Iron reduction: a mechanism for dynamic cycling of occluded cations in tropical forest soils?

Nutrient cations can limit plant productivity in highly weathered soils, but have received much less attention than phosphorus and nitrogen. The reduction of iron (Fe) in anaerobic microsites of surface soils can solubilize organic matter and P sorbed or occluded with short-range-ordered (SRO) Fe phases. This mechanism might also release occluded cations. In the Luquillo Experimental Forest, Puerto Rico, we measured cation release during anaerobic laboratory incubations, and assessed patterns of cation availability in surface soils spanning ridge-slope-valley catenas. During anaerobic incubations, potassium (K), calcium (Ca) and magnesium (Mg) significantly increased with reduced Fe (Fe(II)) in both water and 0.5 M HCl extractions, but did not change during aerobic incubations. In the field, 0.5 M HCl-extractable Fe(II) and Fe(III) were the strongest predictors of K, Mg, and Ca on ridges (R² 0.57–0.75). Here, both Ca and Mg decreased with Fe(III), while K, Ca, and Mg increased with Fe(II), consistent with release of Fe-occluded cations following Fe reduction. Manganese in ridge soils was extremely low, consistent with leaching following reductive dissolution of Mn(IV). On slopes, soil C was the strongest cation predictor, consistent with the importance of organic matter for cation exchange in these highly weathered Oxisols. In riparian valleys, cation concentrations were up to 16-fold greater than in other topographic positions but were weakly or unrelated to measured predictors, potentially reflecting cation-rich groundwater. Predictors of cation availability varied with topography, but were consistent with the potential importance of microsite Fe reduction in liberating occluded cations, particularly in the highly productive ridges. This mechanism may explain discrepancies among indices of “available” soil cations and plant cation uptake observed in other tropical forests.     

Does the redox status of cytochrome C act as a fail-safe mechanism in the regulation of programmed cell death?

It has now become recognized that one of the key events in the induction of apoptosis, or programmed cell death, in both plants and animals is the release of cytochrome c from mitochondria. It is also known that oxidative stress imposed on cells can have a profound effect on the onset or progression of apoptosis. Here, we discuss how the redox status of cytochrome c, and thus its structure, can be altered by the presence of reactive oxygen species (ROS) and reduced glutathione (GSH). We suggest that cytochrome c will only induce programmed cell death if present in the cytoplasm in the oxidized state, and that the presence of high levels of cytoplasmic GSH maintain cytochrome c in an inactive (reduced) state, thus behaving as a fail-safe mechanism if cytochrome c is released by mitochondria when programmed cell death is not the required outcome. If the redox status of the cell is disturbed however, perhaps in the presence of hydrogen peroxide, GSH concentrations will drop, the cellular E(h) will rise, and cytochrome c will tend towards the oxidized state, allowing programmed cell death to proceed. Therefore, we propose that the redox state of cytoplasmic cytochrome c may be a key regulator of programmed cell death.     

The vitamin K-dependent carboxylase generates γ-carboxylated glutamates by using CO2 to facilitate glutamate deprotonation in a concerted mechanism that drives catalysis

The γ-glutamyl carboxylase converts Glu to carboxylated Glu (Gla) to activate a large number of vitamin K-dependent proteins with diverse functions, and this broad physiological impact makes it critical to understand the mechanism of carboxylation. Gla formation is thought to occur in two independent steps (i.e. Glu deprotonation to form a carbanion that then reacts with CO(2)), based on previous studies showing unresponsiveness of Glu deprotonation to CO(2). However, our recent studies on the kinetic properties of a variant enzyme (H160A) showing impaired Glu deprotonation prompted a reevaluation of this model. Glu deprotonation monitored by tritium release from the glutamyl γ-carbon was dependent upon CO(2), and a proportional increase in both tritium release and Gla formation occurred over a range of CO(2) concentrations. This discrepancy with the earlier studies using microsomes is probably due to the known accessibility of microsomal carboxylase to water, which reprotonates the carbanion. In contrast, tritium incorporation experiments with purified carboxylase showed very little carbanion reprotonation and consequently revealed the dependence of Glu deprotonation on CO(2). Cyanide stimulated Glu deprotonation and carbanion reprotonation to the same extent in wild type enzyme but not in the H160A variant. Glu deprotonation that depends upon CO(2) but that also occurs when water or cyanide are present strongly suggests a concerted mechanism facilitated by His-160 in which an electrophile accepts the negative charge on the developing carbanion. This revised mechanism provides important insight into how the carboxylase catalyzes the reaction by avoiding the formation of a high energy discrete carbanion.     

