Biogeosciences Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science.

This article is composed of three independent commentaries about the state of Integrated, Coordinated, Open, Networked (ICON) principles in the American Geophysical Union Biogeosciences section, and discussion on the opportunities and challenges of adopting them. Each commentary focuses on a different topic: (a) Global collaboration, technology transfer, and application (Section 2), (b) Community engagement, community science, education, and stakeholder involvement (Section 3), and (c) Field, experimental, remote sensing, and real-time data research and application (Section 4). We discuss needs and strategies for implementing ICON and outline short- and long-term goals. The inclusion of global data and international community engagement are key to tackling grand challenges in biogeosciences. Although recent technological advances and growing open-access information across the world have enabled global collaborations to some extent, several barriers, ranging from technical to organizational to cultural, have remained in advancing interoperability and tangible scientific progress in biogeosciences. Overcoming these hurdles is necessary to address pressing large-scale research questions and applications in the biogeosciences, where ICON principles are essential. Here, we list several opportunities for ICON, including coordinated experimentation and field observations across global sites, that are ripe for implementation in biogeosciences as a means to scientific advancements and social progress.

A trial comparing emergency front of neck airway performance in a novel obese-synthetic neck, meat-modified obese neck and conventional slim manikin.

Conventional emergency front of neck airway training manikins mimic slim patients and are associated with unrealistic procedural ease. We have described previously a pork belly-modified manikin that more realistically simulated an obese patient's neck. In this study, we compared a novel obese-synthetic manikin (obese-synthetic manikin) with a pork belly-modified manikin (obese-meat manikin) and a conventional slim manikin (slim manikin). Thirty-three experienced anaesthetists undertook simulated emergency front of neck airway procedures on each manikin (total 99 procedures). Time to ventilation was longer on both obese manikins compared with the slim manikin (median (IQR [range]) time to intubation 159 (126-243 [73-647]) s in the obese-synthetic, 105 (72-138 [43-279]) s in the obese-meat and 58 (47-74 [30-370]) s in the slim manikin; p < 0.001 between each manikin). Cricothyroidotomy success rate was similar in the both obese manikins but lower when compared with the slim manikin (15/33 obese-synthetic vs. 14/33 obese-meat vs. 27/33 slim manikin). Participant feedback indicated performance difficulty was similar between both obese manikins, which were both more difficult than the slim manikin. The tissues of the obese-meat manikin were judged more realistic than those of either other manikin. Overall, the obese-synthetic manikin performed broadly similarly to the obese-meat manikin and was technically more difficult than the conventional slim manikin. The novel obese-synthetic manikin maybe useful for training and research in front of neck airway procedures.

Characterisation of the Medipix3 detector for 60 and 80keV electrons.

In this paper we report quantitative measurements of the imaging performance for the current generation of hybrid pixel detector, Medipix3, used as a direct electron detector. We have measured the modulation transfer function and detective quantum efficiency at beam energies of 60 and 80keV. In single pixel mode, energy threshold values can be chosen to maximize either the modulation transfer function or the detective quantum efficiency, obtaining values near to, or exceeding those for a theoretical detector with square pixels. The Medipix3 charge summing mode delivers simultaneous, high values of both modulation transfer function and detective quantum efficiency. We have also characterized the detector response to single electron events and describe an empirical model that predicts the detector modulation transfer function and detective quantum efficiency based on energy threshold. Exemplifying our findings we demonstrate the Medipix3 imaging performance recording a fully exposed electron diffraction pattern at 24-bit depth together with images in single pixel and charge summing modes. Our findings highlight that for transmission electron microscopy performed at low energies (energies <100keV) thick hybrid pixel detectors provide an advantageous architecture for direct electron imaging.

The effects of injury and illness on haemoglobin mass.

