Publications by authors named "Julia Kubanek"

81 Publications

Microbial and chemical dynamics of a toxic dinoflagellate bloom.

PeerJ 2020 21;8:e9493. Epub 2020 Jul 21.

School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America.

Harmful Algal Blooms (HABs) exert considerable ecological and economic damage and are becoming increasingly frequent worldwide. However, the biological factors underlying HABs remain uncertain. Relationships between algae and bacteria may contribute to bloom formation, strength, and duration. We investigated the microbial communities and metabolomes associated with a HAB of the toxic dinoflagellate off the west coast of Florida in June 2018. Microbial communities and intracellular metabolite pools differed based on both bacterial lifestyle and bloom level, suggesting a complex role for blooms in reshaping microbial processes. Network analysis identified as an ecological hub in the planktonic ecosystem, with significant connections to diverse microbial taxa. These included four flavobacteria and one sequence variant unidentified past the domain level, suggesting uncharacterized diversity in phytoplankton-associated microbial communities. Additionally, intracellular metabolomic analyses associated high levels with higher levels of aromatic compounds and lipids. These findings reveal water column microbial and chemical characteristics with potentially important implications for understanding HAB onset and duration.
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http://dx.doi.org/10.7717/peerj.9493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7676380PMC
July 2020

Pentagalloyl glucose from Schinus terebinthifolia inhibits growth of carbapenem-resistant Acinetobacter baumannii.

Sci Rep 2020 09 18;10(1):15340. Epub 2020 Sep 18.

Department of Dermatology, Emory University School of Medicine, Atlanta, GA, USA.

The rise of antibiotic resistance has necessitated a search for new antimicrobials with potent activity against multidrug-resistant gram-negative pathogens, such as carbapenem-resistant Acinetobacter baumannii (CRAB). In this study, a library of botanical extracts generated from plants used to treat infections in traditional medicine was screened for growth inhibition of CRAB. A crude extract of Schinus terebinthifolia leaves exhibited 80% inhibition at 256 µg/mL and underwent bioassay-guided fractionation, leading to the isolation of pentagalloyl glucose (PGG), a bioactive gallotannin. PGG inhibited growth of both CRAB and susceptible A. baumannii (MIC 64-256 µg/mL), and also exhibited activity against Pseudomonas aeruginosa (MIC 16 µg/mL) and Staphylococcus aureus (MIC 64 µg/mL). A mammalian cytotoxicity assay with human keratinocytes (HaCaTs) yielded an IC for PGG of 256 µg/mL. Mechanistic experiments revealed iron chelation as a possible mode of action for PGG's activity against CRAB. Passaging assays for resistance did not produce any resistant mutants over a period of 21 days. In conclusion, PGG exhibits antimicrobial activity against CRAB, but due to known pharmacological restrictions in delivery, translation as a therapeutic may be limited to topical applications such as wound rinses and dressings.
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http://dx.doi.org/10.1038/s41598-020-72331-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7501240PMC
September 2020

A blueprint for academic laboratories to produce SARS-CoV-2 quantitative RT-PCR test kits.

J Biol Chem 2020 11 3;295(46):15438-15453. Epub 2020 Sep 3.

School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA; Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA.

Widespread testing for the presence of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise, and/or instrumentation necessary to detect the virus by quantitative RT-PCR (RT-qPCR), the most robust, sensitive, and specific assay currently available. Here we show that academic biochemistry and molecular biology laboratories equipped with appropriate expertise and infrastructure can replicate commercially available SARS-CoV-2 RT-qPCR test kits and backfill pipeline shortages. The Georgia Tech COVID-19 Test Kit Support Group, composed of faculty, staff, and trainees across the biotechnology quad at Georgia Institute of Technology, synthesized multiplexed primers and probes and formulated a master mix composed of enzymes and proteins produced in-house. Our in-house kit compares favorably with a commercial product used for diagnostic testing. We also developed an environmental testing protocol to readily monitor surfaces for the presence of SARS-CoV-2. Our blueprint should be readily reproducible by research teams at other institutions, and our protocols may be modified and adapted to enable SARS-CoV-2 detection in more resource-limited settings.
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http://dx.doi.org/10.1074/jbc.RA120.015434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7667971PMC
November 2020

Buzz about RT-qPCR: An RT-qPCR formulation for SARS-CoV-2 detection using reagents produced at Georgia Institute of Technology.

medRxiv 2020 Jul 31. Epub 2020 Jul 31.