Whole-exome sequencing reveals a recurrent mutation in the cathepsin C gene that causes Papillon–Lefevre syndrome in a Saudi family

Papillon–Lefevre syndrome (PALS) is a rare, autosomal recessive disorder characterized by periodontitis and hyperkeratosis over the palms and soles. Mutations in the cathepsin C gene (CTSC) have been recognized as the cause of PALS since the late 1990s. More than 75 mutations in CTSC have been identified, and phenotypic variability between different mutations has been described. Next generation sequencing is widely used for efficient molecular diagnostics in various clinical practices. Here we investigated a large consanguineous Saudi family with four affected and four unaffected individuals. All of the affected individuals suffered from hyperkeratosis over the palms and soles and had anomalies of both primary and secondary dentition. For molecular diagnostics, we combined whole-exome sequencing and genome-wide homozygosity mapping procedures, and identified a recurrent homozygous missense mutation (c.899G>A; p.Gly300Asp) in exon 7 of CTSC. Validation of all eight family members by Sanger sequencing confirmed co-segregation of the pathogenic variant (c.899G>A) with the disease phenotype. This is the first report of whole-exome sequencing performed for molecular diagnosis of PALS in Saudi Arabia. Our findings provide further insights into the genotype–phenotype correlation of CTSC pathogenicity in PALS.     

Striking a growth–defense balance: Stress regulators that function in maize development

Maize(Zea mays) cultivation is strongly affected by both abiotic and biotic stress, leading to reduced growth and productivity. It has recently become clear that regulators of plant stress responses, including the phytohormones abscisic acid(ABA),ethylene(ET), and jasmonic acid(JA), together with reactive oxygen species(ROS), shape plant growth and development. Beyond their well established functions in stress responses, these molecules play crucial roles in balancing growth and defense, which m...     

Pattern and variation of C:N:P ratios in China’s soils: a synthesis of observational data

Inspired by previous studies that have indicated consistent or even well-constrained (relatively low variability) relations among carbon (C), nitrogen (N) and phosphorus (P) in soils, we have endeavored to explore general soil C:N:P ratios in China on a national scale, as well as the changing patterns of these ratios with soil depth, developmental stages and climate; we also attempted to determine if well-constrained C:N:P stoichiometrical ratios exist in China’s soil. Based on an inventory data set of 2,384 soil profiles, our analysis indicated that the mean C:N, C:P and N:P ratios for the entire soil depth (as deep as 250 cm for some soil profiles) in China were 11.9, 61 and 5.2, respectively, showing a C:N:P ratio of ~60:5:1. C:N ratios showed relatively small variation among different climatic zones, soil orders, soil depth and weathering stages, while C:P and N:P ratios showed a high spatial heterogeneity and large variations in different climatic zones, soil orders, soil depth and weathering stages. No well-constrained C:N:P ratios were found for the entire soil depth in China. However, for the 0–10 cm organic-rich soil, which has the most active organism–environment interaction, we found a well-constrained C:N ratio (14.4, molar ratio) and relatively consistent C:P (136) and N:P (9.3) ratios, with a general C:N:P ratio of 134:9:1. Finally, we suggested that soil C:N, C:P and N:P ratios in organic-rich topsoil could be a good indicator of soil nutrient status during soil development.     

