ALBERT

Description: The macroalga Fucus vesiculosus carries a specific community of surface bacteria. To identify chemical compounds that possibly mediate abundance and community composition of algae-associated bacteria, we tested the effect of surface-available algal compounds on bacterial settlement and community composition under field conditions. Compounds on algal thalli were separated from the surface by extraction with organic solvents and investigated on growth inhibition and settlement of bacterial isolates. Based on in vitro data, partially purified extract fractions were then exposed to bacterial colonizers in vivo followed by bacterial enumeration and community analysis. The polar fraction of the algal surface extract revealed a significant profouling effect for Vibrionales, whereas the nonpolar fraction containing the xanthophyll pigment fucoxanthin and other unidentified nonpolar surface compounds revealed a significant 80% reduction of surface colonizing bacteria. The analysis of bacterial surface communities by 454 pyrosequencing demonstrated that the antifouling activity of nonpolar algal surface compounds was targeting the abundance of natural bacterial colonizers rather than the relative composition of bacterial members within the community. Moreover, the bacterial community composition on F.vesiculosus was markedly different from artificial control substrates and chemically manipulated experimental treatments, suggesting that other, nonextractable surface features and/or physical properties render algal-specific epiphytic bacterial communities.

Description: Following their transmission from the human to the mosquito with the bloodmeal, malaria parasites have to persevere in the mosquito midgut for approximately 1 d. During this period the parasites are highly vulnerable to factors of the mosquito midgut, including bacteria. We here aimed at determining the microbial diversity of gut bacteria of the Asian malaria vector Anophebs stephensi (Liston) during development and under different feeding regimes, including feeds on malaria parasite-infected blood. 16S rRNA and denaturing gradient gel electrophoresis analyses demonstrated an increasing reduction in the microbial diversity during mosquito development from egg to adult and identified the gram-negative bacterium Elizabethkingia meningoseptica King as the dominant species in the midgut of lab-reared male and female mosquitoes. E. meningoseptica is transmitted between generations and its predominance in the mosquito midgut was not altered by diet, when the gut microbiota was compared between sugar-fed and blood-fed female mosquitoes. Furthermore, feeds on blood infected with malaria parasites did not impact the presence of E. meningoseptica in the gut. Extracts from cultured E. meningoseptica were active against gram-positive and negative bacteria and yeast and against the blood and gametocyte transmission stages of the malaria parasite Plasmodium falciparum Welch. The antimicrobial and antiplasmodial activities of E. meningoseptica may account for its dominance in the midgut of the malaria vector.

Description: Consumer preference for natural food ingredients has increased in recent decades, and the natural food colorant market has grown to over one billion dollars annually. A variety of red, orange, and yellow natural colorants are approved and in use, but there still exists a lack of available blue and purple natural colorant options. The occurrence of blue colored compounds in the natural world is relatively rare. The isolation, identification, and characterization of natural blue and purple pigments obtained from underexplored natural sources such as from obscure terrestrial organisms and marine microorganisms will be discussed.

Description: The concentration of CO2 in global surface ocean waters is increasing due to rising atmospheric CO2 emissions, resulting in lower pH and a lower saturation state of carbonate ions. Such changes in seawater chemistry are expected to impact calcification in calcifying marine organisms. However, other physiological processes related to calcification might also be affected, including enzyme activity. In a mesocosm experiment, macroalgal communities were exposed to three CO2 concentrations (380, 665, and 1486 µatm) to determine how the activity of two enzymes related to inorganic carbon uptake and nutrient assimilation in Corallina officinalis, an abundant calcifying rhodophyte, will be affected by elevated CO2 concentrations. The activity of external carbonic anhydrase, an important enzyme functioning in macroalgal carbon-concentrating mechanisms, was inversely related to CO2 concentration after long-term exposure (12 weeks). Nitrate reductase, the enzyme responsible for reduction of nitrate to nitrite, was stimulated by CO2 and was highest in algae grown at 665 µatm CO2. Nitrate and phosphate uptake rates were inversely related to CO2, while ammonium uptake was unaffected, and the percentage of inorganic carbon in the algal skeleton decreased with increasing CO2. The results indicate that the processes of inorganic carbon and nutrient uptake and assimilation are affected by elevated CO2 due to changes in enzyme activity, which change the energy balance and physiological status of C. officinalis, therefore affecting its competitive interactions with other macroalgae. The ecological implications of the physiological changes in C. officinalis in response to elevated CO2 are discussed.

Description: The sheer scale of the metagenomic and metatranscriptomic datasets that are now available warrants the development of automated protocols for organizing, annotating and comparing the samples in terms of their metabolic profiles. We describe a user-friendly java program FROMP (Fragment Recruitment on Metabolic Pathways) for mapping and visualizing enzyme annotations onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways or custom-made pathways and comparing the samples in terms of their Pathway Completeness Scores,their relative Activity Scores or enzyme enrichment odds ratios. This program along with our fully-configurable PERL based annotation organization pipeline Meta2Pro (METAbolic PROfiling of META-omic data) offers a quick and accurate standalone solution for metabolic profiling of environmental samples or cultures from different treatments. Apart from pictorial comparisons, FROMP can also generate score matrices for multiple meta-omics samples which can be used directly by other statistical programs

Description: Two new natural products, 3 and 4, and their predecessor 7-isocyanoisoneoamphilecta-1(14),15-diene (2), of the rare isoneoamphilectane class of marine diterpenes, along with the known amphilectane diterpenes 6–8, were isolated from the n-hexane extract of the marine sponge Svenzea flava collected at Great Inagua Island, Bahamas. The molecular structures of compounds 3 and 4 were established by spectroscopic (1D/2D NMR, IR, UV, HRMS) methods and confirmed by a series of chemical correlation studies. In a first ever case study of the assignment of the absolute configuration of a molecule based on the isoneoamphilectane carbon skeleton, the absolute configuration of compound 5 was established as 3S,4R,7S,8S,11R,12S,13R by application of vibrational circular dichroism (VCD). In vitro anti-TB screenings revealed that metabolites 2–4 and, in particular, semisynthetic analogue 5, are strong growth inhibitors of Mycobacterium tuberculosis H37Rv.

Description: Chemicals targeting the liver stage (LS) of the malaria parasite are useful for causal prophylaxis of malaria. In this study, four lichen metabolites, evernic acid (1); vulpic acid (2), psoromic acid (3), and, (+)-usnic acid (4), were evaluated against LS parasites of Plasmodium berghei. Inhibition Of P. falciparum blood Stage (BS) parasites was also assessed to determine stage specificity. Compound 4 displayed the highest LS activity and stage specificity (LS IC50 value 2.3 mu M, BS IC50 value 47.3 mu M). The compounds 1 - 3 inhibited one Or more enzymes (Pf FabI, PfFabG, and pfFabZ), from the Plasmodial fatty acid biosynthesis (FAS-II) pathway, a potential drug. target for LS activity. To determine species specificity and to clarify the mechanism of reported antibacterial effects, 1-4 were also evaluated against FabI homologues and Whole cells of various pathogens -(S. aureus, E. coli M. tuberculosis). Molecular modeling studies suggest that lichen acids act indirectly via binding to allosteric sites on the protein surface of the FAS-II enzymes. Potential. toxicity, of compounds was assessed in human hepatocyte and cancer cells (in vitro) as well as in a zebrafish model (in vivo):. This study indicates the therapeutic and prophylactic potential of lichen metabolites as antibacterial and antiplasmodial agents.

Description: We investigated the gelatinous carnivore zooplankton community in the coastal waters of northeast Taiwan during the period 20072010. The community assemblage was composed of 45 species, of which only 14 appeared recurrent in Taiwanese waters. Although there was no clear seasonality, higher richness and abundances occurred in spring and autumn. Examination of potential physical drivers of coastal biomass accumulation did not show any link with water mass transport; instead, peak events were associated with typhoon disturbances, suggesting a potential resource pulse effect.

