Estimating Annual Soil Carbon Loss in Agricultural Peatland Soils Using a Nitrogen Budget Approach

Around the world, peatland degradation and soil subsidence is occurring where these soils have been converted to agriculture. Since initial drainage in the mid-1800s, continuous farming of such soils in the California Sacramento-San Joaquin Delta (the Delta) has led to subsidence of up to 8 meters in places, primarily due to soil organic matter (SOM) oxidation and physical compaction. Rice (Oryza sativa) production has been proposed as an alternative cropping system to limit SOM oxidation. Preliminary research on these soils revealed high N uptake by rice in N fertilizer omission plots, which we hypothesized was the result of SOM oxidation releasing N. Testing this hypothesis, we developed a novel N budgeting approach to assess annual soil C and N loss based on plant N uptake and fallow season N mineralization. Through field experiments examining N dynamics during growing season and winter fallow periods, a complete annual N budget was developed. Soil C loss was calculated from SOM-N mineralization using the soil C:N ratio. Surface water and crop residue were negligible in the total N uptake budget (3 – 4 % combined). Shallow groundwater contributed 24 – 33 %, likely representing subsurface SOM-N mineralization. Assuming 6 and 25 kg N ha-1 from atmospheric deposition and biological N2 fixation, respectively, our results suggest 77 – 81 % of plant N uptake (129 – 149 kg N ha^-1) was supplied by SOM mineralization. Considering a range of N uptake efficiency from 50 – 70 %, estimated net C loss ranged from 1149 – 2473 kg C ha^-1. These findings suggest that rice systems, as currently managed, reduce the rate of C loss from organic delta soils relative to other agricultural practices.     

Microbial Utilization of Estuarine Dissolved Organic Carbon: a Stable Isotope Tracer Approach Tested by Mass Balance

The natural stable isotope values of different plants have been used to trace the fate of organic carbon that enters estuarine ecosystems. Experiments were designed to determine the magnitude of (delta) (sup13)C changes of dissolved organic carbon (DOC) derived from tidal marsh vegetation that occurred during bacterial decomposition. Bacteria were grown on DOC leached from estuarine Spartina alterniflora and Typhus angustifolia plants. In four experiments, 25 to 80% of the initial carbon (2.6 to 9.1 mM organic C) was converted to bacterial biomass and CO(inf2). Mass balance calculations showed good recovery of total C and (sup13)C at the end of these experiments (100% (plusmn) 14% total C; (plusmn) 1(permil) (delta) (sup13)C). The (delta) (sup13)C values of DOC, bacterial biomass, and respired CO(inf2) changed only slightly in the four experiments by average values of -0.6, +1.4, and +0.5(permil), respectively. These changes are small relative to the range of (delta) (sup13)C values represented by different organic carbon sources to estuaries. Thus, microbial (delta) (sup13)C values determined in the field helped to identify the source of the carbon assimilated by bacteria.     

Woody Plant Encroachment by <Emphasis Type="Italic">Juniperus virginiana</Emphasis> in a Mesic Native Grassland Promotes Rapid Carbon and Nitrogen Accrual

The cover and abundance of Juniperus virginiana L. in the U.S. Central Plains are rapidly increasing, largely as a result of changing land-use practices that alter fire regimes in native grassland communities. Little is known about how conversion of native grasslands to Juniperus-dominated forests alters soil nutrient availability and ecosystem storage of carbon (C) and nitrogen (N), although such land-cover changes have important implications for local ecosystem dynamics, as well as regional C and N budgets. Four replicate native grasslands and adjacent areas of recent J. virginiana encroachment were selected to assess potential changes in soil N availability, leaf-level photosynthesis, and major ecosystem C and N pools. Net N mineralization rates were assessed in situ over two years, and changes in labile soil organic pools (potential C and N mineralization rates and microbial biomass C and N) were determined. Photosynthetic nitrogen use efficiencies (PNUE) were used to examine differences in instantaneous leaf-level N use in C uptake. Comparisons of ecosystem C and N stocks revealed significant C and N accrual in both plant biomass and soils in these newly established forests, without changes in labile soil N pools. There were few differences in monthly in situ net N mineralization rates, although cumulative annual net N mineralization was greater in forest soils compared to grasslands. Conversely, potential C mineralization was significantly reduced in forest soils. Encroachment by J. virginiana into grasslands results in rapid accretion of ecosystem C and N in plant and soil pools with little apparent change in N availability. Widespread increases in the cover of woody plants, like J. virginiana, in areas formerly dominated by graminoid species suggest an increasing role of expanding woodlands and forests as regional C sinks in the central U.S.     

