Quantitative proteomics to study the response of potato to contrasting fertilisation regimes

There is concern over the sustainability and environmental impact of mineral fertilisers and crop protection inputs used in intensive arable crop production systems. However, replacing mineral with organic fertilisers (animal and green manures) and restricting the use of chemosynthetic crop protection may significantly reduce crop yields. The effects of (a) replacing mineral with composted cattle manure fertiliser input and (b) omitting pesticide-based crop protection on potato (Solanum tuberosum) tuber yield, leaf and tuber mineral nutrient content and leaf protein profiles were investigated. Switching to organic fertiliser had a greater effect on yield and protein profiles than the omission of chemosynthetic crop protection. Leaf N and P composition were significant drivers of protein expression, particularly proteins involved in photosynthesis such as the large subunit of RuBisCO, RuBisCO activase and the photosystem I reaction centre, which were at higher abundances in potato leaves grown under mineral fertiliser regimes. Proteins known to be induced in response to stress, such as dehydroascorbate reductase and Glutathione S-transferases, were also shown to be up-regulated under mineral fertilisation, possibly associated with higher Cd composition, whereas two proteins known to be involved in biotic stress (1,3-β-d-glucan glucanohydrolase; putative Kunitz-type tuber invertase inhibitor) were more abundant under compost fertilisation. Results showed that switching from mineral to organic fertilisers led to reduced N availability, a significant change in leaf protein expression and lower tuber yield. In contrast, omission of chemosynthetic crop protection inputs had limited effects on protein expression and no significant effect on tuber yield. This study provides information on the effects of changes in nutrient supply on protein expression patterns. It is a prerequisite for the development of functional molecular markers for a directed strategy to inform breeding programmes to improve potato nutrient use efficiency.     

Organic Production Enhances Milk Nutritional Quality by Shifting Fatty Acid Composition: A United States–Wide, 18-Month Study

Over the last century, intakes of omega-6 (ω-6) fatty acids in Western diets have dramatically increased, while omega-3 (ω-3) intakes have fallen. Resulting ω-6/ω-3 intake ratios have risen to nutritionally undesirable levels, generally 10 to 15, compared to a possible optimal ratio near 2.3. We report results of the first large-scale, nationwide study of fatty acids in U.S. organic and conventional milk. Averaged over 12 months, organic milk contained 25% less ω-6 fatty acids and 62% more ω-3 fatty acids than conventional milk, yielding a 2.5-fold higher ω-6/ω-3 ratio in conventional compared to organic milk (5.77 vs. 2.28). All individual ω-3 fatty acid concentrations were higher in organic milk—α-linolenic acid (by 60%), eicosapentaenoic acid (32%), and docosapentaenoic acid (19%)—as was the concentration of conjugated linoleic acid (18%). We report mostly moderate regional and seasonal variability in milk fatty acid profiles. Hypothetical diets of adult women were modeled to assess milk fatty-acid-driven differences in overall dietary ω-6/ω-3 ratios. Diets varied according to three choices: high instead of moderate dairy consumption; organic vs. conventional dairy products; and reduced vs. typical consumption of ω-6 fatty acids. The three choices together would decrease the ω-6/ω-3 ratio among adult women by ∼80% of the total decrease needed to reach a target ratio of 2.3, with relative impact “switch to low ω-6 foods” > “switch to organic dairy products” ≈ “increase consumption of conventional dairy products.” Based on recommended servings of dairy products and seafoods, dairy products supply far more α-linolenic acid than seafoods, about one-third as much eicosapentaenoic acid, and slightly more docosapentaenoic acid, but negligible docosahexaenoic acid. We conclude that consumers have viable options to reduce average ω-6/ω-3 intake ratios, thereby reducing or eliminating probable risk factors for a wide range of developmental and chronic health problems.     