School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.

Widespread testing for the presence novel coronavirus SARS-CoV-2 in patients remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. The early testing shortfall in some parts of the US can be traced to an initial shortage of supplies, expertise and/or instrumentation necessary to detect the virus by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Here we show that academic biochemistry and molecular biology laboratories equipped with appropriate expertise and infrastructure can produce the RT-qPCR assay and backfill pipeline shortages. The Georgia Tech COVID-19 Test Kit Support Group synthesized multiplexed primers and probes and formulated a master mix composed of enzymes and proteins produced in-house. We compare the performance of our in-house kit to a commercial product used for diagnostic testing and describe implementation of environmental testing to monitor surfaces across various campus laboratories for the presence of SARS-CoV-2.
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http://dx.doi.org/10.1101/2020.07.29.20163949DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402063PMC
July 2020

Antimalarial Peptide and Polyketide Natural Products from the Fijian Marine Cyanobacterium .

Mar Drugs 2020 03 18;18(3). Epub 2020 Mar 18.

School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.

A new cyclic peptide, kakeromamide B (), and previously described cytotoxic cyanobacterial natural products ulongamide A (), lyngbyabellin A (), 18-lyngbyaloside C (), and lyngbyaloside () were identified from an antimalarial extract of the Fijian marine cyanobacterium . Compounds and exhibited moderate activity against blood-stages with EC values of 0.89 and 0.99 µM, respectively, whereas was more potent with an EC value of 0.15 nM, respectively. Compounds , , and displayed moderate liver-stage antimalarial activity against liver schizonts with EC values of 1.1, 0.71, and 0.45 µM, respectively. The threading-based computational method FINDSITE predicted the binding of and to potentially druggable proteins of , prompting formulation of hypotheses about possible mechanisms of action. Kakeromamide B () was predicted to bind to several actin-like proteins and a sortilin protein suggesting possible interference with parasite invasion of host cells. When 1 was tested in a mammalian actin polymerization assay, it stimulated actin polymerization in a dose-dependent manner, suggesting that 1 does, in fact, interact with actin.
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http://dx.doi.org/10.3390/md18030167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142784PMC
March 2020

New methods for isolation and structure determination of natural products.

Nat Prod Rep 2019 07 28;36(7):942-943. Epub 2019 Jun 28.

Department of Medicinal Chemistry, College of Pharmacy, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, USA.

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http://dx.doi.org/10.1039/c9np90023cDOI Listing
July 2019

Peyssonnosides A-B, Unusual Diterpene Glycosides with a Sterically Encumbered Cyclopropane Motif: Structure Elucidation Using an Integrated Spectroscopic and Computational Workflow.

J Org Chem 2019 07 18;84(13):8531-8541. Epub 2019 Jun 18.

Parker H. Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.

Two sulfated diterpene glycosides featuring a highly substituted and sterically encumbered cyclopropane ring have been isolated from the marine red alga Peyssonnelia sp. Combination of a wide array of 2D NMR spectroscopic experiments, in a systematic structure elucidation workflow, revealed that peyssonnosides A-B (1-2) represent a new class of diterpene glycosides with a tetracyclo [7.5.0.0.0] tetradecane architecture. A salient feature of this workflow is the unique application of quantitative interproton distances obtained from the rotating frame Overhauser effect spectroscopy (ROESY) NMR experiment, wherein the β-d-glucose moiety of 1 was used as an internal probe to unequivocally determine the absolute configuration, which was also supported by optical rotatory dispersion (ORD). Peyssonnoside A (1) exhibited promising activity against liver stage Plasmodium berghei and moderate antimethicillin-resistant Staphylococcus aureus (MRSA) activity, with no cytotoxicity against human keratinocytes. Additionally, 1 showed strong growth inhibition of the marine fungus Dendryphiella salina indicating an antifungal ecological role in its natural environment. The high natural abundance and novel carbon skeleton of 1 suggests a rare terpene cyclase machinery, exemplifying the chemical diversity in this phylogenetically distinct marine red alga.
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http://dx.doi.org/10.1021/acs.joc.9b00884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6614789PMC
July 2019

A marine chemical defense partnership.

