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Cody RB, Espinoza EO, Price ER, McClure PJ. Wood from Hardwood Angiosperms and Coniferous Gymnosperms Shows Distinctive Lignin Peaks in Direct Analysis in Real Time (DART) Mass Spectra. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:784-789. [PMID: 36947165 DOI: 10.1021/jasms.2c00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A data set was constructed consisting of 3021 mass spectra randomly selected from all available families in the ForeST© (Forensic Spectra of Trees) database of mass spectra for wood analyzed by Direct Analysis in Real Time ionization coupled with time-of-flight mass spectrometry (DART-TOFMS). Clear and reproducible differences were observed between the lignin peaks for hardwood angiosperms and coniferous gymnosperms, with DART-TOFMS spectra of angiosperms showing significantly higher relative abundances for peaks associated with syringyl subunits. Application of the method to processed wood samples demonstrated that these differences can be used to provide support for enforcing trade laws by accurately identifying the source of finished wood products from hardwood angiosperms and coniferous gymnosperms.
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Affiliation(s)
- Robert B Cody
- JEOL USA, Inc., 11 Dearborn Rd., Peabody Massachusetts 01960 United States
| | - Edgard O Espinoza
- US Fish and Wildlife Service, Office of Law Enforcement, National Fish & Wildlife Forensic Laboratory, 1490 East Main Street, Ashland, Oregon 97520, United States
| | - Erin R Price
- US Forest Service International Programs Wood Identification and Screening Center, 1490 East Main Street, Ashland, Oregon 97520, United States
| | - Pamela J McClure
- US Fish and Wildlife Service, Office of Law Enforcement, National Fish & Wildlife Forensic Laboratory, 1490 East Main Street, Ashland, Oregon 97520, United States
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Deklerck. Timber origin verification using mass spectrometry: challenges, opportunities, and way forward. FORENSIC SCIENCE INTERNATIONAL: ANIMALS AND ENVIRONMENTS 2022. [DOI: 10.1016/j.fsiae.2022.100057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Deklerck V, Fowble KL, Coon AM, Espinoza EO, Beeckman H, Musah RA. Opportunities in phytochemistry, ecophysiology and wood research via laser ablation direct analysis in real time imaging-mass spectrometry. THE NEW PHYTOLOGIST 2022; 234:319-331. [PMID: 34861069 DOI: 10.1111/nph.17893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Analysis of wood transects in a manner that preserves the spatial distribution of the metabolites present is highly desirable to among other things: (1) facilitate ecophysiology studies that reveal the association between chemical make-up and environmental factors or climatic events over time; and (2) investigate the mechanisms of the synthesis and trafficking of small molecules within specialised tissues. While a variety of techniques could be applied to achieve these goals, most remain challenging and impractical. Laser ablation direct analysis in real time imaging-mass spectrometry (LADI-MS) was successfully used to survey the chemical profile of wood, while also preserving the small-molecule spatial distributions. The tree species Entandrophragma candollei Harms, Millettia laurentii DeWild., Pericopsis elata (Harms) Meeuwen, Dalbergia nigra (Vell.) Benth. and Dalbergia normandii Bosser & R.Rabev were analysed. Several compounds were associated with anatomical features. A greater diversity was detected in the vessels and parenchyma compared with the fibres. Analysis of single vessels revealed that the chemical fingerprint used for timber identification is mainly determined by vessel content. Laser ablation direct analysis in real time imaging-mass spectrometry offers unprecedented opportunities to investigate the distribution of metabolites within wood samples, while circumventing the issues associated with previous methods. This technique opens up new vistas for the discovery of small-molecule biomarkers that are linked to environmental events.
