Functional significance of shade-induced leaf senescence in dense canopies: an experimental test using transgenic tobacco

Canopy photosynthesis models have predicted an optimal leaf area index (LAI; leaf area per unit surface area) and leaf nitrogen distribution at which whole-plant carbon gain per unit N is maximized. In this study we experimentally tested these models, using transgenic P(SAG12)-IPT tobacco (SAG; Nicotiana tabacum L.) plants with delayed leaf senescence and therefore a greater LAI and more uniform N distribution than the wild type (WT). In a competition experiment, the increased density of surrounding WT plants caused a greater reduction in dry mass of mature SAG target plants than in that of WT target plants, indicating negative effects of delayed leaf senescence on performance at high canopy density. Vegetative SAG plants achieved a lower calculated daily carbon gain than competing WT plants because the former retained leaves with a negative carbon gain in the shaded, lower part of the canopy. Sensitivity analyses showed that the carbon gain of SAG plants would increase if these lower leaves were shed and the N reallocated from these leaves were used to form additional leaf area at the canopy top. This strategy, which is adopted by the WT, is most advantageous because it results in the shading of competing neighbors.     

A general approach for detecting folding intermediates from steady-state and time-resolved fluorescence of single-tryptophan-containing proteins

During denaturant-induced equilibrium (un)folding of wild-type apoflavodoxin from Azotobacter vinelandii, a molten globule-like folding intermediate is formed. This wild-type protein contains three tryptophans. In this study, we use a general approach to analyze time-resolved fluorescence and steady-state fluorescence data that are obtained upon denaturant-induced unfolding of a single-tryptophan-containing variant of apoflavodoxin [i.e., W74/F128/F167 (WFF) apoflavodoxin]. The experimental data are assembled in matrices, and subsequent singular-value decomposition of these matrices (i.e., based on either steady-state or time-resolved fluorescence data) shows the presence of three significant, and independent, components. Consequently, to further analyze the denaturation trajectories, we use a three-state protein folding model in which a folding intermediate and native and unfolded protein molecules take part. Using a global analysis procedure, we determine the relative concentrations of the species involved and show that the stability of WFF apoflavodoxin against global unfolding is ～4.1 kcal/mol. Analysis of time-resolved anisotropy data of WFF apoflavodoxin unfolding reveals the remarkable observation that W74 is equally well fixed within both the native protein and the molten globule-like folding intermediate. Slight differences between the direct environments of W74 in the folding intermediate and native protein cause different rotameric populations of the indole in both folding species as fluorescence lifetime analysis reveals. Importantly, thermodynamic analyses of the spectral denaturation trajectories of the double-tryptophan-containing protein variants WWF apoflavodoxin and WFW apoflavodoxin show that these variants are significantly more stable (5.9 kcal/mol and 6.8 kcal/mol, respectively) than WFF apoflavodoxin (4.1 kcal/mol) Hence, tryptophan residues contribute considerably to the 10.5 kcal/mol thermodynamic stability of native wild-type apoflavodoxin.     

Effects of grazing by fish and waterfowl on the biomass and species composition of submerged macrophytes

Biomanipulation improved water transparency of Lake Zwemlust (The Netherlands) drastically. Before biomanipulation no submerged vegetation was present in the lake, but in summer 1987, directly after the measure, submerged macrophyte stands developed following a clear-water phase caused by high zooplankton grazing in spring. During the summers of 1988 and 1989 Elodea nuttallii was the most dominant species and reached a high biomass, but in the summers of 1990 and 1991 Ceratophyllum demersum became dominant. The total macrophyte biomass decreased in 1990 and 1991. In 1992 and 1993 C. demersum and E. nuttallii were nearly absent and Potamogeton berchtholdii became the dominant species, declining to very low abundance during late summer. Successively algal blooms appeared in autumn of those years reaching chlorophyll-a concentrations between 60–130 µg l^–1. However, in experimental cages placed on the lake bottom, serving as exclosures for larger fish and birds, E. nuttallii still reached a high abundance during 1992 and 1993. Herbivory by coots (Fulica atra) in autumn/winter, and by rudd (Scardinius erythrophthalmus) in summer, most probably caused the decrease in total abundance of macrophytes and the shift in species composition.     

Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes

Background

Array-based comparative genomic hybridization (aCGH) is a high-throughput method for measuring genome-wide DNA copy number changes. Current aCGH methods have limited resolution, sensitivity and reproducibility. Microarrays for aCGH are available only for a few organisms and combination of aCGH data with expression data is cumbersome.

