Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils

We describe solid-state nuclear magnetic resonance (NMR) measurements on fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (Abeta(1-40)) that place constraints on the identity and symmetry of contacts between in-register, parallel beta-sheets in the fibrils. We refer to these contacts as internal and external quaternary contacts, depending on whether they are within a single molecular layer or between molecular layers. The data include (1) two-dimensional 13C-13C NMR spectra that indicate internal quaternary contacts between side chains of L17 and F19 and side chains of I32, L34, and V36, as well as external quaternary contacts between side chains of I31 and G37; (2) two-dimensional 15N-13C NMR spectra that indicate external quaternary contacts between the side chain of M35 and the peptide backbone at G33; (3) measurements of magnetic dipole-dipole couplings between the side chain carboxylate group of D23 and the side chain amine group of K28 that indicate salt bridge interactions. Isotopic dilution experiments allow us to make distinctions between intramolecular and intermolecular contacts. On the basis of these data and previously determined structural constraints from solid-state NMR and electron microscopy, we construct full molecular models using restrained molecular dynamics simulations and restrained energy minimization. These models apply to Abeta(1-40) fibrils grown with gentle agitation. We also present evidence for different internal quaternary contacts in Abeta(1-40) fibrils grown without agitation, which are morphologically distinct.

Source partitioning using stable isotopes: coping with too many sources

Stable isotopes are increasingly being used as tracers in environmental studies. One application is to use isotopic ratios to quantitatively determine the proportional contribution of several sources to a mixture, such as the proportion of various pollution sources in a waste stream. In general, the proportional contributions of n+1 different sources can be uniquely determined by the use of n different isotope system tracers (e.g., delta13C, delta15N, delta18O) with linear mixing models based on mass balance equations. Often, however, the number of potential sources exceeds n+1, which prevents finding a unique solution of source proportions. What can be done in these situations? While no definitive solution exists, we propose a method that is informative in determining bounds for the contributions of each source. In this method, all possible combinations of each source contribution (0-100%) are examined in small increments (e.g., 1%). Combinations that sum to the observed mixture isotopic signatures within a small tolerance (e.g., +/-0.1 per thousand ) are considered to be feasible solutions, from which the frequency and range of potential source contributions can be determined. To avoid misrepresenting the results, users of this procedure should report the distribution of feasible solutions rather than focusing on a single value such as the mean. We applied this method to a variety of environmental studies in which stable isotope tracers were used to quantify the relative magnitude of multiple sources, including (1) plant water use, (2) geochemistry, (3) air pollution, and (4) dietary analysis. This method gives the range of isotopically determined source contributions; additional non-isotopic constraints specific to each study may be used to further restrict this range. The breadth of the isotopically determined ranges depends on the geometry of the mixing space and the similarity of source and mixture isotopic signatures. A sensitivity analysis indicated that the estimated ranges vary only modestly with different choices of source increment and mass balance tolerance parameter values. A computer program (IsoSource) to perform these calculations for user-specified data is available at http://www.epa.gov/wed/pages/models.htm.

Sources of variation in consumer-diet delta 15N enrichment: a meta-analysis

Measurements of delta15N of consumers are usually higher than those of their diet. This general pattern is widely used to make inferences about trophic relationships in ecological studies, although the underlying mechanisms causing the pattern are poorly understood. However, there can be substantial variation in consumer-diet delta15N enrichment within this general pattern. We conducted an extensive literature review, which yielded 134 estimates from controlled studies of consumer-diet delta15N enrichment, to test the significance of several potential sources of variation by means of meta-analyses. We found patterns related to processes of nitrogen assimilation and excretion. There was a significant effect of the main biochemical form of nitrogenous waste: ammonotelic organisms show lower delta15N enrichment than ureotelic or uricotelic organisms. There were no significant differences between animals feeding on plant food, animal food, or manufactured mixtures, but detritivores yielded significantly lower estimates of enrichment. delta15N enrichment was found to increase significantly with the C:N ratio of the diet, suggesting that a nitrogen-poor diet can have an effect similar to that already documented for fasting organisms. There were also differences among taxonomic classes: molluscs and crustaceans generally yielded lower delta15N enrichment. The lower delta 15N enrichment might be related to the fact that molluscs and crustaceans excrete mainly ammonia, or to the fact that many were detritivores. Organisms inhabiting marine environments yielded significantly lower estimates of delta15N enrichment than organisms inhabiting terrestrial or freshwater environments, a pattern that was influenced by the number of marine, ammonotelic, crustaceans and molluscs. Overall, our analyses point to several important sources of variation in delta15N enrichment and suggest that the most important of them are the main biochemical form of nitrogen excretion and nutritional status. The variance of estimates of delta15N enrichment, as well as the fact that enrichment may be different in certain groups of organisms should be taken into account in statistical approaches for studying diet and trophic relationships.

