ALBERT

Description: Looking beyond stratification: a model-based analysis of the biological drivers of oxygen depletion in the North Sea Biogeosciences Discussions, 12, 12543-12610, 2015 Author(s): F. Große, N. Greenwood, M. Kreus, H. J. Lenhart, D. Machoczek, J. Pätsch, L. A. Salt, and H. Thomas The problem of low oxygen conditions, often referred to as hypoxia, occurs regularly in the North Sea, a temperate European shelf sea. Stratification represents a major process regulating the seasonal dynamics of bottom oxygen. However, lowest oxygen conditions in the North Sea do not occur in the regions of strongest stratification. This suggests that stratification is an important prerequisite for hypoxia, but that the complex interaction between hydrodynamics and the biological processes drives its development. In this study we use the ecosystem model HAMSOM-ECOHAM5 to provide a general characteristic of the different North Sea oxygen regimes, and to quantify the impact of the different physical and biological factors driving the oxygen dynamics below the thermocline and in the bottom layer. We show that the North Sea can be subdivided into three different regimes in terms of oxygen dynamics: (1) a highly productive, non-stratified coastal regime, (2) a productive, seasonally stratified regime with a small sub-thermocline volume, and (3) a productive, seasonally stratified regime with a large sub-thermocline volume, with regime 2 being highly susceptible to hypoxic conditions. Our analysis of the different processes driving the oxygen development reveals that inter-annual variations in the oxygen conditions are caused by variations in primary production, while spatial differences can be attributed to differences in stratification and water depth. In addition, we show that benthic bacteria represent the main oxygen consumers in the bottom layer, consistently accounting for more than 50 % of the overall consumption. By providing these valuable insights, we show that ecosystem models can be a useful tool for the interpretation of observations and the estimation of the impact of anthropogenic drivers on the North Sea oxygen conditions.

Description: Optimizing the impact of temperature on bio-hydrogen production from food waste and its derivatives under no pH control using statistical modelling Biogeosciences Discussions, 12, 12823-12850, 2015 Author(s): A. Sattar, C. Arslan, C. Ji, S. Sattar, K. Yousaf, and S. Hashim The effect of temperature on bio-hydrogen production by co-digestion of sewerage sludge with food waste and its two derivatives, i.e. noodle waste and rice waste, was investigated by statistical modelling. Experimental results showed that increasing temperature from mesophilic (37 °C) to thermophilic (55 °C) was an effective mean for increasing bio-hydrogen production from food waste and noodle waste, but it caused a negative impact on bio-hydrogen production from rice waste. The maximum cumulative bio-hydrogen production of 650 mL was obtained from noodle waste under mesophilic temperature condition. Most of the production was observed during 48 h of incubation that continued till 72 h of incubation, and a decline in pH during this interval was 4.3 and 4.4 from a starting value of 7 under mesophilic and thermophilic conditions, respectively. Most of glucose consumption was also observed during 72 h of incubation and the maximum consumption was observed during the first 24 h, which was the same duration where the maximum pH drop occurred. The maximum hydrogen yields of 82.47 mL VS −1 , 131.38 mL COD −1 , and 44.90 mL glucose −1 were obtained from mesophilic food waste, thermophilic noodle waste and mesophilic rice waste respectively. The production of volatile fatty acids increased with an increase in time and temperature from food waste and noodle waste reactors whereas it decreased with temperature in rice waste reactors. The statistical modelling returned good results with high values of coefficient of determination ( R 2 ) for each waste type when it was opted for the study of cumulative hydrogen production, glucose consumption and volatile fatty acid production. The 3-D response surface plots developed by the statistical models helped a lot in developing better understanding of the impact of temperature and incubation time.

Description: As internet technologies make their way into developing areas, so too does the possibility of education and training being delivered to the people living in those previously unserved areas. The growing catalogue of free, high quality courseware, when combined with the newly acquired means of delivery, creates the potential for millions of people in the developing world to acquire a good education. Yet a good education obviously requires more than simply delivering information; students must also receive high quality feedback on their assessments. They must be told how their performance compares with the ideal, and be shown how to close the gap between the two. However, delivering high quality feedback is labor-intensive, and therefore expensive, and has long been recognized as a problematic issue by educators. This paper outlines a case study that uses a Learning Management System (LMS) to efficiently deliver detailed feedback that is informed by the principles of best practice. We make the case that the efficiencies of this method allow for large-scale courses with thousands of enrolments that are accessible to developing and developed areas alike. We explore the question; is computer-mediated feedback delivery efficient and effective and might it be applied to large-scale courses at low-cost?

Description: Stable isotope study of a new chondrichthyan fauna (Kimmeridgian, Porrentruy, Swiss Jura): an unusual freshwater-influenced isotopic composition for the hybodont shark Asteracanthus Biogeosciences Discussions, 12, 12899-12921, 2015 Author(s): L. Leuzinger, L. Kocsis, J.-P. Billon-Bruyat, S. Spezzaferri, and T. Vennemann Chondrichthyan teeth (sharks, rays and chimaeras) are mineralised in isotopic equilibrium with the surrounding water, and parameters such as water temperature and salinity can be inferred from the oxygen isotopic composition (δ 18 O p ) of their bioapatite. We analysed a new chondrichthyan assemblage, as well as teeth from bony fish (Pycnodontiformes). All specimens are from Kimmeridgian coastal marine deposits of the Swiss Jura (vicinity of Porrentruy, Ajoie district, NW Switzerland). While the overall faunal composition and the isotopic composition of bony fish are consistent with marine conditions, unusually low δ 18 O p values were measured for the hybodont shark Asteracanthus . These values are also lower compared to previously published data from older European Jurassic localities. Additional analyses on material from Solothurn (Kimmeridgian, NW Switzerland) also have comparable, low- 18 O isotopic compositions for Asteracanthus . The data are hence interpreted to represent a so far unique, freshwater-influenced isotopic composition for this shark that is classically considered as a marine genus. While reproduction in freshwater or brackish realms is established for other hybodonts, a similar behaviour for Asteracanthus is proposed here. Regular excursions into lower salinity waters can be linked to the age of the deposits and correspond to an ecological adaptation, most likely driven by the Kimmeridgian transgression and by the competition of the primitive shark Asteracanthus with the rapidly diversifying neoselachians (modern sharks).

Description: Climate change impacts on net primary production (NPP) and export production (EP) regulated by increasing stratification and phytoplankton community structure in CMIP5 models Biogeosciences Discussions, 12, 12851-12897, 2015 Author(s): W. Fu, J. Randerson, and J. K. Moore We examine climate change impacts on net primary production (NPP) and export production (sinking particulate flux; EP) with simulations from nine Earth System Models (ESMs) performed in the framework of the fifth Coupled Model Inter-comparison Project (CMIP5). Global NPP and EP are reduced considerably by the end of the century for the intense warming scenario of Representative Concentration Pathway (RCP) 8.5. Relative to the 1990s, global NPP in the 2090s is reduced by 2.3–16 % and EP by 7–18 %. The models with the largest increases in stratification (and largest relative reductions in NPP and EP) also show the largest positive biases in stratification for the contemporary period, suggesting some potential overestimation of climate impacts on NPP and EP. All of the CMIP5 models show an increase in stratification in response to surface ocean warming and freshening that is accompanied by decreases in NPP, EP, and surface macronutrient concentrations. There is considerable variability across models in the absolute magnitude of these fluxes, surface nutrient concentrations, and their perturbations by climate change, indicating large model uncertainties. The negative response of NPP and EP to stratification increases reflects a bottom-up control, as nutrient flux to the euphotic zone declines. Models with dynamic phytoplankton community structure show larger declines in EP than in NPP. This is driven by phytoplankton community composition shifts, with a reduced percentage of NPP by large phytoplankton under RCP 8.5, as smaller phytoplankton are favored under the increasing nutrient stress. Thus, projections of the NPP response to climate change in the CMIP5 models are critically dependent on the simulated phytoplankton community structure, the efficiency of the biological pump, and the resulting (highly variable) levels of regenerated production. Community composition is represented relatively simply in the CMIP5 models, and should be expanded to better capture the spatial patterns and the changes in export efficiency that are necessary for predicting climate impacts on NPP.

Description: Technical Note: A simple calculation algorithm to separate high-resolution CH 4 flux measurements into ebullition and diffusion-derived components Biogeosciences Discussions, 12, 12923-12945, 2015 Author(s): M. Hoffmann, M. Schulz-Hanke, J. Garcia Alba, N. Jurisch, U. Hagemann, T. Sachs, M. Sommer, and J. Augustin Processes driving the production, transformation and transport of methane (CH 4 ) in wetland ecosystems are highly complex. Thus, serious challenges are constitutes in terms of the mechanistic process understanding, the identification of potential environmental drivers and the calculation of reliable CH 4 emission estimates. We present a simple calculation algorithm to separate open-water CH 4 fluxes measured with automatic chambers into diffusion- and ebullition-derived components, which helps facilitating the identification of underlying dynamics and potential environmental drivers. Flux separation is based on ebullition related sudden concentration changes during single measurements. A variable ebullition filter is applied, using the lower and upper quartile and the interquartile range (IQR). Automation of data processing is achieved by using an established R-script, adjusted for the purpose of CH 4 flux calculation. The algorithm was tested using flux measurement data (July to September 2013) from a former fen grassland site, converted into a shallow lake as a result of rewetting ebullition and diffusion contributed 46 and 55 %, respectively, to total CH 4 emissions, which is comparable to those previously reported by literature. Moreover, the separation algorithm revealed a concealed shift in the diurnal trend of diffusive fluxes throughout the measurement period.

Description: Nitrogen export from a boreal stream network following forest harvesting: seasonal nitrate removal and conservative export of organic forms Biogeosciences Discussions, 12, 12061-12089, 2015 Author(s): J. Schelker, R. Sponseller, E. Ring, L. Högbom, S. Löfgren, and H. Laudon Boreal streams are under pressure from large scale disturbance by forestry. Recent scenarios predict an increase in forest production in Scandinavia to meet market demands and to mitigate higher anthropogenic CO 2 emissions. Increased fertilization and shorter forest rotations are anticipated which will likely enhance the pressure on boreal streams in the near future. Among the major environmental impacts of forest harvesting is the increased mobilization of inorganic nitrogen (N), primarily as nitrate (NO 3 - ) into surface waters. But whereas NO 3 - inputs to first-order streams have been previously described, their downstream fate and impact is not well understood. We evaluated the downstream fate of N inputs in a boreal landscape that has been altered by forest harvests over a 10 year period to estimate the effects of multiple clear-cuts on aquatic N export in a boreal stream network. Small streams showed substantial leaching of NO 3 - in response to harvests with concentrations increasing by ~ 15 fold. NO 3 - concentrations at two sampling stations further downstream in the network were strongly seasonal and increased significantly in response to harvesting at the medium size, but not at the larger stream. Nitrate removal efficiency, E r , calculated as the percentage of "forestry derived" NO 3 - that was retained within the landscape using a mass balance model was highest during the snow melt season followed by the growing season, but declined continuously throughout the dormant season. In contrast, export of organic N from the landscape indicated little removal and was essentially conservative. Overall, net removal of NO 3 - between 2008 and 2011 accounted for ~ 70 % of the total NO 3 - mass exported from harvested patches distributed across the landscape. These results highlight the capacity and limitation of N-limited terrestrial and aquatic ecosystems to buffer inorganic N mobilization that arises from multiple clear-cuts within meso-scale boreal watersheds.

Description: by Eliseo Ferrante, Ali Emre Turgut, Edgar Duéñez-Guzmán, Marco Dorigo, Tom Wenseleers Division of labor is ubiquitous in biological systems, as evidenced by various forms of complex task specialization observed in both animal societies and multicellular organisms. Although clearly adaptive, the way in which division of labor first evolved remains enigmatic, as it requires the simultaneous co-occurrence of several complex traits to achieve the required degree of coordination. Recently, evolutionary swarm robotics has emerged as an excellent test bed to study the evolution of coordinated group-level behavior. Here we use this framework for the first time to study the evolutionary origin of behavioral task specialization among groups of identical robots. The scenario we study involves an advanced form of division of labor, common in insect societies and known as “task partitioning”, whereby two sets of tasks have to be carried out in sequence by different individuals. Our results show that task partitioning is favored whenever the environment has features that, when exploited, reduce switching costs and increase the net efficiency of the group, and that an optimal mix of task specialists is achieved most readily when the behavioral repertoires aimed at carrying out the different subtasks are available as pre-adapted building blocks. Nevertheless, we also show for the first time that self-organized task specialization could be evolved entirely from scratch, starting only from basic, low-level behavioral primitives, using a nature-inspired evolutionary method known as Grammatical Evolution. Remarkably, division of labor was achieved merely by selecting on overall group performance, and without providing any prior information on how the global object retrieval task was best divided into smaller subtasks. We discuss the potential of our method for engineering adaptively behaving robot swarms and interpret our results in relation to the likely path that nature took to evolve complex sociality and task specialization.

Description: by Patrícia Santos-Oliveira, António Correia, Tiago Rodrigues, Teresa M Ribeiro-Rodrigues, Paulo Matafome, Juan Carlos Rodríguez-Manzaneque, Raquel Seiça, Henrique Girão, Rui D. M. Travasso Sprouting angiogenesis, where new blood vessels grow from pre-existing ones, is a complex process where biochemical and mechanical signals regulate endothelial cell proliferation and movement. Therefore, a mathematical description of sprouting angiogenesis has to take into consideration biological signals as well as relevant physical processes, in particular the mechanical interplay between adjacent endothelial cells and the extracellular microenvironment. In this work, we introduce the first phase-field continuous model of sprouting angiogenesis capable of predicting sprout morphology as a function of the elastic properties of the tissues and the traction forces exerted by the cells. The model is very compact, only consisting of three coupled partial differential equations, and has the clear advantage of a reduced number of parameters. This model allows us to describe sprout growth as a function of the cell-cell adhesion forces and the traction force exerted by the sprout tip cell. In the absence of proliferation, we observe that the sprout either achieves a maximum length or, when the traction and adhesion are very large, it breaks. Endothelial cell proliferation alters significantly sprout morphology, and we explore how different types of endothelial cell proliferation regulation are able to determine the shape of the growing sprout. The largest region in parameter space with well formed long and straight sprouts is obtained always when the proliferation is triggered by endothelial cell strain and its rate grows with angiogenic factor concentration. We conclude that in this scenario the tip cell has the role of creating a tension in the cells that follow its lead. On those first stalk cells, this tension produces strain and/or empty spaces, inevitably triggering cell proliferation. The new cells occupy the space behind the tip, the tension decreases, and the process restarts. Our results highlight the ability of mathematical models to suggest relevant hypotheses with respect to the role of forces in sprouting, hence underlining the necessary collaboration between modelling and molecular biology techniques to improve the current state-of-the-art.

Description: by Sayed-Rzgar Hosseini, Aditya Barve, Andreas Wagner All biological evolution takes place in a space of possible genotypes and their phenotypes. The structure of this space defines the evolutionary potential and limitations of an evolving system. Metabolism is one of the most ancient and fundamental evolving systems, sustaining life by extracting energy from extracellular nutrients. Here we study metabolism’s potential for innovation by analyzing an exhaustive genotype-phenotype map for a space of 10 15 metabolisms that encodes all possible subsets of 51 reactions in central carbon metabolism. Using flux balance analysis, we predict the viability of these metabolisms on 10 different carbon sources which give rise to 1024 potential metabolic phenotypes. Although viable metabolisms with any one phenotype comprise a tiny fraction of genotype space, their absolute numbers exceed 10 9 for some phenotypes. Metabolisms with any one phenotype typically form a single network of genotypes that extends far or all the way through metabolic genotype space, where any two genotypes can be reached from each other through a series of single reaction changes. The minimal distance of genotype networks associated with different phenotypes is small, such that one can reach metabolisms with novel phenotypes – viable on new carbon sources – through one or few genotypic changes. Exceptions to these principles exist for those metabolisms whose complexity (number of reactions) is close to the minimum needed for viability. Increasing metabolic complexity enhances the potential for both evolutionary conservation and evolutionary innovation.

Description: by Pengxing Cao, Ada W. C. Yan, Jane M. Heffernan, Stephen Petrie, Robert G. Moss, Louise A. Carolan, Teagan A. Guarnaccia, Anne Kelso, Ian G. Barr, Jodie McVernon, Karen L. Laurie, James M. McCaw Influenza is an infectious disease that primarily attacks the respiratory system. Innate immunity provides both a very early defense to influenza virus invasion and an effective control of viral growth. Previous modelling studies of virus–innate immune response interactions have focused on infection with a single virus and, while improving our understanding of viral and immune dynamics, have been unable to effectively evaluate the relative feasibility of different hypothesised mechanisms of antiviral immunity. In recent experiments, we have applied consecutive exposures to different virus strains in a ferret model, and demonstrated that viruses differed in their ability to induce a state of temporary immunity or viral interference capable of modifying the infection kinetics of the subsequent exposure. These results imply that virus-induced early immune responses may be responsible for the observed viral hierarchy. Here we introduce and analyse a family of within-host models of re-infection viral kinetics which allow for different viruses to stimulate the innate immune response to different degrees. The proposed models differ in their hypothesised mechanisms of action of the non-specific innate immune response. We compare these alternative models in terms of their abilities to reproduce the re-exposure data. Our results show that 1) a model with viral control mediated solely by a virus-resistant state, as commonly considered in the literature, is not able to reproduce the observed viral hierarchy; 2) the synchronised and desynchronised behaviour of consecutive virus infections is highly dependent upon the interval between primary virus and challenge virus exposures and is consistent with virus-dependent stimulation of the innate immune response. Our study provides the first mechanistic explanation for the recently observed influenza viral hierarchies and demonstrates the importance of understanding the host response to multi-strain viral infections. Re-exposure experiments provide a new paradigm in which to study the immune response to influenza and its role in viral control.

Description: Hydroxy fatty acids in fresh snow samples from northern Japan: long-range atmospheric transport of Gram-negative bacteria by Asian winter monsoon Biogeosciences Discussions, 12, 13375-13397, 2015 Author(s): P. Tyagi, S. Yamamoto, and K. Kawamura Hydroxy fatty acids (FAs) in fresh snow from Sapporo, one of the heaviest snowfall regions in the world, have been studied to ascertain the airborne bacterial endotoxin concentrations and their biomass. The presence of β-hydroxy FAs (C 9 –C 28 ), constituents of Gram-negative bacteria (GNB), suggests long-range transport of soil microbes. Likewise, the occurrence of α- and ω-hydroxy FAs (C 9 –C 30 and C 9 –C 28 , respectively) in snow reveals their contribution from epicuticular waxes and soil microorganisms. Estimated endotoxin and GNB mass can aid in assessing their possible impacts on the diversity and functioning of aquatic and terrestrial ecosystems, as well as lethal effects on pedestrians through dispersal of microbes. Air mass back trajectories together with hydroxy FAs unveil their sources from Siberia, Russian Far East and North China by the Asian monsoon. This study highlights the role of fresh snow that reduces the human health risk of GNB and endotoxin by scavenging from the air.

