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Ceccopieri M, Farias CO, Araújo M, Soares MLG, Estrada GCD, Wagener A, Hamacher C. Aliphatic and polycyclic aromatic hydrocarbons in surface sediments as a tool for the assessment of the contamination status of mangrove forests in Rio de Janeiro (Brazil). MARINE POLLUTION BULLETIN 2023; 192:115049. [PMID: 37201352 DOI: 10.1016/j.marpolbul.2023.115049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/26/2023] [Accepted: 05/07/2023] [Indexed: 05/20/2023]
Abstract
The distribution of aliphatic and polycyclic aromatic hydrocarbons (PAHs) in surface sediments from mangrove forests of the Rio de Janeiro State was investigated. Ten sampling stations were selected in the mangroves of Sepetiba Bay and the Jacarepaguá Lagoon Complex (JLC), which are areas affected by multiple human activities. The total aliphatic hydrocarbons concentrations showed marked variation between samples (27-407 μg g-1), mostly related to the total organic carbon contents. The total PAHs concentration ranged between 38 and 792 ng g-1. Diagnostic indices and statistical analysis showed that the mangrove forests can be divided into three groups: the western portion of Sepetiba Bay with the lowest level of contamination; the inner portion of the bay with the most intense presence of local sources of contamination, especially of pyrolytic character; and the JLC with a greater accumulation of hydrocarbons, mainly derived from petroleum combustion, resultant from the intense urbanization.
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Affiliation(s)
- Milena Ceccopieri
- Institute of Environment, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA; Laboratório de Geoquímica Orgânica Marinha (LAGOM), Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, RJ 20550-013, Brazil.
| | - Cássia O Farias
- Laboratório de Geoquímica Orgânica Marinha (LAGOM), Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, RJ 20550-013, Brazil
| | - Michelle Araújo
- Laboratório de Geoquímica Orgânica Marinha (LAGOM), Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, RJ 20550-013, Brazil
| | - Mario L G Soares
- Núcleo de Estudos em Manguezais (NEMA), Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, RJ 20550-013, Brazil
| | - Gustavo C D Estrada
- Núcleo de Estudos em Manguezais (NEMA), Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, RJ 20550-013, Brazil
| | - Angela Wagener
- Laboratório de Estudos Marinhos e Ambientais (LabMAM), Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, RJ 22451-900, Brazil
| | - Cláudia Hamacher
- Laboratório de Geoquímica Orgânica Marinha (LAGOM), Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, RJ 20550-013, Brazil
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Natkaniec-Nowak L, Drzewicz P, Stach P, Mroczkowska-Szerszeń M, Żukowska G. The overview of analytical methods for studying of fossil natural resins. Crit Rev Anal Chem 2023:1-23. [PMID: 37083454 DOI: 10.1080/10408347.2023.2200855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The review presents methods that are used frequently for multi-analytical study of fossil resins. The preliminary characterization relies on physical methods such as microhardness, density and fluorescence in UV light measurements. The spectroscopic methods: infrared spectroscopy, Raman spectroscopy, fluorescence spectroscopy are also presented in the paper. Besides that, the review also contains examples of the application of chromatographic methods: gas chromatography, thin layer chromatography, high-performance liquid chromatography, two-dimensional gas chromatography coupled to time-of-flight mass spectrometry as well as sample preparation methods for chromatographic studies such as pyrolysis. Additionally, thermal methods such as thermogravimetric analysis and differential scanning calorimetry also are covered by the review. Beside the examples of application, a detailed description with development history and perspective for further improvement are presented for each method. Moreover, fit-for-purpose assessment of each method is illustrated based on many examples from literature. The paper also contains examples of the application of multivariate statistical analysis and chemometric methods for comparing multiple properties of different fossil resin specimens for differentiation and classification purposes.
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Affiliation(s)
- Lucyna Natkaniec-Nowak
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Krakow, Poland
| | | | - Pawel Stach
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Krakow, Poland
| | | | - Grażyna Żukowska
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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Wang B, Shan T, Wang J, Huang F, Liu W, Tu W, Li S, Chen Q. Sources, distribution and decomposition of soil organic matter based on an effective biomarker in the pastoral areas of Zoige Plateau, China. CHEMOSPHERE 2023; 312:137295. [PMID: 36410503 DOI: 10.1016/j.chemosphere.2022.137295] [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: 09/08/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
The degradation of organic matter in soils plays an important role in the carbon cycle. Lignin is the main source of soil organics and it can be used to trace the source, distribution and turnover of organic matter. In this study the distribution and degradation of lignin were investigated to identify the source and degradation of soil organic matter during the succession of China's Zoige Plateau. Lignin monomers were determined by gas chromatography-mass spectrometry with alkaline CuO oxidation and the soils' δ13C and δ15N contents were interpreted to explore the turnover rate of lignin and organic matter. The main source of organics was identified as C3 non-woody angiosperm tissues. Lignin in the topsoil (0-30 cm) was derived from litter and roots, and it then migrated vertically to the deep soil (30-80 cm). Correlations of δ13C/δ15N with the soil's elemental composition showed that the organics degraded more quickly in meadow soil than in bog soil. The soil communities in the meadow and bog soils were generally similar, but there were certain differences in the dominant microbial phyla at different depths. The meadow soil's effectiveness as a carbon sink was gradually weakened, while that of the bog soil strengthened with depth. These results provide a scientific basis for accurately assessing the carbon sink capacity of the soils in Zoige Plateau.
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Affiliation(s)
- Bin Wang
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China; Key Laboratory of Solid Waste Treatment and Resource Recycle, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China.
| | - Tingqian Shan
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China; Key Laboratory of Solid Waste Treatment and Resource Recycle, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China
| | - Junjie Wang
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China; Key Laboratory of Solid Waste Treatment and Resource Recycle, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China
| | - Fuyang Huang
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China; Key Laboratory of Solid Waste Treatment and Resource Recycle, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China.
| | - Wei Liu
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China; Key Laboratory of Solid Waste Treatment and Resource Recycle, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China
| | - Weiguo Tu
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China; Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, Sichuan 610015, People's Republic of China
| | - Sen Li
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, Sichuan 610015, People's Republic of China
| | - Qingsong Chen
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, Sichuan 610015, People's Republic of China
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Dynamics of Leaf- and Root-Specific Biomarkers during 1-Year of Litter Decomposition. FORESTS 2021. [DOI: 10.3390/f12121732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Root-specific and leaf-specific biomarkers have been used for decades to identify the origin of organic materials in soils and sediments. However, quantitative approaches require appropriate knowledge about the fate of these indicator molecules during degradation. To clarify this issue, we performed a 1-year incubation experiment with fine root and leaf material of six temperate tree species: European ash (Fraxinus excelsior), European beech (Fagus sylvatica), Oak spec. (Quercus spec.), Linden spec. (Tilia spec.), Norway spruce (Picea abies) and Scots pine (Pinus sylvatica). Only one molecule, x,16-dihydroxy hexadecanoic acid (x,16-C16), could be validated as a general leaf-specific biomarker for the set of all species. For roots, no general root biomarker was found. Ester-bound tricosanol (C23-OH) could be validated for five out of six species; 20-hydroxy eicosanoic acid (ωC20) could be validated for four out of six species, leaving Norway spruce without a suitable root biomarker. The results of this study suggest that the validity of leaf- and root-derived ester-bound lipids as biomarkers is highly species dependent and does not always coincide with previous findings. Concentrations of root- and leaf-derived ester-bound lipids did not stay constant within 1 year of degradation and changed without a linear trend. The change of concentrations seems to be highly species dependent. This might be due to a different structure and arrangement of the individual monomers in cutin and suberin per species, and, therefore, a different accessibility of bond cleaving enzymes. The usefulness of root and leaf biomarkers is context dependent. Our results suggest that general assumptions about litter input to forest soils solely based on biomarker analysis have to be considered carefully.
