Dual metabolomics: A novel approach to understanding plant–pathogen interactions

One of the most well-characterised plant pathogenic interactions involves Arabidopsis thaliana and the bacteria Pseudomonas syringae pathovar tomato (Pst). The standard Pst inoculation procedure involves infiltration of large populations of bacteria into plant leaves which means that metabolite changes cannot be readily assigned to the host or pathogen. A plant cell–pathogen co-culture based approach has been developed where the plant and pathogen cells are separated after 12 h of co-culture via differential filtering and centrifugation. Fourier transform infrared (FT-IR) spectroscopy was employed to assess the intracellular metabolomes (metabolic fingerprints) of both host and pathogen and their extruded (extracellular) metabolites (metabolic footprints) under conditions relevant to disease and resistance. We propose that this system will enable the metabolomic profiling of the separated host and pathogen (i.e. ‘dual metabolomics’) and will facilitate the modelling of reciprocal responses.     

Varying foraging patterns in response to competition? A multicolony approach in a generalist seabird

Reducing resource competition is a crucial requirement for colonial seabirds to ensure adequate self‐ and chick‐provisioning during breeding season. Spatial segregation is a common avoidance strategy among and within species from neighboring breeding colonies. We determined whether the foraging behaviors of incubating lesser black‐backed gulls (Larus fuscus) differed between six colonies varying in size and distance to mainland, and whether any differences could be related to the foraging habitats visited. Seventy‐nine incubating individuals from six study colonies along the German North Sea coast were equipped with GPS data loggers in multiple years. Dietary information was gained by sampling food pellets, and blood samples were taken for stable isotope analyses. Foraging patterns clearly differed among and within colonies. Foraging range increased with increasing colony size and decreased with increasing colony distance from the mainland, although the latter might be due to the inclusion of the only offshore colony. Gulls from larger colonies with consequently greater density‐dependent competition were more likely to forage at land instead of at sea. The diets of the gulls from the colonies furthest from each other differed, while the diets from the other colonies overlapped with each other. The spatial segregation and dietary similarities suggest that lesser black‐backed gulls foraged at different sites and utilized two main habitat types, although these were similar across foraging areas for all colonies except the single offshore island. The avoidance of intraspecific competition results in colony‐specific foraging patterns, potentially causing more intensive utilization of terrestrial foraging sites, which may offer more predictable and easily available foraging compared with the marine environment.     

CCN2/decorin interactions: a novel approach to combating fibrosis?

CCN2 (connective tissue growth factor, CTGF), a member of the CCN family is overexpressed in fibrotic disease and is essential for the development of experimental fibrosis. Drugs targeting CCN2 action may therefore prove to be useful anti-fibrotic approaches. CCN2 acts via integrins and heparan sulfate-containing proteoglycans (HSPGs). In a recent study, Vial and colleagues (2011) show that decorin can bind CCN2. A peptide corresponding to the leucine rich repeats peptide 12 region of decorin can neutralize CCN2-mediated activity on C2C12 cells in vitro. Thus it is conceivable that this peptide could be used in the future as a novel antifibrotic approach.     

Non-statistical isotope fractionation as a novel “retro-biosynthetic” approach to understanding alkaloid metabolic pathways

During the biosynthesis of natural products, isotope fractionation occurs due to the selectivity of enzymes for the heavier or lighter isotopomers. As only some of the positions in the molecule are implicated in a given reaction mechanism, position-specific fractionation occurs. Thus, the position-specific ¹³C/¹²C ratios in these compounds can be related to their known precursors and to the known isotope effects of enzymes involved in their biosynthesis, or similar reaction mechanisms. This can be accessed by isotope ratio monitoring NMR spectrometry. In this short review, how isotope fractionation occurs and when it is manifest is described. Then, the way that ¹³C NMR spectrometry has been applied to study certain aspects of the biosynthesis of the solanaceous alkaloids S-(−)-nicotine and tropine is outlined. Notably, it is shown how similar isotope fractionation is found in the steps of the pathway to the common intermediate, N-methyl-Δ¹-pyrrolinium, but that in the moieties derived from different origins no such similarity is found, the isotopic composition of these atoms reflecting their specific metabolic ancestry. In a second example, tramadol, it is shown how this technique can be used in retro-biosynthesis to give direction as to what precursors and pathway intermediates are probable. It is shown how the observed fractionation in the site-specific ¹³C/¹²C ratios can be effectively explained by known metabolism and the properties of enzymes proposed for the pathway. Furthermore, it can give indications of possible mechanisms of those enzymes that are as yet to be described for a number of key steps.     

