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Barry A, Thomson S, Dimayuga I, Chaudhuri A, Do T. Isotope ratio method: state-of-the-art of forensic applications to CBRNE materials. CANADIAN SOCIETY OF FORENSIC SCIENCE JOURNAL 2022. [DOI: 10.1080/00085030.2022.2054109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Aaron Barry
- Canadian Nuclear Laboratories, Chalk River, ON, Canada
| | | | - Ike Dimayuga
- Canadian Nuclear Laboratories, Chalk River, ON, Canada
| | | | - Than Do
- Canadian Nuclear Laboratories, Chalk River, ON, Canada
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2
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A machine learning toolkit for genetic engineering attribution to facilitate biosecurity. Nat Commun 2020; 11:6293. [PMID: 33293535 PMCID: PMC7722865 DOI: 10.1038/s41467-020-19612-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 10/05/2020] [Indexed: 12/21/2022] Open
Abstract
The promise of biotechnology is tempered by its potential for accidental or deliberate misuse. Reliably identifying telltale signatures characteristic to different genetic designers, termed 'genetic engineering attribution', would deter misuse, yet is still considered unsolved. Here, we show that recurrent neural networks trained on DNA motifs and basic phenotype data can reach 70% attribution accuracy in distinguishing between over 1,300 labs. To make these models usable in practice, we introduce a framework for weighing predictions against other investigative evidence using calibration, and bring our model to within 1.6% of perfect calibration. Additionally, we demonstrate that simple models can accurately predict both the nation-state-of-origin and ancestor labs, forming the foundation of an integrated attribution toolkit which should promote responsible innovation and international security alike.
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Oliveira M, Mason-Buck G, Ballard D, Branicki W, Amorim A. Biowarfare, bioterrorism and biocrime: A historical overview on microbial harmful applications. Forensic Sci Int 2020; 314:110366. [PMID: 32683271 PMCID: PMC7305902 DOI: 10.1016/j.forsciint.2020.110366] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022]
Abstract
Microbial Forensics is a field that continues to grow in interest and application among the forensic community. This review, divided into two sections, covers several topics associated with this new field. The first section presents a historic overview concerning the use of microorganisms (or its product, i.e. toxins) as harmful biological agents in the context of biological warfare (biowarfare), bioterrorism, and biocrime. Each case is illustrated with the examination of case reports that span from prehistory to the present day. The second part of the manuscript is devoted to the role of MF and highlights the necessity to prepare for the pressing threat of the harmful use of biological agents as weapons. Preventative actions, developments within the field to ensure a timely and effective response and are discussed herein.
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MESH Headings
- Bacterial Infections
- Biological Warfare/history
- Bioterrorism/history
- Crime/history
- Forensic Sciences
- HIV Infections
- High-Throughput Screening Assays
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- History, Ancient
- History, Medieval
- Humans
- Machine Learning
- Microbiological Techniques
- Toxins, Biological/adverse effects
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Affiliation(s)
- Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
| | | | - David Ballard
- King's Forensics, King's College London, London, United Kingdom
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - António Amorim
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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4
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Dekas AE, Parada AE, Mayali X, Fuhrman JA, Wollard J, Weber PK, Pett-Ridge J. Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP. Front Microbiol 2019; 10:2682. [PMID: 31920997 PMCID: PMC6927911 DOI: 10.3389/fmicb.2019.02682] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 11/05/2019] [Indexed: 11/28/2022] Open
Abstract
Characterizing and quantifying in situ metabolisms remains both a central goal and challenge for environmental microbiology. Here, we used a single-cell, multi-isotope approach to investigate the anabolic activity of marine microorganisms, with an emphasis on natural populations of Thaumarchaeota. After incubating coastal Pacific Ocean water with 13C-bicarbonate and 15N-amino acids, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to isotopically screen 1,501 individual cells, and 16S rRNA amplicon sequencing to assess community composition. We established isotopic enrichment thresholds for activity and metabolic classification, and with these determined the percentage of anabolically active cells, the distribution of activity across the whole community, and the metabolic lifestyle—chemoautotrophic or heterotrophic—of each cell. Most cells (>90%) were anabolically active during the incubation, and 4–17% were chemoautotrophic. When we inhibited bacteria with antibiotics, the fraction of chemoautotrophic cells detected via nanoSIMS increased, suggesting archaea dominated chemoautotrophy. With fluorescence in situ hybridization coupled to nanoSIMS (FISH-nanoSIMS), we confirmed that most Thaumarchaeota were living chemoautotrophically, while bacteria were not. FISH-nanoSIMS analysis of cells incubated with dual-labeled (13C,15N-) amino acids revealed that most Thaumarchaeota cells assimilated amino-acid-derived nitrogen but not carbon, while bacteria assimilated both. This indicates that some Thaumarchaeota do not assimilate intact amino acids, suggesting intra-phylum heterogeneity in organic carbon utilization, and potentially their use of amino acids for nitrification. Together, our results demonstrate the utility of multi-isotope nanoSIMS analysis for high-throughput metabolic screening, and shed light on the activity and metabolism of uncultured marine archaea and bacteria.
