Description and quantification of pteropod shell dissolution: a sensitive bioindicator of ocean acidification

Anthropogenic ocean acidification is likely to have negative effects on marine calcifying organisms, such as shelled pteropods, by promoting dissolution of aragonite shells. Study of shell dissolution requires an accurate and sensitive method for assessing shell damage. Shell dissolution was induced through incubations in CO₂‐enriched seawater for 4 and 14 days. We describe a procedure that allows the level of dissolution to be assessed and classified into three main types: Type I with partial dissolution of the prismatic layer; Type II with exposure of underlying crossed‐lamellar layer, and Type III, where crossed‐lamellar layer shows signs of dissolution. Levels of dissolution showed a good correspondence to the incubation conditions, with the most severe damage found in specimens held for 14 days in undersaturated condition (Ω ~ 0.8). This methodology enables the response of small pelagic calcifiers to acidified conditions to be detected at an early stage, thus making pteropods a valuable bioindicator of future ocean acidification.     

Magnitude of mesozooplankton variability: a case study from the Marginal Ice Zone of the Barents Sea in spring

Zooplankton was studied on eight stations in the marginal icezone (MIZ) of the Barents Sea, in May 1999, along two transectsacross the ice edge. On each station, physical background measurementsand zooplankton samples were taken every 6 h over a 24 h periodat five discrete depth intervals. Cluster analysis revealedseparation of open water stations from all ice stations as wellas high similarity level among replicates belonging to particularstation. Based on five replicates per station, analysis of variance(ANOVA) confirmed significant differences (P < 0.05) in abundancesof the main mesozooplankton taxa among stations. Relations betweenthe zooplankton community and environmental parameters wereestablished using redundancy analysis (CANOCO). In total, 55%of mesozooplankton variability within studied area was explainedby eight variables with significant conditional effects: depthstratum, fluorescence, temperature, salinity, bottom depth,latitude, bloom situation, and ice concentration. GLM modelssupported supposition about clear and negative relationshipbetween concentration of Oithona similis, and overall mesozooplanktondiversity. The analyses showed a dynamic relationship betweenmesozooplankton distribution and hydrological conditions onshort-term scale. Furthermore, our study demonstrated that variabilityin the physical environment of dynamic MIZ of the Barents Seahas measurable effect on the Arctic pelagic ecosystem.     

Flow cytometric analysis of the Vbeta repertoire in healthy controls

BACKGROUND: Analysis of the T-cell receptor (TCR)-Vbeta repertoire has been used for studying selective T-cell responses in autoimmune disease, alloreactivity in transplantation, and protective immunity against microbial and tumor antigens. For the interpretation of these studies, we need information about the Vbeta repertoire usage in healthy individuals. METHODS: We analyzed blood T-lymphocyte (sub)populations of 36 healthy controls (age range: from neonates to 86 years) with a carefully selected most complete panel of 22 Vbeta monoclonal antibodies, which together recognized 70-75% of all blood TCRalphabeta(+) T lymphocytes. Subsequently, we developed a six-tube test kit with selected Vbeta antibody combinations for easy and rapid detection of single ("clonal") Vbeta domain usage in large T-cell expansions. RESULTS: The mean values of the Vbeta repertoire usage were stable during aging in blood TCRalphabeta(+) T lymphocytes as well as in the CD4(+) and CD8(+) T-cell subsets, although the standard deviations increased in the elderly. The increased standard deviations were caused by the occurrence of oligoclonal T-cell expansions in the elderly, mainly consisting of CD8(+) T lymphocytes. The 15 detected T-cell expansions did not reach 40% of total TCRalphabeta(+) T lymphocytes and represented less than 0.4 x 10(9) cells per liter in our study. Vbeta usage of the CD4(+) and CD8(+) subsets was comparable for most tested Vbeta domains, but significant differences (P < 0.01) between the two subsets were found for Vbeta2, Vbeta5.1, Vbeta6.7, Vbeta9.1, and Vbeta22 (higher in CD4(+)), as well as for Vbeta1, Vbeta7.1, Vbeta14, and Vbeta23 (higher in CD8(+)). Finally, single Vbeta domain expression in large T-cell expansions can indeed be detected by the six-tube test kit. CONCLUSIONS: The results of our study can now be used as reference values in studies on distortions of the Vbeta repertoire in disease states. The six-tube test kit can be used for detection of single Vbeta domain expression in large T-cell expansions (>2.0 x 10(9)/l), which are clinically suspicious of T-cell leukemia.     