Photosynthetic Activity in Seed Wings of Dipterocarpaceae in a Masting Year: Does Wing Photosynthesis Contribute to Reproduction?

The photosynthetic rate of seed wings developed from sepals was compared with the leaf photosynthetic rate in nine dipterocarp tree species (Dipterocarpus pachyphyllus, Dryobalanops aromatica, Dryobalanops lanceolata, Shorea beccariana, Shorea ferruginea, Shorea macroptera ssp. bailonii, Shorea macroptera ssp. macropterifolia, Shorea pilosa, and Vatica spp.). The wings showed positive photosynthetic activity, but at much lower rates than in the leaves. The daily CO₂ uptake of wings showed slightly negative values in diurnal gas exchange measurements, even in D. aromatica that showed the highest photosynthetic capacity of all nine species. This low photosynthetic rate in the wings may be the result of low nitrogen and chlorophyll contents in the wing compared with leaves. However, the wings had a higher C/N ratio than leaves, and were thicker. Hence, dipterocarp wings have physical strength and defence against herbivores as higher priorities than photosynthetic activity.     

Are clinical parameters sufficient to model gait patterns in patients with cerebral palsy using a multilinear approach?

The aim of this study was to evaluate whether clinical parameters are sufficient using, a multilinear regression model, to reproduce the sagittal plane joint angles (hip, knee, and ankle) in cerebral palsy gait. A total of 154 patients were included. The two legs were considered (308 observations). Thirty-six clinical parameters were used as regressors (range of motion, muscle strength, and spasticity of the lower). From the clinical gait analysis, the joint angles of the sagittal plane were selected. Results showed that clinical parameter does not provide sufficient information to recover joint angles and/or that the multilinear regression model is not an appropriate solution.     

When to approach novel prey cues? Social learning strategies in frog-eating bats

Animals can use different sources of information when making decisions. Foraging animals often have access to both self-acquired and socially acquired information about prey. The fringe-lipped bat, Trachops cirrhosus, hunts frogs by approaching the calls that frogs produce to attract mates. We examined how the reliability of self-acquired prey cues affects social learning of novel prey cues. We trained bats to associate an artificial acoustic cue (mobile phone ringtone) with food rewards. Bats were assigned to treatments in which the trained cue was either an unreliable indicator of reward (rewarded 50% of the presentations) or a reliable indicator (rewarded 100% of the presentations), and they were exposed to a conspecific tutor foraging on a reliable (rewarded 100%) novel cue or to the novel cue with no tutor. Bats whose trained cue was unreliable and who had a tutor were significantly more likely to preferentially approach the novel cue when compared with bats whose trained cue was reliable, and to bats that had no tutor. Reliability of self-acquired prey cues therefore affects social learning of novel prey cues by frog-eating bats. Examining when animals use social information to learn about novel prey is key to understanding the social transmission of foraging innovations.     

Presence of a dinucleotide fold in cholera toxin: Possible approach to chemoprophylaxis?

The ADP-ribosyltransferase activity of the A₁. subunit of cholera toxin is specifically inhibited by the dye cibacron blue 3GA. The presence of a ‘dinucleotide fold’ in the A₁ subunit is thus established for the first time. This specific inhibition observed in vitro is successfully exploited in vivo for the inhibition of the diarrheal response brought out by the pure toxin in the rabbit ileal-loop test.     