Radical S-adenosylmethionine maquette chemistry: Cx3Cx2C peptide coordinated redox active [4Fe–4S] clusters

JBIC Journal of Biological Inorganic Chemistry - The synthesis and characterization of short peptide-based maquettes of metalloprotein active sites facilitate an inquiry into their...     

Haemoglobin C and S in natural selection against Plasmodium falciparum malaria: a plethora or a single shared adaptive mechanism?

Conclusive evidence exists on the protective role against clinical Plasmodium falciparum malaria of Haemoglobin S (beta 6Glu-->Val) and HbC (HbC; beta 6Glu-->Lys), both occurring in sub-Saharan Africa. However, the mechanism/s of the protection exerted remain/s debated for both haemoglobin variants, HbC and HbS. Recently, an abnormal display of PfEMP1, an antigen involved in malaria pathogenesis, was reported on HbAC and HbCC infected erythrocytes that showed reduced cytoadhesion and impaired rosetting in vitro. On this basis it has been proposed that HbC protection might be attributed to the reduced PfEMP1-mediated adherence of parasitized erythrocytes in the microvasculature. Furthermore, impaired cytoadherence was observed in HbS carriers suggesting for the first time a convergence in the protection mechanism of these two haemoglobin variants. We investigated the impact of this hypothesis on the development of acquired immunity against P. falciparum variant surface antigens (VSA) encoding PfEMP1 in HbC and HbS carriers in comparison with HbA of Burkina Faso. Higher immune response against a VSA panel and several malaria antigens were observed in all adaptive genotypes containing at least one allelic variant HbC or HbS in the low transmission urban area whereas no differences were detected in the high transmission rural area. In both contexts the response against tetanus toxoid was not influenced by the beta-globin genotype. Thus, these findings suggest that both HbC and HbS affect the early development of naturally acquired immunity against malaria. We reviewed the hypothesized mechanisms so far proposed in light of these recent results.     

Looking for the minimum common denominator in haem–copper oxygen reductases: Towards a unified catalytic mechanism

Haem–copper oxygen reductases are transmembrane protein complexes that reduce dioxygen to water and pump protons across the mitochondrial or periplasmatic membrane, contributing to the transmembrane difference of electrochemical potential. Seven years ago we proposed a classification of these enzymes into three different families (A, B and C), based on the amino acid residues of their proton channels and amino acid sequence comparison, later supported by the so far identified characteristics of the catalytic centre of members from each family. The three families have in common the same general structural fold of the catalytic subunit, which contains the same or analogous prosthetic groups, and proton channels. These observations raise the hypothesis that the mechanisms for dioxygen reduction, proton pumping and the coupling of the two processes may be the same for all these enzymes. Under this hypothesis, they should be performed and controlled by the same or equivalent elements/events, and the identification of retained elements in all families will reveal their importance and may prompt the definition of the enzyme operating mode. Thus, we believe that the search for a minimum common denominator has a crucial importance, and in this article we highlight what is already established for the haem–copper oxygen reductases and emphasize the main questions still unanswered in a comprehensive basis.     

Exploration of disease mechanism in acute kidney injury using a multiplex bead array assay: a nested case–control pilot study

Background: Acute kidney injury (AKI) following cardiac surgery with cardiopulmonary bypass (CPB) causes increased morbidity and mortality.

Objective: To evaluate the plasma profile of biomarkers potentially involved in AKI development following CPB.

Methods: In a nested case–control study, plasma levels of 27 biomarkers in 11 AKI cases were compared with 25 controls.

Results: Pre-CPB, plasma levels of epidermal growth factor and macrophage inflammatory protein-1β, 2?h following CPB, soluble vascular cell adhesion molecule-1 (sVCAM-1), fractalkine and macrophage inflammatory protein-1α, and at later time points, sVCAM-1 and interleukin-6 were associated with AKI.

Conclusion: Biomarkers associated with AKI following CPB may merit further study.     