Description: This study aimed to examine interactive effects between ocean acidification and temperature on the photosynthetic and growth performance of Neosiphonia harveyi. N. harveyi was cultivated at 10 and 17.5 °C at present (~380 µatm), expected future (~800 µatm), and high (~1500 µatm) pCO2. Chlorophyll a fluorescence, net photosynthesis, and growth were measured. The state of the carbon-concentrating mechanism (CCM) was examined by pH-drift experiments (with algae cultivated at 10 °C only) using ethoxyzolamide, an inhibitor of external and internal carbonic anhydrases (exCA and intCA, respectively). Furthermore, the inhibitory effect of acetazolamide (an inhibitor of exCA) and Tris (an inhibitor of the acidification of the diffusive boundary layer) on net photosynthesis was measured at both temperatures. Temperature affected photosynthesis (in terms of photosynthetic efficiency, light saturation point, and net photosynthesis) and growth at present pCO2, but these effects decreased with increasing pCO2. The relevance of the CCM decreased at 10 °C. A pCO2 effect on the CCM could only be shown if intCA and exCA were inhibited. The experiments demonstrate for the first time interactions between ocean acidification and temperature on the performance of a non-calcifying macroalga and show that the effects of low temperature on photosynthesis can be alleviated by increasing pCO2. The findings indicate that the carbon acquisition mediated by exCA and acidification of the diffusive boundary layer decrease at low temperatures but are not affected by the cultivation level of pCO2, whereas the activity of intCA is affected by pCO2. Ecologically, the findings suggest that ocean acidification might affect the biogeographical distribution of N. harveyi.

Description: The vast majority of microbes inhabiting the subseafloor remain uncultivated and their energy sources unknown. Thus, a focus of ocean drilling expeditions over the past decade has been to characterize the distribution of microbes associated with specific metabolic reactions. An important question has been whether microbes involved in key microbial processes, such as sulfate reduction and methanogenesis, differ fundamentally from their counterparts in surface environments. To this end, functional genes of anaerobic methane cycling (mcrA), sulfate reduction (dsrAB), acetogenesis (fhs), and dehalorespiration (rdhA) have been examined. A compilation of existing functional gene data suggests that subseafloor microbes involved in anaerobic methane cycling, sulfate reduction, acetogenesis, and dehalorespiration are not fundamentally different from their counterparts in the surface world. Moreover, quantifications of mcrA and dsrAB suggest that, unless the majority of subseafloor microbes involved in methane cycling and sulfate reduction are too genetically divergent to be detected with conventional methods, these processes only support a small fraction (〈 1%) of total microbial biomass in the deep biosphere. Ecological explanations for the observed trends, target processes and methods for future investigations, and strategies for tackling the unresolved issue of microbial contamination in samples obtained by ocean drilling are discussed.

Description: New indicators for optical CO2 sensors are synthesized in two steps from the commercially available diketo-pyrrolo-pyrrole (DPP) pigments Irgazin Ruby and Irgazin Scarlet. After introduction of bis(2-ethylhexyl) sulfonamide groups via a simple two-step synthesis, the pigments are rendered highly soluble in organic solvents and in polymers and show pH-dependent absorption and emission spectra. The new indicators have molar absorption coefficients in a 20 000–50 000 M–1 cm–1 range, possess quantum yields close to unity, and feature good photostability. The indicators along with a quaternary ammonium base are embedded into ethyl cellulose to give optical carbon dioxide sensors. The absorption and emission spectra of the deprotonated form are bathochromically shifted by more than 100 nm compared to the neutral form (λmax absorption 496–550 nm; λmax emission 564–587 nm). This enables colorimetric read-out and self-referenced ratiometric fluorescence intensity measurements. Importantly, the dynamic range of the sensors based on the new indicators is significantly different (0–10 kPa and 1–100 kPa CO2) that enables a broad variety of applications. New DPP dyes are conveniently prepared from commercially available pigments and represent a new class of colorimetric and fluorescent pH indicators for optical carbon dioxide sensors.

Description: Undaria pinnatifida, commonly known as wakame in Japan, is one species of brown seaweeds containing valuable bioactive organic compounds such as fucoxanthin, a carotenoid, which has numerous functional properties. However, most of the seaweeds that do not meet strict quality standards are normally discarded as wastes or returned to the sea, a situation which is becoming an environmental concern. In this research, supercritical carbon dioxide (SCCO2) extraction was investigated for the isolation of fucoxanthin. SCCO2 extraction experiments were carried out at temperature range of 25–60 °C and pressure range of 20–40 MPa, at a carbon dioxide flow rate of 1.0–4.0 mL/min. Results showed that fucoxanthin recovery closed to 80% could be obtained at 40 °C and 40 MPa in extraction time of 180 min. The recovery increased with decreasing temperature and increasing pressure. Pretreatment with microwave (MW) also enhanced the efficiency of extraction due most likely to disruption of the cell membrane. Application of SCCO2, generally regarded as safe and environmentally benign solvent, for extraction of useful bioactive compounds from unwanted or substandard seaweeds look promising in the near future. The extracts obtained using the method can be utilized as food and pharmaceutical additive, and can be used in the development of new health supplements.

Description: Trophodynamics of meso-zooplankton in the North Sea (NS) were assessed at a site in the southern NS, and at a shallow and a deep site in the central NS. Offshore and neritic species from different ecological niches, including Calanus spp., Temora spp. and Sagitta spp., were collected during seven cruises over 14 months from 2007 to 2008. Bulk stable isotope (SI) analysis, phospholipid-derived fatty acid (PLFA) compositions, and δ 13CPLFA data of meso-zooplankton and particulate organic matter (POM) were used to describe changes in zooplankton relative trophic positions (RTPs) and trophodynamics. The aim of the study was to test the hypothesis that the RTPs of zooplankton in the North Sea vary spatially and seasonally, in response to hydrographic variability, with the microbial food web playing an important role at times. Zooplankton RTPs tended to be higher during winter and lower during the phytoplankton bloom in spring. RTPs were highest for predators such as Sagitta sp. and Calanus helgolandicus and lowest for small copepods such as Pseudocalanus elongatus and zoea larvae (Brachyura). δ 15NPOM-based RTPs were only moderate surrogates for animals’ ecological niches, because of the plasticity in source materials from the herbivorous and the microbial loop food web. Common (16:0) and essential (eicosapentaenoic acid, EPA and docosahexaenoic acid, DHA) structural lipids showed relatively constant abundances. This could be explained by incorporation of PLFAs with δ 13C signatures which followed seasonal changes in bulk δ 13CPOM and PLFA δ 13CPOM signatures. This study highlighted the complementarity of three biogeochemical approaches for trophodynamic studies and substantiated conceptual views of size-based food web analysis, in which small individuals of large species may be functionally equivalent to large individuals of small species. Seasonal and spatial variability was also important in altering the relative importance of the herbivorous and microbial food webs.

Description: Effects of epibiotic bacteria associated with macroalgae on barnacle larval attachment were investigated. Eight bacterial isolates obtained from samples of three macroalga species were cultured as monospecies bacterial films and tested for their activity against barnacle (Amphibalanus improvisus) attachment in field experiments (Western Baltic Sea). Furthermore, natural biofilm communities associated with the surface of the local brown alga, Fucus vesiculosus, which were exposed to different temperatures (5, 15 and 20 °C), were harvested and subsequently tested. Generally, monospecies bacterial biofilms, as well as natural microbial assemblages, inhibited barnacle attachment by 20-67%. denaturing gradient gel electrophoresis fingerprints showed that temperature treatment shifted the bacterial community composition and weakened the repellent effects at 20 °C. Repellent effects were absent when settlement pressure of cyprids was high. Nonviable bacteria tended to repel cyprids when compared to the unfilmed surfaces. We conclude that biofilms can have a repellent effect benefiting the host by preventing heavy fouling on its surface. However, severe settlement pressure, as well as stressful temperature, may reduce the protective effects of the alga's biofilm. Our results add to the notion that the performance of F. vesiculosus may be reduced by multiple stressors in the course of global warming.

