ALBERT

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 29 Author(s): José Filipe T. Ganança, José Gregório F. Freitas, Humberto Gil M. Nóbrega, Vanessa Rodrigues, Gonçalo Antunes, Miguel Rodrigues, Miguel Ângelo A. Pinheiro de Carvalho, Vincent Lebot Taro ( Colocasia esculenta (L.) Schott) is a vegetative propagated tropical root occupying the 9th position among world food crops. Taro is an important staple food for many local populations of Asia and Africa. The crop is dependent of wet and highly irrigated growth conditions. Under the scenario of undergoing climatic changes, is estimated that taro production could decrease in the next 30 years as result of drought constraints. The project EU Aid Taro, DCI-Food/2009/45 “adapting propagated crops to climatic and commercial changes” aims to study ways to adapt this clonally propagated root to these climatic changes. A set of drought stress assays were realized at ISOPlexis Genebank (Madeira University), using local taro cultivars (Macaronesian taro genepool) and elite cultivars and seedlings provided by the Secretariat of the Pacific Community (SPC). The 1st pilot assay was realized in a small greenhouse, included 3 local cultivars and aimed to modelate the wattering regimes and their influence on crop growth. The 2nd full assay was realized in two greenhouses, during a full plant growth cycle. Thirty four taro cultivars, 15 elite lines provided by SPC, and 19 local cultivars, from Madeira (10), Canary Islands (6), Azores (2), and Cyprus (1) were screened. Plants were individually cultivated in pots under 2 contrasting wattering regimes, high (0,36 liters/day) and low (0,18 liters/day). Data for 14 morpho-agronomic traits, biomass and yield parameters were collected from 5 plants for each cultivar, per treatment. Preliminary results show significant differences in the ability to cope with drought stress among elite and local varieties. A classification of cultivars according to their relative drougth tolerance was made. The most resilient of these varieties will be subject to a new complete assay, in order to better assess their level of tolerance and recommend for breeding programs in Asian countries.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 29 Author(s): Fereshteh Pourazari, Giulia Vico, Birgitta Båth, Martin Weih One of the most important resources within agriculture is nitrogen (N), and depletion of N resources is an important element in the evaluation of sustainability in agriculture. Therefore, identifying crops with high nitrogen use efficiency (NUE) is important for the sustainability of the system. In an energy crop context, sustainability in crop production could aim at enhanced energy output with maintained or reduced depletion of N resources. Crops with different photosynthetic pathways (C 3 vs. C 4 ) and life histories (perennials vs. annuals) are expected to differ in NUE and also energy harvest per unit N lost from the system. The aim is to characterize the growth, NUE and energy output per unit N lost for three common crops frequently used for energy; maize, winter wheat and perennial grassland (ley). These crops differ in photosynthetic and life history strategies. Above ground biomass of wheat, grassland ley and maize was sampled within a long-term experiment in Central Sweden. The experiment has a split-plot design with four replicates. Four aboveground harvests were conducted during the growth period and plant N contents were determined. Biomass growth, yield (above ground biomass in ley and maize, grain biomass in wheat) and some functional traits were assessed, and the NUE components N uptake efficiency, yield-specific N efficiency and yield N concentration were calculated according to Weih, et al. (2011). Energy output per N lost with the harvested product was calculated assuming crop-specific higher heating values for biofuel use. The N uptake efficiency and yield-specific N efficiency were higher in maize than wheat and ley. The yield N concentration was higher in the perennial ley than the annual crops, and lowest in maize. Energy output per N lost in the harvested product was greater in maize compared to wheat and ley. The results are discussed in a agricultural sustainability perspective.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 29 Author(s): Maendy Fritz, Anja Hartmann Perennial crops can be used as renewable resource but only rare information concerning their site-specific biomass production are available. Also, their yield stability as well as the quality of the produced biomass, whether for energetic or material utilisation, is relatively unknown. Perennial crops offer several ecological benefits such as protection of soil and waterbodies, long flowering and cover for wild animals during winter. Most of these crops have a high yield potential and are – after planting and establishing is completed – labour efficient to cultivate. Concerning climate change and the presumed higher risk of extreme weather conditions, perennial crops might be a good supplement to common annual crops. The aim of a Bavarian project, started 2014, is to evaluate several perennial crops at six Bavarian sites with varying soils and climatic conditions. Cup plant ( Silphium perfoliatum ), sida ( Sida hermaphrodita ), tall wheatgrass ( Agropyron elongatum ), switchgrass ( Panicum virgatum ) and miscanthus ( Miscanthus x giganteus ) are cultivated in field trials in 100 m 2 plots and four replications. The annual crops maize and rye are similarly grown as references. Besides plant development and yield measurement, the potential methane yield and/or fuel properties will be determined to assess the quality and suitability of these crops for different usages. Trials concerning cultivation techniques and weed control complement the agricultural investigations. Ecological aspects of perennial cropping will be evaluated by measuring carbon levels in the soil as well as stocking rates of earthworms used as indicator for changes in soil biota as a result of perennial crop cultivation. Yield and quality results from foregoing trials for the various crops and first data of the now started field trials will be presented. The data and experiences will allow detailed consulting of farmers who are interested in increasing the biodiversity in their fields and minimising their climate-caused production risks.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 29 Author(s): Abdullah A. Jaradat Macro- and micro-nutrients estimated in leaves, stems and seed of eleven genotypes of five physiologically diverse crop species (chickpeas, corn, safflower, soybean, and wheat, respectively producing protein, carbohydrates, oil, protein-oil, and carbohydrates-protein, as main seed storage macromolecules) were used in assessing species and genotypic responses to multiple, long-term abiotic stresses. Crops were subjected to two phases, three years each, of multiple abiotic stresses by manipulating length of the growing season and population density under typical management practices of each crop in the upper Midwest, USA. In Phase II, crops were rotated to release the additional edaphic stress of no-rotation in Phase I. Nutrient densities were estimated using LECO analyzer (Carbon and Nitrogen) or ICP instrument (Calcium, Copper, Iron, Manganese, Magnesium, Phosphorus, Potassium, Sulfur and Zinc). Comparisons of functional relationships among nutrients were based on statistics (α, β, and R2) derived from 1000-permutations using reduced major axis (RMA) regression analyses. Genotypic differences in nutrients functional relationships were modulated, in decreasing order, by Carbon:Nitrogen ratio, stress treatments, and storage macromolecules. Comparisons between the β statistics for each nutrient in Phases I and II suggested that differences in nutrient functional relationships between crop species were significantly larger than differences between genotypes within species. Nitrogen, rather than Carbon content, followed by plant density, but not short growing season, influenced some (Phosphorus, Potassium, Sulfur, and Zinc) nutrient relationships and their allocations to leaves, stems and seed of crop species. Functional relationships between Copper, Iron, Sulfur and Zinc, at the seed storage macromolecules level in Phase I and II indicated that oil and protein producing crop species are more prone to larger adverse effects of abiotic stresses than those producing carbohydrates alone or in combination with protein. A thorough understanding of these relationships is critical for screening genetic diversity and designing nutritionally-balanced crop genotypes under abiotic stress.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 29 Author(s): Jana Zinkernagel, Nadine Schmidt, Katrin Kahlen Today, vegetable production is already limited by local climate and water availability. Knowledge has to be generated for crop management adapted to climate change. Evaluating potential consequences for vegetable production in a model growing region is the scope of this investigation. Simulations of climate conditions and in that respect the use of different climate models allow estimating a broad range of scenarios affecting cultivation. Analysis focuses on climatic parameters relevant for future irrigation demand. By estimating the climatic water balance (CWB), seasonal water demand and crop specific vulnerabilities to water deficit can be revealed. These objectives require knowledge of potential changes in time and duration of vegetable cultivation, gained from analysing thermal growing season (TGS). A broad range of scenarios was achieved for the German region “Hessian Reed” by applying A1B scenario and using the regional models WETTREG 2010, C-CLM and REMO, driven by the global models ECHAM5 and HadCM3, respectively. Simulations cover the period from 1971 to 2100; the validation is based on the period 1971 to 2000. For onion, crop specific CWB was calculated by employing crop coefficients of the Geisenheim Irrigation Scheduling, following FAO-56. TGS was derived from simulated onset and duration of plant growth stages based on temperature sum. Precipitation pattern vary between the models, but still follow a similar trend to higher evaporative demand. CWB decreases by 3 mm/d (WETTREG) and 2 mm/d (C-CLM), respectively. Maximum duration of dry periods increases from 33 to 53 d and occur more frequently from 343 to 457 times for REMO, representing maxima compared to C-CLM and WETTREG. TGS shifts from DOY 60 to 21 for sowing date, but extends from DOY 183 to 208 due to lower temperature (C-CLM). In contrast to the expected increasing irrigation demand in case of unchanged TGS, CWB becomes less negative with TGS-shift.