Science 2019 06;364(6445):1034-1035

School of Biological Sciences and School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.

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http://dx.doi.org/10.1126/science.aax8964DOI Listing
June 2019

Antibacterial Oligomeric Polyphenols from the Green Alga Cladophora socialis.

J Org Chem 2019 05 3;84(9):5035-5045. Epub 2019 Apr 3.

Aquatic Chemical Ecology Center , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.

A series of oligomeric phenols including the known natural product 3,4,3',4'-tetrahydroxy-1,1'-biphenyl (3), the previously synthesized 2,3,8,9-tetrahydroxybenzo[ c]chromen-6-one (4), and eight new related natural products, cladophorols B-I (5-12), were isolated from the Fijian green alga Cladophora socialis and identified by a combination of NMR spectroscopy, mass spectrometric analysis, and computational modeling using DFT calculations. J-resolved spectroscopy and line width reduction by picric acid addition aided in resolving the heavily overlapped aromatic signals. A panel of Gram-positive and Gram-negative pathogens used to evaluate pharmacological potential led to the determination that cladophorol C (6) exhibits potent antibiotic activity selective toward methicillin-resistant Staphylococcus aureus (MRSA) with an MIC of 1.4 μg/mL. Cladophorols B (5) and D-H (7-11) had more modest but also selective antibiotic potency. Activities of cladophorols A-I (4-12) were also assessed against the asexual blood stages of Plasmodium falciparum and revealed cladophorols A (4) and B (5) to have modest activity with EC values of 0.7 and 1.9 μg/mL, respectively.
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http://dx.doi.org/10.1021/acs.joc.8b03218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503470PMC
May 2019

Chemical ecology of the marine plankton.

Nat Prod Rep 2019 08;36(8):1093-1116

School of Biological Sciences, Aquatic Chemical Ecology Center, Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA.

Covering: January 2015 through December 2017 This review focuses on recent studies on the chemical ecology of planktonic marine ecosystems, with the objective of presenting a comprehensive overview of new findings in the field in the time period covered. In order to highlight the role of chemically mediated interactions in the marine plankton this review has been organized by ecological concepts starting with intraspecific communication, followed by interspecific interactions (including facilitation and mutualism, host-parasite, allelopathy, and predator-prey), and finally the effects of plankton secondary metabolites on community and ecosystem-wide interactions.
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http://dx.doi.org/10.1039/c8np00085aDOI Listing
August 2019

Correction: Recent trends in the structural revision of natural products.

Nat Prod Rep 2018 09;35(9):1015

School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.

Correction for 'Recent trends in the structural revision of natural products' by Bhuwan Khatri Chhetri et al., Nat. Prod. Rep., 2018, 35, 514-531.
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http://dx.doi.org/10.1039/c8np90031kDOI Listing
September 2018

Molecules as Biotic Messengers.

ACS Omega 2018 Apr 10;3(4):4048-4053. Epub 2018 Apr 10.

School of Biological Sciences and School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.

Chemical ecology has grown as a scientific discipline from its earliest days of tracking the exquisitely potent chemistry of insect pheromones to a deep understanding of the molecular, physiological, and behavioral interactions governed by naturally occurring small molecules. The current practice of the field relies on knowledge of genomes and gene expression patterns, protein biology, and small-molecule chemistry, providing illustrations of ecological and evolutionary patterns in natural communities.
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http://dx.doi.org/10.1021/acsomega.8b00268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6044985PMC
April 2018

Karenia brevis allelopathy compromises the lipidome, membrane integrity, and photosynthesis of competitors.

Sci Rep 2018 06 22;8(1):9572. Epub 2018 Jun 22.

School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr, Atlanta, GA, 30332, USA.