Impact assessment of an invasive macrophyte community on ecosystem properties: A Mass Balance Approach for Chilika lagoon,India

Phragmites karka (commonly known as Nala grass) is considered an invasive macrophyte, covering an area of 105.1 sq. km, hindering navigation and impacting the ecosystem functioning of Chilika Lagoon (1165 sq.km). The mass balanced models of three different scenarios of Chilika Lagoon were developed using Ecopath to assess the impact of the invasive macrophyte P. karka on the various ecological attributes of the ecosystem. The three different scenarios modelled were (1) a real-time scenario with 23 functional groups that includes P. karka as a group, (2) a virtual scenario with only 22 functional groups where the system is devoid of P. karka, and (3) a virtual scenario that has 22 groups but is devoid of the functional group seagrass and other macrophytes. The results of our study indicate that scenario-2, which is devoid of the macrophyte P. karka, was found to be a relatively mature and resilient ecosystem with the highest utilisation of primary production within the system. This scenario also possesses the highest overhead (67.47%) and Finn's cycling index (FCI) (4.226%) in comparison to the other two scenarios. The ecosystem indices showed a negative impact of P. karka on the trophic functioning of the Chilika Lagoon, which warrants an urgent need to remove the macrophyte to improve the resilience of the ecosystem.     

Recommendations for a Core Outcome Set for Measuring Standing Balance in Adult Populations: A Consensus-Based Approach

Background

Standing balance is imperative for mobility and avoiding falls. Use of an excessive number of standing balance measures has limited the synthesis of balance intervention data and hampered consistent clinical practice.

Objective

To develop recommendations for a core outcome set (COS) of standing balance measures for research and practice among adults.

Methodology

A combination of scoping reviews, literature appraisal, anonymous voting and face-to-face meetings with fourteen invited experts from a range of disciplines with international recognition in balance measurement and falls prevention. Consensus was sought over three rounds using pre-established criteria.

Data sources

The scoping review identified 56 existing standing balance measures validated in adult populations with evidence of use in the past five years, and these were considered for inclusion in the COS.

Results

Fifteen measures were excluded after the first round of scoring and a further 36 after round two. Five measures were considered in round three. Two measures reached consensus for recommendation, and the expert panel recommended that at a minimum, either the Berg Balance Scale or Mini Balance Evaluation Systems Test be used when measuring standing balance in adult populations.

Limitations

Inclusion of two measures in the COS may increase the feasibility of potential uptake, but poses challenges for data synthesis. Adoption of the standing balance COS does not constitute a comprehensive balance assessment for any population, and users should include additional validated measures as appropriate.

Conclusions

The absence of a gold standard for measuring standing balance has contributed to the proliferation of outcome measures. These recommendations represent an important first step towards greater standardization in the assessment and measurement of this critical skill and will inform clinical research and practice internationally.     

Priming of Soil Carbon Decomposition in Two Inner Mongolia Grassland Soils following Sheep Dung Addition: A Study Using 13C Natural Abundance Approach

To investigate the effect of sheep dung on soil carbon (C) sequestration, a 152 days incubation experiment was conducted with soils from two different Inner Mongolian grasslands, i.e. a Leymus chinensis dominated grassland representing the climax community (2.1% organic matter content) and a heavily degraded Artemisia frigida dominated community (1.3% organic matter content). Dung was collected from sheep either fed on L. chinensis (C₃ plant with δ¹³C = −26.8‰; dung δ¹³C = −26.2‰) or Cleistogenes squarrosa (C₄ plant with δ¹³C = −14.6‰; dung δ¹³C = −15.7‰). Fresh C₃ and C₄ sheep dung was mixed with the two grassland soils and incubated under controlled conditions for analysis of ¹³C-CO₂ emissions. Soil samples were taken at days 17, 43, 86, 127 and 152 after sheep dung addition to detect the δ¹³C signal in soil and dung components. Analysis revealed that 16.9% and 16.6% of the sheep dung C had decomposed, of which 3.5% and 2.8% was sequestrated in the soils of L. chinensis and A. frigida grasslands, respectively, while the remaining decomposed sheep dung was emitted as CO₂. The cumulative amounts of C respired from dung treated soils during 152 days were 7–8 times higher than in the un-amended controls. In both grassland soils, ca. 60% of the evolved CO₂ originated from the decomposing sheep dung and 40% from the native soil C. Priming effects of soil C decomposition were observed in both soils, i.e. 1.4 g and 1.6 g additional soil C kg⁻¹ dry soil had been emitted as CO₂ for the L. chinensis and A. frigida soils, respectively. Hence, the net C losses from L. chinensis and A. frigida soils were 0.6 g and 0.9 g C kg⁻¹ soil, which was 2.6% and 7.0% of the total C in L. chinensis and A. frigida grasslands soils, respectively. Our results suggest that grazing of degraded Inner Mongolian pastures may cause a net soil C loss due to the positive priming effect, thereby accelerating soil deterioration.     

