Isolation, structure, chemistry, and photochemistry of cis-bis(2,2'-bipyridyl)carbonylchlororuthenium(II) perchlorate

The molecular structure and chemical and photochemical reactions of [Ru(bpy)2(CO)Cl]+ClO4–, which has been isolated from the reaction of ruthenium trichloride and 2,2′-bipyridyl(bpy) in dimethylformamide, are described.

Testing for a unit root in a process exhibiting a structural break in the presence of GARCH errors

This paper considers the effect of GARCH errors on the tests proposed byPerron (1997) for a unit root in the presence of a structural break. We assessthe impact of degeneracy and integratedness of the conditional varianceindividually and find that, apart from in the limit, the testing procedure isinsensitive to the degree of degeneracy but does exhibit an increasingover-sizing as the process becomes more integrated. When we consider the GARCHspecifications that we are likely to encounter in empirical research, we findthat the Perron tests are reasonably robust to the presence of GARCH and donot suffer from severe over-or under-rejection of a correct null hypothesis.

Stability of pollination services decreases with isolation from natural areas despite honey bee visits

Sustainable agricultural landscapes by definition provide high magnitude and stability of ecosystem services, biodiversity and crop productivity. However, few studies have considered landscape effects on the stability of ecosystem services. We tested whether isolation from florally diverse natural and semi-natural areas reduces the spatial and temporal stability of flower-visitor richness and pollination services in crop fields. We synthesised data from 29 studies with contrasting biomes, crop species and pollinator communities. Stability of flower-visitor richness, visitation rate (all insects except honey bees) and fruit set all decreased with distance from natural areas. At 1 km from adjacent natural areas, spatial stability decreased by 25, 16 and 9% for richness, visitation and fruit set, respectively, while temporal stability decreased by 39% for richness and 13% for visitation. Mean richness, visitation and fruit set also decreased with isolation, by 34, 27 and 16% at 1 km respectively. In contrast, honey bee visitation did not change with isolation and represented > 25% of crop visits in 21 studies. Therefore, wild pollinators are relevant for crop productivity and stability even when honey bees are abundant. Policies to preserve and restore natural areas in agricultural landscapes should enhance levels and reliability of pollination services.

Fine root turnover

Fine roots constitute an interface between plants and soils and thus play a crucial part in forest carbon, nutrient and water cycles. Their continuous growth and dieback, often termed turnover of fine roots, may constitute a major carbon input to soils and significantly contribute to belowground carbon cycle. For this reason, it is of importance to accurately estimate not only the standing biomass of fine roots, but also its rate of turnover. To date, no direct and reliable method of measuring fine root turnover exists. The main reason for this is that the two component processes of root turnover, namely growth and dieback of fine roots, nearly always happen in the same place and at the same time. Further, the estimation of fine root turnover is complicated by the inaccessibility of tree root systems, its labour intensiveness and is often compounded by artefacts created by soil disturbance. Despite the fact that the elucidation of the patterns and controls of forest fine root turnover is of utmost importance for the development of realistic carbon cycle models, our knowledge of the contribution of fine root turnover to carbon and nutrient cycles in forests remains uncertain. This chapter will detail all major methods currently used for estimating fine root turnover and highlight their advantages, as well as drawbacks.

Arabidopsis annexin1 mediates the radical-activated plasma membrane Ca2+ - and K+ -permeable conductance in root cells

Plant cell growth and stress signaling require Ca2+ influx through plasma membrane transport proteins that are regulated by reactive oxygen species. In root cell growth, adaptation to salinity stress, and stomatal closure, such proteins operate downstream of the plasma membrane NADPH oxidases that produce extracellular superoxide anion, a reactive oxygen species that is readily converted to extracellular hydrogen peroxide and hydroxyl radicals, OH_. In root cells, extracellular OH_ activates a plasma membrane Ca2+-permeable conductance that permits Ca2+ influx. In Arabidopsis thaliana, distribution of this conductance resembles that of annexin1 (ANN1). Annexins are membrane binding proteins that can form Ca2+-permeable conductances in vitro. Here, the Arabidopsis loss-of-function mutant for annexin1 (Atann1) was found to lack the root hair and epidermal OH_-activated Ca2+- and K+-permeable conductance. This manifests in both impaired root cell growth and ability to elevate root cell cytosolic free Ca2+ in response to OH_. An OH_-activated Ca2+ conductance is reconstituted by recombinant ANN1 in planar lipid bilayers. ANN1 therefore presents as a novel Ca2+-permeable transporter providing a molecular link between reactive oxygen species and cytosolic Ca2+ in plants.