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 29 Author(s): S.C. Bertolli, G.M. Souza The strategy adopted by plants for exploit environments with low moisture may depend on the neighbor's identity. Roots of the plants have the ability to discriminate self (roots of the same plant) of non-self (roots of other plants), even without physical contact and while other plants are genetically identical. We investigated if there is any change in the plant behavior that self ( Sd ) and non-self ( NSd ) discriminate in situations of water limitation, and whether such behavior can be varied in individuals more or less kin. It was used two Eucalyptus urophylla groups: clones (high kinship- Hk ); and population (low kinship- Lk ). Split-root plants were planted so that each pot contained either two roots of the same plant ( Sd ) or of two different plants ( NSd ). The plants were subjected to full irrigation ( Irr ) or water deficit ( WD ) for thirty days, and biomass parameters of were evaluated. Plants of both groups and both discrimination conditions reduced their total dry mass ( DMt ) under WD . In Hk group, the WD increased the root/shoot ratio (23% compared to irrigated plants) by NSd , indicating that even when plants show a reduction in growth mediated by lack of water, there is an increase in biomass allocation to the roots when the plants interact each plants. In Hk group, the NSd reduced the dry mass ( DMr ) and volume ( Vr ) of roots only in Irr . In Lk group, DMt , DMr , Vr , and leaf area were reduced in NSd under Irr condition, whereas under WD , the NSd reduced just the specific leaf area (21% compared to Sd ), indicating a change in biomass allocation to leaves. The results suggest that the discrimination is more evident in population group and in non-stressful environments, and although not so pronounced in situations of WD , these responses also occur as observed in Lk plants.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 29 Author(s): I. McFarlane, J.R. Park Break crops and multi-crop rotations are common in arable farm management, and the soil quality inherited from a previous crop is one of the parameters that determine the gross margin that is achieved with a given crop from a given parcel of land. In previous work we developed a dynamic economic model to calculate the potential yield and gross margin of a set of crops grown in a selection of typical rotation scenarios, and we reported use of the model to calculate coexistence costs for GM maize grown in a crop rotation. The model predicts economic effects of pest and weed pressures in monthly time steps. Validation of the model in respect of specific traits is proceeding as data from trials with novel crop varieties is published. Alongside this aspect of the validation process, we are able to incorporate data representing the economic impact of abiotic stresses on conventional crops, and then use the model to predict the cumulative gross margin achievable from a sequence of conventional crops grown at varying levels of abiotic stress. We report new progress with this aspect of model validation. In this paper, we report the further development of the model to take account of abiotic stress arising from drought, flood, heat or frost; such stresses being introduced in addition to variable pest and weed pressure. The main purpose is to assess the economic incentive for arable farmers to adopt novel crop varieties having multiple ‘stacked’ traits introduced by means of various biotechnological tools available to crop breeders.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 29 Author(s): Martin Erbs, Remy Manderscheid, Adam Luig, Henning Kage, Hans-Joachim Weigel Among the parameters of global climate change the increases of the atmospheric CO 2 concentration and of temperature, both of which affect plant growth and development, are of prime importance. However, with respect to the importance of these climate changes for global food security little is known on the possible interactions of these prominent changes on crop growth. This is holds also true for anticipated increases in mean temperatures as well as for short-term high temperature events (i.e. heat stress). Form previous studies it is known that wheat is particularly sensitive to temperatures of 30 °C and above during the anthesis and early grain filling. Short-term heat stress may decrease yield by impairing grain set. Higher average temperatures during grain filling may influence yield by reducing grain filling duration. If and to what extend elevated CO 2 may affect crop responses to heat stresses remains a matter of debate, particularly because of a lack of suitable experiments. While there are a few model projections addressing the interactive impacts of these climate change elements on crops, these models nearly exclusively rely on data from non-field experiments. At the Thünen-Institute of Biodiversity (Braunschweig, Germany) for the first time field experiments with winter wheat were conducted, in which elevated canopy temperature treatments (free-air temperature enrichment = FATE) were applied to the plants in 2013 and combined with free-air CO 2 enrichment (FACE, 600 μmol mol -1 ) in 2014 and 2015. The temperature treatments comprised 1.) at anthesis a short-term heat stress treatment (5 or 12 h d -1 for 5 days, maximum increase up to +6 °C) and 2.) during grain filling a long-term increase (24 h d -1 for 28 days, average increase up to +3 °C). Here we present details of the experimental set-up, the system performance and among others results of heat stress effects at anthesis on yield components.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 29 Author(s): Renan Le Roux, Etienne Neethling, Cornelis Van Leeuwen, Laure De Resseguier, Malika Madelin, Cyril Bonnefoy, Gerard Barbeau, Hervé Quenol Firstly this study illustrate regional climate projections for several European vineyards areas at mean- and long-term. Secondly, from a network of data loggers, a modeling approach at local scale is presented to reveal climate variability as an important component to reduce local uncertainties and its impacts on plant behaviour. 3 First part of study concerns all of ADVICLIM vineyards sites. Downscaled Regional Euro-Cordex models are used to map average temperatures and growing degree days differences between 1970-2000, 2020-2050 and 2050-2070. Simulated data from two scenarios are used to show the potential impact of climate change on grapevine behavior at regional scale. Second part of study draws on data obtained from two sites: Saint-Emilion and Coteaux du Layon, France. Daily temperature data are used to quantify and model local climate variability in relation with local environmental features .1,2 At regional scale, a large variability of climate appears inter- and intrasites Projected directional climate change demonstrate significant warming and changes in rainfall patterns, however results reveal great uncertainties as a result of natural climate variability, climate models and socio-economic scenarios. Local scale study show important variability of temperature and growing degree days over very short distances which is related to grapevine phenology and productivity. Regional models are not accurate enough to take into account local climate variability. For this reason Working with nested scales (local and regional) allow to better frame adaptations options to future climate change.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 29 Author(s): L.A. Avila, M.G. Marchezan, E.R. Camargo, D. Agostinetto, C.E. Schaedler, B.S. Moraes, A.C. Langaro, C. Oliveira Extreme rainfall events are expected to be more frequent with the climate change, increasing the chances of prolonged flooding in rice producing areas. Therefore, it is important to understand the response of rice plants to flooding events that would result in plant submersion and it is interaction with herbicide applications. To achieve the objectives two studies were conducted in Southern Brazil (Pelotas, RS). Experiment 1 was conducted with ten rice cultivars and six submersion periods (one, five, seven, 15 e 20 days of plant submersion plus a check treatment. In the check treatment plants were keep under a flooding regime (water layer of 10 cm).). Experiment 2 was conducted with two cultivars, two water regimes (flooded and submerged) and six herbicides (clomazone, bispyribac sodium, penoxsulam, imazethapyr + imazapic, imazapyr + imazapic and an untreated check). Shoot dry matter, chlorophyll levels, total carotenoids, total phenolic content, levels of hydrogen peroxide and activity of catalase (CAT), ascorbate peroxidase (APX) and superoxide dismutase (SOD) were assessed in plant samples. The results observed in the first experiment showed that cultivars Puitá INTA CL, IRGA 417 and IRGA 422 CL were the most tolerant to submergence. The most susceptible cultivars were IRGA 424, BRS Querência, EPAGRI 108 and BRS Taim. In general, the cultivar Puitá INTA CL has lower oxidative damage than BRS Querência when submerged. In order to cope with excessive free radicals, BRS Querência demonstrated higher activity of SOD, APX and CAT enzymes compared to cultivar Puitá INTA CL. Imidazolinone formulated mixtures of herbicides imazethapyr + imazapic and imazapyr + imazapic caused greater reduction in total chlorophyll content and carotenoids.