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Famiyeh L, Chen K, Xu J, Sun Y, Guo Q, Wang C, Lv J, Tang YT, Yu H, Snape C, He J. A review on analysis methods, source identification, and cancer risk evaluation of atmospheric polycyclic aromatic hydrocarbons. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:147741. [PMID: 34058584 DOI: 10.1016/j.scitotenv.2021.147741] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 06/12/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) have gained attention because of their environmental persistence and effects on ecosystems, animals, and human health. They are mutagenic, carcinogenic, and teratogenic. The review provides background knowledge about their sources, metabolism, temporal variations, and size distribution in atmospheric particulate matter. The review article briefly discusses the analytical methods suitable for the extraction, characterization, and quantification of nonpolar and polar PAHs, addressing the challenges. Herein, we discussed the molecular diagnostic ratios (DRs), stable carbon isotopic analysis (SCIA), and receptor models, with much emphasis on the positive matrix factorization (PMF) model, for apportioning PAH sources. Among which, DRs and PCA identified as the most widely employed method, but their accuracy for PAH source identification has received global criticism. Therefore, the review recommends compound-specific isotopic analysis (CSIA) and PMF as the best alternative methods to provide detailed qualitative and quantitative source analysis. The compound-specific isotopic signatures are not affected by environmental degradation and are considered promising for apportioning PAH sources. However, isotopic fractions of co-eluted compounds like polar PAHs and aliphatic hydrocarbons make the PAHs isotopic fractions interpretation difficult. The interference of unresolved complex mixtures is a limitation to the application of CSIA for PAH source apportionment. Hence, for CSIA to further support PAH source apportionment, fast and cost-effective purification techniques with no isotopic fractionation effects are highly desirable. The present review explains the concept of stable carbon isotopic analysis (SCIA) relevant to PAH source analysis, identifying the techniques suitable for sample extract purification. We demonstrate how the source apportioned PAHs can be applied in assessing the health risk of PAHs using the incremental lifetime cancer risk (ILCR) model, and in doing so, we identify the key factors that could undermine the accuracy of the ILCR and research gaps that need further investigation.
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Affiliation(s)
- Lord Famiyeh
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, 199 Taikang E Rd, Ningbo 315100, China
| | - Ke Chen
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, 199 Taikang E Rd, Ningbo 315100, China
| | - Jingsha Xu
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Yong Sun
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, 199 Taikang E Rd, Ningbo 315100, China
| | - Qingjun Guo
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Chengjun Wang
- College of Resources and Environmental Science, South-Central University of Nationalities, Wuhan 430074, China
| | - Jungang Lv
- Procuratoral Technology and Information Research Center, Supreme People's Procuratorate, Beijing 100144, China
| | - Yu-Ting Tang
- Department of Geographical Sciences, University of Nottingham Ningbo China, 199 Taikang E Rd, Ningbo 315100, China
| | - Huan Yu
- Department of Atmospheric Science, School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Collin Snape
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Jun He
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, 199 Taikang E Rd, Ningbo 315100, China; Key Laboratory of Carbonaceous Wastes Processing and Process Intensification Research of Zhejiang Province. University of Nottingham Ningbo China, Ningbo 315100, China.
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6
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Formation of Thiophene under Simulated Volcanic Hydrothermal Conditions on Earth-Implications for Early Life on Extraterrestrial Planets? Life (Basel) 2021; 11:life11020149. [PMID: 33669362 PMCID: PMC7920246 DOI: 10.3390/life11020149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 11/17/2022] Open
Abstract
Thiophene was detected on Mars during the Curiosity mission in 2018. The compound was even suggested as a biomarker due to its possible origin from diagenesis or pyrolysis of biological material. In the laboratory, thiophene can be synthesized at 400 °C by reacting acetylene and hydrogen sulfide on alumina. We here show that thiophene and thiophene derivatives are also formed abiotically from acetylene and transition metal sulfides such as NiS, CoS and FeS under simulated volcanic, hydrothermal conditions on Early Earth. Exactly the same conditions were reported earlier to have yielded a plethora of organic molecules including fatty acids and other components of extant metabolism. It is therefore tempting to suggest that thiophenes from abiotic formation could indicate sites and conditions well-suited for the evolution of metabolism and potentially for the origin-of-life on extraterrestrial planets.
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7
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Porter J, Dit Fouque KJ, Miksovska J, Fernandez-Lima F. Salt bridges govern the structural heterogeneity of heme protein interactions and porphyrin networks: microperoxidase-11. RSC Adv 2020; 10:33861-33867. [PMID: 35519052 PMCID: PMC9056719 DOI: 10.1039/d0ra04956e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/01/2020] [Indexed: 11/21/2022] Open
Abstract
In this work, a proteolytic digest of cytochrome c (microperoxidase 11, MP-11) was used as a model to study the structural aspects of heme protein interactions and porphyrin networks. The MP-11 structural heterogeneity was studied as a function of the starting pH (e.g., pH 3.1-6.1) and concentration (e.g., 1-50 μM) conditions and adduct coordination. Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) showed the MP-11 structural dependence of the charge state distribution and molecular ion forms with the starting pH conditions. The singly charged (e.g., [M]+, [M - 2H + NH4]+, [M - H + Na]+ and [M - H + K]+) and doubly charged (e.g., [M + H]2+, [M - H + NH4]2+, [M + Na]2+ and [M + K]2+) molecular ion forms were observed for all solvent conditions, although the structural heterogeneity (e.g., number of mobility bands) significantly varied with the pH value and ion form. The MP-11 dimer formation as a model for heme-protein protein interactions showed that dimer formation is favored toward more neutral pH and favored when assisted by salt bridges (e.g., NH4 +, Na+ and K+ vs. H+). Inspection of the dimer mobility profiles (2+ and 3+ charge states) showed a high degree of structural heterogeneity as a function of the solution pH and ion form; the observation of common mobility bands suggest that the different salt bridges can stabilize similar structural motifs. In addition, the salt bridge influence on the MP-11 dimer formations was measured using collision induced dissociation and showed a strong dependence with the type of salt bridge (i.e., a CE50 of 10.0, 11.5, 11.8 and 13.0 eV was observed for [2M + H]3+, [2M - H + NH4]3+, [2M + Na]3+ and [2M + K]3+, respectively). Measurements of the dimer equilibrium constant showed that the salt bridge interactions increase the binding strength of the dimeric species.
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Affiliation(s)
- J Porter
- Department of Chemistry and Biochemistry, Florida International University Miami FL 33199 USA
| | - K Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University Miami FL 33199 USA
| | - J Miksovska
- Department of Chemistry and Biochemistry, Florida International University Miami FL 33199 USA
- Biomolecular Science Institute, Florida International University Miami FL 33199 USA
| | - F Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University Miami FL 33199 USA
- Biomolecular Science Institute, Florida International University Miami FL 33199 USA
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Isaacman-VanWertz G, Lu X, Weiner E, Smiley E, Widdowson M. Characterization of Hydrocarbon Groups in Complex Mixtures Using Gas Chromatography with Unit-Mass Resolution Electron Ionization Mass Spectrometry. Anal Chem 2020; 92:12481-12488. [DOI: 10.1021/acs.analchem.0c02308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Gabriel Isaacman-VanWertz
- The Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061-0105, United States
| | - Xin Lu
- The Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061-0105, United States
| | - Ellen Weiner
- The Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061-0105, United States
| | - Elizabeth Smiley
- The Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061-0105, United States
| | - Mark Widdowson
- The Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061-0105, United States
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9
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Havelcová M, Machovič V, Novák F, Lapčák L, Mizera J, Hendrych J. Chemical characterization of mountain forest soils: impact of long-term atmospheric deposition loadings (Czech-Polish-German border region). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:20344-20357. [PMID: 32239414 DOI: 10.1007/s11356-020-08558-x] [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: 10/21/2019] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
The composition of lipids in soil offers clues to soil degradation processes due their persistency and selectivity in soil, and close relation to long-term processes in the ecosystem, thanks to their role in cell membranes of organisms. Organic solvent-extractable compounds were recovered from soils collected at two sites differing in the degree of forest damage. Gas chromatography/mass spectroscopy and Fourier transform infrared spectroscopy were applied in order to characterize solvent-extractable lipids. Raman spectroscopy was also applied as it provides distinct advantages for determining the structural order of carbonaceous materials. The organic matter measurement techniques were combined with an established simultaneous multi-element measurement technique. Variations in individual soil horizons from the sites were reflected in the crystallinity of epicuticular waxes, presence of long-chain aliphatic hydrocarbons, concentrations of n-alkanes, saturated and unsaturated fatty acids, dicarboxylic acids, and in the content of aromatic structures, hydroxyl, ester, and carboxylic acid groups. The results are explained by differently transformed organic matter. The concentrations of elements in the soils were also affected by atmospheric depositions, including higher accumulations of arsenic and antimony, and lower contents of natural nutrients. These data have potential to be used as sensitive biogenic indicators of ecosystem damage by long-term atmospheric depositions.
