Chp8, a diguanylate cyclase from Pseudomonas syringae pv tomato DC3000 suppresses the PAMP flagellin, increases EPS and promotes plant immune evasion.

The bacterial plant pathogen Pseudomonas syringae causes disease in a wide range of plants. The associated decrease in crop yields results in economic losses and threatens global food security. Competition exists between the plant immune system and the pathogen, the basic principles of which can be applied to animal infection pathways. P. syringae uses a type III secretion system (T3SS) to deliver virulence factors into the plant that promote survival of the bacterium. The P. syringae T3SS is a product of the hypersensitive response and pathogenicity (hrp) and hypersensitive response and conserved (hrc) gene cluster, which is strictly controlled by the codependent enhancer-binding proteins HrpR and HrpS. Through a combination of bacterial gene regulation and phenotypic studies, plant infection assays, and plant hormone quantifications, we now report that Chp8 (i) is embedded in the Hrp regulon and expressed in response to plant signals and HrpRS, (ii) is a functional diguanylate cyclase, (iii) decreases the expression of the major pathogen-associated molecular pattern (PAMP) flagellin and increases extracellular polysaccharides (EPS), and (iv) impacts the salicylic acid/jasmonic acid hormonal immune response and disease progression. We propose that Chp8 expression dampens PAMP-triggered immunity during early plant infection.

Efficiency of starfish mopping in reducing predation on cultivated benthic mussels (Mytilus edulis Linnaeus)

The starfish, Asterias rubens, preys on mussels (Mytilus edulis), which are relaid during benthic cultivation processes. Starfish mops, a modified dredge used to remove starfish from mussel cultivation beds, are used in several fisheries today but few studies have attempted to quantify the effectiveness of this method in removing starfish. This study tested the effectiveness of starfish mopping to reduce starfish numbers on mussel beds in Belfast Lough, Northern Ireland. Video surveys to determine starfish densities on mussel beds were conducted between October 2013 and December 2014 using a GoPro™ camera attached to starfish mops. This allowed us to firstly test whether starfish density varied among mussel beds and to investigate how fluctuations in starfish numbers may vary in relationship to starfish ecology. We then estimated the efficiency of mops at removing starfish from mussel beds by comparing densities of starfish on beds, as determined using video footage, with densities removed by mops. Starfish abundance was similar among different mussel beds during this study. The efficiency of mops at removing estimated starfish aggregations varied among mussel beds (4–78%) and the mean reduction in starfish abundance was 27% (± SE 3.2). The effectiveness of mops at reducing starfish abundance was shown to decline as the initial density of starfish on mussel beds increased. It can be recommended that the exact deployment technique of mops on mussel beds should vary depending on the density of starfish locally. The area of mussel bed covered by mops during a tow, for example, should be less when starfish densities are high, to maintain efficiencies throughout the full length of tows and to optimise the removal of starfish from mussel beds. This strategy, by reducing abundance of a major predator, could assist in reducing losses in the mussel cultivation industry.

Breaking and Entering: Examining the role of stress and aerial exposure in predator-prey relationships between the common shore crab (Carcinus maenas) and cultivated blue mussels (Mytilus edulis).

During benthic cultivation Mytilus edulis (blue mussels) are subject to predation pressure from a number of predators including Carcinus maenas (shore crabs). This predator can be responsible for substantial losses of mussels from the fishery and a full understanding of the predator–prey relationship between M. edulis and C. maenas is required to ensure attempts that reduce predatory pressure and subsequent commercial loss are successful. Whilst much work has examined the prey–predator size relationships between C. maenas and M. edulis, far less research has investigated how stress, such as periods of extended aerial exposure, may affect these relationships. We tested whether profit in terms of calories gained by crabs consuming mussels stressed by aerial exposure for 48 h differed from that of mussels at ambient conditions and whether being stressed affected the mussel's likelihood of predation. We also tested whether the size relationship between predators and their prey differed when mussels were stressed. We found that the profitability of prey (calories gained per second of handling time) did not vary between stressed and unstressed mussels. Handling times for stressed and unstressed mussels were similar, even when crabs were presented with mussels of the maximum size that they are able to consume. Small crabs were more likely to reject a mussel of preferred size if it was unstressed, suggesting that crabs may be able to assess that these mussels would require extra effort to break into and consume. Our findings suggest that the predator–prey relationship between mussels and crabs is not altered when mussels are stressed. C. maenas remains a voracious predator and regardless of the condition of mussels laid on commercial beds there is a need to control this predator in attempt to reduce losses in the benthic fishery.