Highly Enantioselective Michael Addition Promoted by a New Diterpene‐Derived Bifunctional Thiourea Catalyst: A Doubly Stereocontrolled Approach to Chiral Succinimide Derivatives

A doubly stereocontrolled organocatalytic asymmetric Michael addition to the synthesis of substituted succinimides is described. Starting from aldehydes and maleimides, both enantiomers of the succinimides could be obtained in high to excellent yields (up to 98%) and enantioselectivities (up to 99%) when one of the two special chiral diterpene‐derived bifunctional thioureas was individually used as a catalyst. Moreover, these catalysts can be efficiently used in large‐scale catalytic synthesis with the same level of yield and enantioselectivity. Chirality 00:000–000, 2014. © 2014 Wiley Periodicals, Inc.     

Compensatory Roles of Nitrogen Uptake and Photosynthetic N-use Efficiency in Determining Plant Growth Response to Elevated CO2: Evaluation Using a Functional Balance Model

We used a modified functional balance (FB) model to predictgrowth response of Helianthus annuus L. to elevated CO₂. Modelpredictions were evaluated against measurements obtained twiceduring the experiment. There was a good agreement between modelpredictions of relative growth rate (RGR) responses to elevatedCO₂and observations, particularly at the second harvest. Themodel was then used to compare the relative effects of biomassallocation to roots, nitrogen (N) uptake and photosyntheticN-use efficiency (PNUE) in determining plant growth responseto elevated CO₂. The model predicted that a rather substantialincrease in biomass allocation to root growth had little effecton whole plant growth response to elevated CO₂, suggesting thatplasticity in root allocation is relatively unimportant in determininggrowth response. Average N uptake rate at elevated comparedto ambient CO₂was decreased by 21–29%. In contrast, elevatedCO₂increased PNUE by approx. 50% due to a corresponding risein the CO₂-saturation factor for carboxylation at elevated CO₂.The model predicted that the decreased N uptake rate at elevatedCO₂lowered RGR modestly, but this effect was counterbalancedby an increase in PNUE resulting in a positive CO₂effect ongrowth. Increased PNUE may also explain why in many experimentselevated CO₂enhances biomass accumulation despite a significantdrop in tissue nitrogen concentration. The formulation of theFB model as presented here successfully predicted plant growthresponses to elevated CO₂. It also proved effective in resolvingwhich plant properties had the greatest leverage on such responses.Copyright 2000 Annals of Botany Company Elevated CO₂, functional balance model, Helianthus annuus L., N uptake, photosynthetic nitrogen use efficiency, root:shoot ratio     

Estimating a Logistic Discrimination Functions When One of the Training Samples Is Subject to Misclassification: A Maximum Likelihood Approach

The problem of discrimination and classification is central to much of epidemiology. Here we consider the estimation of a logistic regression/discrimination function from training samples, when one of the training samples is subject to misclassification or mislabeling, e.g. diseased individuals are incorrectly classified/labeled as healthy controls. We show that this leads to zero-inflated binomial model with a defective logistic regression or discrimination function, whose parameters can be estimated using standard statistical methods such as maximum likelihood. These parameters can be used to estimate the probability of true group membership among those, possibly erroneously, classified as controls. Two examples are analyzed and discussed. A simulation study explores properties of the maximum likelihood parameter estimates and the estimates of the number of mislabeled observations.     