The formation, propagation, and maintenance of harmful algal blooms are of interest due to their negative effects on marine life and human health. Some bloom-forming algae utilize allelopathy, the release of compounds that inhibit competitors, to exclude other species dependent on a common pool of limiting resources. Allelopathy is hypothesized to affect bloom dynamics and is well established in the red tide dinoflagellate Karenia brevis. K. brevis typically suppresses competitor growth rather than being acutely toxic to other algae. When we investigated the effects of allelopathy on two competitors, Asterionellopsis glacialis and Thalassiosira pseudonana, using nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS)-based metabolomics, we found that the lipidomes of both species were significantly altered. However, A. glacialis maintained a more robust metabolism in response to K. brevis allelopathy whereas T. pseudonana exhibited significant alterations in lipid synthesis, cell membrane integrity, and photosynthesis. Membrane-associated lipids were significantly suppressed for T. pseudonana exposed to allelopathy such that membranes of living cells became permeable. K. brevis allelopathy appears to target lipid biosynthesis affecting multiple physiological pathways suggesting that exuded compounds have the ability to significantly alter competitor physiology, giving K. brevis an edge over sensitive species.
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http://dx.doi.org/10.1038/s41598-018-27845-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015087PMC
June 2018

Recent trends in the structural revision of natural products.

Nat Prod Rep 2018 06;35(6):514-531

School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.

Covering: 2012 to 2017 This article reviews recent reports on the structural revision of natural products. Through a critical assessment of the original and revised published structures, the article addresses why each structure was targeted for revision, discusses the techniques and key discrepancies that led to the proposal of the revised structure, and offers measures that may have been taken during the original structure determination to prevent error. With the revised structures in hand, weaknesses of original proposals are assessed, providing a better understanding on the logic behind structure determination.
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http://dx.doi.org/10.1039/c8np00011eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013367PMC
June 2018

Chemical encoding of risk perception and predator detection among estuarine invertebrates.

Proc Natl Acad Sci U S A 2018 01 8;115(4):662-667. Epub 2018 Jan 8.

School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332;

An effective strategy for prey to survive in habitats rich in predators is to avoid being noticed. Thus, prey are under selection pressure to recognize predators and adjust their behavior, which can impact numerous community-wide interactions. Many animals in murky and turbulent aquatic environments rely on waterborne chemical cues. Previous research showed that the mud crab, , recognizes the predatory blue crab, , via a cue in blue crab urine. This cue is strongest if blue crabs recently preyed upon mud crabs. Subsequently, mud crabs suppress their foraging activity, reducing predation by blue crabs. Using NMR spectroscopy- and mass spectrometry-based metabolomics, chemical variation in urine from blue crabs fed different diets was related to prey behavior. We identified the urinary metabolites trigonelline and homarine as components of the cue that mud crabs use to detect blue crabs, with concentrations of each metabolite dependent on the blue crab's diet. At concentrations found naturally in blue crab urine, trigonelline and homarine, alone as well as in a mixture, alerted mud crabs to the presence of blue crabs, leading to decreased foraging by mud crabs. Risk perception by waterborne cues has been widely observed by ecologists, but the molecular nature of these cues has not been previously identified. Metabolomics provides an opportunity to study waterborne cues where other approaches have historically failed, advancing our understanding of the chemical nature of a wide range of ecological interactions.
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http://dx.doi.org/10.1073/pnas.1713901115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789921PMC
January 2018

Variable allelopathy among phytoplankton reflected in red tide metabolome.

Harmful Algae 2018 01 15;71:50-56. Epub 2017 Dec 15.

School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr, Atlanta, GA, 30332, USA; School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA; Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA; Aquatic Chemical Ecology Center, Georgia Institute of Technology, Atlanta, GA 30332, USA. Electronic address:

Harmful algae are known to utilize allelopathy, the release of compounds that inhibit competitors, as a form of interference competition. Competitor responses to allelopathy are species-specific and allelopathic potency of producing algae is variable. In the current study, the biological variability in allelopathic potency was mapped to the underlying chemical variation in the exuded metabolomes of five genetic strains of the red tide dinoflagellate Karenia brevis using H nuclear magnetic resonance (NMR) spectroscopy. The impacts of K. brevis allelopathy on growth of a model competitor, Asterionellopsis glacialis, ranged from strongly inhibitory to negligible to strongly stimulatory. Unique metabolomes of K. brevis were visualized as chemical fingerprints, suggesting three distinct metabolic modalities - allelopathic, non-allelopathic, and stimulatory - with each modality distinguished from the others by different concentrations of several metabolites. Allelopathic K. brevis was characterized by enhanced concentrations of fatty acid-derived lipids and aromatic or other polyunsaturated compounds, relative to less allelopathic K. brevis. These findings point to a previously untapped source of information in the study of allelopathy: the chemical variability of phytoplankton, which has been underutilized in the study of bloom dynamics and plankton chemical ecology.
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http://dx.doi.org/10.1016/j.hal.2017.12.002DOI Listing
January 2018

RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions.

Database (Oxford) 2017 01;2017

School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA 30332, USA.

Database Url: http://rampdb.biology.gatech.edu.
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http://dx.doi.org/10.1093/database/bax067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737055PMC
January 2017

Zebrafish aversive taste co-receptor is expressed in both chemo- and mechanosensory cells and plays a role in lateral line development.

Sci Rep 2017 10 18;7(1):13475. Epub 2017 Oct 18.

School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.

Fishes rely on both chemical and tactile senses to orient themselves to avoid predators, and to detect and taste food. This is likely achieved by highly coordinated reception of signals by mechano- and chemosensory receptors in fish. A small co-receptor from zebrafish, receptor activity modifying protein (RAMP)-like triterpene glycoside receptor (RL-TGR), was previously found to be involved in recognition of triterpene glycosides, a family of naturally occurring compounds that act as chemical defenses in various prey species. However, its localization, function, and how it impacts sensory organ development in vivo is not known. Here we show that RL-TGR is expressed in zebrafish in both i) apical microvilli of the chemosensory cells of taste buds including the epithelium of lips and olfactory epithelium, and ii) mechanosensory cells of neuromasts belonging to the lateral line system. Loss-of-function analyses of RL-TGR resulted in significantly decreased number of neuromasts in the posterior lateral line system and decreased body length, suggesting that RL-TGR is involved in deposition and migration of the neuromasts. Collectively, these results provide the first in vivo genetic evidence of sensory cell-specific expression of this unusual co-receptor and reveal its additional role in the lateral line development in zebrafish.
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http://dx.doi.org/10.1038/s41598-017-14042-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647393PMC
October 2017

Olfaction, taste and chemoreception: scientific evidence replaces "Essays in biopoetry".

Nat Prod Rep 2017 05;34(5):469-471

Dipartimento di Scienze del Farmaco, Largo Donegani 2, 28100 Novara, Italy.

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http://dx.doi.org/10.1039/c7np90016cDOI Listing
May 2017

Iodinated Meroditerpenes from a Red Alga Callophycus sp.

J Org Chem 2017 04 13;82(8):4160-4169. Epub 2017 Apr 13.

School of Chemistry and Biochemistry and ‡School of Biological Sciences, Aquatic Chemical Ecology Center, Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States.

Unique iodine-containing meroditerpenes iodocallophycoic acid A (1) and iodocallophycols A-D (2-5) were discovered from the Fijian red alga Callophycus sp. Because flexibility of the molecular skeleton impaired full characterization of relative stereochemistries by NMR spectroscopy, a DFT-based theoretical model was developed to derive relevant interproton distances which were compared to those calculated from NOE measurements, yielding the relative stereochemistries. The correct 2S,6S,7S,10S,14S enantiomers were then identified by comparison of theoretical and experimental ECD spectra. Biological activities of these iodinated and brominated meroditerpenes and additional new, related bromophycoic acid F (6) and bromophycoic acid A methyl ester (7), were evaluated for relevant human disease targets. Iodocallophycoic acid A (1) showed moderate antibiotic activity against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VREF) with MIC values of 1.4 and 2.2 μg mL, respectively. It also potentiated the anti-MRSA activity of oxacillin in a synergistic fashion, resulting in an 8-fold increase in oxacillin potency, for a MIC of 16 μg mL.
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http://dx.doi.org/10.1021/acs.joc.7b00096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538829PMC
April 2017

Chemical ecology of marine plankton.

Nat Prod Rep 2016 Jul 19;33(7):843-60. Epub 2016 Apr 19.