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Affiliation(s)
- Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, United States.,Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Alma E Parada
- Department of Earth System Science, Stanford University, Stanford, CA, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
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5
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Bishop AH. The signatures of microorganisms and of human and environmental biomes can now be used to provide evidence in legal cases. FEMS Microbiol Lett 2019; 366:5303725. [PMID: 30689874 DOI: 10.1093/femsle/fnz021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/26/2019] [Indexed: 12/28/2022] Open
Abstract
The microorganisms with which we share our world go largely unnoticed. We are, however, beginning to be able to exploit their apparently silent presence as witnesses to events that are of legal concern. This information can be used to link forensic samples to criminal events and even perpetrators. Once dead, our bodies are rapidly colonised, internally and externally. The progress of these events can be charted to inform how long and even by what means a person has died. A small number of microbial species could actually be the cause of such deaths as a result of biocrime or bioterrorism. The procedures and techniques to respond to such attacks have matured in the last 20 years. The capability now exists to identify malicious intent, characterise the threat agent to isolate level and potentially link it to perpetrators with a high level of confidence.
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Affiliation(s)
- A H Bishop
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Devon, PL4 8AA, UK
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6
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Abstract
Isotopic information determined by mass spectrometry can be used in a wide variety of applications. Broadly speaking these could be classified as "passive" applications, meaning that they use naturally occurring isotopic information, and "active" applications, meaning that the isotopic distributions are manipulated in some way. The classic passive application is the determination of chemical composition by comparing observed isotopic patterns of molecules to theoretically calculated isotopic patterns. Active applications include isotope exchange experiments of a variety of types, as well as isotope labeling in tracing studies and to provide references for quantitation. Regardless of the type of application considered, the problem of theoretical calculation of isotopic patterns almost invariably arises. This chapter reviews a number of application examples and computational approaches for isotopic studies in mass spectrometry.
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7
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Mahoney CM, Kelly RT, Alexander L, Newburn M, Bader S, Ewing RG, Fahey AJ, Atkinson DA, Beagley N. Bayesian Integration and Classification of Composition C-4 Plastic Explosives Based on Time-of-Flight-Secondary Ion Mass Spectrometry and Laser Ablation-Inductively Coupled Plasma Mass Spectrometry. Anal Chem 2016; 88:3598-607. [PMID: 26913559 DOI: 10.1021/acs.analchem.5b04151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Time-of-flight-secondary ion mass spectrometry (TOF-SIMS) and laser ablation-inductively coupled plasma mass spectrometry (LA-ICPMS) were used for characterization and identification of unique signatures from a series of 18 Composition C-4 plastic explosives. The samples were obtained from various commercial and military sources around the country. Positive and negative ion TOF-SIMS data were acquired directly from the C-4 residue on Si surfaces, where the positive ion mass spectra obtained were consistent with the major composition of organic additives, and the negative ion mass spectra were more consistent with explosive content in the C-4 samples. Each series of mass spectra was subjected to partial least squares-discriminant analysis (PLS-DA), a multivariate statistical analysis approach which serves to first find the areas of maximum variance within different classes of C-4 and subsequently to classify unknown samples based on correlations between the unknown data set and the original data set (often referred to as a training data set). This method was able to successfully classify test samples of C-4, though with a limited degree of certainty. The classification accuracy of the method was further improved by integrating the positive and negative ion data using a Bayesian approach. The TOF-SIMS data was combined with a second analytical method, LA-ICPMS, which was used to analyze elemental signatures in the C-4. The integrated data were able to classify test samples with a high degree of certainty. Results indicate that this Bayesian integrated approach constitutes a robust classification method that should be employable even in dirty samples collected in the field.
