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  • 1
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    Differences in Leaf Chemistry and Glandular Trichome Density between Wild Southwestern American Hop ( Humulus neomexicanus ) and Commercial Hop Cultivars (2021)
    American Chemical Society
    In:  Journal of Agricultural and Food Chemistry, 69 (27). pp. 7798-7814.
    Details
    Publication Date: 2022-01-07
    Description: The female flowers (“cones”) of the hop plant (Humulus L.) produce compounds that contribute to the flavor and other properties of beer. Hop leaves and cones produce many of the same compounds, which also confer agronomic traits such as insect and disease resistance. Targeted and untargeted ultraperformance liquid chromatography-quadrupole time-of-flight–mass spectrometry with Waters MSE technology (UPLC-QTof-MSE) metabolomics were used to compare leaf phytochemical compositions of greenhouse-grown southwestern American wild Humulus neomexicanus (A. Nelson and Cockerell) Rydb. against a group of commercial hop cultivars consisting of both pure European Humulus lupulus L. and European–North American hybrids. Principal component analysis showed a clear distinction in chemical profiles between the two groups. H. neomexicanus leaves had a significantly higher content of total α acids (p = 4.4 × 10–9), total bitter acids (p = 2.6 × 10–6), cohumulone (p = 1.0 × 10–13), humulone + adhumulone (p = 9.1 × 10–4), and the prenylflavonoids xanthohumol (p = 0.013) and desmethylxanthohumol (p = 0.029) as well as significantly higher densities of glandular trichomes (p = 1.3 × 10–6), the biosynthetic site of those compounds. Most flavonol glycosides measured were also significantly more abundant in H. neomexicanus (p = 1.5 × 10–22 to 0.0027), whereas phenolic acids were consistently, but generally nonsignificantly (p 〉 0.05), more abundant in the cultivars. The higher bitter acid, prenylflavonoid, and flavonol glycoside content of H. neomexicanus leaves may help to confer more favorable insect and disease-resistance properties.
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  • 2
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    Iron Acquisition Systems of Gram-negative Bacterial Pathogens Define TonB-Dependent Pathways to Novel Antibiotics (2021)
    American Chemical Society
    In:  Chemical Reviews, 121 (9). pp. 5193-5239.
    Details
    Publication Date: 2022-01-07
    Description: Iron is an indispensable metabolic cofactor in both pro- and eukaryotes, which engenders a natural competition for the metal between bacterial pathogens and their human or animal hosts. Bacteria secrete siderophores that extract Fe3+ from tissues, fluids, cells, and proteins; the ligand gated porins of the Gram-negative bacterial outer membrane actively acquire the resulting ferric siderophores, as well as other iron-containing molecules like heme. Conversely, eukaryotic hosts combat bacterial iron scavenging by sequestering Fe3+ in binding proteins and ferritin. The variety of iron uptake systems in Gram-negative bacterial pathogens illustrates a range of chemical and biochemical mechanisms that facilitate microbial pathogenesis. This document attempts to summarize and understand these processes, to guide discovery of immunological or chemical interventions that may thwart infectious disease.
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  • 3
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    Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics (2021)
    American Chemical Society
    In:  ACS Chemical Biology .
    Details
    Publication Date: 2022-01-07
    Description: While thousands of environmental metagenomes have been mined for the presence of novel biosynthetic gene clusters, such computational predictions do not provide evidence of their in vivo biosynthetic functionality. Using fluorescent in situ enzyme assay targeting carrier proteins common to polyketide (PKS) and nonribosomal peptide synthetases (NRPS), we applied fluorescence-activated cell sorting to tunicate microbiome to enrich for microbes with active secondary metabolic capabilities. Single-cell genomics uncovered the genetic basis for a wide biosynthetic diversity in the enzyme-active cells and revealed a member of marine Oceanospirillales harboring a novel NRPS gene cluster with high similarity to phylogenetically distant marine and terrestrial bacteria. Interestingly, this synthase belongs to a larger class of siderophore biosynthetic gene clusters commonly associated with pestilence and disease. This demonstrates activity-guided single-cell genomics as a tool to guide novel biosynthetic discovery.
