SALARECON connects the Atlantic salmon genome to growth and feed efficiency.

Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species such as salmon.

The role of the cadmium-binding protein response of the digestive gland of the Yesso scallop Mizuhopecten yessoensis (Jay, 1857) for marine environmental assessments.

The ability of Pectinidae to accumulate heavy metals and store them in their tissues allows the use of scallops for biomonitoring marine pollution. High molecular weight metallothionein (MT)-like proteins (MTlps) play a central role in this process. Two major MTlps (72 and 43 kDa) have been identified in the digestive glands of Mizuhopecten yessoensis (Yesso scallop).

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Sensitivity analysis of a pathway with respect to fast and small temperature change.

Temperature affects all enzymes simultaneously in a metabolic system. The enzyme concentration in a biochemical system can be considered as invariant under fast and small temperature change. Therefore, the total sensitivity of a steady state flux through a pathway with respect to the temperature can be expressed as: the apparent activation energy of a steady state pathway flux equals the sum of weighted activation energies of the individual reactions contributing to the flux, where the weighting factors are the flux control coefficients of these reactions in the context of the network.

Using a Multi-compartmental Metabolic Model to Predict Carbon Allocation in Arabidopsis thaliana.

The molecular mechanism of loading/unloading of sucrose into/from the phloem plays an important role in sucrose translocation among plant tissues. Perturbation of this mechanism results in growth phenotypes of a plant. In order to better understand the coupling of sucrose translocation with metabolic processes a multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized with respect to biomass growth, both in light and in dark conditions.

Cell size and morphological properties of yeast Saccharomyces cerevisiae in relation to growth temperature.

Cell volume is an important parameter for modelling cellular processes. Temperature-induced variability of cellular size, volume, intracellular granularity, a fraction of budding cells of yeast Saccharomyces cerevisiae CEN.PK 113-7D (in anaerobic glucose unlimited batch cultures) were measured by flow cytometry and matched with the performance of the biomass growth (maximal specific growth rate (μmax), specific rate of glucose consumption, the rate of maintenance, biomass yield on glucose).

Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation.

Background: Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of these metabolic and underlying regulatory processes allow a detailed understanding of carbon distribution within the plant and the formation of associated phenotypic traits. Sucrose translocation from 'source' tissues (e.

From Phosphoproteome to Modeling of Plant Signaling Pathways.

Quantitative proteomic experiments in recent years became almost routine in many aspects of biology. Particularly the quantification of peptides and corresponding phosphorylated counterparts from a single experiment is highly important for understanding of dynamics of signaling pathways. We developed an analytical method to quantify phosphopeptides (pP) in relation to the quantity of the corresponding non-phosphorylated parent peptides (P).

The new facile and straightforward method for the synthesis of 4H-1,2,3-thiadiazolo[5,4-b]indoles and determination of their antiproliferative activity.

A series of 4H-1,2,3-thiadiazolo[5,4-b]indoles were synthesized by novel tandem of oxidative cyclization of 3-alkoxycarbonylhydrazonoindoline-2-thiones, 1,5-H-shift and elimination of tert-butoxy(ethoxy)carbonyl group. The simple method for their modifications by the reactions with electrophilic agents were elaborated and as a result of the synthetic investigation a number of N-alkyl-, N-acyl- and N-sulfonyl-4H-1,2,3-thiadiazolo[5,4-b]indoles were prepared in good yields. Preliminary biological tests for the three examples of synthesized compounds with different substituents at the nitrogen atom indole ring have shown that the biological behavior of the investigated 1,2,3-thiadiazolo[5,4-b]indoles is substantially directed by this structural fragment.

Metabolic efficiency in yeast Saccharomyces cerevisiae in relation to temperature dependent growth and biomass yield.

Canonized view on temperature effects on growth rate of microorganisms is based on assumption of protein denaturation, which is not confirmed experimentally so far. We develop an alternative concept, which is based on view that limits of thermal tolerance are based on imbalance of cellular energy allocation. Therefore, we investigated growth suppression of yeast Saccharomyces cerevisiae in the supraoptimal temperature range (30-40°C), i.

'Domino' systems biology and the 'A' of ATP.

We develop a strategic 'domino' approach that starts with one key feature of cell function and the main process providing for it, and then adds additional processes and components only as necessary to explain provoked experimental observations. The approach is here applied to the energy metabolism of yeast in a glucose limited chemostat, subjected to a sudden increase in glucose. The puzzles addressed include (i) the lack of increase in adenosine triphosphate (ATP) upon glucose addition, (ii) the lack of increase in adenosine diphosphate (ADP) when ATP is hydrolyzed, and (iii) the rapid disappearance of the 'A' (adenine) moiety of ATP.

Simplified absolute metabolite quantification by gas chromatography-isotope dilution mass spectrometry on the basis of commercially available source material.

In the field of metabolomics, GC-MS has rather established itself as a tool for semi-quantitative strategies like metabolic fingerprinting or metabolic profiling. Absolute quantification of intra- or extracellular metabolites is nowadays mostly accomplished by application of diverse LC-MS techniques. Only few groups have so far adopted GC-MS technology for this exceptionally challenging task.

Miniaturized device for agitating a high-density yeast suspension that is suitable for in vivo nuclear magnetic resonance applications.

In vivo nuclear magnetic resonance (NMR) monitoring requires a high-density cell suspension, where cell precipitation should be avoided. We have designed a miniaturized cell agitator that fits entirely into an 8-mm NMR probe but that, being mounted into the instrument, is situated outside of the sensitive area. The device consists of two glass tubes connected in a way that, when gas flow is blown through them, creates influx of cell suspension into the device that returns through apertures.