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Affiliation(s)
- Christine M Mahoney
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , 902 Battelle Boulevard, Richland, Washington 99352, United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , 902 Battelle Boulevard, Richland, Washington 99352, United States
| | - Liz Alexander
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , 902 Battelle Boulevard, Richland, Washington 99352, United States
| | - Matt Newburn
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , 902 Battelle Boulevard, Richland, Washington 99352, United States
| | - Sydney Bader
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , 902 Battelle Boulevard, Richland, Washington 99352, United States
| | - Robert G Ewing
- National Security Directorate, Pacific Northwest National Laboratory , 902 Battelle Boulevard, Richland, Washington 99352, United States
| | - Albert J Fahey
- National Security Directorate, Pacific Northwest National Laboratory , 902 Battelle Boulevard, Richland, Washington 99352, United States
| | - David A Atkinson
- National Security Directorate, Pacific Northwest National Laboratory , 902 Battelle Boulevard, Richland, Washington 99352, United States
| | - Nathaniel Beagley
- Johns Hopkins University , Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
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8
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Abstract
This article critically reviews the literature on the history of biological warfare, bioterrorism, and biocrimes. The first serious effort to review this entire history, made in 1969, had numerous limitations. In recent decades, several authors have filled many of the gaps in our understanding of the past use of biological agents (including both pathogens and toxins), making it possible to reconstruct that history with greater fidelity than previously possible. Nevertheless, there are numerous remaining gaps, and closer inspection indicates that some supposed uses of biological weapons never took place or are poorly substantiated. Topics requiring additional research are identified.
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Affiliation(s)
- W Seth Carus
- W. Seth Carus, PhD, is Distinguished Research Fellow, Center for the Study of WMD, National Defense University , Ft. McNair, Washington, DC
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9
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Isotope ratio mass spectrometry as a tool for source inference in forensic science: A critical review. Forensic Sci Int 2015; 251:139-58. [DOI: 10.1016/j.forsciint.2015.03.031] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/17/2015] [Accepted: 03/31/2015] [Indexed: 11/19/2022]
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10
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Effects of low-level deuterium enrichment on bacterial growth. PLoS One 2014; 9:e102071. [PMID: 25033078 PMCID: PMC4102507 DOI: 10.1371/journal.pone.0102071] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 06/14/2014] [Indexed: 11/22/2022] Open
Abstract
Using very precise (±0.05%) measurements of the growth parameters for bacteria E. coli grown on minimal media, we aimed to determine the lowest deuterium concentration at which the adverse effects that are prominent at higher enrichments start to become noticeable. Such a threshold was found at 0.5% D, a surprisingly high value, while the ultralow deuterium concentrations (≤0.25% D) showed signs of the opposite trend. Bacterial adaptation for 400 generations in isotopically different environment confirmed preference for ultralow (≤0.25% D) enrichment. This effect appears to be similar to those described in sporadic but multiple earlier reports. Possible explanations include hormesis and isotopic resonance phenomena, with the latter explanation being favored.
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11
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Cappuccio JA, Falso MJS, Kashgarian M, Buchholz BA. 14C Analysis of protein extracts from Bacillus spores. Forensic Sci Int 2014; 240:54-60. [PMID: 24814329 DOI: 10.1016/j.forsciint.2014.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 03/28/2014] [Accepted: 04/01/2014] [Indexed: 10/25/2022]
Abstract
Investigators of bioagent incidents or interdicted materials need validated, independent analytical methods that will allow them to distinguish between recently made bioagent samples versus material drawn from the archives of a historical program. Heterotrophic bacteria convert the carbon in their food sources, growth substrate or culture media, into the biomolecules they need. The F(14)C (fraction modern radiocarbon) of a variety of media, Bacillus spores, and separated proteins from Bacillus spores was measured by accelerator mass spectrometry (AMS). AMS precisely measures F(14)C values of biological materials and has been used to date the synthesis of biomaterials over the bomb pulse era (1955 to present). The F(14)C of Bacillus spores reflects the radiocarbon content of the media in which they were grown. In a survey of commercial media we found that the F(14)C value indicated that carbon sources for the media were alive within about a year of the date of manufacture and generally of terrestrial origin. Hence, bacteria and their products can be dated using their (14)C signature. Bacillus spore samples were generated onsite with defined media and carbon free purification and also obtained from archived material. Using mechanical lysis and a variety of washes with carbon free acids and bases, contaminant carbon was removed from soluble proteins to enable accurate (14)C bomb-pulse dating. Since media is contemporary, (14)C bomb-pulse dating of isolated soluble proteins can be used to distinguish between historical archives of bioagents and those produced from recent media.