Root growth models: towards a new generation of continuous approaches

Models of root system growth emerged in the early 1970s, and were based on mathematical representations of root length distribution in soil. The last decade has seen the development of more complex architectural models and the use of computer-intensive approaches to study developmental and environmental processes in greater detail. There is a pressing need for predictive technologies that can integrate root system knowledge, scaling from molecular to ensembles of plants. This paper makes the case for more widespread use of simpler models of root systems based on continuous descriptions of their structure. A new theoretical framework is presented that describes the dynamics of root density distributions as a function of individual root developmental parameters such as rates of lateral root initiation, elongation, mortality, and gravitropsm. The simulations resulting from such equations can be performed most efficiently in discretized domains that deform as a result of growth, and that can be used to model the growth of many interacting root systems. The modelling principles described help to bridge the gap between continuum and architectural approaches, and enhance our understanding of the spatial development of root systems. Our simulations suggest that root systems develop in travelling wave patterns of meristems, revealing order in otherwise spatially complex and heterogeneous systems. Such knowledge should assist physiologists and geneticists to appreciate how meristem dynamics contribute to the pattern of growth and functioning of root systems in the field.

Elevated atmospheric carbon dioxide impairs the performance of root-feeding vine weevils by modifying root growth and secondary metabolites

Predicting how insect crop pests will respond to global climate change is an important part of increasing crop production for future food security, and will increasingly rely on empirically based evidence. The effects of atmospheric composition, especially elevated carbon dioxide (eCO(2)), on insect herbivores have been well studied, but this research has focussed almost exclusively on aboveground insects. However, responses of root-feeding insects to eCO(2) are unlikely to mirror these trends because of fundamental differences between aboveground and belowground habitats. Moreover, changes in secondary metabolites and defensive responses to insect attack under eCO(2) conditions are largely unexplored for root herbivore interactions. This study investigated how eCO(2) (700 mu mol mol-1) affected a root-feeding herbivore via changes to plant growth and concentrations of carbon (C), nitrogen (N) and phenolics. This study used the root-feeding vine weevil, Otiorhynchus sulcatus and the perennial crop, Ribes nigrum. Weevil populations decreased by 33% and body mass decreased by 23% (from 7.2 to 5.4 mg) in eCO(2). Root biomass decreased by 16% in eCO(2), which was strongly correlated with weevil performance. While root N concentrations fell by 8%, there were no significant effects of eCO(2) on root C and N concentrations. Weevils caused a sink in plants, resulting in 8-12% decreases in leaf C concentration following herbivory. There was an interactive effect of CO(2) and root herbivory on root phenolic concentrations, whereby weevils induced an increase at ambient CO(2), suggestive of defensive response, but caused a decrease under eCO(2). Contrary to predictions, there was a positive relationship between root phenolics and weevil performance. We conclude that impaired root-growth underpinned the negative effects of eCO(2) on vine weevils and speculate that the plant's failure to mount a defensive response at eCO(2) may have intensified these negative effects.

Root phenomics of crops: opportunities and challenges

Reliable techniques for screening large numbers of plants for root traits are still being developed, but include aeroponic, hydroponic and agar plate systems. Coupled with digital cameras and image analysis software, these systems permit the rapid measurement of root numbers, length and diameter in moderate ( typically <1000) numbers of plants. Usually such systems are employed with relatively small seedlings, and information is recorded in 2D. Recent developments in X-ray microtomography have facilitated 3D non-invasive measurement of small root systems grown in solid media, allowing angular distributions to be obtained in addition to numbers and length. However, because of the time taken to scan samples, only a small number can be screened (typically<10 per day, not including analysis time of the large spatial datasets generated) and, depending on sample size, limited resolution may mean that fine roots remain unresolved. Although agar plates allow differences between lines and genotypes to be discerned in young seedlings, the rank order may not be the same when the same materials are grown in solid media. For example, root length of dwarfing wheat ( Triticum aestivum L.) lines grown on agar plates was increased by similar to 40% relative to wild-type and semi-dwarfing lines, but in a sandy loam soil under well watered conditions it was decreased by 24-33%. Such differences in ranking suggest that significant soil environment-genotype interactions are occurring. Developments in instruments and software mean that a combination of high-throughput simple screens and more in-depth examination of root-soil interactions is becoming viable.

