ALBERT

Description: Shallow gas occurs between 0 and 1000 m below the sea floor. It consists mainly of microbial-formed or thermogenic methane or a combination of both, sometimes with a limited admixture of higher hydrocarbons (propane, butane, etc.).

Description: Microbial mats collected at cold methane seeps in the Black Sea carry out anaerobic oxidation of methane (AOM) to carbon dioxide using sulfate as the electron acceptor. These mats, which predominantly consist of sulfate-reducing bacteria and archaea of the ANME-1 and ANME-2 type, contain large amounts of proteins very similar to methyl-coenzyme M reductase from methanogenic archaea. Mass spectrometry of mat samples revealed the presence of two nickel-containing cofactors in comparable amounts, one with the same mass as coenzyme F430 from methanogens (m/z = 905) and one with a mass that is 46 Da higher (m/z = 951). The two cofactors were isolated and purified, and their constitution and absolute configuration were determined. The cofactor with m/z = 905 was proven to be identical to coenzyme F430 from methanogens. For the m/z = 951 species, high resolution ICP-MS pointed to F430 + CH2S as the molecular formula, and LA-ICP-SF MS finally confirmed the presence of one sulfur atom per nickel. Esterification gave two stereoisomeric pentamethyl esters with m/z = 1021, which could be purified by reverse phase HPLC and were subjected to comprehensive NMR analysis, allowing determination of their constitution and configuration as (172S)−172-methylthio-F430 pentamethyl ester and (172R)−172-methylthio-F430 pentamethyl ester. The corresponding diastereoisomeric pentaacids could also be separated by HPLC and were correlated to the esters via mild hydrolysis of the latter. Equilibration of the pentaacids under acid catalysis showed that the (172S) isomer is the naturally occurring albeit thermodynamically less stable one. The more stable (172R) isomer (80% at equilibrium) is an isolation artifact generated under the acidic conditions necessary for the isolation of the cofactors from the calcium carbonate-encrusted mats.

Description: The definition of noise and signal in seismic data will vary widely with the viewer's perspective and methods to process and visualize the data. Thus we begin with our definition from the perspective of presenting structural subsurface information.

Description: A new equation is proposed for the calculation of sound speed in seawater as a function of temperature, salinity, depth, and latitude in all oceans and open seas, including the Baltic and the Black Sea. The proposed equation agrees to better than ±0.2m∕s with two reference complex equations, each fitting the best available data corresponding to existing waters of different salinities. The only exceptions are isolated hot brine spots that may be found at the bottom of some seas. The equation is of polynomial form, with 14 terms and coefficients of between one and three significant figures. This is a substantial reduction in complexity compared to the more complex equations using pressure that need to be calculated according to depth and location. The equation uses the 1990 universal temperature scale (an elementary transformation is given for data based on the 1968 temperature scale). It is hoped that the equation will be useful to those who need to calculate sound speed in applications of marine acoustics.

Description: Metabolomics offers great potential for understanding the metabolic consequences of exposure to chemicals and other stressors in the environment. Biological systems encompass humans exposed to chemicals in the environment as well as the diverse organisms inhabiting an ecosystem and exposed to environmental contaminants. An overall goal of environmental metabolomics is to understand what is metabolomically “normal” or adaptive and what constitutes a threat to human health and the environment.

Description: Anthecularin (1), a minor sesquiterpene lactone with a novel ring system was isolated from Greek Anthemis auriculata (Asteraceae). Its structure was elucidated by means of NMR, HRMS, and X-ray crystallography. Anthecularin showed antitrypanosomal (IC50 = 10.1 μg/mL) and antiplasmodial activity (IC50 = 23.3 μg/mL) and inhibited two key enzymes of the plasmodial type II fatty acid biosynthesis pathway, PfFabI and PfFabG (IC50 values = 14 and 28.3 μg/mL, respectively). A probable biogenesis of 1 is also proposed and discussed.

Description: The water-soluble part of the methanolic extract from the aerial parts of Scrophularia crypthophila, through chromatographic methods, yielded three new resin glycosides, crypthophilic acids A−C (1−3). Compounds 1−3 are tetraglycosides of (+)-3S,12S-dihydroxypalmitic acid. The structures of these and 10 known compounds were elucidated by spectroscopic and chemical means. All natural resin glycosides known so far have been obtained from Convolvulaceae plants; this is the first report of such glycosides from another, taxonomically unrelated family (Scrophulariaceae).