Production of N(2) through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments

In the global nitrogen cycle, bacterial denitrification is recognized as the only quantitatively important process that converts fixed nitrogen to atmospheric nitrogen gas, N(2), thereby influencing many aspects of ecosystem function and global biogeochemistry. However, we have found that a process novel to the marine nitrogen cycle, anaerobic oxidation of ammonium coupled to nitrate reduction, contributes substantially to N(2) production in marine sediments. Incubations with (15)N-labeled nitrate or ammonium demonstrated that during this process, N(2) is formed through one-to-one pairing of nitrogen from nitrate and ammonium, which clearly separates the process from denitrification. Nitrite, which accumulated transiently, was likely the oxidant for ammonium, and the process is thus similar to the anammox process known from wastewater bioreactors. Anaerobic ammonium oxidation accounted for 24 and 67% of the total N(2) production at two typical continental shelf sites, whereas it was detectable but insignificant relative to denitrification in a eutrophic coastal bay. However, rates of anaerobic ammonium oxidation were higher in the coastal sediment than at the deepest site and the variability in the relative contribution to N(2) production between sites was related to large differences in rates of denitrification. Thus, the relative importance of anaerobic ammonium oxidation and denitrification in N(2) production appears to be regulated by the availability of their reduced substrates. By shunting nitrogen directly from ammonium to N(2), anaerobic ammonium oxidation promotes the removal of fixed nitrogen in the oceans. The process can explain ammonium deficiencies in anoxic waters and sediments, and it may contribute significantly to oceanic nitrogen budgets.

Reprogramming of proline and glutamine metabolism contributes to the proliferative and metabolic responses regulated by oncogenic transcription factor c-MYC

In addition to glycolysis, the oncogenic transcription factor c-MYC (MYC) stimulates glutamine catabolism to fuel growth and proliferation of cancer cells through up-regulating glutaminase (GLS). Glutamine is converted to glutamate by GLS, entering the tricarboxylic acid cycle as an important energy source. Less well-recognized, glutamate can also be converted to proline through Δ(1)-pyrroline-5-carboxylate (P5C) and vice versa. This study suggests that some MYC-induced cellular effects are due to MYC regulation of proline metabolism. Proline oxidase, also known as proline dehydrogenase (POX/PRODH), the first enzyme in proline catabolism, is a mitochondrial tumor suppressor that inhibits proliferation and induces apoptosis. MiR-23b* mediates POX/PRODH down-regulation in human kidney tumors. MiR-23b* is processed from the same transcript as miR-23b; the latter inhibits the translation of GLS. Using MYC-inducible human Burkitt lymphoma model P493 and PC3 human prostate cancer cells, we showed that MYC suppressed POX/PRODH expression primarily through up-regulating miR-23b*. The growth inhibition in the absence of MYC was partially reversed by POX/PRODH knockdown, indicating the importance of suppression of POX/PRODH in MYC-mediated cellular effects. Interestingly, MYC not only inhibited POX/PRODH, but also markedly increased the enzymes of proline biosynthesis from glutamine, including P5C synthase and P5C reductase 1. MYC-induced proline biosynthesis from glutamine was directly confirmed using (13)C,(15)N-glutamine as a tracer. The metabolic link between glutamine and proline afforded by MYC emphasizes the complexity of tumor metabolism. Further studies of the relationship between glutamine and proline metabolism should provide a deeper understanding of tumor metabolism while enabling the development of novel therapeutic strategies.

Global patterns of foliar nitrogen isotopes and their relationships with climate, mycorrhizal fungi, foliar nutrient concentrations, and nitrogen availability

Ratios of nitrogen (N) isotopes in leaves could elucidate underlying patterns of N cycling across ecological gradients. To better understand global-scale patterns of N cycling, we compiled data on foliar N isotope ratios (delta(15)N), foliar N concentrations, mycorrhizal type and climate for over 11,000 plants worldwide. Arbuscular mycorrhizal, ectomycorrhizal, and ericoid mycorrhizal plants were depleted in foliar delta(15)N by 2 per thousand, 3.2 per thousand, 5.9 per thousand, respectively, relative to nonmycorrhizal plants. Foliar delta(15)N increased with decreasing mean annual precipitation and with increasing mean annual temperature (MAT) across sites with MAT >or= -0.5 degrees C, but was invariant with MAT across sites with MAT < -0.5 degrees C. In independent landscape-level to regional-level studies, foliar delta(15)N increased with increasing N availability; at the global scale, foliar delta(15)N increased with increasing foliar N concentrations and decreasing foliar phosphorus (P) concentrations. Together, these results suggest that warm, dry ecosystems have the highest N availability, while plants with high N concentrations, on average, occupy sites with higher N availability than plants with low N concentrations. Global-scale comparisons of other components of the N cycle are still required for better mechanistic understanding of the determinants of variation in foliar delta(15)N and ultimately global patterns in N cycling.