Description: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Bettina Schreiner, Elisa Romanelli, Pawel Liberski, Barbara Ingold-Heppner, Bettina Sobottka-Brillout, Tom Hartwig, Vijay Chandrasekar, Helge Johannssen, Hanns Ulrich Zeilhofer, Adriano Aguzzi, Frank Heppner, Martin Kerschensteiner, Burkhard Becher Although the importance of reactive astrocytes during CNS pathology is well established, the function of astroglia in adult CNS homeostasis is less well understood. With the use of conditional, astrocyte-restricted protein synthesis termination, we found that selective paralysis of GFAP + astrocytes in vivo led to rapid neuronal cell loss and severe motor deficits. This occurred while structural astroglial support still persisted and in the absence of any major microvascular damage. Whereas loss of astrocyte function did lead to microglial activation, this had no impact on the neuronal loss and clinical decline. Neuronal injury was caused by oxidative stress resulting from the reduced redox scavenging capability of dysfunctional astrocytes and could be prevented by the in vivo treatment with scavengers of reactive oxygen and nitrogen species (ROS/RNS). Our results suggest that the subpopulation of GFAP + astrocytes maintain neuronal health by controlling redox homeostasis in the adult CNS. Graphical abstract Teaser Schreiner et al. examine the functional contribution of astrocytes to tissue homeostasis in the adult CNS and identify the redox-scavenging capacity of GFAP + astrocytes as a key factor for neuronal health in vivo. The importance of the metabolic integrity of the glia-neuron interface highlights potential therapies for the treatment of neurodegenerative diseases.

Description: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Priya Srikanth, Karam Han, Dana G. Callahan, Eugenia Makovkina, Christina R. Muratore, Matthew A. Lalli, Honglin Zhou, Justin D. Boyd, Kenneth S. Kosik, Dennis J. Selkoe, Tracy L. Young-Pearse Genetic and clinical association studies have identified disrupted in schizophrenia 1 ( DISC1 ) as a candidate risk gene for major mental illness. DISC1 is interrupted by a balanced chr(1;11) translocation in a Scottish family in which the translocation predisposes to psychiatric disorders. We investigate the consequences of DISC1 interruption in human neural cells using TALENs or CRISPR-Cas9 to target the DISC1 locus. We show that disruption of DISC1 near the site of the translocation results in decreased DISC1 protein levels because of nonsense-mediated decay of long splice variants. This results in an increased level of canonical Wnt signaling in neural progenitor cells and altered expression of fate markers such as Foxg1 and Tbr2. These gene expression changes are rescued by antagonizing Wnt signaling in a critical developmental window, supporting the hypothesis that DISC1-dependent suppression of basal Wnt signaling influences the distribution of cell types generated during cortical development. Graphical abstract Teaser Srikanth et al. report the generation of isogenic hiPSC lines with engineered mutations in two locations within the DISC1 gene. This disease-relevant disruption shows a loss of long isoforms, which, in turn, affects neural progenitor cell proliferation, baseline WNT signaling, and the expression of NPC fate markers such as FoxG1 and Tbr2.

Description: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Ivana Vonkova, Antoine-Emmanuel Saliba, Samy Deghou, Kanchan Anand, Stefano Ceschia, Tobias Doerks, Augustinus Galih, Karl G. Kugler, Kenji Maeda, Vladimir Rybin, Vera van Noort, Jan Ellenberg, Peer Bork, Anne-Claude Gavin Many cellular processes involve the recruitment of proteins to specific membranes, which are decorated with distinctive lipids that act as docking sites. The phosphoinositides form signaling hubs, and we examine mechanisms underlying recruitment. We applied a physiological, quantitative, liposome microarray-based assay to measure the membrane-binding properties of 91 pleckstrin homology (PH) domains, the most common phosphoinositide-binding target. 10,514 experiments quantified the role of phosphoinositides in membrane recruitment. For most domains examined, the observed binding specificity implied cooperativity with additional signaling lipids. Analyses of PH domains with similar lipid-binding profiles identified a conserved motif, mutations in which—including some found in human cancers—induced discrete changes in binding affinities in vitro and protein mislocalization in vivo. The data set reveals cooperativity as a key mechanism for membrane recruitment and, by enabling the interpretation of disease-associated mutations, suggests avenues for the design of small molecules targeting PH domains. Graphical abstract Teaser Vonkova et al. systematically quantify the lipid-binding properties of 91 pleckstrin homology (PH) domains using a physiological, quantitative, liposome microarray-based assay. The data set reveals that cooperativity between lipids is a key mechanism for membrane recruitment of PH domains.