    Type: Article , PeerReviewed
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  • 4
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    Microplastics in the Weddell Sea (Antarctica): A Forensic Approach for Discrimination between Environmental and Vessel-Induced Microplastics (2021)
    American Chemical Society
    In:  EPIC3Environmental Science & Technology, American Chemical Society, ISSN: 0013-936X
    Details
    Publication Date: 2022-01-07
    Description: Microplastic (MP) pollution has been found in the Southern Ocean surrounding Antarctica, but many local regions within this vast area remain uninvestigated. The remote Weddell Sea contributes to the global thermohaline circulation, and one of the two Antarctic gyres is located in that region. In the present study, we evaluate MP (〉300 μm) concentration and composition in surface (n = 34) and subsurface water samples (n = 79, ∼11.2 m depth) of the Weddell Sea. All putative MP were analyzed by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. MP was found in 65% of surface and 11.4% of subsurface samples, with mean (±standard deviation (SD)) concentrations of 0.01 (±0.01 SD) MP m–3 and 0.04 (±0.1 SD) MP m–3, respectively, being within the range of previously reported values for regions south of the Polar Front. Additionally, we aimed to determine whether identified paint fragments (n = 394) derive from the research vessel. Environmentally sampled fragments (n = 101) with similar ATR-FTIR spectra to reference paints from the research vessel and fresh paint references generated in the laboratory were further subjected to micro-X-ray fluorescence spectroscopy (μXRF) to compare their elemental composition. This revealed that 45.5% of all recovered MP derived from vessel-induced contamination. However, 11% of the measured fragments could be distinguished from the reference paints via their elemental composition. This study demonstrates that differentiation based purely on visual characteristics and FTIR spectroscopy might not be sufficient for accurately determining sample contamination sources.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
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    Flow-through quantification of microplastics using impedance spectroscopy (2021)
    American Chemical Society
    Details
    Publication Date: 2022-10-21
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Colson, B. C., & Michel, A. P. M. Flow-through quantification of microplastics using impedance spectroscopy. ACS Sensors, 6(1), (2021): 238–244, doi:10.1021/acssensors.0c02223.
    Description: Understanding the sources, impacts, and fate of microplastics in the environment is critical for assessing the potential risks of these anthropogenic particles. However, our ability to quantify and identify microplastics in aquatic ecosystems is limited by the lack of rapid techniques that do not require visual sorting or preprocessing. Here, we demonstrate the use of impedance spectroscopy for high-throughput flow-through microplastic quantification, with the goal of rapid measurement of microplastic concentration and size. Impedance spectroscopy characterizes the electrical properties of individual particles directly in the flow of water, allowing for simultaneous sizing and material identification. To demonstrate the technique, spike and recovery experiments were conducted in tap water with 212–1000 μm polyethylene beads in six size ranges and a variety of similarly sized biological materials. Microplastics were reliably detected, sized, and differentiated from biological materials via their electrical properties at an average flow rate of 103 ± 8 mL/min. The recovery rate was ≥90% for microplastics in the 300–1000 μm size range, and the false positive rate for the misidentification of the biological material as plastic was 1%. Impedance spectroscopy allowed for the identification of microplastics directly in water without visual sorting or filtration, demonstrating its use for flow-through sensing.
    Description: The authors thank the Richard Saltonstall Charitable Foundation and the National Academies Keck Futures Initiative (NAKFI DBS13) for their funding support.
    Keywords: Microplastics ; Plastics ; Impedance spectroscopy ; Dielectric properties ; Instrumentation ; Particle detection ; Flow-through ; Environmental sensing
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Plastic formulation is an emerging control of its photochemical fate in the ocean (2021)
    American Chemical Society
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Walsh, A. N., Reddy, C. M., Niles, S. F., McKenna, A. M., Hansel, C. M., & Ward, C. P. Plastic formulation is an emerging control of its photochemical fate in the ocean. Environmental Science & Technology, 55(18), (2021): 12383–12392, https://doi.org/10.1021/acs.est.1c02272.