Estimating genetic variance contributed by a quantitative trait locus: A random model approach

Detecting quantitative trait loci (QTL) and estimating QTL variances (represented by the squared QTL effects) are two main goals of QTL mapping and genome-wide association studies (GWAS). However, there are issues associated with estimated QTL variances and such issues have not attracted much attention from the QTL mapping community. Estimated QTL variances are usually biased upwards due to estimation being associated with significance tests. The phenomenon is called the Beavis effect. However, estimated variances of QTL without significance tests can also be biased upwards, which cannot be explained by the Beavis effect; rather, this bias is due to the fact that QTL variances are often estimated as the squares of the estimated QTL effects. The parameters are the QTL effects and the estimated QTL variances are obtained by squaring the estimated QTL effects. This square transformation failed to incorporate the errors of estimated QTL effects into the transformation. The consequence is biases in estimated QTL variances. To correct the biases, we can either reformulate the QTL model by treating the QTL effect as random and directly estimate the QTL variance (as a variance component) or adjust the bias by taking into account the error of the estimated QTL effect. A moment method of estimation has been proposed to correct the bias. The method has been validated via Monte Carlo simulation studies. The method has been applied to QTL mapping for the 10-week-body-weight trait from an F₂ mouse population.     

Description and Prediction of the Development of Metabolic Syndrome: A Longitudinal Analysis Using a Markov Model Approach

Background

Delineating the natural history of metabolic syndrome (MetS) is prerequisite to prevention. This study aimed to build Markov models to simulate each component’s progress and to test the effect of different initial states on the development of MetS.

Methods

MetS was defined with revised AHA/NHLBI criteria. Each reversible multistate Markov chain consisted of 8 states (no component, five isolated component states, 2-component state, and MetS state). Yearly transition probabilities were calculated from a five-year population-based follow up studywhich enrolled 2,247 individuals with mean aged 32.4 years at study entry.

Results

In men, high BP or a 2-component state was most likely to initiate the progress of MetS. In women, abdominal obesity or low HDL were the most likely initiators. Metabolic components were likely to occur together. The development of MetS was an increasing monotonic function of time. MetS was estimated to develop within 15 years in 12.7% of young men with no component, and 2 components developed in 16.3%. MetS was estimated to develop in 10.6% of women with at the age of 47, and 2 components developed in 14.3%. MetS was estimated to develop in 24.6% of men and 27.6% of women with abdominal obesity, a rate higher than in individuals initiating with no component.

Conclusions

This modeling study allows estimation of the natural history of MetS. Men tended to develop this syndrome sooner than women did, i.e., before their fifth decade of life. Individuals with 1 or 2 components showed increased development of MetS.     

The Source for the Difference Between Sulfhydryl and Hydroxyl Anions in Their Nucleophilic Addition Reaction to a Carbonyl Group: A DFT Approach.

Ab initio calculations show that sulfhydryl anion has a significantly lower potential than the hydroxide anion for stabilizing the products of its attack on carbonyl moieties - the tetrahedral complexes (TC). In this paper we analyze the factors that contribute to this phenomenon. Quantum mechanical MO ab initio calculations were used for studies of two reaction series, one for the attack of hydroxyl and one for the attack of sulfhydryl anion on different carbonyl compounds and their analogs. All of the anionic TCs formed by HS^- are characterized by higher charge transfer, but are significantly less stable than the relevant TC of HO^-. To explain the phenomenon we used a simple qualitative model based on Density Functional Theory (DFT). The crucial role of the occupied valence MOs is demonstrated in the process of electronegativity equalization between the donor and acceptor fragments in the final TC product. The sulfhydryl anion has significantly lower potential to stabilize TC products in comparison with the hydroxide anion because of the larger extent of electron back-donation from the electrophiles HOMO_A to the nucleophiles LUMO_D. This electron back-donation thus reduces the stability of the anionic TC in the case of HS^- and may account for the calculational results. Applications of this work to enzyme reactions help in understanding the differences in mechanisms of serine and cysteine proteases and may be used to guide the design of inhibitors for these enzymes. In perspective, the back-donation phenomenon discussed here may be applied to the study of electron transfer processes involving oxidation-reduction enzymes.     

