Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef

To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.     

Crystal structure of the human supernatant protein factor

Supernatant protein factor (SPF) promotes the epoxidation of squalene catalyzed by microsomes. Several studies suggest its in vivo role in the cholesterol biosynthetic pathway by a yet unknown mechanism. SPF belongs to a family of lipid binding proteins called CRAL_TRIO, which include yeast phosphatidylinositol transfer protein Sec14 and tocopherol transfer protein TTP. The crystal structure of human SPF at a resolution of 1.9 A reveals a two domain topology. The N-terminal 275 residues form a Sec14-like domain, while the C-terminal 115 residues consist of an eight-stranded jelly-roll barrel similar to that found in many viral protein structures. The ligand binding cavity has a peculiar horseshoe-like shape. Contrary to the Sec14 crystal structure, the lipid-exchange loop is in a closed conformation, suggesting a mechanism for lipid exchange.     

Domain analysis of the calcium-activated potassium channel SK1 from rat brain. Functional expression and toxin sensitivity

Two small conductance, calcium-activated potassium channels (SK channels), SK2 and SK3, have been shown to contribute to the afterhyperpolarization (AHP) and to shape the firing behavior in neurons for example in the hippocampal formation, the dorsal vagal nucleus, the subthalamic nucleus, and the cerebellum. In heterologous expression systems, SK2 and SK3 currents are blocked by the bee venom toxin apamin, just as well as the corresponding neuronal AHP currents. However, the functional role and pharmacological profile of SK1 channels from rat brain (rSK1) is still largely unknown, as so far rSK1 homomeric channels could not be functionally expressed. We have performed a domain analysis to elucidate the pharmacological profile and the molecular determinants of rSK1 channel expression by using channel chimeras in combination with immunocytochemistry, immunoblot analysis, and electrophysiology. Our results reveal that the rSK1 subunit is synthesized in cells but does not form functional homomeric channels. Exchanging the carboxyl terminus of rSK1 for that of hSK1 or rSK2 is sufficient to rescue the functional expression of rSK1 channels. Additionally, transplantation of both amino and carboxyl termini of rSK1 onto hSK1 subunits, normally forming functional homomeric channel, hinders their functional expression, while hSK1 channels containing only the rSK1 carboxyl terminus are functional. These results suggest that the lack of functional expression of rSK1 channels is probably due to problems in their assembly and tetramerization but not in their calmodulin-dependent gating. Finally, we show that chimeric channels containing the core domain (S1-S6) of rSK1, unlike hSK1, are apamin-insensitive.     

Experimental verification of the behavioral foundation of bacterial transport parameters using microfluidics

We present novel microfluidic experiments to quantify population-scale transport parameters (chemotactic sensitivity χ₀ and random motility μ) of a population of bacteria. Previously, transport parameters have been derived theoretically from single-cell swimming behavior using probabilistic models, yet the mechanistic foundations of this upscaling process have not been verified experimentally. We designed a microfluidic capillary assay to generate and accurately measure gradients of chemoattractant (α-methylaspartate) while simultaneously capturing the swimming trajectories of individual Escherichia coli bacteria using videomicroscopy and cell tracking. By measuring swimming speed and bias in the swimming direction of single cells for a range of chemoattractant concentrations and concentration gradients, we directly computed the chemotactic velocity V_C and the associated chemotactic sensitivity χ₀. We then show how μ can also be readily determined using microfluidics but that a population-scale microfluidic approach is experimentally more convenient than a single-cell analysis in this case. Measured values of both χ₀ [(12.4 ± 2.0) × 10⁻⁴ cm² s⁻¹] and μ [(3.3 ± 0.8) × 10⁻⁶ cm² s⁻¹] are comparable to literature results. This microscale approach to bacterial chemotaxis lends experimental support to theoretical derivations of population-scale transport parameters from single-cell behavior. Furthermore, this study shows that microfluidic platforms can go beyond traditional chemotaxis assays and enable the quantification of bacterial transport parameters.     

Monitoring of a Hot Melt Coating Process via a Novel Multipoint Near-Infrared Spectrometer

The aim of the present work was to develop a PAT strategy for the supervision of hot melt coating processes. Optical fibers were placed at various positions in the process chamber of a fluid bed device. Experiments were performed to determine the most suitable position for in-line process monitoring, taking into account such requirements as a good signal to noise ratio, the mitigation of dead zones, the ability to monitor the product over the entire process, and reproducibility. The experimental evidence suggested that the position at medium fluid bed height, looking towards the center, i.e., normal to particle movement, proved to be the most reliable position. In this study, the advantages of multipoint monitoring are shown, and an in-line-implementation was created. This enabled the real-time supervision of the process, including the fast detection of inhomogeneities and disturbances in the process chamber, and the compensation of sensor malfunction. In addition, a model for estimating the particle size distribution via NIR was successfully created. This ensures that the quality of the product and the endpoint of the coating process can be determined correctly.     

