Copper uptake and translocation in chicory (Cichorium intybus L. cv Grasslands Puna) and tomato (Lycopersicon esculentum Mill. cv Rondy) plants grown in NFT system. II. The role of nicotianamine and histidine in xylem sap copper transport

The effect of rooting media Cu concentration (0.05–20 mg Cu L^-1) on amino acid concentrations and copper speciation in the xylem sap of chicory and tomato plants was measured using 6 week old plants grown in a nutrient film technique system (NFT). Irrespective of the Cu concentration in the nutrient solutions, more than 99.68% and 99.74% of total Cu in tomato and chicory xylem sap was in a bound form. When exposed to high Cu concentrations in the rooting media, amino acid concentrations in the sap increased. Relative to other amino acids, the concentrations of glutamine (Gln), histidine (His), asparagine (Asn), valine (Val), nicotianamine (NA) and proline (Pro) in tomato xylem saps, and His, γ-aminobutyric acid (Gaba), glutamic acid (Glu), leucine (Leu), NA and phenylalanine (Phe) in chicory xylem saps showed the greatest increases. The data indicate that induced synthesis of some free amino acids as a specific and proportional response to Cu treatment. For a single complexation amino acid, the solution Cu²⁺concentration vs pH titration curve for NA at 0.06–0.07 mM was most similar, closely followed by His at 0.5–0.6 mM, to the solution Cu²⁺concentration behaviour in both tomato and chicory xylem sap. It is concluded that increased Cu concentrations in the rooting media induced selective synthesis of certain amino acid which include NA, His, Asn and Gln which have high stability constants with Cu. NA and His have the highest binding constants for Cu and the concentrations of NA and His in chicory and tomato xylem saps can account for all the bound Cu carried in the sap. This revised version was published online in June 2006 with corrections to the Cover Date.     

Accommodating dynamic oceanographic processes and pelagic biodiversity in marine conservation planning

Pelagic ecosystems support a significant and vital component of the ocean's productivity and biodiversity. They are also heavily exploited and, as a result, are the focus of numerous spatial planning initiatives. Over the past decade, there has been increasing enthusiasm for protected areas as a tool for pelagic conservation, however, few have been implemented. Here we demonstrate an approach to plan protected areas that address the physical and biological dynamics typical of the pelagic realm. Specifically, we provide an example of an approach to planning protected areas that integrates pelagic and benthic conservation in the southern Benguela and Agulhas Bank ecosystems off South Africa. Our aim was to represent species of importance to fisheries and species of conservation concern within protected areas. In addition to representation, we ensured that protected areas were designed to consider pelagic dynamics, characterized from time-series data on key oceanographic processes, together with data on the abundance of small pelagic fishes. We found that, to have the highest likelihood of reaching conservation targets, protected area selection should be based on time-specific data rather than data averaged across time. More generally, we argue that innovative methods are needed to conserve ephemeral and dynamic pelagic biodiversity.     

The cover of living and dead corals from airborne remote sensing

Trends in coral cover are widely used to indicate the health of coral reefs but are costly to obtain from field survey over large areas. In situ studies of reflected spectra at the coral surface show that living and recently dead colonies can be distinguished. Here, we investigate whether such spectral differences can be detected using an airborne remote sensing instrument. The Compact Airborne Spectrographic Imager (Itres Research Ltd, Canada) was flown in two configurations: 10 spectral bands with 1-m² pixels and 6 spectral bands with 0.25-m² pixels. First, we show that an instrument with 10 spectral bands possesses adequate spectral resolution to distinguish living Porites, living Pocillopora spp., partially dead Porites, recently dead Porites (total colony mortality within 6 months), old dead (>6 months) Porites, Halimeda spp., and coralline red algae when there is no water column to confuse spectra. All substrata were distinguished using fourth-order spectral derivatives around 538 nm and 562 nm. Then, at a shallow site (Tivaru) at Rangiroa Atoll, Tuamotu Archipelago (French Polynesia), we show that live and dead coral can be distinguished from the air to a depth of at least 4 m using first- and fourth-order spectral derivatives between 562–580 nm. However, partially dead and recently dead Porites colonies could not be distinguished from an airborne platform. Spectral differences among substrata are then exploited to predict the cover of reef substrata in ten 25-m² plots at nearby Motu Nuhi (max depth 8 m). The actual cover in these plots was determined in situ using quadrats with a 0.01-m² grid. Considerable disparity occurred between field and image-based measures of substrate cover within individual 25-m² quadrats. At this small scale, disparity, measured as the absolute difference in cover between field and remote-sensing methods, reached 25% in some substrata but was always less than 10% for living coral (99% of which consisted of Porites spp.). At the scale of the reef (all ten 25-m² quadrats), however, disparities in percent cover between imagery and field data were less than 10% for all substrata and extremely low for some classes (e.g. <3% for living Porites, recently dead Porites and Halimeda). The least accurately estimated substrata were sand and coralline red algae, which were overestimated by absolute values 7.9% and 6.6%, respectively. The precision of sampling was similar for field and remote-sensing methods: field methods required 19 plots to detect a 10% difference in coral cover among three reefs with a statistical power of 95%. Remote-sensing methods required 21 plots. However, it took 1 h to acquire imagery over 92,500 m² of reef, which represents 3,700 plots of 25 m² each, compared with 3 days to survey 10 such plots underwater. There were no significant differences in accuracy between 1-m² and 0.25-m² image resolutions, suggesting that the advantage of using smaller pixels is offset by reduced spectral information and an increase in noise (noise was observed to be 1.6–1.8 times greater in 0.25-m² pixels). We show that airborne remote sensing can be used to monitor coral and algal cover over large areas, providing that water is shallow and clear, and that brown fleshy macroalgae are scarce, that depth is known independently (e.g. from sonar survey).     