Description: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Ju-Hyun Lee, Mary Kate McBrayer, Devin M. Wolfe, Luke J. Haslett, Asok Kumar, Yutaka Sato, Pearl P.Y. Lie, Panaiyur Mohan, Erin E. Coffey, Uday Kompella, Claire H. Mitchell, Emyr Lloyd-Evans, Ralph A. Nixon Presenilin 1 (PS1) deletion or Alzheimer’s disease (AD)-linked mutations disrupt lysosomal acidification and proteolysis, which inhibits autophagy. Here, we establish that this phenotype stems from impaired glycosylation and instability of vATPase V0a1 subunit, causing deficient lysosomal vATPase assembly and function. We further demonstrate that elevated lysosomal pH in Presenilin 1 knockout (PS1KO) cells induces abnormal Ca 2+ efflux from lysosomes mediated by TRPML1 and elevates cytosolic Ca 2+ . In WT cells, blocking vATPase activity or knockdown of either PS1 or the V0a1 subunit of vATPase reproduces all of these abnormalities. Normalizing lysosomal pH in PS1KO cells using acidic nanoparticles restores normal lysosomal proteolysis, autophagy, and Ca 2+ homeostasis, but correcting lysosomal Ca 2+ deficits alone neither re-acidifies lysosomes nor reverses proteolytic and autophagic deficits. Our results indicate that vATPase deficiency in PS1 loss-of-function states causes lysosomal/autophagy deficits and contributes to abnormal cellular Ca 2+ homeostasis, thus linking two AD-related pathogenic processes through a common molecular mechanism. Graphical abstract Teaser Lee et al. present evidence establishing that Presenilin 1 loss of function elevates lysosomal pH via loss of V0a1 vATPase subunits. Besides disrupting autophagy, elevated lysosomal pH hyperactivates the TRPML1 calcium channel, causing increased lysosomal calcium efflux and cytosolic calcium elevation, thus linking two AD-related presenilin phenotypes to vATPase deficiency.

Description: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Soraia Barão, Annette Gärtner, Eduardo Leyva-Díaz, Galina Demyanenko, Sebastian Munck, Tine Vanhoutvin, Lujia Zhou, Melitta Schachner, Guillermina López-Bendito, Patricia F. Maness, Bart De Strooper ΒACE1 is the major drug target for Alzheimer’s disease, but we know surprisingly little about its normal function in the CNS. Here, we show that this protease is critically involved in semaphorin 3A (Sema3A)-mediated axonal guidance processes in thalamic and hippocampal neurons. An active membrane-bound proteolytic CHL1 fragment is generated by BACE1 upon Sema3A binding. This fragment relays the Sema3A signal via ezrin-radixin-moesin (ERM) proteins to the neuronal cytoskeleton. APH1B-γ-secretase-mediated degradation of this fragment stops the Sema3A-induced collapse and sensitizes the growth cone for the next axonal guidance cue. Thus, we reveal a cycle of proteolytic activity underlying growth cone collapse and restoration used by axons to find their correct trajectory in the brain. Our data also suggest that BACE1 and γ-secretase inhibition have physiologically opposite effects in this process, supporting the idea that combination therapy might attenuate some of the side effects associated with these drugs. Graphical abstract Teaser Barão et al. show that the Alzheimer’s-disease-related proteases, BACE1 and APH1B-γ-secretase, control axonal guidance by regulating growth cone dynamics. BACE1 cleaves CHL1, inducing growth cone collapse. Subsequently, γ-secretase activity stops the collapse and axonal growth resumes. Therefore, testing of inhibitors of these proteases in humans should proceed with caution.

Description: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Alexander Harms, Frédéric Valentin Stanger, Patrick Daniel Scheu, Imke Greet de Jong, Arnaud Goepfert, Timo Glatter, Kenn Gerdes, Tilman Schirmer, Christoph Dehio Toxin-antitoxin (TA) modules are ubiquitous molecular switches controlling bacterial growth via the release of toxins that inhibit cell proliferation. Most of these toxins interfere with protein translation, but a growing variety of other mechanisms hints at a diversity that is not yet fully appreciated. Here, we characterize a group of FIC domain proteins as toxins of the conserved and abundant FicTA family of TA modules, and we reveal that they act by suspending control of cellular DNA topology. We show that FicTs are enzymes that adenylylate DNA gyrase and topoisomerase IV, the essential bacterial type IIA topoisomerases, at their ATP-binding site. This modification inactivates both targets by blocking their ATPase activity, and, consequently, causes reversible growth arrest due to the knotting, catenation, and relaxation of cellular DNA. Our results give insight into the regulation of DNA topology and highlight the remarkable plasticity of FIC domain proteins. Graphical abstract Teaser Harms et al. reveal that the FicTA toxin-antitoxin module acts via adenylylation of DNA gyrase and topoisomerase IV. This modification inactivates both targets by blocking the ATPase activity that is central to their enzymatic functions, and it reversibly inhibits bacterial growth via the knotting, catenation, and relaxation of cellular DNA.

Description: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Takaharu Kanno, Davide G. Berta, Camilla Sjögren The structural maintenance of chromosome (SMC) protein complexes cohesin and condensin and the Smc5/6 complex (Smc5/6) are crucial for chromosome dynamics and stability. All contain essential ATPase domains, and cohesin and condensin interact with chromosomes through topological entrapment of DNA. However, how Smc5/6 binds DNA and chromosomes has remained largely unknown. Here, we show that purified Smc5/6 binds DNA through a mechanism that requires ATP hydrolysis by the complex and circular DNA to be established. This also promotes topoisomerase 2-dependent catenation of plasmids, suggesting that Smc5/6 interconnects two DNA molecules using ATP-regulated topological entrapment of DNA, similar to cohesin. We also show that a complex containing an Smc6 mutant that is defective in ATP binding fails to interact with DNA and chromosomes and leads to cell death with concomitant accumulation of DNA damage when overexpressed. Taken together, these results indicate that Smc5/6 executes its cellular functions through ATP-regulated intermolecular DNA linking. Graphical abstract Teaser Kanno et al. have found that Smc5/6 interacts with DNA by two different mechanisms. One is based on electrostatic interactions that require ATP binding to Smc6. The other leads to topological entrapment and demands ATP hydrolysis by the complex. The results show that Smc5/6 is an ATP-dependent intermolecular DNA linker.

Description: Publication date: September 2015 Source: Journal of Hydrology: Regional Studies, Volume 4, Part B Author(s): J.S. Lessels, T.F.A. Bishop Study region South eastern Australia. Study focus This region is characterised with rainfall events that are associated with large exports of nutrients and sediments. Many water quality monitoring schemes use a form of event-based sampling to quantify these exports. Previous water quality studies that have evaluated different sampling schemes often rely on continuously monitored water quality data. However, many catchment authorities only have access to limited historical data which consists of event-based and monthly routine samples. Therefore there is a need to develop a method that assesses the importance of sampling events using information from limited historical data. This work presents a simulation based approach using unconditional simulation based on historical stream discharge. Such an approach offers site-specific information on optimal sampling schemes. A linear mixed model is used to model the relationship between total phosphorus and stream discharge and the auto-correlation of total phosphorus. New hydrological insights for the region The inclusion of event-based sampling improved annual load estimates of all sites with a maximum RMSE difference of 16.11 tonnes between event-based and routine sampling. Based on the accuracy of annual loads, event-based sampling was found to be more important in catchments with a large relief and high annual rainfall in this region. Using this approach, different sampling schemes can be compared based on limited historical data.

Description: Publication date: 18 August 2015 Source: Cell Reports, Volume 12, Issue 7 Author(s): Marvin L. Meistrich, Gunapala Shetty In this issue of Cell Reports , DeFalco et al. (2015) characterize a novel macrophage population associated with the peritubular lamina of mouse testes. These macrophages may create a niche not for the self-renewal of stem cells but rather the induction of their differentiation.