Description: Microscopy, confocal Raman spectroscopy and powder X-ray diffraction (PXRD) were used for in situ investigations of the CO2-hydrocarbon exchange process in gas hydrates and its driving forces. The study comprises the exposure of simple structure I CH4 hydrate and mixed structure II CH4–C2H6 and CH4–C3H8 hydrates to gaseous CO2 as well as the reverse reaction, i.e., the conversion of CO2-rich structure I hydrate into structure II mixed hydrate. In the case of CH4–C3H8 hydrates, a conversion in the presence of gaseous CO2 from a supposedly more stable structure II hydrate to a less stable structure I CO2-rich hydrate was observed. PXRD data show that the reverse process requires longer initiation times, and structural changes seem to be less complete. Generally, the exchange process can be described as a decomposition and reformation process, in terms of a rearrangement of molecules, and is primarily induced by the chemical potential gradient between hydrate phase and the provided gas phase. The results show furthermore the dependency of the conversion rate on the surface area of the hydrate phase, the thermodynamic stability of the original and resulting hydrate phase, as well as the mobility of guest molecules and formation kinetics of the resulting hydrate phase.

Description: Calculations of the size and density of atmospheric aerosols are complicated by the fact that they can exist at concentrations highly supersaturated with respect to dissolved salts and supercooled with respect to ice. Densities and apparent molar volumes of solutes in aqueous solutions containing the solutes H2SO4, HNO3, HCl, Na2SO4, NaNO3, NaCl, (NH4)2SO4, NH4NO3, and NH4Cl have been critically evaluated and represented using fitted equations from 0 to 50 °C or greater and from infinite dilution to concentrations saturated or supersaturated with respect to the dissolved salts. Using extrapolated densities of high-temperature solutions and melts, the relationship between density and concentration is extended to the hypothetical pure liquid solutes. Above a given reference concentration of a few mol kg−1, it is observed that density increases almost linearly with decreasing temperature, and comparisons with available data below 0 °C suggest that the fitted equations for density can be extrapolated to very low temperatures. As concentration is decreased below the reference concentration, the variation of density with temperature tends to that of water (which decreases as temperature is reduced below 3.98 °C). In this region below the reference concentration, and below 0 °C, densities are calculated using extrapolated apparent molar volumes which are constrained to agree at the reference concentrations with an equation for the directly fitted density. Calculated volume properties agree well with available data at low temperatures, for both concentrated and dilute solutions. Comparisons are made with literature data for temperatures of maximum density. Apparent molar volumes at infinite dilution are consistent, on a single ion basis, to better than ±0.1 cm3 mol−1 from 0 to 50 °C. Volume properties of aqueous NaHSO4, NaOH, and NH3 have also been evaluated, at 25 °C only. In part 2 of this work (ref 1) an ion interaction (Pitzer) model has been used to calculate apparent molar volumes of H2SO4 in 0−3 mol kg−1 aqueous solutions of the pure acid and to represent directly the effect of the HSO4− ↔ H+ + SO42− reaction. The results are incorporated into the treatment of aqueous H2SO4 density described here. Densities and apparent molar volumes from −20 to 50 °C, and from 0 to 100 wt % of solute, are tabulated for the electrolytes listed in the title and have also been incorporated into the extended aerosol inorganics model (E-AIM, http://www.aim.env.uea.ac.uk/aim/aim.php) together with densities of the solid salts and hydrates.

Description: The aim of this study was to examine sponge orange band (SOB) disease affecting the prominent Caribbean sponge Xestospongia muta. Scanning and transmission electron microscopy revealed that SOB is accompanied by the massive destruction of the pinacoderm. Chlorophyll a content and the main secondary metabolites, tetrahydrofurans, characteristic of X. muta, were significantly lower in bleached than in healthy tissues. Denaturing gradient gel electrophoresis using cyanobacteria-specific 16S rRNA gene primers revealed a distinct shift from the Synechococcus/Prochlorococcus clade of sponge symbionts towards several clades of unspecific cyanobacteria, including lineages associated with coral disease (i.e. Leptolyngbya sp.). Underwater infection experiments were conducted by transplanting bleached cores into healthy individuals, but revealed no signs of SOB development. This study provided no evidence for the involvement of a specific microbial pathogen as an etiologic agent of disease; hence, the cause of SOB disease in X. muta remains unidentified.

Description: A total of 19 naturally occurring bromophenols, with six new and 13 known structures, were isolated and identified from the methanolic extract of the marine red alga Rhodomela confervoides. The new compounds were identified by spectroscopic methods as 3,4-dibromo-5-((methylsulfonyl)methyl)benzene-1,2-diol (1), 3,4-dibromo-5-((2,3-dihydroxypropoxy)methyl)benzene-1,2-diol (2), 5-(aminomethyl)-3,4-dibromobenzene-1,2-diol (3), 2-(2,3-dibromo-4,5-dihydroxyphenyl)acetic acid (4), 2-methoxy-3-bromo-5-hydroxymethylphenol (5), and (E)-4-(2-bromo-4,5-dihydroxyphenyl)but-3-en-2-one (6). Each compound was evaluated for free radical scavenging activity against DPPH (α,α-diphenyl-β-dipicrylhydrazyl) and ABTS [2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid)diammonium salt] radicals. Most of them exhibited potent activities stronger than or comparable to the positive controls butylated hydroxytoluene (BHT) and ascorbic acid. The results from this study suggest that R. confervoides is an excellent source of natural antioxidants, and inclusion of these antioxidant-rich algal components would likely help prevent the oxidative deterioration of food.

Description: Shallow coastal waters, where phototrophic purple sulfur bacteria (PSB) regularly form massive blooms, are subjected to massive diurnal and event-driven changes of physicochemical conditions including temperature and salinity. To analyze the ability of PSB to cope with these environmental factors and to compete in complex communities we have studied changes of the environmental community of PSB of a Baltic Sea lagoon under experimental enrichment conditions with controlled variation of temperature and NaCl concentration. For the first time, changes within a community of PSB were specifically analyzed using the photosynthetic reaction center genes pufL and M by RFLP and cloning experiments. The most abundant PSB phylotypes in the habitat were found along the NaCl gradient from freshwater conditions up to 7.5% NaCl. They were accompanied by smaller numbers of purple nonsulfur bacteria and aerobic anoxygenic phototrophic bacteria. Major components of the PSB community of the brackish lagoon were affiliated to PSB genera and species known as marine, halophilic or salt-tolerant, including species of Marichromatium, Halochromatium, Thiorhodococcus, Allochromatium, Thiocapsa, Thiorhodovibrio, and Thiohalocapsa. A dramatic shift occurred at elevated temperatures of 41 and 44°C when Marichromatium gracile became most prominent which was not detected at lower temperatures.

Description: Titanium (Ti) is present as a trace element in seawater at extremely low concentrations (5-350 pM, where 1 pM = 10(-12) mol L(-1)) throughout the water column. Presently, little is known about the marine biogeochemistry of Ti and there is a distinct lack of oceanic measurements of Ti, because of the combined difficulties of trace-metal clean sampling for an element at such low levels and the lack of a suitable shipboard method of analysis. Here, a new cathodic stripping voltammetry procedure is presented for the rapid determination of Ti at pM concentrations in seawater that is capable of being used directly at sea. This method utilizes the catalytic enhancement of the reduction of the complex formed between Cupferron (N-nitrosophenylhydroxylamine) and Ti(IV). While Cupferron itself acts as both a complexing agent and an oxidizing agent, it was found that the optimal sensitivity was with bromate as an auxiliary oxidant. An advantage of this method is that it is useable over the pH range of 5.5-8. Under the conditions employed in this work, detection limits ranged from 5 pM to 12 pM. This new catalytic method is significantly more sensitive than existing methods and has been extensively tested at sea in the Atlantic and Southern Oceans.