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Affiliation(s)
- Jenny A Cappuccio
- Biosciences & Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94551, United States
| | - Miranda J Sarachine Falso
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA 94551, United States
| | - Michaele Kashgarian
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA 94551, United States
| | - Bruce A Buchholz
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA 94551, United States.
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12
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Abstract
Isotopic information determined by mass spectrometry can be used in a wide variety of applications. Broadly speaking these could be classified as "passive" applications, meaning that they use naturally occurring isotopic information, and "active" applications, meaning that the isotopic distributions are manipulated in some way. The classic passive application is the determination of chemical composition by comparing observed isotopic patterns of molecules to theoretically calculated isotopic patterns. Active applications include isotope exchange experiments of a variety of types, as well as isotope labeling in tracing studies and to provide references for quantitation. Regardless of the type of application considered, the problem of theoretical calculation of isotopic patterns almost invariably arises. This paper reviews a number of application examples and computational approaches for isotopic studies in mass spectrometry.
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Affiliation(s)
- Alan L Rockwood
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
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13
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Wunschel D, Tulman E, Engelmann H, Clowers BH, Geary S, Robinson A, Liao X. Forensic proteomics of poxvirus production. Analyst 2013; 138:6385-97. [PMID: 23979794 DOI: 10.1039/c3an00711a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The field of microbial forensics has recently sought to develop methods to discern biological signatures to indicate production methods for biological agents. Viral agents have received less attention to date. Their obligate propagation in living cells makes purification from cellular material a challenge. This leads to potential carryover of protein-rich signatures of their production system. Here we have explored a proteomic analysis of vaccinia virus as a model poxvirus system in which to compare samples of virus propagated in different cell lines and subjected to different purification schemes. The proteomic data sets indicated viral, host cell and culture medium proteins. Several layers of data analysis were applied to build confidence in the peptide identification and capture information on the taxonomic utility of each. The analysis showed clear shifts in protein profiles with virus purification, with successive gradient purification steps showing different levels of viral protein enrichment. Peptides from cellular proteins, including those present in purified virus preparations, provided signatures which enabled discrimination of cell line substrates, including distinguishing between cells derived from different primate species. The ability to discern multiple aspects of viral production demonstrates the potential value of proteomic analysis as tool for microbial forensics.
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Affiliation(s)
- David Wunschel
- Chemical and Biological Signature Sciences Group, Pacific Northwest National Laboratory, Richland, Washington, USA.
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14
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Webb-Robertson BJ, Corley C, McCue LA, Wahl K, Kreuzer H. Fusion of laboratory and textual data for investigative bioforensics. Forensic Sci Int 2013; 226:118-24. [PMID: 23313599 DOI: 10.1016/j.forsciint.2012.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 12/04/2012] [Accepted: 12/16/2012] [Indexed: 10/27/2022]
Abstract
Chemical and biological forensic programs focus on the identification of a threat and acquisition of laboratory measurements to determine how a threat agent may have been produced. However, to generate investigative leads, it might also be useful to identify institutions where the same agent has been produced by the same or a very similar process, since the producer of the agent may have learned methods at a university or similar institution. We have developed a Bayesian network framework that fuses hard and soft data sources to assign probability to production practices. It combines the results of laboratory measurements with an automatic text reader to scan scientific literature and rank institutions that had published papers on the agent of interest in order of the probability that the institution has the capability to generate the sample of interest based on laboratory data. We demonstrate the Bayesian network on an example case from microbial forensics, predicting the methods used to produce Bacillus anthracis spores based on mass spectrometric measurements and identifying institutions that have a history of growing Bacillus spores using the same or highly similar methods. We illustrate that the network model can assign a higher posterior probability than expected by random chance to appropriate institutions when trained using only a small set of manually analyzed documents. This is the first example of an automated methodology to integrate experimental and textual data for the purpose of investigative forensics.