Description: by Paul M. Harrison, Laurent Badel, Mark J. Wall, Magnus J. E. Richardson Models of neocortical networks are increasingly including the diversity of excitatory and inhibitory neuronal classes. Significant variability in cellular properties are also seen within a nominal neuronal class and this heterogeneity can be expected to influence the population response and information processing in networks. Recent studies have examined the population and network effects of variability in a particular neuronal parameter with some plausibly chosen distribution. However, the empirical variability and covariance seen across multiple parameters are rarely included, partly due to the lack of data on parameter correlations in forms convenient for model construction. To addess this we quantify the heterogeneity within and between the neocortical pyramidal-cell classes in layers 2/3, 4, and the slender-tufted and thick-tufted pyramidal cells of layer 5 using a combination of intracellular recordings, single-neuron modelling and statistical analyses. From the response to both square-pulse and naturalistic fluctuating stimuli, we examined the class-dependent variance and covariance of electrophysiological parameters and identify the role of the h current in generating parameter correlations. A byproduct of the dynamic I-V method we employed is the straightforward extraction of reduced neuron models from experiment. Empirically these models took the refractory exponential integrate-and-fire form and provide an accurate fit to the perisomatic voltage responses of the diverse pyramidal-cell populations when the class-dependent statistics of the model parameters were respected. By quantifying the parameter statistics we obtained an algorithm which generates populations of model neurons, for each of the four pyramidal-cell classes, that adhere to experimentally observed marginal distributions and parameter correlations. As well as providing this tool, which we hope will be of use for exploring the effects of heterogeneity in neocortical networks, we also provide the code for the dynamic I-V method and make the full electrophysiological data set available.

Description: Nitrogen cycling in the subsurface biosphere: nitrate isotopes in porewaters underlying the oligotrophic North Atlantic Biogeosciences Discussions, 12, 13545-13591, 2015 Author(s): S. D. Wankel, C. Buchwald, W. Ziebis, C. B. Wenk, and M. F. Lehmann Nitrogen (N) is a key component of fundamental biomolecules. Hence, the cycling and availability of N is a central factor governing the extent of ecosystems across the Earth. In the organic-lean sediment porewaters underlying the oligotrophic ocean, where low levels of microbial activity persist despite limited organic matter delivery from overlying water, the extent and modes of nitrogen transformations have not been widely investigated. Here we use the N and oxygen (O) isotopic composition of porewater nitrate (NO 3 − ) from a site in the oligotrophic North Atlantic (IODP) to determine the extent and magnitude of microbial nitrate production (via nitrification) and consumption (via denitrification). We find that NO 3 − accumulates far above bottom seawater concentrations (∼ 21 μM) throughout the sediment column (up to ∼ 50 μM) down to the oceanic basement as deep as 90 mbsf, reflecting the predominance of aerobic nitrification/remineralization within the deep marine sediments. Large changes in the δ 15 N and δ 18 O of nitrate, however, reveal variable influence of nitrate respiration across the three sites. We use an inverse porewater diffusion–reaction model, constrained by the N and O isotope systematics of nitrification and denitrification and the porewater NO 3 − isotopic composition, to estimate rates of nitrification and denitrification throughout the sediment column. Results indicate variability of reaction rates across and within the three boreholes that are generally consistent with the differential distribution of dissolved oxygen at this site, though not necessarily with the canonical view of how redox thresholds separate nitrate regeneration from dissimilative consumption spatially. That is, we provide isotope evidence for expanded zones of co-ocurring nitrification and denitrification. The isotope biogeochemical modeling also yielded estimates for the δ 15 N and δ 18 O of newly produced nitrate (δ 15 N NTR and δ 18 O NTR ), as well as the isotope effect for denitrification ( 15 ϵ DNF ), parameters with high relevance to global ocean models of N cycling. Estimated values of δ 15 N NTR were generally lower than previously reported δ 15 N values for sinking PON in this region. We suggest that these values can be related to sedimentary N-fixation and remineralization of the newly fixed organic N. Values of δ 18 O NTR generally ranged between −2.8 and 0.0 ‰, consistent with recent estimates based on lab cultures of nitrifying bacteria. Notably, some δ 18 O NTR values were elevated, suggesting incorporation of 18 O-enriched dissolved oxygen during nitrification, and possibly indicating a tight coupling of NH 4 + and NO 2 − oxidation in this metabolically sluggish environment. Our findings indicate that the production of organic matter by in situ autotrophy (e.g., nitrification, nitrogen fixation) supply a large fraction of the biomass and organic substrate for heterotrophy in these sediments, supplementing the small organic matter pool derived from the overlying euphotic zone. This work sheds new light on an active nitrogen cycle operating, despite exceedingly low carbon inputs, in the deep sedimentary biosphere.

Description: Spring bloom onset in the Nordic Seas Biogeosciences Discussions, 12, 13631-13673, 2015 Author(s): A. Mignot, R. Ferrari, and K. A. Mork The North Atlantic spring bloom is a massive annual growth event of marine phytoplankton, tiny free-floating algae that form the base of the ocean's food web and generates a large fraction of the global primary production of organic matter. The conditions that trigger the onset of the spring bloom in the Nordic Seas, at the northern edge of the North Atlantic, are studied using in-situ data from five bio-optical floats released above the Arctic Circle. It is often assumed that spring blooms start as soon as phytoplankton cells daily irradiance is sufficiently abundant that division rates exceed losses. The bio-optical float data instead suggest the tantalizing hypothesis that Nordic Seas blooms start when the photoperiod, the number of daily light hours experienced by phytoplankton, exceeds a critical value, independently of division rates. This bloom behavior may be explained by realizing that photosynthesis is impossible during polar nights and phytoplankton enters in a dormant stage in winter, only to be awaken by a photoperiodic trigger. While the first accumulation of biomass recorded by the bio-optical floats is consistent with the photoperiod hypothesis, it is possible that some biomass accumulation started before the critical photoperiod but at levels too low to be detected by the fluorometers. Thus more precise observations are needed to test the photoperiod hypothesis.

Description: Unusual biogenic calcite structures in two shallow lakes, James Ross Island, Antarctica Biogeosciences Discussions, 12, 13593-13629, 2015 Author(s): J. Elster, L. Nedbalová, R. Vodrážka, K. Láska, J. Haloda, and J. Komárek The floors of two shallow endorheic lakes, located on volcanic surfaces on James Ross Island, are covered with calcareous organosedimentary structures. Their biological and chemical composition, lake water characteristics, and seasonal variability of the thermal regime are introduced. The lakes are frozen down to the bottom eight-nine months per year and their water chemistry is characterized by low conductivity and neutral to slightly alkaline pH. The photosynthetic microbial mat is composed of filamentous cyanobacteria and microalgae that are considered to be Antarctic endemic species. The mucilaginous black biofilm is covered by green spots formed by a green microalga and the macroscopic structures are packed together with fine material. Thin sections consist of rock substrate, soft biofilm, calcite spicules and mineral grains originating from different sources. The morphology of the spicules is typical of calcium carbonate monocrystals having a layered structure and worn surface, which reflect growth and degradation processes. The spicules chemical composition and structure correspond to pure calcite. Lakes age, altitude, morphometry, geomorphological and hydrological stability, including low sedimentation rates, together with thermal regime predispose the existence of this community. We hypothesize that the precipitation of calcite is connected with the photosynthetic activity of the green microalgae that were not recorded in any other lake in the region. This study has shown that the unique community producing biogenic calcite spicules is quite different to any yet described.

Description: by Ariel Afek, Hila Cohen, Shiran Barber-Zucker, Raluca Gordân, David B. Lukatsky Recent genome-wide experiments in different eukaryotic genomes provide an unprecedented view of transcription factor (TF) binding locations and of nucleosome occupancy. These experiments revealed that a large fraction of TF binding events occur in regions where only a small number of specific TF binding sites (TFBSs) have been detected. Furthermore, in vitro protein-DNA binding measurements performed for hundreds of TFs indicate that TFs are bound with wide range of affinities to different DNA sequences that lack known consensus motifs. These observations have thus challenged the classical picture of specific protein-DNA binding and strongly suggest the existence of additional recognition mechanisms that affect protein-DNA binding preferences. We have previously demonstrated that repetitive DNA sequence elements characterized by certain symmetries statistically affect protein-DNA binding preferences. We call this binding mechanism nonconsensus protein-DNA binding in order to emphasize the point that specific consensus TFBSs do not contribute to this effect. In this paper, using the simple statistical mechanics model developed previously, we calculate the nonconsensus protein-DNA binding free energy for the entire C . elegans and D . melanogaster genomes. Using the available chromatin immunoprecipitation followed by sequencing (ChIP-seq) results on TF-DNA binding preferences for ~100 TFs, we show that DNA sequences characterized by low predicted free energy of nonconsensus binding have statistically higher experimental TF occupancy and lower nucleosome occupancy than sequences characterized by high free energy of nonconsensus binding. This is in agreement with our previous analysis performed for the yeast genome. We suggest therefore that nonconsensus protein-DNA binding assists the formation of nucleosome-free regions, as TFs outcompete nucleosomes at genomic locations with enhanced nonconsensus binding. In addition, here we perform a new, large-scale analysis using in vitro TF-DNA preferences obtained from the universal protein binding microarrays (PBM) for ~90 eukaryotic TFs belonging to 22 different DNA-binding domain types. As a result of this new analysis, we conclude that nonconsensus protein-DNA binding is a widespread phenomenon that significantly affects protein-DNA binding preferences and need not require the presence of consensus (specific) TFBSs in order to achieve genome-wide TF-DNA binding specificity.

Description: by The PLOS Computational Biology Staff

Description: by James Tamerius, Cécile Viboud, Jeffrey Shaman, Gerardo Chowell While a relationship between environmental forcing and influenza transmission has been established in inter-pandemic seasons, the drivers of pandemic influenza remain debated. In particular, school effects may predominate in pandemic seasons marked by an atypical concentration of cases among children. For the 2009 A/H1N1 pandemic, Mexico is a particularly interesting case study due to its broad geographic extent encompassing temperate and tropical regions, well-documented regional variation in the occurrence of pandemic outbreaks, and coincidence of several school breaks during the pandemic period. Here we fit a series of transmission models to daily laboratory-confirmed influenza data in 32 Mexican states using MCMC approaches, considering a meta-population framework or the absence of spatial coupling between states. We use these models to explore the effect of environmental, school–related and travel factors on the generation of spatially-heterogeneous pandemic waves. We find that the spatial structure of the pandemic is best understood by the interplay between regional differences in specific humidity (explaining the occurrence of pandemic activity towards the end of the school term in late May-June 2009 in more humid southeastern states), school vacations (preventing influenza transmission during July-August in all states), and regional differences in residual susceptibility (resulting in large outbreaks in early fall 2009 in central and northern Mexico that had yet to experience fully-developed outbreaks). Our results are in line with the concept that very high levels of specific humidity, as present during summer in southeastern Mexico, favor influenza transmission, and that school cycles are a strong determinant of pandemic wave timing.

Description: by Alireza Alemi, Carlo Baldassi, Nicolas Brunel, Riccardo Zecchina Understanding the theoretical foundations of how memories are encoded and retrieved in neural populations is a central challenge in neuroscience. A popular theoretical scenario for modeling memory function is the attractor neural network scenario, whose prototype is the Hopfield model. The model simplicity and the locality of the synaptic update rules come at the cost of a poor storage capacity, compared with the capacity achieved with perceptron learning algorithms. Here, by transforming the perceptron learning rule, we present an online learning rule for a recurrent neural network that achieves near-maximal storage capacity without an explicit supervisory error signal, relying only upon locally accessible information. The fully-connected network consists of excitatory binary neurons with plastic recurrent connections and non-plastic inhibitory feedback stabilizing the network dynamics; the memory patterns to be memorized are presented online as strong afferent currents, producing a bimodal distribution for the neuron synaptic inputs. Synapses corresponding to active inputs are modified as a function of the value of the local fields with respect to three thresholds. Above the highest threshold, and below the lowest threshold, no plasticity occurs. In between these two thresholds, potentiation/depression occurs when the local field is above/below an intermediate threshold. We simulated and analyzed a network of binary neurons implementing this rule and measured its storage capacity for different sizes of the basins of attraction. The storage capacity obtained through numerical simulations is shown to be close to the value predicted by analytical calculations. We also measured the dependence of capacity on the strength of external inputs. Finally, we quantified the statistics of the resulting synaptic connectivity matrix, and found that both the fraction of zero weight synapses and the degree of symmetry of the weight matrix increase with the number of stored patterns.

Description: Characterizing Leaf Area Index (LAI) and Vertical Foliage Profile (VFP) over the United States Biogeosciences Discussions, 12, 13675-13710, 2015 Author(s): H. Tang, S. Ganguly, G. Zhang, M. A. Hofton, R. F. Nelson, and R. Dubayah Leaf area index (LAI) and vertical foliage profile (VFP) are among the important canopy structural variables. Recent advances in lidar remote sensing technology have demonstrated the capability of accurately mapping LAI and VFP over large areas. The primary objective of this study was to derive and validate a LAI and VFP product over the contiguous United States using spaceborne waveform lidar data. This product was derived at the footprint level from the Geoscience Laser Altimeter System (GLAS) using a biophysical model. We validated GLAS derived LAI and VFP across major forest biomes using airborne waveform lidar. The comparison results showed that GLAS retrievals of total LAI were generally accurate with little bias ( r 2 = 0.67, bias = −0.13, RMSE = 0.75). The derivations of GLAS retrievals of VFP within layers was not as accurate overall ( r 2 = 0.36, bias = −0.04, RMSE = 0.26), and these varied as a function of height, increasing from understory to overstory −0 to 5 m layer: r 2 = 0.04, bias = 0.09, RMSE = 0.31; 10 to 15 m layer: r 2 = 0.53, bias = −0.08, RMSE = 0.22; and 15 to 20 m layer: r 2 = 0.66, bias =−0.05, RMSE = 0.20. Significant relationships were also found between GLAS LAI products and different environmental factors, in particular elevation and annual precipitation. In summary, our results provide a unique insight into vertical canopy structure distribution across North American ecosystems. This data set is a first step towards a baseline of canopy structure needed for evaluating climate and land use induced forest changes at continental scale in the future and should help deepen our understanding of the role of vertical canopy structure on terrestrial ecosystem processes across varying scales.

Description: Application of the 15 N-Gas Flux method for measuring in situ N 2 and N 2 O fluxes due to denitrification in natural and semi-natural terrestrial ecosystems and comparison with the acetylene inhibition technique Biogeosciences Discussions, 12, 12653-12689, 2015 Author(s): F. Sgouridis, S. Ullah, and A. Stott Soil denitrification is considered the most un-constrained process in the global N cycle due to uncertain in situ N 2 flux measurements, particularly in natural and semi-natural terrestrial ecosystems. 15 N tracer approaches can provide in situ measurements of both N 2 and N 2 O simultaneously, but their use has been limited to fertilised agro-ecosystems due to the need for large 15 N additions in order to detect 15 N 2 production against the high atmospheric N 2 . For 15 N-N 2 analyses, we have used an "in house" laboratory designed and manufactured N 2 preparation instrument which can be interfaced to any commercial continuous flow isotope ratio mass spectrometer (CF-IRMS). The N 2 prep unit has gas purification steps, a copper based reduction furnace, and allows the analysis of small gas injection volumes (4 μL) for 15 N-N 2 analysis. For the analysis of N 2 O, an automated Tracegas Pre-concentrator (Isoprime Ltd) coupled to an IRMS was used to measure the 15 N-N 2 O (4 mL gas injection volume). Consequently, the coefficient of variation for the determination of isotope ratios for N 2 in air and in standard N 2 O (0.5 ppm) was better than 0.5 %. The 15 N Gas-Flux method was adapted for application in natural and semi-natural land use types (peatlands, forests and grasslands) by lowering the 15 N tracer application rate to 0.04–0.5 kg 15 N ha −1 . For our chamber design (volume / surface = 8:1) and a 20 h incubation period, the minimum detectable flux rates were 4 μg N m −2 h −1 and 0.2 ng N m −2 h −1 for the N 2 and N 2 O fluxes respectively. The N 2 flux ranged between 2.4 and 416.6 μg N m −2 h −1 , and the grassland soils showed on average 3 and 14 times higher denitrification rates than the woodland and organic soils respectively. The N 2 O flux was on average 20 to 200 times lower than the N 2 flux, while the denitrification product ratio (N 2 O/N 2 + N 2 O) was low, ranging between 0.03 and 13 %. Total denitrification rates measured by the acetylene inhibition technique under the same field conditions correlated ( r = 0.58) with the denitrification rates measured under the 15 N Gas-Flux method but were underestimated by a factor of 4 and this was attributed to the incomplete inhibition of N 2 O reduction to N 2 under relatively high soil moisture content. The results show that the 15 N Gas-Flux method can be used for quantifying N 2 and N 2 O production rates in natural terrestrial ecosystems, thus significantly improving our ability to constrain ecosystem N budgets.

Description: by Sander Land, Steven A. Niederer Biophysical models of cardiac tension development provide a succinct representation of our understanding of force generation in the heart. The link between protein kinetics and interactions that gives rise to high cooperativity is not yet fully explained from experiments or previous biophysical models. We propose a biophysical ODE-based representation of cross-bridge (XB), tropomyosin and troponin within a contractile regulatory unit (RU) to investigate the mechanisms behind cooperative activation, as well as the role of cooperativity in dynamic tension generation across different species. The model includes cooperative interactions between regulatory units (RU-RU), between crossbridges (XB-XB), as well more complex interactions between crossbridges and regulatory units (XB-RU interactions). For the steady-state force-calcium relationship, our framework predicts that: (1) XB-RU effects are key in shifting the half-activation value of the force-calcium relationship towards lower [Ca 2+ ], but have only small effects on cooperativity. (2) XB-XB effects approximately double the duty ratio of myosin, but do not significantly affect cooperativity. (3) RU-RU effects derived from the long-range action of tropomyosin are a major factor in cooperative activation, with each additional unblocked RU increasing the rate of additional RU’s unblocking. (4) Myosin affinity for short (1–4 RU) unblocked stretches of actin of is very low, and the resulting suppression of force at low [Ca 2+ ] is a major contributor in the biphasic force-calcium relationship. We also reproduce isometric tension development across mouse, rat and human at physiological temperature and pacing rate, and conclude that species differences require only changes in myosin affinity and troponin I/troponin C affinity. Furthermore, we show that the calcium dependence of the rate of tension redevelopment k tr is explained by transient blocking of RU’s by a temporary decrease in XB-RU effects.