Description: The seismic trace is a complex aggregate of reflected and scattered signals from subsurface formation interfaces and heterogeneities. Although many varieties of random noise may also be present in the trace, we know from reacquiring the same seismic survey that seismic data are highly repeatable, indicating that significant information about the subsurface is contained in the trace but not yet used by our standard analysis methods. Seismic scattering is a type of signal contained in the data that is generally not utilized.

Description: Significant changes have occurred in the anthropogenic emissions of many compounds related to the Kyoto and Montreal Protocols within the past 20 years and many of their atmospheric abundances have responded dramatically. Additionally, there are a number of related natural compounds with underdetermined source or sink budgets. A new instrument, Medusa, was developed to make the high frequency in situ measurements required for the determination of the atmospheric lifetimes and emissions of these compounds. This automated system measures a wide range of halocarbons, hydrocarbons, and sulfur compounds involved in ozone depletion and/or climate forcing, from the very volatile perfluorocarbons (PFCs, e.g., CF4 and CF3CF3) and hydrofluorocarbons (HFCs, e.g., CH3CF3) to the higher-boiling point solvents (such as CH3CCl3 and CCl2CCl2) and CHBr3. A network of Medusa systems worldwide provides 12 in situ ambient air measurements per day of more than 38 compounds of part per trillion mole fractions and precisions up to 0.1% RSD at the five remote field stations operated by the Advanced Global Atmospheric Gases Experiment (AGAGE). This custom system couples gas chromatography/mass spectrometry (GC/MSD) with a novel scheme for cryogen-free low-temperature preconcentration (−165 °C) of analytes from 2 L samples in a two-trap process using HayeSep D adsorbent.

Description: Gas-hydrate accumulations located onshore in Arctic permafrost regions are seen as a potential source of natural gas. Surprisingly, most of the gas hydrate found in the Mackenzie Delta and Beaufort Sea areas was indirectly discovered or inferred from conventional hydrocarbon exploration programs. One of these occurrences, the Mallik gas-hydrate field (Figure 1), has received particular attention over the last 10 years. Two internationally partnered research well programs have intersected three intervals of gas hydrates and have allowed successful extraction of subpermafrost core samples with significant gas hydrates. The gas-hydrate intervals are up to 40 m thick and have high gas-hydrate saturation, sometimes exceeding 80% of pore volume of unconsolidated clastic sediments with average porosities from 25–40%. At Mallik, the gas-hydrate intervals are located at depths of 900–1100 m and are localized on the crest of an anticline.

Description: A bottom-simulating reflection (BSR) is a seismic reflectivity phenomenon that is widely accepted as indicating the base of the gas-hydrate stability zone. The acoustic impedance difference between sediments invaded with gas hydrate above the BSR and sediments without gas hydrate, but commonly with free gas below, are accepted as the conditions that create this reflection. The relationship between BSRs and marine gas hydrate has become so well known since the 1970s that investigators, when asked to define the most important seismic attribute of marine gas-hydrate systems, usually reply, “a BSR event.” Research conducted over the last decade has focused on calibrating seafloor seismic reflectivity across the geology of the northern Gulf of Mexico (GoM) continental slope surface to the seafloor. This research indicates that the presence and character of seafloor bright spots (SBS) can be indicators of gas hydrates in surface and near-surface sediments (Figure 1). It has become apparent that SBSs on the continental slope generally are responses to fluid and gas expulsion processes. Gas-hydrate formation is, in turn, related to these processes. As gas-hydrate research expands around the world, it will be interesting to find if SBS behavior in other deepwater settings is as useful for identifying gas-hydrate sites as in the GoM.

Description: Two new cyclic peroxides, 2 and 3, were isolated from a sample of the Norwegian sponge Plakortis simplex. Their structures including relative stereochemistry were elucidated by interpretation of MS and NMR data. Compound 3 exhibited moderate in vitro activity against six solid human tumor cell lines with IC50 values in the range 7−15 μg/mL.