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Affiliation(s)
- Martina Havelcová
- Institute of Rock Structure and Mechanics, AS CR V Holešovičkách 41, 182 09, Prague, Czech Republic.
| | - Vladimír Machovič
- Institute of Rock Structure and Mechanics, AS CR V Holešovičkách 41, 182 09, Prague, Czech Republic
- University of Chemistry and Technology Prague, Technická 5, 166 28, Prague, Czech Republic
| | - František Novák
- Technopark Kralupy, University of Chemistry and Technology Prague, 278 01, Kralupy nad Vltavou, Czech Republic
| | - Ladislav Lapčák
- University of Chemistry and Technology Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Jiří Mizera
- Institute of Nuclear Physic, Řež 130, 250 68, Řež, Czech Republic
| | - Jiří Hendrych
- University of Chemistry and Technology Prague, Technická 5, 166 28, Prague, Czech Republic
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Abstract
The question whether organic compounds occur on Mars remained unanswered for decades. However, the recent discovery of various classes of organic matter in martian sediments by the Curiosity rover seems to strongly suggest that indigenous organic compounds exist on Mars. One intriguing group of detected organic compounds were thiophenes, which typically occur on Earth in kerogen, coal, and crude oil as well as in stromatolites and microfossils. Here we provide a brief synopsis of conceivable pathways for the generation and degradation of thiophenes on Mars. We show that the origin of thiophene derivatives can either be biotic or abiotic, for example, through sulfur incorporation in organic matter during early diagenesis. The potential of thiophenes to represent martian biomarkers is discussed as well as a correlation between abundances of thiophenes and sulfate-bearing minerals. Finally, this study provides suggestions for future investigations on Mars and in Earth-based laboratories to answer the question whether the martian thiophenes are of biological origin.
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Affiliation(s)
- Jacob Heinz
- Center for Astronomy and Astrophysics (ZAA), Astrobiology Research Group, Technische Universität Berlin, Berlin, Germany
| | - Dirk Schulze-Makuch
- Center for Astronomy and Astrophysics (ZAA), Astrobiology Research Group, Technische Universität Berlin, Berlin, Germany
- German Research Centre for Geosciences (GFZ), Section Geomicrobiology, Potsdam, Germany
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
- School of the Environment, Washington State University, Pullman, WA, USA
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11
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Miller AZ, De la Rosa JM, Jiménez-Morillo NT, Pereira MFC, Gonzalez-Perez JA, Knicker H, Saiz-Jimenez C. Impact of wildfires on subsurface volcanic environments: New insights into speleothem chemistry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134321. [PMID: 31783462 DOI: 10.1016/j.scitotenv.2019.134321] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Siliceous speleothems frequently reported in volcanic caves have been traditionally interpreted as resulting from basalt weathering combined with the activity of microbial communities. A characteristic feature in lava tubes from Hawaii, Azores and Canary Islands is the occurrence of black jelly-like speleothems. Here we describe the formation process of siliceous black speleothems found in a lava tube from La Palma, Canary Islands, Spain, based on mineralogy, microscopy, light stable isotopes, analytical pyrolysis, NMR spectroscopy and chemometric analyses. The data indicate that the black speleothems are composed of a hydrated gel matrix of amorphous aluminum silicate materials containing charred vegetation and thermally degraded resins from pines or triterpenoids from Erica arborea, characteristic of the overlying laurel forest. This is the first observation of a connection between fire and speleothem chemistry from volcanic caves. We conclude that wildfires and organic matter from the surface area overlying caves may play an important role in the formation of speleothems found in La Palma and demonstrate that siliceous speleothems are potential archives for past fires.
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Affiliation(s)
- Ana Z Miller
- Laboratório HERCULES, Universidade de Évora, Largo Marquês de Marialva 8, 7000-676 Évora, Portugal; Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas (IRNAS-CSIC), Av. Reina Mercedes 10, 41012 Sevilla, Spain.
| | - José M De la Rosa
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas (IRNAS-CSIC), Av. Reina Mercedes 10, 41012 Sevilla, Spain
| | | | - Manuel F C Pereira
- CERENA, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - José A Gonzalez-Perez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas (IRNAS-CSIC), Av. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Heike Knicker
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas (IRNAS-CSIC), Av. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas (IRNAS-CSIC), Av. Reina Mercedes 10, 41012 Sevilla, Spain
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12
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Garcia MR, Cattani AP, da Cunha Lana P, Figueira RCL, Martins CC. Petroleum biomarkers as tracers of low-level chronic oil contamination of coastal environments: A systematic approach in a subtropical mangrove. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 249:1060-1070. [PMID: 31146312 DOI: 10.1016/j.envpol.2019.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/01/2019] [Accepted: 03/03/2019] [Indexed: 06/09/2023]
Abstract
Petroleum biomarkers (hopanes, terpanes and steranes) are frequently assessed in estuarine sediments as tracers of oil input. In order to compare distinct patterns of hydrocarbon accumulation in mudflats, salt marsh and mangrove, sediments from two transects (control and impacted areas) were sampled in Paranaguá Bay, SW Atlantic. Concentrations of n-alkanes, polycyclic aromatic hydrocarbons (PAHs) and petroleum biomarkers (hopanes, terpanes and steranes) were determined, as well as bulk parameters (TOC, grain size and δ13C). N-alkanes concentrations were similar between control and impacted sites (respectively, 3.03 ± 1.20 μg g-1 and 4.11 ± 3.02 μg g-1) and reflected a high biogenic input. Conversely, PAHs and petroleum biomarker concentrations were three to six times higher in impacted site than the control site (respectively, 60.4 ± 23.3 ng g-1 and 22.0 ± 25.0 ng g-1 for PAHs and 197.7 ± 51.8 ng g-1 and 40.2 ± 32. ng g-1 for hopanes). Despite these differences, concentrations were lower than those reported for highly impacted areas worldwide. Diagnostic ratios and hydrocarbon parameters (e.g. total PAHs and total petroleum biomarkers) helped to distinguish human impact in the ecological zones, suggesting different sources and/or levels of weathering, confirmed by ANOVA tests. TOC played a fundamental role to the concentration of hydrocarbons, showing similar distributions along the transects. Petroleum biomarkers could clearly indicate the preferential sites of deposition and assign different levels of anthropic contamination by hydrocarbons, thus providing clear information about the chronic petroleum pollution in coastal sediments.
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Affiliation(s)
- Marina Reback Garcia
- Programa de Pós-Graduação em Sistemas Costeiros e Oceânicos (PGSISCO), Universidade Federal do Paraná, Caixa Postal 61, 83255-976, Pontal do Paraná, PR, Brazil.
| | - André Pereira Cattani
- Centro de Estudos do Mar, Universidade Federal do Paraná, Caixa Postal 61, 83255-976, Pontal do Paraná, PR, Brazil
| | - Paulo da Cunha Lana
- Centro de Estudos do Mar, Universidade Federal do Paraná, Caixa Postal 61, 83255-976, Pontal do Paraná, PR, Brazil
| | - Rubens César Lopes Figueira
- Instituto Oceanográfico da Universidade de São Paulo, Praça do Oceanográfico, 191, 05508-900, São Paulo, SP, Brazil
| | - César C Martins
- Centro de Estudos do Mar, Universidade Federal do Paraná, Caixa Postal 61, 83255-976, Pontal do Paraná, PR, Brazil.
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Gas Chromatography Coupled to High Resolution Time-of-Flight Mass Spectrometry as a High-Throughput Tool for Characterizing Geochemical Biomarkers in Sediments. Int J Anal Chem 2019; 2018:2560498. [PMID: 30627163 PMCID: PMC6304594 DOI: 10.1155/2018/2560498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/30/2018] [Accepted: 11/04/2018] [Indexed: 11/17/2022] Open
Abstract
The performance of gas chromatography coupled to high-resolution time-of-flight mass spectrometry (GC-HRTofMS) for characterizing geochemical biomarkers from sediment samples was evaluated. Two approaches to obtain the geochemical biomarkers were tested: (1) extraction with organic solvent and subsequent derivatization and (2) in-situ derivatization thermal desorption. Results demonstrated that both approaches can be conveniently applied for simultaneous characterization of many geochemical biomarkers (alkanes, alkanols, sterols, and fatty acids), avoiding conventional time-consuming purification procedures. GC-HRTofMS reduces both sample preparation time and the number of chromatographic runs compared to traditional methodologies used in organic geochemistry. Particularly, the approach based on in-situ derivatization thermal desorption represents a very simple method that can be performed in-line employing few milligrams of sediment, eliminating the need for any sample preparation and solvent use. The high resolving power (m/Δm50% 25,000) and high mass accuracy (error ≤ 1 ppm) offered by the “zig-zag” time-of-flight analyzer were indispensable to resolve the complexity of the total ion chromatograms, representing a high-throughput tool. Extracted ion chromatograms using exact m/z were useful to eliminate many isobaric interferences and to increase significantly the signal to noise ratio. Characteristic fragment ions allowed the identification of homologous series, such as alkanes, alkanols, fatty acids, and sterols. Polycyclic aromatic hydrocarbons were also identified in the samples by their molecular ions. The characterization of geochemical biomarkers along a sedimentary core collected in the area of Valo Grande Channel (Cananéia-Iguape Estuarine-Lagunar System (São Paulo, Brazil)) provided evidences of environmental changes. Sediments deposited before opening of channel showed dominance of biomarkers from mangrove vegetation, whereas sediments of the pos-opening period showed an increase of biomarkers from aquatic macrophyte (an invasive vegetation).
