Ethanol contamination of cerebrospinal fluid during standardized sampling and its effect on (1)H-NMR metabolomics.

Standardization of body fluid sampling, processing and storage procedures is pivotal to ensure data quality in metabolomics studies. Yet, despite strict adherence to standard sampling guidelines, we detected variable levels of ethanol in the (1)H-NMR spectra of human cerebrospinal fluid (CSF) samples (range 9.2 × 10(-3)-10.0 mM). The presence of ethanol in all samples and the wide range of concentrations clearly indicated contamination of the samples of some sort, which affected the (1)H-NMR spectra quality and the interpretation. To determine where in the sampling protocol the ethanol contamination occurs, we performed a CSF sampling protocol simulation with 0.9 % NaCl (saline) instead of CSF and detected ethanol in all simulation samples. Ethanol diffusion through air during sampling and preparation stages appeared the only logical explanation. With a bench study, we showed that ethanol easily diffuses into ex vivo CSF samples via air transmission. Ethanol originated from routinely used skin disinfectants containing ethanol and from laboratory procedures. Ethanol affected the CSF sample matrix at concentrations above ~9.4 mM and obscured a significant part of the (1)H-NMR spectrum. CSF sample preparation for (1)H-NMR-based metabolomics analyses should therefore be carried out in a well-ventilated atmosphere with laminar flow, and use of ethanol should be avoided.

Polyketide assembly lines of uncultivated sponge symbionts from structure-based gene targeting.

There is increasing evidence that uncultivated bacterial symbionts are the true producers of numerous bioactive compounds isolated from marine sponges. The localization and heterologous expression of biosynthetic genes could clarify this issue and provide sustainable supplies for a wide range of pharmaceuticals. However, identification of genes in the usually highly complex symbiont communities remains a challenging task. For polyketides, one of the most important groups of sponge-derived drug candidates, we have developed a general strategy that allows one to rapidly access biosynthetic gene clusters based on chemical moieties. Using this method, we targeted polyketide synthase genes from two different sponge metagenomes. We have obtained from a sponge-bacterial association a complete pathway for the rare and potent antitumor agent psymberin from Psammocinia aff. bulbosa. The data support the symbiont hypothesis and provide insights into natural product evolution in previously inaccessible bacteria.

Biosynthesis of spiro-mamakone A, a structurally unprecedented fungal metabolite.

Biosynthetic studies on spiro-mamakone A (1), a potently cytotoxic and antimicrobial compound from an endophytic fungus isolated from the New Zealand native tree Knightia excelsa (rewarewa), confirm the polyketide origins of this unique compound belonging to the spirobisnaphthalene class of compounds. The biosynthesis proceeds via an unprecedented symmetric enedione with the two halves of the molecule being formed from two separate pentaketide units connected by oxidative coupling.

Evolving trends in the dereplication of natural product extracts: new methodology for rapid, small-scale investigation of natural product extracts.

The use of an HPLC bioactivity profiling/microtiter plate technique in conjunction with capillary probe NMR instrumentation and access to appropriate databases effectively short-circuits conventional dereplication procedures, necessarily based on multimilligram extracts, to a single, more rapid submilligram operation. This approach to dereplication is illustrated using fungal or bacterial extracts that contain known compounds. In each case the dereplication steps were carried out on microgram quantities of extract and demonstrate the discriminating power of (1)H NMR spectroscopy as a definitive dereplication tool.

Lanostane triterpenoids from the Sri Lankan basidiomycete Ganoderma applanatum.

Two new lanostane-type triterpenoids, 3alpha,16alpha-dihydroxylanosta-7,9(11),24-trien-21-oic acid (1) and 3alpha,16alpha,26-trihydroxylanosta-7,9(11),24-trien-21-oic acid (2), along with three known lanostanoids, 16alpha-hydroxy-3-oxolanosta-7,9(11),24-trien-21-oic acid (3), 3alpha-carboxyacetoxy-24-methylen-23-oxolanost-8-en-26-oic acid (4), and 3alpha-carboxyacetoxy-24-methyl-23-oxolanost-8-en-26-oic acid (5), have been isolated from the EtOAc extract of the fruiting body of Ganoderma applanatum. The structures of 1, 2, and 3 were determined directly by the interpretation of spectroscopic data, while the structures of 4 and 5 were assigned by comparison of spectroscopic data against literature values.

spiro-Mamakone A: a unique relative of the spirobisnaphthalene class of compounds.

[structure: see text] A spirobisnaphthalene derivative with a new spiro-nonadiene skeleton, spiro-mamakone A (1), has been isolated from the extract of a cultured nonsporulating fungal endophyte derived from the New Zealand native tree Knightia excelsa (rewarewa). The carbon skeleton of spiro-mamakone A represents a new structural entity and an intriguing addition to the structurally diverse spirobisnaphthalene group of compounds. spiro-Mamakone A is potently cytotoxic and is also antimicrobial.

Bioactivity profiling using HPLC/microtiter-plate analysis: application to a New Zealand marine alga-derived fungus, Gliocladium sp.

Using HPLC/microtiter-plate-based generation of activity profiles the extract of a marine alga-derived fungus, identified as Gliocladium sp., was shown to contain the known strongly cytotoxic metabolite 4-keto-clonostachydiol (1) and also clonostachydiol (2) as well as gliotide (3), a new cyclodepsipeptide containing several D-amino acids. The absolute configuration of 1 was elucidated by reduction to 2, and two further oxidized derivatives of clonostachydiol (5, 6) were prepared and evaluated for biological activity.

Dichlorinated pulvinic acid derivative from a Malaysian Scleroderma sp.

A new dichlorinated pulvinic acid derivative, methyl-3',5'-dichloro-4,4'-di-O-methylatromentate, was isolated from the fruiting body of a Scleroderma sp. The structure was determined using spectroscopic methods, and an X-ray analysis was carried out for confirmation of the structure. Compound was found to display moderate antimicrobial activity against Bacillus subtilis.