This study sought to quantify the effects of reduced training, surgery and changes in body mass on haemoglobin mass (Hbmass) in athletes. Hbmass of 15 athletes (6 males, 9 females) was measured 9±6 (mean±SD) times over 162±198 days, during reduced training following injury or illness. Additionally, body mass (n=15 athletes) and episodes of altitude training (n=2), iron supplementation (n=5), or surgery (n=3) were documented. Training was recorded and compared with pre-injury levels. Analysis used linear mixed models for ln(Hbmass), with Sex, Altitude, Surgery, Iron, Training and log(Body Mass) as fixed effects, and Athlete as a fixed and random effect. Reduced training and surgery led to 2.3% (p=0.02) and 2.7% (p=0.04) decreases in Hbmass, respectively. Altitude and iron increased Hbmass by 2.4% (p=0.03) and 4.2% (p=0.05), respectively. The effect of changes in body mass on Hbmass was not statistically significant (p=0.435).The estimates for the effects of surgery and altitude on Hbmass should be confirmed by future research using a larger sample of athletes. These estimates could be used to inform the judgements of experts examining athlete biological passports, improving their interpretation of Hbmass perturbations, which athletes claim are related to injury, thereby protecting innocent athletes from unfair sanctioning.

Spurious Hb mass increases following exercise.

Sensitivity of the Athlete Blood Passport for blood doping could be improved by including total haemoglobin mass (Hb(mass)), but this measure may be unreliable immediately following strenuous exercise. We examined the stability of Hb(mass) following ultra-endurance triathlon (3.8 km swim, 180 km bike, 42.2 km run). 26 male sub-elite triathletes, 18 Racers and 8 Controls, were tested for Hb(mass) using CO re-breathing, twice 1-5 days apart. Racers were measured before and 1-3 h after the triathlon. Controls did no vigorous exercise on either test day. Serum haptoglobin concentration and urine haemoglobin concentration were measured to assess intravascular haemolysis. There was a 3.2% (p<0.01) increase in Racers' Hb(mass) from pre-race (976 g ± 14.6%, mean ±% coefficient of variation) to post-race (1 007 g ± 13.8%), as opposed to a - 0.5% decrease in Controls (pre-race 900 g ± 13.9%, post-race 896 g ± 12.4%). Haptoglobin was - 67% (p<0.01) reduced in Racers (pre-race 0.48 g / L ± 150%, post-race 0.16 g / L ± 432%), compared to - 6% reduced in Controls (pre-race 1.08 g / L ± 37%, post-race 1.02 g / L ± 37%). Decreased serum haptoglobin concentration in Racers, which is suggestive of mild intravascular blood loss, was contrary to the apparent Hb(mass) increase post-race. Ultra-endurance triathlon racing may confound the accuracy of post-exercise Hb(mass) measures, possibly due to splenic contraction or an increased rate of CO diffusion to intramuscular myoglobin.

Quality control technique to reduce the variability of longitudinal measurement of hemoglobin mass.

The sensitivity of the athlete blood passport to detect blood doping may be improved by the inclusion of total hemoglobin mass (Hb(mass)), but the comparability of Hb(mass) from different laboratories is unknown. To optimize detection sensitivity, the analytical variability associated with Hb(mass) measurement must be minimized. The aim of this study was to investigate the efficacy of using quality controls to minimize the variation in Hb(mass) between laboratories. Three simulated laboratories were set up in one location. Nine participants completed three carbon monoxide (CO) re-breathing tests in each laboratory. One participant completed two CO re-breathing tests in each laboratory. Simultaneously, quality controls containing Low (1-3%) and High (8-11%) concentrations of percent carboxyhemoglobin (%HbCO) were measured to compare hemoximeters in each laboratory. Linear mixed modeling was used to estimate the within-subject variation in Hb(mass), expressed as the coefficient of variation, and to estimate the effect of different laboratories. The analytic variation of Hb(mass) was 2.4% when tests were conducted in different laboratories, which reduced to 1.6% when the model accounted for between-laboratory differences. Adjustment of Hb(mass) values using quality controls achieved a comparable analytic variation of 1.7%. The majority of between-laboratory variation in Hb(mass) originated from the difference between hemoximeters, which could be eliminated using appropriate quality controls.

Laser-photofield emission from needle cathodes for low-emittance electron beams.

Illumination of a ZrC needle with short laser pulses (16 ps, 266 nm) while high voltage pulses (-60 kV, 2 ns, 30 Hz) are applied, produces photo-field emitted electron bunches. The electric field is high and varies rapidly over the needle surface so that quantum efficiency (QE) near the apex can be much higher than for a flat photocathode due to the Schottky effect. Up to 150 pC (2.9 A peak current) have been extracted by photo-field emission from a ZrC needle. The effective emitting area has an estimated radius below 50 microm leading to a theoretical intrinsic emittance below 0.05 mm mrad.