    Description: Sunlight exposure is a control of long-term plastic fate in the environment that converts plastic into oxygenated products spanning the polymer, dissolved, and gas phases. However, our understanding of how plastic formulation influences the amount and composition of these photoproducts remains incomplete. Here, we characterized the initial formulations and resulting dissolved photoproducts of four single-use consumer polyethylene (PE) bags from major retailers and one pure PE film. Consumer PE bags contained 15–36% inorganic additives, primarily calcium carbonate (13–34%) and titanium dioxide (TiO2; 1–2%). Sunlight exposure consistently increased production of dissolved organic carbon (DOC) relative to leaching in the dark (3- to 80-fold). All consumer PE bags produced more DOC during sunlight exposure than the pure PE (1.2- to 2.0-fold). The DOC leached after sunlight exposure increasingly reflected the 13C and 14C isotopic composition of the plastic. Ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry revealed that sunlight exposure substantially increased the number of DOC formulas detected (1.1- to 50-fold). TiO2-containing bags photochemically degraded into the most compositionally similar DOC, with 68–94% of photoproduced formulas in common with at least one other TiO2-containing bag. Conversely, only 28% of photoproduced formulas from the pure PE were detected in photoproduced DOC from the consumer PE. Overall, these findings suggest that plastic formulation, especially TiO2, plays a determining role in the amount and composition of DOC generated by sunlight. Consequently, studies on pure, unweathered polymers may not accurately represent the fates and impacts of the plastics entering the ocean.
    Description: Funding was provided by the Seaver Institute, the Gerstner Family Foundation, Woods Hole Oceanographic Institution, and the National Science Foundation Graduate Research Fellowship Program (A.N.W.). The Ion Cyclotron Resonance user facility at the National High Magnetic Field Laboratory is supported by the National Science Foundation Division of Chemistry and Division of Materials Research through DMR-1644779 and the State of Florida.
    Keywords: Plastic pollution ; Marine debris ; Additives ; Dissolved organic carbon ; Photochemical oxidation ; FT-ICR-MS ; Titanium dioxide
    Repository Name: Woods Hole Open Access Server
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  • 7
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    A cross-institutional analysis of the effects of broadening trainee professional development on research productivity (2021)
    Public Library of Science
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Brandt, P. D., Sturzenegger Varvayanis, S., Baas, T., Bolgioni, A. F., Alder, J., Petrie, K. A., Dominguez, I., Brown, A. M., Stayart, C. A., Singh, H., Van Wart, A., Chow, C. S., Mathur, A., Schreiber, B. M., Fruman, D. A., Bowden, B., Wiesen, C. A., Golightly, Y. M., Holmquist, C. E., Arneman, D., Hall, J. D., Hyman, L. E., Gould, K. L., Chalkley, R., Brennwald, P. J., Layton, R. L. A cross-institutional analysis of the effects of broadening trainee professional development on research productivity. Plos Biology, 19(7), (2021): e3000956, https://doi.org/10.1371/journal.pbio.3000956.
    Description: PhD-trained scientists are essential contributors to the workforce in diverse employment sectors that include academia, industry, government, and nonprofit organizations. Hence, best practices for training the future biomedical workforce are of national concern. Complementing coursework and laboratory research training, many institutions now offer professional training that enables career exploration and develops a broad set of skills critical to various career paths. The National Institutes of Health (NIH) funded academic institutions to design innovative programming to enable this professional development through a mechanism known as Broadening Experiences in Scientific Training (BEST). Programming at the NIH BEST awardee institutions included career panels, skill-building workshops, job search workshops, site visits, and internships. Because doctoral training is lengthy and requires focused attention on dissertation research, an initial concern was that students participating in additional complementary training activities might exhibit an increased time to degree or diminished research productivity. Metrics were analyzed from 10 NIH BEST awardee institutions to address this concern, using time to degree and publication records as measures of efficiency and productivity. Comparing doctoral students who participated to those who did not, results revealed that across these diverse academic institutions, there were no differences in time to degree or manuscript output. Our findings support the policy that doctoral students should participate in career and professional development opportunities that are intended to prepare them for a variety of diverse and important careers in the workforce.