A CHARMm Based Force Field for Carbohydrates Using the CHEAT Approach: Carbohydrate Hydroxyl Groups Represented by Extended Atoms

Abstract

Computational studies of carbohydrates that do not consider explicit solvent molecules suffer from the strong tendency of the carbohydrate pendant hydroxyl groups to form intramolecular hydrogen bonds that are unlikely to be present in protic media. In this paper a novel approach towards molecular modelling of carbohydrates is described. The average effect of intra- and intermolecular hydrogen bonding is introduced into the potential energy function by adding a new (extended) atom type representing a carbohydrate hydroxyl group to the CHARMm force field; we coin the name CHEAT (Carbohydrate Hydroxyls represented by Extended AToms) for the resulting force field. As a training set for the parametrisation of CHEAT we used ethylene glycol, 10 cyclohexanols, 5 inositols, and 12 glycopyranoses for which in total 64 conformational energy differences were estimated using a set of steric interaction energies between hydroxyl and/or methyl groups on six-membered ring compounds as derived by Angyal (Angew. Chem., 8, 172-182, (1969)). The root-mean-square deviation between the estimated energy differences and the corresponding values obtained by our CHEAT approach amounts to 0.37 kcal/mol (n = 64). The CHEAT approach, which is claimed to calculate aqueous state compatible energetical and conformational properties of carbohydrates, is computationally very efficient and facilitates the calculation of nanosecond range MD trajectories as well as systematic conformational searches of oligosaccharides.     

Influence of a Polyphenol-Enriched Protein Powder on Exercise-Induced Inflammation and Oxidative Stress in Athletes: A Randomized Trial Using a Metabolomics Approach

Objectives

Polyphenol supplementation was tested as a countermeasure to inflammation and oxidative stress induced by 3-d intensified training.

Methods

Water soluble polyphenols from blueberry and green tea extracts were captured onto a polyphenol soy protein complex (PSPC). Subjects were recruited, and included 38 long-distance runners ages 19–45 years who regularly competed in road races. Runners successfully completing orientation and baseline testing (N = 35) were randomized to 40 g/d PSPC (N = 17) (2,136 mg/d gallic acid equivalents) or placebo (N = 18) for 17 d using double-blinded methods and a parallel group design, with a 3-d running period inserted at day 14 (2.5 h/d, 70% VO_2max). Blood samples were collected pre- and post-14 d supplementation, and immediately and 14 h after the third day of running in subjects completing all aspects of the study (N = 16 PSPC, N = 15 placebo), and analyzed using a metabolomics platform with GC-MS and LC-MS.

Results

Metabolites characteristic of gut bacteria metabolism of polyphenols were increased with PSPC and 3 d running (e.g., hippurate, 4-hydroxyhippurate, 4-methylcatechol sulfate, 1.8-, 1.9-, 2.5-fold, respectively, P<0.05), an effect which persisted for 14-h post-exercise. Fatty acid oxidation and ketogenesis were induced by exercise in both groups, with more ketones at 14-h post-exercise in PSPC (3-hydroxybutyrate, 1.8-fold, P<0.05). Established biomarkers for inflammation (CRP, cytokines) and oxidative stress (protein carbonyls) did not differ between groups.

Conclusions

PSPC supplementation over a 17-d period did not alter established biomarkers for inflammation and oxidative stress but was linked to an enhanced gut-derived phenolic signature and ketogenesis in runners during recovery from 3-d heavy exertion.

Trial Registration

ClinicalTrials.gov, U.S. National Institutes of Health, identifier: {"type":"clinical-trial","attrs":{"text":"NCT01775384","term_id":"NCT01775384"}}NCT01775384     

Comparative Proteomics Studies of Insect Cuticle by Tandem Mass Spectrometry: Application of a Novel Proteomics Approach to the Pea Aphid Cuticular Proteins

The cuticle is a biological composite material consisting principally of N‐acetylglucosamine polymer embedded in cuticular proteins (CPs). CPs have been studied and characterized by mass spectrometry in several cuticular structures and in many arthropods. Such analyses were carried out by protein extraction using SDS followed by electrophoresis, allowing detection and identification of numerous CPs. To build a repertoire of cuticular structures from Bombyx mori, Apis mellifera and Anopheles gambiae the use of SDS and electrophoresis was avoided. Using the combination of hexafluoroisopropanol and of a surfactant compatible with MS, a high number of CPs was identified in An. gambiae wings, legs and antennae, and in the thoracic integument cuticle of Ap. mellifera pupae. The exoskeleton analysis of B. mori larvae allowed to identify 85 CPs from a single larva. Finally, the novel proteomics approach was tested on cuticles left behind after the molt from the fourth instar of Acyrthosiphon pisum. Analysis of these cast cuticles allowed to identify 100 Ac. pisum CPs as authentic cuticle constituents. These correspond to 68% of the total putative CPs previously annotated for this pea aphid. While this paper analyzes only the recovered cuticular proteins, peptides from many other proteins were also detected.