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Affiliation(s)
- Victor Deklerck
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- Royal Botanic Gardens, Kew, Richmond,, TW9 3AE, UK
| | - Kristen L Fowble
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Allix M Coon
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Edgard O Espinoza
- US National Fish and Wildlife Forensic Laboratory, 1490 East Main Street, Ashland, OR, 97520, USA
| | - Hans Beeckman
- Service of Wood Biology, Royal Museum for Central Africa (RMCA), Leuvensesteensweg 13, Tervuren, 3080, Belgium
| | - Rabi A Musah
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
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Gupta S, Samal N. Application of direct analysis in real-time mass spectrometry (DART-MS) in forensic science: a comprehensive review. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2022. [DOI: 10.1186/s41935-022-00276-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
As the rate of crime is constantly increasing, the workload on the forensic analyst also piles up. The availability of a limited number of seized samples makes it crucial to directly analyze the sample, thereby preventing wastage in the prior steps of sample preparation. Due to such needs, the forensic community is consistently working on broadening the usage of direct analysis in real-time mass spectrometry (DART-MS). DART-MS is a relatively new technique for rapid mass spectral analysis. Its use for chemical analysis credits its ability to analyze the sample at atmospheric pressure.
Main body
This article gives insight into the ionization mechanisms, data analysis tools, and the use of hyphenated techniques like thermal-desorption-DART-MS, infrared-thermal-desorption-DART-MS, Joule-heating thermal-desorption-DART-MS, etc. This review summarizes the applications of DART-MS in the field of Forensic Science reported from 2005 to 2021. The applications include analysis of drugs, warfare agents, gun-shot residues, ink differentiation, and other forensically relevant samples. The paper also presents the relation between the type of DART-MS technique and the ionization mode used for a particular class of compounds.
Conclusion
The review follows that the high-resolution mass-spectrometers or low-resolution mass-spectrometers systems in the positive or negative mode were highly dependent on the type of analyte under investigation. Drugs, inks, dyes, and paints were mainly analyzed using the positive ionization mode in the HRMS technique. The examinations of fire accelerants predominantly used the positive ionization mode in the LRMS technique. Moreover, the limit of detection values obtained from the qualitative screening of street drugs were of ppb level, indicating high sensitivity of DART-MS. Considering the work done in the past years, there are potential future research needs of this technology, especially in forensic science.
Graphical Abstract
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Price ER, Miles-Bunch I, Gasson PE, Lancaster CA. Inference of origin of Pterocarpus timber by chemical profiling of ambient ionization mass spectra. FORENSIC SCIENCE INTERNATIONAL: ANIMALS AND ENVIRONMENTS 2021. [DOI: 10.1016/j.fsiae.2021.100032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Cronn RC, Finch KN, Hauck LL, Parker-Forney M, Milligan BG, Dowling J, Scientists A. Range-wide assessment of a SNP panel for individualization and geolocalization of bigleaf maple (Acer macrophyllum Pursh). FORENSIC SCIENCE INTERNATIONAL: ANIMALS AND ENVIRONMENTS 2021. [DOI: 10.1016/j.fsiae.2021.100033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Ó Marcaigh F, Kelly DJ, O'Connell DP, Dunleavy D, Clark A, Lawless N, Karya A, Analuddin K, Marples NM. Evolution in the understorey: The Sulawesi babbler Pellorneum celebense (Passeriformes: Pellorneidae) has diverged rapidly on land-bridge islands in the Wallacean biodiversity hotspot. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Moore HE, Hall MJR, Drijfhout FP, Cody RB, Whitmore D. Cuticular hydrocarbons for identifying Sarcophagidae (Diptera). Sci Rep 2021; 11:7732. [PMID: 33833323 PMCID: PMC8032779 DOI: 10.1038/s41598-021-87221-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/15/2021] [Indexed: 11/28/2022] Open
Abstract
The composition and quantity of insect cuticular hydrocarbons (CHCs) can be species-specific as well as sexually dimorphic within species. CHC analysis has been previously used for identification and ageing purposes for several insect orders including true flies (Diptera). Here, we analysed the CHC chemical profiles of adult males and females of eleven species of flesh flies belonging to the genus Sarcophaga Meigen (Sarcophagidae), namely Sarcophaga africa (Wiedemann), S. agnata Rondani, S. argyrostoma Robineau-Desvoidy, S. carnaria (Linnaeus), S. crassipalpis Macquart, S. melanura Meigen, S. pumila Meigen, S. teretirostris Pandellé, S. subvicina Rohdendorf, S. vagans Meigen and S. variegata (Scopoli). Cuticular hydrocarbons extracted from pinned specimens from the collections of the Natural History Museum, London using a customised extraction technique were analysed using Gas Chromatography-Mass Spectrometry. Time of preservation prior to extraction ranged between a few weeks to over one hundred years. CHC profiles (1) allowed reliable identification of a large majority of specimens, (2) differed between males and females of the same species, (3) reliably associated males and females of the same species, provided sufficient replicates (up to 10) of each sex were analysed, and (4) identified specimens preserved for up to over one hundred years prior to extraction.
