Genome streamlining in a cosmopolitan oceanic bacterium

The SAR11 clade consists of very small, heterotrophic marine alpha-proteobacteria that are found throughout the oceans, where they account for about 25% of all microbial cells. Pelagibacter ubique, the first cultured member of this clade, has the smallest genome and encodes the smallest number of predicted open reading frames known for a free-living microorganism. In contrast to parasitic bacteria and archaea with small genomes, P. ubique has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors. P. ubique has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins; few paralogs; and the shortest intergenic spacers yet observed for any cell.     

Nod2 mutation in Crohn's disease potentiates NF-kappaB activity and IL-1beta processing

Variants of NOD2, an intracellular sensor of bacteria-derived muramyl dipeptide (MDP), increase susceptibility to Crohn's disease (CD). These variants are thought to be defective in activation of nuclear factor kappaB (NF-kappaB) and antibacterial defenses, but CD clinical specimens display elevated NF-kappaB activity. To illuminate the pathophysiological function of NOD2, we introduced such a variant to the mouse Nod2 locus. Mutant mice exhibited elevated NF-kappaB activation in response to MDP and more efficient processing and secretion of the cytokine interleukin-1beta (IL-1beta). These effects are linked to increased susceptibility to bacterial-induced intestinal inflammation and identify NOD2 as a positive regulator of NF-kappaB activation and IL-1beta secretion.     

Dynamic complex formation during the yeast cell cycle

To analyze the dynamics of protein complexes during the yeast cell cycle, we integrated data on protein interactions and gene expression. The resulting time-dependent interaction network places both periodically and constitutively expressed proteins in a temporal cell cycle context, thereby revealing previously unknown components and modules. We discovered that most complexes consist of both periodically and constitutively expressed subunits, which suggests that the former control complex activity by a mechanism of just-in-time assembly. Consistent with this, we show that additional regulation through targeted degradation and phosphorylation by Cdc28p (Cdk1) specifically affects the periodically expressed proteins.     

The structure of ferrihydrite, a nanocrystalline material

Despite the ubiquity of ferrihydrite in natural sediments and its importance as an industrial sorbent, the nanocrystallinity of this iron oxyhydroxide has hampered accurate structure determination by traditional methods that rely on long-range order. We uncovered the atomic arrangement by real-space modeling of the pair distribution function (PDF) derived from direct Fourier transformation of the total x-ray scattering. The PDF for ferrihydrite synthesized with the use of different routes is consistent with a single phase (hexagonal space group P6(3)mc; a = approximately 5.95 angstroms, c = approximately 9.06 angstroms). In its ideal form, this structure contains 20% tetrahedrally and 80% octahedrally coordinated iron and has a basic structural motif closely related to the Baker-Figgis delta-Keggin cluster. Real-space fitting indicates structural relaxation with decreasing particle size and also suggests that second-order effects such as internal strain, stacking faults, and particle shape contribute to the PDFs.     

Structure of the polycrystalline zeolite catalyst IM-5 solved by enhanced charge flipping

Despite substantial advances in crystal structure determination methodology for polycrystalline materials, some problems have remained intractable. A case in point is the zeolite catalyst IM-5, whose structure has eluded determination for almost 10 years. Here we present a charge-flipping structure-solution algorithm, extended to facilitate the combined use of powder diffraction and electron microscopy data. With this algorithm, we have elucidated the complex structure of IM-5, with 24 topologically distinct silicon atoms and an unusual two-dimensional medium-pore channel system. This powerful approach to structure solution can be applied without modification to any type of polycrystalline material (e.g., catalysts, ceramics, pharmaceuticals, complex metal alloys) and is therefore pertinent to a diverse range of scientific disciplines.     

Automated image analysis as a tool to quantify the colour and composition of rainbow trout (Oncorhynchus mykiss W.) cutlets

The goal of this paper is to propose and evaluate automated image analysis methods for describing muscle cutlets in rainbow trout. The proposed automated image analysis methods were tested on a total of 983 scanned images of trout cutlets, and included quality traits such as fat percentage, flesh colour and the size of morphologically distinguishable subparts of the cutlet. A sub-sample of 50 images was randomly selected for manual segmentation of the cutlet, the dorsal fat depot and the red muscle and regions. The identification of these regions by manual and automatic image analysis correlated strongly (r = 0.97, r = 0.95 and r = 0.91, respectively). The estimated fat percentage obtained from image analysis, based on the area of visible fat and the colour of the cutlet flesh, correlated well with chemical fat percentage measured by mid-infrared transmission spectroscopy (MIT) (r = 0.78). The automated image analysis methods are therefore a reliable means of predicting the fat percentage of trout cutlets. Principal component analysis (PCA) loading plots were used to identify subsets of variables from the image analysis of special significance for further studies; cutlet area, dorsal fat depot area, red muscle area, back height, cutlet width, and width of left and right abdomen wall were among the variables selected. PCA loading plots of different colour variables indicated that simple statistical coefficients such as percentiles and mean values can be used to quantify different aspects of flesh colour. In conclusion, the methods presented here provide a powerful toolbox for describing important morphological structures and quality traits of trout cutlets.     