Methodological underestimation of oceanic nitrogen fixation rates

The two commonly applied methods to assess dinitrogen (N₂) fixation rates are the ¹⁵N₂-tracer addition and the acetylene reduction assay (ARA). Discrepancies between the two methods as well as inconsistencies between N₂ fixation rates and biomass/growth rates in culture experiments have been attributed to variable excretion of recently fixed N₂. Here we demonstrate that the ¹⁵N₂-tracer addition method underestimates N₂ fixation rates significantly when the ¹⁵N₂ tracer is introduced as a gas bubble. The injected ¹⁵N₂ gas bubble does not attain equilibrium with the surrounding water leading to a ¹⁵N₂ concentration lower than assumed by the method used to calculate ¹⁵N₂-fixation rates. The resulting magnitude of underestimation varies with the incubation time, to a lesser extent on the amount of injected gas and is sensitive to the timing of the bubble injection relative to diel N₂ fixation patterns. Here, we propose and test a modified ¹⁵N₂ tracer method based on the addition of ¹⁵N₂-enriched seawater that provides an instantaneous, constant enrichment and allows more accurate calculation of N₂ fixation rates for both field and laboratory studies. We hypothesise that application of N₂ fixation measurements using this modified method will significantly reduce the apparent imbalances in the oceanic fixed-nitrogen budget.

Anaerobic ammonium oxidation measured in sediments along the Thames estuary, United Kingdom

Until recently, denitrification was thought to be the only significant pathway for N(2) formation and, in turn, the removal of nitrogen in aquatic sediments. The discovery of anaerobic ammonium oxidation in the laboratory suggested that alternative metabolisms might be present in the environment. By using a combination of (15)N-labeled NH(4)(+), NO(3)(-), and NO(2)(-) (and (14)N analogues), production of (29)N(2) and (30)N(2) was measured in anaerobic sediment slurries from six sites along the Thames estuary. The production of (29)N(2) in the presence of (15)NH(4)(+) and either (14)NO(3)(-) or (14)NO(2)(-) confirmed the presence of anaerobic ammonium oxidation, with the stoichiometry of the reaction indicating that the oxidation was coupled to the reduction of NO(2)(-). Anaerobic ammonium oxidation proceeded at equal rates via either the direct reduction of NO(2)(-) or indirect reduction, following the initial reduction of NO(3)(-). Whether NO(2)(-) was directly present at 800 micro M or it accumulated at 3 to 20 micro M (from the reduction of NO(3)(-)), the rate of (29)N(2) formation was not affected, which suggested that anaerobic ammonium oxidation was saturated at low concentrations of NO(2)(-). We observed a shift in the significance of anaerobic ammonium oxidation to N(2) formation relative to denitrification, from 8% near the head of the estuary to less than 1% at the coast. The relative importance of anaerobic ammonium oxidation was positively correlated (P < 0.05) with sediment organic content. This report of anaerobic ammonium oxidation in organically enriched estuarine sediments, though in contrast to a recent report on continental shelf sediments, confirms the presence of this novel metabolism in another aquatic sediment system.

Factors that influence assimilation rates and fractionation of nitrogen and carbon stable isotopes in avian blood and feathers

By switching great skuas Catharacta skua from one isotopically distinct diet to another, we measured diet-tissue discrimination factors and tested the assumption that dietary nitrogen and carbon isotope signatures are incorporated into blood and feathers at similar rates. We also examined the effects of metabolic rate and looked for evidence of isotopic routing. We found that blood delta(15)N and delta(13)C signatures altered after the diet switch at similar rates (14.4 d and 15.7 d, respectively). Qualitative analyses imply that the same was true with feathers. Mass balance calculations suggest that only a small amount of lipid is likely to be involved in the synthesis of blood and feathers. Differences in diet-tissue discrimination factors before and after the diet switch may mean that toward the end of the experiment, some of the nutrients for blood synthesis had been coming from stores. Repeated measures mixed models provided evidence that increases in metabolic rate might accelerate fractional turnover rates in blood. There is a need for more laboratory-based experimental isotope studies in order to address further questions that this study has raised.