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Affiliation(s)
- Hannah E Moore
- Cranfield Forensic Institute, Cranfield University, Defence Academy of the United Kingdom, Shrivenham, Wiltshire, SN6 8LA, UK.
| | - Martin J R Hall
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Falko P Drijfhout
- Chemical Ecology Group, School of Chemical and Physical Science, Keele University, Keele, ST5 5BG, England, UK
| | - Robert B Cody
- JEOL USA, Inc. 11 Dearborn Rd., Peabody, MA, 01969, USA
| | - Daniel Whitmore
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191, Stuttgart, Germany
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Aoyagi S, Fujiwara Y, Takano A, Vorng JL, Gilmore IS, Wang YC, Tallarek E, Hagenhoff B, Iida SI, Luch A, Jungnickel H, Lang Y, Shon HK, Lee TG, Li Z, Matsuda K, Mihara I, Miisho A, Murayama Y, Nagatomi T, Ikeda R, Okamoto M, Saiga K, Tsuchiya T, Uemura S. Evaluation of Time-of-Flight Secondary Ion Mass Spectrometry Spectra of Peptides by Random Forest with Amino Acid Labels: Results from a Versailles Project on Advanced Materials and Standards Interlaboratory Study. Anal Chem 2021; 93:4191-4197. [PMID: 33635050 DOI: 10.1021/acs.analchem.0c04577] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the results of a VAMAS (Versailles Project on Advanced Materials and Standards) interlaboratory study on the identification of peptide sample TOF-SIMS spectra by machine learning. More than 1000 time-of-flight secondary ion mass spectrometry (TOF-SIMS) spectra of six peptide model samples (one of them was a test sample) were collected using 27 TOF-SIMS instruments from 25 institutes of six countries, the U. S., the U. K., Germany, China, South Korea, and Japan. Because peptides have systematic and simple chemical structures, they were selected as model samples. The intensity of peaks in every TOF-SIMS spectrum was extracted using the same peak list and normalized to the total ion count. The spectra of the test peptide sample were predicted by Random Forest with 20 amino acid labels. The accuracy of the prediction for the test spectra was 0.88. Although the prediction of an unknown peptide was not perfect, it was shown that all of the amino acids in an unknown peptide can be determined by Random Forest prediction and the TOF-SIMS spectra. Moreover, the prediction of peptides, which are included in the training spectra, was almost perfect. Random Forest also suggests specific fragment ions from an amino acid residue Q, whose fragment ions detected by TOF-SIMS have not been reported, in the important features. This study indicated that the analysis using Random Forest, which enables translation of the mathematical relationships to chemical relationships, and the multi labels representing monomer chemical structures, is useful to predict the TOF-SIMS spectra of an unknown peptide.