Description: The effects of dissolved organic compounds on the determination of nanomolar concentrations of Fe(II) have been compared using two luminol-based flow injection chemiluminescence (FI-CL) methods. One used the direct injection of sample into the luminol reagent stream, and the other incorporated on-line solid-phase extraction of the analyte on an 8-hydroxyquinoline microcolumn. The CL signals from analyses of dissolved iron species (Fe(II) and Fe(III)) with model ligands and organic compounds were examined in high-purity water and seawater. The organic compounds included natural reducing agents (e.g., ascorbic acid), nitrogen σ-donor/π-acceptor compounds (e.g., 1,4-dipyridine, protoporphyrin IX), aromatic compounds (e.g., 1,4-dihydroxybenzene), synthetic iron chelators (e.g., EDTA), and natural iron binding compounds (e.g., desferrioxamine B, ferrichrome A). Fe(II) determinations for both luminol FI-CL methods were affected by submicromolar concentrations of redox-active compounds, strong iron binding ligands (i.e., log KFeL > 6), and compounds with electron-donating functional groups in both high-purity water and seawater. This was due to reactions between organic molecules and iron species before and during analysis, rather than chemiluminescence caused by the individual organic compounds. In addition, the effects of strong ligands and size speciation on Fe(II) recoveries from seawater following acidification (pH 2) and reduction (100 μM sodium sulfite) were investigated. © 2005 American Chemical Society.

Description: A critical examination of published data obtained primarily from recent nuclear magnetic resonance spectroscopy, X-ray absorption near-edge structure spectroscopy, electrospray ionization-mass spectrometry, and pyrolysis studies reveals an evolving new view of the molecular structure of soil humic substances. According to the new view, humic substances are collections of diverse, relatively low molecular mass components forming dynamic associations stabilized by hydrophobic interactions and hydrogen bonds. These associations are capable of organizing into micellar structures in suitable aqueous environments. Humic components display contrasting molecular motional behavior and may be spatially segregated on a scale of nanometers. Within this new structural context, these components comprise any molecules intimately associated with a humic substance, such that they cannot be separated effectively by chemical or physical methods. Thus biomolecules strongly bound within humic fractions are by definition humic components, a conclusion that necessarily calls into question key biogeochemical pathways traditionally thought to be required for the formation of humic substances. Further research is needed to elucidate the intermolecular interactions that link humic components into supramolecular associations and to establish the pathways by which these associations emerge from the degradation of organic litter.

Description: Microcionamides A (1) and B (2) have been isolated from the Philippine marine sponge Clathria (Thalysias) abietina. These new linear peptides are cyclized via a cystine moiety and have their C-terminus blocked by a 2-phenylethylenamine group. Their total structures, including absolute stereochemistry, were determined by a combination of spectral and chemical methods. Compound 1 was shown to slowly isomerize about the C-36/C-37 double bond when stored in DMSO. Microcionamides A (1) and B (2) exhibited significant cytotoxicity against the human breast tumor cells lines MCF-7 and SKBR-3 and displayed inhibitory activity against Mycobacterium tuberculosis H37Ra.

Description: Penicillium expansum is known for its destructive rot and patulin production in apple juice. According to the literature, P. expansum can, among other compounds, produce citrinin, ochratoxin A, patulin, penitrem A, and rubratoxin B. In this study the qualitative production of metabolites was examined using TLC (260 isolates), HPLC (85 isolates), and MS (22 isolates). The results showed that none of the 260 isolates produced ochratoxin A, penitrem A, or rubratoxin B. However, chaetoglobosin A and communesin B were produced consistently by all 260 isolates. Patulin and roquefortine C were produced by 98% of the isolates. Expansolides A/B and citrinin were detected in 91 and 85% of the isolates, respectively. Chaetoglobosins and communesins were detected in naturally infected juices and potato pulp, whereas neither patulin nor citrinin was found. Because most P. expansum isolates produce patulin, citrinin, chaetoglobosins, communesins, roquefortine C, and expansolides A and B, foods contaminated with this fungus should ideally be examined for chaetoglobosin A as well as patulin.

Description: We determined the coordination environment of Zn2+ in aqueous Cl- brines at 25 °C and 300 °C using ab initio molecular dynamics simulations. The ZnCl+ and ZnCl2 complexes exist as pseudo-octahedral ZnClm(H2O)6-m clusters at 25 °C but occur as pseudo-tetrahedral ZnClm(H2O)4-m clusters at 300 °C. The ZnCl3- complex occurs as the pseudo-tetrahedral ZnCl3(H2O)- cluster at 25 and 300 °C. The tetrahedral ZnCl42- complex, however, is the dominant Zn−Cl complex at 25 °C, at least in highly concentrated (7.4 m) Cl- brines. The change in hydration number with temperature for the ZnCl+ and ZnCl2 complexes will complicate extrapolations of solvation energies to hydrothermal conditions using a Born-model-based equation of state.