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Garabedian A, Leng F, Ridgeway ME, Park MA, Fernandez-Lima F. Tailoring peptide conformational space with organic gas modifiers in TIMS-MS. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s12127-018-0231-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Wang JJ, Pisani O, Lin LH, Lun OOY, Bowden RD, Lajtha K, Simpson AJ, Simpson MJ. Long-term litter manipulation alters soil organic matter turnover in a temperate deciduous forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:865-875. [PMID: 28711848 DOI: 10.1016/j.scitotenv.2017.07.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/09/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Understanding soil organic matter (OM) biogeochemistry at the molecular-level is essential for assessing potential impacts from management practices and climate change on shifts in soil carbon storage. Biomarker analyses and nuclear magnetic resonance (NMR) spectroscopy were used in an ongoing detrital input and removal treatment experiment in a temperate deciduous forest in Pennsylvania, USA, to examine how above- and below-ground plant inputs control soil OM quantity and quality at the molecular-level. From plant material to surface soils, the free acyclic lipids and cutin, suberin, and lignin biomarkers were preferentially retained over free sugars and free cyclic lipids. After 20years of above-ground litter addition (Double Litter) or exclusion (No Litter) treatments, soil OM composition was relatively more degraded, as revealed by solid-state 13C NMR spectroscopy. Under Doubled Litter inputs, soil carbon and phospholipid fatty acid (PLFA) concentrations were unchanged, suggesting that the current OM degradation status is a reflection of microbial-mediated degradation that occurred prior to the 20-year sampling campaign. Soil OM degradation was higher in the No Litter treatments, likely due to the decline in fresh, above-ground litter inputs over time. Furthermore, root and root and litter exclusion treatments (No Roots and No Inputs, respectively) both significantly reduced free sugars and PLFAs and increased preservation of suberin-derived compounds. PLFA stress ratios and the low N-acetyl resonances from diffusion edited 1H NMR also indicate substrate limitations and reduced microbial biomass with these treatments. Overall, we highlight that storage of soil carbon and its biochemical composition do not linearly increase with plant inputs because the microbial processing of soil OM is also likely altered in the studied forest.
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Affiliation(s)
- Jun-Jian Wang
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Oliva Pisani
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Lisa H Lin
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Olivia O Y Lun
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Richard D Bowden
- Department of Environmental Science, Allegheny College, Meadville, PA 16335, USA
| | - Kate Lajtha
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
| | - André J Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Myrna J Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada.
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Worton DR, Decker M, Isaacman-VanWertz G, Chan AWH, Wilson KR, Goldstein AH. Improved molecular level identification of organic compounds using comprehensive two-dimensional chromatography, dual ionization energies and high resolution mass spectrometry. Analyst 2017; 142:2395-2403. [PMID: 28555694 DOI: 10.1039/c7an00625j] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A new analytical methodology combining comprehensive two-dimensional gas chromatography (GC×GC), dual ionization energies and high resolution time of flight mass spectrometry has been developed that improves molecular level identification of organic compounds in complex environmental samples. GC×GC maximizes compound separation providing cleaner mass spectra by minimizing erroneous fragments from interferences and co-eluting peaks. Traditional electron ionization (EI, 70 eV) provides MS fragmentation patterns that can be matched to published EI MS libraries while vacuum ultraviolet photoionization (VUV, 10.5 eV) yields MS with reduced fragmentation enhancing the abundance of the molecular ion providing molecular formulas when combined with high resolution mass spectrometry. We demonstrate this new approach by applying it to a sample of organic aerosol. In this sample, 238 peaks were matched to EI MS library data with FM ≥ 800 but a fifth (42 compounds) were determined to be incorrectly identified because the molecular formula was not confirmed by the VUV MS data. This highlights the importance of using a complementary technique to confirm compound identifications even for peaks with very good matching statistics. In total, 171 compounds were identified by EI MS matching to library spectra with confirmation of the molecular formula from the high resolution VUV MS data and were not dependent on the matching statistics being above a threshold value. A large number of unidentified peaks were still observed with FM < 800, which in routine analysis would typically be neglected. Where possible, these peaks were assigned molecular formulas from the VUV MS data (211 in total). In total, the combination of EI and VUV MS data provides more than twice as much molecular level peak information than traditional approaches and improves confidence in the identification of individual organic compounds. The molecular formula data from the VUV MS data was used, in conjunction with GC×GC retention times and the observed EI MS, to generate a new, searchable EI MS library compatible with the standard NIST MS search program. This library is deliberately dynamic and editable so that other end users can add new entries and update existing entries as new information becomes available.
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Affiliation(s)
- David R Worton
- Department of Environmental Sciences Policy and Management, University of California, Berkeley, CA 94720, USA.
| | - Monika Decker
- Department of Environmental Sciences Policy and Management, University of California, Berkeley, CA 94720, USA.
| | - Gabriel Isaacman-VanWertz
- Department of Environmental Sciences Policy and Management, University of California, Berkeley, CA 94720, USA.
| | - Arthur W H Chan
- Department of Environmental Sciences Policy and Management, University of California, Berkeley, CA 94720, USA.
| | - Kevin R Wilson
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Allen H Goldstein
- Department of Environmental Sciences Policy and Management, University of California, Berkeley, CA 94720, USA. and Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720, USA
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17
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Pisani O, Haddix ML, Conant RT, Paul EA, Simpson MJ. Molecular composition of soil organic matter with land-use change along a bi-continental mean annual temperature gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 573:470-480. [PMID: 27572539 DOI: 10.1016/j.scitotenv.2016.08.154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 08/12/2016] [Accepted: 08/21/2016] [Indexed: 06/06/2023]
Abstract
Soil organic matter (SOM) is critical for maintaining soil fertility and long-term agricultural sustainability. The molecular composition of SOM is likely altered due to global climate and land-use change; but rarely are these two aspects studied in tandem. Here we used molecular-level techniques to examine SOM composition along a bi-continental (from North to South America) mean annual temperature (MAT) gradient from seven native grassland/forest and cultivated/pasture sites. Biomarker methods included solvent extraction, base hydrolysis and cupric (II) oxide oxidation for the analysis of free lipids of plant and microbial origin, ester-bound lipids from cutin and suberin, and lignin-derived phenols, respectively. Solid-state 13C nuclear magnetic resonance (NMR) was used to examine the overall composition of SOM. Soil cultivation was found to increase the amount of microbial-derived compounds at warmer temperatures (up to 17% increase). The cultivated soils were characterized by much lower contributions of plant-derived SOM components compared to the native soils (up to 64% lower at the coldest site). In addition, cultivation caused an increase in lignin and cutin degradation (up to 68 and 15% increase, respectively), and an increase in the amount of suberin-derived inputs (up to 54% increase). Clear differences in the molecular composition of SOM due to soil cultivation were observed in soils of varying mineral composition and were attributed to disturbance, different vegetation inputs, soil aggregate destruction and MAT. A high organic allophanic tropical soil was characterized by its protection of carbohydrates and nitrogen-containing compounds. The conversion of native to cultivated land shows significant shifts in the degradation stage of SOM. In particular, cutin-derived compounds which are believed to be part of the stable SOM pool may undergo enhanced degradation with long-term cultivation and disruption of soil aggregates. On a per year basis, the total amount of cutin decreased only at the two forest sites that were converted to pasture, likely due to cutin degradation or to changes in vegetation and litter quality associated with land-use change. Overall, our study highlights that the implementation of different agricultural management practices enhances the degradation of recalcitrant SOM compounds that may become a source of atmospheric CO2 with increasing land-use and climate change.
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Affiliation(s)
- Oliva Pisani
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Michelle L Haddix
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80523, USA
| | - Richard T Conant
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80523, USA
| | - Eldor A Paul
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80523, USA
| | - Myrna J Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada.