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Affiliation(s)
- Satoka Aoyagi
- Faculty of Science and Technology, Seikei University, Musashino, Tokyo 180-8633, Japan
| | - Yukio Fujiwara
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Akio Takano
- Toyama Co., Ltd., 3816-1 Kishi, Yamakita-machi, Ashigarakami-gun, Kanagawa 258-0112, Japan
| | - Jean-Luc Vorng
- National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, UK
| | - Ian S Gilmore
- National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, UK
| | - Yung-Chen Wang
- Medtronic, Corporate Science & Technology, 710 Medtronic Parkway, Mailstop LT240, Minneapolis Minnesota 55432, United States
| | | | | | - Shin-Ichi Iida
- ULVAC-PHI, Inc., 2500 Hagisono, Chigasaki, Kanagawa 253-8522, Japan
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Strasse 8-10, Berlin 10589, Germany
| | - Harald Jungnickel
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Strasse 8-10, Berlin 10589, Germany
| | - Yusheng Lang
- Analytical Science Team, Common Base Technology Division, Innovative Technology Laboratories, AGC Inc., 1150 Hazawa-cho, Kanagawa-ku, Yokohama-shi, Kanagawa 221-8755, Japan
| | - Hyun Kyong Shon
- Bio-imaging Team, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea
| | - Tae Geol Lee
- Bio-imaging Team, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea
| | - Zhanping Li
- Department of Chemistry, Tsinghua University, No. 30, Shuangqing Road, Haidian District, Beijing 100084, China
| | - Kazuhiro Matsuda
- Faculty of Science and Technology, Seikei University, Musashino, Tokyo 180-8633, Japan.,Surface Science Laboratories, Toray Research Center, Inc., 3-3-7, Sonoyama, Otsu, Shiga 520-8567, Japan
| | - Ichiro Mihara
- Analytical Technology and Solutions Laboratory, Kurashiki Research Center, KURARAY CO., LTD, 2045-1, Sakazu, Kurashiki, Okayama 710-0801, Japan
| | - Ako Miisho
- KOBELCO RESEARCH INSTITUTE, INC., 1-5-5, Takatsukadai, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Yohei Murayama
- Specialty Chemicals Development Center, Peripheral Products Operations, Canon Inc., 4202, Fukara, Susono, Shizuoka 410-1196, Japan
| | - Takaharu Nagatomi
- Platform Laboratory for Science and Technology, Asahi Kasei Corporation, 2-1 Samejima, Fuji, Shizuoka 416-8501, Japan
| | - Reiko Ikeda
- Analytical Science Research Laboratory, Kao Corp., Minato 1334. Wakayama-shi, Wakayama 640-8580, Japan
| | - Masayuki Okamoto
- Analytical Science Research Laboratory, Kao Corp., Minato 1334. Wakayama-shi, Wakayama 640-8580, Japan
| | - Kunio Saiga
- Mitsui Chemical Analysis & Consulting Service Inc., 580-32 Nagaura, Sodegaura, Chiba 299-0265, Japan
| | - Toshihiko Tsuchiya
- Mitsui Chemical Analysis & Consulting Service Inc., 580-32 Nagaura, Sodegaura, Chiba 299-0265, Japan
| | - Shigeaki Uemura
- Sumitomo Electric Industries, Ltd., 1-1-1, Koyakita, Itami, Hyogo 664-0016, Japan
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Creydt M, Ludwig L, Köhl M, Fromm J, Fischer M. Wood profiling by non-targeted high-resolution mass spectrometry: Part 1, Metabolite profiling in Cedrela wood for the determination of the geographical origin. J Chromatogr A 2021; 1641:461993. [PMID: 33611119 DOI: 10.1016/j.chroma.2021.461993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 11/18/2022]
Abstract
The determination of the geographical origin of wood can be highly relevant for several reasons: On the one hand, it can help to prevent illegal logging and timber trade, on the other hand, it is of special interest for archaeological artefacts made of wood, as well as for a variety of biological questions. For this reason, different extraction methods were first tested for the analysis of polar and non-polar metabolites using liquid chromatography coupled electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). A two-phase extraction with chloroform, methanol and water proved to be particularly successful. Subsequently, cedrela (Cedrela odorata) samples from South America were measured to distinguish geographic origin. Using multivariate data analysis, numerous origin-dependent differences could be extracted. The identification of the marker substances indicated that several metabolic pathways were affected by the geographical influences, some of them probably indicating pest infections.