Plato: a genetic algorithm approach to run-time reconfiguration in?autonomic computing systems

Increasingly, applications need to be able to self-reconfigure in response to changing requirements and environmental conditions. Autonomic computing has been proposed as a means for automating software maintenance tasks. As the complexity of adaptive and autonomic systems grows, designing and managing the set of reconfiguration rules becomes increasingly challenging and may produce inconsistencies. This paper proposes an approach to leverage genetic algorithms in the decision-making process of an autonomic system. This approach enables a system to dynamically evolve target reconfigurations at run time that balance tradeoffs between functional and non-functional requirements in response to changing requirements and environmental conditions. A key feature of this approach is incorporating system and environmental monitoring information into the genetic algorithm such that specific changes in the environment automatically drive the evolutionary process towards new viable solutions. We have applied this genetic-algorithm based approach to the dynamic reconfiguration of a collection of remote data mirrors, demonstrating an effective decision-making method for diffusing data and minimizing operational costs while maximizing data reliability and network performance, even in the presence of link failures.     

Can the narrow red bands of dragonflies be used to perceive wing interference patterns?

Despite numerous studies of selection on position and number of spectral vision bands, explanations to the function of narrow spectral bands are lacking. We investigate dragonflies (Odonata), which have the narrowest spectral bands reported, in order to investigate what features these narrow spectral bands may be used to perceive. We address whether it is likely that narrow red bands can be used to identify conspecifics by the optical signature from wing interference patterns (WIPs). We investigate the optical signatures of Odonata wings using hyperspectral imaging, laser profiling, ellipsometry, polarimetric modulation spectroscopy, and laser radar experiments. Based on results, we estimate the prospects for Odonata perception of WIPs to identify conspecifics in the spectral, spatial, intensity, polarization, angular, and temporal domains. We find six lines of evidence consistent with an ability to perceive WIPs. First, the wing membrane thickness of the studied Odonata is 2.3 μm, coinciding with the maximal thickness perceivable by the reported bandwidth. Second, flat wings imply that WIPs persist from whole wings, which can be seen at a distance. Third, WIPs constitute a major brightness in the visual environment only second after the solar disk. Fourth, WIPs exhibit high degree of polarization and polarization vision coincides with frontal narrow red bands in Odonata. Fifth, the angular light incidence on the Odonata composite eye provides all prerequisites for direct assessment of the refractive index which is associated with age. Sixth, WIPs from conspecifics in flight make a significant contribution even to the fundamental wingbeat frequency within the flicker fusion bandwidth of Odonata vision. We conclude that it is likely that WIPs can be perceived by the narrow red bands found in some Odonata species and propose future behavioral and electrophysiological tests of this hypothesis.     

Kalisomes in corals: a novel KCl concentrating organelle?

Large membrane-bound inclusions were clearly visible within the gastrodermis and lipid-containing cells of planulae and settled larvae of the zooxanthellate coral, Pocillopora damicornis after fixation or freeze-substitution. We suggest that these inclusions may be a novel potassium (kalium) chloride concentrating organelle, for which we propose the name kalisome. The inclusions were more abundant in settled larvae than in planulae and were not present in mature polyps. In planulae of the azooxanthellate coral, Dendrophyllia sp. these inclusions were extremely rare. Quantitative X-ray microanalysis of freeze-substituted preparations showed that the inclusions in P. damicornis settled larvae contained very high, positively correlated, concentrations of K (2.5 mol x kg(-1)) and Cl (2.5 mol x kg(-1)). Lower concentrations of both K (1.2 mol x kg(-1)) and Cl (1.3 mol x kg(-1)) were detected in P. damicornis planulae, yet higher concentrations were measured in Dendrophyllia planulae (K=6.0 mol x kg(-1); Cl=5.1 mol x kg(-1)). No significant (P>0.05) differences in concentration were observed between inclusions in freeze-substituted and freeze-dried sections of planulae. Symbiotic algae (zooxanthellae) in P. damicornis planulae and settled larvae also contained deposits with high levels of K and Cl, but these were not positively correlated and no structures associated with them were retained by fixation. Significant (P<0.05) concentration differences were also observed between deposits in freeze-substituted and freeze-dried sections. However, similar to 'kalisomes,' zooxanthellae deposits were more abundant in settled larvae than planulae and absent in mature polyps. Higher concentrations of K and Cl were also detected in settled larvae (K=0.7 mol x kg(-1); Cl=1.1 mol x kg(-1)) in comparison to planulae (K=0.4 mol x kg(-1); Cl=0.5 mol x kg(-1)).     