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18
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Kune C, Far J, De Pauw E. Accurate Drift Time Determination by Traveling Wave Ion Mobility Spectrometry: The Concept of the Diffusion Calibration. Anal Chem 2016; 88:11639-11646. [PMID: 27934120 DOI: 10.1021/acs.analchem.6b03215] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion mobility spectrometry (IMS) is a gas phase separation technique, which relies on differences in collision cross section (CCS) of ions. Ionic clouds of unresolved conformers overlap if the CCS difference is below the instrumental resolution expressed as CCS/ΔCCS. The experimental arrival time distribution (ATD) peak is then a superimposition of the various contributions weighted by their relative intensities. This paper introduces a strategy for accurate drift time determination using traveling wave ion mobility spectrometry (TWIMS) of poorly resolved or unresolved conformers. This method implements through a calibration procedure the link between the peak full width at half-maximum (fwhm) and the drift time of model compounds for wide range of settings for wave heights and velocities. We modified a Gaussian equation, which achieves the deconvolution of ATD peaks where the fwhm is fixed according to our calibration procedure. The new fitting Gaussian equation only depends on two parameters: The apex of the peak (A) and the mean drift time value (μ). The standard deviation parameter (correlated to fwhm) becomes a function of the drift time. This correlation function between μ and fwhm is obtained using the TWIMS calibration procedure which determines the maximum instrumental ion beam diffusion under limited and controlled space charge effect using ionic compounds which are detected as single conformers in the gas phase. This deconvolution process has been used to highlight the presence of poorly resolved conformers of crown ether complexes and peptides leading to more accurate CCS determinations in better agreement with quantum chemistry predictions.
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Affiliation(s)
- Christopher Kune
- Laboratory of Mass Spectrometry, University of Liege , Quartier Agora, Allée du Six Aout 11, B-4000, Liege, Belgium
| | - Johann Far
- Laboratory of Mass Spectrometry, University of Liege , Quartier Agora, Allée du Six Aout 11, B-4000, Liege, Belgium
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, University of Liege , Quartier Agora, Allée du Six Aout 11, B-4000, Liege, Belgium
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19
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Garabedian A, Butcher D, Lippens JL, Miksovska J, Chapagain PP, Fabris D, Ridgeway ME, Park MA, Fernandez-Lima F. Structures of the kinetically trapped i-motif DNA intermediates. Phys Chem Chem Phys 2016; 18:26691-26702. [PMID: 27711445 PMCID: PMC5652045 DOI: 10.1039/c6cp04418b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In the present work, the conformational dynamics and folding pathways of i-motif DNA were studied in solution and in the gas-phase as a function of the solution pH conditions using circular dichroism (CD), photoacoustic calorimetry analysis (PAC), trapped ion mobility spectrometry-mass spectrometry (TIMS-MS), and molecular dynamics (MD). Solution studies showed at thermodynamic equilibrium the existence of a two-state folding mechanism, whereas during the pH = 7.0 → 4.5 transition a fast and slow phase (ΔHfast + ΔHslow = 43 ± 7 kcal mol-1) with a volume change associated with the formation of hemiprotonated cytosine base pairs and concomitant collapse of the i-motif oligonucleotide into a compact conformation were observed. TIMS-MS experiments showed that gas-phase, kinetically trapped i-motif DNA intermediates produced by nanoESI are preserved, with relative abundances depending on the solution pH conditions. In particular, a folded i-motif DNA structure was observed in nanoESI-TIMS-MS for low charge states in both positive and negative ion mode (e.g., z = ±3 to ±5) at low pH conditions. As solution pH increases, the cytosine neutralization leads to the loss of cytosine-cytosine+ (C·CH+) base pairing in the CCC strands and in those conditions we observe partially unfolded i-motif DNA conformations in nanoESI-TIMS-MS for higher charge states (e.g., z = -6 to -9). Collisional induced activation prior to TIMS-MS showed the existence of multiple local free energy minima, associated with the i-motif DNA unfolding at z = -6 charge state. For the first time, candidate gas-phase structures are proposed based on mobility measurements of the i-motif DNA unfolding pathway. Moreover, the inspection of partially unfolded i-motif DNA structures (z = -7 and z = -8 charge states) showed that the presence of inner cations may or may not induce conformational changes in the gas-phase. For example, incorporation of ammonium adducts does not lead to major conformational changes while sodium adducts may lead to the formation of sodium mediated bonds between two negatively charged sides inducing the stabilization towards more compact structures in new local, free energy minima in the gas-phase.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA.
| | - David Butcher
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA.
| | | | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. and Biomolecular Science Institute, Florida International University, Miami, USA
| | - Prem P Chapagain
- Biomolecular Science Institute, Florida International University, Miami, USA and Department of Physics, Florida International University, Miami, USA
| | | | | | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. and Biomolecular Science Institute, Florida International University, Miami, USA
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20
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Reiffarth DG, Petticrew EL, Owens PN, Lobb DA. Sources of variability in fatty acid (FA) biomarkers in the application of compound-specific stable isotopes (CSSIs) to soil and sediment fingerprinting and tracing: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 565:8-27. [PMID: 27155260 DOI: 10.1016/j.scitotenv.2016.04.137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/15/2016] [Accepted: 04/17/2016] [Indexed: 05/23/2023]
Abstract
Determining soil redistribution and sediment budgets in watersheds is often challenging. One of the methods for making such determinations employs soil and sediment fingerprinting techniques, using sediment properties such as geochemistry, fallout radionuclides, and mineral magnetism. These methods greatly improve the estimation of erosion and deposition within a watershed, but are limited when determining land use-based soil and sediment movement. Recently, compound-specific stable isotopes (CSSIs), which employ fatty acids naturally occurring in the vegetative cover of soils, offer the possibility of refining fingerprinting techniques based on land use, complementing other methods that are currently in use. The CSSI method has been met with some success; however, challenges still remain with respect to scale and resolution due to a potentially large degree of biological, environmental and analytical uncertainty. By better understanding the source of tracers used in CSSI work and the inherent biochemical variability in those tracers, improvement in sample design and tracer selection is possible. Furthermore, an understanding of environmental and analytical factors affecting the CSSI signal will lead to refinement of the approach and the ability to generate more robust data. This review focuses on sources of biological, environmental and analytical variability in applying CSSI to soil and sediment fingerprinting, and presents recommendations based on past work and current research in this area for improving the CSSI technique. A recommendation, based on current information available in the literature, is to use very-long chain saturated fatty acids and to avoid the use of the ubiquitous saturated fatty acids, C16 and C18.
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Affiliation(s)
- D G Reiffarth
- Natural Resources and Environmental Studies Program, University of Northern British Columbia, 3333 University Way, Prince George, BC V2N 4Z9, Canada.
| | - E L Petticrew
- Geography Program and Quesnel River Research Centre, University of Northern British Columbia, 3333 University Way, Prince George, BC V2N 4Z9, Canada.
| | - P N Owens
- Environmental Science Program and Quesnel River Research Centre, University of Northern British Columbia, 3333 University Way, Prince George, BC, V2N 4Z9, Canada.
| | - D A Lobb
- Watershed Systems Research Program, University of Manitoba, 13 Freedman Crescent, Winnipeg, MB R3T 2N2, Canada.
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21
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Benigni P, Marin R, Molano-Arevalo JC, Garabedian A, Wolff JJ, Ridgeway ME, Park MA, Fernandez-Lima F. Towards the Analysis of High Molecular Weight Proteins and Protein complexes using TIMS-MS. INTERNATIONAL JOURNAL FOR ION MOBILITY SPECTROMETRY : OFFICIAL PUBLICATION OF THE INTERNATIONAL SOCIETY FOR ION MOBILITY SPECTROMETRY 2016; 19:95-104. [PMID: 27818614 PMCID: PMC5091298 DOI: 10.1007/s12127-016-0201-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 05/26/2016] [Accepted: 05/29/2016] [Indexed: 01/02/2023]
Abstract
In the present work, we demonstrate the potential and versatility of TIMS for the analysis of proteins, DNA-protein complexes and protein-protein complexes in their native and denatured states. In addition, we show that accurate CCS measurement are possible and in good agreement with previously reported CCS values using other IMS analyzers (<5% difference). The main challenges for the analysis of high mass proteins and protein complexes in the mobility and m/z domain are described. That is, the analysis of high molecular weight systems in their native state may require the use of higher electric fields or a compromise in the TIMS mobility resolution by reducing the bath gas velocity in order to effectively trap at lower electric fields. This is the first report of CCS measurements of high molecular weight biomolecules and biomolecular complexes (~ 150 kDa) using TIMS-MS.