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Affiliation(s)
- Marina Creydt
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany; Cluster of Excellence, Understanding Written Artefacts, University of Hamburg, Warburgstraße 26, 20354 Hamburg, Germany.
| | - Lea Ludwig
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Michael Köhl
- Institute of Wood Science, Research Unit World Forestry, University of Hamburg, Leuschnerstrasse 91e, 21031, Hamburg, Germany
| | - Jörg Fromm
- Cluster of Excellence, Understanding Written Artefacts, University of Hamburg, Warburgstraße 26, 20354 Hamburg, Germany; Institute of Wood Science, Research Unit Wood Biology, University of Hamburg, Leuschnerstrasse 91d, 21031, Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany; Cluster of Excellence, Understanding Written Artefacts, University of Hamburg, Warburgstraße 26, 20354 Hamburg, Germany
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Cody RB. Saccharomyces cerevisiae and S. pastorianus species and strain differentiation by direct analysis in real time time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8835. [PMID: 32430915 DOI: 10.1002/rcm.8835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Seventeen different dried yeast strains, including twelve strains of Saccharomyces cerevisiae and five strains of S. pastorianus, were analyzed using direct analysis in real time (DART) time-of-flight mass spectrometry. The resulting mass spectra were used for rapid species and strain differentiation based upon small-molecule metabolomic profiles. METHODS Yeast strains purchased from local shops were suspended in a 1:1 water-methanol solution. Solutions were sampled by dipping the sealed end of a melting point capillary into each vial. Six replicates were measured in positive-ion and negative-ion mode for each strain using an automated linear rail with the DART source operated with helium gas and a gas heater temperature of 350°C. Averaged and centroided mass spectra were exported for analysis with chemometric software. RESULTS Negative-ion DART mass spectra exhibited less chemical background and more distinctive components than positive-ion DART mass spectra. An on-line search of the Yeast Metabolome Database provided candidate metabolites for selection as features for chemometric analysis. Negative-ion DART mass spectra could distinguish both species and all strains. The DART analysis was also able to identify potential metabolomic differences between top-fermenting and bottom-fermenting yeast, between beer and baking yeast, and between red wine and champagne yeast. CONCLUSIONS All strains could be distinguished by their negative-ion DART mass spectra with 97.7% validation accuracy. Clear differences were observed between dry and liquid forms and Saccharomyces strains with different applications to baking or beverage fermentation. Possible differences in metabolite profiles were suggested, but not confirmed, by accurate mass data.
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Affiliation(s)
- Robert B Cody
- JEOL USA Inc., 11 Dearborn Road, Peabody, 01960, USA
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Predicting the geographic origin of Spanish Cedar (Cedrela odorata L.) based on DNA variation. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01282-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Shang D, Brunswick P, Yan J, Bruno J, Duchesne I, Isabel N, VanAggelen G, Kim M, Evans PD. Chemotyping and identification of protected Dalbergiatimber using gas chromatography quadrupole time of flight mass spectrometry. J Chromatogr A 2020; 1615:460775. [DOI: 10.1016/j.chroma.2019.460775] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/03/2019] [Accepted: 12/06/2019] [Indexed: 11/26/2022]
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Chemical Fingerprinting of Wood Sampled along a Pith-to-Bark Gradient for Individual Comparison and Provenance Identification. FORESTS 2020. [DOI: 10.3390/f11010107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Background and Objectives: The origin of traded timber is one of the main questions in the enforcement of regulations to combat the illegal timber trade. Substantial efforts are still needed to develop techniques that can determine the exact geographical provenance of timber and this is vital to counteract the destructive effects of illegal logging, ranging from economical loss to habitat destruction. The potential of chemical fingerprints from pith-to-bark growth rings for individual comparison and geographical provenance determination is explored. Materials and Methods: A wood sliver was sampled per growth ring from four stem disks from four individuals of Pericopsis elata (Democratic Republic of the Congo) and from 14 stem disks from 14 individuals of Terminalia superba (Côte d’Ivoire and Democratic Republic of the Congo). Chemical fingerprints were obtained by analyzing these wood slivers with Direct Analysis in Real Time Time-Of-Flight Mass Spectrometry (DART TOFMS). Results: Individual distinction for both species was achieved but the accuracy was dependent on the dataset size and number of individuals included. As this is still experimental, we can only speak of individual comparison and not individual distinction at this point. The prediction accuracy for the country of origin increases with increasing sample number and a random sample can be placed in the correct country. When a complete disk is removed from the training dataset, its rings (samples) are correctly attributed to the country with an accuracy ranging from 43% to 100%. Relative abundances of ions appear to contribute more to differentiation compared to frequency differences. Conclusions: DART TOFMS shows potential for geographical provenancing but is still experimental for individual distinction; more research is needed to make this an established method. Sampling campaigns should focus on sampling tree cores from pith-to-bark, paving the way towards a chemical fingerprint database for species provenance.