Two decades of tropical cyclone impacts on North Carolina’s estuarine carbon,nutrient and phytoplankton dynamics: implications for biogeochemical cycling and water quality in a stormier world

Coastal North Carolina (USA) has experienced 35 tropical cyclones over the past 2 decades; the frequency of these events is expected to continue in the foreseeable future. Individual storms had unique and, at times, significant hydrologic, nutrient-, and carbon (C)-loading impacts on biogeochemical cycling and phytoplankton responses in a large estuarine complex, the Pamlico Sound (PS) and Neuse River Estuary (NRE). Major storms caused up to a doubling of annual nitrogen and tripling of phosphorus loading compared to non-storm years; magnitudes of loading depended on storm tracks, forward speed, and precipitation in NRE-PS watersheds. With regard to C cycling, NRE-PS was a sink for atmospheric CO₂ during dry, storm-free years and a significant source of CO₂ in years with at least one storm, although responses were storm-specific. Hurricane Irene (2011) mobilized large amounts of previously-accumulated terrigenous C in the watershed, mainly as dissolved organic carbon, and extreme winds rapidly released CO₂ to the atmosphere. Historic flooding after Hurricanes Joaquin (2015) and Matthew (2016) provided large inputs of C from the watershed, modifying the annual C balance of NRE-PS and leading to sustained CO₂ efflux for months. Storm type affected biogeochemical responses as C-enriched floodwaters enhanced air–water CO₂ exchange during ‘wet’ storms, while CO₂ fluxes during ‘windy’ storms were largely supported by previously-accumulated C. Nutrient loading and flushing jointly influenced spatio-temporal patterns of phytoplankton biomass and composition. These findings suggest the importance of incorporating freshwater discharge and C dynamics in nutrient management strategies for coastal ecosystems likely to experience a stormier future.     

Purification and properties of glycolate oxidase from plants with different photosynthetic pathways: Distinctness of C4 enzyme from that of a C3 species and a C3–C4 intermediate

Glycolate oxidase (GO; EC 1.1.3.1) was purified from the leaves of three plant species:Amaranthus hypochondriacus L.(NAD-ME type C₄ dicot),Pisum sativum L. (C₃ species) andParthenium hysterophorus L. (C₃–C₄. intermediate). A flavin moiety was present in the enzyme from all the three species. The enzyme from the C₄ plant had a low specific activity, exhibited lower K_M for glycolate, and required a lower pH for maximal activity, compared to the C₃ enzyme. The enzyme from the C₄ species oxidized glyoxylate at <10% of the rate with glycolate, while the GO from the C₃ plant oxidized glyoxylate at a rate of about 35 to 40% of that with glycolate. The sensitivity of GO from C₄ plant to -hydroxypyridinemethane sulfonate, 2-hydroxy-3-butynoate and other inhibitors was less than that of the enzyme from C₃ source. The properties of GO fromParthenium hysterophorus, were similar to those of the enzyme fromPisum sativum. The characteristics of glycolate oxidase from leaves of a C₄ plant,Amaranthus hypochondriacus are different from those of the C₃ species or the C₃–C₄ intermediate.     

Specialist by preference,generalist by need: availability of quality hosts drives parasite choice in a natural multihost–parasite system

Encountering suitable hosts is key for parasite success. A general assumption for disease transmission is that the contact of a parasite with a potential host is driven by the density or relative frequency of hosts. That assumption ignores the potential role of differential host attractiveness for parasites that can drive the encounter of hosts. It has been posited that hosts may be chosen by parasites as a function of their suitability, but the existing literature addressing that hypothesis is still very scarce. In a natural system involving a parasitic Philornis botfly and its multiple bird hosts, there are profound differences in host quality. The Great Kiskadee tolerates and does not invest in resisting the infection, which makes it an optimal host. Alternative hosts are frequently used, but whilst some of them may be good options, others are bad alternatives. Here we examined the host selection processes that drive parasite dynamics in this system with 8 years of data from a longitudinal study under natural conditions. We found that the use of an alternative host was not driven by its density or relative frequency, but instead selection of these hosts was strongly dependent on availability of more suitable hosts. When optimal hosts are plentiful, the parasite tends to ignore alternative ones. As broods of optimal hosts become limited, good alternative hosts are targeted. The parasite chooses bad alternative hosts only when better alternatives are not sufficiently available. These results add evidence from a natural system that some parasites choose their hosts as a function of their profitability, and show that host selection by this parasite is plastic and context-dependent. Such findings could have important implications for the epidemiology of some parasitic and vector-borne infections which should be considered when modelling and managing those diseases. The facultative host selection observed here can be of high relevance for public health, animal husbandry, and biodiversity conservation, because reductions in the richness of hosts might cause humans, domestic animals, or endangered species to become increasingly targeted by parasites that can drive the encounter of hosts.     