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Rebecca Marin
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | - Alyssa Garabedian
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
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23
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Laitano MV, Castro ÍB, Costa PG, Fillmann G, Cledón M. Butyltin and PAH Contamination of Mar del Plata Port (Argentina) Sediments and Their Influence on Adjacent Coastal Regions. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2015; 95:513-520. [PMID: 26310126 DOI: 10.1007/s00128-015-1637-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 08/18/2015] [Indexed: 06/04/2023]
Abstract
The distribution of butyltins (BTs) and polycyclic aromatic hydrocarbons (PAHs) were studied in surface sediments to assess how relevant is Mar del Plata port (Argentina) as a source of contamination to the surrounding environments. Within the port, TBT concentrations ranged from 24.2 to 150 ng Sn g(-1) and PAHs (Σ16) from 180 to 17,094 ng g(-1). At the surrounding beaches, PAHs were detected at low concentrations and TBT concentrations reached 10.9 ng Sn g(-1). Although those low levels indicate that the Port might not be an important source of contamination to the surrounding beaches, the very low TOC content and the coarse grain size of the beaches sediments could explain the sedimentary levels. The results show a reduction in TBT levels in Mar del Plata port after national and international use restrictions of TBT-based antifouling paints.
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Affiliation(s)
- María V Laitano
- IIMyC, Instituto de Investigaciones Marinas y Costeras, CONICET-FCEN, Universidad Nacional de Mar del Plata, Funes 3350, 7600, Mar del Plata, Provincia de Buenos Aires, Argentina.
| | - Ítalo B Castro
- Laboratório de Microcontaminantes Orgânicos e Ecotoxicologia Aquática (CONECO), Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, RS, 96203-900, Brazil
- Departamento de Ciências do Mar, Universidade Federal de São Paulo (UNIFESP), Santos, SP, 11030-400, Brazil
| | - Patrícia G Costa
- Laboratório de Microcontaminantes Orgânicos e Ecotoxicologia Aquática (CONECO), Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, RS, 96203-900, Brazil
| | - G Fillmann
- Laboratório de Microcontaminantes Orgânicos e Ecotoxicologia Aquática (CONECO), Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, RS, 96203-900, Brazil
| | - M Cledón
- IIMyC, Instituto de Investigaciones Marinas y Costeras, CONICET-FCEN, Universidad Nacional de Mar del Plata, Funes 3350, 7600, Mar del Plata, Provincia de Buenos Aires, Argentina
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Organic matter source and degradation as revealed by molecular biomarkers in agricultural soils of Yuanyang terrace. Sci Rep 2015; 5:11074. [PMID: 26046574 PMCID: PMC4457134 DOI: 10.1038/srep11074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 04/27/2015] [Indexed: 11/29/2022] Open
Abstract
Three soils with different tillage activities were collected and compared for their organic matter sources and degradation. Two soils (TD and TP) with human activities showed more diverse of chemicals in both free lipids and CuO oxidation products than the one (NS) without human activities. Branched alkanoic acids only accounted for less than 5% of lipids, indicating limited microbial inputs in all three investigated soils. The degradation of lignin in NS and TD was relatively higher than TP, probably because of the chemical degradation, most likely UV light-involved photodegradation. Lignin parameters obtained from CuO oxidation products confirmed that woody gymnosperm tissue (such as pine trees) may be the main source for NS, while angiosperm tissues from vascular plant may be the predominant source for the lignins in TD and TP. Analysis of BPCAs illustrated that BC in NS may be mainly originated from soot or other fossil carbon sources, whereas BC in TD and TP may be produced during corn stalk and straw burning. BC was involved in mineral interactions for TD and TP. The dynamics of organic matter needs to be extensively examined for their nonideal interactions with contaminants.
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25
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Cho YT, Su H, Wu WJ, Wu DC, Hou MF, Kuo CH, Shiea J. Biomarker Characterization by MALDI-TOF/MS. Adv Clin Chem 2015; 69:209-54. [PMID: 25934363 DOI: 10.1016/bs.acc.2015.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometric techniques frequently used in clinical diagnosis, such as gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, ambient ionization mass spectrometry, and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF/MS), are discussed. Due to its ability to rapidly detect large biomolecules in trace amounts, MALDI-TOF/MS is an ideal tool for characterizing disease biomarkers in biologic samples. Clinical applications of MS for the identification and characterization of microorganisms, DNA fragments, tissues, and biofluids are introduced. Approaches for using MALDI-TOF/MS to detect various disease biomarkers including peptides, proteins, and lipids in biological fluids are further discussed. Finally, various sample pretreatment methods which improve the detection efficiency of disease biomarkers are introduced.
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Affiliation(s)
- Yi-Tzu Cho
- Department of Cosmetic Applications and Management, Yuh-Ing Junior College of Health Care & Management, Kaohsiung, Taiwan
| | - Hung Su
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wen-Jeng Wu
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Feng Hou
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chao-Hung Kuo
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan.
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Castellanos A, Benigni P, Hernandez DR, DeBord JD, Ridgeway ME, Park MA, Fernandez-Lima F. Fast Screening of Polycyclic Aromatic Hydrocarbons using Trapped Ion Mobility Spectrometry - Mass Spectrometry. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2014; 6:9328-9332. [PMID: 25558291 PMCID: PMC4280789 DOI: 10.1039/c4ay01655f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In the present paper, we showed the advantages of trapped ion mobility spectrometry coupled too mass spectrometry (TIMS-MS) combined with theoretical calculations for fast identification (millisecond timescale) of polycyclic aromatic hydrocarbons (PAH) compounds from complex mixtures. Accurate PAH collision cross sections (CCS, in nitrogen as a bath gas) are reported for the most commonly encountered PAH compounds and the ability to separate PAH geometric isomers is shown for three isobaric pairs with mobility resolution exceeding 150 (3-5 times higher than conventional IMS devices). Theoretical candidate structures (optimized at the DFT/B3LYP level) are proposed for the most commonly encountered PAH compounds showing good agreement with the experimental CCS values (<5%). The potential of TIMS-MS for the separation and identification of PAH compounds from complex mixtures without the need of lengthy pre-separation steps is illustrated for the case of a complex soil mixture.
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Affiliation(s)
- A Castellanos
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - P Benigni
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - D R Hernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - J D DeBord
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - M E Ridgeway
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - M A Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - F Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
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Visentin M, Pietrogrande MC. Determination of polar organic compounds in atmospheric aerosols by gas chromatography with ion trap tandem mass spectrometry. J Sep Sci 2014; 37:1561-9. [PMID: 24723391 DOI: 10.1002/jssc.201301332] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/28/2014] [Accepted: 04/01/2014] [Indexed: 01/13/2023]
Abstract
A gas chromatography with ion trap mass spectrometry method has been developed and validated for the analysis of 27 polar organic compounds in atmospheric aerosols. The target analytes were low-molecular-weight carboxylic acids and methoxyphenols, as relevant markers of source emissions and photochemical processes of organic aerosols. The operative parameters were optimized in order to achieve the best sensitivity and selectivity for the analysis. In comparison with the previous gas chromatography with mass spectrometry procedure based on single ion monitoring detection, the tandem mass spectrometry technique increased the analytical sensitivity by reducing detection limits for standard solutions from 1-2.6 to 0.1-0.4 ng/μL ranges (concentrations in the injected solution). In addition, it enhanced selectivity by reducing matrix interferences and chemical noise in the chromatogram. The applicability of the developed method in air quality monitoring campaigns was effectively checked by analyzing environmental samples collected in the Po Valley (Northern Italy) in different seasons. The obtained results indicate that the ion trap mass spectrometer may be an ideal alternative to high-resolution mass spectrometers for the user-friendly and cost-effective determination of a wide range of molecular tracers in airborne particulate matter.
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Affiliation(s)
- Marco Visentin
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
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29
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Ménager M, Azémard C, Vieillescazes C. Study of Egyptian mummification balms by FT-IR spectroscopy and GC–MS. Microchem J 2014. [DOI: 10.1016/j.microc.2013.11.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Ghanem E, Al-Hariri S. Separation of Isomers on Nematic Liquid Crystal Stationary Phases in Gas Chromatography: A Review. Chromatographia 2014. [DOI: 10.1007/s10337-014-2675-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Mohd Tahir N, Pang SY, Abdullah NA, Suratman S. Composition and sources of aliphatic lipids and sterols in sediments of a tropical island, southern South China Sea: preliminary assessment. ENVIRONMENTAL MONITORING AND ASSESSMENT 2013; 185:10209-10216. [PMID: 23856812 DOI: 10.1007/s10661-013-3325-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 06/26/2013] [Indexed: 06/02/2023]
Abstract
Near-shore surface sediment was collected from five stations off Redang Island located on the eastern coast of Peninsular Malaysia. Freeze-dried sediments were Soxhlet extracted and then fractionated using column chromatography into aliphatic and polar fractions. Determination of these fractions was carried out using gas chromatography mass spectrometry. The concentration of total resolved aliphatic hydrocarbons in sediments ranged from 157 to 308 ng/g. The distribution of aliphatic fraction showed the presence of n-alkanes ranging from nC15 to nC33 with a minor odd-to-even predominance exhibiting carbon maximum, depending on station, at nC17, nC26, nC29 or nC31. Calculation of Carbon Preference Index (CPI) for CPI(15-33) gave values ranging from 1.09 to 1.46. n-Alkanol in all sediment exhibits even-to-odd carbon predominance ranging from nC16 to nC28 and maximising at nC22. n-Fatty acids distribution ranged from nC14 to nC24 with a dominant maximum at nC16 and exhibiting high values of short chain fatty acids (≤nC20) to long chain fatty acids (>nC20) ratios. Unsaturated fatty acids, particularly nC16:1 and nC18:1 is also ubiquitous in all samples. Cholesterol is the most abundant compound amongst the sterol group ranging from 42.8 to 62.6% of the total sterols. β-Sitosterol, brassicasterol and stigmasterol, are also present but of relatively lower amount. These observations suggest that the aliphatic lipids and sterols in the study area originate, mainly, from biogenic sources of marine microbial with minor contribution from epiticular waxes of terrestrial plants.