Description: by Jonas Paulsen, Odin Gramstad, Philippe Collas The three-dimensional (3D) structure of the genome is important for orchestration of gene expression and cell differentiation. While mapping genomes in 3D has for a long time been elusive, recent adaptations of high-throughput sequencing to chromosome conformation capture (3C) techniques, allows for genome-wide structural characterization for the first time. However, reconstruction of "consensus" 3D genomes from 3C-based data is a challenging problem, since the data are aggregated over millions of cells. Recent single-cell adaptations to the 3C-technique, however, allow for non-aggregated structural assessment of genome structure, but data suffer from sparse and noisy interaction sampling. We present a manifold based optimization (MBO) approach for the reconstruction of 3D genome structure from chromosomal contact data. We show that MBO is able to reconstruct 3D structures based on the chromosomal contacts, imposing fewer structural violations than comparable methods. Additionally, MBO is suitable for efficient high-throughput reconstruction of large systems, such as entire genomes, allowing for comparative studies of genomic structure across cell-lines and different species.

Description: by Hiroo Kenzaki, Shoji Takada Nucleosomes, basic units of chromatin, are known to show spontaneous DNA unwrapping dynamics that are crucial for transcriptional activation, but its structural details are yet to be elucidated. Here, employing a coarse-grained molecular model that captures residue-level structural details up to histone tails, we simulated equilibrium fluctuations and forced unwrapping of single nucleosomes at various conditions. The equilibrium simulations showed spontaneous unwrapping from outer DNA and subsequent rewrapping dynamics, which are in good agreement with experiments. We found several distinct partially unwrapped states of nucleosomes, as well as reversible transitions among these states. At a low salt concentration, histone tails tend to sit in the concave cleft between the histone octamer and DNA, tightening the nucleosome. At a higher salt concentration, the tails tend to bound to the outer side of DNA or be expanded outwards, which led to higher degree of unwrapping. Of the four types of histone tails, H3 and H2B tail dynamics are markedly correlated with partial unwrapping of DNA, and, moreover, their contributions were distinct. Acetylation in histone tails was simply mimicked by changing their charges, which enhanced the unwrapping, especially markedly for H3 and H2B tails.

Description: by Sebastian Bitzer, Jelle Bruineberg, Stefan J. Kiebel Even for simple perceptual decisions, the mechanisms that the brain employs are still under debate. Although current consensus states that the brain accumulates evidence extracted from noisy sensory information, open questions remain about how this simple model relates to other perceptual phenomena such as flexibility in decisions, decision-dependent modulation of sensory gain, or confidence about a decision. We propose a novel approach of how perceptual decisions are made by combining two influential formalisms into a new model. Specifically, we embed an attractor model of decision making into a probabilistic framework that models decision making as Bayesian inference. We show that the new model can explain decision making behaviour by fitting it to experimental data. In addition, the new model combines for the first time three important features: First, the model can update decisions in response to switches in the underlying stimulus. Second, the probabilistic formulation accounts for top-down effects that may explain recent experimental findings of decision-related gain modulation of sensory neurons. Finally, the model computes an explicit measure of confidence which we relate to recent experimental evidence for confidence computations in perceptual decision tasks.

Description: Natural variability in the surface ocean carbonate ion concentration Biogeosciences Discussions, 12, 13123-13157, 2015 Author(s): N. S. Lovenduski, M. C. Long, and K. Lindsay We investigate variability in the surface ocean carbonate ion concentration ([CO 3 2− ]) on the basis of a long control simulation with a fully-coupled Earth System Model. The simulation is run with a prescribed, pre-industrial atmospheric CO 2 concentration for 1000 years, permitting investigation of natural [CO 3 2− ] variability on interannual to multi-decadal timescales. We find high interannual variability in surface [CO 3 2− ] in the tropical Pacific and at the boundaries between the subtropical and subpolar gyres in the Northern Hemisphere, and relatively low interannual variability in the centers of the subtropical gyres and in the Southern Ocean. Statistical analysis of modeled [CO 3 2− ] variance and autocorrelation suggests that significant anthropogenic trends in the saturation state of aragonite (Ω aragonite ) are already or nearly detectable at the sustained, open-ocean timeseries sites, whereas several decades of observations are required to detect anthropogenic trends in Ω aragonite in the tropical Pacific, North Pacific, and North Atlantic. The detection timescale for anthropogenic trends in pH is shorter than that for Ω aragonite , due to smaller noise-to-signal ratios and lower autocorrelation in pH. In the tropical Pacific, the leading mode of surface [CO 3 2− ] variability is primarily driven by variations in the vertical advection of dissolved inorganic carbon (DIC) in association with El Niño–Southern Oscillation. In the North Pacific, surface [CO 3 2− ] variability is caused by circulation-driven variations in surface DIC and strongly correlated with the Pacific Decadal Oscillation, with peak spectral power at 20–30 year periods. North Atlantic [CO 3 2− ] variability is also driven by variations in surface DIC, and exhibits weak correlations with both the North Atlantic Oscillation and the Atlantic Multidecadal Oscillation. As the scientific community seeks to detect the anthropogenic influence on ocean carbonate chemistry, these results will aid the interpretation of trends calculated from spatially- and temporally-sparse observations.

Description: Spatial and temporal trends in summertime climate and water quality indicators in the coastal embayments of Buzzards Bay, Massachusetts Biogeosciences Discussions, 12, 13159-13192, 2015 Author(s): J. E. Rheuban, S. C. Williamson, J. E. Costa, D. M. Glover, R. W. Jakuba, D. C. McCorkle, C. Neill, T. Williams, and S. C. Doney Degradation of coastal ecosystems by eutrophication is largely defined by nitrogen loading from land via surface and groundwater flows. However, indicators of water quality are highly variable due to a myriad of other drivers, including temperature and precipitation. To evaluate these drivers, we examined spatial and temporal trends in a 22 year record of summer water quality data from 122 stations in 17 embayments within Buzzards Bay, MA (USA), collected through a citizen science monitoring program managed by Buzzards Bay Coalition. To identify spatial patterns across Buzzards Bay's embayments, we used a principle component and factor analysis and found that rotated factor loadings indicated little correlation between inorganic nutrients and organic matter and chlorophyll a (Chl a ) concentration. Factor scores showed that embayment geomorphology in addition to nutrient loading was a strong driver of water quality, where embayments with surface water inputs showed larger biological impacts than embayments dominated by groundwater influx. A linear regression analysis of annual summertime water quality indicators over time revealed that from 1992 to 2013, most embayments (15 of 17) exhibited an increase in temperature (mean rate of 0.082 ± 0.025 (SD) °C yr −1 ) and Chl a (mean rate of 0.0171 ± 0.0088 log 10 (Chl a ; mg m −3 ) yr −1 , equivalent to a 4.0 % increase per year). However, only 7 embayments exhibited an increase in total nitrogen (TN) concentration (mean rate 0.32 ± 0.47 (SD) μM yr −1 ). Average summertime log 10 (TN) and log 10 (Chl a ) were correlated with an indication that yield of Chl a per unit total nitrogen increased with time suggesting the estuarine response to TN may have changed because of other stressors such as warming, altered precipitation patterns, or changing light levels. These findings affirm that nitrogen loading and physical aspects of embayments are essential in explaining observed ecosystem response. However, climate-related stressors may also need to be considered by managers because increased temperature and precipitation may worsen water quality and partially offset benefits achieved by reducing nitrogen loading.

Description: Carbon dynamics in highly heterotrophic subarctic thaw ponds Biogeosciences Discussions, 12, 11707-11749, 2015 Author(s): T. Roiha, I. Laurion, and M. Rautio Global warming has accelerated the formation of permafrost thaw ponds in several subarctic and arctic regions. These ponds are net heterotrophic as evidenced by their greenhouse gas (GHG) supersaturation levels (CO 2 and CH 4 ), and generally receive large terrestrial carbon inputs from the thawing and eroding permafrost. We measured seasonal and vertical variations in the concentration and type of dissolved organic matter (DOM) in five subarctic thaw (thermokarst) ponds in northern Quebec, and explored how environmental gradients influenced heterotrophic and phototrophic biomass and productivity. Late winter DOM had low aromaticity indicating reduced inputs of terrestrial carbon, while the high concentration of dissolved organic carbon (DOC) suggests that some production of non-chromophoric dissolved compounds by the microbial food web took place under the ice cover. Summer DOM had a strong terrestrial signature, but was also characterized with significant inputs of algal-derived carbon, especially at the pond surface. During late winter, bacterial production was low (maximum of 0.8 mg C m −3 d −1 ) and was largely based on free-living bacterioplankton (58 %). Bacterial production in summer was high (up to 58 mg C m −3 d −1 ), dominated by particle-attached bacteria (67 %), and strongly correlated to the amount of terrestrial carbon. Primary production was restricted to summer surface waters due to strong light limitation deeper in the water column or in winter. The phototrophic biomass was equal to the heterotrophic biomass, but as the algae were mostly composed of mixotrophic species, most probably they used bacteria rather than solar energy in such shaded ponds. According to the δ 13 C analyses, non-algal carbon supported 51 % of winter and 37 % of summer biomass of the phantom midge larvae, Chaoborus sp., that are at the top of the trophic chain. Our results point to a strong heterotrophic energy pathway in these thaw pond ecosystems, where bacterioplankton dominates the production of new carbon in both summer and winter.

Description: Phototrophic pigment diversity and picophytoplankton abundance in permafrost thaw lakes Biogeosciences Discussions, 12, 12121-12156, 2015 Author(s): A. Przytulska, J. Comte, S. Crevecoeur, C. Lovejoy, I. Laurion, and W. F. Vincent Permafrost thaw lakes (thermokarst lakes) are widely distributed across the northern landscape, and are known to be biogeochemically active sites that emit large amounts of carbon to the atmosphere as CH 4 and CO 2 . However, the abundance and composition of the photosynthetic communities that consume CO 2 have been little explored in this ecosystem type. In order to identify the major groups of phototrophic organisms and their controlling variables, we sampled 12 permafrost thaw lakes along a permafrost degradation gradient in northern Québec, Canada. Additional samples were taken from 5 rock-basin reference lakes in the region to determine if the thaw waters differed in limnological properties and phototrophs. Phytoplankton community structure was determined by high performance liquid chromatography analysis of their photoprotective and photosynthetic pigments, and autotrophic picoplankton concentrations were assessed by flow cytometry. One of the black colored lakes located in a andscape of rapidly degrading palsas (permafrost mounds) was selected for high-throughput 18S rRNA sequencing to help interpret the pigment and cytometry data. The results showed that the limnological properties of the thaw lakes differed significantly from the reference lakes, and were more highly stratified. However, both waterbody types contained similarly diverse phytoplankton groups, with dominance of the pigment assemblages by fucoxanthin-containing taxa, as well as chlorophytes, cryptophytes and cyanobacteria. Chlorophyll a concentrations (Chl a ) were correlated with total phosphorus (TP), and both were significantly higher in the thaw lakes (overall means of 3.3 μg Chl a L −1 and 34 μg TP L −1 ) relative to the reference lakes (2.0 μg Chl a L −1 and 8.2 μg TP L −1 ). Stepwise multiple regression of Chl a against the other algal pigments showed that it was largely a function of lutein, fucoxanthin and peridinin ( R 2 = 0.78). The bottom waters of two of the thaw lakes also contained high concentrations of bacteriochlorophyll d , showing the presence of green photosynthetic sulphur bacteria. The molecular analyses indicated a relatively minor contribution of diatoms, while chrysophytes, dinoflagellates and chlorophytes were well represented; the heterotrophic eukaryote fraction was dominated by numerous ciliate taxa, and also included Heliozoa, Rhizaria, chytrids and flagellates. Autotrophic picoplankton occurred in cell concentrations up to 8.8 × 10 5 mL −1 (picocyanobacteria) and 4.6 × 10 5 mL −1 (picoeukaryotes). Both groups of picophytoplankton were positively correlated with total phytoplankton abundance, as measured by Chl a ; picocyanobacteria were inversely correlated with dissolved organic carbon, while picoeukaryotes were correlated with conductivity. Despite their net heterotrophic character, subarctic thaw lakes are rich habitats for diverse phototrophic communities.

Description: by Malachi Griffith, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential expression, and alternative splicing analysis methods. These tutorials and additional training resources are accompanied by complete analysis pipelines and test datasets made available without encumbrance at www.rnaseq.wiki.

Description: by Arjun Bharioke, Dmitri B. Chklovskii Neurons must faithfully encode signals that can vary over many orders of magnitude despite having only limited dynamic ranges. For a correlated signal, this dynamic range constraint can be relieved by subtracting away components of the signal that can be predicted from the past, a strategy known as predictive coding, that relies on learning the input statistics. However, the statistics of input natural signals can also vary over very short time scales e.g., following saccades across a visual scene. To maintain a reduced transmission cost to signals with rapidly varying statistics, neuronal circuits implementing predictive coding must also rapidly adapt their properties. Experimentally, in different sensory modalities, sensory neurons have shown such adaptations within 100 ms of an input change. Here, we show first that linear neurons connected in a feedback inhibitory circuit can implement predictive coding. We then show that adding a rectification nonlinearity to such a feedback inhibitory circuit allows it to automatically adapt and approximate the performance of an optimal linear predictive coding network, over a wide range of inputs, while keeping its underlying temporal and synaptic properties unchanged. We demonstrate that the resulting changes to the linearized temporal filters of this nonlinear network match the fast adaptations observed experimentally in different sensory modalities, in different vertebrate species. Therefore, the nonlinear feedback inhibitory network can provide automatic adaptation to fast varying signals, maintaining the dynamic range necessary for accurate neuronal transmission of natural inputs.

Description: by Murat Alp, Vipan K. Parihar, Charles L. Limoli, Francis A. Cucinotta In this work, a stochastic computational model of microscopic energy deposition events is used to study for the first time damage to irradiated neuronal cells of the mouse hippocampus. An extensive library of radiation tracks for different particle types is created to score energy deposition in small voxels and volume segments describing a neuron’s morphology that later are sampled for given particle fluence or dose. Methods included the construction of in silico mouse hippocampal granule cells from neuromorpho.org with spine and filopodia segments stochastically distributed along the dendritic branches. The model is tested with high-energy 56 Fe, 12 C, and 1 H particles and electrons. Results indicate that the tree-like structure of the neuronal morphology and the microscopic dose deposition of distinct particles may lead to different outcomes when cellular injury is assessed, leading to differences in structural damage for the same absorbed dose. The significance of the microscopic dose in neuron components is to introduce specific local and global modes of cellular injury that likely contribute to spine, filopodia, and dendrite pruning, impacting cognition and possibly the collapse of the neuron. Results show that the heterogeneity of heavy particle tracks at low doses, compared to the more uniform dose distribution of electrons, juxtaposed with neuron morphology make it necessary to model the spatial dose painting for specific neuronal components. Going forward, this work can directly support the development of biophysical models of the modifications of spine and dendritic morphology observed after low dose charged particle irradiation by providing accurate descriptions of the underlying physical insults to complex neuron structures at the nano-meter scale.

Description: by Brinda Vallat, Carlos Madrid-Aliste, Andras Fiser Predicting the three-dimensional structure of proteins from their amino acid sequences remains a challenging problem in molecular biology. While the current structural coverage of proteins is almost exclusively provided by template-based techniques, the modeling of the rest of the protein sequences increasingly require template-free methods. However, template-free modeling methods are much less reliable and are usually applicable for smaller proteins, leaving much space for improvement. We present here a novel computational method that uses a library of supersecondary structure fragments, known as Smotifs, to model protein structures. The library of Smotifs has saturated over time, providing a theoretical foundation for efficient modeling. The method relies on weak sequence signals from remotely related protein structures to create a library of Smotif fragments specific to the target protein sequence. This Smotif library is exploited in a fragment assembly protocol to sample decoys, which are assessed by a composite scoring function. Since the Smotif fragments are larger in size compared to the ones used in other fragment-based methods, the proposed modeling algorithm, SmotifTF, can employ an exhaustive sampling during decoy assembly. SmotifTF successfully predicts the overall fold of the target proteins in about 50% of the test cases and performs competitively when compared to other state of the art prediction methods, especially when sequence signal to remote homologs is diminishing. Smotif-based modeling is complementary to current prediction methods and provides a promising direction in addressing the structure prediction problem, especially when targeting larger proteins for modeling.

Description: Skeletal mineralogy of coral recruits under high temperature and p CO 2 Biogeosciences Discussions, 12, 12485-12500, 2015 Author(s): T. Foster and P. L. Clode Aragonite, which is the polymorph of CaCO 3 precipitated by modern corals during skeletal formation, has a higher solubility than the more stable polymorph calcite. This higher solubility leaves animals that produce aragonitic skeletons more vulnerable to anthropogenic ocean acidification. It is therefore, important to determine whether scleractinian corals have the plasticity to adapt and produce calcite in their skeletons in response to changing environmental conditions. Both high p CO 2 and lower Mg / Ca ratios in seawater are thought to have driven changes in the skeletal mineralogy of major marine calcifiers in the past ∼540 myr. Experimentally reduced Mg / Ca ratios in ambient seawater have been shown to induce some calcite precipitation in both adult and newly settled modern corals, however, the impact of high p CO 2 on the mineralogy of recruits is unknown. Here we determined the skeletal mineralogy of one-month old Acropora spicifera coral recruits grown under high temperature (+3 °C) and p CO 2 (∼900 μatm) conditions, using X-ray diffraction and Raman spectroscopy. We found that newly settled coral recruits produced entirely aragonitic skeletons regardless of the treatment. Our results show that elevated p CO 2 alone is unlikely to drive changes in the skeletal mineralogy of young corals. Not having an ability to switch from aragonite to calcite precipitation may leave corals and ultimately coral reef ecosystems more susceptible to predicted ocean acidification. An important area for prospective research would be to investigate the combined impact of high p CO 2 and reduced Mg / Ca ratio on coral skeletal mineralogy.