Advances in sequential data assimilation and numerical weather forecasting: an Ensemble Transform Kalman-Bucy Filter, a study on clustering in deterministic Ensemble Square Root Filters, and a test of a new time stepping scheme in an atmospheric model

This dissertation deals with aspects of sequential data assimilation (in particular ensemble Kalman filtering) and numerical weather forecasting. In the first part, the recently formulated Ensemble Kalman-Bucy (EnKBF) filter is revisited. It is shown that the previously used numerical integration scheme fails when the magnitude of the background error covariance grows beyond that of the observational error covariance in the forecast window. Therefore, we present a suitable integration scheme that handles the stiffening of the differential equations involved and doesn’t represent further computational expense. Moreover, a transform-based alternative to the EnKBF is developed: under this scheme, the operations are performed in the ensemble space instead of in the state space. Advantages of this formulation are explained. For the first time, the EnKBF is implemented in an atmospheric model. The second part of this work deals with ensemble clustering, a phenomenon that arises when performing data assimilation using of deterministic ensemble square root filters in highly nonlinear forecast models. Namely, an M-member ensemble detaches into an outlier and a cluster of M-1 members. Previous works may suggest that this issue represents a failure of EnSRFs; this work dispels that notion. It is shown that ensemble clustering can be reverted also due to nonlinear processes, in particular the alternation between nonlinear expansion and compression of the ensemble for different regions of the attractor. Some EnSRFs that use random rotations have been developed to overcome this issue; these formulations are analyzed and their advantages and disadvantages with respect to common EnSRFs are discussed. The third and last part contains the implementation of the Robert-Asselin-Williams (RAW) filter in an atmospheric model. The RAW filter is an improvement to the widely popular Robert-Asselin filter that successfully suppresses spurious computational waves while avoiding any distortion in the mean value of the function. Using statistical significance tests both at the local and field level, it is shown that the climatology of the SPEEDY model is not modified by the changed time stepping scheme; hence, no retuning of the parameterizations is required. It is found the accuracy of the medium-term forecasts is increased by using the RAW filter.

Tree species diversity interacts with elevated CO2 to induce a greater root system response

As a consequence of land use change and the burning of fossil fuels, atmospheric concentrations of CO2 are increasing and altering the dynamics of the carbon cycle in forest ecosystems. In a number of studies using single tree species, fine root biomass has been shown to be strongly increased by elevated CO2. However, natural forests are often intimate mixtures of a number of co-occurring species. To investigate the interaction between tree mixture and elevated CO2, Alnus glutinosa, Betula pendula and Fagus sylvatica were planted in areas of single species and a three species polyculture in a free-air CO2 enrichment study (BangorFACE). The trees were exposed to ambient or elevated CO2 (580 µmol mol-1) for four years. Fine and coarse root biomass, together with fine root turnover and fine root morphological characteristics were measured. Fine root biomass, and morphology responded differentially to elevated CO2 at different soil depths in the three species when grown in monocultures. In polyculture, a greater response to elevated CO2 was observed in coarse roots to a depth of 20 cm, and fine root area index to a depth of 30 cm. Total fine root biomass was positively affected by elevated CO2 at the end of the experiment, but not by species diversity. Our data suggest that existing biogeochemical cycling models parameterised with data from species grown in monoculture may be underestimating the belowground response to global change.

Fine-root turnover rates of European forests revisited: an analysis of data from sequential coring and ingrowth cores

Background and Aims Forest trees directly contribute to carbon cycling in forest soils through the turnover of their fine roots. In this study we aimed to calculate root turnover rates of common European forest tree species and to compare them with most frequently published values. Methods We compiled available European data and applied various turnover rate calculation methods to the resulting database. We used Decision Matrix and Maximum-Minimum formula as suggested in the literature. Results Mean turnover rates obtained by the combination of sequential coring and Decision Matrix were 0.86 yr−1 for Fagus sylvatica and 0.88 yr−1 for Picea abies when maximum biomass data were used for the calculation, and 1.11 yr−1 for both species when mean biomass data were used. Using mean biomass rather than maximum resulted in about 30 % higher values of root turnover. Using the Decision Matrix to calculate turnover rate doubled the rates when compared to the Maximum-Minimum formula. The Decision Matrix, however, makes use of more input information than the Maximum-Minimum formula. Conclusions We propose that calculations using the Decision Matrix with mean biomass give the most reliable estimates of root turnover rates in European forests and should preferentially be used in models and C reporting.