Results

We present a novel method of using commercial oligonucleotide expression microarrays for aCGH, enabling DNA copy number measurements and expression profiles to be combined using the same platform. This method yields aCGH data from genomic DNA without complexity reduction at a median resolution of approximately 17,500 base pairs. Due to the well-defined nature of oligonucleotide probes, DNA amplification and deletion can be defined at the level of individual genes and can easily be combined with gene expression data.

Conclusion

A novel method of gene resolution analysis of copy number variation (graCNV) yields high-resolution maps of DNA copy number changes and is applicable to a broad range of organisms for which commercial oligonucleotide expression microarrays are available. Due to the standardization of oligonucleotide microarrays, graCNV results can reliably be compared between laboratories and can easily be combined with gene expression data using the same platform.     

Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution

Accurate species identification often relies on public repositories to compare the barcode sequences of the investigated individual(s) with taxonomically assigned sequences. However, the accuracy of identifications in public repositories is often questionable, and the names originally given are rarely updated. For instance, species of the Sea Lettuce (Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) are frequently misidentified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding unreliable. We DNA barcoded 295 individual distromatic foliose strains of Ulva from the North-East Atlantic for three loci (rbcL, tufA, ITS1). Seven distinct species were found, and we compared our results with all worldwide Ulva spp. sequences present in the NCBI database for the three barcodes rbcL, tufA and the ITS1. Our results demonstrate a large degree of species misidentification, where we estimate that 24%–32% of the entries pertaining to foliose species are misannotated and provide an exhaustive list of NCBI sequences reannotations. An analysis of the global distribution of registered samples from foliose species also indicates possible geographical isolation for some species, and the absence of U. lactuca from Northern Europe. We extended our analytical framework to three other genera, Fucus, Porphyra and Pyropia and also identified erroneously labelled accessions and possibly new synonymies, albeit less than for Ulva spp. Altogether, exhaustive taxonomic clarification by aggregation of a library of barcode sequences highlights misannotations and delivers an improved representation of species diversity and distribution.     

Unearthing the transition rates between photoreceptor conformers

Background

Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. In many cases experimental limitations mean that some enzymatic rates cannot be measured directly, requiring mathematical algorithms to estimate them. Here, we describe a methodology that calculates rates at which light-regulated proteins switch between conformational states. We focus our analysis on the phytochrome family of photoreceptors found in cyanobacteria, plants and many optogenetic tools. Phytochrome proteins change between active (P _A ) and inactive (P _I ) states at rates that are proportional to photoconversion cross-sections and influenced by light quality, light intensity, thermal reactions and dimerisation. This work presents a method that can accurately calculate these photoconversion cross-sections in the presence of multiple non-light regulated reactions.

Results

Our approach to calculating the photoconversion cross-sections comprises three steps: i) calculate the thermal reversion reaction rate(s); ii) develop search spaces from which all possible sets of photoconversion cross-sections exist, and; iii) estimate extinction coefficients that describe our absorption spectra. We confirm that the presented approach yields accurate results through the use of simulated test cases. Our test cases were further expanded to more realistic scenarios where noise, multiple thermal reactions and dimerisation are considered. Finally, we present the photoconversion cross-sections of an Arabidopsis phyB N-terminal fragment commonly used in optogenetic tools.

Conclusions

The calculation of photoconversion cross-sections has implications for both photoreceptor and synthetic biologists. Our method allows, for the first time, direct comparisons of photoconversion cross-sections and response speeds of photoreceptors in different cellular environments and synthetic tools. Due to the generality of our procedure, as shown by the application to multiple test cases, the photoconversion cross-sections and quantum yields of any photoreceptor might now, in principle, be obtained.

     

Respiratory energy requirements of roots vary with the potential growth rate of a plant species

The rates of growth, net rate of nitrate uptake and root respiration of 24 wild species were compared under conditions of optimum nutrient supply. The relative growth rate (RGR)of the roots of these species varied between 110 and 370 mg g^-1 day^-1 and the net rate of nitrate uptake between 1 and 7 mmol (g root dry weight)^-1 day^-1. The rate of root respiration was positively correlated with the RGR of the roots. Root respiration was also calculated from the measured rate of growth and nitrate uptake, using previously determined values for the costs of maintenance, growth and ion uptake of two slow-growing species. The calculated rate of respiration was slightly lower than the measured one for slow-growing species, but twice as high as measured rates for rapid-growing species. This discrepancy was not due to a relatively smaller electron flow through the alternative pathway and, consequently, a more efficient ATP production in the fast-growing species. Neither could variation in specific costs for root growth or maintenance explain these differences. Therefore, we conclude that fast-growing species have lower specific respiratory costs for ion uptake than slow-growing ones. Due partly to these lower specific costs of nutrient uptake, the fraction of respiration that rapid-growing species spend on anion uptake is lower than that of slow-growing species, in spite of the much higher rate of ion uptake of the fast-growing ones.