Root exudation from Hordeum vulgare in response to localized nitrate supply

Root proliferation as a response to exploit zones of nutrient enrichment in soil has been demonstrated for a wide range of plant species. However, the effectiveness of this as a strategy to acquire nutrients is also dependent on interactions with the soil microbial community. Specifically, C-flow from roots modifies microbial activity and probably the balance between nutrient mineralization and immobilization processes in the rhizosphere. In this study, near-natural abundance 13C-labelling and gene-reporter methods were applied to determine the effects of uneven nitrate supply to roots of Hordeum vulgare on assimilate partitioning and root exudation. Plants were initially grown in uniform nitrate supply in split-root, sand microcosms after which one treatment continued to receive uniform supply, and the other received nitrate to one root compartment only. At the time of imposing the treatments, the CO2 supplied to the plants was switched to a cylinder source, providing a distinct delta13C-signature and allowing the fate of new assimilate within the plants to be determined. The labelling approach allowed quantification of the expected preferential allocation of new C-assimilate to roots in enriched nitrate, prior to any measurable effect on whole biomass or root architecture. Biosensor (lux-marked Pseudomonas fluorescens 10586 pUCD607) bioluminescence, quantified spatially by CCD imaging, demonstrated that root exudation was significantly increased for roots in enriched nitrate. This response of root exudation, being primarily associated with root apices and concurrent with enhanced assimilate supply, strongly suggests that C-flow from roots is an integral component of the proliferation response to nitrate.     

Effect of sediment type on microphytobenthos vertical distribution: Modelling the productive biomass and improving ground truth measurements

Intertidal flats are frequently colonised by microphytobenthos (MPB) assemblages that form transient biofilms at the sediment surface which are responsible for large fractions of estuarine primary production. The large spatio-temporal variability in MPB biomass distribution in concert with the fact that tidal flats can cover many km² makes the use of remote sensing particularly useful in assessing MPB distribution. Water content, sediment type and MPB vertical migration are variables that affect the relationship between ground truth measurements and remote sensing of benthic chlorophyll. The effect of chlorophyll depth distribution (top 2 mm) on the relationship between benthic chlorophyll and several remote sensing indices (NDVI, PI, R562/R647, derivative indices and PAM fluorescence) was investigated over a 2 year sampling period at 6 sites (Tagus estuary, Portugal). Additionally, the effect of the dark adaptation time required to measure the minimum fluorescence parameter (F₀) was also tested. Sediment type strongly affected MPB depth distribution with muddy sites showing a strong negative exponential decay in chlorophyll with distance from the surface while sandy sites had a homogenous distribution over the same scale (2 mm). Chlorophyll content (mass per unit mass, μg g^− 1) in the top 2 mm was better correlated with remote sensing indices than concentration (mass per unit volume, mg m^− 3), both for NDVI (0.72 vs. 0.45) and for PAM fluorescence (0.70 vs. 0.55). Separating the data by transect increased the correlation values in all situations. A fitted model of chlorophyll depth distribution showed that the effect of asymmetrical chlorophyll depth distribution was stronger on the correlations between chlorophyll concentration and NDVI than on chlorophyll content and NDVI (0.46-2 mm vs. 0.74-125 μm, muddy site) the same was valid for fluorescence (0.66-2 mm vs. 0.92-125 μm, muddy site). Dark adapting the samples for more than 5 min did not result in any significant difference in the relationship between F₀ and chlorophyll a. The residuals from the regression of chlorophyll content on NDVI were positively correlated (0.7) with the mass per unit of mass of sediment < 63 μm and negatively (− 0.6) with chlorophyll concentration, this indicates that if no correction is performed to account for chlorophyll depth distribution both units will be strongly affected by the mass of < 63 μm particles. The results demonstrate that although expressing chlorophyll a as concentration is generally a better option for ground truth measurements care should be taken to account for chlorophyll depth distribution since strong asymmetries within the sampling depth can introduce large errors.     

Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon

Genome duplication is potentially a good source of new genes, but such genes take time to evolve. We have found a group of "duplication-resistant" genes, which have undergone convergent restoration to singleton status following several independent genome duplications. Restoration of duplication-resistant genes to singleton status could be important to long-term survival of a polyploid lineage. Angiosperms show more frequent polyploidization and a higher degree of duplicate gene preservation than other paleopolyploids, making them well-suited to further study of duplication-resistant genes.     

Laccase activity from the fungus Trametes hirsuta using an air-lift bioreactor

AIM: To produce high laccase activities from the white-rot fungus Trametes hirsuta in an in-house air-lift bioreactor (ALB). METHODS AND RESULTS: Trametes hirsuta was grown in a 6-l ALB. A fed-batch strategy with glycerol as an addition resulted in maximum laccase activity of 19,400 U l(-1), which was the highest reported from the fungus. CONCLUSION: The ALB configuration with additional glycerol resulted in high laccase activities. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides useful information on how to produce high concentrations of laccase.     