Future challenges in coupled C–N–P cycle models for terrestrial ecosystems under global change: a review

Climate change has consequences for terrestrial functioning, but predictions of plant responses remain uncertain because of the gaps in the representation of nutrient cycles and C–N–P interactions in ecosystem models. Here, we review the processes that are included in ecosystem models, but focus on coupled C–N–P cycle models. We highlight important plant adjustments to climate change, elevated atmospheric CO₂, and/or nutrient limitations that are currently not—or only partially—incorporated in ecosystem models by reviewing experimental studies and compiling data. Plant adjustments concern C:N:P stoichiometry, photosynthetic capacity, nutrient resorption rates, allocation patterns, symbiotic N₂ fixation and root exudation (phosphatases, carboxylates) and the effect of root exudation on nutrient mobilization in the soil rhizosphere (P solubilization, biochemical mineralization of organic P and priming effect). We showed that several plant adjustments could be formulated and calibrated using existing experimental data in the literature. Finally, we proposed a roadmap for future research because improving ecosystem models necessitate specific data and collaborations between modelers and empiricists.     

Source and age of dissolved and gaseous carbon in a peatland–riparian–stream continuum: a dual isotope (14C and δ13C) analysis

Radiocarbon isotopes are increasingly being used to investigate the age and source of carbon released from peatlands. Here we use combined ¹⁴C and δ¹³C measurements to determine the isotopic composition of soil and soil decomposition products [dissolved organic carbon (DOC), CO₂ and CH₄] in a peatland–riparian–stream transect, to establish the isotopic signature and potential connectivity between carbon pools. Sampling was conducted during two time periods in 2012 to investigate processes under different temperature, hydrological and flux conditions. Isotopic differences existed in the peatland and riparian zone soil organic matter as a result of the riparian depositional formation. The peatland had a mean radiocarbon age of 551 ± 133 years BP, with age increasing with depth, and δ¹³C values consistent with C3 plant material as the primary source. In contrast the riparian zone had a much older radiocarbon age of 1,055 ± 107 years BP and showed no age/depth relationship; δ¹³C in the riparian zone was also consistent with C3 plant material. With the exception of DOC in September, soil decomposition products were predominately >100 %modern with ¹⁴C values consistent with derivation from organic matter fixed in the previous 5 years. Emissions of CO₂ and CH₄ from the soil surface were also modern. In contrast, CO₂ and CH₄ evaded from the stream surface was older (CH₄: 310–537 years BP, CO₂: 36 years BP to modern) and contained a more complex mix of sources combining soil organic matter and geogenic carbon. The results suggest considerable vertical transport of modern carbon to depth within the soil profile. The importance of modern recently fixed carbon and the differences between riparian and stream isotopic signatures suggests that the peatland (not the riparian zone) is the most important source of carbon to stream water.     