Description: The impact of sedimentary alkalinity release on the water column CO 2 system in the North Sea Biogeosciences Discussions, 12, 12395-12453, 2015 Author(s): H. Brenner, U. Braeckman, M. Le Guitton, and F. J. R. Meysman Recently, it has been proposed that alkalinity release from sediments can play an important role in the carbonate dynamics on continental shelves, lowering the p CO 2 of seawater and hence increasing the CO 2 uptake from the atmosphere. To test this hypothesis, sedimentary alkalinity generation was quantified within permeable and muddy sediments across the North Sea during two cruises in September 2011 (basin-wide) and June 2012 (Dutch coastal zone). Benthic fluxes of alkalinity ( A T ) and dissolved inorganic carbon (DIC) were determined using shipboard closed sediment incubations. These results show that sediments can be an important source for alkalinity, particularly in the shallow southern North Sea, where high A T and DIC fluxes were recorded in near shore sediments of the Belgian, Dutch and German coastal zone. In contrast, fluxes of A T and DIC are substantially lower in the deeper, seasonally stratified, northern part of the North Sea. Overall, our results show that sedimentary alkalinity generation should be considered an important factor in the CO 2 dynamics of shallow coastal systems.

Description: Contribution of Marine Group II Euryarchaeota to cyclopentyl tetraethers in the Pearl River estuary and coastal South China Sea: impact on the TEX 86 paleothermometer Biogeosciences Discussions, 12, 12455-12484, 2015 Author(s): J. X. Wang, C. L. Zhang, W. Xie, Y. G. Zhang, and P. Wang TEX 86 (TetraEther indeX of glycerol dialkyl glycerol tetraethers (GDGTs) with 86 carbon atoms) has been widely applied to reconstruct (paleo-) sea surface temperature (SST). While Marine Group I (MG I) Thaumarchaeota have been commonly believed to be the source for GDGTs, Marine Group II (MG II Euryarchaeota ) have recently been suggested to contribute significantly to the GDGT pool in the ocean. However, little is known how the MG II Euryarchaeota -derived GDGTs may influence TEX 86 in marine sediment record. In this study, we characterize MG II Euryarchaeota -produced GDGTs and assess the likely effect of these tetraether lipids on TEX 86 . Analyses of core lipid (CL-) and intact polar lipid (IPL-) based GDGTs, 454 sequencing and quantitative polymerase chain reaction (qPCR) targeting MG II Euryarchaeota were performed on suspended particulate matter (SPM) and surface sediments collected along a salinity gradient from the lower Pearl River (river water) and its estuary (mixing water) to the coastal South China Sea (seawater). The results showed that the community composition varied along the salinity gradient with MG II Euryarchaeota as the second dominant group in the mixing water and seawater. qPCR data indicated that the abundance of MG II Euryarchaeota in the mixing water was three to four orders of magnitude higher than the river water and seawater. Significant linear correlations were observed between the gene abundance ratio of MG II Euryarchaeota vs. total archaea and the relative abundance of GDGTs-1, -2, -3, or -4 as well as the ring index based on these compounds, which collectively suggest that MG II Euryarchaeota may actively produce GDGTs in the water column. These results also show strong evidence that MG II Euryarchaeota synthesizing GDGTs with 1–4 cyclopentane moieties may bias TEX 86 in the water column and sediments. This study highlights that valid interpretation of TEX 86 in sediment record, particularly in coastal oceans, needs to consider the contribution from MG II Euryarchaeota .

Description: Fate of peat-derived carbon and associated CO 2 and CO emissions from two Southeast Asian estuaries Biogeosciences Discussions, 12, 8299-8340, 2015 Author(s): D. Müller, T. Warneke, T. Rixen, M. Müller, A. Mujahid, H. W. Bange, and J. Notholt Coastal peatlands in Southeast Asia release large amounts of organic carbon to rivers, which transport it further to the adjacent estuaries. However, little is known about the fate of this terrestrial material in the coastal ocean. Although Southeast Asia is, by area, considered a hotspot of estuarine CO 2 emissions, studies in this region are very scarce. We measured dissolved and particulate organic carbon, carbon dioxide (CO 2 ) partial pressure and carbon monoxide (CO) concentrations in two tropical estuaries in Sarawak, Malaysia, whose coastal area is covered by peatlands. We surveyed the estuaries of the rivers Lupar and Saribas during the wet and dry season, respectively. The spatial distribution and the carbon-to-nitrogen ratios of dissolved organic matter (DOM) suggest that peat-draining rivers convey terrestrial organic carbon to the estuaries. We found evidence that a large fraction of this carbon is respired. The median p CO 2 in the estuaries ranged between 618 and 5064 μatm with little seasonal variation. CO 2 fluxes were determined with a floating chamber and estimated to amount to 14–272 mol m −2 yr −1 , which is high compared to other studies from tropical and subtropical sites. In contrast, CO concentrations and fluxes were relatively moderate (0.3–1.4 nmol L −1 and 0.8–1.9 mmol m −2 yr −1 ) if compared to published data for oceanic or upwelling systems. We attributed this to the large amounts of suspended matter (4–5004 mg L −1 ), limiting the light penetration depth. However, the diurnal variation of CO suggests that it is photochemically produced, implying that photodegradation might play a role for the removal of DOM from the estuary as well. We concluded that unlike smaller peat-draining tributaries, which tend to transport most carbon downstream, estuaries in this region function as an efficient filter for organic carbon and release large amounts of CO 2 to the atmosphere. The Lupar and Saribas mid-estuaries release 0.4 ± 0.2 Tg C yr −1 , which corresponds to approximately 80% of the emissions from the aquatic systems in these two catchments.

Description: Carbonate saturation state of surface waters in the Ross Sea and Southern Ocean: controls and implications for the onset of aragonite undersaturation Biogeosciences Discussions, 12, 8429-8465, 2015 Author(s): H. B. DeJong, R. B. Dunbar, D. A. Mucciarone, and D. A. Koweek Predicting when surface waters of the Ross Sea and Southern Ocean will become undersaturated with respect to biogenic carbonate minerals is challenging in part due to the lack of baseline high resolution carbon system data. Here we present ~ 1700 surface total alkalinity measurements from the Ross Sea and along a transect between the Ross Sea and southern Chile from the austral autumn (February–March 2013). We calculate the saturation state of aragonite (Ω Ar ) and calcite (Ω Ca ) using measured total alkalinity and p CO 2 . In the Ross Sea and south of the Polar Front, variability in carbonate saturation state (Ω) is mainly driven by algal photosynthesis. Freshwater dilution and calcification have minimal influence on Ω variability. We estimate an early spring surface water Ω Ar value of ~ 1.2 for the Ross Sea using a total alkalinity–salinity relationship and historical p CO 2 measurements. Our results suggest that the Ross Sea is not likely to become undersaturated with respect to aragonite until the year 2070.

Description: Biodegradability of dissolved organic carbon in permafrost soils and waterways: a meta-analysis Biogeosciences Discussions, 12, 8353-8393, 2015 Author(s): J. E. Vonk, S. E. Tank, P. J. Mann, R. G. M. Spencer, C. C. Treat, R. G. Striegl, B. W. Abbott, and K. P. Wickland As Arctic regions warm, the large organic carbon pool stored in permafrost becomes increasingly vulnerable to thaw and decomposition. The transfer of newly mobilized carbon to the atmosphere and its potential influence upon climate change will largely depend on the reactivity and subsequent fate of carbon delivered to aquatic ecosystems. Dissolved organic carbon (DOC) is a key regulator of aquatic metabolism and its biodegradability will determine the extent and rate of carbon release from aquatic ecosystems to the atmosphere. Knowledge of the mechanistic controls on DOC biodegradability is however currently poor due to a scarcity of long-term data sets, limited spatial coverage of available data, and methodological diversity. Here, we performed parallel biodegradable DOC (BDOC) experiments at six Arctic sites (16 experiments) using a standardized incubation protocol to examine the effect of methodological differences used as common practice in the literature. We further synthesized results from 14 aquatic and soil leachate BDOC studies from across the circum–arctic permafrost region to examine pan-Arctic trends in BDOC. An increasing extent of permafrost across the landscape resulted in higher BDOC losses in both soil and aquatic systems. We hypothesize that the unique composition of permafrost-derived DOC combined with limited prior microbial processing due to low soil temperature and relatively shorter flow path lengths and transport times, resulted in higher overall terrestrial and freshwater BDOC loss. Additionally, we found that the fraction of BDOC decreased moving down the fluvial network in continuous permafrost regions, i.e. from streams to large rivers, suggesting that highly biodegradable DOC is lost in headwater streams. We also observed a seasonal (January–December) decrease in BDOC losses in large streams and rivers, but no apparent change in smaller streams and soil leachates. We attribute this seasonal change to a combination of factors including shifts in carbon source, changing DOC residence time related to increasing thaw-depth, increasing water temperatures later in the summer, as well as decreasing hydrologic connectivity between soils and surface water as the seasons progress. Our results suggest that future, climate warming-induced shifts of continuous permafrost into discontinuous permafrost regions could affect the degradation potential of thaw-released DOC as well as its variability throughout the Arctic summer. We lastly present a recommended standardized BDOC protocol to facilitate the comparison of future work and improve our knowledge of processing and transport of DOC in a changing Arctic.

Description: Ideas and perspectives: use of tree-ring width as an indicator of tree growth Biogeosciences Discussions, 12, 8341-8352, 2015 Author(s): R. A. Hember, W. A. Kurz, and J. M. Metsaranta By taking core samples, dendroecological studies can reconstruct radial growth over the lifespan of a tree, providing a valuable way to estimate the sensitivity of tree productivity to environmental change. With increasing prevalence of such studies in global change science, it is worth cautioning that the incremental growth rate of a sub-dimension of a tree organ, such as annual ring width ( w ), does not respond to extrinsic perturbations with the same relative magnitude as the primary production of that organ. For example, if an extrinsic force causes a two-fold increase in the absolute growth rate of stemwood biomass (AGR), it should only theoretically translate into a 1.3-fold increase in w , or a 1.7-fold increase in basal area increment (BAI), when a 2:1 ratio in resource allocation to lateral and apical meristems is assumed. Expressing the magnitude of a response in relative terms does not, therefore, provide a valid means of comparing estimates of relative growth derived from measurement of different dimensional traits of the tree. From our perspective, enough conformity to facilitate comparison of environmental sensitivity across studies of tree growth is warranted so we emphasize the benefit of dimension analysis to transform measurements of w and BAI into the AGR. Although conversion to AGR introduces an error from the use of allometric equations, the approach is widely accepted in mainstream ecology and global change science at least partially because it avoids discrepancies in response magnitude owing to differences in dimension. Studies of organ elongation have historically provided invaluable information, yet it must be recognized that they systematically underestimate the response magnitude of primary production, and confound comparisons of growth sensitivity between many dendroecological studies that focus on w and studies of primary production.

Description: Spatial variability of diploptene δ 13 C values in thermokarst lakes: the potential to analyse the complexity of lacustrine methane cycling Biogeosciences Discussions, 12, 12157-12189, 2015 Author(s): K. L. Davies, R. D. Pancost, M. E. Edwards, K. M. Walter Anthony, P. G. Langdon, and L. Chaves Torres Cryospheric changes in northern high latitudes are linked to significant greenhouse gas flux to the atmosphere, including methane release that originates from organic matter decomposition in thermokarst lakes. The connections between methane production in sediments, transport pathways and oxidation are not well understood and this has implications for any attempts to reconstruct methane production from sedimentary archives. We assessed methane oxidation as represented by methane oxidising bacteria across the surface sediments of two interior Alaska thermokarst lakes in relation to methane emissions via ebullition (bubbling). The bacterial biomarker diploptene was present and had low δ 13 C values (lower than −38 ‰) in all sediments analysed, suggesting methane oxidation was widespread. The most δ 13 C-depleted diploptene was found in the area of highest methane ebullition emissions in Ace Lake (δ 13 C diplotene values between −68.2 and −50.1 ‰), suggesting a positive link between methane production, oxidation, and emission in this area. In contrast, significantly less depleted diploptene δ 13 C values (between −42.9 and −38.8 ‰) were found in the area of highest methane ebullition emissions in Smith Lake. Lower δ 13 C values of diploptene were found in the central area of Smith Lake (between −56.8 and −46.9 ‰), where methane ebullition rates are low but methane diffusion appears high. Using δ 13 C-diplotene as a proxy for methane oxidation activity, we suggest the observed differences in methane oxidation levels among sites within the two lakes could be linked to differences in source area of methane production (e.g. age and type of organic carbon) and bathymetry as it relates to varying oxycline depths and changing pressure gradients. As a result, methane oxidation is highly lake-dependent. The diploptene δ 13 C values also highlight strong within-lake variability, implying that single-value, down-core records of hopanoid isotopic signatures are not secure indicators of changing methane flux at the whole-lake scale.

Description: Metagenomic analyses of the late Pleistocene permafrost – additional tools for reconstruction of environmental conditions Biogeosciences Discussions, 12, 12091-12119, 2015 Author(s): E. Rivkina, L. Petrovskaya, T. Vishnivetskaya, K. Krivushin, L. Shmakova, M. Tutukina, A. Meyers, and F. Kondrashov A comparative analysis of the metagenomes from two 30 000 year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which have been characterized by the absence of methane with lower values of redox-potential and Fe 2+ content) showed both a low abundance of methanogenic archaea and enzymes from the carbon, nitrogen and sulfur cycles. The metagenomic and geochemical analyses described in the paper provide evidence that the formation of the late Pleistocene Ice Complex sediments likely took place under much more aerobic conditions than lake-alluvial sediments.

Description: by Po-Wei Chen, Luis L. Fonseca, Yusuf A. Hannun, Eberhard O. Voit The article demonstrates that computational modeling has the capacity to convert metabolic snapshots, taken sequentially over time, into a description of cellular, dynamic strategies. The specific application is a detailed analysis of a set of actions with which Saccharomyces cerevisiae responds to heat stress. Using time dependent metabolic concentration data, we use a combination of mathematical modeling, reverse engineering, and optimization to infer dynamic changes in enzyme activities within the sphingolipid pathway. The details of the sphingolipid responses to heat stress are important, because they guide some of the longer-term alterations in gene expression, with which the cells adapt to the increased temperature. The analysis indicates that all enzyme activities in the system are affected and that the shapes of the time trends in activities depend on the fatty-acyl CoA chain lengths of the different ceramide species in the system.

Description: Nonlinear thermal and moisture dynamics of high Arctic wetland polygons following permafrost disturbance Biogeosciences Discussions, 12, 11797-11831, 2015 Author(s): E. Godin, D. Fortier, and E. Lévesque Low-centre polygonal terrain developing within gentle sloping surfaces and lowlands in the high Arctic have a potential to retain snowmelt water in their bowl-shaped centre and as such are considered high latitude wetlands. Such wetlands in the continuous permafrost regions have an important ecological role in an otherwise generally arid region. In the valley of the glacier C-79 on Bylot Island (Nunavut, Canada), thermal erosion gullies are rapidly eroding the permafrost along ice wedges affecting the integrity of the polygons by breaching and collapsing the surrounding rims. While intact polygons were characterized by a relative homogeneity (topography, snow cover, maximum active layer thaw depth, ground moisture content, vegetation cover), eroded polygons had a non-linear response for the same elements following their perturbation. The heterogeneous nature of disturbed terrains impacts active layer thickness, ground ice aggradation in the upper portion of permafrost, soil moisture and vegetation dynamics, carbon storage and terrestrial green-house gas emissions.

Description: Controls on microalgal community structures in cryoconite holes upon high Arctic glaciers, Svalbard Biogeosciences Discussions, 12, 11751-11795, 2015 Author(s): T. R. Vonnahme, M. Devetter, J. D. Žárský, M. Šabacká, and J. Elster Glaciers are known to harbor surprisingly complex ecosystems. On their surface, distinct cylindrical holes filled with meltwater and sediments are considered as hot spots for microbial life. The present paper addresses possible biological interactions within the community of prokaryotic cyanobacteria and eukaryotic microalgae (microalgae) and relations to their potential grazers, additional to their environmental controls. Svalbard glaciers with substantial allochthonous input of material from local sources reveal high microalgal densities. Small valley glaciers with high sediment coverages and high impact of birds show high biomasses and support a high biological diversity. Invertebrate grazer densities do not show any significant negative correlation with microalgal abundances, but a positive correlation with eukaryotic microalgae. Most microalgae found in this study form large colonies ( 〈 10 cells, or 〉 25 μm), which may protect them against invertebrate grazing. This finding rather indicates grazing as a positive control on eukaryotic microalgae by nutrient recycling. Density differences between the eukaryotic microalgae and prokaryotic cyanobacteria and their high distinction in RDA and PCA analyses indicate that these two groups are in strong contrast. Eukaryotic microalgae occurred mainly in unstable cryoconite holes with high sediment loads, high N : P ratios, and a high impact of bird guano, as a proxy for nutrients. In these environments autochthonous nitrogen fixation appears to be negligible. Selective wind transport of Oscillatoriales via soil and dust particles is proposed to explain their dominance in cryoconites further away from the glacier margins. We propose that, for the studied glaciers, nutrient levels related to recycling of limiting nutrients is the main factor driving variation in the community structure of microalgae and grazers.

Description: Thermo-erosion gullies boost the transition from wet to mesic vegetation Biogeosciences Discussions, 12, 12191-12228, 2015 Author(s): N. Perreault, E. Lévesque, D. Fortier, and L. J. Lamarque Continuous permafrost zones with well-developed polygonal ice-wedge networks are particularly vulnerable to climate change. Thermo-mechanical erosion can initiate the development of gullies that lead to substantial drainage of adjacent wet habitats. How vegetation responds to this particular disturbance is currently unknown but has the potential to strongly disrupt function and structure of Arctic ecosystems. Focusing on three major gullies of Bylot Island, Nunavut, we aimed at estimating the effects of thermo-erosion processes in shaping plant community changes. Over two years, we explored the influence of environmental factors on plant species richness, abundance and biomass studying 197 polygons that covered the whole transition from intact wet to disturbed and mesic habitats. While gullying decreased soil moisture by 40 % and thaw front depth by 10 cm in breached polygons, we observed a gradual vegetation shift within five to ten years with mesic habitat plant species such as Arctagrostis latifolia and Salix arctica replacing wet habitat dominant Carex aquatilis and Dupontia fisheri . This transition was accompanied by a five time decrease in graminoid above-ground biomass in mesic sites. Our results illustrate that wetlands are highly vulnerable to thermo-erosion processes that may rapidly promote the decrease of food availability for herbivores and reduce methane emissions of Arctic ecosystems.