Impact of long-term storage at ambient temperatures on the total quality and stability of high-pressure processed tomato juice

High-pressure processing (HPP) can produce tomato juice of high quality and safety with a short shelf life under refrigeration temperatures. Long-term higher temperature storage studies are rare and temperature tolerant products are challenging to develop. The effect of high-pressure processing (HPP) on the total quality (colour, microbial counts, phytochemical levels, antioxidant and enzymatic activities) and stability (retention over time) of tomato juice during long-term storage was investigated. Thermal processing (TP) was used as a control treatment, and overall, two different ambient conditions (20 °C and 28 °C) were tested. Immediately after processing, HPP products proved superior to TP ones (enhanced redness, total carotenoids and lycopene, stable total phenols and inactivation of pectin methyl esterase). During initial storage (30 d) most quality attributes of HPP juice remained stable. Prolonged storage, however, led to losses of most quality attributes, although HPP (20 °C) showed lower quality degradation rate constants comparison to TP and HPP (28 °C). Industrial Relevance: There is a demand for ambient stable tomato products, especially in some parts of the world, and current industrial practices (canning, pasteurisation) either compromise in product quality or require refrigeration conditions. High-pressure processing has been investigated as milder technology, with a potential to deliver superior quality. The drawback is that is also requires chill storage. The results of this study show how quality parameters behave in a high-pressured tomato product and pave the way for further development that could optimise this technology. This could be of economic importance for the tomato juice industry to develop new products stable in ambient temperatures and perhaps beneficial for cutting down the refrigeration costs under specific conditions.

Industrial scale microwave processing of tomato juice using a novel continuous microwave system

This study evaluated the effect of an industrial scale continuous flow microwave volumetric heating system in comparison to conventional commercial scale pasteurisation for the processing of tomato juice in terms of physicochemical properties, microbial characteristics and antioxidant capacity. The effect against oxidative stress in Caco-2 cells, after in vitro digestion was also investigated. Physicochemical and colour characteristics of juices were very similar between technologies and during storage. Both conventional and microwave pasteurisation inactivated microorganisms and kept them in low levels throughout storage. ABTS⁺ values, but not ORAC, were higher for the microwave pasteurised juice at day 0 however no significant differences between juices were observed during storage. Juice processed with the microwave system showed an increased cytoprotective effect against H₂O₂ induced oxidation in Caco-2 cells. Organoleptic analysis revealed that the two tomato juices were very similar. The continuous microwave volumetric heating system appears to be a viable alternative to conventional pasteurisation.

Integration of design of experiment, surface response methodology and multi-layer validation to predict the effect of blanching on colour of tomato juice

Response surface methodology was used to develop models to predict the effect of tomato cultivar, juice pH, blanching temperature and time on colour change of tomato juice after blanching. The juice from three tomato cultivars with adjusted pH levels ranging from 3.9 to 4.6 were blanched at temperatures from 60-100 °C for 1-5 min using the central composite design (CCD). The colour change was assessed by calculating the redness (a/b) and total colour change (∆E) after measuring the Hunter L, a and b values. Developed models for both redness and ∆E were significant (p<0.0001) with satisfactory coefficient of determination (R2 = 0.99 and 0.97) and low coefficient of variation (CV% = 1.89 and 7.23), respectively. Multilevel validation that was implemented revealed that the variation between the predicted and experimental values obtained for redness and ∆E were within the acceptable error range of 7.3 and 22.4%, respectively

Do vesicle cells of the red alga Asparagopsis (Falkenbergia stage) play a role in bromocarbon production?

