FLUXNET and modelling the global carbon cycle

Measurements of the net CO₂ flux between terrestrial ecosystems and the atmosphere using the eddy covariance technique have the potential to underpin our interpretation of regional CO₂ source–sink patterns, CO₂ flux responses to forcings, and predictions of the future terrestrial C balance. Information contained in FLUXNET eddy covariance data has multiple uses for the development and application of global carbon models, including evaluation/validation, calibration, process parameterization, and data assimilation. This paper reviews examples of these uses, compares global estimates of the dynamics of the global carbon cycle, and suggests ways of improving the utility of such data for global carbon modelling. Net ecosystem exchange of CO₂ (NEE) predicted by different terrestrial biosphere models compares favourably with FLUXNET observations at diurnal and seasonal timescales. However, complete model validation, particularly over the full annual cycle, requires information on the balance between assimilation and decomposition processes, information not readily available for most FLUXNET sites. Site history, when known, can greatly help constrain the model‐data comparison. Flux measurements made over four vegetation types were used to calibrate the land‐surface scheme of the Goddard Institute for Space Studies global climate model, significantly improving simulated climate and demonstrating the utility of diurnal FLUXNET data for climate modelling. Land‐surface temperatures in many regions cool due to higher canopy conductances and latent heat fluxes, and the spatial distribution of CO₂ uptake provides a significant additional constraint on the realism of simulated surface fluxes. FLUXNET data are used to calibrate a global production efficiency model (PEM). This model is forced by satellite‐measured absorbed radiation and suggests that global net primary production (NPP) increased 6.2% over 1982–1999. Good agreement is found between global trends in NPP estimated by the PEM and a dynamic global vegetation model (DGVM), and between the DGVM and estimates of global NEE derived from a global inversion of atmospheric CO₂ measurements. Combining the PEM, DGVM, and inversion results suggests that CO₂ fertilization is playing a major role in current increases in NPP, with lesser impacts from increasing N deposition and growing season length. Both the PEM and the inversion identify the Amazon basin as a key region for the current net terrestrial CO₂ uptake (i.e. 33% of global NEE), as well as its interannual variability. The inversion's global NEE estimate of −1.2 Pg [C] yr⁻¹ for 1982–1995 is compatible with the PEM‐ and DGVM‐predicted trends in NPP. There is, thus, a convergence in understanding derived from process‐based models, remote‐sensing‐based observations, and inversion of atmospheric data. Future advances in field measurement techniques, including eddy covariance (particularly concerning the problem of night‐time fluxes in dense canopies and of advection or flow distortion over complex terrain), will result in improved constraints on land‐atmosphere CO₂ fluxes and the rigorous attribution of mechanisms to the current terrestrial net CO₂ uptake and its spatial and temporal heterogeneity. Global ecosystem models play a fundamental role in linking information derived from FLUXNET measurements to atmospheric CO₂ variability. A number of recommendations concerning FLUXNET data are made, including a request for more comprehensive site data (particularly historical information), more measurements in undisturbed ecosystems, and the systematic provision of error estimates. The greatest value of current FLUXNET data for global carbon cycle modelling is in evaluating process representations, rather than in providing an unbiased estimate of net CO₂ exchange.     

Bootstrapping phylogenies inferred from rearrangement data

ABSTRACT: Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its support values follow a similar scale and its receiver-operating characteristics are nearly identical, indicating that it provides similar levels of sensitivity and specificity. Thus our assessment method makes it possible to conduct phylogenetic analyses on whole genomes with the same degree of confidence as for analyses on aligned sequences. Extensions to search-based inference methods such as maximum parsimony and maximum likelihood are possible, but remain to be thoroughly tested.     

Effect of melanin concentrating hormone on pigment and adrenal cells in vitro

Highly purified synthetic salmonid melanin concentrating hormone (MCH) and some analogs were investigated for their ability to concentrate the pigment in scale melanophores of the Chinese grass carp, Ctenopharyngodon idellus, to produce melanin dispersion in frog or lizard melanophores and to inhibit alpha-MSH in its action on mouse melanoma and rat adrenal glomerulosa cells in vitro. In the grass carp, MCH produced half-maximal pigment aggregation at 6 X 10(-11) M and its oxidized form at 7 X 10(-11) M. Replacement of the two methionines at position 3 and 6 with norvaline lowered the potency by a factor of 2.7 and with propargylglycine by a factor of about 7. Linear, Cys5,14-Acm-protected MCH was a full agonist of MCH but with a 345-fold lower potency. Iodinated MCH showed similar, low activity. In tetrapods, salmonid MCH and its analogs displayed only marginal pigment dispersion at concentrations greater than 10(-5) M. Alkali-treatment of MCH increased the pigment-dispersing potency by a factor of about 30 whereas the activity for pigment aggregation in the grass carp was destroyed. At high concentrations (10(-6), 10(-5) M) MCH also stimulated tyrosinase activity in B-16 mouse melanoma cells but did not modify the effects of alpha-MSH in this system. By contrast, when tested on rat adrenal glomerulosa cells, salmonid MCH had no effect alone but at a concentration of greater than 10(-10) M it slightly reduced corticosterone production by an alpha-MSH concentration of 10(-7) M. Aldosterone production was not affected and MCH did not influence the response to ACTH.     