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Affiliation(s)
- N Mohd Tahir
- Environmental Research Group, Department of Chemical Sciences, Faculty of Science & Technology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia,
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32
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Kumano S, Sugiyama M, Yamada M, Nishimura K, Hasegawa H, Morokuma H, Inoue H, Hashimoto Y. Development of a Portable Mass Spectrometer Characterized by Discontinuous Sample Gas Introduction, a Low-Pressure Dielectric Barrier Discharge Ionization Source, and a Vacuumed Headspace Technique. Anal Chem 2013; 85:5033-9. [DOI: 10.1021/ac4002904] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Shun Kumano
- Hitachi, Ltd., Central Research Laboratory, Kokubunji, Japan
| | | | | | | | - Hideki Hasegawa
- Hitachi, Ltd., Central Research Laboratory, Kokubunji, Japan
| | | | - Hiroyuki Inoue
- National Research Institute of Police Science, Kashiwa, Japan
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33
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Simpson MJ, Simpson AJ. The chemical ecology of soil organic matter molecular constituents. J Chem Ecol 2012; 38:768-84. [PMID: 22549555 DOI: 10.1007/s10886-012-0122-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 04/02/2012] [Accepted: 04/15/2012] [Indexed: 11/26/2022]
Abstract
Soil organic matter (OM) contains vast stores of carbon, and directly supports microbial, plant, and animal life by retaining essential nutrients and water in the soil. Soil OM plays important roles in biological, chemical, and physical processes within the soil, and arguably plays a major role in maintaining long-term ecological stability in a changing world. Despite its importance, there is a great deal still unknown about soil OM chemical ecology. The development of sophisticated analytical methods have reshaped our understanding of soil OM composition, which is now believed to be comprised of plant and microbial products at various stages of decomposition. The methods also have recently been applied to study environmental change in various settings and have provided unique insight with respect to soil OM chemical ecology. The goal of this review is to highlight the methods used to characterize soil OM structure, source, and degradation that have enabled precise observations of OM and associated ecological shifts. Although the chemistry of soil OM is important in its overall fate in ecosystems, the studies conducted to date suggest that ecological function is not defined by soil OM chemistry alone. The long-standing questions regarding soil OM stability and recalcitrance will likely be answered when several molecular methods are used in tandem to closely examine structure, source, age, degradation stage, and interactions of specific OM components in soil.
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Affiliation(s)
- Myrna J Simpson
- Environmental NMR Centre and Department of Chemistry, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.
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34
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Isaacman G, Wilson KR, Chan AWH, Worton DR, Kimmel JR, Nah T, Hohaus T, Gonin M, Kroll JH, Worsnop DR, Goldstein AH. Improved Resolution of Hydrocarbon Structures and Constitutional Isomers in Complex Mixtures Using Gas Chromatography-Vacuum Ultraviolet-Mass Spectrometry. Anal Chem 2012; 84:2335-42. [DOI: 10.1021/ac2030464] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriel Isaacman
- Environmental Science, Policy,
and Management, University of California, Berkeley, California, United States
| | - Kevin R. Wilson
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California,
United States
| | - Arthur W. H. Chan
- Environmental Science, Policy,
and Management, University of California, Berkeley, California, United States
| | - David R. Worton
- Environmental Science, Policy,
and Management, University of California, Berkeley, California, United States
- Aerosol Dynamics Inc., Berkeley, California, United States
| | - Joel R. Kimmel
- Center for Aerosol and Cloud
Chemistry, Aerodyne Research, Inc., Billerica,
Massachusetts, United States
- Cooperative Institute for Research
in the Environmental Sciences and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States
- Tofwerk AG, Thun, Switzerland
| | - Theodora Nah
- Chemistry, University of California, Berkeley, California, United States
| | - Thorsten Hohaus
- Center for Aerosol and Cloud
Chemistry, Aerodyne Research, Inc., Billerica,
Massachusetts, United States
| | | | - Jesse H. Kroll
- Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
United States
- Chemical
Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
United States
| | - Douglas R. Worsnop
- Center for Aerosol and Cloud
Chemistry, Aerodyne Research, Inc., Billerica,
Massachusetts, United States
| | - Allen H. Goldstein
- Environmental Science, Policy,
and Management, University of California, Berkeley, California, United States
- Environmental
and Energy Technologies
Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States
- Civil and Environmental Engineering, University of California, Berkeley, California, United
States
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35
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Marchal A, Waffo-Téguo P, Génin E, Mérillon JM, Dubourdieu D. Identification of new natural sweet compounds in wine using centrifugal partition chromatography-gustatometry and Fourier transform mass spectrometry. Anal Chem 2011; 83:9629-37. [PMID: 22044220 DOI: 10.1021/ac202499a] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sweetness contributes notably to the taste-balance of dry wines and increases during oak-barrel aging owing to the release of natural sweeteners from wood. The search for such taste-active molecules, which are sometimes present at very low concentrations in wine or other complex matrixes, requires both reliable purification tools and powerful identification techniques. Here, we report the development of an original inductive method using centrifugal partition chromatography (CPC) and sensorial analysis. This method, called CPC-gustatometry, was implemented to isolate a sweet fraction with only four compounds from a complex oak wood extract. The recently developed Fourier transform mass spectrometry (FT-MS, Orbitrap analyzer) was used jointly with two-dimensional nuclear magnetic resonance (2D (1)H and (13)C NMR) to obtain the structural elucidation of the purified compounds. The tandem mass spectrometry (MS/MS) spectra obtained with resonant and nonresonant fragmentation modes were compared, thus providing complementary information about the molecular structure. Two oleanane-type triterpenoids substituted with galloyl and glucosyl moieties were identified, one of which exhibits sweet properties. We term these compounds which have never been reported, Quercotriterpenoside I and II.
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Affiliation(s)
- Axel Marchal
- Université de Bordeaux, ISVV, EA 4577, Unité de Recherche OENOLOGIE, Villenave d'Ornon, France.
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36
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Pautler BG, Simpson AJ, McNally DJ, Lamoureux SF, Simpson MJ. Arctic permafrost active layer detachments stimulate microbial activity and degradation of soil organic matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:4076-4082. [PMID: 20459054 DOI: 10.1021/es903685j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Large quantities of soil organic carbon in Arctic permafrost zones are becoming increasingly unstable due to a warming climate. High temperatures and substantial rainfall in July 2007 in the Canadian High Arctic resulted in permafrost active layer detachments (ALDs) that redistributed soils throughout a small watershed in Nunavut, Canada. Molecular biomarkers and NMR spectroscopy were used to measure how ALDs may lead to microbial activity and decomposition of previously unavailable soil organic matter (SOM). Increased concentrations of extracted bacterial phospholipid fatty acids (PLFAs) and large contributions from bacterial protein/peptides in the NMR spectra at recent ALDs suggest increased microbial activity. PLFAs were appreciably depleted in a soil sample where ALDs occurred prior to 2003. However an enrichment of bacterial derived peptidoglycan was observed by (1)H-(13)C heteronuclear multiple quantum coherence (HMQC) and (1)H diffusion edited (DE) NMR and enhanced SOM degradation was observed by (13)C solid-state NMR. These data suggest that a previous rise in microbial activity, as is currently underway at the recent ALD site, led to degradation and depletion of labile SOM components. Therefore, this study indicates that ALDs may amplify climate change due to the release of labile SOM substrates from thawing High Arctic permafrost.