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Affiliation(s)
- Bobbie-Jo Webb-Robertson
- Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, USA.
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15
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Kreuzer HW, West JB, Ehleringer JR. Forensic Applications of Light-Element Stable Isotope Ratios ofRicinus communisSeeds and Ricin Preparations. J Forensic Sci 2012; 58 Suppl 1:S43-51. [DOI: 10.1111/1556-4029.12000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 12/16/2011] [Accepted: 12/22/2011] [Indexed: 11/27/2022]
Affiliation(s)
- Helen W. Kreuzer
- Department of Biology; University of Utah; 257 South 1400 East, Salt Lake City; UT 84112
| | - Jason B. West
- Department of Biology; University of Utah; 257 South 1400 East, Salt Lake City; UT 84112
| | - James R. Ehleringer
- Department of Biology; University of Utah; 257 South 1400 East, Salt Lake City; UT 84112
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16
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Auclair J, Lépine F, Villemur R. A liquid chromatography - mass spectrometry method to measure ¹³C-isotope enrichment for DNA stable-isotope probing. Can J Microbiol 2012; 58:287-92. [PMID: 22356592 DOI: 10.1139/w11-133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA stable-isotope probing (DNA-SIP) is a cultivation-independent technique that makes it possible to associate metabolic function and taxonomic identity in a wide range of terrestrial and aquatic environments. In DNA-SIP, DNA is labeled via the assimilation of a labeled growth substrate that is subsequently used to identify microorganisms involved in assimilation of the substrate. However, the labeling time has to be sufficient to obtain labeled DNA but not so long such that cross-feeding of ¹³C-labeled metabolites from the primary consumers to nontarget species can occur. Confirmation that the DNA is isotopically labeled in DNA-SIP assays can be achieved using an isotope ratio mass spectrometer. In this study, we describe the development of a method using liquid chromatography (HPLC) coupled to a quadrupole mass spectrometer (QMS) to measure the ¹³C enrichment of thymine incorporated into DNA in Escherichia coli cultures fed with [¹³C]acetate. The method involved the hydrolysis of DNA extracted from the cultures that released the nucleotides, followed by the separation of the thymine by HPLC on a reverse-phase C₈ column in isocratic elution mode and the detection and quantification of ¹³C-labeled thymine by QMS. To mimic a DNA-SIP assay, a DNA mixture was made using ¹³C-labeled E. coli DNA with DNA extracted from five bacterial species. The HPLC-MS method was able to measure the correct proportion of ¹³C-DNA in the mix. This method can then be used as an alternative to the use of isotope ratio mass spectrometry in DNA-SIP assays.
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Affiliation(s)
- Julie Auclair
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
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17
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Kreuzer HW, Horita J, Moran JJ, Tomkins BA, Janszen DB, Carman A. Stable Carbon and Nitrogen Isotope Ratios of Sodium and Potassium Cyanide as a Forensic Signature. J Forensic Sci 2011; 57:75-9. [DOI: 10.1111/j.1556-4029.2011.01946.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Zubarev RA. Role of stable isotopes in life--testing isotopic resonance hypothesis. GENOMICS PROTEOMICS & BIOINFORMATICS 2011; 9:15-20. [PMID: 21641558 PMCID: PMC5054155 DOI: 10.1016/s1672-0229(11)60003-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 02/14/2011] [Indexed: 11/17/2022]
Abstract
Stable isotopes of most important biological elements, such as C, H, N and O, affect living organisms. In rapidly growing species, deuterium and to a lesser extent other heavy isotopes reduce the growth rate. At least for deuterium it is known that its depletion also negatively impacts the speed of biological processes. As a rule, living organisms “resist” changes in their isotopic environment, preferring natural isotopic abundances. This preference could be due to evolutionary optimization; an additional effect could be due to the presence of the “isotopic resonance”. The isotopic resonance phenomenon has been linked to the choice of earliest amino acids, and thus affected the evolution of genetic code. To test the isotopic resonance hypothesis, literature data were analyzed against quantitative and qualitative predictions of the hypothesis. Four studies provided five independent datasets, each in very good quantitative agreement with the predictions. Thus, the isotopic resonance hypothesis is no longer simply plausible; it can now be deemed likely. Additional testing is needed, however, before full acceptance of this hypothesis.