Respiratory carbon losses and the carbon-use efficiency of a northern hardwood forest, 1999-2003.

Quantitative assessment of carbon (C) storage by forests requires an understanding of climatic controls over respiratory C loss. Ecosystem respiration can be estimated biometrically as the sum (R Sigma) of soil (Rs), leaf (Rl) and wood (Rw) respiration, and meteorologically by measuring above-canopy nocturnal CO2 fluxes (Fcn). Here we estimated R Sigma over 5 yr in a forest in Michigan, USA, and compared R Sigma and Fcn on turbulent nights. We also evaluated forest carbon-use efficiency (Ec = P(NP)/P(GP)) using biometric estimates of net primary production (P(NP)) and R Sigma and Fcn-derived estimates of gross primary production (P(GP)). Interannual variation in R Sigma was modest (142 g C m(-2) yr(-1)). Mean annual R Sigma was 1425 g C m(-2) yr(-1); 71% from Rs, 18% from Rl, and 11% from Rw. Hourly R Sigma was well correlated with Fcn, but 11 to 58% greater depending on the time of year. Greater R Sigma compared with Fcn resulted in higher estimated annual P(GP) and lower annual Ec (0.42 vs 0.54) using biometric and meteorological data, respectively. Our results provide one of the first multiyear estimates of R Sigma in a forested ecosystem, and document the responses of component respiratory C losses to major climatic drivers. They also provide the first assessment of Ec in a deciduous forest using independent estimates of P(GP).

The HCL gene of Medicago truncatula controls Rhizobium-induced root hair curling.

The symbiotic infection of the model legume Medicago truncatula by Sinorhizobium meliloti involves marked root hair curling, a stage where entrapment of the microsymbiont occurs in a chamber from which infection thread formation is initiated within the root hair. We have genetically dissected these early symbiotic interactions using both plant and rhizobial mutants and have identified a M. truncatula gene, HCL, which controls root hair curling. S. meliloti Nod factors, which are required for the infection process, induced wild-type epidermal nodulin gene expression and root hair deformation in hcl mutants, while Nod factor induction of cortical cell division foci was reduced compared to wild-type plants. Studies of the position of nuclei and of the microtubule cytoskeleton network of hcl mutants revealed that root hair, as well as cortical cells, were activated in response to S. meliloti. However, the asymmetric microtubule network that is typical of curled root hairs, did not form in the mutants, and activated cortical cells did not become polarised and did not exhibit the microtubular cytoplasmic bridges characteristic of the pre-infection threads induced by rhizobia in M. truncatula. These data suggest that hcl mutations alter the formation of signalling centres that normally provide positional information for the reorganisation of the microtubular cytoskeleton in epidermal and cortical cells.

[Calcium oscillations and Nod signal transduction in Rhizobium-legume symbiosis]. / Oscillations calciques et transduction du signal Nod dans la symbiose Rhizobium-Légumineuses.

Rhizobium nodulation (Nod) factors are lipo-chitooligosaccharides that act as symbiotic signals, eliciting a number of key developmental responses in the roots of legume hosts. One of the earliest responses of root hairs to Nod factors is the induction of sharp oscillations of cytoplasmic calcium ion concentration ("calcium spiking"). This response was first characterised in Medicago sativa and Nod factors were found to be unable to induce calcium spiking in a nodulation-defective mutant of M. sativa. The fact that this mutant lacked any morphological response to Nod factors raised the question of whether calcium spiking could be part of a Nod factor-induced signal transduction pathway leading to nodulation. More recently, calcium spiking has been described in a model legume, Medicago truncatula, and in pea. When nodulation-defective mutants were tested for the induction of calcium spiking in response to Nod factors, three loci of pea and two of M. truncatula were found to be necessary for Nod factor-induced calcium spiking. These loci are also known to be necessary for Nod factor-induction of symbiotic responses such as root hair deformation, nodulin gene expression and cortical cell division. These results therefore constitute strong genetic evidence for the role of calcium spiking in Nod factor transduction. This system provides an opportunity to use genetics to study ligand-stimulated calcium spiking as a signal transduction event.

Genetic analysis of calcium spiking responses in nodulation mutants of Medicago truncatula.