Stable isotope turnover and half-life in animal tissues: a literature synthesis

Stable isotopes of carbon, nitrogen, and sulfur are used as ecological tracers for a variety of applications, such as studies of animal migrations, energy sources, and food web pathways. Yet uncertainty relating to the time period integrated by isotopic measurement of animal tissues can confound the interpretation of isotopic data. There have been a large number of experimental isotopic diet shift studies aimed at quantifying animal tissue isotopic turnover rate λ (%·day(-1), often expressed as isotopic half-life, ln(2)/λ, days). Yet no studies have evaluated or summarized the many individual half-life estimates in an effort to both seek broad-scale patterns and characterize the degree of variability. Here, we collect previously published half-life estimates, examine how half-life is related to body size, and test for tissue- and taxa-varying allometric relationships. Half-life generally increases with animal body mass, and is longer in muscle and blood compared to plasma and internal organs. Half-life was longest in ecotherms, followed by mammals, and finally birds. For ectotherms, different taxa-tissue combinations had similar allometric slopes that generally matched predictions of metabolic theory. Half-life for ectotherms can be approximated as: ln (half-life) = 0.22*ln (body mass) + group-specific intercept; n = 261, p<0.0001, r2 = 0.63. For endothermic groups, relationships with body mass were weak and model slopes and intercepts were heterogeneous. While isotopic half-life can be approximated using simple allometric relationships for some taxa and tissue types, there is also a high degree of unexplained variation in our models. Our study highlights several strong and general patterns, though accurate prediction of isotopic half-life from readily available variables such as animal body mass remains elusive.

Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps

Carbonate communities: The activity of anaerobic methane oxidizing microbes facilitates precipitation of vast quantities of authigenic carbonate at methane seeps. Here we demonstrate the significant role of carbonate rocks in promoting diversity by providing unique habitat and food resources for macrofaunal assemblages at seeps on the Costa Rica margin (400–1850 m). The attendant fauna is surprisingly similar to that in rocky intertidal shores, with numerous grazing gastropods (limpets and snails) as dominant taxa. However, the community feeds upon seep-associated microbes. Macrofaunal density, composition, and diversity on carbonates vary as a function of seepage activity, biogenic habitat and location. The macrofaunal community of carbonates at non-seeping (inactive) sites is strongly related to the hydrography (depth, temperature, O₂) of overlying water, whereas the fauna at sites of active seepage is not. Densities are highest on active rocks from tubeworm bushes and mussel beds, particularly at the Mound 12 location (1000 m). Species diversity is higher on rocks exposed to active seepage, with multiple species of gastropods and polychaetes dominant, while crustaceans, cnidarians, and ophiuroids were better represented on rocks at inactive sites. Macro-infauna (larger than 0.3 mm) from tube cores taken in nearby seep sediments at comparable depths exhibited densities similar to those on carbonate rocks, but had lower diversity and different taxonomic composition. Seep sediments had higher densities of ampharetid, dorvilleid, hesionid, cirratulid and lacydoniid polychaetes, whereas carbonates had more gastropods, as well as syllid, chrysopetalid and polynoid polychaetes. Stable isotope signatures and metrics: The stable isotope signatures of carbonates were heterogeneous, as were the food sources and nutrition used by the animals. Carbonate δ¹³C_inorg values (mean = -26.98‰) ranged from -53.3‰ to +10.0‰, and were significantly heavier than carbonate δ¹³C_org (mean = -33.83‰), which ranged from -74.4‰ to -20.6‰. Invertebrates on carbonates had average δ¹³C (per rock) = -31.0‰ (range -18.5‰ to -46.5‰) and δ¹⁵N = 5.7‰ (range -4.5‰ to +13.4‰). Average δ¹³C values did not differ between active and inactive sites; carbonate fauna from both settings depend on chemosynthesis-based nutrition. Community metrics reflecting trophic diversity (SEAc, total Hull Area, ranges of δ¹³C and δ¹⁵N) and species packing (mean distance to centroid, nearest neighbor distance) also did not vary as a function of seepage activity or site. However, distinct isotopic signatures were observed among related, co-occurring species of gastropods and polychaetes, reflecting intense microbial resource partitioning. Overall, the substrate and nutritional heterogeneity introduced by authigenic seep carbonates act to promote diverse, uniquely adapted assemblages, even after seepage ceases. The macrofauna in these ecosystems remain largely overlooked in most surveys, but are major contributors to biodiversity of chemosynthetic ecosystems and the deep sea in general.

The effect of dietary protein quality on nitrogen isotope discrimination in mammals and birds

We tested the competing hypotheses that (1) nitrogen discrimination in mammals and birds increases with dietary nitrogen concentration or decreasing C:N ratios and, therefore, discrimination will increase with trophic level as carnivores ingest more protein than herbivores and omnivores or (2) nitrogen discrimination increases as dietary protein quality decreases and, therefore, discrimination will decrease with trophic level as carnivores ingest higher quality protein than do herbivores. Discrimination factors were summarized for five major diet groupings and 21 different species of birds and mammals. Discrimination did not differ between mammals and birds and decreased as protein quality (expressed as biological value) increased with trophic level (i.e., herbivores to carnivores). Relationships between discrimination factors and dietary nitrogen concentration or C:N ratios were either the opposite of what was hypothesized or non-significant. Dietary protein quality accounted for 72% of the variation in discrimination factors across diet groupings. We concluded that protein quality established the baseline for discrimination between dietary groupings, while other variables, such as dietary protein intake relative to animal requirements, created within-group variation. We caution about the care needed in developing studies to understand variation in discrimination and subsequently applying those discrimination factors to estimate assimilated diets of wild animals.

