Small conductance Ca2+-activated K+ channels and calmodulin: cell surface expression and gating

Small conductance Ca2+-activated K+ channels (SK channels) are heteromeric complexes of pore-forming alpha subunits and constitutively bound calmodulin (CaM). The binding of CaM is mediated in part by the electrostatic interaction between residues Arg-464 and Lys-467 of SK2 and Glu-84 and Glu-87 of CaM. Heterologous expression of the double charge reversal in SK2, SK2 R464E/K467E (SK2:64/67), did not yield detectable surface expression or channel activity in whole cell or inside-out patch recordings. Coexpression of SK2:64/67 with wild type CaM or CaM1,2,3,4, a mutant lacking the ability to bind Ca2+, rescued surface expression. In patches from cells coexpressing SK2:64/67 and wild type CaM, currents were recorded immediately following excision into Ca2+-containing solution but disappeared within minutes after excision or immediately upon exposure to Ca2+-free solution and were not reactivated upon reapplication of Ca2+-containing solution. Channel activity was restored by application of purified recombinant Ca2+-CaM or exposure to Ca2+-free CaM followed by application of Ca2+-containing solution. Coexpression of the double charge reversal E84R/E87K in CaM (CaM:84/87) with SK2:64/67 reconstituted stable Ca2+-dependent channel activity that was not lost with exposure to Ca2+-free solution. Therefore, Ca2+-independent interactions with CaM are required for surface expression of SK channels, whereas the constitutive association between the two channel subunits is not an essential requirement for gating.     

Growth response of komatsuna (Brassica rapa var. peruviridis) to root and foliar applications of phosphite

Soil and hydroponic culture experiments were conducted to investigate the effects of phosphite (Phi) as phosphorus (P) fertilizer via root and foliar applications on the growth and P supply of komatsuna. In both experiments, root P treatments were combinations of Phi and phosphate (Pi) at different Pi:Phi ratios, for a total of high P level (92 mg P pot^?1; the soil experiment) or low P level (0.05 mM P; the hydroponic experiment). Foliar P treatments were deionized water (control), a Pi solution and a Phi solution at low concentration of 0.05% P₂O₅. In both experiments, shoot dry weight of plants significantly decreased as Pi:Phi ratio decreased. In the soil experiment, plants grew abnormally at a Pi:Phi ratio of 25:75 and died when P was applied to soil entirely as Phi form (0:100 treatment). In the hydroponic experiment, no visible damage was found in shoot but root growth was strongly inhibited with severe damage symptoms at low Pi:Phi ratios. Total P concentration in plant decreased significantly with decreasing Pi:Phi ratio, especially in the hydroponic experiment. Foliar application of Phi although greatly increased total P of plants compared to that of Pi in both experiments, it did not improve but further decreased plant growth at low Pi:Phi ratios in the soil experiment and at all Pi:Phi ratios in the hydroponic experiment. The results of this study clearly indicated that Phi could not be used as P fertilizer by komatsuna plants via both application methods and could not substitute P at any rate at either low or high level. No beneficial effect of Phi was detected even when it was applied at low rate or applied in combination with Pi at different ratios. The effects of Phi were strongly dependent on the P nutrition status of plants; and plants that were not sufficiently fertilized with Pi may become vulnerable to Phi even at low levels.     

Enhanced biomethanation of kitchen waste by different pre-treatments

Five different pre-treatments were investigated to enhance the solubilisation and anaerobic biodegradability of kitchen waste (KW) in thermophilic batch and continuous tests. In the batch solubilisation tests, the highest and the lowest solubilisation efficiency were achieved with the thermo-acid and the pressure-depressure pre-treatments, respectively. However, in the batch biodegradability tests, the highest cumulative biogas production was obtained with the pressure-depressure method. In the continuous tests, the best performance in terms of an acceptable biogas production efficiency of 60% and stable in-reactor COD_s and VFA concentrations corresponded to the pressure-depressure reactor, followed by freeze-thaw, acid, thermo-acid, thermo and control. The maximum OLR (5 g COD L⁻¹ d⁻¹) applied in the pressure-depressure and freeze-thaw reactors almost doubled the control reactor. From the overall analysis, the freeze-thaw pre-treatment was the most profitable process with a net potential profit of around 11.5 € ton⁻¹ KW.     

Adaptive phenotypic plasticity contributes to divergence between lake and river populations of an East African cichlid fish

Adaptive phenotypic plasticity and fixed genotypic differences have long been considered opposing strategies in adaptation. More recently, these mechanisms have been proposed to act complementarily and under certain conditions jointly facilitate evolution, speciation, and even adaptive radiations. Here, we investigate the relative contributions of adaptive phenotypic plasticity vs. local adaptation to fitness, using an emerging model system to study early phases of adaptive divergence, the generalist cichlid fish species Astatotilapia burtoni. We tested direct fitness consequences of morphological divergence between lake and river populations in nature by performing two transplant experiments in Lake Tanganyika. In the first experiment, we used wild‐caught juvenile lake and river individuals, while in the second experiment, we used F1 crosses between lake and river fish bred in a common garden setup. By tracking the survival and growth of translocated individuals in enclosures in the lake over several weeks, we revealed local adaptation evidenced by faster growth of the wild‐caught resident population in the first experiment. On the other hand, we did not find difference in growth between different types of F1 crosses in the second experiment, suggesting a substantial contribution of adaptive phenotypic plasticity to increased immigrant fitness. Our findings highlight the value of formally comparing fitness of wild‐caught and common garden‐reared individuals and emphasize the necessity of considering adaptive phenotypic plasticity in the study of adaptive divergence.     