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Wiedenhoeft AC, Simeone J, Smith A, Parker-Forney M, Soares R, Fishman A. Fraud and misrepresentation in retail forest products exceeds U.S. forensic wood science capacity. PLoS One 2019; 14:e0219917. [PMID: 31344141 PMCID: PMC6657862 DOI: 10.1371/journal.pone.0219917] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/03/2019] [Indexed: 11/19/2022] Open
Abstract
Fraud and misrepresentation in forest products supply chains is often associated with illegal logging, but the extent of fraud in the U.S. forest products market, and the availability of forensic expertise to detect it, is unknown. We used forensic wood anatomy to test 183 specimens from 73 consumer products acquired from major U.S. retailers, surveyed U.S. experts regarding their forensic wood anatomy capacity, and conducted a proficiency-testing program of those experts. 62% of tested products (45 of 73) had one or more type of fraudulent or misrepresented claim. Survey respondents reported a total capacity of 830 wood specimens per year, and participants' identification accuracy ranged from 6% to 92%. Given the extent of fraud and misrepresentation, U.S. wood forensic wood anatomy capacity does not scale with the need for such expertise. We call for increased training in forensic wood anatomy and its broader application in forest products supply chains to eliminate fraud and combat illegal logging.
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Affiliation(s)
- Alex C. Wiedenhoeft
- Center for Wood Anatomy Research, Forest Products Laboratory, Madison, WI, United States of America
- Department of Botany, University of Wisconsin, Madison, WI, United States of America
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, United States of America
- Ciências Biológicas (Botânica), Universidade Estadual Paulista–Botucatu, São Paulo, Brasil
- * E-mail:
| | - John Simeone
- Simeone Consulting, LLC, Anchorage, AK, United States of America
- World Wildlife Fund, Washington, DC, United States of America
| | - Amy Smith
- World Wildlife Fund, Washington, DC, United States of America
| | | | - Richard Soares
- Center for Wood Anatomy Research, Forest Products Laboratory, Madison, WI, United States of America
- Department of Botany, University of Wisconsin, Madison, WI, United States of America
| | - Akiva Fishman
- World Wildlife Fund, Washington, DC, United States of America
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Tang K, Ren J, Cronn R, Erickson DL, Milligan BG, Parker-Forney M, Spouge JL, Sun F. Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA. BMC Genomics 2018; 19:896. [PMID: 30526482 PMCID: PMC6288960 DOI: 10.1186/s12864-018-5253-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/15/2018] [Indexed: 01/14/2023] Open
Abstract
Background The application of genomic data and bioinformatics for the identification of restricted or illegally-sourced natural products is urgently needed. The taxonomic identity and geographic provenance of raw and processed materials have implications in sustainable-use commercial practices, and relevance to the enforcement of laws that regulate or restrict illegally harvested materials, such as timber. Improvements in genomics make it possible to capture and sequence partial-to-complete genomes from challenging tissues, such as wood and wood products. Results In this paper, we report the success of an alignment-free genome comparison method, \documentclass[12pt]{minimal}
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\begin{document}$$ {d}_2^{\ast }, $$\end{document}d2∗, that differentiates different geographic sources of white oak (Quercus) species with a high level of accuracy with very small amount of genomic data. The method is robust to sequencing errors, different sequencing laboratories and sequencing platforms. Conclusions This method offers an approach based on genome-scale data, rather than panels of pre-selected markers for specific taxa. The method provides a generalizable platform for the identification and sourcing of materials using a unified next generation sequencing and analysis framework. Electronic supplementary material The online version of this article (10.1186/s12864-018-5253-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kujin Tang
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jie Ren
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA
| | - Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA.