Description: The conversion of alkylboranes to the corresponding alkanes is classically per-formed via protonolysis of alkylboranes. This simple reaction requires the use of severe reaction conditions, that is, treatment with a carboxylic acid at high temperature (〉150 °C). We report here a mild radical procedure for the transformation of organoboranes to alkanes. 4-tert-Butylcatechol, a well-established radical inhibitor and antioxidant, is acting as a source of hydrogen atoms. An efficient chain reaction is observed due to the exceptional reactivity of phenoxyl radicals toward alkylboranes. The reaction has been applied to a wide range of organoboron derivatives such as B-alkylcatecholboranes, trialkylboranes, pinacolboronates, and alkylboronic acids. Furthermore, the so far elusive rate constants for the hydrogen transfer between secondary alkyl radical and catechol derivatives have been experimentally determined. Interestingly, they are less than 1 order of magnitude slower than that of tin hydride at 80 °C, making catechols particularly attractive for a wide range of transformations involving C−C bond formation.

Description: The activity of the human armpit microbiota triggers the formation of body odor. We used differential 16S rRNA gene (rDNA)- and rRNA-based terminal-restriction fragment length polymorphism fingerprinting in combination with cloning and sequencing to identify active members of the human armpit microbiota. DNA and RNA were isolated from skin scrub samples taken from both armpits of 10 preconditioned, healthy males. The fingerprint profiles indicated pronounced similarities between the armpit microbiota in the right and the left axillae of an individual test person, but larger differences between the axilla microbiota of different individuals. Using 16S rDNA and rRNA sequence data, the majority of peaks in the armpit profiles were assigned to bacteria affiliated with well-known genera of skin bacteria. The relative abundances of all groups were similar among the rDNA and rRNA samples, suggesting that all groups of armpit bacteria were active. Surprisingly, the relative abundance of sequences affiliated with Peptoniphilus sp. was by far and with statistical significance the highest in the rRNA samples of the right armpits. Thus, bacteria affiliated with Peptoniphilus sp. might have been particularly active in the right axillae of the test persons, possibly owing to the handedness of the test persons, which might cause different environmental conditions in the right axillae.

Description: Macroalgae have for centuries been consumed whole among the East Asian populations of China, Korea, and Japan. Due to the environment in which they grow, macroalgae produce unique and interesting biologically active compounds. Protein can account for up to 47% of the dry weight of macroalgae depending on species and time of cultivation and harvest. Peptides derived from marcoalgae are proven to have hypotensive effects in the human circulatory system. Hypertension is one of the major, yet controllable, risk factors in cardiovascular disease (CVD). CVD is the main cause of death in Europe, accounting for over 4.3 million deaths each year. In the United States it affects one in three individuals. Hypotensive peptides derived from marine and other sources have already been incorporated into functional foods such as beverages and soups. The purpose of this review is to highlight the potential of heart health peptides from macroalgae and to discuss the feasibility of expanding the variety of foods these peptides may be used in.

Description: Mixing processes of reduced hydrothermal fluids with oxygenated seawater and fluid-rock reactions contribute to the chemical signatures of diffuse venting and likely determine the geochemical constraints on microbial life. We examined the influence of fluid chemistry on microbial diversity and activity by sampling diffuse fluids emanating through mussel beds at two contrasting hydrothermal vents. The H(2) concentration was very low at the basalt-hosted Clueless site, and mixing models suggest O(2) availability throughout much of the habitat. In contrast, effluents from the ultramafic-hosted Quest site were considerably enriched in H(2) , while O(2) is likely limited to the mussel layer. Only two different hydrogenase genes were identified in clone libraries from the H(2) -poor Clueless fluids, but these fluids exhibited the highest H(2) uptake rates in H(2) -spiked incubations (oxic conditions, at 18 °C). In contrast, a phylogenetically diverse H(2) -oxidizing potential was associated with distinct thermal conditions in the H(2) -rich Quest fluids, but under oxic conditions, H(2) uptake rates were extremely low. Significant stimulation of CO(2) fixation rates by H(2) addition was solely illustrated in Quest incubations (P-value 〈0.02), but only in conjunction with anoxic conditions (at 18 °C). We conclude that the factors contributing toward differences in the diversity and activity of H(2) oxidizers at these sites include H(2) and O(2) availability.

Description: Methane hydrate, a potential future energy resource, is known to occur naturally in vast quantities beneath the ocean floor and in permafrost regions. It is important to evaluate how much methane is recoverable from these hydrate reserves. This article introduces the theoretical background of HydrateResSim, the National Energy Technology Laboratory (NETL) methane production simulator for hydrate-containing reservoirs, originally developed for NETL by Lawrence Berkeley National Laboratory (LBNL). It describes the mathematical model that governs the dissociation of methane hydrate by depressurization or thermal stimulation of the system, including the transport of multiple temperature-dependent components in multiple phases through a porous medium. The model equations are obtained by incorporating the multiphase Darcy’s law for gas and liquid into both the mass component balances and the energy conservation equations. Two submodels in HydrateResSim for hydrate dissociation are also considered: a kinetic model and a pure thermodynamic model. Contrary to more traditional reservoir simulations, the set of model unknowns or primary variables in HydrateResSim changes throughout the simulation as a result of the formation or dissociation of ice and hydrate phases during the simulation. The primary variable switch method (PVSM) is used to effectively track these phase changes. The equations are solved by utilizing the implicit time finite-difference method on the grid system, which can properly describe phase appearance or disappearance as well as the boundary conditions. The Newton-Raphson method is used to solve the linear equations after discretization and setup of the Jacobian matrix. We report here the application of HydrateResSim to a three-component, four-phase flow system in order to predict the methane produced from a laboratory-scale reservoir. The first results of HydrateResSim code in a peer-reviewed publication are presented in this article. The numerical solution was verified against the state-of-the art simulator TOUGH+Hydrate. The model was then used to compare twodissociation theories: kinetic and pure equilibrium. Generally, the kinetic model revealed a lower dissociation rate than the equilibrium model. The hydrate dissociation patterns differed significantly when the thermal boundary condition was shifted from adiabatic to constant-temperature. The surface area factor was found to have an important effect on the rate of hydrate dissociation for the kinetic model. The deviation between the kinetic and equilibrium models was found to increase with decreasing surface area factor.

Description: Phototrophic bacteria are important primary producers of salt lakes in the Salar de Atacama and at times form visible mass developments within and on top of the lake sediments. The communities of phototrophic bacteria from two of these lakes were characterized by molecular genetic approaches using key genes for the biosynthesis of the photosynthetic apparatus in phototrophic purple bacteria (pufLM) and in green sulfur bacteria (fmoA). Terminal restriction fragment length polymorphism of the pufLM genes indicated high variability of the community composition between the two lakes and subsamples thereof. The communities were characterized by the dominance of a novel, so far undescribed lineage of pufLM containing bacteria and the presence of representatives related to known halophilic Chromatiaceae and Ectothiorhodospiraceae. In addition, the presence of BChl b-containing anoxygenic phototrophic bacteria and of aerobic anoxygenic bacteria was indicated. Green sulfur bacteria were not detected in the environmental samples, although a bacterium related to Prosthecochloris indicum was identified in an enrichment culture. This is the first comprehensive description of phototrophic bacterial communities in a salt lake of South America made possible only due to the application of the functional pufLM genes.