Structural and mechanistic insights into ras association domains of phospholipase C epsilon

Ras proteins signal to a number of distinct pathways by interacting with diverse effectors. Studies of ras/effector interactions have focused on three classes, Raf kinases, ral guanylnucleotide-exchange factors, and phosphatidylinositol-3-kinases. Here we describe ras interactions with another effector, the recently identified phospholipase C epsilon (PLCepsilon). We solved structures of PLCepsilon RA domains (RA1 and RA2) by NMR and the structure of the RA2/ras complex by X-ray crystallography. Although the similarity between ubiquitin-like folds of RA1 and RA2 proves that they are homologs, only RA2 can bind ras. Some of the features of the RA2/ras interface are unique to PLCepsilon, while the ability to make contacts with both switch I and II regions of ras is shared only with phosphatidylinositol-3-kinase. Studies of PLCepsilon regulation suggest that, in a cellular context, the RA2 domain, in a mode specific to PLCepsilon, has a role in membrane targeting with further regulatory impact on PLC activity.     

Sea ice microbial dynamics over an annual ice cycle in Prydz Bay, Antarctica

Microbial community dynamics within the fast sea ice of Prydz Bay (68°S?78°E) were investigated over an annual cycle at two sites (1 and 3?km offshore) between April and November 2008. There are few long-term sea ice studies, and few that cover the phase of winter darkness when autotrophic processes are curtailed. Mean chlorophyll a concentrations in the ice column ranged between 0.76 and 44.8?μg?L^?1 at the 1-km site (Site 1) and 3.11–144.6?μg?L^?1 at the 3-km site (Site 2). Highest chlorophyll a usually occurred at the base of the ice. Bacterial concentrations ranged between 0.30 and 2.08?×?10⁸?cells?L^?1, heterotrophic nanoflagellates (HNAN) between 0.21?×?10⁵ and 2.98?×?10⁵?cells?L^?1 and phototrophic nanoflagellates (PNAN) 0–1.06?×?10⁵?cells?L^?1. While HNAN occurred throughout the year, PNAN were largely absent in winter. Dinoflagellates were a conspicuous and occasionally an abundant element of the community (maximum 17,460?cells?L^?1), while ciliates were sparse. The bacterial community showed considerable morphological diversity with a dominance of filamentous forms. Bacterial production continued throughout the year ranging between 0 and 22.92?μg?C?L^?1?day^?1 throughout the ice column. Lowest rates occurred between late June and early August. The sea ice sustained an active and diverse microbial community through its annual extent. The data suggest that during winter darkness the microbial community is dominated by heterotrophic processes, sustained by a pool of dissolved organic carbon.     

A computational study of odorant transport and deposition in the canine nasal cavity: implications for olfaction

Olfaction begins when an animal draws odorant-laden air into its nasal cavity by sniffing, thus transporting odorant molecules from the external environment to olfactory receptor neurons (ORNs) in the sensory region of the nose. In the dog and other macrosmatic mammals, ORNs are relegated to a recess in the rear of the nasal cavity that is comprised of a labyrinth of scroll-like airways. Evidence from recent studies suggests that nasal airflow patterns enhance olfactory sensitivity by efficiently delivering odorant molecules to the olfactory recess. Here, we simulate odorant transport and deposition during steady inspiration in an anatomically correct reconstructed model of the canine nasal cavity. Our simulations show that highly soluble odorants are deposited in the front of the olfactory recess along the dorsal meatus and nasal septum, whereas moderately soluble and insoluble odorants are more uniformly deposited throughout the entire olfactory recess. These results demonstrate that odorant deposition patterns correspond with the anatomical organization of ORNs in the olfactory recess. Specifically, ORNs that are sensitive to a particular class of odorants are located in regions where that class of odorants is deposited. The correlation of odorant deposition patterns with the anatomical organization of ORNs may partially explain macrosmia in the dog and other keen-scented species.     

Examination of the distribution of arsenic in hydrated and fresh cowpea roots using two- and three-dimensional techniques

Arsenic (As) is considered to be the environmental contaminant of greatest concern due to its potential accumulation in the food chain and in humans. Using novel synchrotron-based x-ray fluorescence techniques (including sequential computed tomography), short-term solution culture studies were used to examine the spatial distribution of As in hydrated and fresh roots of cowpea (Vigna unguiculata 'Red Caloona') seedlings exposed to 4 or 20 μm arsenate [As(V)] or 4 or 20 μm arsenite. For plants exposed to As(V), the highest concentrations were observed internally at the root apex (meristem), with As also accumulating in the root border cells and at the endodermis. When exposed to arsenite, the endodermis was again a site of accumulation, although no As was observed in border cells. For As(V), subsequent transfer of seedlings to an As-free solution resulted in a decrease in tissue As concentrations, but growth did not improve. These data suggest that, under our experimental conditions, the accumulation of As causes permanent damage to the meristem. In addition, we suggest that root border cells possibly contribute to the plant's ability to tolerate excess As(V) by accumulating high levels of As and limiting its movement into the root.