A novel human tocopherol-associated protein: cloning, in vitro expression, and characterization

Vitamin E (alpha-tocopherol) is an essential dietary nutrient for humans and animals. The mechanisms involved in cellular regulation as well as in the preferential cellular and tissue accumulation of alpha-tocopherol are not yet well established. We previously reported (Stocker, A., Zimmer, S., Spycher, S. E., and Azzi, A. (1999) IUBMB Life 48, 49-55) the identification of a novel 46-kDa tocopherol-associated protein (TAP) in the cytosol of bovine liver. Here, we describe the identification, the molecular cloning into Escherichia coli, and the in vitro expression of the human homologue of bovine TAP, hTAP. This protein appears to belong to a family of hydrophobic ligand binding proteins, which have the CRAL (cis-retinal binding motif) sequence in common. By using a biotinylated alpha-tocopherol derivative and the IASys resonant mirror biosensor, the purified recombinant protein was shown to bind tocopherol at a specific binding site with K(d) 4.6 x 10(-7) m. Northern analyses showed that hTAP mRNA has a size of approximately 2800 base pairs and is ubiquitously expressed. The highest amounts of hTAP message are found in liver, brain, and prostate. In conclusion, hTAP has sequence homology to proteins containing the CRAL_TRIO structural motif. TAP binds to alpha-tocopherol and biotinylated tocopherol, suggesting the existence of a hydrophobic pocket, possibly analogous to that of SEC14.     

Apparent antimutagenic effect of ultraviolet irradiation

Strain SL3367 is a S. typhimurium LT2 hisG46 stock which spontaneously reverts to His⁺ at a high frequency. Plates of defined medium with 1% (v/v) nutrient broth inoculated with ca. 10⁸ washed SL3367 cells were incubated, untreated or after UV irradiation. After 2 days at 37°C, an average of 165 His⁺ colonies were obtained per control plate but significantly fewer, 105 His⁺ colonies, on plates irradiated at a fluence of 7 J/m². The dry weight of bacteria in washings from plates incubated 14 h (by which time growth of His^? cells had ceased) was the same for irradiated and non-irradiated plates but the yield of colony-forming units from irradiated plates was less than from control plates, by about the same factor as the reduction in yield of His⁺ colonies caused by the same fluence. Washings from incubated irradiated plates, but not those from control plates, contained long filaments as well as bacteria of normal size; on transfer to nutrient-agar slide cultures cells normal size grew into microcolonies but filaments did not grow. The reduced plateau yield of viable His^? cells caused by consumption of much of the growth-limiting supply of histidine by irradiated cells growing into non-viable filaments reduces the number of auxotrophic bacteria at risk for spontaneous reversion and so accounts for the apparent antimutagenic effect of UV irradiation. This effect was partly reversed by the presence of d,l-pantoyl lactone in the selection medium, and was also observed for yield of Trp⁺ colonies from trpE8 cultures with a high spontaneous reversion rate. Treatments not inducing cell filamentation did not result in the depression of spontaneous revertants and were detected as being mutagenic. The apparent antimutagenic effect may be expected for reversion of any auxotroph, unless masked by induced revertants and is particularly apparent in an auxotroph which reverts spontaneously at high frequency.     

Coenzyme Q improves LDL resistance to ex vivo oxidation but does not enhance endothelial function in hypercholesterolemic young adults

Oxidative modification of low-density lipoprotein (LDL) may cause arterial endothelial dysfunction in hyperlipidemic subjects. Antioxidants can protect LDL from oxidation and therefore improve endothelial function. Dietary supplementation with coenzyme Q (CoQ(10)) raises its level within LDL, which may subsequently become more resistant to oxidation. Therefore, the aim of this study was to assess whether oral supplementation of CoQ(10) (50 mg three times daily) is effective in reducing ex vivo LDL oxidizability and in improving vascular endothelial function. Twelve nonsmoking healthy adults with hypercholesterolemia (age 34+/-10 years, nine women and three men, total cholesterol 7.4+/-1.1 mmol/l) and endothelial dysfunction (below population mean) at baseline were randomized to receive CoQ(10) or matching placebo in a double-blind crossover study (active/placebo phase 4 weeks, washout 4 weeks). Flow-mediated (FMD, endothelium-dependent) and nitrate-mediated (NMD, smooth muscle-dependent) arterial dilatation were measured by high-resolution ultrasound. CoQ(10) treatment increased plasma CoQ(10) levels from 1.1 +/-0.5 to 5.0+/-2.8 micromol/l (p =.009) but had no significant effect on FMD (4.3+/-2.4 to 5.1+/-3.6 %, p =.99), NMD (21.6+/-6.1 to 20.7+/-7.8 %, p = .38) or serum LDL-cholesterol levels (p = .51). Four subjects were selected randomly for detailed analysis of LDL oxidizability using aqueous peroxyl radicals as the oxidant. In this subgroup, CoQ(10) supplementation significantly increased the time for CoQ(10)H(2) depletion upon oxidant exposure of LDL by 41+/-19 min (p = .04) and decreased the extent of lipid hydroperoxide accumulation after 2 hours by 50+/-37 micromol/l (p =.04). We conclude that dietary supplementation with CoQ(10) decreases ex-vivo LDL oxidizability but has no significant effect on arterial endothelial function in patients with moderate hypercholesterolemia.