School of Biology, Aquatic Chemical Ecology Center, Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA.

Covering: January 2013 to online publication December 2014This review summarizes recent research in the chemical ecology of marine pelagic ecosystems, and aims to provide a comprehensive overview of advances in the field in the time period covered. In order to highlight the role of chemical cues and toxins in plankton ecology this review has been organized by ecological interaction types starting with intraspecific interactions, then interspecific interactions (including facilitation and mutualism, host-parasite, allelopathy, and predator-prey), and finally community and ecosystem-wide interactions.
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http://dx.doi.org/10.1039/c6np00015kDOI Listing
July 2016

Marine and terrestrial herbivores display convergent chemical ecology despite 400 million years of independent evolution.

Proc Natl Acad Sci U S A 2015 Sep 31;112(39):12110-5. Epub 2015 Aug 31.

School of Biology, Georgia Institute of Technology, Atlanta, GA 30332; Aquatic Chemical Ecology Center, Georgia Institute of Technology, Atlanta, GA 30332;

Chemical cues regulate key ecological interactions in marine and terrestrial ecosystems. They are particularly important in terrestrial plant-herbivore interactions, where they mediate both herbivore foraging and plant defense. Although well described for terrestrial interactions, the identity and ecological importance of herbivore foraging cues in marine ecosystems remain unknown. Here we show that the specialist gastropod Elysia tuca hunts its seaweed prey, Halimeda incrassata, by tracking 4-hydroxybenzoic acid to find vegetative prey and the defensive metabolite halimedatetraacetate to find reproductive prey. Foraging cues were predicted to be polar compounds but instead were nonpolar secondary metabolites similar to those used by specialist terrestrial insects. Tracking halimedatetraacetate enables Elysia to increase in abundance by 12- to 18-fold on reproductive Halimeda, despite reproduction in Halimeda being rare and lasting for only ∼36 h. Elysia swarm to reproductive Halimeda where they consume the alga's gametes, which are resource rich but are chemically defended from most consumers. Elysia sequester functional chloroplasts and halimedatetraacetate from Halimeda to become photosynthetic and chemically defended. Feeding by Elysia suppresses the growth of vegetative Halimeda by ∼50%. Halimeda responds by dropping branches occupied by Elysia, apparently to prevent fungal infection associated with Elysia feeding. Elysia is remarkably similar to some terrestrial insects, not only in its hunting strategy, but also its feeding method, defense tactics, and effects on prey behavior and performance. Such striking parallels indicate that specialist herbivores in marine and terrestrial systems can evolve convergent ecological strategies despite 400 million years of independent evolution in vastly different habitats.
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http://dx.doi.org/10.1073/pnas.1508133112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593077PMC
September 2015

Editorial: Chemical Ecology.

Nat Prod Rep 2015 Jul;32(7):886-7

Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.

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http://dx.doi.org/10.1039/c5np90027aDOI Listing
July 2015

Reception of Aversive Taste.

Integr Comp Biol 2015 Sep 28;55(3):507-17. Epub 2015 May 28.

*School of Chemistry and Biochemistry, Aquatic Chemical Ecology Center, Institute for Bioengineering and Biosciences, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332, USA; School of Biology, Aquatic Chemical Ecology Center, Institute for Bioengineering and Biosciences, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332, USA

Many organisms encounter noxious or unpalatable compounds in their diets. Thus, a robust reception-system for aversive taste is necessary for an individual's survival; however, mechanisms for perceiving aversive taste vary among organisms. Possession of a system sensitive to aversive taste allows for recognition of a vast array of noxious molecules via membrane-bound receptors, co-receptors, and ion channels. These receptor-ligand interactions trigger signal transduction pathways resulting in activation of nerves and in neural processing, which in turn dictates behavior, including rejection of the noxious item. The impacts of these molecular processes on behavior differ among species, and these differences have impacts at the ecosystem level by driving feeding-behavior, organization of communities, and ultimately, speciation. For example, when comparing mammalian carnivores and herbivores, it is not surprising that herbivores that encounter a variety of toxic plants in their diets express a larger number of aversive taste receptors than carnivores. Comparing the molecular mechanisms and ecological consequences of aversive-taste reception among organisms in a variety of types of ecosystems and ecological niches will illuminate the role of taste in ecology and evolution.
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http://dx.doi.org/10.1093/icb/icv058DOI Listing
September 2015

Predator lipids induce paralytic shellfish toxins in bloom-forming algae.

