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Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, da Silva EB, O'Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small molecule in situ resin capture provides a compound first approach to natural product discovery. Nat Commun 2024; 15:5230. [PMID: 38898025 PMCID: PMC11187115 DOI: 10.1038/s41467-024-49367-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Culture-based microbial natural product discovery strategies fail to realize the extraordinary biosynthetic potential detected across earth's microbiomes. Here we introduce Small Molecule In situ Resin Capture (SMIRC), a culture-independent method to obtain natural products directly from the environments in which they are produced. We use SMIRC to capture numerous compounds including two new carbon skeletons that were characterized using NMR and contain structural features that are, to the best of our knowledge, unprecedented among natural products. Applications across diverse marine habitats reveal biome-specific metabolomic signatures and levels of chemical diversity in concordance with sequence-based predictions. Expanded deployments, in situ cultivation, and metagenomics facilitate compound discovery, enhance yields, and link compounds to candidate producing organisms, although microbial community complexity creates challenges for the later. This compound-first approach to natural product discovery provides access to poorly explored chemical space and has implications for drug discovery and the detection of chemically mediated biotic interactions.
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Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Mariam N Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alexander B Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Mitchell N Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Tadeusz F Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Paul R Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.
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Tang J, Zhang C, Xu W, Li X, Jia Y, Fang J, Mai BX. Indirect Impact of Eutrophication on Occurrence, Air-Water Exchange, and Vertical Sinking Fluxes of Antibiotics in a Subtropical River. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8932-8945. [PMID: 38710016 DOI: 10.1021/acs.est.4c00960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
A significant challenge that warrants attention is the influence of eutrophication on the biogeochemical cycle of emerging contaminants (ECs) in aquatic environments. Antibiotics pollution in the eutrophic Pearl River in South China was examined to offer new insights into the effects of eutrophication on the occurrence, air-water exchange fluxes (Fair-water), and vertical sinking fluxes (Fsinking) of antibiotics. Antibiotics transferred to the atmosphere primarily through aerosolization controlled by phytoplankton biomass and significant spatiotemporal variations were observed in the Fair-water of individual antibiotics throughout all sites and seasons. The Fsinking of ∑AB14 (defined as a summary of 14 antibiotics) was 750.46 ± 283.19, 242.71 ± 122.87, and 346.74 ± 249.52 ng of m-2 d-1 in spring, summer, and winter seasons. Eutrophication indirectly led to an elevated pH, which reduced seasonal Fair-water of antibiotics, sediment aromaticity, and phytoplankton hydrophobicity, thereby decreasing antibiotic accumulation in sediments and phytoplankton. Negative correlations were further found between Fsinking and the water column daily loss of antibiotics with phytoplankton biomass. The novelty of this study is to provide new complementary knowledge for the regulation mechanisms of antibiotics by phytoplankton biological pump, offering novel perspectives and approaches to understanding the coupling between eutrophication and migration and fate of antibiotics in a subtropical eutrophic river.
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Affiliation(s)
- Jinpeng Tang
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107 Guangdong, PR China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Chencheng Zhang
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107 Guangdong, PR China
| | - Wang Xu
- Shenzhen Ecological and Environmental Monitoring Center of Guangdong Province, Shenzhen 518049, PR China
| | - Xuxia Li
- Shenzhen Ecological and Environmental Monitoring Center of Guangdong Province, Shenzhen 518049, PR China
| | - Yanyan Jia
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107 Guangdong, PR China
| | - Ji Fang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, PR China
| | - Bi-Xian Mai
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Resources Utilization and Protection, Guangzhou Institute of Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Chinese Academy of Sciences, Guangzhou 510640, PR China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, PR China
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Fan H, Huang Z, Feng C, Wu Z, Tian Y, Ma F, Li H, Huang J, Qin X, Zhou Z, Zhang X. Functional keystone taxa promote N and P removal of the constructed wetland to mitigate agricultural nonpoint source pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169155. [PMID: 38065493 DOI: 10.1016/j.scitotenv.2023.169155] [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: 08/25/2023] [Revised: 10/23/2023] [Accepted: 12/05/2023] [Indexed: 01/18/2024]
Abstract
Characterized by irregular spatial and temporal variations of pollutant loading and complex occurrence mechanisms, agricultural nonpoint source pollution (ANPSP) has always been a great challenge in field restoration worldwide. Returning farmlands to wetlands (RFWs) as an ecological restoration mode among various constructed wetlands was selected to manage ANPSP in this study. Triarrhena lutarioriparia, Nelumbo nucifera and Zizania latifolia monocultures were designed and the water pollutants was monitored. N. nucifera and Z. latifolia could reach the highest TN (53.28 %) and TP (53.22 %) removal efficiency, respectively. By 16s high-throughput sequencing of rhizosphere bacteria, 45 functional species were the main contributors for efficient N and P removal, and 38 functional keystone taxa (FKT) were found with significant ecological niche roles and metabolic functions. To our knowledge, this is the first study to explore the microbial driving N and P removal mechanism in response to ANPSP treated by field scale RFWs.