Description: Effects of dust additions on phytoplankton growth and DMS production in high CO 2 northeast Pacific HNLC waters Biogeosciences Discussions, 12, 12281-12319, 2015 Author(s): J. Mélançon, M. Levasseur, M. Lizotte, M. Scarratt, J.-É. Tremblay, P. Tortell, G.-P. Yang, G.-Y. Shi, H.-W. Gao, D. M. Semeniuk, M. Robert, M. Arychuk, K. Johnson, N. Sutherland, M. Davelaar, N. Nemcek, A. Peña, and W. Richardson Ocean acidification (OA) is likely to have an effect on the fertilizing potential of desert dust in high-nutrient, low-chlorophyll oceanic regions, either by modifying Fe speciation and bioavailability, or by altering phytoplankton Fe requirements and acquisition. To address this issue, short incubations (4 days) of northeast subarctic Pacific waters enriched with either FeSO 4 or dust, and set at pH 8.0 (in situ) and 7.8 were conducted in August 2010. We assessed the impact of a decrease in pH on dissolved Fe concentration, phytoplankton biomass, taxonomy and productivity, and the production of dimethylsulfide (DMS) and its algal precursor dimethylsulfoniopropionate (DMSP). Chlorophyll a (chl a ) remained unchanged in the controls and doubled in both the FeSO 4 -enriched and dust-enriched incubations, confirming the Fe-limited status of the plankton assemblage during the experiment. In the acidified treatments, a significant reduction (by 16–38 %) of the final concentration of chl a was measured compared to their non-acidified counterparts, and a 15 % reduction in particulate organic carbon (POC) concentration was measured in the dust-enriched acidified treatment compared to the dust-enriched non-acidified treatment. FeSO 4 and dust additions had a fertilizing effect mainly on diatoms and cyanobacteria. Lowering the pH affected mostly the haptophytes, but pelagophyte concentrations were also reduced in some acidified treatments. Acidification did not significantly alter DMSP and DMS concentrations. These results show that dust deposition events in a low-pH iron-limited Northeast subarctic Pacific are likely to stimulate phytoplankton growth to a lesser extent than in today's ocean during the few days following fertilization and point to a low initial sensitivity of the DMSP and DMS dynamics to OA.

Description: Projected climate change impacts on North Sea and Baltic Sea: CMIP3 and CMIP5 model based scenarios Biogeosciences Discussions, 12, 12229-12279, 2015 Author(s): D. Pushpadas, C. Schrum, and U. Daewel Climate change impacts on the marine biogeochemistry and lower trophic level dynamics in the North Sea and Baltic Sea have been assessed using regional downscaling in a number of recent studies. However, most of these where only forced by physical conditions from Global Climate Models (GCMs) and regional downscaling considering the climate change impact on oceanic nutrient conditions from Global Earth System Models (ESMs) are rare and so far solely based on CMIP3-generation climate models. The few studies published show a large range in projected future primary production and hydrodynamic condition. With the addition of CMIP5 models and scenarios, the demand to explore the uncertainty in regional climate change projections increased. Moreover, the question arises how projections based on CMIP5-generation models compare to earlier projections and multi-model ensembles comprising both AR4 and AR5 generation forcing models. Here, we investigated the potential future climate change impacts to the North Sea and the Baltic Sea ecosystem using a coherent regional downscaling strategy based on the regional coupled bio-physical model ECOSMO. ECOSMO was forced by output from different ESMs from both CMIP3 and CMIP5 models. Multi-model ensembles using CMIP3/A1B and CMIP5/RCP4.5 scenarios are examined, where the selected CMIP5 models are the successors of the chosen CMIP3 models. Comparing projected changes with the present day reference condition, all these simulations predicted an increase in Sea Surface Temperature (SST) in both North Sea and Baltic Sea, reduction in sea ice in the Baltic, decrease in primary production in the North Sea and an increase in primary production in the Baltic Sea. Despite these largely consistent results on the direction of the projected changes, our results revealed a broad range in the amplitude of projected climate change impacts. Our study strengthens the claim that the choice of the ESM is a major factor for regional climate projections. The change in oceanic nutrient input appeared to be the major driver for the projected changes in North Sea primary production. Assessing the spread in ensemble groups, we found that there is for the North Sea a significant reduction in the spread of projected changes among CMIP5 forced model simulations compared to those forced by CMIP3 ESMs, except for salinity. The latter was due to an unexpected salinification observed in one of the CMIP5 model while all other models exhibit freshening in the future. However, for the Baltic Sea substantial differences in inter-model variability in projected climate change impact to primary production is lacking.

Description: This paper proposes a discussion concerning the use of social media-related geographic information in the context of the strategic environmental assessment (SEA) of Sardinian Municipal masterplans (MMPs). We show that this kind of information improves, substantially, the SEA process since it provides planners, evaluators, and the local communities with information retrieved from social media that would have not been available otherwise. This information integrates authoritative data collection, which comes from official sources, and enlightens tastes and preferences of the users of services and infrastructure, and their expectations concerning their spatial organization. A methodological approach related to the collection of social media-related geographic information is implemented and discussed with reference to the urban context of the city of Cagliari (Sardinia, Italy). The results are very effective in terms of provision of information, which may possibly increase the spatial knowledge available for planning policy definition and implementation. In this perspective, this kind of information discloses opportunities for building analytical scenarios related to urban and regional planning and it offers useful suggestions for sustainable development based on tourism strategies.

Description: by Pengyi Yang, Xiaofeng Zheng, Vivek Jayaswal, Guang Hu, Jean Yee Hwa Yang, Raja Jothi Cell signaling underlies transcription/epigenetic control of a vast majority of cell-fate decisions. A key goal in cell signaling studies is to identify the set of kinases that underlie key signaling events. In a typical phosphoproteomics study, phosphorylation sites (substrates) of active kinases are quantified proteome-wide. By analyzing the activities of phosphorylation sites over a time-course, the temporal dynamics of signaling cascades can be elucidated. Since many substrates of a given kinase have similar temporal kinetics, clustering phosphorylation sites into distinctive clusters can facilitate identification of their respective kinases. Here we present a knowledge-based CLUster Evaluation (CLUE) approach for identifying the most informative partitioning of a given temporal phosphoproteomics data. Our approach utilizes prior knowledge, annotated kinase-substrate relationships mined from literature and curated databases, to first generate biologically meaningful partitioning of the phosphorylation sites and then determine key kinases associated with each cluster. We demonstrate the utility of the proposed approach on two time-series phosphoproteomics datasets and identify key kinases associated with human embryonic stem cell differentiation and insulin signaling pathway. The proposed approach will be a valuable resource in the identification and characterizing of signaling networks from phosphoproteomics data.

Description: Dissolved organic carbon lability and stable isotope shifts during microbial decomposition in a tropical river system Biogeosciences Discussions, 12, 12761-12782, 2015 Author(s): N. Geeraert, F. O. Omengo, G. Govers, and S. Bouillon A significant amount of carbon is transported to the ocean as dissolved organic carbon (DOC) in rivers. During transport, it can be transformed through microbial consumption and photochemical oxidation. In dark incubation experiments with water from the Tana River, Kenya, we examined the consumption of DOC through microbial decomposition and the associated change in its carbon stable isotope composition (δ 13 C). In 15 of the 18 incubations, DOC concentrations decreased significantly by 10 to 60 %, with most of the decomposition taking place within the first 24–48 h. After 8 days, the remaining DOC was up to 3 ‰ more depleted in 13 C compared with the initial pool, and the change in δ 13 C correlated strongly with the fraction of DOC remaining. We propose that the shift in δ 13 C is consistent with greater microbial lability of DOC originating from herbaceous C 4 vegetation than DOC derived from woody C 3 vegetation in the semi-arid lower Tana. The findings complement earlier data that riverine C sources do not necessarily reflect their proportion in the catchment: besides spatial distribution, also processing within the river can further influence the riverine δ 13 C.

Description: Ocean dynamic processes causing spatially heterogeneous distribution of sedimentary caesium-137 massively released from the Fukushima Dai-ichi Nuclear Power Plant Biogeosciences Discussions, 12, 12713-12759, 2015 Author(s): H. Higashi, Y. Morino, N. Furuichi, and T. Ohara Massive amounts of anthropogenic radiocaesium 137 Cs that was released into the environment by the Fukushima Dai-ichi Nuclear Power Plant accident on March 2011 are widely known to have extensively migrated to Pacific oceanic sediment off of east Japan. Several recent reports have stated that the sedimentary 137 Cs is now stable with a remarkably heterogeneous distribution. The present study elucidates ocean dynamic processes causing this heterogeneous sedimentary 137 Cs distribution in and around the shelf off Fukushima and adjacent prefectures. We performed a numerical simulation of oceanic 137 Cs behaviour for about 10 months after the accident, using a comprehensive dynamic model involving advection–diffusion transport in seawater, adsorption and desorption to and from particulate matter, sedimentation and suspension on and from the bottom, and vertical diffusion transport in the sediment. A notable simulated result was that the sedimentary 137 Cs significantly accumulated in a swath just offshore of the shelf break (along the 50–100 m isobath) as in recent observations, although the seabed in the entire simulation domain was assumed to have ideal properties such as identical bulk density, uniform porosity, and aggregation of particles with a single grain diameter. This result indicated that the heterogeneous sedimentary 137 Cs distribution was not necessarily a result of the spatial distribution of 137 Cs sediment adsorptivity. The present simulation suggests that the shape of the swath is mainly associated with spatiotemporal variation between bottom shear stress in the shallow shelf ( 〈 50 m depths) and that offshore of the shelf break. In a large part of the shallow shelf, the simulation indicated that strong bottom friction suspending particulate matter from the seabed frequently occurred via a periodic spring tide about every 2 weeks and via occasional strong wind. The sedimentary 137 Cs thereby could hardly stay on the surface of the seabed with the result that the simulated sediment-surface 137 Cs activity tended to decrease steadily for a long term after the initial 137 Cs migration. By contrast, in the offshore region, neither the spring tide nor the strong wind caused bottom disturbance. Hence, the particulate matter incorporated with 137 Cs, which was horizontally transported from the adjacent shallow shelf, readily settled and remained on the surface of the sediment just offshore of the shelf break. The present simulation also clearly demonstrated that the bottom disturbance influenced the sedimentary 137 Cs distributions not only horizontally but also vertically. In particular, within a part of the near-shore off the nuclear power plant, the simulation indicated that large amounts of the sedimentary 137 Cs were present in both upper and deeper sediments. As a result, total sedimentary 137 Cs in the entire simulation domain (1.4 x 10 5 km 2 ) at the end of 2011 was 3.2 x 10 15 Bq, more than 10 times that in previous estimates using samples of upper sediments.

Description: Soil N 2 O and NO emissions from land use and land-use change in the tropics and subtropics: a meta-analysis Biogeosciences Discussions, 12, 12783-12821, 2015 Author(s): J. van Lent, K. Hergoualc'h, and L. V. Verchot Deforestation and forest degradation in the tropics may substantially alter soil N-oxide emissions. It is particularly relevant to accurately quantify those changes to properly account for them in a REDD+ climate change mitigation scheme that provides financial incentives to reduce the emissions. With this study we provide updated land use (LU)-based emission rates (103 studies, 387 N 2 O and 111 NO case studies), determine the trend and magnitude of flux changes with land-use change (LUC) using a meta-analysis approach (43 studies, 132 N 2 O and 37 NO cases) and evaluate biophysical drivers of N 2 O and NO emissions and emission changes for the tropics. The average N 2 O and NO emissions in intact upland tropical forest amounted to 2.0 ± 0.2 ( n = 88) and 1.7 ± 0.5 ( n = 36) kg N ha −1 yr −1 , respectively. In agricultural soils annual N 2 O emissions were exponentially related to N fertilization rates and average water-filled pore space (WFPS) whereas in non-agricultural sites a Gaussian response to WFPS fit better the observed NO and N 2 O emissions. The sum of soil N 2 O and NO fluxes and the ratio of N 2 O to NO increased exponentially and significantly with increasing nitrogen availability (expressed as NO 3 − /[NO 3 − +NH 4 + ]) and WFPS, respectively; following the conceptual Hole-In-the-Pipe model. Nitrous and nitric oxide fluxes did not overall increase significantly as a result of LUC (Hedges's d of 0.11 ± 0.11 and 0.16 ± 0.19, respectively), however individual LUC trajectories or practices did. Nitrous oxide fluxes increased significantly after intact upland forest conversion to croplands (Hedges's d = 0.78 ± 0.24) and NO increased significantly following the conversion of low forest cover (secondary forest younger than 30 years, woodlands, shrublands) (Hedges's d of 0.44 ± 0.13). Forest conversion to fertilized systems significantly and highly raised both N 2 O and NO emission rates (Hedges's d of 1.03 ± 0.23 and 0.52 ± 0.09, respectively). Changes in nitrogen availability and WFPS were the main factors explaining changes in N 2 O emissions following LUC, therefore it is important that experimental designs monitor their spatio-temporal variation. Gaps in the literature on N oxide fluxes included geographical gaps (Africa, Oceania) and LU gaps (degraded forest, wetland (notably peat) forest, oil palm plantation and soy cultivation).

Description: Phytoplankton calcification as an effective mechanism to prevent cellular calcium poisoning Biogeosciences Discussions, 12, 12691-12712, 2015 Author(s): M. N. Müller, J. Barcelos e Ramos, K. G. Schulz, U. Riebesell, J. Kaźmierczak, F. Gallo, L. Mackinder, Y. Li, P. N. Nesterenko, T. W. Trull, and G. M. Hallegraeff Marine phytoplankton has developed the remarkable ability to tightly regulate the concentration of free calcium ions in the intracellular cytosol at a level of ~ 0.1 μmol L −1 in the presence of seawater Ca 2+ concentrations of 10 mmol L −1 . The low cytosolic calcium ion concentration is of utmost importance for proper cell signalling function. While the regulatory mechanisms responsible for the tight control of intracellular Ca 2+ concentration are not completely understood, phytoplankton taxonomic groups appear to have evolved different strategies, which may affect their ability to cope with changes in seawater Ca 2+ concentrations in their environment on geological time scales. For example, the Cretaceous (145 to 66 Ma ago), an era known for the high abundance of coccolithophores and the production of enormous calcium carbonate deposits, exhibited seawater calcium concentrations up to four times present-day levels. We show that calcifying coccolithophore species ( Emiliania huxleyi , Gephyrocapsa oceanica and Coccolithus braarudii ) are able to maintain their relative fitness (in terms of growth rate and photosynthesis) at simulated Cretaceous seawater calcium concentrations, whereas these rates are severely reduced under these conditions in some non-calcareous phytoplankton species ( Chaetoceros sp., Ceratoneis closterium and Heterosigma akashiwo ). Most notably, this also applies to a non-calcifying strain of E. huxleyi which displays a calcium-sensitivity similar to the non-calcareous species. We hypothesize that the process of calcification in coccolithophores provides an efficient mechanism to prevent cellular calcium poisoning and thereby offered a potential key evolutionary advantage, responsible for the proliferation of coccolithophores during times of high seawater calcium concentrations.

Description: by Deborah A. Striegel, Manami Hara, Vipul Periwal Pancreatic islets of Langerhans consist of endocrine cells, primarily α, β and δ cells, which secrete glucagon, insulin, and somatostatin, respectively, to regulate plasma glucose. β cells form irregular locally connected clusters within islets that act in concert to secrete insulin upon glucose stimulation. Due to the central functional significance of this local connectivity in the placement of β cells in an islet, it is important to characterize it quantitatively. However, quantification of the seemingly stochastic cytoarchitecture of β cells in an islet requires mathematical methods that can capture topological connectivity in the entire β-cell population in an islet. Graph theory provides such a framework. Using large-scale imaging data for thousands of islets containing hundreds of thousands of cells in human organ donor pancreata, we show that quantitative graph characteristics differ between control and type 2 diabetic islets. Further insight into the processes that shape and maintain this architecture is obtained by formulating a stochastic theory of β-cell rearrangement in whole islets, just as the normal equilibrium distribution of the Ornstein-Uhlenbeck process can be viewed as the result of the interplay between a random walk and a linear restoring force. Requiring that rearrangements maintain the observed quantitative topological graph characteristics strongly constrained possible processes. Our results suggest that β-cell rearrangement is dependent on its connectivity in order to maintain an optimal cluster size in both normal and T2D islets.

Description: EUROSPEC: at the interface between remote sensing and ecosystem CO 2 flux measurements in Europe Biogeosciences Discussions, 12, 13069-13121, 2015 Author(s): A. Porcar-Castell, A. Mac Arthur, M. Rossini, L. Eklundh, J. Pacheco-Labrador, K. Anderson, M. Balzarolo, M. P. Martín, H. Jin, E. Tomelleri, S. Cerasoli, K. Sakowska, A. Hueni, T. Julitta, C. J. Nichol, and L. Vescovo Resolving the spatial and temporal dynamics of gross primary productivity (GPP) of terrestrial ecosystems across different scales remains a challenge. Remote sensing is regarded as the solution to upscale point observations conducted at the ecosystem level, using the eddy covariance (EC) technique, to the landscape and global levels. In addition to traditional vegetation indices, the photochemical reflectance index (PRI) and the emission of solar-induced chlorophyll fluorescence (SIF), now measurable from space, provide a new range of opportunities to monitor the global carbon cycle using remote sensing. However, the scale mismatch between EC observations and the much coarser satellite-derived data complicates the integration of the two sources of data. The solution is to establish a network of in situ spectral measurements that can act as bridge between EC measurements and remote sensing data. In situ spectral measurements have been already conducted for many years at EC sites, but using variable instrumentation, setups, and measurement standards. In Europe in particular, in situ spectral measurements remain highly heterogeneous. The goal of EUROSPEC Cost Action ES0930 was to promote the development of common measuring protocols and new instruments towards establishing best practices and standardization of in situ spectral measurements. In this review we describe the background and main tradeoffs of in situ spectral measurements, review the main results of EUROSPEC Cost Action, and discuss the future challenges and opportunities of in situ spectral measurements for improved estimation of local and global carbon cycle.