Description: Publication date: Available online 19 August 2015 Source: Geoscience Frontiers Author(s): Noreen Mary Vielreicher, David Ian Groves, Neal Jesse McNaughton The Neoarchaean Kalgoorlie Gold Field contains the giant Golden Mile and world-class Mt Charlotte deposits, which have been the subject of much research for over 100 years. The Golden Mile deposit is a complex array of ductile to brittle vein and breccia lodes that are predominantly hosted in the highly-fractionated Golden Mile Dolerite sill. The Fimiston lodes comprise an array of narrow lodes that evolved broadly syn- to late-formation of the regional D2 NW-trending foliation. The lodes are characterized by pyrite veinlets and disseminations, quartz veinlets and breccias, and banded quartz-carbonate veins with sericite, carbonate, and pyrite-dominated alteration. Bonanza Green-Leader, or Oroya-style, lodes, with grades in excess of 1000g/t Au, are similar to the Fimiston-style lodes, but are characterized by abundant visible gold, native tellurium and more abundant telluride minerals within roscoelite-bearing alteration zones. The arguably structurally younger Mt Charlotte-style lodes are characterized by a pipe-shaped, coarse-grained quartz, carbonate and scheelite vein-stockwork with distinct vertically-zoned, carbonate-sericite-albite-pyrite±pyrrhotite dominant alteration assemblages around veins within Unit 8 of the Golden Mile Dolerite and porphyry dykes. The network of steep- and gently-dipping extension and shear fracture-fill veins are associated with NE-trending fault sets that cross cut the regional NW-trend. The deposit area is intruded by swarms of porphyry dykes, including syn-volcanic mafic dykes, early and volumetrically most significant c. 2.67 Ga feldspar-phyric porphyry dykes, as well as later c. 2.66‒2.65Ga calc-alkaline hornblende-phyric dykes associated with younger c. 2.65‒2.64Ga lamprophyre dykes. All post-volcanic dykes have similar orientations to the Fimiston lodes. The feldspar dykes are clearly overprinted by all styles of mineralization, although the relationship between hornblende-phyric and lamprophyre dykes and gold mineralization is more ambiguous. Most agree that gold mineralization was post-peak regional metamorphism of host rocks, although its relative structural timing is controversial. Direct timing constraints on gold mineralization indicate that Fimiston- and Mt Charlotte-style mineralization formed within a relative short period of time around 2.64Ga, and, as such, support a model of progressive deformation of a rheologically heterogeneous rock package late in the structural history. Fluid charactersitics, combined with the structural, metamorphic and absolute timing, support description of gold mineralization at the Golden Mile as orogenic and mesozonal, and this allows direct correlation with orogenic gold deposits worldwide, which classically formed during accretion along convergent margins throughout Earth history. Graphical abstract

Description: Publication date: Available online 24 August 2015 Source: Journal of Asian Ceramic Societies Author(s): Dmytro Demirskyi, Yoshio Sakka, Oleg Vasylkiv The in situ synthesis/consolidation of B 4 C-TaB 2 eutectic composites by spark plasma sintering (SPS) is reported. The microstructure–property relations were determined for composites with the B 4 C-TaB 2 eutectic composition as functions of TaB 2 content, and TaB 2 -TaB 2 interlamellar spacing. A clear maximum in fracture toughness was identified (∼4.5 MPa m 1/2 ) for eutectic composites with interlamellar spacing between 0.9 and 1.1 μm. The composites with the hypereutectic composition of 40 mol.% TaB 2 obtained by SPS exhibited lower Vickers hardness (25–26 GPa) but higher indentation fracture toughness (up to 4.9 MPa m 1/2 ) than eutectic composites with 30–35 mol.% of TaB 2 .

Description: Publication date: September 2015 Source: Journal of Hydrology: Regional Studies, Volume 4, Part B Author(s): Hayet Chihi, Ghislain de Marsily, Habib Belayouni, Houcine Yahyaoui Study region “Jeffara de Medenine” aquifer system in south-eastern Tunisia. Study focus This study investigates the role of fault structures in the distribution of hydrogeochemical facies and groundwater compartmentalization for the aquifer system. New hydrological insights for the region The proposed methodology, including seismic structural study, hierarchical cluster analysis and geostatistical methods, allowed an efficient multi-element characterization of the spatial patterns of the structural elements in the aquifers and of the hydrogeological parameters used in a spatial cross-correlation to explore the dependence of the geochemical properties in each “geochemical population” on the hosting structural compartment to delineate the different geochemical compartments. The tectonic studies showed that the lateral extent of the aquifers is controlled by normal faults. The multivariate statistical analysis revealed a strong spatial coherence between hydrogeochemical facies clustering and the reservoir compartments at both large and small scales. The kriged maps of major-ion concentrations and of total dissolved solids in the aquifers were then analyzed and compared with the reservoir facies distribution for each compartment, the geometric characteristics of the aquifer, and the piezometric level trends. This allowed to characterize the hydraulic behavior of the Medenine fault and to understand the underlying physical and chemical processes having led to the spatial distribution of the geochemical properties, and thus, the hydrogeochemical functioning of the aquifers.