Distinguishing nitrous oxide production from nitrification and denitrification on the basis of isotopomer abundances

The intramolecular distribution of nitrogen isotopes in N2O is an emerging tool for defining the relative importance of microbial sources of this greenhouse gas. The application of intramolecular isotopic distributions to evaluate the origins of N2O, however, requires a foundation in laboratory experiments in which individual production pathways can be isolated. Here we evaluate the site preferences of N2O produced during hydroxylamine oxidation by ammonia oxidizers and by a methanotroph, ammonia oxidation by a nitrifier, nitrite reduction during nitrifier denitrification, and nitrate and nitrite reduction by denitrifiers. The site preferences produced during hydroxylamine oxidation were 33.5 +/- 1.2 per thousand, 32.5 +/- 0.6 per thousand, and 35.6 +/- 1.4 per thousand for Nitrosomonas europaea, Nitrosospira multiformis, and Methylosinus trichosporium, respectively, indicating similar site preferences for methane and ammonia oxidizers. The site preference of N2O from ammonia oxidation by N. europaea (31.4 +/- 4.2 per thousand) was similar to that produced during hydroxylamine oxidation (33.5 +/- 1.2 per thousand) and distinct from that produced during nitrifier denitrification by N. multiformis (0.1 +/- 1.7 per thousand), indicating that isotopomers differentiate between nitrification and nitrifier denitrification. The site preferences of N2O produced during nitrite reduction by the denitrifiers Pseudomonas chlororaphis and Pseudomonas aureofaciens (-0.6 +/- 1.9 per thousand and -0.5 +/- 1.9 per thousand, respectively) were similar to those during nitrate reduction (-0.5 +/- 1.9 per thousand and -0.5 +/- 0.6 per thousand, respectively), indicating no influence of either substrate on site preference. Site preferences of approximately 33 per thousand and approximately 0 per thousand are characteristic of nitrification and denitrification, respectively, and provide a basis to quantitatively apportion N2O.

Light-induced structural changes in a putative blue-light receptor with a novel FAD binding fold sensor of blue-light using FAD (BLUF); Slr1694 of synechocystis sp. PCC6803

The sensor of blue-light using FAD (BLUF) domain is the flavin-binding fold categorized to a new class of blue-light sensing domain found in AppA from Rhodobacter sphaeroides and PAC from Euglena gracilis, but little is known concerning the mechanism of blue-light perception. An open reading frame slr1694 in a cyanobacterium Synechocystis sp. PCC6803 encodes a protein possessing the BLUF domain. Here, a full-length Slr1694 protein retaining FAD was expressed and purified and found to be present as an oligomeric form (trimer or tetramer). Using the purified Slr1694, spectroscopic properties of Slr1694 were characterized. Slr1694 was found to show the same red-shift of flavin absorption and quenching of flavin fluorescence by illumination as those of AppA. These changes reversed in the dark although the rate of dark state regeneration was much faster in Slr1694 than AppA, indicating that Slr1694 is a blue-light receptor based on BLUF with the similar photocycle to that of AppA. The dark decay in D(2)O was nearly four times slower than in H(2)O. Light-induced Fourier transform infrared (FTIR) difference spectroscopy was applied to examine the light-induced structure change of a chromophore and apo-protein with deuteration and universal (13)C and (15)N isotope labeling. The FTIR results indicate that light excitation induced distinct changes in the amide I modes of peptide backbone but relatively limited changes in flavin chromophore. Light excitation predominantly weakened the C(4)=O and C(2)=O bonding and strengthened the N1C10a and/or C4aN5 bonding, indicating formational changes of the isoalloxazine ring II and III of FAD but little formational change in the isoalloxazine ring I. The photocycle of the BLUF is unique in the sense that light excitation leads to the structural rearrangements of the protein moieties coupled with a minimum formational change of the chromophore.