Reductive activation of the heme iron–nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study

Cytochrome c nitrite reductase catalyzes the six-electron, seven-proton reduction of nitrite to ammonia without release of any detectable reaction intermediate. This implies a unique flexibility of the active site combined with a finely tuned proton and electron delivery system. In the present work, we employed density functional theory to study the recharging of the active site with protons and electrons through the series of reaction intermediates based on nitrogen monoxide [Fe(II)-NO(+), Fe(II)-NO·, Fe(II)-NO(-), and Fe(II)-HNO]. The activation barriers for the various proton and electron transfer steps were estimated in the framework of Marcus theory. Using the barriers obtained, we simulated the kinetics of the reduction process. We found that the complex recharging process can be accomplished in two possible ways: either through two consecutive proton-coupled electron transfers (PCETs) or in the form of three consecutive elementary steps involving reduction, PCET, and protonation. Kinetic simulations revealed the recharging through two PCETs to be a means of overcoming the predicted deep energetic minimum that is calculated to occur at the stage of the Fe(II)-NO· intermediate. The radical transfer role for the active-site Tyr(218), as proposed in the literature, cannot be confirmed on the basis of our calculations. The role of the highly conserved calcium located in the direct proximity of the active site in proton delivery has also been studied. It was found to play an important role in the substrate conversion through the facilitation of the proton transfer steps.     

MMP-2 −1306C > T polymorphism in breast cancer: a case–control study in a South European population

This case control study aims to investigate the role of MMP-2 ?1306C > T polymorphism as a potential risk factor and possible prognostic marker for breast cancer in a South European population. 113 consecutive incident cases of histologically confirmed ductal breast cancer and 124 healthy controls were recruited. MMP-2 ?1306C > T polymorphism was genotyped; multivariate logistic regression as well as Cox regression analysis were performed. MMP-2 ?1306C > T status was not associated with breast cancer risk either at the total sample or at the subanalyses on premenopausal and postmenopausal women. At the survival analysis, a trend towards a favorable association between MMP-2 ?1306C > T allele and disease-free survival as well as overall survival was observed. Regarding subanalyses on ER-negative and ER-positive cases, the favorable association implicating MMP-2 ?1306C > T allele was particularly evident among ER-positive cases; no significant associations emerged among ER-negative cases. MMP-2 ?1306C > T polymorphism does not seem to be a risk factor for breast cancer in South European population; however, a trend towards a favorable association with survival has been observed.     

DCMU inhibits in vivo nitrate reduction in illuminated barley (C(3)) leaves but not in maize (C(4)): a new mechanism for the role of light?

The leaves of C(4) plants possess a superior metabolic efficiency not only in terms of photosynthetic carbon assimilation, but also in terms of inorganic nitrogen assimilation, when compared to C(3)plants. In vivo nitrate assimilation efficiency of leaves is dependent on light, but the obligatory presence of light has been debated and its role remains confounded. This problem has not been addressed from the standpoint of the C(3) vs. C(4) nature of the species investigated, which may actually hold the key to resolve the controversy. Here, we present the first report providing evidence for differential photo-regulation of leaf nitrate reduction in barley ( Hordeum vulgare L.) vs. maize ( Zea mays L.) plants, which may help explain the superior nitrogen-use efficiency (and hence superior productivity) of maize plants. The novel finding that carbohydrate-depleted maize leaves were able to reduce nitrate when photosynthesis was inhibited by 3-(3',4'-dichlorophenyl)-1,1'-dimethylurea (DCMU) in the presence of light, raises a very important question about the possibilities of a new photo-regulatory mechanism for supporting nitrate reduction in maize leaves operating independently of photosynthetic carbon dioxide fixation. On the other hand, leaves of barley could not carry out any in vivo nitrate assimilation, whatsoever, under these conditions. We find another fundamental difference between the two species in terms of differential regulation of nitrate reductase (NR; EC 1.6.6.1). In barley leaves, NR activity and activation state remained unaffected due to DCMU, but in sharp contrast, both were appreciably upregulated in maize. Collectively, the results indicate that enzyme capacity is not limiting for nitrate reduction in leaves, as the NR activity was higher in barley than in maize. The maize leaves may have had a selective advantage due to C(4) morphology/metabolism in terms of maintaining a better reductant/carbon skeleton supply for nitrate reduction.