Isolation of Actinomyces hyovaginalis from sheep and comparison with isolates obtained from pigs

Actinomyces hyovaginalis, an organism initially described from pigs, was recovered from nine sheep and a moufflon. Further strains of A. hyovaginalis were recovered from five samples from pigs over the same period. 16S rRNA sequencing and extensive phenotyping demonstrated high similarity between the ovine and porcine isolates; however differences with respect to erythritol, adonitol and l-arabitol fermentation were detected. Ovine isolates were made from various sample sites including abscesses and highlight the importance of the accurate identification of the various coryneform isolates which affect sheep. A. hyovaginalis can be added to the growing list of coryneforms which can cause disease in sheep including Corynebacterium pseudotuberculosis, Trueperella pyogenes and Arcanobacterium pluranimalium.

Isolation from a sheep of an attaching and effacing Escherichia coli O115:H- with a novel combination of virulence factors

Attaching and effacing (AE) lesions were observed in the caecum, proximal colon and rectum of one of four lambs experimentally inoculated at 6 weeks. of age with Escherichia coli O157:H7. However, the attached bacteria did not immunostain with O157-specific antiserum. Subsequent bacteriological analysis of samples from this animal yielded two E. coli O115:H- strains, one from the colon (CO) and one from the rectum (RC), and those bacteria forming the AE lesions were shown to be of the O115 serogroup by immunostaining. The O115:H(-)isolates formed microcolonies and attaching and effacing lesions, as demonstrated by the fluorescence actin staining test, on HEp-2 tissue culture cells. Both isolates were confirmed by PCR to encode the epsilon (epsilon) subtype of intimin. Supernates of both O115:H- isolates induced cytopathic effects on Vero cell monolayers, and PCR analysis verified that both isolates encoded EAST1, CNF1 and CNF2 toxins but not Shiga-like toxins. Both isolates harboured similar sized plasmids but-PCR analysis indicated that only one of the O115:H- isolates (CO) possessed the plasmid-associated virulence determinants ehxA and etpD. Neither strain possessed the espP, katP or bfpA plasmid-associated virulence determinants. These E. coli O115:H- strains exhibited a novel combination of virulence determinants and are the first isolates found to possess both CNF1 and CNF2.

Isolation of recombinant antibodies against EspA and intimin of Escherichia coli O157:H7

Intimin, Tir, and EspA proteins are expressed by attaching-effacing Escherichia coli, which include enteropathogenic and enterohemorrhagic E. coli pathotypes. EspA proteins are part of the type three secretion system needle complex that delivers Tir to the host epithelial cell, while surface arrayed intimin docks the bacterium to the translocated Tir. This intimate attachment leads to attaching and effacing lesions. Recombinant forms of these effector proteins from enterohemorrhagic E. coli O157:H7 were produced by using E. coli expression vectors. Binding of intimin and Tir fragments in enzyme-linked immunosorbent assay (ELISAs) demonstrated the interaction of intimin fragments containing the C-terminal 282 or 188 amino acids to a Tir fragment containing amino acid residues 258 to 361. Recombinant intimin and EspA proteins were used to elicit immune responses in rabbits and immune phage-display antibody libraries were produced. Screening of these immune libraries by conventional phage-antibody panning and colony filter screening produced a panel of antibodies with specificity for EspA or intimin. Antibodies recognizing different C-terminal epitopes on intimin bound specifically to the gamma intimin of O157:H7 and not to other classes of intimin. Antibodies recognizing EspA from E. coli O157 also recognized the protein from the eae-deficient O157 mutant DM3 and from E. coli O111. Anti-intimin antibodies were also produced as fusion proteins coupled to the reporter molecule alkaline phosphatase, allowing the one-step detection of gamma intimin. The isolated recombinant monoclonal antibodies were functional in a range of assay formats, including ELISA, Western blotting, and dot blots, thus demonstrating their diagnostic potential.