Nitrogen recycling and remobilization are differentially controlled by leaf senescence and development stage in Arabidopsis under low nitrogen nutrition

Five recombinant inbred lines (RILs) of Arabidopsis (Arabidopsis thaliana), previously selected from the Bay-0 x Shahdara RIL population on the basis of differential leaf senescence phenotypes (from early senescing to late senescing) when cultivated under nitrogen (N)-limiting conditions, were analyzed to monitor metabolic markers related to N assimilation and N remobilization pathways. In each RIL, a decrease of total N, free amino acid, and soluble protein contents with leaf aging was observed. In parallel, the expression of markers for N remobilization such as cytosolic glutamine synthetase, glutamate dehydrogenase, and CND41-like protease was increased. This increase occurred earlier and more rapidly in early-senescing lines than in late-senescing lines. We measured the partitioning of (15)N between sink and source leaves during the vegetative stage of development using (15)N tracing and showed that N remobilization from the source leaves to the sink leaves was more efficient in the early-senescing lines. The N remobilization rate was correlated with leaf senescence severity at the vegetative stage. Experiments of (15)N tracing at the reproductive stage showed, however, that the rate of N remobilization from the rosettes to the flowering organs and to the seeds was similar in early- and late-senescing lines. At the reproductive stage, N remobilization efficiency did not depend on senescence phenotypes but was related to the ratio between the biomasses of the sink and the source organs.

‘Are fish what they eat’ all year round?

Isotope turnover in muscle of ectotherms depends primarily on growth rather than on metabolic replacement. Ectotherms, such as fish, have a discontinuous pattern of growth over the year, so the isotopic signature of muscle (delta13C and delta15N) may only reflect food consumed during periods of growth. In contrast, the liver is a regulatory tissue, with a continuous protein turnover. Therefore, the isotopic composition of liver should respond year round to changes in the isotopic signature of food sources. Therefore, we predicted that (1) Whitefish in Lake Geneva would have larger seasonal variation in the isotopic variation of the liver compared to that of the muscle tissue, and (2) the isotope composition of fish muscle would reflect a long-term image of the isotope composition of the food consumed only throughout the growth period. To test these expectations, we compared the isotope compositions of Whitefish muscle, liver and food in a 20-month study. We found that the seasonal amplitude of isotope variation was two to three times higher in liver compared to muscle tissue. During the autumn and winter, when growth was limited, only the isotopic signature of liver responded to changes in the isotope composition of the food sources. The delta13C and delta15N of muscle tissue only reflected the food consumed during the spring and summer growth period.

Quantitative imaging of nitrogen fixation by individual bacteria within animal cells

Biological nitrogen fixation, the conversion of atmospheric nitrogen to ammonia for biosynthesis, is exclusively performed by a few bacteria and archaea. Despite the essential importance of biological nitrogen fixation, it has been impossible to quantify the incorporation of nitrogen by individual bacteria or to map the fate of fixed nitrogen in host cells. In this study, with multi-isotope imaging mass spectrometry we directly imaged and measured nitrogen fixation by individual bacteria within eukaryotic host cells and demonstrated that fixed nitrogen is used for host metabolism. This approach introduces a powerful way to study microbes and global nutrient cycles.

15N IN SYMBIOTIC FUNGI AND PLANTS ESTIMATES NITROGEN AND CARBON FLUX RATES IN ARCTIC TUNDRA

When soil nitrogen is in short supply, most terrestrial plants form symbioses with fungi (mycorrhizae): hyphae take up soil nitrogen, transport it into plant roots, and receive plant sugars in return. In ecosystems, the transfers within the pathway fractionate nitrogen isotopes so that the natural abundance of 15N in fungi differs from that in their host plants by as much as 12% per hundred. Here we present a new method to quantify carbon and nitrogen fluxes in the symbiosis based on the fractionation against 15N during transfer of nitrogen from fungi to plant roots. We tested this method, which is based on the mass balance of 15N, with data from arctic Alaska where the nitrogen cycle is well studied. Mycorrhizal fungi provided 61-86% of the nitrogen in plants; plants provided 8-17% of their photosynthetic carbon to the fungi for growth and respiration. This method of analysis avoids the disturbance of the soil-microbe-root relationship caused by collecting samples, mixing the soil, or changing substrate concentrations. This analytical technique also can be applied to other nitrogen-limited ecosystems, such as many temperate and boreal forests, to quantify the importance for terrestrial carbon and nitrogen cycling of nutrient transfers mediated by mycorrhizae at the plant-soil interface.

Characterization of the magnitude and kinetics of xanthine oxidase-catalyzed nitrate reduction: evaluation of its role in nitrite and nitric oxide generation in anoxic tissues