Description: Improved end-member characterization of modern organic matter pools in the Ohrid Basin (Albania, Macedonia) and evaluation of new palaeoenvironmental proxies Biogeosciences Discussions, 12, 12975-13039, 2015 Author(s): J. Holtvoeth, D. Rushworth, A. Imeri, M. Cara, H. Vogel, T. Wagner, and G. A. Wolff We present elemental, lipid biomarker and compound-specific isotope (δ 13 C, δ 2 H) data for soils and leaf litter collected in the catchment of Lake Ohrid (Albania, Macedonia), as well as macrophytes, particulate organic matter and sediments from the lake itself. Lake Ohrid provides an outstanding archive of continental environmental change of at least 1.2 M years and the purpose of our study is to ground truth organic geochemical proxies that we developed in order to study past changes in the terrestrial biome. We show that soils dominate the lipid signal of the lake sediments rather than the vegetation or aquatic biomass, while compound-specific isotopes (δ 13 C, δ 2 H) determined for n-alkanoic acids confirm a dominant terrestrial source of organic matter to the lake. There is a strong imprint of suberin monomers on the composition of total lipid extracts and chain-length distributions of n-alkanoic acids, n-alcohols, ω-hydroxy acids and α,ω-dicarboxylic acids. Our end-member survey identifies that ratios of mid-chain length suberin-derived to long-chain length cuticular-derived alkyl compounds as well as their average chain length distributions can be used as new molecular proxies of organic matter sources to the lake. We tested these for the 8.2 ka event, a pronounced and widespread Holocene climate fluctuation. In SE Europe climate became drier and cooler in response to the event, as is clearly recognizable in the carbonate and organic carbon records of Lake Ohrid sediments. Our new proxies indicate biome modification in response to hydrological changes, identifying two phases of increased soil OM supply, first from topsoils and then from mineral soils. Our study demonstrates that geochemical fingerprinting of terrestrial OM should focus on the main lipid sources, rather than the living biomass. Both can exhibit climate-controlled variability, but are generally not identical.

Description: The root economics spectrum: divergence of absorptive root strategies with root diameter Biogeosciences Discussions, 12, 13041-13067, 2015 Author(s): D. Kong, J. Wang, P. Kardol, H. Wu, H. Zeng, X. Deng, and Y. Deng Plant roots usually vary along a dominant ecological axis, the root economics spectrum (RES), depicting a tradeoff between resource acquisition and conservation. For absorptive roots, which are mainly responsible for resource acquisition, we hypothesized that root strategies as predicted from the RES shift with increasing root diameter. To test this hypothesis, we used seven contrasting plant species for which we separated absorptive roots into two categories: thin roots ( 〈 247 μm diameter) and thick roots. For each category, we analyzed a~range of root traits closely related to resource acquisition and conservation, including root tissue density, carbon (C) and nitrogen (N) fractions as well as root anatomical traits. The results showed that trait relationships for thin absorptive roots followed the expectations from the RES while no clear trait relationships were found in support of the RES for thick absorptive roots. Our results suggest divergence of absorptive root strategies in relation to root diameter, which runs against a single economics spectrum for absorptive roots.

Description: Millennial changes in North Atlantic oxygen concentrations Biogeosciences Discussions, 12, 12947-12973, 2015 Author(s): B. A. A. Hoogakker, D. J. R. Thornalley, and S. Barker Glacial–interglacial changes in bottom water oxygen concentrations [O 2 ] in the deep Northeast Atlantic have been linked to decreased ventilation relating to changes in ocean circulation and the biological pump (Hoogakker et al., 2015). In this paper we discuss seawater [O 2 ] changes in relation to millennial climate oscillations in the North Atlantic ocean over the last glacial cycle, using bottom water [O 2 ] reconstructions from 2 cores: (1) MD95-2042 from the deep northeast Atlantic (Hoogakker et al., 2015), and (2) ODP 1055 from the intermediate northwest Atlantic. Deep northeast Atlantic core MD95-2042 shows decreased bottom water [O 2 ] during millennial scale cool events, with lowest bottom water [O 2 ] of 170, 144, and 166 ± 17 μmol kg −1 during Heinrich ice rafting events H6, H4 and H1. Importantly, at intermediate core ODP 1055 bottom water [O 2 ] was lower during parts of Marine Isotope Stage 4 and millennial cool events, with lowest values of 179 and 194 μmol kg −1 recorded during millennial cool events C21 and a cool event following Dansgaard–Oeschger event 19. Our reconstructions agree with previous model simulations suggesting that glacial cold events may be associated with lower seawater [O 2 ] across the North Atlantic below ~1 km (Schmittner et al., 2007), although in our reconstructions the changes are less dramatic. The decreases in bottom water [O 2 ] during North Atlantic Heinrich events and earlier cold events at the deep site can be linked to water mass changes in relation to ocean circulation changes, and possibly productivity changes. At the intermediate depth site a strong North Atlantic Intermediate Water cell precludes water mass changes as a cause for decreased bottom water [O 2 ]. Instead we propose that the lower bottom [O 2 ] there can be linked to productivity changes through increased export of organic material from the surface ocean.

Description: by Ghanim Ullah, Yina Wei, Markus A Dahlem, Martin Wechselberger, Steven J Schiff Cell volume changes are ubiquitous in normal and pathological activity of the brain. Nevertheless, we know little of how cell volume affects neuronal dynamics. We here performed the first detailed study of the effects of cell volume on neuronal dynamics. By incorporating cell swelling together with dynamic ion concentrations and oxygen supply into Hodgkin-Huxley type spiking dynamics, we demonstrate the spontaneous transition between epileptic seizure and spreading depression states as the cell swells and contracts in response to changes in osmotic pressure. Our use of volume as an order parameter further revealed a dynamical definition for the experimentally described physiological ceiling that separates seizure from spreading depression, as well as predicted a second ceiling that demarcates spreading depression from anoxic depolarization. Our model highlights the neuroprotective role of glial K buffering against seizures and spreading depression, and provides novel insights into anoxic depolarization and the relevant cell swelling during ischemia. We argue that the dynamics of seizures, spreading depression, and anoxic depolarization lie along a continuum of the repertoire of the neuron membrane that can be understood only when the dynamic ion concentrations, oxygen homeostasis,and cell swelling in response to osmotic pressure are taken into consideration. Our results demonstrate the feasibility of a unified framework for a wide range of neuronal behaviors that may be of substantial importance in the understanding of and potentially developing universal intervention strategies for these pathological states.

Description: by John R. Houser, Craig Barnhart, Daniel R. Boutz, Sean M. Carroll, Aurko Dasgupta, Joshua K. Michener, Brittany D. Needham, Ophelia Papoulas, Viswanadham Sridhara, Dariya K. Sydykova, Christopher J. Marx, M. Stephen Trent, Jeffrey E. Barrick, Edward M. Marcotte, Claus O. Wilke How do bacteria regulate their cellular physiology in response to starvation? Here, we present a detailed characterization of Escherichia coli growth and starvation over a time-course lasting two weeks. We have measured multiple cellular components, including RNA and proteins at deep genomic coverage, as well as lipid modifications and flux through central metabolism. Our study focuses on the physiological response of E . coli in stationary phase as a result of being starved for glucose, not on the genetic adaptation of E . coli to utilize alternative nutrients. In our analysis, we have taken advantage of the temporal correlations within and among RNA and protein abundances to identify systematic trends in gene regulation. Specifically, we have developed a general computational strategy for classifying expression-profile time courses into distinct categories in an unbiased manner. We have also developed, from dynamic models of gene expression, a framework to characterize protein degradation patterns based on the observed temporal relationships between mRNA and protein abundances. By comparing and contrasting our transcriptomic and proteomic data, we have identified several broad physiological trends in the E . coli starvation response. Strikingly, mRNAs are widely down-regulated in response to glucose starvation, presumably as a strategy for reducing new protein synthesis. By contrast, protein abundances display more varied responses. The abundances of many proteins involved in energy-intensive processes mirror the corresponding mRNA profiles while proteins involved in nutrient metabolism remain abundant even though their corresponding mRNAs are down-regulated.

Description: by Shaun S. Sanders, Dale D. O. Martin, Stefanie L. Butland, Mathieu Lavallée-Adam, Diego Calzolari, Chris Kay, John R. Yates, Michael R. Hayden Palmitoylation involves the reversible posttranslational addition of palmitate to cysteines and promotes membrane binding and subcellular localization. Recent advancements in the detection and identification of palmitoylated proteins have led to multiple palmitoylation proteomics studies but these datasets are contained within large supplemental tables, making downstream analysis and data mining time-consuming and difficult. Consequently, we curated the data from 15 palmitoylation proteomics studies into one compendium containing 1,838 genes encoding palmitoylated proteins; representing approximately 10% of the genome. Enrichment analysis revealed highly significant enrichments for Gene Ontology biological processes, pathway maps, and process networks related to the nervous system. Strikingly, 41% of synaptic genes encode a palmitoylated protein in the compendium. The top disease associations included cancers and diseases and disorders of the nervous system, with Schizophrenia, HD, and pancreatic ductal carcinoma among the top five, suggesting that aberrant palmitoylation may play a pivotal role in the balance of cell death and survival. This compendium provides a much-needed resource for cell biologists and the palmitoylation field, providing new perspectives for cancer and neurodegeneration.

Description: by Liat Rockah-Shmuel, Ágnes Tóth-Petróczy, Dan S. Tawfik Systematic mappings of the effects of protein mutations are becoming increasingly popular. Unexpectedly, these experiments often find that proteins are tolerant to most amino acid substitutions, including substitutions in positions that are highly conserved in nature. To obtain a more realistic distribution of the effects of protein mutations, we applied a laboratory drift comprising 17 rounds of random mutagenesis and selection of M.HaeIII, a DNA methyltransferase. During this drift, multiple mutations gradually accumulated. Deep sequencing of the drifted gene ensembles allowed determination of the relative effects of all possible single nucleotide mutations. Despite being averaged across many different genetic backgrounds, about 67% of all nonsynonymous, missense mutations were evidently deleterious, and an additional 16% were likely to be deleterious. In the early generations, the frequency of most deleterious mutations remained high. However, by the 17th generation, their frequency was consistently reduced, and those remaining were accepted alongside compensatory mutations. The tolerance to mutations measured in this laboratory drift correlated with sequence exchanges seen in M.HaeIII’s natural orthologs. The biophysical constraints dictating purging in nature and in this laboratory drift also seemed to overlap. Our experiment therefore provides an improved method for measuring the effects of protein mutations that more closely replicates the natural evolutionary forces, and thereby a more realistic view of the mutational space of proteins.

Description: The carbon cycle in Mexico: past, present and future of C stocks and fluxes Biogeosciences Discussions, 12, 12501-12541, 2015 Author(s): G. Murray-Tortarolo, P. Friedlingstein, S. Sitch, V. J. Jaramillo, F. Murguía-Flores, A. Anav, Y. Liu, A. Arneth, A. Arvanitis, A. Harper, A. Jain, E. Kato, C. Koven, B. Poulter, B. D. Stocker, A. Wiltshire, S. Zaehle, and N. Zeng We modelled the carbon (C) cycle in Mexico with a process-based approach. We used different available products (satellite data, field measurements, models and flux towers) to estimate C stocks and fluxes in the country at three different time frames: present (defined as the period 2000–2005), the past century (1901–2000) and the remainder of this century (2010–2100). Our estimate of the gross primary productivity (GPP) for the country was 2137 ± 1023 Tg C yr −1 and a total C stock of 34 506 ± 7483 Tg C, with 20 347 ± 4622 Pg C in vegetation and 14 159 ± 3861 in the soil. Contrary to other current estimates for recent decades, our results showed that Mexico was a C sink over the period 1990–2009 (+31 Tg C yr −1 ) and that C accumulation over the last century amounted to 1210 ± 1040 Tg C. We attributed this sink to the CO 2 fertilization effect on GPP, which led to an increase of 3408 ± 1060 Tg C, while both climate and land use reduced the country C stocks by −458 ± 1001 and −1740 ± 878 Tg C, respectively. Under different future scenarios the C sink will likely continue over 21st century, with decreasing C uptake as the climate forcing becomes more extreme. Our work provides valuable insights on relevant driving processes of the C-cycle such as the role of drought in marginal lands (e.g. grasslands and shrublands) and the impact of climate change on the mean residence time of C in tropical ecosystems.

Description: Influence of timing of sea ice retreat on phytoplankton size during marginal ice zone bloom period in the Chukchi and Bering shelves Biogeosciences Discussions, 12, 12611-12651, 2015 Author(s): A. Fujiwara, T. Hirawake, K. Suzuki, L. Eisner, I. Imai, S. Nishino, T. Kikuchi, and S. I. Saitoh Timing of sea ice retreat (TSR) as well as cell size of primary producers (i.e., phytoplankton) plays crucial roles in seasonally ice-covered marine ecosystem. Thus, it is important to monitor the temporal and spatial distribution of phytoplankton community size structure. Prior to this study, an ocean color algorithm has been developed to derive phytoplankton size index F L , which is defined as the ratio of chlorophyll a derived from the cells larger than 5 μm to the total chl a using satellite remote sensing for the Chukchi and Bering shelves. Using this method, we analyzed pixel-by-pixel relationships between F L during marginal ice zone (MIZ) bloom period and TSR over a period of 1998–2013. The influence of TSR on sea surface temperature (SST) and changes in ocean heat content (ΔOHC) during the MIZ bloom period were also investigated. A significant negative relationship between F L and TSR was widely found in the shelf region during MIZ bloom season. On the other hand, we found a significant positive (negative) relationship between SST (ΔOHC) and TSR. That is, earlier sea-ice retreat was associated with a dominance of larger phytoplankton during a colder and weakly stratified MIZ bloom season, suggesting that duration of nitrate supply, which is important for large-sized phytoplankton growth in this region (i.e., diatoms), can change according to TSR. In addition, under-ice phytoplankton blooms are likely to occur in years with late ice retreat, because sufficient light for phytoplankton growth can pass through the ice and penetrate into the water columns due to an increase in solar radiation toward the summer solstice. Moreover, we found not only the length of ice-free season but also annual median of F L positively correlated with annual net primary production (APP). Thus, both phytoplankton community composition and growing season are important for APP in the study area. Our findings showed quantitative relationship between the inter-annual variability of F L , TSR and APP suggesting satellite remote sensing of phytoplankton community size structure is suitable to document the impact of recent rapid sea ice loss on ecosystem of the study region.

Description: by Shuai Yuan, H. Richard Johnston, Guosheng Zhang, Yun Li, Yi-Juan Hu, Zhaohui S. Qin With rapid decline of the sequencing cost, researchers today rush to embrace whole genome sequencing (WGS), or whole exome sequencing (WES) approach as the next powerful tool for relating genetic variants to human diseases and phenotypes. A fundamental step in analyzing WGS and WES data is mapping short sequencing reads back to the reference genome. This is an important issue because incorrectly mapped reads affect the downstream variant discovery, genotype calling and association analysis. Although many read mapping algorithms have been developed, the majority of them uses the universal reference genome and do not take sequence variants into consideration. Given that genetic variants are ubiquitous, it is highly desirable if they can be factored into the read mapping procedure. In this work, we developed a novel strategy that utilizes genotypes obtained a priori to customize the universal haploid reference genome into a personalized diploid reference genome. The new strategy is implemented in a program named RefEditor. When applying RefEditor to real data, we achieved encouraging improvements in read mapping, variant discovery and genotype calling. Compared to standard approaches, RefEditor can significantly increase genotype calling consistency (from 43% to 61% at 4X coverage; from 82% to 92% at 20X coverage) and reduce Mendelian inconsistency across various sequencing depths. Because many WGS and WES studies are conducted on cohorts that have been genotyped using array-based genotyping platforms previously or concurrently, we believe the proposed strategy will be of high value in practice, which can also be applied to the scenario where multiple NGS experiments are conducted on the same cohort. The RefEditor sources are available at https://github.com/superyuan/refeditor.

Description: by Alexey A. Gritsenko, Marc Hulsman, Marcel J. T. Reinders, Dick de Ridder Translation of RNA to protein is a core process for any living organism. While for some steps of this process the effect on protein production is understood, a holistic understanding of translation still remains elusive. In silico modelling is a promising approach for elucidating the process of protein synthesis. Although a number of computational models of the process have been proposed, their application is limited by the assumptions they make. Ribosome profiling (RP), a relatively new sequencing-based technique capable of recording snapshots of the locations of actively translating ribosomes, is a promising source of information for deriving unbiased data-driven translation models. However, quantitative analysis of RP data is challenging due to high measurement variance and the inability to discriminate between the number of ribosomes measured on a gene and their speed of translation. We propose a solution in the form of a novel multi-scale interpretation of RP data that allows for deriving models with translation dynamics extracted from the snapshots. We demonstrate the usefulness of this approach by simultaneously determining for the first time per-codon translation elongation and per-gene translation initiation rates of Saccharomyces cerevisiae from RP data for two versions of the Totally Asymmetric Exclusion Process (TASEP) model of translation. We do this in an unbiased fashion, by fitting the models using only RP data with a novel optimization scheme based on Monte Carlo simulation to keep the problem tractable. The fitted models match the data significantly better than existing models and their predictions show better agreement with several independent protein abundance datasets than existing models. Results additionally indicate that the tRNA pool adaptation hypothesis is incomplete, with evidence suggesting that tRNA post-transcriptional modifications and codon context may play a role in determining codon elongation rates.

Description: Southwestern Tropical Atlantic coral growth response to atmospheric circulation changes induced by ozone depletion in Antarctica Biogeosciences Discussions, 12, 13193-13213, 2015 Author(s): H. Evangelista, I. Wainer, A. Sifeddine, T. Corrège, R. C. Cordeiro, S. Lamounier, D. Godiva, C.-C. Shen, F. Le Cornec, B. Turcq, C. E. Lazareth, and C.-Y. Hu Climate changes induced by stratospheric ozone depletion over Antarctica have been recognized as an important consequence of the recently observed Southern Hemisphere atmospheric circulation. Here we present evidences that the Brazilian coast (Southwestern Atlantic) may have been impacted from both winds and sea surface temperature changes derived from this process. Skeleton analysis of massive coral species living in shallow waters off Brazil are very sensitive to air–sea interactions, and seem to record this impact. Growth rates of Brazilian corals show a trend reversal that fits the ozone depletion evolution, confirming that ozone impacts are far reaching and potentially affect coastal ecosystems in tropical environments.