Description: Publication date: September 2015 Source: Journal of Hydrology: Regional Studies, Volume 4, Part B Author(s): Marnie L. Atkins, Isaac R. Santos, Damien T. Maher Study region This study investigates dissolved methane distribution in groundwater from the Richmond River Catchment (New South Wales, Australia) before proposed coal seam gas (CSG, or coal bed methane) development. Study focus Unconventional gas exploration has rapidly expanded in recent years. However, the impact of these operations on groundwater systems is poorly understood. A total of 91 groundwater samples were analyzed from 6 geological units. Our observations act as regional baseline research prior to CSG extraction and may assist with long term impact assessment. New hydrological insights for the region Methane was found in all geological units ranging between 0.26 and 4427 μg L −1 (median 10.68 μg L −1 ). Median methane concentrations were highest in chloride-type groundwater (13.26 μg L −1 , n = 58) while bicarbonate-type groundwater had lower concentrations (3.71 μg L −1 ). Groundwater from alluvial sediments had significantly higher median methane concentrations (91.46 μg L −1 ) than groundwater from both the basalt aquifers (0.7 μg L −1 ) and bedrock aquifers (4.63 μg L −1 ); indicating geology was a major driver of methane distribution. Methane carbon stable isotope ratios ranged from –90.9‰ to –29.5‰, suggesting a biogenic origin with some methane oxidation. No significant correlations were observed between methane concentrations and redox indicators (nitrate, manganese, iron and sulphate) except between iron and methane in the Lismore Basalt ( r 2 = 0.66, p 〈 0.001), implying redox conditions were not the main predictor of methane distribution.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Kavita R. Sharma, Brittany L. Enzmann, Yvonne Schmidt, Dani Moore, Graeme R. Jones, Jane Parker, Shelley L. Berger, Danny Reinberg, Laurence J. Zwiebel, Bernhard Breit, Jürgen Liebig, Anandasankar Ray The sophisticated organization of eusocial insect societies is largely based on the regulation of complex behaviors by hydrocarbon pheromones present on the cuticle. We used electrophysiology to investigate the detection of cuticular hydrocarbons (CHCs) by female-specific olfactory sensilla basiconica on the antenna of Camponotus floridanus ants through the utilization of one of the largest family of odorant receptors characterized so far in insects. These sensilla, each of which contains multiple olfactory receptor neurons, are differentially sensitive to CHCs and allow them to be classified into three broad groups that collectively detect every hydrocarbon tested, including queen and worker-enriched CHCs. This broad-spectrum sensitivity is conserved in a related species, Camponotus laevigatus , allowing these ants to detect CHCs from both nestmates and non-nestmates. Behavioral assays demonstrate that these ants are excellent at discriminating CHCs detected by the antenna, including enantiomers of a candidate queen pheromone that regulates the reproductive division of labor. Graphical abstract Teaser Sharma et al. show that ants can detect a number of hydrocarbons present on the cuticle, therefore recognizing different castes such as workers and queens from their own colony as well as different colonies. They also show that ants are able to smell and discriminate minor differences among hydrocarbons.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Sanjeev Kumar, Jing Liu, Paul Pang, A. Michaela Krautzberger, Antoine Reginensi, Haruhiko Akiyama, Andreas Schedl, Benjamin D. Humphreys, Andrew P. McMahon After acute kidney injury (AKI), surviving cells within the nephron proliferate and repair. We identify Sox9 as an acute epithelial stress response in renal regeneration. Translational profiling after AKI revealed a rapid upregulation of Sox9 within proximal tubule (PT) cells, the nephron cell type most vulnerable to AKI. Descendants of Sox9 + cells generate the bulk of the nephron during development and regenerate functional PT epithelium after AKI-induced reactivation of Sox9 after renal injury. After restoration of renal function post-AKI, persistent Sox9 expression highlights regions of unresolved damage within injured nephrons. Inactivation of Sox9 in PT cells pre-injury indicates that Sox9 is required for the normal course of post-AKI recovery. These findings link Sox9 to cell intrinsic mechanisms regulating development and repair of the mammalian nephron. Graphical abstract Teaser Surviving tubular epithelial cells repair the nephron after acute kidney injury (AKI). Kumar et al. identify Sox9 activation as a rapid response to AKI within repairing cells of the damaged proximal tubule segment. Sox9 activation is required for a normal repair process.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Rheinallt M. Jones, Chirayu Desai, Trevor M. Darby, Liping Luo, Alexandra A. Wolfarth, Christopher D. Scharer, Courtney S. Ardita, April R. Reedy, Erin S. Keebaugh, Andrew S. Neish An optimal gut microbiota influences many beneficial processes in the metazoan host. However, the molecular mechanisms that mediate and function in symbiont-induced host responses have not yet been fully characterized. Here, we report that cellular ROS enzymatically generated in response to contact with lactobacilli in both mice and Drosophila has salutary effects against exogenous insults to the intestinal epithelium via the activation of Nrf2 responsive cytoprotective genes. These data show that the xenobiotic-inducible Nrf2 pathway participates as a signaling conduit between the prokaryotic symbiont and the eukaryotic host. Indeed, our data imply that the capacity of lactobacilli to induce redox signaling in epithelial cells is a highly conserved hormetic adaptation to impel cellular conditioning to exogenous biotic stimuli. These data also highlight the role the microbiota plays in eukaryotic cytoprotective pathways and may have significant implications in the characterization of a eubiotic microbiota. Graphical abstract Teaser Jones et al. report that the commensal gut bacterial taxa lactobacilli are able to mediate beneficial cytoprotective effects in the gut of both flies and mice. These highly conserved events are mediated by ROS-dependent activation of the Nrf2 xenobiotic pathway and conserved effector genes.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Neel Mehta, Arthur H. Cheng, Cheng-Kang Chiang, Lucia Mendoza-Viveros, Harrod H. Ling, Abhilasha Patel, Bo Xu, Daniel Figeys, Hai-Ying M. Cheng The pacemaker properties of the suprachiasmatic nucleus (SCN) circadian clock are shaped by mechanisms that influence the expression and behavior of clock proteins. Here, we reveal that G-protein-coupled receptor kinase 2 (GRK2) modulates the period, amplitude, and entrainment characteristics of the SCN. Grk2 -deficient mice show phase-dependent alterations in light-induced entrainment, slower recovery from jetlag, and longer behavioral rhythms. Grk2 ablation perturbs intrinsic rhythmic properties of the SCN, increasing amplitude and decreasing period. At the cellular level, GRK2 suppresses the transcription of the mPeriod1 gene and the trafficking of PERIOD1 and PERIOD2 proteins to the nucleus. Moreover, GRK2 can physically interact with PERIOD1/2 and promote PERIOD2 phosphorylation at Ser545, effects that may underlie its ability to regulate PERIOD1/2 trafficking. Together, our findings identify GRK2 as an important modulator of circadian clock speed, amplitude, and entrainment by controlling PERIOD at the transcriptional and post-translational levels. Graphical abstract Teaser Mehta et al. demonstrate the importance of GRK2 in regulating both the pace of the circadian clock and its response to environmental time cues (i.e., light). GRK2 functionally interacts with the molecular clock at the transcriptional and post-translational levels, dampening mPeriod1 gene transcription and suppressing nuclear trafficking of PERIOD1/2 proteins.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Juan F. Linares, Angeles Duran, Miguel Reina-Campos, Pedro Aza-Blanc, Alex Campos, Jorge Moscat, Maria T. Diaz-Meco The mTORC1 complex is central to the cellular response to changes in nutrient availability. The signaling adaptor p62 contributes to mTORC1 activation in response to amino acids and interacts with TRAF6, which is required for the translocation of mTORC1 to the lysosome and the subsequent K63 polyubiquitination and activation of mTOR. However, the signal initiating these p62-driven processes was previously unknown. Here, we show that p62 is phosphorylated via a cascade that includes MEK3/6 and p38δ and is driven by the PB1-containing kinase MEKK3. This phosphorylation results in the recruitment of TRAF6 to p62, the ubiquitination and activation of mTOR, and the regulation of autophagy and cell proliferation. Genetic inactivation of MEKK3 or p38δ mimics that of p62 in that it leads to inhibited growth of PTEN-deficient prostate organoids. Analysis of human prostate cancer samples showed upregulation of these three components of the pathway, which correlated with enhanced mTORC1 activation. Graphical abstract Teaser Linares et al. identify a kinase cascade that regulates the phosphorylation of the signal adaptor p62 in response to amino acids to control mTORC1 activation. This nutrient-sensing mechanism is relevant for autophagy regulation and tumor growth.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Yui Masuki This study clarifies the role of an NGO in transforming the discriminatory social status of the Dalits (Untouchables), and its implications for sustainable community development. Subduing the discriminatory relationship between Dalits and other local people will not only uplift them socioeconomically, but also expand their opportunity for communication, enabling the construction of inter-personal relationships between the discriminating and the discriminated against. The NGO plays an important role in facilitating this communication and implementing national and global level sanitation. This study illustrates the dynamic process of transforming discriminatory social relationships and the complicated mechanism of Dalit discrimination in contemporary India.