Arctic seabird food chains explored by fatty acid composition and stable isotopes in Kongsfjorden, Svalbard

Marine birds are important predators in the marine ecosystem, and dietary studies can give useful information about their feeding ecology, food webs and oceanographic variability. The aim of this study was to increase our understanding of the diet and trophic level of the seabirds breeding in Kongsfjorden, Svalbard. We have used fatty acids and stable isotopes, both of which integrate diet information over space and time, to determine trophic relationships in marine food webs. Fatty acid compositions of muscle from Little auk (Alle alle), Brünnich’s guillemot (Uria lomvia), Black-legged kittiwake (Rissa tridactyla), Northern fulmar (Fulmarus glacialis) and Glaucous gull (Larus hyperboreus) were determined and compared with their prey species. Canonical analysis (CA) showed that fatty acid composition differed among the five seabird species. Little auk, Black-legged kittiwake and Northern fulmar had high levels of the Calanus markers 20:1n9 and 22:1, indicating that these seabirds are a part of the Calanus food chain. Brünnich’s guillemot differed from the other species with much lower levels of 20:1n9 and 22:1. Brünnich’s guillemot is a pursuit diver feeding on fish and amphipods deeper in the water column, below 30 m. Glaucous gull also differed from the other seabird species, with a larger variation in the fatty acid composition indicating a more diverse diet. Trophic level analysis placed Little auk at the lowest trophic level, Brünnich’s guillemot and Black-legged kittiwake at intermediate levels and Glaucous gull and Northern fulmar at the highest trophic level.     

Ice algal assemblages and vertical export of organic matter from sea ice in the Barents Sea and Nansen Basin (Arctic Ocean)

Algal communities and export of organic matter from sea ice were studied in the offshore marginal ice zone (MIZ) of the northern Barents Sea and Nansen Basin of the Arctic Ocean north of Svalbard by means of ice cores and short-term deployed sediment traps. The observations cover a total of ten stations within the drifting pack ice, visited over a period of 3 years during the period of ice melt in May and July. Maximum flux of particulate organic carbon and chlorophyll a from the ice at 1 m depth (1,537 mg C m⁻² per day and 20 mg Chl a m⁻² per day) exceeded the flux at 30 m by a factor of 2 during spring, a pattern that was reversed later in the season. Although diatoms dominated the ice-associated algal biomass, flagellates at times revealed similarly high biomass and typically dominated the exported algal carbon. Importance of flagellates to the vertical flux increased as melting progressed, whereas diatoms made the highest contribution during the early melting stage. High export of ice-derived organic matter and phytoplankton took place simultaneously in the offshore MIZ, likely as a consequence of ice drift dynamics and the mosaic structure of ice-covered and open water characteristic of this region.     

A modular treatment of molecular traffic through the active site of cholinesterase

We present a model for the molecular traffic of ligands, substrates, and products through the active site of cholinesterases (ChEs). First, we describe a common treatment of the diffusion to a buried active site of cationic and neutral species. We then explain the specificity of ChEs for cationic ligands and substrates by introducing two additional components to this common treatment. The first module is a surface trap for cationic species at the entrance to the active-site gorge that operates through local, short-range electrostatic interactions and is independent of ionic strength. The second module is an ionic-strength-dependent steering mechanism generated by long-range electrostatic interactions arising from the overall distribution of charges in ChEs. Our calculations show that diffusion of charged ligands relative to neutral isosteric analogs is enhanced approximately 10-fold by the surface trap, while electrostatic steering contributes only a 1.5- to 2-fold rate enhancement at physiological salt concentration. We model clearance of cationic products from the active-site gorge as analogous to the escape of a particle from a one-dimensional well in the presence of a linear electrostatic potential. We evaluate the potential inside the gorge and provide evidence that while contributing to the steering of cationic species toward the active site, it does not appreciably retard their clearance. This optimal fine-tuning of global and local electrostatic interactions endows ChEs with maximum catalytic efficiency and specificity for a positively charged substrate, while at the same time not hindering clearance of the positively charged products.     

Metabolic activation of the nontricyclic antidepressant trazodone to electrophilic quinone-imine and epoxide intermediates in human liver microsomes and recombinant P4503A4