Description: Analyses of clone libraries from water and sediments of different sites from Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano, revealed the presence of five unique clusters of uncultured Archaea that have not been previously reported or specifically assigned. These sequences were distantly related (83–96% sequence identity) to a limited number of other clone sequences and revealed no identity to cultured Archaea. The abundance of Archaea and Bacteria was estimated using qPCR and community composition was examined through the construction of clone libraries of archaeal 16S rRNA gene. Archaea were found to be dominant over Bacteria in sediments from two saline sites (sites H4: 6.31 × 104 and site H6: 1.37 × 104 μS cm−1) and in one of the water samples (freshwater from site H0: 607 μS cm−1). Euryarchaeotal sequences were more abundant than crenarchaeotal sequences. Many of the clone sequences (52%) were similar to uncultured archaeal groups found in marine ecosystems having identity values between 99% and 97%. A major fraction of the sequences (40%) were members of Methanobacteria, while others were included in the Marine Benthic Groups B and D, the Miscellaneous Crenarchaeotic Group, the Terrestrial Miscellaneous Euryarchaeotal Group, Marine Group I and Halobacteria. The presence of uncultured archaeal groups in Salar de Huasco extends their known distribution in inland waters, providing new clues about their possible function in the environment.

Description: Life at deep-sea hydrothermal vents depends on chemolithoautotrophic microorganisms as primary producers mediating the transfer of energy from hydrothermal fluids to higher trophic levels. A comprehensive molecular survey was performed with microbial communities in a mussel patch at the Irina II site of the Logatchev hydrothermal field by combining the analysis of 16S rRNA gene sequences with studies of functional key genes involved in biochemical pathways of sulfur oxidation–reduction (soxB, aprA) and autotrophic carbon fixation (aclB, cbbM, cbbL). Most significantly, major groups of chemoautotrophic sulfur oxidizers in the diffuse fluids differed in their biosynthetic pathways of both carbon fixation and sulfur oxidation. One important component of the community, the Epsilonproteobacteria, has the potential to grow chemoautotrophically by means of the reductive tricarboxylic acid cycle and to gain energy through the oxidation of reduced sulfur compounds using the Sox pathway. The majority of soxB and all retrieved aclB gene sequences were assigned to this group. Another important group in this habitat, the Gammaproteobacteria, may use the adenosine 5'-phosphosulfate pathway and the Calvin–Benson–Bassham cycle, deduced from the presence of aprA and cbbM genes. Hence, two important groups of primary producers at the investigated site might use different pathways for sulfur oxidation and carbon fixation.

Description: The chemical composition of the Caribbean sponge Pandaros acanthifolium was reinvestigated and led to the isolation of 12 new steroidal glycosides, namely, pandarosides E-J (1-6) and their methyl esters (7-12). Their structures were determined on the basis of extensive spectroscopic analyses, including two-dimensional NMR and HRESIMS data. Like the previously isolated pandarosides A-D (13-16), the new compounds 1-12 share an unusual oxidized D-ring and a cis C/D ring junction. The absolute configurations of the aglycones were assigned by interpretation of CD spectra, whereas the absolute configurations of the monosaccharide units were determined by chiral GC analyses of the acid methanolysates. The majority of the metabolites showed in vitro activity against three or four parasitic protozoa. Particularly active were the compounds 3 (pandaroside G) and its methyl ester (9), which potently inhibited the growth of Trypanosoma brucei rhodesiense (IC(50) values 0.78 and 0.038 mu M, respectively) and Leishmania donovani (IC(50)'s 1.3 and 0.051 mu M, respectively).

Description: The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (≤2 μm diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer-probes targeting a subset of these, as well as housekeeping genes, in RCC299. All those investigated showed expression either under standard growth conditions or under nitrogen depletion. Like other recent publications, our findings show a higher degree of "mixed lineage gene affiliations" among eukaryotes than anticipated, and even the most phylogenetically anomalous versions appear to be functional. Nitrogen is often considered a regulating factor for phytoplankton populations. This study provides a springboard for exploring the use and functional diversification of inorganic nitrogen transporters and related genes in eukaryotic phytoplankton. © 2010 The Author.

Description: The metabolic demands of a rare paper nautilus, Argonauta nouryi, in the eastern tropical Pacific (ETP) are evaluated. After adjusting for temperature and size, the rates of oxygen consumption and of aerobic and anaerobic metabolic potential (as evidenced by citrate synthase and octopine dehydrogenase activities, respectively) of A. nouryi were much higher than those in holopelagic octopods that exhibit float-and-wait predation strategies. In fact, the rates were similar to those found in small epipelagic squids and benthic octopods. The critical oxygen partial pressure was 4.9 kPa at 20°C, suggesting that the strong oxygen minimum layer found at intermediate depths in the ETP may constrain the vertical distribution of A. nouryi to the upper few metres of the water column. We also report the occurrence of a chain of shelled females at the surface, in which each animal was attached, as if on the benthos, to the next individual in the chain. Although it may constitute an effective strategy to increase the rates of mate encounter in the vast open ocean, there may be an important ecological trade-off for such behaviour, namely the increase in visibility at the surface with concomitant attraction of predators.

Description: The distribution of paralarvae and small juvenile cephalopods sampled by a rectangular midwater trawl (opening area 8 m2) over the continental shelf off Cape Santa Marta Grande, southern Brazil (28°09′S–29°56′S) during spring 1989 is discussed. An intrusion of Brazil Current Tropical Water (22°C; 36.5) separates warm, less-saline water (22°C; 35.2) from cooler, more-saline water (15°C; 36.4). Prevailing northeasterly winds led to upwelling of South Atlantic Central Water over the shelf, promoting high Chl a concentrations. Three species constituted 99% of the 628 cephalopods collected: Illex argentinus (n = 540; 4–40 mm mantle length, ML), Argonauta nodosa (n = 46; 2–19 mm ML), and Loligo sanpaulensis (n = 42, 2–21 mm ML). Segregation of I. argentinus juveniles of similar size suggests school formation as small as 10 mm ML. The presence of mature males along with fertilized female A. nodosa indicates mating early in life. There was a consistent and direct link between high plankton production and high densities of juvenile cephalopods through a short and ecologically efficient food chain. The relationship between production, pycnocline intensity, and the density of paralarvae and juveniles revealed suitable conditions for survival and growth during the upwelling season.

Description: As ecosystem engineers, seagrasses are angiosperms of paramount ecological importance in shallow shoreline habitats around the globe. Furthermore, the ancestors of independent seagrass lineages have secondarily returned into the sea in separate, independent evolutionary events. Thus, understanding the molecular adaptation of this clade not only makes significant contributions to the field of ecology, but also to principles of parallel evolution as well. With the use of Dr. Zompo, the first interactive seagrass sequence database presented here, new insights into the molecular adaptation of marine environments can be inferred. The database is based on a total of 14 597 ESTs obtained from two seagrass species, Zostera marina and Posidonia oceanica, which have been processed, assembled and comprehensively annotated. Dr. Zompo provides experimentalists with a broad foundation to build experiments and consider challenges associated with the investigation of this class of non-domesticated monocotyledon systems. Our database, based on the Ruby on Rails framework, is rich in features including the retrieval of experimentally determined heat-responsive transcripts, mining for molecular markers (SSRs and SNPs), and weighted key word searches that allow access to annotation gathered on several levels including Pfam domains, GeneOntology and KEGG pathways. Well established plant genome sites such as The Arabidopsis Information Resource (TAIR) and the Rice Genome Annotation Project are interfaced by Dr. Zompo. With this project, we have initialized a valuable resource for plant biologists in general and the seagrass community in particular. The database is expected to grow together with more data to come in the near future, particularly with the recent initiation of the Zostera genome sequencing project. The Dr. Zompo database is available at http://drzompo.uni-muenster.de/

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: The taxonomy of two sympatric surf clams Donax marincovichi Coan, 1983 and Donax obesulus Reeve, 1854, inhabiting the coastal Humboldt Current Upwelling System is revisited. Because both species are exploited by artisanal fisheries, it is essential to verify that they are indeed distinct species that have to be managed separately. In this study, both taxa were sampled across their shared distributional area and specimens were indentified according to their respective morphological characteristics. Although width/height and height/length ratios revealed significant differences within sampling areas, the two morphotypes were frequently incongruent for taxonomically important morphometric parameters. In addition, they showed no significant mitochondrial genetic differentiation within or among populations and exhibited indistinguishable sperm ultrastructure. We conclude that the two morphotypes do not represent distinct species and should be included together under D. obesulus.