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Affiliation(s)
- Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
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19
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The effect of growth medium on B. anthracis Sterne spore carbohydrate content. J Microbiol Methods 2011; 85:183-9. [PMID: 21396405 DOI: 10.1016/j.mimet.2011.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 02/23/2011] [Accepted: 02/28/2011] [Indexed: 11/21/2022]
Abstract
The expressed characteristics of biothreat agents may be impacted by variations in the culture environment, including growth medium formulation. The carbohydrate composition of B. anthracis spores has been well studied, particularly for the exosporium, which is the outermost spore structure. The carbohydrate composition of the exosporium has been demonstrated to be distinct from the vegetative form containing unique monosaccharides. We have investigated the carbohydrate composition of B. anthracis Sterne spores produced using four different medium types formulated with different sources of medium components. The amount of rhamnose, 3-O-methyl rhamnose and galactosamine was found to vary significantly between spores cultured using different medium formulations. The relative abundance of these monosaccharides compared to other monosaccharides such as mannosamine was also found to vary with medium type. Specific medium components were also found to impact the carbohydrate profile. Xylose has not been previously described in B. anthracis spores but was detected at low levels in two media. This may represent residual material from the brewery yeast extract used to formulate these two media. These results illustrate the utility of this method to capture the impact of growth medium on carbohydrate variation in spores. Detecting carbohydrate profiles in B. anthracis evidentiary material may provide useful forensic information on the growth medium used for sporulation.
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20
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Hagopian WM, Jahren AH. Minimization of sample requirement for delta18O in benzoic acid. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:2542-2546. [PMID: 20740528 DOI: 10.1002/rcm.4669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The measurement of the oxygen stable isotope content in organic compounds has applications in many fields, ranging from paleoclimate reconstruction to forensics. Conventional High-Temperature Conversion (HTC) techniques require >20 microg of O for a single delta(18)O measurement. Here we describe a system that converts the CO produced by HTC into CO(2) via reduction within a Ni-furnace. This CO(2) is then concentrated cryogenically, and 'focused' into the isotope ratio mass spectrometry (IRMS) source using a low-flow He carrier gas (6-8 mL/min). We report analyses of benzoic acid (C(7)H(6)O(2)) reference materials that yielded precise delta(18)O measurement down to 1.3 microg of O, suggesting that our system could be used to decrease sample requirement for delta(18)O by more than an order of magnitude.
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Affiliation(s)
- William M Hagopian
- Department of Geology and Geophysics, University of Hawaii, Honolulu, HI 96822, USA
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Wahl KL, Colburn HA, Wunschel DS, Petersen CE, Jarman KH, Valentine NB. Residual agar determination in bacterial spores by electrospray ionization mass spectrometry. Anal Chem 2010; 82:1200-6. [PMID: 20073479 DOI: 10.1021/ac901491c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Presented here is an analytical method to detect residual agar from a bacterial spore sample as an indication of culturing on an agar plate. This method is based on the resolubilization of agar polysaccharide from a bacterial spore sample, enzymatic digestion, followed by electrospray ionization tandem mass spectrometry (ESI-MS(n)) analysis for detection of a specific agar fragment ion. A range of Bacillus species and strains were selected to demonstrate the effectiveness of this approach. The characteristic agar fragment ion was detected in the spores grown on agar that were washed from 1 to 5 times, irradiated or nonirradiated, and not in the spores grown in broth. A sample containing approximately 10(8) spores is currently needed for confident detection of residual agar from culture on agar plates in the presence of bacterial spores with a limit of detection of approximately 1 ppm agar spiked into a broth-grown spore sample. The results of a proficiency test with 42 blinded samples are presented demonstrating the utility of this method with no false positives and only three false negatives for samples that were below the detection level of the method as documented.
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Affiliation(s)
- Karen L Wahl
- Pacific Northwest National Laboratory, P.O. Box 999, MS P7-50, Richland, Washington 99352, USA.