    Description: Funding sources included the Common Fund NIH Director’s Biomedical Research Workforce Innovation Broadening Experiences in Scientific Training (BEST) Award. The following institutional NIH BEST awards (alphabetical by institution) included: DP7OD020322 (Boston University; AFB, ID, BMS, LEH); DP7OD020316 (University of Chicago; CAS); DP7OD018425 (Cornell University; SSV); DP7OD018428 (Virginia Polytechnic Institute; AVW, BB); DP7OD020314 (Rutgers University; JA); DP7OD020315 (University of Rochester; TB); DP7OD018423 (Vanderbilt University; KAP, AMB, KLG, RC); DP7OD020321 (University of California, Irvine; HS, DAF); DP7OD020317 (University of North Carolina, Chapel Hill; PDB, PJB, RLL); DP7 OD018427 (Wayne State University; CSC, AM). National Institutes of Health (NIH) General Medical Sciences - Science of Science Policy Approach to Analyzing and Innovating the Biomedical Research Enterprise (SCISIPBIO) Award (GM-19-011) - 1R01GM140282-01 (University of North Carolina at Chapel Hill; RLL, PDB, PJB).
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum (2021)
    American Chemical Society
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gosselin, K. M., Nelson, R. K., Spivak, A. C., Sylva, S. P., Van Mooy, B. A. S., Aeppli, C., Sharpless, C. M., O’Neil, G. W., Arrington, E. C., Reddy, C. M., & Valentine, D. L. Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum. ACS Omega, 6(35), (2021): 22803–22810, https://doi.org/10.1021/acsomega.1c03196.
    Description: The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism.
    Description: This work was funded with grants from the National Science Foundation grants OCE-1333148, OCE-1333162, and OCE-1756254 and the Woods Hole Oceanographic Institution (IR&D). GCxGC analysis made possible by WHOI’s Investment in Science Fund.
    Keywords: Lipids ; Alkyls ; Bacteria ; Genetics ; Chromatography
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Lingering Chukchi Sea sea ice and Chukchi Sea mean winds influence population age structure of euphausiids (krill) found in the bowhead whale feeding hotspot near Pt. Barrow, Alaska (2021)
    Public Library of Science
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ashjian, C. J., Okkonen, S. R., Campbell, R. G., & Alatalo, P. Lingering Chukchi Sea sea ice and Chukchi Sea mean winds influence population age structure of euphausiids (krill) found in the bowhead whale feeding hotspot near Pt. Barrow, Alaska. Plos One, 16(7), (2021): e0254418, https://doi.org/10.1371/journal.pone.0254418.
    Description: Interannual variability in euphausiid (krill) abundance and population structure and associations of those measures with environmental drivers were investigated in an 11-year study conducted in late August–early September 2005–2015 in offshelf waters (bottom depth 〉 40 m) in Barrow Canyon and the Beaufort Sea just downstream of Distributed Biological Observatory site 5 (DBO5) near Pt. Barrow, Alaska. Statistically-significant positive correlations were observed among krill population structure (proportion of juveniles and adults), the volume of Late Season Melt Water (LMW), and late-spring Chukchi Sea sea ice extent. High proportions of juvenile and adult krill were seen in years with larger volumes of LMW and greater spring sea ice extents (2006, 2009, 2012–2014) while the converse, high proportions of furcilia, were seen in years with smaller volumes of LMW and lower spring sea ice extent (2005, 2007, 2010, 2011, 2015). These different life stage, sea ice and water mass regimes represent integrated advective responses to mean fall and/or spring Chukchi Sea winds, driven by prevailing atmospheric pressure distributions in the two sets of years. In years with high proportions of juveniles and adults, late-spring and preceding-fall winds were weak and variable while in years with high proportions of furcilia, late-spring and preceding-fall winds were strong, easterly and consistent. The interaction of krill life history with yearly differences in the northward transports of krill and water masses along with sea ice retreat determines the population structure of late-summer krill populations in the DBO5 region near Pt. Barrow. Years with higher proportions of mature krill may provide larger prey to the Pt. Barrow area bowhead whale prey hotspot. The characteristics of prey near Pt. Barrow is dependent on krill abundance and size, large-scale environmental forcing, and interannual variability in recruitment success of krill in the Bering Sea.