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 diversity of Cyanobacteria in water and sediment samples from four representative sites of the Salar de Huasco was examined using denaturing gradient gel electrophoresis and analysis of clone libraries of 16S rRNA gene PCR products. Salar de Huasco is a high altitude (3800 m altitude) saline wetland located in the Chilean Altiplano. We analyzed samples from a tributary stream (H0) and three shallow lagoons (H1, H4, H6) that contrasted in their physicochemical conditions and associated biota. Seventy-eight phylotypes were identified in a total of 268 clonal sequences deriving from seven clone libraries of water and sediment samples. Oscillatoriales were frequently found in water samples from sites H0, H1 and H4 and in sediment samples from sites H1 and H4. Pleurocapsales were found only at site H0, while Chroococcales were recovered from sediment samples of sites H0 and H1, and from water samples of site H1. Nostocales were found in sediment samples from sites H1 and H4, and water samples from site H1 and were largely represented by sequences highly similar to Nodularia spumigena. We suggest that cyanobacterial communities from Salar de Huasco are unique - they include sequences related to others previously described from the Antarctic, along with others from diverse, but less extreme environments.

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: The functional gene amoA was used to compare the diversity of ammonia-oxidizing bacteria (AOB) in the water column and sediment-water interface of the two freshwater lakes Plusssee and Schöhsee and the Baltic Sea. Nested amplifications were used to increase the sensitivity of amoA detection, and to amplify a 789-bp fragment from which clone libraries were prepared. The larger part of the sequences was only distantly related to any of the cultured AOB and is considered to represent new clusters of AOB within the Nitrosomonas/Nitrosospira group. Almost all sequences from the water column of the Baltic Sea and from 1-m depth of Schöhsee were related to different Nitrosospira clusters 0 and 2, respectively. The majority of sequences from Plusssee and Schöhsee were associated with sequences from Chesapeake Bay, from a previous study of Plusssee and from rice roots in Nitrosospira-like cluster A, which lacks sequences from Baltic Sea. Two groups of sequences from Baltic Sea sediment were related to clonal sequences from other brackish/marine habitats in the purely environmental Nitrosospira-like cluster B and the Nitrosomonas-like cluster. This confirms previous results from 16S rRNA gene libraries that indicated the existence of hitherto uncultivated AOB in lake and Baltic Sea samples, and showed a differential distribution of AOB along the water column and sediment of these environments

Description: Bacterial communities associated with the brown alga Laminaria saccharina from the Baltic Sea and from the North Sea were investigated using denaturing gradient gel electrophoresis and 16S rRNA gene clone libraries. The rhizoid, cauloid, meristem and phyloid revealed different 16S rRNA gene denaturing gradient gel electrophoresis banding patterns indicating a specific association of bacterial communities with different parts of the alga. Associations with cauloid and meristem were more specific, while less specific associations were obtained from the old phyloid. In addition, seasonal and geographical differences in the associated communities were observed. Results from 16S rRNA gene libraries supported these findings. Bacterial phylotypes associated with the alga were affiliated with the Alphaproteobacteria (nine phylotypes), Gammaproteobacteria (nine phylotypes) and the Bacteroidetes group (four phylotypes). A number of bacteria associated with other algae and other marine macroorganisms were among the closest relatives of phylotypes associated with L. saccharina.

Description: Over recent years, several PCR primers have been described to amplify genes encoding the structural subunits of ammonia monooxygenase (AMO) from ammonia-oxidizing bacteria (AOB). Most of them target amoA, while amoB and amoC have been neglected so far. This study compared the nucleotide sequence of 33 primers that have been used to amplify different regions of the amoCAB operon with alignments of all available sequences in public databases. The advantages and disadvantages of these primers are discussed based on the original description and the spectrum of matching sequences obtained. Additionally, new primers to amplify the almost complete amoCAB operon of AOB belonging to Betaproteobacteria (betaproteobacterial AOB), a primer pair for DGGE analysis of amoA and specific primers for gammaproteobacterial AOB, are also described. The specificity of these new primers was also evaluated using the databases of the sequences created during this study.

Description: We studied the effect of the quorum-sensing (QS) blockers 5-hydroxy-3[(1R)-1-hydroxypropyl]-4-methylfuran-2(5H)-one (FUR1), (5R)-3,4-dihydroxy-5-[(1S)-1,2-dihydroxyethyl]furan-2(5H)-one (FUR2) and triclosan (TRI) on the formation of bacterial biofilms, and the effect of these biofilms on the larval attachment of the polychaete Hydroides elegans and the bryozoan Bugula neritina. 14-day-old subtidal biofilms were harvested from artificial substrata and were allowed to develop in the laboratory with and without QS blockers. QS blockers inhibited the production of violacein by the QS reporter strain Chromobacterium violaceum CV026 and did not affect the metabolic activity of bacteria in multispecies biofilms. At a concentration of 10(-3) M all three tested compounds inhibited the establishment of microbial communities, but at one of 10(-4) M only FUR2 inhibited establishment. The tested QS blockers caused changes in bacterial density and bacterial community structure, as revealed by terminal restriction fragment length polymorphism and FISH. The groups most affected by QS blockers were Alphaproteobacteria, Gammaproteobacteria and the Cytophagales. Larvae of H. elegans and B. neritina avoided settling on biofilms that had developed in the presence of QS blockers. Our results suggest that QS blockers directly control the formation of multi-species biofilms, and indirectly - by means of biofilm properties - affect larval attachment on these modified biofilms.

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: Microbial isolate Z143-1 found to be associated with an unidentified tunicate was characterized due to its significant antimicrobial activity. Z143-1 is similar to Pseudovibrio ascidiaceicola and Pseudovibrio denitrificans in morphological, physiological and biochemical characteristics, except for its ability to ferment glucose and produce a characteristic red pigment. Fatty acid methyl ester analysis revealed a predominance of the fatty acid 18:1 ω7c at 80.55%, at levels slightly lower than the Pseudovibrio denitrificans type strain DN34T (87.7%). The mol% G+C of Z143-1 is 54.02, relatively higher than the Pseudovibrio denitrificans type strain DN34T and Pseudovibrio ascidiaceicola with mol% G+C of 51.7 and 51.4, respectively. However, phylogenetic analysis of the 16S rRNA gene sequence of Z143-1 showed 100% similarity with the Pseudovibrio denitrificans type strain DN34T. In this study, the bacterium Z143-1 is reported as a new strain of Pseudovibrio denitrificans. While there is no report of a secondary metabolite for Pseudovibrio denitrificans, Z143-1 produces the red pigment heptylprodigiosin, also known as 16-methyl-15-heptyl-prodiginine, which shows anti-Staphylococcus aureus activity.

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: Mechanisms that affect thermal tolerance of ectothermic organisms have recently received much interest, mainly due to global warming and climate-change debates in both the public and in the scientific community. In physiological terms, thermal tolerance of several marine ectothermic taxa can be linked to oxygen availability, with capacity limitations in ventilatory and circulatory systems contributing to oxygen limitation at extreme temperatures. The present review briefly summarizes the processes that define thermal tolerance in a model cephalopod organism, the cuttlefish Sepia officinalis, with a focus on the contribution of the cephalopod oxygen-carrying blood pigment, hemocyanin. When acutely exposed to either extremely high or low temperatures, cuttlefish display a gradual transition to an anaerobic mode of energy production in key muscle tissues once critical temperatures (Tcrit) are reached. At high temperatures, stagnating metabolic rates and a developing hypoxemia can be correlated with a progressive failure of the circulatory system, well before Tcrit is reached. However, at low temperatures, declining metabolic rates cannot be related to ventilatory or circulatory failure. Rather, we propose a role for hemocyanin functional characteristics as a major limiting factor preventing proper tissue oxygenation. Using information on the oxygen binding characteristics of cephalopod hemocyanins, we argue that high oxygen affinities (= low P50 values), as found at low temperatures, allow efficient oxygen shuttling only at very low venous oxygen partial pressures. Low venous PO2s limit rates of oxygen diffusion into cells, thus eventually causing the observed transition to anaerobic metabolism. On the basis of existing blood physiological, molecular, and crystallographical data, the potential to resolve the role of hemocyanin isoforms in thermal adaptation by an integrated molecular physiological approach is discussed.