The internalization signal in the cytoplasmic tail of lysosomal acid phosphatase consists of the hexapeptide PGYRHV.

Lysosomal acid phosphatase (LAP) is rapidly internalized from the cell surface due to a tyrosine-containing internalization signal in its 19 amino acid cytoplasmic tail. Measuring the internalization of a series of LAP cytoplasmic tail truncation and substitution mutants revealed that the N-terminal 12 amino acids of the cytoplasmic tail are sufficient for rapid endocytosis and that the hexapeptide 411-PGYRHV-416 is the tyrosine-containing internalization signal. Truncation and substitution mutants of amino acid residues following Val416 can prevent internalization even though these residues do not belong to the internalization signal. It was shown recently that part of the LAP cytoplasmic tail peptide corresponding to 410-PPGY-413 forms a well-ordered beta turn structure in solution. Two-dimensional NMR spectroscopy of two modified LAP tail peptides, in which the single tyrosine was substituted either by phenylalanine or by alanine, revealed that the tendency to form a beta turn is reduced by 25% in the phenylalanine-containing peptide and by approximately 50% in the alanine-containing mutant peptide. Our results suggest, that in the short cytoplasmic tail of LAP tyrosine is required for stabilization of the right turn and that the aromatic ring system of the tyrosine residue is a contact point to the putative cytoplasmic receptor.     

Specialty oilseed crops provide an abundant source of pollen for pollinators and beneficial insects

The continuing pollinator crisis is due, in part, to the lack of year‐round floral resources. In intensive farming regions, such as the Upper Midwest (UMW) of the USA, natural and pastoral vegetation largely has been replaced by annual crops such as maize (Zea mays L.), soyabean (Glycine max L.) and wheat (Triticum spp.). Neither the energy (nectar) nor protein (pollen) needs of pollinating and other beneficial insects are being met sufficiently by the new, high‐intensity, agricultural landscape. Several potentially useful oilseed crops can be grown in the UMW, and many of these oilseeds are highly attractive to beneficial insects. Prior research showed that some of these oilseeds produced abundant nectar, but their corresponding values for pollen production are unknown. Accordingly, the aim of our research was to document pollen (and protein) production per unit area of twelve oilseed crops grown in Minnesota and associate these values with levels of beneficial insect visitation during anthesis. Our results show that oilseed crops such as camelina (Camelina sativa L.), flax (Linum usitatissimum L.) and pennycress (Thlaspi arvense L.) produce relatively little pollen (≤40 kg/ha); borage (Borago officinalis L.), calendula (Calendula officinalis L.), canola (Brassica napus L.), crambe (Crambe abyssianica Hochst) and cuphea (Cuphea viscosissima Jacq. × Cuphea lanceolata W. T. Aiton) produce bountiful pollen resources (50–150 kg/ha); and oilseed echium (Echium plantagineum L.) generates massive amounts of pollen (>400 kg/ha), about 50% of which is protein. Our study is unique in presenting a season‐long perspective of pollen production in alternative oilseed crops, a resource valuable to pollen‐feeding insects such as managed and wild bees. Diversification of UMW landscapes that includes alternative oilseed crops such as oilseed echium and cuphea can potentially provide a ready source of pollen and protein to help combat pollinator decline.     

Glyoxal as an alternative fixative to formaldehyde in immunostaining and super‐resolution microscopy

Paraformaldehyde (PFA) is the most commonly used fixative for immunostaining of cells, but has been associated with various problems, ranging from loss of antigenicity to changes in morphology during fixation. We show here that the small dialdehyde glyoxal can successfully replace PFA. Despite being less toxic than PFA, and, as most aldehydes, likely usable as a fixative, glyoxal has not yet been systematically tried in modern fluorescence microscopy. Here, we tested and optimized glyoxal fixation and surprisingly found it to be more efficient than PFA‐based protocols. Glyoxal acted faster than PFA, cross‐linked proteins more effectively, and improved the preservation of cellular morphology. We validated glyoxal fixation in multiple laboratories against different PFA‐based protocols and confirmed that it enabled better immunostainings for a majority of the targets. Our data therefore support that glyoxal can be a valuable alternative to PFA for immunostaining.     

Contribution of sucrose synthase, ADP-glucose pyrophosphorylase and starch synthase to starch synthesis in developing pea seeds

Using genetic variability existing amongst nine pea genotypes (Pisum sativum L.), the biochemical basis of sink strength in developing pea seeds was investigated. Sink strength was considered to be reflected by the rate of starch synthesis (RSS) in the embryo, and sink activity in the seed was reflected by the relative rate of starch synthesis (RRSS). These rates were compared to the activities of three enzymes of the starch biosynthetic pathway [sucrose synthase (Sus), ADP-glucose pyrophosphorylase and starch synthase] at three developmental stages during seed filling (25, 50 and 75% of the dry seed weight). Complete sets of data collected during seed filling for the nine genotypes showed that, for all enzyme activities (expressed on a protein basis), only Sus in the embryo and seed coat was linearly and significantly correlated to RRSS. The contribution of the three enzyme activities to the variability in RSS and RRSS was evaluated by multiple regression analysis for the first two developmental stages. Only Sus activity in the embryo could explain, at least in part, the significant variability observed for both the RSS and the RRSS at each developmental stage. We conclude that Sus activity is a reliable marker of sink activity in developing pea seeds.