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Affiliation(s)
- Huixin Fan
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, PR China
| | - Zhongliang Huang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, PR China
| | - Chongling Feng
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha, Hunan 410004, PR China
| | - Zijian Wu
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, PR China
| | - Yuxin Tian
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, PR China
| | - Fengfeng Ma
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, PR China
| | - Hui Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, PR China
| | - Jing Huang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, PR China
| | - Xiaoli Qin
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, PR China
| | - Zhou Zhou
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha, Hunan 410004, PR China
| | - Xuan Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, PR China.
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McLamb F, Feng Z, Shea D, Bozinovic K, Vasquez MF, Stransky C, Gersberg RM, Wang W, Kong X, Xia XR, Bozinovic G. Evidence of transboundary movement of chemicals from Mexico to the U.S. in Tijuana River Estuary sediments. CHEMOSPHERE 2024; 348:140749. [PMID: 38000551 DOI: 10.1016/j.chemosphere.2023.140749] [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: 06/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
The Tijuana River Estuary (TRE) has been a public health hazard and point of contention between the United States and Mexico for decades, with sources of pollution on both sides of the border. The goal of our study is to determine the presence and dynamics of chemical contamination in the TRE. We sampled sediment from four TRE locations in the U.S. during stable dry conditions and immediately after a wet weather period. Organic chemicals were initially screened with non-targeted analysis using gas chromatography high-resolution mass spectrometry (GC/HRMS) that tentatively identified 6978 chemicals in the NIST 20 database. These tentative identifications were filtered using the USEPA CompTox database to guide quantitative targeted analysis at detection limits below 1 ng/g dry weight sediment. Quantitative targeted analysis of 152 organic pollutants and 18 inorganic elements via GC/HRMS revealed generally higher concentrations of contaminants in dry weather sediments compared to wet weather sediments. The highest concentrations of all chemical classes were detected at the site closest to the U.S.-Mexico border, followed by an urban area near Imperial Beach, California, U.S. All sites exhibited a mixture of petrogenic and pyrogenic polycyclic aromatic hydrocarbons (PAHs). Current-use pesticides were dominated by pyrethroid insecticides and the thiocarbamate herbicide s-Ethyl dipropylthiocarbamate (EPTC), while the U.S.-banned organochlorine pesticides were dominated by chlordanes, dieldrin, and dichlorodiphenyltrichloroethane (DDT) and its degradation byproducts. Polychlorinated biphenyl (PCB) concentrations were greatest at the site closest to the U.S.-Mexico border but in the low nanogram-per-gram range. Phthalates were only found at the same site, with relatively high concentrations of bis(2-ethylhexyl) phthalate. This study provides positive identification and quantitative concentrations for organic pollutants in TRE sediments. Our data suggest that there are multiple sources of chemical contamination in the estuary, including possible transboundary movement of pollutants from Mexico.