Description: Contrasting pH buffering patterns in neutral-alkaline soils along a 3600 km transect in northern China Biogeosciences Discussions, 12, 13215-13240, 2015 Author(s): W. Luo, P. N. Nelson, M.-H. Li, J. Cai, Y. Zhang, Y. Zhang, Y. Shan, R. Wang, X. Han, and Y. Jiang Soil pH buffering capacity (pHBC) plays a crucial role in predicting acidification rates, yet its large-scale patterns and controls are poorly understood, especially for neutral-alkaline soils. Here, we evaluated the spatial patterns and drivers of pHBC along a 3600 km long transect (1900 km sub-transect with carbonate containing soils and 1700 km sub-transect with non-carbonate containing soils) across northern China. Soil pHBC was greater in the carbonate containing soils than in the non-carbonate containing soils. Acid addition decreased soil pH in the non-carbonate containing soils more markedly than in the carbonate containing soils. Within the carbonate soil sub-transect, soil pHBC was positively correlated with cation exchange capacity (CEC), carbonate content and exchangeable sodium (Na) concentration, but negatively correlated with initial pH and clay content, and not correlated with soil organic carbon (SOC) content. Within the non-carbonate sub-transect, soil pHBC was positively related to initial pH, clay content, CEC and exchangeable Na concentration, but not related to SOC content. Carbonate content was the primary determinant of pHBC in the carbonate containing soils and CEC was the main determinant of buffering capacity in the non-carbonate containing soils. Soil pHBC was positively related to aridity index and carbonate content across the carbonate containing soil sub-transect. Our results indicated that mechanisms controlling pHBC differ among neutral-alkaline soils of northern China, especially between carbonate and non-carbonate containing soils, leading to different rates, risks, and impacts of acidification. This understanding should be incorporated into the acidification risk assessment and landscape management in a changing world.

Description: To monitor multiple environmental factors of henhouses in modern chicken farms, a henhouse online monitoring system based on wireless sensor network was developed using wireless sensor technology and computer network technology. Sensor data compensation and correction were designed to be achieved using software and data fitting methods, data reliable transmission achieved using a data loss recovery strategy, and data missing during monitoring addressed using a self-decision and online filling method. Operation test of the system showed that: The system was economic and reliable; it enabled wireless monitoring and Web display of the environmental factors of a henhouse; and the root mean square errors (RMSEs) between the estimated values from the self-decision and on-line filling method and experimental values of the four environmental factors were 0.1698, 3.0859, 77 and 0.094, respectively, indicative of high estimation accuracy. The system can provide support for modern management of henhouses and can be transplanted to related monitoring scenarios in the agricultural field.

Description: by Santiago Schnell

Description: by Alexander Ullrich, Mathias A. Böhme, Johannes Schöneberg, Harald Depner, Stephan J. Sigrist, Frank Noé Synaptic vesicle fusion is mediated by SNARE proteins forming in between synaptic vesicle (v-SNARE) and plasma membrane (t-SNARE), one of which is Syntaxin-1A. Although exocytosis mainly occurs at active zones, Syntaxin-1A appears to cover the entire neuronal membrane. By using STED super-resolution light microscopy and image analysis of Drosophila neuro-muscular junctions, we show that Syntaxin-1A clusters are more abundant and have an increased size at active zones. A computational particle-based model of syntaxin cluster formation and dynamics is developed. The model is parametrized to reproduce Syntaxin cluster-size distributions found by STED analysis, and successfully reproduces existing FRAP results. The model shows that the neuronal membrane is adjusted in a way to strike a balance between having most syntaxins stored in large clusters, while still keeping a mobile fraction of syntaxins free or in small clusters that can efficiently search the membrane or be traded between clusters. This balance is subtle and can be shifted toward almost no clustering and almost complete clustering by modifying the syntaxin interaction energy on the order of only 1 k B T. This capability appears to be exploited at active zones. The larger active-zone syntaxin clusters are more stable and provide regions of high docking and fusion capability, whereas the smaller clusters outside may serve as flexible reserve pool or sites of spontaneous ectopic release.

Description: by Stephan Köhler, Friederike Schmid, Giovanni Settanni Fibrinogen is a serum multi-chain protein which, when activated, aggregates to form fibrin, one of the main components of a blood clot. Fibrinolysis controls blood clot dissolution through the action of the enzyme plasmin, which cleaves fibrin at specific locations. Although the main biochemical factors involved in fibrin formation and lysis have been identified, a clear mechanistic picture of how these processes take place is not available yet. This picture would be instrumental, for example, for the design of improved thrombolytic or anti-haemorrhagic strategies, as well as, materials with improved biocompatibility. Here, we present extensive molecular dynamics simulations of fibrinogen which reveal large bending motions centered at a hinge point in the coiled-coil regions of the molecule. This feature, likely conserved across vertebrates according to our analysis, suggests an explanation for the mechanism of exposure to lysis of the plasmin cleavage sites on fibrinogen coiled-coil region. It also explains the conformational variability of fibrinogen observed during its adsorption on inorganic surfaces and it is supposed to play a major role in the determination of the hydrodynamic properties of fibrinogen. In addition the simulations suggest how the dynamics of the D region of fibrinogen may contribute to the allosteric regulation of the blood coagulation cascade through a dynamic coupling between the a- and b-holes, important for fibrin polymerization, and the integrin binding site P1.

Description: by Sergei Maslov, Kim Sneppen Populations of species in ecosystems are often constrained by availability of resources within their environment. In effect this means that a growth of one population, needs to be balanced by comparable reduction in populations of others. In neutral models of biodiversity all populations are assumed to change incrementally due to stochastic births and deaths of individuals. Here we propose and model another redistribution mechanism driven by abrupt and severe reduction in size of the population of a single species freeing up resources for the remaining ones. This mechanism may be relevant e.g. for communities of bacteria, with strain-specific collapses caused e.g. by invading bacteriophages, or for other ecosystems where infectious diseases play an important role. The emergent dynamics of our system is characterized by cyclic ‘‘diversity waves’’ triggered by collapses of globally dominating populations. The population diversity peaks at the beginning of each wave and exponentially decreases afterwards. Species abundances have bimodal time-aggregated distribution with the lower peak formed by populations of recently collapsed or newly introduced species while the upper peak - species that has not yet collapsed in the current wave. In most waves both upper and lower peaks are composed of several smaller peaks. This self-organized hierarchical peak structure has a long-term memory transmitted across several waves. It gives rise to a scale-free tail of the time-aggregated population distribution with a universal exponent of 1.7. We show that diversity wave dynamics is robust with respect to variations in the rules of our model such as diffusion between multiple environments, species-specific growth and extinction rates, and bet-hedging strategies.

Description: by Hannah Edwards, Charlotte M. Deane Several protein structure classification schemes exist that partition the protein universe into structural units called folds. Yet these schemes do not discuss how these units sit relative to each other in a global structure space. In this paper we construct networks that describe such global relationships between folds in the form of structural bridges. We generate these networks using four different structural alignment methods across multiple score thresholds. The networks constructed using the different methods remain a similar distance apart regardless of the probability threshold defining a structural bridge. This suggests that at least some structural bridges are method specific and that any attempt to build a picture of structural space should not be reliant on a single structural superposition method. Despite these differences all representations agree on an organisation of fold space into five principal community structures: all- α , all- β sandwiches, all- β barrels, α / β and α + β . We project estimated fold ages onto the networks and find that not only are the pairings of unconnected folds associated with higher age differences than bridged folds, but this difference increases with the number of networks displaying an edge. We also examine different centrality measures for folds within the networks and how these relate to fold age. While these measures interpret the central core of fold space in varied ways they all identify the disposition of ancestral folds to fall within this core and that of the more recently evolved structures to provide the peripheral landscape. These findings suggest that evolutionary information is encoded along these structural bridges. Finally, we identify four highly central pivotal folds representing dominant topological features which act as key attractors within our landscapes.

Description: by Ayal Lavi, Omri Perez, Uri Ashery Neuronal microcircuits generate oscillatory activity, which has been linked to basic functions such as sleep, learning and sensorimotor gating. Although synaptic release processes are well known for their ability to shape the interaction between neurons in microcircuits, most computational models do not simulate the synaptic transmission process directly and hence cannot explain how changes in synaptic parameters alter neuronal network activity. In this paper, we present a novel neuronal network model that incorporates presynaptic release mechanisms, such as vesicle pool dynamics and calcium-dependent release probability, to model the spontaneous activity of neuronal networks. The model, which is based on modified leaky integrate-and-fire neurons, generates spontaneous network activity patterns, which are similar to experimental data and robust under changes in the model's primary gain parameters such as excitatory postsynaptic potential and connectivity ratio. Furthermore, it reliably recreates experimental findings and provides mechanistic explanations for data obtained from microelectrode array recordings, such as network burst termination and the effects of pharmacological and genetic manipulations. The model demonstrates how elevated asynchronous release, but not spontaneous release, synchronizes neuronal network activity and reveals that asynchronous release enhances utilization of the recycling vesicle pool to induce the network effect. The model further predicts a positive correlation between vesicle priming at the single-neuron level and burst frequency at the network level; this prediction is supported by experimental findings. Thus, the model is utilized to reveal how synaptic release processes at the neuronal level govern activity patterns and synchronization at the network level.

Description: Smallholder African farms in western Kenya have limited greenhouse gas fluxes Biogeosciences Discussions, 12, 15301-15336, 2015 Author(s): D. E. Pelster, M. C. Rufino, T. Rosenstock, J. Mango, G. Saiz, E. Diaz-Pines, G. Baldi, and K. Butterbach-Bahl Few field studies examine greenhouse gas (GHG) emissions from African agricultural systems resulting in high uncertainty for national inventories. We provide here the most comprehensive study in Africa to date, examining annual CO 2 , CH 4 and N 2 O emissions from 59 plots, across different vegetation types, field types and land classes in western Kenya. The study area consists of a lowland area (approximately 1200 m a.s.l.) rising approximately 600 m to a highland plateau. Cumulative annual fluxes ranged from 2.8 to 15.0 Mg CO 2 -C ha −1 , −6.0 to 2.4 kg CH 4 -C ha −1 and −0.1 to 1.8 kg N 2 O-N ha −1 . Management intensity of the plots did not result in differences in annual fluxes for the GHGs measured ( P = 0.46, 0.67 and 0.14 for CO 2 , N 2 O and CH 4 respectively). The similar emissions were likely related to low fertilizer input rates (≤ 20 kg ha −1 ). Grazing plots had the highest CO 2 fluxes ( P = 0.005); treed plots were a larger CH 4 sink than grazing plots ( P = 0.05); while N 2 O emissions were similar across vegetation types ( P = 0.59). This case study is likely representative for low fertilizer input, smallholder systems across sub-Saharan Africa, providing critical data for estimating regional or continental GHG inventories. Low crop yields, likely due to low inputs, resulted in high (up to 67 g N 2 O-N kg −1 aboveground N uptake) yield-scaled emissions. Improving crop production through intensification of agricultural production (i.e. water and nutrient management) may be an important tool to mitigate the impact of African agriculture on climate change.

Description: Combining two complementary micrometeorological methods to measure CH 4 and N 2 O fluxes over pasture Biogeosciences Discussions, 12, 15245-15299, 2015 Author(s): J. Laubach, M. Barthel, A. Fraser, J. E. Hunt, and D. W. T. Griffith New Zealand's largest industrial sector is pastoral agriculture, giving rise to a large fraction of the country's emissions of methane (CH 4 ) and nitrous oxide (N 2 O). We designed a system to continuously measure CH 4 and N 2 O fluxes at the field scale on two adjacent pastures that differed with respect to management. At the core of this system was a closed-cell Fourier-transform infrared spectrometer (FTIR), measuring the mole fractions of CH 4 , N 2 O and carbon dioxide (CO 2 ) at two heights at each site. In parallel, CO 2 fluxes were measured using eddy-covariance instrumentation. We applied two different micrometeorological ratio methods to infer the CH 4 and N 2 O fluxes from their respective mole fractions and the CO 2 fluxes. The first is a variant of the flux-gradient method, where it is assumed that the turbulent diffusivities of CH 4 and N 2 O equal that of CO 2 . This method was reliable when the CO 2 mole-fraction difference between heights was at least 4 times greater than the FTIR's resolution of differences. For the second method, the temporal increases of mole fractions in the stable nocturnal boundary layer, which are correlated for concurrently-emitted gases, are used to infer the unknown fluxes of CH 4 and N 2 O from the known flux of CO 2 . This method was sensitive to "contamination" from trace gas sources other than the pasture of interest and therefore required careful filtering. With both methods combined, estimates of mean daily CH 4 and N 2 O fluxes were obtained for 60 % of days at one site and 77 % at the other. Both methods indicated both sites as net sources of CH 4 and N 2 O. Mean emission rates for one year at the unfertilised, winter-grazed site were 8.2 (± 0.91) nmol CH 4 m −2 s −1 and 0.40 (± 0.018) nmol N 2 O m −2 s −1 . During the same year, mean emission rates at the irrigated, fertilised and rotationally-grazed site were 7.0 (± 0.89) nmol CH 4 m −2 s −1 and 0.57 (± 0.019) nmol N 2 O m −2 s −1 . At this site, the N 2 O emissions amounted to 1.19 (± 0.15) % of the nitrogen inputs from animal excreta and fertiliser application.

Description: by Michael A. Cerullo

Description: by Jasmine Foo, Lin L Liu, Kevin Leder, Markus Riester, Yoh Iwasa, Christoph Lengauer, Franziska Michor The traditional view of cancer as a genetic disease that can successfully be treated with drugs targeting mutant onco-proteins has motivated whole-genome sequencing efforts in many human cancer types. However, only a subset of mutations found within the genomic landscape of cancer is likely to provide a fitness advantage to the cell. Distinguishing such “driver” mutations from innocuous “passenger” events is critical for prioritizing the validation of candidate mutations in disease-relevant models. We design a novel statistical index, called the Hitchhiking Index, which reflects the probability that any observed candidate gene is a passenger alteration, given the frequency of alterations in a cross-sectional cancer sample set, and apply it to a mutational data set in colorectal cancer. Our methodology is based upon a population dynamics model of mutation accumulation and selection in colorectal tissue prior to cancer initiation as well as during tumorigenesis. This methodology can be used to aid in the prioritization of candidate mutations for functional validation and contributes to the process of drug discovery.

Description: by Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam Arkin, Jay D. Keasling Current limitations in quantitatively predicting biological behavior hinder our efforts to engineer biological systems to produce biofuels and other desired chemicals. Here, we present a new method for calculating metabolic fluxes, key targets in metabolic engineering, that incorporates data from 13 C labeling experiments and genome-scale models. The data from 13 C labeling experiments provide strong flux constraints that eliminate the need to assume an evolutionary optimization principle such as the growth rate optimization assumption used in Flux Balance Analysis (FBA). This effective constraining is achieved by making the simple but biologically relevant assumption that flux flows from core to peripheral metabolism and does not flow back. The new method is significantly more robust than FBA with respect to errors in genome-scale model reconstruction. Furthermore, it can provide a comprehensive picture of metabolite balancing and predictions for unmeasured extracellular fluxes as constrained by 13 C labeling data. A comparison shows that the results of this new method are similar to those found through 13 C Metabolic Flux Analysis ( 13 C MFA) for central carbon metabolism but, additionally, it provides flux estimates for peripheral metabolism. The extra validation gained by matching 48 relative labeling measurements is used to identify where and why several existing COnstraint Based Reconstruction and Analysis (COBRA) flux prediction algorithms fail. We demonstrate how to use this knowledge to refine these methods and improve their predictive capabilities. This method provides a reliable base upon which to improve the design of biological systems.

Description: Increasing P-stress and viral infection impact lipid remodeling of the picophytoplankter Micromonas pusilla Biogeosciences Discussions, 12, 15583-15610, 2015 Author(s): D. S. Maat, N. J. Bale, E. C. Hopmans, J. S. Sinninghe Damsté, S. Schouten, and C. P. D. Brussaard The intact polar lipid (IPL) composition of phytoplankton is plastic and dependent on environmental factors. Previous studies have shown that phytoplankton under phosphorus (P)-stress substitute phosphatidylglycerols (PGs) with sulphoquinovosyldiacylglycerols (SQDGs) and digalactosyldiacylglycerols (DGDGs). However, these studies focused merely on P-depletion, while phytoplankton in the natural environment often experience P-limitation whereby the degree of limitation depends on the supply rate of the limiting nutrient. Here we demonstrate a linear increase in SQDG : PG and DGDG : PG ratios with increasing cellular P-stress in the picophotoeukaryote Micromonas pusilla , obtained by P-replete, P-limited (chemostat) and P-starved (no supply of P) culturing conditions. These ratios were not affected by the degree of the P-limiting conditions itself (i.e. 0.97 and 0.32 μ max chemostats), suggesting there is a minimum requirement of PGs for the maintenance of cell growth. Viral infection reduced the increase in SQDG : PG and DGDG : PG ratios in P-starved cells, but the extent did depend on the growth rate of the cultures before infection. The membrane of M. pusilla virus MpV itself was lacking some IPLs compared to the host as, e.g. no monogalactosyldiacylglycerols could be detected. Growth of the phytoplankton cultures under enhanced CO 2 concentration did not affect the lipid remodeling results. The present study provides new insights into how the P-related trophic state of an ecosystem as well as viral infection can affect phytoplankton IPL composition, and therefore influence food web dynamics and biogeochemical cycling.

Description: No-tillage lessens soil CO 2 emissions the most under arid and sandy soil conditions: results from a meta-analysis Biogeosciences Discussions, 12, 15495-15535, 2015 Author(s): K. Abdalla, P. Chivenge, P. Ciais, and V. Chaplot The management of agroecosystems plays a crucial role in the global carbon cycle with soil tillage leading to known organic carbon redistributions within soils and changes in soil CO 2 emissions. Yet, discrepancies exist on the impact of tillage on soil CO 2 emissions and on the main soil and environmental controls. A meta-analysis was conducted using 46 peer-reviewed publications totaling 174 paired observations comparing CO 2 emissions over entire seasons or years from tilled and untilled soils across different climates, crop types and soil conditions with the objective of quantifying tillage impact on CO 2 emissions and assessing the main controls. On average, tilled soils emitted 21 % more CO 2 than untilled soils, which corresponded to a significant difference at P 〈 0.05. The difference increased to 29 % in sandy soils from arid climates with low soil organic carbon content (SOC C 〈 1 %) and low soil moisture, but tillage had no impact on CO 2 fluxes in clayey soils with high background SOC C (〉 3 %). Finally, nitrogen fertilization and crop residue management had little effect on the CO 2 responses of soils to no-tillage. These results suggest no-tillage is an effective mitigation measure of carbon dioxide losses from dry land soils. They emphasize the importance of including information on soil factors such as texture, aggregate stability and organic carbon content in global models of the carbon cycle.