The symbiotic interaction between Medicago truncatula and Sinorhizobium meliloti results in the formation of nitrogen-fixing nodules on the roots of the host plant. The early stages of nodule formation are induced by bacteria via lipochitooligosaccharide signals known as Nod factors (NFs). These NFs are structurally specific for bacterium-host pairs and are sufficient to cause a range of early responses involved in the host developmental program. Early events in the signal transduction of NFs are not well defined. We have previously reported that Medicago sativa root hairs exposed to NF display sharp oscillations of cytoplasmic calcium ion concentration (calcium spiking). To assess the possible role of calcium spiking in the nodulation response, we analyzed M. truncatula mutants in five complementation groups. Each of the plant mutants is completely Nod- and is blocked at early stages of the symbiosis. We defined two genes, DMI1 and DMI2, required in common for early steps of infection and nodulation and for calcium spiking. Another mutant, altered in the DMI3 gene, has a similar mutant phenotype to dmi1 and dmi2 mutants but displays normal calcium spiking. The calcium behavior thus implies that the DMI3 gene acts either downstream of calcium spiking or downstream of a common branch point for the calcium response and the later nodulation responses. Two additional mutants, altered in the NSP and HCL genes, which show root hair branching in response to NF, are normal for calcium spiking. This system provides an opportunity to use genetics to study ligand-stimulated calcium spiking as a signal transduction event.

Four genes of Medicago truncatula controlling components of a nod factor transduction pathway.

Rhizobium nodulation (Nod) factors are lipo-chitooligosaccharides that act as symbiotic signals, eliciting several key developmental responses in the roots of legume hosts. Using nodulation-defective mutants of Medicago truncatula, we have started to dissect the genetic control of Nod factor transduction. Mutants in four genes (DMI1, DMI2, DMI3, and NSP) were pleiotropically affected in Nod factor responses, indicating that these genes are required for a Nod factor-activated signal transduction pathway that leads to symbiotic responses such as root hair deformations, expressions of nodulin genes, and cortical cell divisions. Mutant analysis also provides evidence that Nod factors have a dual effect on the growth of root hair: inhibition of endogenous (plant) tip growth, and elicitation of a novel tip growth dependent on (bacterial) Nod factors. dmi1, dmi2, and dmi3 mutants are also unable to establish a symbiotic association with endomycorrhizal fungi, indicating that there are at least three common steps to nodulation and endomycorrhization in M. truncatula and providing further evidence for a common signaling pathway between nodulation and mycorrhization.

Structure, properties, and tissue localization of apoplastic alpha-glucosidase in crucifers.

Apoplastic alpha-glucosidases occur widely in plants but their function is unknown because appropriate substrates in the apoplast have not been identified. Arabidopsis contains at least three alpha-glucosidase genes; Aglu-1 and Aglu-3 are sequenced and Aglu-2 is known from six expressed sequence tags. Antibodies raised to a portion of Aglu-1 expressed in Escherichia coli recognize two proteins of 96 and 81 kD, respectively, in vegetative tissues of Arabidopsis, broccoli (Brassica oleracea L.), and mustard (Brassica napus L.). The acidic alpha-glucosidase activity from broccoli flower buds was purified using concanavalin A and ion-exchange chromatography. Two active fractions were resolved and both contained a 96-kD immunoreactive polypeptide. The N-terminal sequence from the 96-kD broccoli alpha-glucosidase indicated that it corresponds to the Arabidopsis Aglu-2 gene and that approximately 15 kD of the predicted N terminus was cleaved. The 81-kD protein was more abundant than the 96-kD protein, but it was not active with 4-methylumbelliferyl-alpha-D-glucopyranoside as the substrate and it did not bind to concanavalin A. In situ activity staining using 5-bromo-4-chloro-3-indolyl-alpha-D-glucopyranoside revealed that the acidic alpha-glucosidase activity is predominantly located in the outer cortex of broccoli stems and in vascular tissue, especially in leaf traces.

Differential stability of the triple helix of (Pro-Pro-Gly)10 in H2O and D2O: thermodynamic and structural explanations.