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Affiliation(s)
- Flannery McLamb
- Boz Life Science Research and Teaching Institute, San Diego, CA, 92109, USA; University of California San Diego, Extended Studies, La Jolla, CA, 92037, USA
| | - Zuying Feng
- Boz Life Science Research and Teaching Institute, San Diego, CA, 92109, USA
| | - Damian Shea
- Statera Environmental, Inc, Raleigh, NC, 27606, USA
| | - Kesten Bozinovic
- Boz Life Science Research and Teaching Institute, San Diego, CA, 92109, USA; Georgetown University, Washington, DC, 20035, USA
| | - Miguel F Vasquez
- Boz Life Science Research and Teaching Institute, San Diego, CA, 92109, USA; University of California San Diego, Extended Studies, La Jolla, CA, 92037, USA
| | | | - Richard M Gersberg
- San Diego State University, Graduate School of Public Health, San Diego, CA, 92182, USA
| | | | - Xiang Kong
- Statera Environmental, Inc, Raleigh, NC, 27606, USA
| | - Xin-Rui Xia
- Statera Environmental, Inc, Raleigh, NC, 27606, USA
| | - Goran Bozinovic
- Boz Life Science Research and Teaching Institute, San Diego, CA, 92109, USA; San Diego State University, Graduate School of Public Health, San Diego, CA, 92182, USA; University of California San Diego, School of Biological Sciences, La Jolla, CA, 92037, USA; Portland State University, Center for Life in Extreme Environments, Portland, OR, 97201, USA.
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de Guia ACM, Guia MRDUD, Monserate JJ, Salazar JR, Velasco RR, Mingala CN, Quiazon KMA. Detection of Aeromonas hydrophila possessing aerolysin gene using gold nanoparticle probe. J Adv Vet Anim Res 2023; 10:593-598. [PMID: 38370905 PMCID: PMC10868686 DOI: 10.5455/javar.2023.j714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/22/2023] [Accepted: 10/20/2023] [Indexed: 02/20/2024] Open
Abstract
Objective The aerolysin (aerA) is a virulence indicator used to identify the pathogenicity of the Aeromonas strain. Targeting a pathogen's crucial virulence gene for detection is essential, as it determines the potential threat to the host. This study aimed to develop a gold nanoparticle (AuNP) probe for detecting the gene aerA in Aeromonas hydrophila among field samples. Materials and Methods Kidney samples among both healthy and sick Nile tilapias in five provinces of Luzon Island were collected for bacterial analysis. Screening using specific primers targeting aerA was conducted in parallel with testing the AuNPs probe on the same sample set. The positive control provided by BFAR-NFLD, confirmed by polymerase chain reaction (PCR) assay, was used as a positive sample containing the target gene. Results The AuNP probe demonstrated a computed accuracy of 81.32%, sensitivity of 100%, and specificity of 81.26%. Among the 257 reactions, 59 were false positives, while no false negative results were observed. The AuNP probe could detect aerA at levels as low as 30 ng/µl. The low prevalence of the target gene may be attributed to the use of general media instead of specific media like Rimler-Shotts agar. Conclusion The established colorimetric detection method for A. hydrophila with the aerA gene offers a swift alternative to PCR, negating the requirement for advanced equipment like a thermal cycler.