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22
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High-pressure highly reduced nitrides and oxides from chromitite of a Tibetan ophiolite. Proc Natl Acad Sci U S A 2009; 106:19233-8. [PMID: 19880742 DOI: 10.1073/pnas.0905514106] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The deepest rocks known from within Earth are fragments of normal mantle ( approximately 400 km) and metamorphosed sediments ( approximately 350 km), both found exhumed in continental collision terranes. Here, we report fragments of a highly reduced deep mantle environment from at least 300 km, perhaps very much more, extracted from chromite of a Tibetan ophiolite. The sample consists, in part, of diamond, coesite-after-stishovite, the high-pressure form of TiO(2), native iron, high-pressure nitrides with a deep mantle isotopic signature, and associated SiC. This appears to be a natural example of the recently discovered disproportionation of Fe(2+) at very high pressure and consequent low oxygen fugacity (fO(2)) in deep Earth. Encapsulation within chromitite enclosed within upwelling solid mantle rock appears to be the only vehicle capable of transporting these phases and preserving their low-fO(2) environment at the very high temperatures of oceanic spreading centers.
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WEBER P, GRAHAM G, TESLICH N, CHAN WMOBERLY, GHOSAL S, LEIGHTON T, WHEELER K. NanoSIMS imaging of Bacillus spores sectioned by focused ion beam. J Microsc 2009; 238:189-99. [DOI: 10.1111/j.1365-2818.2009.03336.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Hu J, Dagle RA, Johnson BR, Kreuzer HW, Gaspar DJ, Roberts BQ, Alexander ML. Development of a Micropyrolyzer for Enhanced Isotope Ratio Measurement. Ind Eng Chem Res 2008. [DOI: 10.1021/ie8009236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jianli Hu
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Robert A. Dagle
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Bradley R. Johnson
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Helen W. Kreuzer
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Daniel J. Gaspar
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Benjamin Q. Roberts
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - M. Lizabeth Alexander
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
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Demirev PA, Fenselau C. Mass spectrometry in biodefense. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:1441-57. [PMID: 18720458 DOI: 10.1002/jms.1474] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Potential agents for biological attacks include both microorganisms and toxins. In mass spectrometry (MS), rapid identification of potential bioagents is achieved by detecting the masses of unique biomarkers, correlated to each agent. Currently, proteins are the most reliable biomarkers for detection and characterization of both microorganisms and toxins, and MS-based proteomics is particularly well suited for biodefense applications. Confident identification of an organism can be achieved by top-down proteomics following identification of individual protein biomarkers from their tandem mass spectra. In bottom-up proteomics, rapid digestion of intact protein biomarkers is again followed by MS/MS to provide unambiguous bioagent identification and characterization. Bioinformatics obviates the need for culturing and rigorous control of experimental variables to create and use MS fingerprint libraries for various classes of bioweapons. For specific applications, MS methods, instruments and algorithms have also been developed for identification based on biomarkers other than proteins and peptides.
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Affiliation(s)
- Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD 20723, USA.
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Ehleringer JR, Cerling TE, West JB, Podlesak DW, Chesson LA, Bowen GJ. Spatial Considerations of Stable Isotope Analyses in Environmental Forensics. ENVIRONMENTAL FORENSICS 2008. [DOI: 10.1039/9781847558343-00036] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Jarman KH, Kreuzer-Martin HW, Wunschel DS, Valentine NB, Cliff JB, Petersen CE, Colburn HA, Wahl KL. Bayesian-integrated microbial forensics. Appl Environ Microbiol 2008; 74:3573-82. [PMID: 18390682 PMCID: PMC2423015 DOI: 10.1128/aem.02526-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Accepted: 03/23/2008] [Indexed: 11/20/2022] Open
Abstract
In the aftermath of the 2001 anthrax letters, researchers have been exploring ways to predict the production environment of unknown-source microorganisms. Culture medium, presence of agar, culturing temperature, and drying method are just some of the broad spectrum of characteristics an investigator might like to infer. The effects of many of these factors on microorganisms are not well understood, but the complex way in which microbes interact with their environments suggests that numerous analytical techniques measuring different properties will eventually be needed for complete characterization. In this work, we present a Bayesian statistical framework for integrating disparate analytical measurements. We illustrate its application to the problem of characterizing the culture medium of Bacillus spores using three different mass spectral techniques. The results of our study suggest that integrating data in this way significantly improves the accuracy and robustness of the analyses.
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Affiliation(s)
- Kristin H Jarman
- Pacific Northwest National Laboratory, PO Box 999/MS K9-72, Richland, WA 99352, USA.
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