(Pro-Pro-Gly)10 [(PPG10)], a collagen-like polypeptide, forms a triple-helical, polyproline-II structure in aqueous solution at temperatures somewhat lower than physiological, with a melting temperature of 24.5 degrees C. In this article, we present circular dichroism spectra that demonstrate an increase of the melting temperature with the addition of increasing amounts of D2O to an H2O solution of (PPG)10, with the melting temperature reaching 40 degrees C in pure D2O. A thermodynamic analysis of the data demonstrates that this result is due to an increasing enthalpy of unfolding in D2O vs. H2O. To provide a theoretical explanation for this result, we have used a model for hydration of (PPG)10 that we developed previously, in which inter-chain water bridges are formed between sterically crowded waters and peptide bond carbonyls. Energy minimizations were performed upon this model using hydrogen bond parameters for water, and altered hydrogen bond parameters that reproduced the differences in carbonyl oxygen-water oxygen distances found in small-molecule crystal structures containing oxygen-oxygen hydrogen bonds between organic molecules and H2O or D2O. It was found that using hydrogen bond parameters that reproduced the distance typical of hydrogen bonds to D2O resulted in a significant lowering of the potential energy of hydrated (PPG)10. This lowering of the energy involved energetic terms that were only indirectly related to the altered hydrogen bond parameters, and were therefore not artifactual; the intra-(PPG10) energy, plus the water-(PPG10) van der Waals energy (not including hydrogen bond interactions), were lowered enough to qualitatively account for the lower enthalpy of the triple-helical conformation, relative to the unfolded state, in D2O vs. H2O. This result indicates that the geometry of the carbonyl-D2O hydrogen bonds allows formation of good hydrogen bonds without making as much of an energetic sacrifice from other factors as in the case of hydration by H2O.

The role of bound water in the stability of the triple-helical conformation of (Pro-Pro-Gly)10.

There is significant experimental evidence for bound water in collagen and related polymers. (Pro-Pro-Gly)10 [(PPG)10] is a polymer that forms a collagen-like triple-helical structure in aqueous solution. Like collagen, (PPG)10 adopts a structure in which side chains are mostly exposed to solvent, and the backbone polar groups are limited in their ability to form hydrogen bonds with each other. (PPG)10, like collagen, also has many of its backbone polar groups in positions that inhibit complete solvation in aqueous solution; thus the necessity of bound waters for stabilization of the structure. We have constructed a model for bound waters in (PPG)10, based on an examination of the geometry and steric environment of the backbone polar groups. As will become clear, the number of bound waters is determined by the geometry of the backbone carbonyl groups and the steric crowding surrounding them. In this model, each water forms one hydrogen bond with each of two backbone carbonyls from a glycine and a proline in different monomer chains, thus bridging the two carbonyls. The carbonyls in question are quite sterically crowded by neighboring (PPG)10 atoms and would not be likely to experience complete solvation by bulk solvent in aqueous solution. The bound waters are therefore likely to be present even in solution, since otherwise the unsatisfied hydrogen-bonding potential of the carbonyls would destabilize the structure. Other carbonyls also are sterically crowded and possibly prevented from experiencing full solvation, but are not in a favorable geometry for such bridging hydrogen bonds. The intra- and interchain interactions found in a previous computational study of (PPG)10 without bound waters are not disrupted by the addition of waters.

Controlling persistent organic pollutants-what next?

Within the context of current international initiatives on the control of persistent organic pollutants (POPs), an overview is given of the scientific knowledge relating to POP sources, emissions, transport, fate and effects. At the regional scale, improvements in mass balance models for well-characterised POPs are resulting in an ability to estimate their environmental concentrations with sufficient accuracy to be of help for some regulatory purposes. The relevance of the parameters used to define POPs within these international initiatives is considered with an emphasis on mechanisms for adding new substances to the initial lists. A tiered approach is proposed for screening the large number of untested chemical substances according to their long-range transport potential, persistence and bioaccumulative potential prior to more detailed risk assessments. The importance of testing candidate POPs for chronic toxicity (i.e. for immunotoxicity, endocrine disruption and carcinogenicity) is emphasised as is a need for the further development of relevant SAR (structure activity relationship) models and in vitro and in vivo tests for these effects. Where there is a high level of uncertainty at the risk assessment stage, decision-makers may have to rely on expert judgement and weight-of-evidence, taking into account the precautionary principle and the views of relevant stake-holders. Close co-operation between the various international initiatives on POPs will be required to ensure that assessment criteria and procedures are as compatible as possible.