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Affiliation(s)
- Brent G Pautler
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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37
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Andreou G, Rapsomanikis S. Origins of n-alkanes, carbonyl compounds and molecular biomarkers in atmospheric fine and coarse particles of Athens, Greece. THE SCIENCE OF THE TOTAL ENVIRONMENT 2009; 407:5750-5760. [PMID: 19692113 DOI: 10.1016/j.scitotenv.2009.07.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 07/11/2009] [Accepted: 07/14/2009] [Indexed: 05/28/2023]
Abstract
The abundance and origin of aliphatic hydrocarbons, carbonyl compounds and molecular biomarkers found in the aliphatic fraction of PM(10-2.5) and PM(2.5) in the centre of Athens Greece are discussed in an attempt to reveal seasonal air pollution characteristics of the conurbation. Each extract was fractionated into individual compound classes and was analyzed using gas chromatography coupled to mass spectrometry. Normal alkanes, ranging from C(14) to C(35), were abundant in PM(10-2.5) and PM(2.5) samples during both sampling campaigns. The daily concentration of total n-alkanes was up to 438 ng m(-3) for PM(10-2.5) and up to 511 ng m(-3) for PM(2.5). Additionally, gaseous concentrations of n-alkanes were calculated, revealing that the relative proportions between gaseous and particle phases of individual compounds may differ significantly between summer and late winter. Normal alkanals and alkan-2-ones were only detected in the fine fraction of particulate matter and their concentrations were much lower than the n-alkane concentrations. Several geochemical parameters were used to qualitatively reconcile the sources of organic aerosol. The carbon preference index (CPI) of the coarse particles in August had the highest value, while in March the leaf wax contribution decreased significantly and the CPI value was very close to unity for both sites. Maximum concentrations of carbonyl compounds were reported in the range of C(15)-C(20), demonstrating that they were formed from anthropogenic activity or from atmospheric oxidative processes. 6, 10, 14-trimethylpentadecan-2-one, a marker of biogenic input, was also detected in our samples. Molecular biomarker compounds confirmed that ca. 60% of the aliphatic fraction on the sampled atmospheric particles originated from petroleum and not from any contemporary biogenic sources. Pristane and phytane were detected in the fine fraction with their presence indicating sources of fossil fuel in the range of C(16)-C(20). At all sites the 17alpha(Eta),21beta(Eta) hopane series was the most abundant hopane group.
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Affiliation(s)
- G Andreou
- Laboratory of Atmospheric Pollution and Pollution Control Engineering of Atmospheric Pollutants, Department of Environmental Engineering, Faculty of Engineering, Democritus University of Thrace, 67100 Xanthi, Greece
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38
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Herbst A, McIlwain S, Schmidt JJ, Aiken JM, Page CD, Li L. Prion disease diagnosis by proteomic profiling. J Proteome Res 2009; 8:1030-6. [PMID: 19133784 DOI: 10.1021/pr800832s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Definitive prion disease diagnosis is currently limited to postmortem assay for the presence of the disease-associated proteinase K-resistant prion protein. Using cerebrospinal fluid (CSF) from prion-infected hamsters, matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS), and support vector machines (SVM), we have identified peptide profiles characteristic of disease state. Using 10-fold leave-one-out cross-validation, we report a predictive accuracy of 72% with a true positive rate of 73% and a false positive rate of 27% demonstrating the suitability of using proteomic profiling and CSF for the development of multiple marker diagnostics of prion disease.
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Affiliation(s)
- Allen Herbst
- Department of Comparative Biosciences, University of Wisconsin-Madison, Wisconsin 53705-222, USA
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Brenner N, Haapala M, Vuorensola K, Kostiainen R. Simple Coupling of Gas Chromatography to Electrospray Ionization Mass Spectrometry. Anal Chem 2008; 80:8334-9. [DOI: 10.1021/ac801406t] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Nina Brenner
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, P.O. Box 56, FI-00014 University of Helsinki, Finland
| | - Markus Haapala
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, P.O. Box 56, FI-00014 University of Helsinki, Finland
| | - Katariina Vuorensola
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, P.O. Box 56, FI-00014 University of Helsinki, Finland
| | - Risto Kostiainen
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, P.O. Box 56, FI-00014 University of Helsinki, Finland
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40
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Dong M, Ding G, Zhou J, Wang H, Zhao Y, Huang H. The Effect of Trophoblasts on T Lymphocytes: Possible Regulatory Effector Molecules - A Proteomic Analysis. Cell Physiol Biochem 2008; 21:463-72. [DOI: 10.1159/000129639] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2008] [Indexed: 01/25/2023] Open
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41
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Medeiros PM, Simoneit BRT. Gas chromatography coupled to mass spectrometry for analyses of organic compounds and biomarkers as tracers for geological, environmental, and forensic research. J Sep Sci 2007; 30:1516-36. [PMID: 17623433 DOI: 10.1002/jssc.200600399] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Gas chromatography, especially when coupled with mass spectrometry, is the analytical method of choice for elucidation of biomarker compounds present in organic mixtures extracted from geological, environmental, and biological samples. This review describes the biomarker concept, i. e., the precursor natural products to the geological/environmental derivatives, and their application as multi-tracers in the geosphere and ambient environment. The mass spectrometric methods currently utilized for such analyses are reviewed with a general key to the literature, and typical examples of applications using GC-MS are also described.
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Affiliation(s)
- Patricia M Medeiros
- Environmental and Petroleum Research Group, College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, USA
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42
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Otto A, Simpson MJ. Analysis of soil organic matter biomarkers by sequential chemical degradation and gas chromatography – mass spectrometry. J Sep Sci 2007; 30:272-82. [PMID: 17390623 DOI: 10.1002/jssc.200600243] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Low molecular weight (LMW) biomarkers can be used to trace the source and stage of soil organic matter. However, methods that selectively isolate these groups of compounds are underdeveloped. In this study, we isolate biomarkers by a successive series of extraction and chemical degradation procedures involving solvent extraction (TSE), base (BHY) and acid hydrolysis (AHY), and CuO oxidation (CUO). GC-MS was used to analyze these fractions and the extraction methods were verified by solid-state 13C NMR spectroscopy. The GC-MS response was high for the BHY products (96%), intermediate for the TSE (30%) and CUO (19%), but very low for the AHY fraction (5%) indicating that the fractions contain polar or high molecular weight compounds. Aliphatic lipids (62%), phenols and benzyls (17%) were the predominant classes, accompanied by minor abundances of mono- and disaccharides, LMW acids, terpenoids, steroids, amino acids, and amino sugars. The TSE and BHY fractions contained mainly aliphatic lipids derived from plant waxes, cutin, and suberin. Lignin-derived phenols are the major products in the CUO fraction, and amino compounds and carbohydrates of various sources were identified in the AHY products. The sequential degradation method is useful for the isolation and identification of apolar, LMW biomarkers in soil.
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Affiliation(s)
- Angelika Otto
- Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
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43
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Liu AX, Zhu YM, Luo Q, Wu YT, Gao HJ, Zhu XM, Xu CM, Huang HF. Specific peptide patterns of follicular fluids at different growth stages analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Biochim Biophys Acta Gen Subj 2007; 1770:29-38. [PMID: 16949757 DOI: 10.1016/j.bbagen.2006.06.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Revised: 05/25/2006] [Accepted: 06/15/2006] [Indexed: 11/29/2022]
Abstract
Human follicular fluid (HFF) has been suggested to influence oocyte development potential, and some of HFF proteins may be potential markers for oocyte maturation during follicular development. Using matrix-assisted laser desorption /ionization-time of flight mass spectrometry (MALDI-TOF MS), the presence of specific peptide peaks in HFF which could represent the follicle development potential was evaluated. HFF from different developmental stages were first digested and the resultant peptide mixtures were directly analyzed by MALDI-TOF MS. It was shown that the frequencies of specific peaks demonstrated higher reproducibility than peak intensities after multiple measurements (>or=6 times) per sample. Using this approach, a reliable peak list for each different sample could be generated by combining the information from multiple measurements. By comparing the peak lists from different samples at different growth stages, we found that 5 specific peaks appeared in the 100% frequency category of 6 replicates in all the HFF samples containing mature oocyte. Similarly, such 25 peptide peaks were also identified for HFF containing immature oocyte. These specific peaks could be used to distinguish HFF from different stages as biomarkers related to follicle development and maturation. After searching the protein database, some proteins that are known to be involved in the development and maturation of oocyte were identified, such as apolipoprotein A-I, collagen type IV, integrin, et al. Identification of such proteins in our experiment further proved that the direct analysis of tryptic digests could be of practical value.
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Affiliation(s)
- Ai-Xia Liu
- Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, 2 Xue-Shi Rd., Hangzhou, Zhejiang 310006, China
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