Assessing the impact of interfering organic matter on soil metaproteomic workflow

Soil organic matter (SOM) is biologically, chemically, and physically complex. As a major store of nutrients within the soil, it plays an important role in nutrient provision to plants. An enhanced understanding of SOM utilisation processes could underpin better fertiliser management for plant growth, with reduced environmental losses. Metaproteomics can allow the characterisation of protein profiles and could help gain insights into SOM microbial decomposition mechanisms. Here, we applied three different extraction methods to two soil types to recover SOM with different characteristics. Specifically, water-extractable organic matter, mineral-associated organic matter and protein-bound organic matter were targeted with the aim to investigate the metaproteome enriched in those extractions. As a proof-of-concept, replicated extracts from one soil were further analysed for peptide identification using liquid chromatography followed by tandem mass spectrometry. We employed a framework for mining mass spectra for both peptide assignment and fragmentation pattern characterisation. Different extracts were found to exhibit contrasting total protein and humic substance content for the two soils investigated. Overall, water extracts displayed the lowest humic substance content (in both soils) and the highest number of peptide identifications (in the soil investigated) with the most frequent peptide hits associated with diverse substrate/ligand binding proteins of Proteobacteria and derived taxa. Our framework also highlighted a strong peptidic signal in unassigned and unmatched spectra, information that is currently not captured by the pipelines employed in this study. Taken together, this work points to specific areas for optimisation in chromatography and mass spectrometry to adequately characterise SOM-associated metaproteomes.     

Assessment of shoreline vegetation in relation to use by molting black brant Branta bernicla nigricans on the Alaska coastal plain

To evaluate the importance of large thaw lakes on the Alaska Coastal Plain for molting Pacific black brant Branta bernicla nigricans, distribution and life form of shoreline vegetation were assessed using several scales: satellite imagery, point-intercept transects, cover quadrats, and a parameter for water regime. Brant population and distribution estimates from aerial surveys were used to classify large lakes into high, moderate, and low use. Correlations between brant and abundance of their preferred feeding site — moss flats — were best demostrated by satellite imagery. Intercepts and cover ratings were not correlated, presumably because these techniques were less efficient at assessing area. General observations suggested that the presence of islands, large ice floes, and possibly other physical attributes of the habitat, influenced brant distribution. This area is unique because of low-lying, drained-lake basins that have ideal combinations of moss flats and large water areas where brant seek protection disturbance is vital to the success of this declining species because alternate habitats may not be available elsewhere on the Coastal Plain. in water or on ice floes. Protection of the area from     

Ability of lipid hydroperoxides to partition into surfactant micelles and alter lipid oxidation rates in emulsions

Lipid hydroperoxides are important factors in lipid oxidation due to their ability to decompose into free radicals. In oil-in-water emulsions, the physical location of lipid hydroperoxides could impact their ability to interact with prooxidants such as iron. Interfacial tension measurements show that linoleic acid, methyl linoleate, and trilinolein hydroperoxides are more surface-active than their non-peroxidized counterparts. In oil-in-water emulsion containing surfactant (Brij 76) micelles in the continuous phase, linoleic acid, methyl linoleate, and trilinolein hydroperoxides were solubilized out of the lipid droplets into the aqueous phase. Brij 76 solubilization of the different hydroperoxides was in the order of linoleic acid > trilinolein > or = methyl linoleate. Brij 76 micelles inhibited lipid oxidation of corn oil-in-water emulsions with greater inhibition of oxidation occurring in emulsions containing linoleic acid hydroperoxides. Surfactant solubilization of lipid hydroperoxides could be responsible for the ability of surfactant micelles to inhibit lipid oxidation in oil-in-water emulsions.     

Role of continuous phase protein on the oxidative stability of fish oil-in-water emulsions

Whey protein isolate (WPI), soy protein isolate (SPI), and sodium caseinate (CAS) can inhibit lipid oxidation when they produce a positive charge at the interface of emulsion droplets. However, when proteins are used to stabilize oil-in-water emulsions, only a fraction of them actually absorb to the emulsion droplets, with the rest remaining in the continuous phase. The impact of these continuous phase proteins on the oxidative stability of protein-stabilized emulsions is not well understood. WPI-stabilized menhaden oil-in-water emulsions were prepared by high-pressure homogenization. In some experiments WPI was removed from the continuous phase of the emulsions through repeated centrifugation and resuspension of the emulsion droplets (washed emulsion). Unwashed emulsions were more oxidatively stable than washed emulsions at pH 7.0, suggesting that continuous phase proteins were antioxidative. The oxidative stability of emulsions containing different kinds of protein in the continuous phase decreased in the order SPI > CAS > WPI, as determined by both hydroperoxide and headspace propanal formation. Iron-binding studies showed that the chelating ability of the proteins decreased in the order CAS > SPI > WPI. The free sulfhydryls of both WPI and SPI were involved in their antioxidant activity. This research shows that continuous phase proteins could be an effective means of protecting omega-3 fatty acids from oxidative deterioration.     