Reconstructing historical trends of small pelagic fish in the Java Sea using standardized commercial trip based catch per unit of effort

Pelagic fish stocks in the Java Sea have been exploited intensively since the beginning of the 1970s. However, due to the effect of increased fishing power of the fleets and the changing nature of spatial and temporal distribution of the fishing effort, assessment of stock trends based on commercial data of catch and effort requires the standardization of both effort and catch data. Here we present the first attempt to reconstruct a standardized time series of commercial catch per unit of effort (CPUE) for the main pelagic species exploited by the purse seine fleet in the Java Sea. The results showed that all the stocks analysed have largely declined since the beginning of the 1990s. For bigeye scad, Indian mackerel and sardine, current estimates are only between 3 and 19% of the maximum observed value while round scads and spotted sardine biomass estimates lie between 18 and 34%. However, our assumptions about the effect of lamp power and level of creeping and the fact that the influence of fish density on catchability and the effect of targeting were not taken into account thus observed decline is a rather conservative estimate of the real decline of the stocks. If effective management actions are not put in place as a matter of urgency in the Java Sea for small pelagic fisheries, one runs the risk of adding those species to the long list of overexploited stocks of the world oceans.     

Lower prevalence of fin erosion in mature than in immature Atlantic salmon (Salmo salar) parr

Samples of hatchery-reared Atlantic salmon parr (age 0+ and 1+) from two different Norwegian river strains were investigated for connections between sexual maturity and prevalence of dorsal fin ray erosion. Mature males showed consistently lower prevalence as well as better recovery than immature males. Among the immature fish, no differences were detected between males and females. The results are discussed relative to morphological and physiological changes in maturing salmon parr.     

Nonlocal wind-driven fjord–coast advection and its potential effect on plankton and fish recruitment

The Bergen Ocean Model (BOM), a three-dimensional physical coastal ocean model, was used for a numerical simulation experiment to investigate short-term effects of wind-generated coastal upwelling and downwelling on the dynamics of adjacent large outer and smaller inner fjords. The effect of the real alongshore wind regime on advection for an idealized fjord topography, resembling Masfjorden, western Norway, is used as an example. This modelling exercise is a supplement to, and its predictions support, the various hypotheses investigated in ecosystem simulation studies of the Masfjorden. The model predicts that coastal winds from the north cause upwelling and transport the upper water layer out from the fjords. Winds from the south cause downwelling and transport the upper water layer into the fjords. The transport is rapid and ≈50% of the upper water layer may be replaced within 1–2 days. Implications of these physical processes for the dispersal and retention of planktonic organisms and the early life stages of fish are discussed. If strong southerly winds occur frequently, this will transport planktonic organisms into the fjord and may increase the carrying capacity for planktivorous fish. In contrast, frequent strong northerly winds may reduce the abundance of planktonic organisms, including the early life stages of marine fish, and thus possibly reduce recruitment to fjord fish populations. Frequent shifts between southerly and northerly winds would cause an exchange of early life stages between neighbouring fjords and thus enhance genetic exchange.     

The effect of cell density on biomass and fatty acid productivity during cultivation of Rhodomonas salina in a tubular photobioreactor

The microalga Rhodomonas salina is widely used in aquaculture. There is a need for optimization of the growth of the microalgae and its content of essential fatty acids. Here, the fatty acid profile of Rhodomonas in relation to cell density during cultivation in a tubular PBR is investigated. It is expected that cell density is an important factor in controlling productivity and fatty acid content of the microalgae because cell density is important in determining light availability due to the self‐shading of the algae. The carbon productivity as a function of cell density is described by a saturation curve. The carbon productivity and the productivity of total fatty acids are lowest at the lowest cell density, and independent of cell density at higher cell densities. The relative contribution of the two poly‐unsaturated fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) increases with increasing cell density and saturates at 1 × 10⁶ cells/ml. We conclude that large‐scale production of Rhodomonas in this tubular PBR should take place at cell densities of 1 × 10⁶ cells/ml, while there are indications for increasing difficulties in maintaining steady‐state production in this PBR at higher cell densities.