Description: High-performance liquid chromatography-electrospray ionization mass spectrometry was applied to the detection of the iron(III) complexes of the hydroxamate siderophores rhodotoluric acid, deferrioxamine B, and deferrichrome. Separation of the iron(III) complexes was obtained using a polystyrene-divinylbenzene stationary phase. The retention and responses of ferrioxamine and ferrichrome were optimal when a gradient elution program with methanol and 0.1% (v/v) formic acid as the mobile phases was used. These conditions were also suitable for the retention and separation of the uncomplexed ligands. Retention of iron(III) rhodotoluate was improved when formic acid was replaced by the ion-pairing reagent heptafluorobutyric acid (0.1%). Detection limits for the ferric complexes, defined as 3 SD of the lowest determined standard, were 26 nM for iron(III) rhodotoluate, 0.23 nM for ferrioxamine, and 0.40 nM for ferrichrome. A protocol for the solid-phase extraction of these hydroxamate siderophores from seawater was developed and applied to the extraction of siderophores from enriched incubated seawater samples.

Description: High-performance liquid chromatography-electrospray ionization mass spectrometry was applied to the detection of the iron(III) complexes of the hydroxamate siderophores rhodotoluric acid, deferrioxamine B, and deferrichrome. Separation of the iron(III) complexes was obtained using a polystyrene-divinylbenzene stationary phase. The retention and responses of ferrioxamine and ferrichrome were optimal when a gradient elution program with methanol and 0.1% (v/v) formic acid as the mobile phases was used. These conditions were also suitable for the retention and separation of the uncomplexed ligands. Retention of iron(III) rhodotoluate was improved when formic acid was replaced by the ion-pairing reagent heptafluorobutyric acid (0.1%). Detection limits for the ferric complexes, defined as 3 SD of the lowest determined standard, were 26 nM for iron(III) rhodotoluate, 0.23 nM for ferrioxamine, and 0.40 nM for ferrichrome. A protocol for the solid-phase extraction of these hydroxamate siderophores from seawater was developed and applied to the extraction of siderophores from enriched incubated seawater samples.

Description: As offshore petroleum exploration and development move into deeper water, industry must contend increasingly with gas hydrate, a solid compound that binds water and a low-molecular-weight gas (usually methane). Gas hydrate has been long studied in industry from an engineering viewpoint, due to its tendency to clog gas pipelines. However, hydrate also occurs naturally wherever there are high pressures, low temperatures, and sufficient concentrations of gas and water. These conditions prevail in two natural environments, both of which are sites of active exploration: permafrost regions and marine sediments on continental slopes. In this article we discuss seismic detection of gas hydrate in marine sediments. Gas hydrate in deepwater sediments poses both new opportunities and new hazards. An enormous quantity of natural gas, likely far exceeding the global inventory of conventional fossil fuels, is locked up worldwide in hydrates. Ex-traction of this unconventional resource presents unique exploration, engineering, and economic challenges, and several countries, including the United States, Japan, Canada, India, and Korea, have initiated joint industry-academic-governmental programs to begin studying those challenges. Hydrates also constitute a potential drilling hazard. Because hydrates are only stable in a restricted range of pressure and temperature, any activity that sufficiently raises temperature or lowers pressure could destabilize them, releasing potentially large volumes of gas and decreasing the shear strength of the host sediments. Assessment of the opportunities and hazards associated with hydrates requires reliable methods of detecting hydrate and accurate maps of their distribution and concentration. Hydrate may occur only within the upper few hundred meters of deepwater sediment, at any depth between the seafloor and the base of the stability zone, which is controlled by local pressure and temperature. Hydrate is occasionally exposed at the seafloor, where it can be detected either visually or acoustically by strong seismic reflection amplitudes or high backscatter …

Description: Two new isomalabaricane triterpenes, stellettin H (1) and stellettin I (2), have been isolated from the marine sponge Rhabdastrella globostellata, collected from the Philippines. Stellettins A−D (3−6), (−)-stellettin E (7), and rhabdastrellic acid-A (8) were also isolated and characterized. Stellettin B (4) and (−)-stellettin E (7) showed selective cytotoxicity toward p21WAF1/Cip1-deficient human colon tumor (HCT-116) cells with IC50 values of 0.043 and 0.039 μM, respectively.