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Affiliation(s)
- Arren Christian M. de Guia
- Livestock Biotechnology Center, Philippine Carabao Center, Science City of Muñoz, The Philippines
- Freshwater Aquaculture Center—College of Fisheries, Central Luzon State University, Science City of Muñoz, The Philippines
| | - Mary Rose D. Uy-de Guia
- Production System and Nutrition Section, Philippine Carabao Center, Science City of Muñoz, The Philippines
| | - Juvy J. Monserate
- Department of Chemistry, College of Science, Central Luzon State University, Science City of Muñoz, The Philippines
| | - Joel R. Salazar
- Department of Chemistry, College of Science, Central Luzon State University, Science City of Muñoz, The Philippines
| | - Ravelina R. Velasco
- Freshwater Aquaculture Center—College of Fisheries, Central Luzon State University, Science City of Muñoz, The Philippines
| | - Claro N. Mingala
- Livestock Biotechnology Center, Philippine Carabao Center, Science City of Muñoz, The Philippines
- Department of Animal Science, College of Agriculture, Institute of Graduate Studies, Central Luzon State University, Science City of Muñoz, The Philippines
| | - Karl Marx A. Quiazon
- Freshwater Aquaculture Center—College of Fisheries, Central Luzon State University, Science City of Muñoz, The Philippines
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Tan J, Deng H, Lu F, Chen W, Su X, Wang H. Antibacterial Nanocellulose-TiO 2/Polyester Fabric for the Recyclable Photocatalytic Degradation of Dyes. Polymers (Basel) 2023; 15:4376. [PMID: 38006100 PMCID: PMC10675286 DOI: 10.3390/polym15224376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
In this paper, we report an antibacterial, recyclable nanocellulose-titanium dioxide/polyester nonwoven fabric (NC-TiO2/PET) composite for the highly efficient photocatalytic degradation of dyes. The NC-TiO2 was loaded onto the surface of flexible PET nonwoven fabric through a simple swelling and dipping method. The NC-TiO2 in the particle size range of ~10 nm were uniformly attached to the surface of the PET fibers. The NC-TiO2/PET composite has the ability to achieve the stable photocatalytic degradation of dyes and presents antibacterial properties. The degradation rates to methylene blue (MB) and acid red (AR) of the NC-TiO2/PET composite reached 90.02% and 91.14%, respectively, and the inhibition rate of Escherichia coli was >95%. After several rounds of cyclic testing, the photocatalytic performance, antibacterial performance, and mechanical stability of the NC-TiO2/PET composite remained robust.
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Affiliation(s)
- Jiacheng Tan
- Key Laboratory of Functional Fibers and Intelligent Textiles, Yuanpei College, Shaoxing University, Shaoxing 312000, China; (J.T.); (H.D.)
| | - Hangjun Deng
- Key Laboratory of Functional Fibers and Intelligent Textiles, Yuanpei College, Shaoxing University, Shaoxing 312000, China; (J.T.); (H.D.)
| | - Fangfang Lu
- Zhoushan Institute of Calibration and Testing for Quality and Technology Supervision, Zhoushan 316000, China;
| | - Wei Chen
- College of Textile Science and Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China;
| | - Xiuping Su
- Key Laboratory of Functional Fibers and Intelligent Textiles, Yuanpei College, Shaoxing University, Shaoxing 312000, China; (J.T.); (H.D.)
| | - Hairong Wang
- Zhoushan Institute of Calibration and Testing for Quality and Technology Supervision, Zhoushan 316000, China;
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Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, Barbosa da Silva E, O’Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small Molecule in situ Resin Capture - A Compound First Approach to Natural Product Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.02.530684. [PMID: 37398257 PMCID: PMC10312467 DOI: 10.1101/2023.03.02.530684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Microbial natural products remain an important resource for drug discovery. Yet, commonly employed discovery techniques are plagued by the rediscovery of known compounds, the relatively few microbes that can be cultured, and laboratory growth conditions that do not elicit biosynthetic gene expression among myriad other challenges. Here we introduce a culture independent approach to natural product discovery that we call the Small Molecule In situ Resin Capture (SMIRC) technique. SMIRC exploits in situ environmental conditions to elicit compound production and represents a new approach to access poorly explored chemical space by capturing natural products directly from the environments in which they are produced. In contrast to traditional methods, this compound-first approach can capture structurally complex small molecules across all domains of life in a single deployment while relying on Nature to provide the complex and poorly understood environmental cues needed to elicit biosynthetic gene expression. We illustrate the effectiveness of SMIRC in marine habitats with the discovery of numerous new compounds and demonstrate that sufficient compound yields can be obtained for NMR-based structure assignment. Two new compound classes are reported including one novel carbon skeleton that possesses a functional group not previously observed among natural products and a second that possesses potent biological activity. We introduce expanded deployments, in situ cultivation, and metagenomics as methods to facilitate compound discovery, enhance yields, and link compounds to producing organisms. This compound first approach can provide unprecedented access to new natural product chemotypes with broad implications for drug discovery.
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Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mariam N. Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander B. Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mitchell N. Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Lani F. Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven J. Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tadeusz F. Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paul R. Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
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