Proc Natl Acad Sci U S A 2015 May 27;112(20):6395-400. Epub 2015 Apr 27.

Department of Biological and Environmental Sciences-Tjärnö, University of Gothenburg, SE 452 96 Strömstad, Sweden; and.

Interactions among microscopic planktonic organisms underpin the functioning of open ocean ecosystems. With few exceptions, these organisms lack advanced eyes and thus rely largely on chemical sensing to perceive their surroundings. However, few of the signaling molecules involved in interactions among marine plankton have been identified. We report a group of eight small molecules released by copepods, the most abundant zooplankton in the sea, which play a central role in food webs and biogeochemical cycles. The compounds, named copepodamides, are polar lipids connecting taurine via an amide to isoprenoid fatty acid conjugate of varying composition. The bloom-forming dinoflagellate Alexandrium minutum responds to pico- to nanomolar concentrations of copepodamides with up to a 20-fold increase in production of paralytic shellfish toxins. Different copepod species exude distinct copepodamide blends that contribute to the species-specific defensive responses observed in phytoplankton. The signaling system described here has far reaching implications for marine ecosystems by redirecting grazing pressure and facilitating the formation of large scale harmful algal blooms.
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http://dx.doi.org/10.1073/pnas.1420154112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443330PMC
May 2015

Experimental validation of FINDSITE(comb) virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders.

J Cheminform 2014 26;6:16. Epub 2014 Apr 26.

Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250, 14th Street, N.W., Atlanta, GA 30318, USA.

Background: Identification of ligand-protein binding interactions is a critical step in drug discovery. Experimental screening of large chemical libraries, in spite of their specific role and importance in drug discovery, suffer from the disadvantages of being random, time-consuming and expensive. To accelerate the process, traditional structure- or ligand-based VLS approaches are combined with experimental high-throughput screening, HTS. Often a single protein or, at most, a protein family is considered. Large scale VLS benchmarking across diverse protein families is rarely done, and the reported success rate is very low. Here, we demonstrate the experimental HTS validation of a novel VLS approach, FINDSITE(comb), across a diverse set of medically-relevant proteins.

Results: For eight different proteins belonging to different fold-classes and from diverse organisms, the top 1% of FINDSITE(comb)'s VLS predictions were tested, and depending on the protein target, 4%-47% of the predicted ligands were shown to bind with μM or better affinities. In total, 47 small molecule binders were identified. Low nanomolar (nM) binders for dihydrofolate reductase and protein tyrosine phosphatases (PTPs) and micromolar binders for the other proteins were identified. Six novel molecules had cytotoxic activity (<10 μg/ml) against the HCT-116 colon carcinoma cell line and one novel molecule had potent antibacterial activity.

Conclusions: We show that FINDSITE(comb) is a promising new VLS approach that can assist drug discovery.
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http://dx.doi.org/10.1186/1758-2946-6-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038399PMC
June 2014

Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton.

Proc Natl Acad Sci U S A 2014 Jun 2;111(24):9009-14. Epub 2014 Jun 2.

Department of Genome Sciences, University of Washington, Seattle, WA 98195

Competition is a major force structuring marine planktonic communities. The release of compounds that inhibit competitors, a process known as allelopathy, may play a role in the maintenance of large blooms of the red-tide dinoflagellate Karenia brevis, which produces potent neurotoxins that negatively impact coastal marine ecosystems. K. brevis is variably allelopathic to multiple competitors, typically causing sublethal suppression of growth. We used metabolomic and proteomic analyses to investigate the role of chemically mediated ecological interactions between K. brevis and two diatom competitors, Asterionellopsis glacialis and Thalassiosira pseudonana. The impact of K. brevis allelopathy on competitor physiology was reflected in the metabolomes and expressed proteomes of both diatoms, although the diatom that co-occurs with K. brevis blooms (A. glacialis) exhibited more robust metabolism in response to K. brevis. The observed partial resistance of A. glacialis to allelopathy may be a result of its frequent exposure to K. brevis blooms in the Gulf of Mexico. For the more sensitive diatom, T. pseudonana, which may not have had opportunity to evolve resistance to K. brevis, allelopathy disrupted energy metabolism and impeded cellular protection mechanisms including altered cell membrane components, inhibited osmoregulation, and increased oxidative stress. Allelopathic compounds appear to target multiple physiological pathways in sensitive competitors, demonstrating that chemical cues in the plankton have the potential to alter large-scale ecosystem processes including primary production and nutrient cycling.
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http://dx.doi.org/10.1073/pnas.1402130111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066504PMC
June 2014