Description: Raf/MEK-1/MAPK cascade inhibitor activity-directed fractionation of the sponge Stylissa massa afforded eight known alkaloids:  aldisine (1), 2-bromoaldisine (2), 10Z-debromohymenialdisine (3), 10E-hymenialdisine (4), 10Z-hymenialdisine (5), hymenin (6), oroidin (7), and 4,5-dibromopyrrole-2-carbonamide (8). Both 4 and 5 showed significant enzyme inhibitory activity (IC50 3 and 6 nM, respectively). Secondary assays identified these compounds as potent MEK-1 inhibitors. Compounds 4 and 5 also inhibited the growth of human tumor LoVo cells.

Description: The increasing environmental pressures on estuarine and coastal waters call for improved monitoring techniques of chemical constituents to aid management decisions. Automated stripping voltammetry is a suitable technique for continuous, near real-time monitoring of trace metals in marine systems. This contribution describes the application of voltammetric monitoring techniques in estuarine and coastal waters of the UK and Spain. The high spatial and temporal resolution of the data obtained, allows a thorough interpretation of the trace metal sources and behaviour. Future trends in this field research include submersible sensors which can be remotely deployed for a period of several weeks.

Description: The valuable nutraceutical γ-linolenic acid (GLA, (6Z,9Z,12Z)-octadecatrienoic acid) is biosynthesized by a series of regio- and stereoselective dehydrogenation reactions that are catalyzed by a set of enzymes known as fatty acid desaturases. As part of ongoing research into the mechanism of these remarkable catalysts, we have examined the cryptoregiochemistry (site of initial oxidation) of Δ6 desaturation as it occurs in the protozoan Tetrahymena thermophila. Two complementary approaches that address this issue are described. In the first set of experiments, we measured the individual primary deuterium kinetic isotope effects associated with the C−H bond cleavages at C-6 and C-7. Competition experiments using appropriately deuterium-labeled 4-thiasubstrates revealed that a large KIE (kH/kD = 7.1 ± 0.5) was observed for the C−H bond-breaking step at C-6, whereas the C−H bond cleavage at C-7 was insensitive to deuterium substitution (kH/kD = 1.04 ± 0.05). These results point to C-6 as the site of initial oxidation in Δ6 desaturation since the first chemical step in this type of reaction is rupture of a strong, unactivated C−H bond, an energetically difficult process that typically exhibits a large KIE. This conclusion was supported by the results of our second approach, which involved locating the position of the putative diiron oxo oxidant with respect to substrate by monitoring the efficiency of oxo transfer to a series of thia fatty acid probes. Thus only a 6-thia-analogue is converted to significant amounts of the corresponding sulfoxide (9% yield). The absolute configuration of this product was determined to be S using (S)-MPAA as a chiral shift reagent. Taken together, these results point to the abstraction of the C-6 pro S hydrogen as the initial event in Δ6 desaturation as it occurs in T. thermophila.

Description: From the aerial parts of Putoria calabrica, two new flavonol triglycosides were isolated and their structures were elucidated as quercetin-3-O-[α-l-rhamnopyranosyl-(1→2)-α-l-arabinopyranoside]-7-O-β-d-glucopyranoside (1, calabricoside A) and quercetin-3-O-[4‘ ‘‘-O-caffeoyl-α-l-rhamnopyranosyl-(1→2)-α-l-arabinopyranoside]-7-O-β-d-glucopyranoside (2, calabricoside B). Additionally, seven iridoid and three lignan glycosides were isolated and characterized. Radical scavenging activities of all compounds were determined by quantifying their effects on luminol-enhanced chemiluminescence in formyl-methionyl-leucyl-phenylalanine (FMLP) stimulated human polymorphonuclear neutrophils (PMNs). Calabricoside A and B showed strong radical scavenging activity with IC50 values of 0.25 and 0.3 μM, respectively.

Description: A new iridoid glucoside, 5β,6β-dihydroxyboschnaloside (1), was isolated from the aerial parts of Euphrasia pectinata. Five known iridoid glucosides, 6β-hydroxyboschnaloside (2), aucubin, euphroside, plantarenaloside, and geniposidic acid, and two known phenylethanoid glycosides, verbascoside (= acteoside) and leucosceptoside A, were also obtained and characterized. The structure of compound 1 was established by spectroscopic evidence.