Description: Recent molecular studies investigating higher-level phylogenetics of coleoid cephalopods (octopuses, squids and cuttlefishes) have produced conflicting results. A wide range of sequence alignment and analysis methods are used in cephalopod phylogenetic studies. The present study investigated the effect of commonly used alignment and analysis methods on higher-level cephalopod phylogenetics. Two sequence homology methods: (1) eye alignment, (2) implied alignment, and three analysis methods: (1) parsimony, (2) maximum likelihood, (3) Bayesian methodologies, were employed on the longest sequence dataset available for the coleoid cephalopods, comprising three mitochondrial and six nuclear loci. The data were also tested for base composition heterogeneity, which was detected in three genes and resolved using RY coding. The Octopoda, Argonautoidea, Oegopsida and Ommastrephidae are monophyletic in the phylogenies resulting from each of the alignment and analysis combinations. Furthermore, the Bathyteuthidae are the sister taxon of the Oegopsida in each case. However many relationships within the Coleoidea differed depending upon the alignment and analysis method used. This study demonstrates how differences in alignment and analysis methods commonly used in cephalopod phylogenetics can lead to different, but often highly supported, relationships.

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: The basal position of the Mamiellales (Prasinophyceae) within the green lineage makes these unicellular organisms key to elucidating early stages in the evolution of chlorophyll a/b-binding light-harvesting complexes (LHCs). Here, we unveil the complete and unexpected diversity of Lhc proteins in Ostreococcus tauri, a member of the Mamiellales order, based on results from complete genome sequencing. Like Mantoniella squamata, O. tauri possesses a number of genes encoding an unusual prasinophyte-specific Lhc protein type herein designated "Lhcp". Biochemical characterization of the complexes revealed that these polypeptides, which bind chlorophylls a, b, and a chlorophyll c-like pigment (Mg-2,4-divinyl-phaeoporphyrin a 5 monomethyl ester) as well as a number of unusual carotenoids, are likely predominant. They are retrieved to some extent in both reaction center I (RCI)- and RCII-enriched fractions, suggesting a possible association to both photosystems. However, in sharp contrast to previous reports on LHCs of M. squamata, O. tauri also possesses other LHC subpopulations, including LHCI proteins (encoded by five distinct Lhca genes) and the minor LHCII polypeptides, CP26 and CP29. Using an antibody against plant Lhca2, we unambiguously show that LHCI proteins are present not only in O. tauri, in which they are likely associated to RCI, but also in other Mamiellales, including M. squamata. With the exception of Lhcp genes, all the identified Lhc genes are present in single copy only. Overall, the discovery of LHCI proteins in these prasinophytes, combined with the lack of the major LHCII polypeptides found in higher plants or other green algae, supports the hypothesis that the latter proteins appeared subsequent to LHCI proteins. The major LHC of prasinophytes might have arisen prior to the LHCII of other chlorophyll a/b-containing organisms, possibly by divergence of a LHCI gene precursor. However, the discovery in O. tauri of CP26-like proteins, phylogenetically placed at the base of the major LHCII protein clades, yields new insight to the origin of these antenna proteins, which have evolved separately in higher plants and green algae. Its diverse but numerically limited suite of Lhc genes renders O. tauri an exceptional model system for future research on the evolution and function of LHC components. © The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.

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: A bioenergetic model for two narwhal (Monodon monoceros) sub-populations was developed to quantify daily gross energy requirements and estimate the biomass of Greenland halibut (Reinhardtius hippoglossoides) needed to sustain the sub-populations for their 5-month stay on wintering grounds in Baffin Bay. Whales in two separate wintering grounds were estimated to require 700 tonnes (s.e. 300) and 90 tonnes (s.e. 40) of Greenland halibut per day, assuming a diet of 50% Greenland halibut. Mean densities and length distributions of Greenland halibut inside and outside of the narwhal wintering grounds were correlated with predicted whale predation levels based on diving behavior. The difference in Greenland halibut biomass between an area with high predation and a comparable area without whales, approximately 19 000 tonnes, corresponded well with the predicted biomass removed by the narwhal sub-population on a diet of 50–75% Greenland halibut.

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: The systematics and distribution of the cirrate octopod genus Grimpoteuthis in the north-east Atlantic are reviewed. Three new species are described and Grimpoteuthis wuelkeri (Grimpe, 1920) is redescribed. A new generic diagnosis is proposed. Five species of Grimpoteuthis are recognized in the north-east Atlantic. The type species, G. umbellata (Fisher, 1883) is known only from the type specimen, which is in such poor condition that comparison with recently captured material was not possible. G. wuelkeri is a large, slope species, caught between 1600 m and 2200 m in the north-east and north-west Atlantic. Of the three new species, both G. boylei and G. challengeri are large abyssal species. G. boylei is found in the north-east Atlantic at the Porcupine Abyssal Plain (PAP) and the Madeira Abyssal Plain and may be found at abyssal depths throughout the north-east Atlantic. G. challengeri is known from the PAP, with a single specimen from the north-west Atlantic. G. discoveryi is a small, lower slope and abyssal species found in the north-east Atlantic. The Grimpoteuthis species can be separated based on shell form, presence of a radula and posterior salivary glands, arrangement of suckers and cirri and gill morphology. Two species, G. megaptera Verrill and G. plena Verrill, have been described from the north-west Atlantic, but the types are either lost (G. megaptera) or in poor condition (G. plena), hindering comparisons. Material examined from the north-west Atlantic included G. wuelkeri, G. challengeri and at least two other species.

Description: Legionella pneumophila is naturally found in fresh water were the bacteria parasitize within protozoa. It also survives planctonically in water or biofilms. Upon aerosol formation via man-made water systems, L. pneumophila can enter the human lung and cause a severe form of pneumonia, called Legionnaires’ disease. The pathogenesis of Legionnaires’ disease is largely due to the ability of L. pneumophila to invade and grow within macrophages. An important characteristic of the intracellular survival strategy is the replication within the host vacuole that does not fuse with endosomes or lysosomes. In recent times a great number of bacterial virulence factors which affect growth of L. pneumophila in both macrophages and protozoa have been identified. The ongoing Legionella genome project and the use of genetically tractable surrogate hosts are expected to significantly contribute to the understanding of bacterium–host interactions and the regulation of virulence traits during the infection cycle. Since person-to-person transmission of legionellosis has never been observed, the measures for disease prevention have concentrated on eliminating the pathogen from water supplies. In this respect detection and analysis of Legionella in complex environmental consortia become increasingly important. With the availability of new molecular tools this area of applied research has gained new momentum.

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: Eight planktonic egg masses of the diamond-shaped Thysanoteuthis rhombus observed from 1995 to 2000 are described. Four were found in the western Mediterranean and the others were found off the Canary Islands. The egg masses from the Canary Islands are the first records for the eastern Atlantic. All were found near the surface at the end of summer and the beginning of autumn. The planktonic egg masses were dense, resilient oblong cylinders with rounded tips ranging from 80 to 130 cm in length and between 15 and 20 cm in diameter. Egg capsule dimensions ranged from 2.8 to 3.4 mm and total length of the newly hatched paralarvae was between 2.5 and 2.8 mm. Each egg mass contained an estimated 24 100–43 800 eggs. Some new characters that should help identification of the paralarvae, such as arm formulae, presence of an incipient keel-shaped membrane on some arms, and the type and chromatophore pattern are given. Ecological factors influencing the presence and distribution of these egg masses are discussed.