| | - David L Erickson
- DNA4 Technologies LLC, bwtech@UMBC Research & Technology Park, Baltimore, MD, 21227, USA
| | - Brook G Milligan
- Conservation Genomics Laboratory, Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | | | - John L Spouge
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Fengzhu Sun
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA. .,Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, 200433, China.
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17
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Deklerck V, Finch K, Gasson P, Van den Bulcke J, Van Acker J, Beeckman H, Espinoza E. Comparison of species classification models of mass spectrometry data: Kernel Discriminant Analysis vs Random Forest; A case study of Afrormosia (Pericopsis elata (Harms) Meeuwen). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1582-1588. [PMID: 28700098 DOI: 10.1002/rcm.7939] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE The genus Pericopsis includes four tree species of which only Pericopsis elata (Harms) Meeuwen is of commercial interest. Enforcement officers might have difficulties discerning this CITES-listed species from some other tropical African timber species. Therefore, we tested several methods to separate and identify these species rapidly in order to enable customs officials to uncover illegal trade. In this study, two classification methods using Direct Analysis in Real Time (DART™) ionization coupled with Time-of-Flight Mass Spectrometry (DART-TOFMS) data to discern between several species are presented. METHODS Metabolome profiles were collected using DART™ ionization coupled with TOFMS analysis of heartwood specimens of all four Pericopsis species and Haplormosia monophylla (Harms) Harms, Dalbergia melanoxylon Guill. & Perr. Harms, and Milicia excelsa (Welw.) C.C. Berg. In total, 95 specimens were analysed and the spectra evaluated. Kernel Discriminant Analysis (KDA) and Random Forest classification were used to discern the species. RESULTS DART-TOFMS spectra obtained from wood slivers and post-processing analysis using KDA and Random Forest classification separated Pericopsis elata from the other Pericopsis taxa and its lookalike timbers Haplormosia monophylla, Milicia excelsa, and Dalbergia melanoxylon. Only 50 ions were needed to achieve the highest accuracy. CONCLUSIONS DART-TOFMS spectra of the taxa were reproducible and the results of the chemometric analysis provided comparable accuracy. Haplormosia monophylla was visually distinguished based on the heatmap and was excluded from further analysis. Both classification methods, KDA and Random Forest, were capable of distinguishing Pericopsis elata from the other Pericopsis taxa, Milicia excelsa, and Dalbergia melanoxylon, timbers that are commonly traded.
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Affiliation(s)
- V Deklerck
- Woodlab-UGent, Ghent University, Laboratory of Wood Technology, Department of Forest and Water Management, Coupure Links 653, B-9000, Ghent, Belgium
- Wood Biology Service, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, 3080, Tervuren, Belgium
| | - K Finch
- Department of Botany and Plant Pathology, Oregon State University, Cordley Hall, 2701 SW Campus Way, Corvalis, OR, USA
| | - P Gasson
- Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - J Van den Bulcke
- Woodlab-UGent, Ghent University, Laboratory of Wood Technology, Department of Forest and Water Management, Coupure Links 653, B-9000, Ghent, Belgium
| | - J Van Acker
- Woodlab-UGent, Ghent University, Laboratory of Wood Technology, Department of Forest and Water Management, Coupure Links 653, B-9000, Ghent, Belgium
| | - H Beeckman
- Wood Biology Service, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, 3080, Tervuren, Belgium
| | - E Espinoza
- U.S. National Fish and Wildlife Forensic Laboratory, 1490 East Main Street, Ashland, OR, USA
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