In addition to nitric oxide (NO) generation from specific NO synthases, NO is also formed during anoxia from nitrite reduction, and xanthine oxidase (XO) catalyzes this process. While in tissues and blood high nitrate levels are present, questions remain regarding whether nitrate is also a source of NO and if XO-mediated nitrate reduction can be an important source of NO in biological systems. To characterize the kinetics, magnitude, and mechanism of XO-mediated nitrate reduction under anaerobic conditions, EPR, chemiluminescence NO-analyzer, and NO-electrode studies were performed. Typical XO reducing substrates, xanthine, NADH, and 2,3-dihydroxybenz-aldehyde, triggered nitrate reduction to nitrite and NO. The rate of nitrite production followed Michaelis-Menten kinetics, while NO generation rates increased linearly following the accumulation of nitrite, suggesting stepwise-reduction of nitrate to nitrite then to NO. The molybdenum-binding XO inhibitor, oxypurinol, inhibited both nitrite and NO production, indicating that nitrate reduction occurs at the molybdenum site. At higher xanthine concentrations, partial inhibition was seen, suggesting formation of a substrate-bound reduced enzyme complex with xanthine blocking the molybdenum site. The pH dependence of nitrite and NO formation indicate that XO-mediated nitrate reduction occurs via an acid-catalyzed mechanism. With conditions occurring during ischemia, myocardial xanthine oxidoreductase and nitrate levels were determined to generate up to 20 microM nitrite within 10-20 min that can be further reduced to NO with rates comparable to those of maximally activated NOS. Thus, XOR catalyzed nitrate reduction to nitrite and NO occurs and can be an important source of NO production in ischemic tissues.

Mutualistic mycorrhiza in orchids: evidence from plant-fungus carbon and nitrogen transfers in the green-leaved terrestrial orchid Goodyera repens

The roles of mycorrhiza in facilitating the acquisition and transfer of carbon (C) and nitrogen (N) to adult orchids are poorly understood. Here, we employed isotopically labelled sources of C and N to investigate these processes in the green forest orchid, Goodyera repens. Fungus-to-orchid transfers of C and N were measured using mass spectrometry after supplying extraradical mycelial systems with double-labelled [13C-15N]glycine. Orchid-to-fungus C transfer was revealed and quantified by radioisotope imaging and liquid scintillation counting of extraradical mycelium following 14CO2 fixation by shoots. Both 13C and 15N were assimilated by the fungus and transferred to the roots and shoots of the orchid. Contrary to previous reports, considerable quantities (2.6% over 72 h) of fixed C were shown to be allocated to the extraradical mycelium of the fungus. This study demonstrates, for the first time, mutualism in orchid mycorrhiza, bidirectional transfer of C between a green orchid and its fungal symbiont, and a fungus-dependent pathway for organic N acquisition by an orchid.

Parallel evolutionary paths to mycoheterotrophy in understorey Ericaceae and Orchidaceae: ecological evidence for mixotrophy in Pyroleae

Several forest understorey achlorophyllous plants, termed mycoheterotrophs (MHs), obtain C from their mycorrhizal fungi. The latter in turn form ectomycorrhizas with trees, the ultimate C source of the entire system. A similar nutritional strategy occurs in some green forest orchids, phylogenetically close to MH species, that gain their C via a combination of MH and photosynthesis (mixotrophy). In orchid evolution, mixotrophy evolved in shaded habitats and preceded MH nutrition. By generalizing and applying this to Ericaceae, we hypothesized that green forest species phylogenetically close to MHs are mixotrophic. Using stable C isotope analysis with fungi, autotrophic, mixotrophic and MH plants as comparisons, we found the first quantitative evidence for substantial fungi-mediated mixotrophy in the Pyroleae, common ericaceous shrubs from boreal forests close to the MH Monotropoideae. Orthilia secunda, Pyrola chlorantha, Pyrola rotundifolia and Chimaphila umbellata acquired between 10.3 and 67.5% of their C from fungi. High N and 15N contents also suggest that Pyroleae nutrition partly rely on fungi. Examination of root fungal internal transcribed spacer sequences at one site revealed that 39 species of mostly endophytic or ectomycorrhizal fungi, including abundant Tricholoma spp., were associated with O. secunda, P. chlorantha and C. umbellata. These fungi, particularly ectomycorrhizal associates, could thus link mixotrophic Pyroleae spp. to surrounding trees, allowing the C flows deduced from isotopic evidence. These data suggest that we need to reconsider ecological roles of understorey plants, which could influence the dynamics and composition of forest communities.

The effect of cold-induced increased metabolic rate on the rate of 13C and 15N incorporation in house sparrows (Passer domesticus)

Animals with high metabolic rates are believed to have high rates of carbon and nitrogen isotopic incorporation. We hypothesized that (1) chronic exposure to cold, and hence an increase in metabolic rate, would increase the rate of isotopic incorporation of both 13C and 15N into red blood cells; and (2) that the rate of isotopic incorporation into red blood cells would be allometrically related to body mass. Two groups of sparrows were chronically exposed to either 5 or 22 degrees C and switched from a 13C-depleted C3-plant diet to a more 13C-enriched C4-plant one. We used respirometry to estimate the resting metabolic rate (VO2) of birds exposed chronically to our two experimental temperatures. The allometric relationship between the rate of 13C incorporation into blood and body mass was determined from published data. The (VO2) of birds at 5 degrees C was 1.9 times higher than that of birds at 22 degrees C. Chronic exposure to a low temperature did not have an effect on the rate of isotopic incorporation of 15N save for a very small effect on the incorporation of 13C. The isotopic incorporation rate of 13C was 1.5 times faster than that of 15N. The fractional rate of 13C incorporation into avian blood was allometrically related to body mass with an exponent similar to -1/4. We conclude that the relationship between metabolic rate and the rate of isotopic incorporation into an animal's tissues is indirect. It is probably mediated by protein turnover and thus more complex than previous studies have assumed.