GPCR-induced dissociation of G-protein subunits in early stage signal transduction

G-protein coupled receptors (GPCRs) form a ternary complex of agonist, receptor and G-proteins during primary signal transduction at the cell membrane. Downstream signalling is thought to be preceded by the process of dissociation of Gα and Gβγ subunits, thus exposing new surfaces to interact with downstream effectors. We demonstrate here for the first time, the dissociation of heterotrimeric G-protein subunits (i.e., Gα and Gβγ) following agonist-induced GPCR (α_2A-adrenergic receptor; α_2A-AR) activation in a cell-free assay system. α_2A-AR membranes were reconstituted with the G-proteins (±hexahistidine-tagged) Gα_i1 and Gβ₁γ₂ and functional signalling was determined following activation of the reconstituted receptor:G-protein complex with the potent agonist UK-14304, and [³⁵S]GTPγS. In the presence of Ni²⁺-coated agarose beads, the activated his-tagged Gα_i1his-[³⁵S]GTPγS complex was captured on the Ni²⁺-presenting surface. When his-tagged Gβ₁γ₂ (Gβ₁γ₂his) was used with Gα_i1, the [³⁵S]GTPγS-bound Gα_i1 was not present on the Ni²⁺-coated beads, but rather, it was separated from the β₁γ₂(his)-beads, demonstrating receptor-induced dissociation of Gα and Gβγ subunits. Treatment of the reconstituted α_2A-AR membranes containing Gβ₁γ₂his:Gα_i1 with imidazole confirmed the specificity for the Ni²⁺:G-protein surface dissociation of Gα_i1 from Gβ₁γ₂his. These data demonstrate for the first time, the complete dissociation of the G-protein subunits and extend observations on the role of G-proteins in the assembly and disassembly of the ternary complex in the primary events of GPCR signalling.     

Ecology of Microbial Saprophytes and Pathogens in Tissue Culture and Field-Grown Plants: Reasons for Contamination Problems In Vitro

This review compares published surveys of microbial populations in plant tissue and cell cultures with the microbial saprophytes and pathogens found on field grown plants and microbial populations in the laboratory environment. From this comparison and the measured reduction in contamination after improvements in working practices in the laboratory, conclusions can be drawn about the importance of the explant and the laboratory as sources of contamination.

Mechanisms of pathogenicity in vitro are described to explain why bacteria, fungi, and yeasts that are not pathogenic to plants in the field become pathogens in plant tissue cultures. Conversely, plant metabolism and its effect on the tissue culture environment are described to explain why prokaryotes, viruses, and viroids that cause disease in the field can stay latent in vitro.

Detection methods for latent contaminants in plant tissue cultures are summarized, and the strategies and methods for prevention or treatment of contamination are discussed.     

Effects of low-chloride solutions on action potentials of sheep cadiac purkinje fibers

The rapid repolarization during phase 1 of the action potential of sheep cardiac purkinje fibers has been attributed to a time- and voltage-dependent chloride current. In part, this conclusion was based on experiments that showed a substantial slowing of phase 1 when larger, presumably impermeant, anions were substituted for chloride in tyrode’s solution. We have re- examined the electrical effects of low-chloride solutions. We recorded action potentials of sheep cardiac purkinje fibers in normal tyrode’s solution and in low-chloride solutions made by substituting sodium propionate, acetylglycinate, methylsulfate, or methanesulfonate for the NaCl of Tyrode’s solution. Total calcium was adjusted to keep calcium ion activity of test solutions equal to that of control solutions. Propionate gave qualitatively variable results in preliminary experiments; it was not tested further. Low-chloride solutions made with the other anions gave much more consistent results: phase 1 and the notch that often occurs between phases 1 and 2 were usually unaffected, and the action potential duration usually increased. The only apparent change in the resting potential was a transient 3-6 mV depolarization when low-chloride solution was first admitted to the chamber, and a symmetrical transient hyperpolarization when chloride was returned to normal. If a time- and voltage-dependent chloride current exists in sheep cardiac purkinje fibers, our results suggest that it plays little role in generating phase 1 of the action potential.     

Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts

Background  

Text-mining can assist biomedical researchers in reducing information overload by extracting useful knowledge from large collections of text. We developed a novel text-mining method based on analyzing the network structure created by symbol co-occurrences as a way to extend the capabilities of knowledge extraction. The method was applied to the task of automatic gene and protein name synonym extraction.     