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Mohammad Razif, Soemarno, Bagyo Yanuwiadi, Arief Rachmansyah, Prawira Fajarindra Belgiawan This study aims to implement the linear regression method to generate a linear regression equation that can be used in the study of EIA (Environmental Impact Assessment) to predict the cost of WWTP (Wastewater Treatment Plant) of the data wastewater flowrate with case study of ten malls in Surabaya city.Some previous researchers have produced data on a linear regression WWTP construction costs and wastewater flowrate.In the EIA study in Indonesia, management and monitoring costs include costs of construction, operation and maintenance costs, and monitoring costs.Therefore, these costs will be calculated for WWTP of malls with unit prices prevailing in Surabaya city. The methodology of the study consists of the calculation of the construction cost, the calculation of operation and maintenance cost, the calculation of monitoring cost, and the process of making a linear regression curve. The result showed that from the ten malls, the smallest flowrate was 0.88 l/sec and 6.72 l/sec the largest, while the calculation of the cost was gained at the least as 577x10 6 IDR and the biggest cost was 2163 x10 6 IDR. The linear regression curve between the flow rate WWTP (as independentvariables in the X axis) and the total cost WWTP (as dependent variables in the Y-axis) has produced a regression equation of Y = 358 + 271X. The result of the linear regression equation can be used directly by the EIA committee in Surabaya city and activityinitiator of mall to predict the cost of WWTP quickly and to decide the environmental feasibility of the mall.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Obie Farobie, Yukihiko Matsumura Biodiesel was produced via non-catalytic transesterification in supercritical methanol using a novel spiral reactor. This spiral reactor could serve as a heat exchanger, thus it provided the advantage of being able to recover the heat. Transesterification was carried out at 270-400°C, a pressure of 20 MPa, oil-to-methanol molar ratio of 1:40, and reaction time of 3-30min. Using this technique, a complete conversion of fatty acid methyl ester (FAME) (100 wt%) was obtained in a short reaction time of 10 min at 350°C and oil-to-methanol molar ratio of 1:40 under a reactor pressure of 20 MPa. The result revealed that biodiesel yield conducted in spiral reactor is higher than that in batch reactor at the same reaction conditions. The kinetic model of canola oil conversion to biodiesel in supercritical methanol was also determined.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Supriyono, Hedi Surahman, Yuni Krisyuningsih Krisnandi, Jarnuzi Gunlazuardi Relationship between loading level and some physical properties of the SnO 2 -F film has been investigated. SnO 2 -F thin films were prepared by spray pyrolysis technique using modified respiratory therapist nebulizer at substrate temperature in the range of 400-520̊C. A stannous chloride solution was used as precursor and ammonium fluoride (NH 4 F) as dopant with 20% [F]/[Sn] ratio. The sheet resistance was found to decrease withthe increasing loading level, and sheet resistancebecame steady after the loading level was greater than0.45 mg/cm 2 . The transmittance was found to decrease with the increase of loading level but the decrease was not significant. The transparent conductive oxide of SnO 2 -F thin films were obtained, with transmittance was greater than 82.5% and sheet resistance of 21.4 Ω/sq. This results are comparable with the reported values (81.9% and 21.8 Ω/sq) [1] and this film can be used for efficient support of dye-sensitized solar cells electrode.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Aziza Hamed Al-Farsi, Hameed Sulaiman, Hassan Ali Al-Reasi Protection of the ecosystems ultimately contributes towards their sustainability. Presence of high levels of toxic metals in seafood is considered as an environmental warning for possible influences on the ecosystem components and public health. This research quantified the concentrations of cadmium (Cd), chromium (Cr), copper (Cu), manganese (Mn), lead (Pb), vanadium (V), and zinc (Zn) in sediments and edible soft tissue of shellfish Strombus ( Conomurex ) persicus from the Sea of Oman. In both matrices, metals exhibited no general trend in the distribution of metals between the sampling sites. In shellfish, metal levels were below the international maximum permissible guidelines, illustrating safe consumption of this seafood item. The calculated risk factor ( E r i ) for Cr, Cu, Pb, and Zn revealed no ecological damage should be anticipated at the reported metal concentrations in the sediment samples. However, Cd had higher E r i range, suggesting moderate to considerable ecological risk. For transfer of metals from sediment to S . persicus , bioaccumulation factors (BAF) estimated for Cd, Cu, and Zn were above 1.0, indicating tendency of these metals to accumulate in S . persicus . While the BAF and E r i values for Zn were insignificantly correlated, BAF values for Cd and Cu were inversely related to their corresponding E r i values. Nevertheless, correlation was not statistically significant for Cu. For Cd, it seems that sediments having higher E r i may not be necessarily resulting in higher tissue Cd burdens of S . persicus . In conclusion, it appears that the use of correlation between BAF and E r i to examine transfer of metals from abiotic component to organisms in natural waters is limited.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Tito Sumandono, Henderson Saragih, Migirin, Takashi Watanabe, Rudianto Amirta In this research, decolorization of Remazol Brilliant Blue R (RBBR) was investigated using a new isolated white rot fungus, strain KRUS-G, collected from Mulwarman University Botanical Garden,Samarinda, East Kalimantan, Indonesia. The results showed that strain KRUS-G decolorized RBBR efectively compared to Phanerochaetecrysosporium and Ceriporiopsissubvermispora . The highest decolorization was obtained at pH 4 with 89% loss of RBBR used. The effective decolorization was also observed in the high concentration of RBBR (1500 ppm).Concentration of RBBR at 500, 1000, and 1500 ppm caused slightly decreasing pattern on mycelia growth. Rapid decolorization was occurred within 4 days of incubation. We suggest that laccase played an important role on the decolorizationeven high activity ofMnP was also detected.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Arry Y. Nurhayati, Yuda C. Hariadi, P. Lestari Demands on an early detection method for lead (Pb), found as a pollutant in soil, are urgently needed to improve awareness on the continuing usage of waste water and industrial effluent for the agricultural practices especially in East Java, Indonesia. Marsilea crenata plant grown in a glasshouse under various concentration of Pb to indicate its tolerance to Pb stress is measured by its weekly biolectrical responses. The result shows that increasing Pb concentration tends to inhibit the plant's growth. It is concluded that the method is viable as an early detection remediation process to protect agricultural economy and human security.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Santosa S. Putra, Mick v.d. Wegen, J. Reyns, Arthur v. Dam, D.P. Solomatine, J.A. Roelvink A model calibration based on the distributed multi stations approach is necessary towards model implementation in the operational phase. In this study, a tree dimensional (3D) hydrodynamic and salinity dynamic model of an estuary was simulated using DFlow Flexible Mesh program, which is developed by Deltares. Specifically, this research was focused on the Columbia Estuary case study, which is situated in Oregon, United States. The preconfigured model was calibrated based on 15 measurement stations that are spread along the estuary. Furthermore, a detail portion data with an average interval of 1 minute were used during the calibration process. The model performances were improved by considering the data denial concept. The data denial concept was introduced by neglecting inconsistence data across its temporal and spatial variability. In this particular case, it was revealed that the downstream data, which have high salinity value, tends to produce high contribution to the root mean square error of the model result. In conclusion, the upstream data have immense variable fluctuation rate and therefore it is more sensitive to give lower coefficient of determination. Therefore, there must be a trade of between good estuary model performance and upstream station data reliability.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Hoang Trung Thanh, Helmut Yabar, Yoshiro Higano Hanoi, the capital of Vietnam, is home to approximately 7 million people. In 2011, the city generated about 2,372,500 tons of municipal solid waste (MSW) (accounting for 11% of national generation) and the collection rate reached 85%, of which 84% was sent directly to landfills (without landfill gas capture systems). This conventional practice has caused not only adverse environmental impacts but also increased greenhouse gas (GHG) emissions and loss of recyclable resources. Since most of the waste generated in the city is organic waste (it accounts for 71% of municipal solid waste), there is high potential for organic waste recovery of MSW in Hanoi. This paper analyzes the potential for environmental benefits of introducing composting of municipal organic waste by proposing five alternative scenarios that range from current situation to composting of both commercial and household organic waste. In order to evaluate the environmental performance of the scenarios, we used three indicators: organic fertilizer production, landfill life extension, and GHG emission reduction. The results show that composting could produce a huge amount of organic fertilizer (i.e. from 6,424to 218,650 tons/year) depending on the scenarios. Diversion of organic waste to composting could reduce the amount of waste disposed in landfills resulting in extending landfill life significantly. Therefore, landfill lifecould be extended from 0.5 to 8.7 years compared to the current situation. Current MSW management practices contributed the highest amount of GHG emission accounting for 1,322,928 tonsCO 2 -eq/year, whereas the proposed scenarios decrease emissions in accordance with increasing the amount of organic waste used for composting. The estimated emission reduction from the proposed scenarios ranges from 15% to 98% compared to the current situation. The results suggest that composting could bring significant environmental benefits and is a key solution toward sustainable solid waste management for Hanoi city. In addition, composting highlights the potential of climate protection in the waste management sector.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Yusuf Wibisono, Slamet Widodo The use of crude vegetable oils without degumming, during biodiesel production, might decrease the conversion rate and be difficult to separate glycerol from biodiesel. Ultrafiltration is promising technology for gum removal from crude vegetable oils. However, since the oil constituents have very close molecular weight, degumming process by membrane is relatively difficult. In order to understand the membrane degumming process of corn-oil, a prediction of concentration boundary layer thickness was calculated using a CFD model. An artificial neural network is developed to learn the relationship between Reynolds and Schmidt numbers of feed solution which affects the boundary layer thickness along the membrane tube.