Description: King Penguins (Aptenodytes patagonicus) from breeding islands in the Indian Ocean (Crozet and Kerguelen Islands) and the Atlantic Ocean (South Georgia and Falkland Islands) were equipped with global location sensors to compare their foraging patterns during different times of the year. In summer, all birds investigated traveled toward the Antarctic Polar Front (APF), irrespective of whether they bred to the north (Crozet Islands, Falkland Islands), within (Kerguelen Islands) or to the south (South Georgia) of this hydrographic feature. Whereas most birds remained north of the APF and foraged in waters of the Antarctic Polar Frontal Zone, some penguins also traveled, or remained (South Georgia), south of the APF and foraged in Antarctic waters. It appeared that food resources in the vicinity of the APF were sufficiently predictable to warrant travel of several hundred km by King Penguins for foraging. Data collected on the winter distribution of King Penguins indicated at least two different foraging strategies. Birds from the oceanic Crozet Islands foraged beyond the APF in the Antarctic waters, whereas birds from the Falkland Islands relied also on the resources provided by the highly diverse and productive slope of the Patagonian Shelf. However, despite these differences, in both cases minimum distances of sometimes more than 10 000 km were covered. Further research on the foraging habitats of King Penguins over the entire breeding season and the temporal and spatial changes of oceanographic features is necessary to obtain a comprehensive picture on the variability in the foraging ranges of King Penguins.

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: A PCR protocol for the detection of sulfur-oxidizing bacteria based on soxB genes that are essential for thiosulfate oxidation by sulfur-oxidizing bacteria of various phylogenetic groups which use the 'Paracoccus sulfur oxidation' pathway was developed. Five degenerate primers were used to specifically amplify fragments of soxB genes from different sulfur-oxidizing bacteria previously shown to oxidize thiosulfate. The PCR yielded a soxB fragment of approximately 1000 bp from most of the bacteria. Amino acid and nucleotide sequences of soxB from reference strains as well as from new isolates and environmental DNA from a hydrothermal vent habitat in the North Fiji Basin were compared and used to infer relationships of soxB between sulfur-oxidizing bacteria belonging to various 16S rDNA-based phylogenetic groups. Major phylogenetic lines derived from 16S rDNA were confirmed by soxB phylogeny. Thiosulfate-oxidizing green sulfur bacteria formed a coherent group by their soxB sequences. Likewise, clearly separated branches demonstrated the distant relationship of representatives of alpha-, beta-, and gamma-Proteobacteria including representative species of the former genus Thiobacillus (now Halothiobacillus - gamma-Proteobacteria, Thiobacillus - beta-Proteobacteria and Starkeya - alpha-Proteobacteria). This general picture emerged although apparent evidence for lateral transfer of the soxB gene is indicated and comparison of soxB phylogeny and 16S rDNA phylogeny points to the significance of this gene transfer in hydrothermal vent bacterial communities of the North Fiji Basin.

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: The food habits of the beaked skate were studied utilising 274 individuals obtained from the incidental catches of the Argentine hake (Merluccius hubbsi) fishery. The most important prey were the Argentine hake, the southern cod (Patagonotothen ramsayi), the Argentine shortfin squid (Illex argentinus), the isopod (Serolis schythei), the “raneya” (Raneya brasiliensis , Pisces: Ophidiidae), and the Argentine anchovy (Engraulis anchoita). A total of 45 prey species was identified. No differences in the diet between sexes, but significant differences among size classes and between immature and mature individuals were found. Two size-related dietary shifts previously reported in this species, at around 35 cm and 85 cm total length were confirmed and related to changes in habitat utilisation. The first shift entails a major change from benthic prey (mostly crustaceans) to demersal-benthic prey (mostly fishes) and the second change from demersal-benthic to demersal-pelagic prey (increased consumption of Argentine hake and decreased consumption of southern cod). The second shift coincides with sexual maturation and may reflect a behavioural response to maturation.

Description: Although morphology of firm-bodied shallow-water octopuses resists preservation-linked deformation, preservation and handling of deep-sea specimens of Graneledone are hypothesized to deform specimens by accelerating fluid loss from mantle and arm tissues. Principal components analysis finds that seven of 39 North Pacific specimens of the genus are exceptionally narrow; the remaining specimens show considerable morphological variation, independent of time in preservation. Five exceptionally narrow specimens, including some paratypes of G. pacifica, were collected and preserved by the same trawling study; a single unrecorded factor in their common preservation history may have caused their deformation. The high morphological variation among the remaining specimens, seemingly unique among octopodids, may reflect factors as subtle as how the specimen was stored in the jar. Two types of change with time in preservation are documented. The mantle wall of formalin-fixed specimens thins unpredictably after storage for 30 months in 70% ethanol, consistent with deformation in preservation. Skin tubercles on the dorsal mantle, important taxonomic characters, become more prominent during the first decade in preservation. To maximize the information specimens with fluid-rich tissues convey and to identify the sources of deformation, the full preservation history and measurements made prior to dissection should be permanently recorded.

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.

Description: Scaphitids are heteromorph ammonites exhibiting morphological trends counter to of those of the other main heteromorph ammonite groups. These trends include the shortening of the body chamber, lateral compression of the whorl, closure of the coil, and more regular, spiral coiling. Scaphitid-like morphologies may have appeared in other heteromorphs, but the Scaphitaceae are monophyletic. The most primitive scaphitids are known from the Albian, but an important radiation occurred in the Western Interior Seaway of North America from the Santonian to Maastrichtian, some of which spread to the Old World. The scaphitid morphology is consistent with improved swimming abilities, but scaphitids remained associated with the seafloor and are best considered to have been nektobenthos similar to modern nautiluses.

Description: Age and growth rates of the Mediterranean short-finned squid Illex coindetii (Ommastrephidae) were studied using statoliths from 704 specimens collected during trawl surveys within the Strait of Sicily in April and October–November 1995. In both samples, almost the whole ontogenetic spectrum was present, from juveniles to spent adults. Most of the squid captured in April had hatched between October and December 1994 (autumn–winter hatched group, AW), whereas most captured in October–November had hatched between May and July 1995 with a peak in June (spring–summer hatched group, SS). Age of the AW squid did not exceed 240 days (mainly 200–210 d), while that of the SS squid did not exceed 191 days (mainly 170–180 d). Growth in length and weight was best described by the logistic growth function. In both groups, daily growth rates (DGR) of males decreased at younger ages than in females, and sexual dimorphism in sizes (females larger than males) became evident in maturing and mature adults. The AW squids grew rather slowly during their juvenile and immature phases, which occurred in cool winter and spring seasons. They were characterized by a maximum DGR in mantle length (ML) and body weight (BW) at old ages, a prolonged period of maturation and old ages of mature specimens. AW squids attained large sizes and spawned at ages of 6–7 months in spring–summer. Their progeny (SS group) grew rapidly during the warm summer and autumn seasons and achieved their maximum DGR in ML and BW at younger ages than their AW predecessors. However, their younger age at maturation (5–6 months) reduced their somatic growth during the late ontogenetic stages, resulting in rather small sizes at maturity and early spawning. It is concluded that I. coindetii in the Strait of Sicily produce at least two alternating generations each year, which are adapted to live in different seasonal environmental conditions.

Description: Fishing can change the biological diversity of an ecosystem substantially, and determining the effects of fishing on marine biodiversity requires a variety of data, chief among them the proper identification of organisms. Because identification of all organisms in an ecosystem is not currently possible, target taxonomic groups (taxa) must be selected. The current status of taxonomic information varies greatly among taxa and among geographic areas within taxa. Problems include nomenclature, diagnoses, and determination of taxonomic relationships. We provide examples of a variety of these problems. We then propose a series of criteria for evaluating available taxonomic information in determining the potential reliability of species identification, including recency and comprehensiveness of revisionary studies, methods used for systematic and phylogenetic studies, adequacy of documentation, and evidence of peer review. When the goal is to explore biodiversity, these criteria must be used differently from when measuring and monitoring biodiversity.