The Rhodophyceae (red algae) are an established source of volatile halocarbons in the marine environment. Some species in the Bonnemaisoniaceae have been reported to contain large amounts of halogens in structures referred to as vesicle cells, suggesting involvement of these specialised cells in the production of halocarbons. We have investigated the role of vesicle cells in the accumulation and metabolism of bromide in an isolate of the red macroalga Asparagopsis (Falkenbergia stage), a species known to release bromocarbons. Studies of laboratory-cultivated alga, using light microscopy, revealed a requirement of bromide for both the maintenance and formation of vesicle cells. Incubation of the alga in culture media with bromide concentrations below 64 mg l-1 (the concentration of Br- in seawater) resulted in a decrease in the proportion of vesicle cells to pericentral cells. The abundance of vesicle cells was correlated with bromide concentration below this level. Induction of vesicle cell formation in cultures of Falkenbergia occurred at concentrations as low as 8 mg l-1, with the abundance of vesicle cells increasing with bromide concentration up to around 100 mg l-1. Further studies revealed a positive correlation between the abundance of vesicle cells and dibromomethane and bromoform production. Interestingly, however, whilst dibromomethane production was stimulated by the presence of bromide in the culture media, bromoform release remained unaffected suggesting that the two compounds are formed by different mechanisms.

Graded Relative Evidence

Relative Evidential Supports (RES) was developed and justified several years ago as a non-numeric apparatus that allows us to compare evidential supports for alternative conclusions when making a decision. An extension called Graded Relative Evidence (GRE) of the RES concept of pairwise balancing and trading-off of evidence is reported here which keeps its basic features of simplicity and perspicacity but enriches its modelling fidelity by permitting very modest and intuitive variations in degrees of outweighing (which the essentially binary RES does not). The formal justification is very simply based on linkages to RES and to the Dempster - Shafer theory of evidence. The use of the simple extension is illustrated and to a small degree further justified empirically by application to a topical scientific debate about what is called the Congo Crossover Conjecture here. This decision-making instance is chosen because of the wealth of evidence that has been accumulated on both sides of the debate and the range of evidence strengths manifested in it. The conjecture is that the advent of Aids was in the late 1950s in the Congo when a vaccine for polio was allegedly cultivated in the kidneys of chimpanzees which allowed the Aids infection to cross over to humans from primates. © 2005 Springer.

High-resolution organellar genome analysis of Triticum and Aegilops sheds new light on cytoplasm evolution in wheat

We have utilised polymorphic chloroplast microsatellites to analyse cytoplasmic relationships between accessions in the genera Triticum and Aegilops. Sequencing of PCR products revealed point mutations and insertions/deletions in addition to the standard repeat length expansion/contraction which most likely represent ancient synapomorphies. Phylogenetic analyses revealed three distinct groups of accessions. One of these contained all the non-Aegilops speltoides S-type cytoplasm species, another comprised almost exclusively A, C, D, M, N, T and U cytoplasm-type accessions and the third contained the polyploid Triticum species and all the Ae. speltoides accessions, further confirming that Ae. speltoides or a closely related but now extinct species was the original B-genome donor of cultivated polyploid wheat. Successive decreases in levels of genetic diversity due to domestication were also observed. Finally, we highlight the importance of elucidating longer-term evolutionary processes operating at microsatellite repeat loci.

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.

Linking past cultural developments to palaeoenvironmental changes in Estonia

Connections between environmental and cultural changes are analysed in Estonia during the past c. 4,500 years. Records of cereal-type pollen as (agri)cultural indices are compared with high-resolution palaeohydrological and annual mean temperature reconstructions from a selection of Estonian bogs and lakes (and Lake Igelsjon in Sweden). A broad-scale comparison shows increases in the percentage of cereal-type pollen during a decreasing trend in annual mean temperatures over the past c. 4,300 years, suggesting a certain independence of agrarian activities from environmental conditions at the regional level. The first cereal-type pollen in the region is found from a period with a warm and dry climate. A slow increase in pollen of cultivated land is seen around the beginning of the late Bronze Age, a slight increase at the end of the Roman Iron Age and a significant increase at the beginning of the Middle Ages. In a few cases increases in agricultural pollen percentages occur in the periods of warming. Stagnation and regression occurs in the periods of cooling, but regression at individual sites may also be related to warmer climate episodes. The cooling at c. 400-300 cal b.p., during the 'Little Ice Age' coincides with declines in cereal-type and herb pollen curves. These may not, however, be directly related to the climate change, because they coincide with war activities in the region.