Stable isotope (N, C, Hg) study of methylmercury sources and trophic transfer in the northern gulf of Mexico

We combined N, C, and Hg stable isotope measurements to identify the most important factors that influence MeHg accumulation in fish from the northern Gulf of Mexico (nGOM), and to determine if coastal species residing in the Mississippi River (MR) plume and migratory oceanic species derive their MeHg from the same, or different, sources. In six coastal species and two oceanic species (blackfin and yellowfin tuna), trophic position as measured by delta(15)N explained most of the variance in log[MeHg] (r(2) approximately 0.8), but coastal species and tuna fell along distinct, nearly parallel lines with significantly different intercepts. The tuna also had significantly higher delta(202)Hg (0.2-0.5 per thousand) and Delta(201)Hg ( approximately 1.5 per thousand) than the coastal fish (delta(202)Hg = 0 to -1.0 per thousand; Delta(201)Hg approximately 0.4 per thousand). The observations can be best explained by largely disconnected food webs rooted in different baseline delta(15)N signatures (MR-plume vs oceanic) and isotopically distinct MeHg sources, with oceanic MeHg having undergone substantial photodegradation ( approximately 50%) before entering the base of the food web. Given the MR's large, productive footprint in the nGOM and the potential for exporting prey and MeHg to the adjacent oligotrophic GOM, the disconnected food webs and different MeHg sources are consistent with recent evidence in other systems of important oceanic MeHg sources.

Using stable isotope analysis with telemetry or mark-recapture data to identify fish movement and foraging

Information about animal movements has often been inferred from stable isotope analysis (SIA), but is dependent on animals assimilating site-specific isotopic signatures via diet. This potential weakness in ecological interpretation can be overcome by using other investigative tools that provide precise information about individual movement patterns. In this paper, we demonstrate the value of combining SIA with telemetry or mark-recapture data from trapping, electrofishing and remote detection of individuals to study the movement and feeding ecology of fishes in different habitats. In a fjord lake system in Newfoundland, Canada, juvenile Atlantic salmon delayed downstream migration (smolts) or actively moved into a large lake (parr) where they foraged for periods reflecting different life history strategies. In the Miramichi River (New Brunswick, Canada), SIA provided evidence of distinct foraging habitats (tributary versus large river). By tracking fish implanted with passive integrated transponder (PIT) tags, we distinguished between movements related to foraging versus seeking cool water refugia during high temperature events. Finally, site fidelity and limited mobility of slimy sculpin, a small benthic fish, was established where delta13C in muscle tissue showed a progressive enrichment downstream and where a median displacement of <10 m was estimated for sculpin tagged with PIT tags. Technological improvements have permitted non-destructive tissue sampling of wild fishes for SIA, and the tagging and remote detection of animals smaller than was previously possible. These advancements and the combination of investigative tools promise new insights into animal ecology.

Folic acid metabolism in human subjects revisited: potential implications for proposed mandatory folic acid fortification in the UK

Following an introduction of the importance of folates and the rationale for seeking to estimate fractional folate absorption from foods (especially for countries not having a mandatory folic acid fortification policy), scientific papers covering the mechanisms of folate absorption and initial biotransformation are discussed. There appears (post-1983) to be a consensus that physiological doses of folic acid undergo biotransformation in the absorptive cells of the upper small intestine to 5-methyltetrahydrofolic acid (as happens for all naturally-occurring reduced 1-carbon-substituted folates). This 'validates' short-term experimental protocols assessing 'relative' folate absorption in human subjects that use folic acid as the 'reference' dose. The underlying scientific premise on which this consensus is based is challenged on three grounds: (i) the apparent absence of a 5-methyltetrahydrofolic acid response in the human hepatic portal vein following absorption of folic acid, (ii) the low dihydrofolate reductase activity peculiar to man and (iii) the implications derived from recent stable-isotope studies of folate absorption. It is concluded that the historically accepted case for folic acid being a suitable 'reference folate' for studies of the 'relative absorption' of reduced folates in human subjects is invalid. It is hypothesised that the liver, and not the absorptive cells of the upper small intestine, is the initial site of folic acid metabolism in man and that this may have important implications for its use as a supplement or fortificant since human liver's low capacity for reduction may eventually give rise to saturation, resulting in significant (and potentially deleterious) unmetabolised folic acid entering the systemic circulation.