    Description: This research was supported by the National Science Foundation through grants PLR-1023331 (CJA), OPP-0436131 (CJA), PLR-1022139 (RGC), OPP-0436110 (RGC), PLR-1023446 (SRO), and OPP-043166 (SRO), the National Oceanic and Atmospheric Administration (NOAA) under cooperative agreement NA08OAR4320751 with the University of Alaska (SRO) and cooperative agreements NA17RJ1223 and NA09OAR4320129 with the Woods Hole Oceanographic Institution (CJA), the Bureau of Ocean Energy Management through Interagency Agreement 0106RU39923/M08PG20021 between the National Marine Fisheries Service and MMS/BOEM (CJA, RGC, SRO) and through the National Oceanographic Partnership Program award number N00014-08-1-0311 from the Office of Naval Research to the Woods Hole Oceanographic Institution (CJA, SRO, RGC). Additional support was provided by the Coastal Marine Institute at the University of Alaska (SRO, RGC) and the James M. and Ruth P. Clark Arctic Research Initiative Fund at the Woods Hole Oceanographic Institution (CJA). The participation of the K-12 teachers was supported by the National Science Foundation through the ARMADA program at the University of Rhode Island (2005, 2006) and through the POLARTrec program at the Arctic Research Consortium of the United States (2012).
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Affinity purification of label-free tubulins from xenopus egg extracts (2021)
    Cell Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Reusch, S., Biswas, A., Hirst, W. G., & Reber, S. Affinity purification of label-free tubulins from xenopus egg extracts. STAR Protocols, 1(3), (2020): 100151, doi:10.1016/j.xpro.2020.100151.
    Description: Cytoplasmic extracts from unfertilized Xenopus eggs have made important contributions to our understanding of microtubule dynamics, spindle assembly, and scaling. Until recently, these in vitro studies relied on the use of heterologous tubulin. This protocol allows for the purification of physiologically relevant Xenopus tubulins in milligram yield, which are a complex mixture of isoforms with various post-translational modifications. The protocol is applicable to any cell or tissue of interest. For complete details on the use and execution of this protocol, please refer to Hirst et al. (2020).
    Description: This article was prompted by our stay at the Marine Biological Laboratory (MBL), Woods Hole, MA, in the summer of 2016 funded by the Princeton-Humboldt Strategic Partnership Grant together with the lab of Sabine Petry (Princeton University). We are grateful to the National Xenopus Resource (NXR) for supplying frogs. For mass spectrometry, we would like to acknowledge the assistance of Benno Kuropka and Chris Weise from the Core Facility BioSupraMol supported by the Deutsche Forschungsgemeinschaft (DFG). We thank the Protein Expression Purification and Characterization (PEPC) facility at the MPI-CBG; in particular, we thank Aliona Bogdanova and Barbara Borgonovo. We thank all former and current members of the Reber lab for discussions and helpful advice, in particular Christoph Hentschel and Soma Zsoter for technical assistance. S.R. acknowledges funding from the IRI Life Sciences (Humboldt-Universität zu Berlin, Excellence Initiative/DFG). W.H. was supported by the Alliance Berlin Canberra co-funded by a grant from the Deutsche Forschungsgemeinschaft (DFG) for the International Research Training Group (IRTG) 2290 and the Australian National University.
    Repository Name: Woods Hole Open Access Server
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