Screening and preliminary characterization of hemagglutinins in Vietnamese marine algae

Extracts from 44 species of Vietnamese marine algae, including 15 Chlorophyta, 18 Rhodophyta and 11 Phaeophyta species, were examined for hemagglutination activity with a variety of different animal and human erythrocytes that were untreated or treated with enzymes. Almost all extracts showed activity toward at least one type of erythrocytes, although those from three Chlorophyta and two Rhodophyta species showed no hemagglutination with any type of erythrocytes examined. Strong activity was detected in extracts from two Chlorophyta (Anadyomene plicata and Avrainvillea erecta) and four Rhodophyta species (Gracilaria eucheumatoides, Gracilaria salicornia, Kappaphycus alvarezii, and Kappaphycus striatum) with enzyme-treated rabbit and sheep erythrocytes. The hemagglutinins of seven Chlorophyta and eight Rhodophyta species were examined for sugar-binding specificity, pH- and temperature-stability, and divalent cation-independency of hemagglutination using ammonium sulfate-precipitates prepared from their extracts. In a hemagglutination-inhibition test with various monosaccharides and glycoproteins, none of the hemagglutinins had affinity for monosaccharides, except the Codium arabicum and Gracilaria euchematoides hemagglutinins, whose activities were inhibited by both N-acetyl-d-galactosamine and N-acetyl-d-glucosamine. On the other hand, all of the hemagglutinins activities were inhibited by some glycoproteins. The inhibition profiles with glycoproteins were different depending on hemagglutinin species, and suggest the presence of lectins specific for high mannose N-glycans, complex N-glycans, or O-glycans. The activities of these algal hemagglutinins were stable over a wide range of pH and temperature, and independent of the presence of divalent cations. These results indicate that Vietnamese marine algae are a good source of novel and useful lectins.     

MASTR-MS: a web-based collaborative laboratory information management system (LIMS) for metabolomics

Background

An increasing number of research laboratories and core analytical facilities around the world are developing high throughput metabolomic analytical and data processing pipelines that are capable of handling hundreds to thousands of individual samples per year, often over multiple projects, collaborations and sample types. At present, there are no Laboratory Information Management Systems (LIMS) that are specifically tailored for metabolomics laboratories that are capable of tracking samples and associated metadata from the beginning to the end of an experiment, including data processing and archiving, and which are also suitable for use in large institutional core facilities or multi-laboratory consortia as well as single laboratory environments.

Results

Here we present MASTR-MS, a downloadable and installable LIMS solution that can be deployed either within a single laboratory or used to link workflows across a multisite network. It comprises a Node Management System that can be used to link and manage projects across one or multiple collaborating laboratories; a User Management System which defines different user groups and privileges of users; a Quote Management System where client quotes are managed; a Project Management System in which metadata is stored and all aspects of project management, including experimental setup, sample tracking and instrument analysis, are defined, and a Data Management System that allows the automatic capture and storage of raw and processed data from the analytical instruments to the LIMS.

Conclusion

MASTR-MS is a comprehensive LIMS solution specifically designed for metabolomics. It captures the entire lifecycle of a sample starting from project and experiment design to sample analysis, data capture and storage. It acts as an electronic notebook, facilitating project management within a single laboratory or a multi-node collaborative environment. This software is being developed in close consultation with members of the metabolomics research community. It is freely available under the GNU GPL v3 licence and can be accessed from, https://muccg.github.io/mastr-ms/.

     

Material Flows in a Social Context: A Vietnamese Case Study Combining the Materials Flow Analysis and Action‐in‐Context Frameworks

Materials flow analysis (MFA) is one of the central achievements of industrial ecology. One direction in which one can move MFA beyond mere accounting is by putting the material flows in their social context. This “socially extended MFA” may be carried out at various levels of aggregation. In this article, specific material flows will be linked to concrete actors and mechanisms that cause these flows—using the action‐in‐context (AiC) framework, which contains, inter alia, both proximate and indirect actors and factors. The case study site is of Tat hamlet in Vietnam, set in a landscape of paddy fields on valley floors surrounded by steep, previously forested slopes. Out of the aggregate MFA of Tat, the study focuses on material flows associated with basic needs and sustainability. The most important actors causing these material flows are farming households, politicians, traders, and agribusiness firms—of which local politicians turned out to be pivotal. The study shows the value of combining MFA with actor‐based social analysis. MFA achieves the balanced quantification of the physical system, thus helping to pinpoint key processes. Actor‐based analysis adds the causal understanding of what drives these key processes, leading to improved scenarios of the future and the effective identification of target groups and instruments for policy making.