Studies with myoglobin variants indicate that released hemin is the primary promoter of lipid oxidation in washed fish muscle

Variants of sperm whale myoglobin (Mb) were used to assess the mechanism of heme protein-mediated lipid oxidation in washed cod muscle. A myoglobin variant with high hemin affinity (V68T) was an exceptionally poor promoter of lipid oxidation, while a Mb variant with low hemin affinity (H97A) was a potent promoter of lipid oxidation. V68T releases hemin slowly due to the ability of threonine to hydrogen bond with coordinated water and the distal histidine within the heme crevice. H97A rapidly releases hemin because the relatively small alanine residue creates a channel for water to easily enter the heme crevice which weakens the covalent linkage of hemin to the proximal histidine. A variant sensitive to heme degradation (L29F/H64Q) was a weaker promoter of lipid oxidation compared to wild-type Mb. This suggests that degrading the heme ring and releasing iron decreased the ability of Mb to promote lipid oxidation. Free radicals resulting from hemin-mediated decomposition of lipid hydroperoxides have the capacity to propagate lipid oxidation and degrade hemin catalyst. This may explain why heme proteins behave as reactants rather than "catalysts" of lipid oxidation in washed cod. Collectively these studies strongly suggest that released hemin is the critical entity that drives heme protein-mediated lipid oxidation in washed fish muscle.     

Extensive dispersal of Roanoke logperch (Percina rex) inferred from genetic marker data

The dispersal ecology of most stream fishes is poorly characterised, complicating conservation efforts for these species. We used microsatellite DNA marker data to characterise dispersal patterns and effective population size (N_e) for a population of Roanoke logperch Percina rex, an endangered darter (Percidae). Juveniles and candidate parents were sampled for 2 years at sites throughout the Roanoke River watershed. Dispersal was inferred via genetic assignment tests (ATs), pedigree reconstruction (PR) and estimation of lifetime dispersal distance under a genetic isolation‐by‐distance model. Estimates of N_e varied from 105 to 1218 individuals, depending on the estimation method. Based on PR, polygamy was frequent in parents of both sexes, with individuals spawning with an average of 2.4 mates. The sample contained 61 half‐sibling pairs, but only one parent–offspring pair and no full‐sib pairs, which limited our ability to discriminate natal dispersal of juveniles from breeding dispersal of their parents between spawning events. Nonetheless, all methods indicated extensive dispersal. The AT indicated unrestricted dispersal among sites ≤15 km apart, while siblings inferred by the PR were captured an average of 14 km and up to 55 km apart. Model‐based estimates of median lifetime dispersal distance (6–24 km, depending on assumptions) bracketed AT and PR estimates, indicating that widely dispersed individuals do, on average, contribute to gene flow. Extensive dispersal of P. rex suggests that darters and other small benthic stream fishes may be unexpectedly mobile. Monitoring and management activities for such populations should encompass entire watersheds to fully capture population dynamics.     

Observation of polymer conformation hysteresis in extensional flow

Highly extensible Escherichia coli DNA molecules in planar extensional flow were visualized in dilute solution by fluorescence microscopy. For a narrow range of flow strengths, the molecules were found in either a coiled or highly extended conformation, depending on the deformation history of the polymer. This conformation hysteresis persists for many polymer relaxation times and is due to conformation-dependent hydrodynamic forces. Polymer conformational free-energy landscapes were calculated from computer simulations and show two free-energy minima for flow strengths near the coil-stretch transition. Hysteresis cycles may directly influence bulk-solution stresses and the development of stress-strain relations for dilute polymer flows.     

基于物质平衡原理的贝类循环水养殖系统的设计与试验

为恢复和保护濒危淡水贝类资源,该文根据物质平衡原理,以具有代表性的淡水彩虹贝类为研究对象,设计并构建了一套小型的室内淡水彩虹贝循环水养殖系统,该系统由养殖池、生物过滤器、蓄水池、循环水泵、充氧系统和自动投饵装置等环节组成。并在该循环水系统中对钩介幼虫2日龄的彩虹贝幼贝进行了为期60 d的养殖(2011年6月21日到2011年8月20日),整个养殖周期内,彩虹贝幼贝养殖系统环境稳定,水质稳定良好,彩虹贝幼贝壳长日增长量为15.2μm/d,彩虹贝幼贝的最大相对增长率发生在第40天到第50天,其相对生长率为32.4%,和之前池塘流水、跑道式等养殖模式相比,该循环水系统养殖的彩虹贝幼贝获得了更高的生长率。该研究可为淡水贝类的人工繁育和养殖提供参考。     

Lipid oxidation in corn oil-in-water emulsions stabilized by casein,whey protein isolate,and soy protein isolate

Proteins can be used to produce cationic oil-in-water emulsion droplets at pH 3.0 that have high oxidative stability. This research investigated differences in the physical properties and oxidative stability of corn oil-in-water emulsions stabilized by casein, whey protein isolate (WPI), or soy protein isolate (SPI) at pH 3.0. Emulsions were prepared with 5% corn oil and 0.2-1.5% protein. Physically stable, monomodal emulsions were prepared with 1.5% casein, 1.0 or 1.5% SPI, and > or =0.5% WPI. The oxidative stability of the different protein-stabilized emulsions was in the order of casein > WPI > SPI as determined by monitoring both lipid hydroperoxide and headspace hexanal formation. The degree of positive charge on the protein-stabilized emulsion droplets was not the only factor involved in the inhibition of lipid oxidation because the charge of the emulsion droplets (WPI > casein > or = SPI) did not parallel oxidative stability. Other potential reasons for differences in oxidative stability of the protein-stabilized emulsions include differences in interfacial film thickness, protein chelating properties, and differences in free radical scavenging amino acids. This research shows that differences can be seen in the oxidative stability of protein-stabilized emulsions; however, further research is needed to determine the mechanisms for these differences.