A Bacterial Enrichment Study and Overview of the Extractable Lipids from Paleosols in the Dry Valleys, Antarctica: Implications for Future Mars Reconnaissance

The Dry Valleys of Antarctica are one of the coldest and driest environments on Earth with paleosols in selected areas that date to the emplacement of tills by warm-based ice during the Early Miocene. Cited as an analogue to the martian surface, the ability of the Antarctic environment to support microbial life-forms is a matter of special interest, particularly with the upcoming NASA/ESA 2018 ExoMars mission. Lipid biomarkers were extracted and analyzed by gas chromatography-mass spectrometry to assess sources of organic carbon and evaluate the contribution of microbial species to the organic matter of the paleosols. Paleosol samples from the ice-free Dry Valleys were also subsampled and cultivated in a growth medium from which DNA was extracted with the explicit purpose of the positive identification of bacteria. Several species of bacteria were grown in solution and the genus identified. A similar match of the data to sequenced DNA showed that Alphaproteobacteria, Gamma-proteobacteria, Bacteriodetes, and Actinobacteridae species were cultivated. The results confirm the presence of bacteria within some paleosols, but no assumptions have been made with regard to in situ activity at present. These results underscore the need not only to further investigate Dry Valley cryosols but also to develop reconnaissance strategies to determine whether such likely Earth-like environments on the Red Planet also contain life.

Early Holocene vegetation, human activity and climate from Sarawak, Malaysian Borneo

A 40mcore from Loagan Bunut,Malaysian Borneo, yielded a high-resolution early Holocene (11.3e6.75 ka) sequence of marginal-marine deposits. Palynological analysis showed relatively stable fire-regulated lowland forest through this time, with the local development and regression of mangrove vegetation. A general trend of rising rainfall and thus strengthening North East monsoonal circulation linked to the migration of the mean position of the ICTZ was interrupted by what may be episodes of drier climate and weakening monsoonal activity at 9250-8890, 7900 and 7600-7545 cal. BP. Magnetic susceptibility peaks suggestmarked short-term ENSO-style activity superimposed upon this record. Repeated markers for openand disturbed habitats, plus occasional imported and probably-cultivated taxa, point towards human impact from the earliest Holocene on the wet tropical forest at Loagan Bunut.

Globalization, Police Reform and Development; Doing it the Western Way?

Under what conditions does successful police reform take place? Can democratic forms of policing exist within undemocratic state structures? What are the motives of donor and recipient nations, and can the norms of global civil society be cultivated in order to promote human rights, democratic governance, and fair and accountable policing? These questions are addressed in this volume, which presents a unique examination of Western-led police reform efforts by theoretically linking neoliberal globalization, police reform and development. The authors present seven country case studies based on this theoretical approach (Afghanistan, Brazil, Iraq, Northern Ireland, South Africa, Trinidad and Tobago, and Turkey) and assess the prospects for successful police reform in a global context.

Neolithic farming in north-western Europe: archaeobotanical evidence from Ireland

This paper presents significant new insights into the appearance of agriculture at the north- western edge of Europe, focusing on Neolithic Ireland (4000-2500 cal BC). Previous studies were based upon a limited plant macro-remains dataset, as much of the Irish evidence is unpublished. A research project, 'Cultivating Societies', was implemented to examine the nature, timing and extent of agricultural activity in Neolithic Ireland through collation and analysis of different strands of published and unpublished archaeological and environmental evidence, with a particular focus on plant macro- remains, pollen, settlement and 14C data. Plant macro-remains from a total of 52 excavated sites were collated and analysed, representing the most comprehensive study to date of Neolithic plant remains from this region. Cereals were present at many locations and site types, sometimes in large quantities and most often at sites dating to the earlier Neolithic (3750-3600 cal BC). Emmer wheat was the dominant crop, at least at this time. Other crops included naked and hulled barley, naked wheat, einkorn wheat and flax. Analysis of arable weeds indicates that early plots were not managed under a shifting cultivation regime, which has important implications for understanding Neolithic settlement practices and how communities engaged with landscapes. The variety of crops cultivated in Neolithic Ireland is similar to those in Britain, reflecting a decreasing diversity in crop types as agriculture spread from south-east to north-west Europe.