There's something in the water: opportunities in marine chemical ecology.

Authors:
Julia Kubanek

J Chem Ecol 2014 Mar;40(3):218-9

School of Biology and School of Chemistry & Biochemistry, Aquatic Chemical Ecology Center, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA, 30332-0230, USA,

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http://dx.doi.org/10.1007/s10886-014-0394-4DOI Listing
March 2014

The smell of moulting: N-acetylglucosamino-1,5-lactone is a premoult biomarker and candidate component of the courtship pheromone in the urine of the blue crab, Callinectes sapidus.

J Exp Biol 2014 Apr 20;217(Pt 8):1286-96. Epub 2013 Dec 20.

Neuroscience Institute, Department of Biology, Brains & Behavior Program, and Center for Behavioral Neuroscience, Georgia State University, Atlanta, GA 30302-5030, USA.

Female blue crabs (Callinectes sapidus) in their pubertal moult stage release unidentified sex pheromone molecules in their urine, causing males to respond with courtship behaviours including a display called courtship stationary paddling and a form of precopulatory guarding called cradle carry. We hypothesized that pheromones are mixtures of molecules and are more concentrated in urine of pubertal premoult females compared with other moulting stages and thus that these molecules are biomarkers (i.e. metabolites that can be used as an indicator of some biological state or condition) of pubertal premoult females. We tested this hypothesis by combining bioassay-guided fractionation and biomarker targeting. To evaluate the molecular mass of the putative pheromone by bioassay-guided fractionation, we separated urine from pubertal premoult females and intermoult males by ultrafiltration into three molecular mass fractions. The <500 Da fraction and the 500-1000 Da fraction but not the >1000 Da fraction of female urine induced male courtship stationary paddling, but none of the fractions of male urine did. Thus, female urine contains molecules of <1000 Da that stimulate courtship behaviours in males. Biomarker targeting using nuclear magnetic resonance (NMR) spectral analysis of the 500-1000 Da fraction of urine from premoult and postmoult males and females revealed a premoult biomarker. Purification, nuclear magnetic resonance, mass spectrometry and high pressure liquid chromatography analysis of this premoult biomarker identified it as N-acetylglucosamino-1,5-lactone (NAGL) and showed that it is more abundant in urine of premoult females and males than in urine of either postmoult or juvenile females and males. NAGL has not been reported before as a natural product or as a molecule of the chitin metabolic pathway. Physiological and behavioural experiments demonstrated that blue crabs can detect NAGL through their olfactory pathway. Thus, we hypothesize that NAGL is a component of the sex pheromone and that it acts in conjunction with other yet unidentified components.
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http://dx.doi.org/10.1242/jeb.099051DOI Listing
April 2014

Pharmacokinetics, metabolism, and efficacy of the antimalarial natural product bromophycolide A.

ACS Med Chem Lett 2013 Oct;4(10):989-993

School of Biology and School of Chemistry and Biochemistry, Aquatic Chemical Ecology Center and Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.

A suite of pharmacokinetic and pharmacological studies show that bromophycolide A (), an inhibitor of drug-sensitive and drug-resistant , displays a typical small molecule profile with low toxicity and good bioavailability. Despite susceptibility to liver metabolism and a short half-life, significantly decreased parasitemia in a malaria mouse model. Combining these data with prior SAR analyses, we demonstrate the potential for future development of and its bioactive ester analogs.
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http://dx.doi.org/10.1021/ml4002858DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3804352PMC
October 2013
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