Description: Predicting biomass of hyperdiverse and structurally complex Central Amazon forests – a virtual approach using extensive field data Biogeosciences Discussions, 12, 15537-15581, 2015 Author(s): D. Magnabosco Marra, N. Higuchi, S. E. Trumbore, G. H. P. M. Ribeiro, J. dos Santos, V. M. C. Carneiro, A. J. N. Lima, J. Q. Chambers, R. I. Negrón-Juárez, F. Holzwarth, B. Reu, and C. Wirth Old-growth forests are subject to substantial changes in structure and species composition due to the intensification of human activities, gradual climate change and extreme weather events. Trees store ca. 90 % of the total AGB above-ground biomass in tropical forests and AGB estimation models are crucial for forest management and conservation. In the Central Amazon, predicting AGB at large spatial-scales is a challenging task due to the heterogeneity of successional stages, high tree species diversity and inherent variations in allometry and architecture. We parameterized generic AGB estimation models applicable across species and a wide range of structural and compositional variation related to species sorting into height layers as well as frequent natural disturbances. We used 727 trees from 101 genera and at least 135 species harvested in a contiguous forest near Manaus, Brazil. Sampling from this dataset we assembled six scenarios designed to span existing gradients in floristic composition and size distribution in order to select models that best predict AGB at the landscape-level across successional gradients. We found that good individual tree model fits do not necessarily translate into good predictions of AGB at the landscape level. When predicting AGB (dry mass) over scenarios using our different models and an available pantropical model, we observed systematic biases ranging from −31 % (pantropical) to +39 %, with RMSE root-mean-square error values of up to 130 Mg ha −1 (pantropical). Our first and second best models had both low mean biases (0.8 and 3.9 %, respectively) and RMSE (9.4 and 18.6 Mg ha −1 ) when applied over scenarios. Predicting biomass correctly at the landscape-level in complex tropical forests, especially allowing good performance at the margins of data availability for model parametrization, requires the inclusion of predictors related to species architecture. The model of interest should comprise the floristic composition and size-distribution variability of the target forest, implying that even generic global or pantropical biomass estimation models can lead to strong biases. Reliable biomass assessments for the Amazon basin still depend on the collection of destructive allometry data at the local/regional scale and forest inventories including species-specific attributes, which are often unavailable or estimated imprecisely in most regions.

Description: by Julia C. Quindlen, Victor K. Lai, Victor H. Barocas Cutaneous mechanoreceptors transduce different tactile stimuli into neural signals that produce distinct sensations of touch. The Pacinian corpuscle (PC), a cutaneous mechanoreceptor located deep within the dermis of the skin, detects high frequency vibrations that occur within its large receptive field. The PC is comprised of lamellae that surround the nerve fiber at its core. We hypothesized that a layered, anisotropic structure, embedded deep within the skin, would produce the nonlinear strain transmission and low spatial sensitivity characteristic of the PC. A multiscale finite-element model was used to model the equilibrium response of the PC to indentation. The first simulation considered an isolated PC with fiber networks aligned with the PC’s surface. The PC was subjected to a 10 μm indentation by a 250 μm diameter indenter. The multiscale model captured the nonlinear strain transmission through the PC, predicting decreased compressive strain with proximity to the receptor’s core, as seen experimentally by others. The second set of simulations considered a single PC embedded epidermally (shallow) or dermally (deep) to model the PC’s location within the skin. The embedded models were subjected to 10 μm indentations at a series of locations on the surface of the skin. Strain along the long axis of the PC was calculated after indentation to simulate stretch along the nerve fiber at the center of the PC. Receptive fields for the epidermis and dermis models were constructed by mapping the long-axis strain after indentation at each point on the surface of the skin mesh. The dermis model resulted in a larger receptive field, as the calculated strain showed less indenter location dependence than in the epidermis model.

Description: Carbon dynamics and changing winter conditions: a review of current understanding and future research directions Biogeosciences Discussions, 12, 15763-15808, 2015 Author(s): M. Haei and H. Laudon Despite the important role of winters for northern ecosystems, it remains the least understood of all the seasons. Here, we summarize existing empirical studies on winter climate and carbon dynamics and highlight some important future research directions. The existing studies include field-scale snow-cover manipulation experiments representing extreme soil climate conditions, laboratory soil incubations studying the influential factors, and time-series of climate and carbon data showing long-term natural variations and existing trends. Most of the field and laboratory experiments indicate an increased soil organic carbon loss due to soil frost. Long-term data demonstrate temporal changes in winter CO 2 efflux and its important contribution to the annual fluxes. A number of research priorities to improve our understanding of winter conditions include (i) ecosystem processes in the fall-winter and winter-spring shoulder seasons, (ii) extreme events, (iii) partitioning into organic- and inorganic carbon, (iv) carry-over effects of winter and growing season on each other, (v) long-term cumulative impacts, and (vi) improved winter process modelling. These areas of research would enable an improved understanding of the role of the snow covered period for carbon cycling, and provide a basis for more realistic models that include winter processes.

Description: by Vipin Narang, Muhamad Azfar Ramli, Amit Singhal, Pavanish Kumar, Gennaro de Libero, Michael Poidinger, Christopher Monterola Human gene regulatory networks (GRN) can be difficult to interpret due to a tangle of edges interconnecting thousands of genes. We constructed a general human GRN from extensive transcription factor and microRNA target data obtained from public databases. In a subnetwork of this GRN that is active during estrogen stimulation of MCF-7 breast cancer cells, we benchmarked automated algorithms for identifying core regulatory genes (transcription factors and microRNAs). Among these algorithms, we identified K-core decomposition, pagerank and betweenness centrality algorithms as the most effective for discovering core regulatory genes in the network evaluated based on previously known roles of these genes in MCF-7 biology as well as in their ability to explain the up or down expression status of up to 70% of the remaining genes. Finally, we validated the use of K-core algorithm for organizing the GRN in an easier to interpret layered hierarchy where more influential regulatory genes percolate towards the inner layers. The integrated human gene and miRNA network and software used in this study are provided as supplementary materials (S1 Data) accompanying this manuscript.

Description: by Jianfei Hu, Johnathan Neiswinger, Jin Zhang, Heng Zhu, Jiang Qian Scaffold proteins play a crucial role in facilitating signal transduction in eukaryotes by bringing together multiple signaling components. In this study, we performed a systematic analysis of scaffold proteins in signal transduction by integrating protein-protein interaction and kinase-substrate relationship networks. We predicted 212 scaffold proteins that are involved in 605 distinct signaling pathways. The computational prediction was validated using a protein microarray-based approach. The predicted scaffold proteins showed several interesting characteristics, as we expected from the functionality of scaffold proteins. We found that the scaffold proteins are likely to interact with each other, which is consistent with previous finding that scaffold proteins tend to form homodimers and heterodimers. Interestingly, a single scaffold protein can be involved in multiple signaling pathways by interacting with other scaffold protein partners. Furthermore, we propose two possible regulatory mechanisms by which the activity of scaffold proteins is coordinated with their associated pathways through phosphorylation process.

Description: by Vassilios Christopoulos, Paul R. Schrater Decisions involve two fundamental problems, selecting goals and generating actions to pursue those goals. While simple decisions involve choosing a goal and pursuing it, humans evolved to survive in hostile dynamic environments where goal availability and value can change with time and previous actions, entangling goal decisions with action selection. Recent studies suggest the brain generates concurrent action-plans for competing goals, using online information to bias the competition until a single goal is pursued. This creates a challenging problem of integrating information across diverse types, including both the dynamic value of the goal and the costs of action. We model the computations underlying dynamic decision-making with disparate value types, using the probability of getting the highest pay-off with the least effort as a common currency that supports goal competition. This framework predicts many aspects of decision behavior that have eluded a common explanation.

Description: by Chakravarthy Marella, Andrew E. Torda, Dominik Schwudke A lipidome is the set of lipids in a given organism, cell or cell compartment and this set reflects the organism’s synthetic pathways and interactions with its environment. Recently, lipidomes of biological model organisms and cell lines were published and the number of functional studies of lipids is increasing. In this study we propose a homology metric that can quantify systematic differences in the composition of a lipidome. Algorithms were developed to 1. consistently convert lipids structure into SMILES, 2. determine structural similarity between molecular species and 3. describe a lipidome in a chemical space model. We tested lipid structure conversion and structure similarity metrics, in detail, using sets of isomeric ceramide molecules and chemically related phosphatidylinositols. Template-based SMILES showed the best properties for representing lipid-specific structural diversity. We also show that sequence analysis algorithms are best suited to calculate distances between such template-based SMILES and we adjudged the Levenshtein distance as best choice for quantifying structural changes. When all lipid molecules of the LIPIDMAPS structure database were mapped in chemical space, they automatically formed clusters corresponding to conventional chemical families. Accordingly, we mapped a pair of lipidomes into the same chemical space and determined the degree of overlap by calculating the Hausdorff distance. We named this metric the ‘Lipidome jUXtaposition (LUX) score’. First, we tested this approach for estimating the lipidome similarity on four yeast strains with known genetic alteration in fatty acid synthesis. We show that the LUX score reflects the genetic relationship and growth temperature better than conventional methods although the score is based solely on lipid structures. Next, we applied this metric to high-throughput data of larval tissue lipidomes of Drosophila. This showed that the LUX score is sufficient to cluster tissues and determine the impact of nutritional changes in an unbiased manner, despite the limited information on the underlying structural diversity of each lipidome. This study is the first effort to define a lipidome homology metric based on structures that will enrich functional association of lipids in a similar manner to measures used in genetics. Finally, we discuss the significance of the LUX score to perform comparative lipidome studies across species borders.

Description: The self-organizing nature of the Mobile Ad hoc Networks (MANETs) provide a communication channel anywhere, anytime without any pre-existing network infrastructure. However, it is exposed to various vulnerabilities that may be exploited by the malicious nodes. One such malicious behavior is introduced by blackhole nodes, which can be easily introduced in the network and, in turn, such nodes try to crumble the working of the network by dropping the maximum data under transmission. In this paper, a new protocol is proposed which is based on the widely used Ad hoc On-Demand Distance Vector (AODV) protocol, Enhanced Secure Trusted AODV (ESTA), which makes use of multiple paths along with use of trust and asymmetric cryptography to ensure data security. The results, based on NS-3 simulation, reveal that the proposed protocol is effectively able to counter the blackhole nodes in three different scenarios.

Description: by Noah Ollikainen, René M. de Jong, Tanja Kortemme Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein–ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art “fixed backbone” design methods perform poorly on these tests, we develop a new “coupled moves” design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein – ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.

Description: Vanishing coccolith vital effects with alleviated CO 2 limitation Biogeosciences Discussions, 12, 15835-15866, 2015 Author(s): M. Hermoso, I. Z. X. Chan, H. L. O. McClelland, A. M. C. Heureux, and R. E. M. Rickaby By recreating a range of geologically relevant concentrations of dissolved inorganic carbon (DIC) in the laboratory, we demonstrate that the magnitude of the vital effects in both carbon and oxygen isotopes of coccolith calcite of multiple species relates to ambient DIC concentration. Under high DIC levels, all the examined coccoliths lacked any offset from inorganic calcite, whereas in low (present-day) DIC concentrations, these vital effects and interspecies differences become substantial. These laboratory observations support the recent hypothesis from field observations that the appearance of interspecific vital effect in coccolithophores coincides with the long-term Neogene decline of atmospheric CO 2 concentrations. The present study brings further valuable constraints on coccolith isotopic compositions by demonstrating the threshold for the absence of vital effects under high DIC regimes. From a mechanistic viewpoint, we show that the vital effect is determined by physiology; growth rate, cell size and relative rates of photosynthesis and calcification, and a modulation of these parameters with ambient carbon availability. This study provides palaeoceanographers with a biogeochemical framework that can be utilised to further develop the use of calcareous nannofossils in palaeoceanography to derive sea surface temperature and p CO 2 levels.

Description: Ocean acidification modulates expression of genes and physiological performance of a marine diatom Biogeosciences Discussions, 12, 15809-15833, 2015 Author(s): Y. Li, S. Zhuang, Y. Wu, H. Ren, F. Cheng, X. Lin, K. Wang, J. Beardall, and K. Gao Ocean Acidification (OA) is known to affect various aspects of the physiological performance of diatoms, but there is little information on the underlining molecular mechanisms involved. Here, we show that in the model diatom Phaeodactylum tricornutum expression of the genes related to light harvesting, carbon acquisition and carboxylation, nitrite assimilation and ATP synthesis are modulated by OA. Growth and photosynthetic carbon fixation were enhanced by elevated CO 2 (1000 μatm) under both constant indoor and fluctuating outdoor light regimes. The genetic expression of nitrite reductase (NiR) was up-regulated by OA regardless of light levels and/or regimes. The transcriptional expression of fucoxanthin chlorophyll a/c protein (lhcf type (FCP)) and mitochondrial ATP synthase (mtATP synthase) genes were also enhanced by OA, but only under high light intensity. OA treatment decreased the expression of β-carbonic anhydrase (β-CA) along with down-regulation of CO 2 concentrating mechanisms (CCMs). Additionally, the genes for these proteins (NiR, FCP, mtATP synthase, β-CA) showed diel expressions either under constant indoor light or fluctuating sunlight. Thus, OA enhanced photosynthetic and growth rates by stimulating nitrogen assimilation and indirectly by down-regulating the energy-costly inorganic carbon acquisition process.

Description: by Pete Riley, Michal Ben-Nun, Jon A. Linker, Angelia A. Cost, Jose L. Sanchez, Dylan George, David P. Bacon, Steven Riley The potential rapid availability of large-scale clinical episode data during the next influenza pandemic suggests an opportunity for increasing the speed with which novel respiratory pathogens can be characterized. Key intervention decisions will be determined by both the transmissibility of the novel strain (measured by the basic reproductive number R 0 ) and its individual-level severity. The 2009 pandemic illustrated that estimating individual-level severity, as described by the proportion p C of infections that result in clinical cases, can remain uncertain for a prolonged period of time. Here, we use 50 distinct US military populations during 2009 as a retrospective cohort to test the hypothesis that real-time encounter data combined with disease dynamic models can be used to bridge this uncertainty gap. Effectively, we estimated the total number of infections in multiple early-affected communities using the model and divided that number by the known number of clinical cases. Joint estimates of severity and transmissibility clustered within a relatively small region of parameter space, with 40 of the 50 populations bounded by: p C , 0.0133–0.150 and R 0 , 1.09–2.16. These fits were obtained despite widely varying incidence profiles: some with spring waves, some with fall waves and some with both. To illustrate the benefit of specific pairing of rapidly available data and infectious disease models, we simulated a future moderate pandemic strain with p C approximately ×10 that of 2009; the results demonstrating that even before the peak had passed in the first affected population, R 0 and p C could be well estimated. This study provides a clear reference in this two-dimensional space against which future novel respiratory pathogens can be rapidly assessed and compared with previous pandemics.

Description: by Gang Li, Karen E. Ross, Cecilia N. Arighi, Yifan Peng, Cathy H. Wu, K. Vijay-Shanker MicroRNAs (miRNAs) regulate a wide range of cellular and developmental processes through gene expression suppression or mRNA degradation. Experimentally validated miRNA gene targets are often reported in the literature. In this paper, we describe miRTex, a text mining system that extracts miRNA-target relations, as well as miRNA-gene and gene-miRNA regulation relations. The system achieves good precision and recall when evaluated on a literature corpus of 150 abstracts with F-scores close to 0.90 on the three different types of relations. We conducted full-scale text mining using miRTex to process all the Medline abstracts and all the full-length articles in the PubMed Central Open Access Subset. The results for all the Medline abstracts are stored in a database for interactive query and file download via the website at http://proteininformationresource.org/mirtex. Using miRTex, we identified genes potentially regulated by miRNAs in Triple Negative Breast Cancer, as well as miRNA-gene relations that, in conjunction with kinase-substrate relations, regulate the response to abiotic stress in Arabidopsis thaliana . These two use cases demonstrate the usefulness of miRTex text mining in the analysis of miRNA-regulated biological processes.

Description: by Greg Jensen, Fabian Muñoz, Yelda Alkan, Vincent P. Ferrera, Herbert S. Terrace Transitive inference (the ability to infer that B 〉 D given that B 〉 C and C 〉 D ) is a widespread characteristic of serial learning, observed in dozens of species. Despite these robust behavioral effects, reinforcement learning models reliant on reward prediction error or associative strength routinely fail to perform these inferences. We propose an algorithm called betasort , inspired by cognitive processes, which performs transitive inference at low computational cost. This is accomplished by (1) representing stimulus positions along a unit span using beta distributions, (2) treating positive and negative feedback asymmetrically, and (3) updating the position of every stimulus during every trial, whether that stimulus was visible or not. Performance was compared for rhesus macaques, humans, and the betasort algorithm, as well as Q -learning, an established reward-prediction error (RPE) model. Of these, only Q -learning failed to respond above chance during critical test trials. Betasort’s success (when compared to RPE models) and its computational efficiency (when compared to full Markov decision process implementations) suggests that the study of reinforcement learning in organisms will be best served by a feature-driven approach to comparing formal models.

Description: Comparing solubility algorithms of greenhouse gases in Earth-System modelling Biogeosciences Discussions, 12, 15925-15945, 2015 Author(s): V. M. N. C. S. Vieira, E. Sahlée, P. Jurus, E. Clementi, H. Pettersson, and M. Mateus Accurate solubility estimates are fundamental for (i) Earth-System models forecasting the climate change taking into consideration the atmosphere–ocean balances and trades of greenhouse gases, and (ii) using field data to calibrate and validate the algorithms simulating those trades. We found important differences between the formulation generally accepted and a recently proposed alternative relying on a different chemistry background. First, we tested with field data from the Baltic Sea, which also enabled finding differences between using water temperatures measured at 0.5 or 4 m depths. Then, we used data simulated by atmospheric (Meteodata application of WRF) and oceanographic (WW3-NEMO) models of the European Coastal Ocean and Mediterranean to compare the use of the two solubility algorithms in Earth-System modelling. The mismatches between both formulations lead to a difference of millions of tons of CO 2 , and hundreds of tons of CH 4 and N 2 O, dissolved in the first meter below the sea surface of the whole modelled region.

Description: This paper is based on the experience of introducing wireless sensor networks (WSNs) into the building industry in Denmark and in a rural area of Greenland. There are very real advantages in the application of the technology and its consequences for the life cycle operation of the building sector. Sensor networks can be seen as an important part of the Internet of Things and may even constitute an Internet of Sensors, since the communication layers can differ from the Internet standards. The current paper describes the case for application, followed by a discussion of the observed adaptive advantages and consequences of the technology. Essentially, WSNs constitute a highly sophisticated technology that is more robust in a rural context due to its extremely simple installation procedures (plug and play) allowing the use of local less-skilled labour, and the possibility of reconfiguring and repurposing its use remotely.