Dietary fish oil alters cardiomyocyte Ca2+ dynamics and antioxidant status

The n-3 polyunsaturated fatty acids (PUFAs) found in fish oil (FO) have been shown to protect against reperfusion arrhythmias, a manifestation of reperfusion injury, which is believed to be induced by the formation of reactive oxygen species (ROS) and intracellular calcium (Ca2+) overload. Adult rats fed a diet supplemented with 10% FO had a higher proportion of myocardial n-3 PUFAs and increased expression of antioxidant enzymes compared with the saturated fat (SF)-supplemented group. Addition of hydrogen peroxide (H2O2) to cardiomyocytes isolated from rats in the SF-supplemented group increased the proportions of cardiomyocytes contracting in an asynchronous manner, increased the rate of Ca2+ influx, and increased the diastolic and systolic [Ca2+]i compared with the FO group. H2O2 exposure increased the membrane fluidity of cardiomyocytes from the FO group. These results demonstrate that dietary FO supplementation is associated with a reduction in the susceptibility of myocytes to ROS-induced injury and this may be related to membrane incorporation of n-3 PUFAs, increased antioxidant defenses, changes in cardiomyocyte membrane fluidity, and the ability to prevent rises in cellular Ca2+ in response to ROS.     

Ground beetle species (Carabidae,Coleoptera) activity and richness in relation to crop type,fertility management and crop protection in a farm management comparison trial

Ground beetle activity and species richness was monitored using pitfall traps in a plot trial system on a farm in northern England where the effects of organic and conventional fertility and crop protection management were separated within different crop types between 2005 and 2008. As well as analyses on species activity the beetles were split into small, medium‐sized and large groups, and into groups of herbivores and specific Collembola feeders. Crop type had significant effects on the activity of the 20 most abundant species and all groups, generally with most in beans and winter barley and least in vegetables and spring barley. Most significant reactions to crop protection and fertility management were in cereals and grass/clover. Activity of small species was highest in conventionally crop‐protected cereals but not in vegetables, with more medium‐sized and herbivorous species in organic plots, but there was little influence of crop protection management on large and Collembola feeding species. However, large species were significantly more active in organically fertilised cereals and grass/clover, but not in vegetables, and there were more Collembola feeders in conventional cereals but not in grass/clover. Small species were more abundant in conventionally fertilised grass/clover but there were more in organic cereals and vegetables. These inconsistent activity reactions to management were also observed with individual species but most preferred organically managed plots. There were few significant crop protection : fertility management interactions. Species richness was also significantly affected by crop type and where management had an influence, more species were found in organically managed plots. Constrained ordination emphasised that ground beetle activity was influenced more by crops than by management. Given the diverse nature of organic crop rotations, crop type should be considered a major influence in any environmental manipulation aimed at increasing ground beetle activity for provision of ecosystem services.     

A pragmatic approach for improving invertebrate biodiversity assessment in the agricultural landscape

Assessments of invertebrate biodiversity in the agricultural landscape have been inconsistent and sometimes contradictory. There is a requirement to improve assessments, especially when quantifying the beneficial effects of low input and organic farming on biodiversity. To generate an improved understanding, data from four crops (organic leek, cabbage and broccoli, conventional calabrese), sampled in eastern England with both pitfall and pan traps, was used. Eight Orders, 55 ground beetle (Carabidae) species, 12 Coleoptera families and 66 Higher taxa (tribes, subfamilies and families) were used to calculate four diversity-related metrics and two fidelity metrics, using data from pitfall traps and from pitfall and pan traps combined. Diversity metrics were taxa richness, Shannon diversity index and Quantitative totals and indexes based on the number of each taxa recorded. Fidelity totals and indexes were used to assess deviations from the basic vegetable field habitat. Order was the least consistent taxa and the Shannon index was a poor diversity indicator. Taxa richness and Quantitative totals were more accurate and the use of quantifications based on the number of appropriate taxa recorded improved metric quality and Fidelity index was an improvement on the Fidelity total. In general, the highest metric values were in broccoli and cabbage, the crops with most weeds, and there were positive correlations between most metrics and weed cover. Metrics using combined epigeal and aerial invertebrate data, utilising the most taxa and the number recorded, were most appropriate for comparisons between crop types.