Therapy with the antidepressant trazodone has been associated with several cases of idiosyncratic hepatotoxicity. While the mechanism of hepatotoxicity remains unknown, it is possible that reactive metabolites of trazodone play a causative role. Studies were initiated to determine whether trazodone undergoes bioactivation in human liver microsomes to electrophilic intermediates. LC/MS/MS analysis of incubations containing trazodone and NADPH-supplemented microsomes or recombinant P4503A4 in the presence of glutathione revealed the formation of conjugates derived from the addition of the sulfydryl nucleophile to mono-hydroxylated- and hydrated-trazodone metabolites. Product ion spectra suggested that mono-hydroxylation and sulfydryl conjugation occurred on the 3-chlorophenyl-ring, whereas hydration and subsequent sulfydryl conjugation had occurred on the triazolopyridinone ring system. These findings are consistent with bioactivation sequences involving: (1) aromatic hydroxylation of the 3-chlorophenyl-ring in trazodone followed by the two-electron oxidation of this metabolite to a reactive quinone-imine intermediate, which reacts with glutathione in a 1,4-Michael fashion and (2) oxidation of the pyridinone ring to an electrophilic epoxide, ring opening of which, by glutathione or water generates the corresponding hydrated-trazodone-thiol conjugate or the stable diol metabolite, respectively. The pathway involving trazodone bioactivation to the quinone-imine has also been observed with many para-hydroxyanilines including the structurally related antidepressant nefazodone. It is proposed that the quinone-imine and/or the epoxide intermediate(s) may represent a rate-limiting step in the initiation of trazodone-mediated hepatotoxicity.     

Determination of GDC-0449, a small-molecule inhibitor of the Hedgehog signaling pathway,in human plasma by solid phase extraction-liquid chromatographic-tandem mass spectrometry

To support clinical development, a solid phase extraction (SPE) liquid chromatographic-tandem mass spectrometry (LC-MS/MS) method for the determination of GDC-0449 concentrations in human plasma has been developed and validated. Samples (200 μl) were extracted using an Oasis MCX 10 mg 96-well SPE plate and the resulting extracts were analyzed using reverse-phase chromatography coupled with a turbo-ionspray interface. The method was validated over calibration curve range 5–5000 ng/mL. Quadratic regression and 1/x² weighing were used. Within-run relative standard deviation (%RSD) was within 10.1% and accuracy ranged from 88.6% to 109.0% of nominal. Between-run %RSD was within 8.6% and accuracy ranged from 92.4% to 105.3% of nominal. Extraction recovery of GDC-0449 was between 88.3% and 91.2% as assessed using quality control sample concentrations. GDC-0449 was stable in plasma for 315 days when stored at ?70 °C and stable in reconstituted sample extracts for 117 h when stored at room temperature. Quantitative matrix effect/ion suppression experiment was performed and no significant matrix ion suppression was observed. This assay allows for the determination of GDC-0449 plasma concentrations over a sufficient time period to determine pharmacokinetic parameters at relevant clinical doses.     

A decoy set for the thermostable subdomain from chicken villin headpiece,comparison of different free energy estimators

Background  

Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently evaluated by discriminating native or native-like conformations from large ensembles of so-called decoy structures.     

Clinical evaluation of lentil lectin-reactive alpha-fetoprotein-L3 in histology-proven hepatocellular carcinoma

INTRODUCTION: Serum alpha-fetoprotein (AFP) is a useful marker of hepatocellular carcinoma (HCC), although the serum AFP concentration is also increased in patients with chronic liver diseases (CLD). The analysis of AFP glycoforms has been known to be of diagnostic value. We applied the lectin-affinity electrophoresis and antibody-affinity blotting techniques to HCC patients in Vietnam in order to better understand the role of lentil lectin-affinity AFP-L3 in the diagnosis and differential diagnosis of HCC, and its relationship with the biological characteristics of HCC. METHODS: Lens culinaris agglutinin-reactive AFP (AFP-L3) was measured in 65 patients with histologically proven HCC and 25 patients with CLD. All patients had serum AFP levels above 54 ng/mL. AFP-L3 levels were determined by lectin affinity electrophoresis coupled with antibody-affinity blotting. The diagnosis of HCC was confirmed histologically by ultrasound-guided biopsy. RESULTS: The mean value of AFP-L3 in the HCC patients was 49.6 +/- 21.6%, which was significantly higher (p<0.001) than that in the 25 CLD patients (10.7 +/- 4.3%). When the cutoff level for AFP-L3 was set at 15% (mean +/- SD), the sensitivity was 96.9%, the specificity 92.0% and the accuracy 95.5% in the 65 HCC patients. There was no clear correlation between serum AFP level and AFP-L3 percentage (r=0.16). There was no correlation between AFP-L3 and the maximum diameter of HCC nodules (r=0.05). However, the mean AFP-L3 value was higher in moderately or poorly differentiated HCC than in well differentiated tumors (p<0.001). CONCLUSIONS: AFP-L3 is potentially a clinically useful marker for the differentiation of increased AFP levels in hepatocellular carcinoma and chronic liver diseases. The AFP-L3 percentage is closely related to HCC differentiation. We consider the analysis of AFP-L3 a useful adjunct in the diagnosis of HCC.