Estimating seasonal and annual carbon inputs,and root decomposition rates in a temperate pasture following field 14C pulse-labelling

Using a ¹⁴C pulse-labelling technique, we studied the seasonal changes in assimilation and partitioning of photoassimilated C in the plant–root–soil components of a temperate pasture. Pasture and soil samples were taken after 4-h, and 35-day chase periods, to examine these seasonal ¹⁴C fluxes. Total C and ¹⁴C were determined in the shoot, root and soil system. The amounts of C translocated annually to roots and soil were also estimated from the seasonal ¹⁴C distribution and pasture growth. The in situ field decomposition of newly formed roots during different seasons, also using ¹⁴C-labelling, was studied for one year in undisturbed rhizosphere soil. The ¹⁴C-labelled roots were sampled five times and decomposition rates were calculated assuming first-order decomposition.Annual pasture production at the site was 16 020 kg DM ha^–1, and pasture growth varied with season being highest (75–79 kg ha^–1 d^–1) in spring and lowest (18–20 kg ha^–1 d^–1) in winter. The above- and below-ground partitioning of ¹⁴C also varied with the season. The respiratory ¹⁴C–CO₂ losses, calculated as the difference between the total amounts of ¹⁴C recovered in the soil-plant system at 4 h and 35 days, were high (66–70%) during the summer, autumn and winter season, and low (37–39%) during the spring and late-spring season. Pasture plants partitioned more C below-ground during spring compared with summer, autumn and winter seasons. Overall, at this high fertility dairy pasture site, 18 220 kg C/ha was respired, 6490 kg remained above-ground in the shoot, and 6820 kg was translocated to roots and 1320 kg to soil. Root decomposition rate constant (k) differed widely with the season and were the highest for the autumn roots. The half-life was highest (111 days) for autumn roots and lowest (64 days) for spring roots. About one-third of the root label measured in the spring season disappeared in the first 5 weeks after the initial 35 Day of allocation period. The late spring, summer, late summer and winter roots had intermediate half-lives (88–94 days). These results indicate that seasonal changes in root growth and decomposition should be accounted for to give a better quantification of root turnover.     

Codon catalog usage and the genome hypothesis.

Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind of genome, appears to possess a "system" for choosing between codons. Frameshift genes, however, have widely different choice strategies from normal genes. Our work indicates that the main factors distinguishing between mRNA sequences relate to choices among degenerate bases. These systematic third base choices can therefore be used to establish a new kind of genetic distance, which reflects differences in coding strategy. The choice patterns we find seem compatible with the idea that the genome and not the individual gene is the unit of selection. Each gene in a genome tends to conform to its species' usage of the codon catalog; this is our genome hypothesis.     

Working of the genetic code

The genetic code is used differently by different kinds of species. Each type of genome has a particular coding strategy, that is, choices among degenerate bases are consistently similar for all genes therein. This uniformity in the selection between degenerate bases within each taxonomic group has been discovered by applying new methods to the study of coding variability. It is now possible to calculate relative distances between genomes, or genome types, based on use of the codon catalog by the mRNAs therein.