Plant-based manipulation of nitrification in soil: a new approach to managing N loss?

Much work has gone into the management of nitrification through applications of chemicals known to inhibit enzyme function in nitrifiers with indifferent outcomes when tested in the field. Much less attention has been focused on the capacity of plants to modify nitrification in situ. Subbarao and coworkers in a series of neat and elegant studies have confirmed that a tropical grass species, Brachiaria humidicola, produces chemicals that inhibit nitrification in soil. Critical to the work was the use of a Nitrosomonas europaea strain (nitrifying bacteria) that had been specifically constructed to produce bioluminescence due to the expression of “luxAB’ genes during nitrification. This application led to the development of an assay that enabled the suppression of nitrification to be assessed directly. They produce evidence that the production of chemicals by Brachiaria humidicola roots, described as biological nitrification inhibitors (BNIs), is under plant control. However, the triggers or molecular controls for BNI production have yet to be ascertained. Examination of the capacity of major crops to produce BNIs, including wheat (Triticum aestivum), barley (Hordeum vulgare), rice (Oryza sativa) and maize (Zea mays) indicate that these do not have this capacity. Work is needed on wild relatives of these crops and the major temperate grass species such as Lolium perenne to determine whether these have the capacity to produce BNIs with an aim to introduce this capacity into domesticated lines. The work of Subbarao et al. highlights how molecular biology can be used to introduce traits into micro-organisms responsible for key soil N transformations in a way that facilitates analysis of the interaction between plants and the soil environment so crucial to their growth and survival.     

Histamine in cardiac sympathetic ganglia: a novel neurotransmitter?

Although ganglia in the heart are well known to be cholinergic, many other neurotransmitters and neuropeptides also influence (and are produced in) cardiac neurons, including adrenergic and purinergic compounds. Recently, histamine was suggested as a possible neurotransmitter in cardiac tissue. Although histamine does elicit many effects in the heart, does it stand up to rigorous scrutiny and fulfill certain criteria that are used to define neurotransmitters?     

Modelling neurodegenerative diseases in Drosophila: a fruitful approach?

Human neurodegenerative diseases are characterized by the progressive loss of specific neuronal populations, resulting in substantial disability and early death. The identification of causative single-gene mutations in families with inherited neurodegenerative disorders has facilitated the modelling of these diseases in experimental organisms, including the fruitfly Drosophila melanogaster. Many neurodegenerative diseases have now been successfully modelled in Drosophila, and genetic analysis is under way in each of these models. Using fruitfly genetics to define the molecular pathways that underlie the neurodegenerative process is likely to improve substantially our understanding of the pathogenesis of the human diseases, and to provide new therapeutic targets.     

Inhibition of farnesyltransferase: a rational approach to treat cancer?

This article presents in brief the development of farnesyltransferase inhibitors (FTIs) and their preclinical and clinical status. In this review the mechanism of action of FTIs is discussed and their selectivity issue towards tumor cells is also addressed. The significant efficacy of FTIs as single or combined agents in preclinical studies stands in contrast with only moderate effects in Clinical Phase II-III studies. This suggests that there is a need to further explore and understand the complex mechanism of action of FTIs and their interaction with cytotoxic agents.