Description: Publication date: Available online 29 July 2015 Source: Geodesy and Geodynamics Author(s): Zhou Rui, Wu Xiaoping How to deal with colored noises of GOCE (Gravity field and steady – state Ocean Circulation Explorer) satellite has been the key to data processing. This paper focused on colored noises of GOCE gradient data and the frequency spectrum analysis. According to the analysis results, gravity field model of the optimal degrees 90–240 is given, which is recovered by GOCE gradient data. This paper presents an iterative Wiener filtering method based on the gravity gradient invariants. By this method a degree-220 model was calculated from GOCE SGG (Satellite Gravity Gradient) data. The degrees above 90 of ITG2010 were taken as the prior gravity field model, replacing the low degree gravity field model calculated by GOCE orbital data. GOCE gradient colored noises was processed by Wiener filtering. Finally by Wiener filtering iterative calculation, the gravity field model was restored by space-wise harmonic analysis method. The results show that the model's accuracy matched well with the ESA's (European Space Agency) results by using the same data.

Description: Publication date: 4 August 2015 Source: Cell Reports, Volume 12, Issue 5 Author(s): Obinna Chijioke, Anne Müller, Regina Feederle, Mario Henrique M. Barros, Carsten Krieg, Vanessa Emmel, Emanuela Marcenaro, Carol S. Leung, Olga Antsiferova, Vanessa Landtwing, Walter Bossart, Alessandro Moretta, Rocio Hassan, Onur Boyman, Gerald Niedobitek, Henri-Jacques Delecluse, Riccarda Capaul, Christian Münz

Description: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Matthew T. Maurano, Hao Wang, Sam John, Anthony Shafer, Theresa Canfield, Kristen Lee, John A. Stamatoyannopoulos Although DNA methylation is commonly invoked as a mechanism for transcriptional repression, the extent to which it actively silences transcription factor (TF) occupancy sites in vivo is unknown. To study the role of DNA methylation in the active modulation of TF binding, we quantified the effect of DNA methylation depletion on the genomic occupancy patterns of CTCF, an abundant TF with known methylation sensitivity that is capable of autonomous binding to its target sites in chromatin. Here, we show that the vast majority (>98.5%) of the tens of thousands of unoccupied, methylated CTCF recognition sequences remain unbound upon abrogation of DNA methylation. The small fraction of sites that show methylation-dependent binding in vivo are in turn characterized by highly variable CTCF occupancy across cell types. Our results suggest that DNA methylation is not a primary groundskeeper of genomic TF landscapes, but rather a specialized mechanism for stabilizing intrinsically labile sites. Graphical abstract Teaser Alterations of DNA methylation in malignancy and development are frequently interpreted as affecting transcriptional activity. Maurano et al. find that, upon genomic abrogation of DNA methylation, binding of the canonically methylation-sensitive transcriptional regulator CTCF is largely unaffected. Their results suggest that a limited set of methylation-sensitive CTCF sites are variable across cell types and that key sequence and chromatin features predict methylation sensitivity of CTCF binding.

Description: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Swea-Ling Khaw, Chua Min-Wen, Cheng-Gee Koh, Bing Lim, Ng Shyh-Chang Oocyte factors not only drive somatic cell nuclear transfer reprogramming but also augment the efficiency and quality of induced pluripotent stem cell (iPSC) reprogramming. Here, we show that the oocyte-enriched factors Tcl1 and Tcl1b1 significantly enhance reprogramming efficiency. Clonal analysis of pluripotency biomarkers further show that the Tcl1 oocyte factors improve the quality of reprogramming. Mechanistically, we find that the enhancement effect of Tcl1b1 depends on Akt, one of its putative targets. In contrast, Tcl1 suppresses the mitochondrial polynucleotide phosphorylase (PnPase) to promote reprogramming. Knockdown of PnPase rescues the inhibitory effect from Tcl1 knockdown during reprogramming, whereas PnPase overexpression abrogates the enhancement from Tcl1 overexpression. We further demonstrate that Tcl1 suppresses PnPase’s mitochondrial localization to inhibit mitochondrial biogenesis and oxidation phosphorylation, thus remodeling the metabolome. Hence, we identified the Tcl1-PnPase pathway as a critical mitochondrial switch during reprogramming. Graphical abstract Teaser Khaw et al. identify the oocyte Tcl1-PnPase pathway as a critical mitochondrial switch during reprogramming into iPSCs. They find that Tcl1 suppresses the mitochondrial localization of PNPase, thus inhibiting mitochondrial biogenesis and oxidation phosphorylation.

Description: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Xinfang Huang, Jingjing Li, Stephanie Dorta-Estremera, Jeremy Di Domizio, Scott M. Anthony, Stephanie S. Watowich, Daniel Popkin, Zheng Liu, Philip Brohawn, Yihong Yao, Kimberly S. Schluns, Lewis L. Lanier, Wei Cao Here, we examine the mechanism by which plasmacytoid dendritic cells (pDCs) and type I interferons promote humoral autoimmunity. In an amyloid-induced experimental autoimmune model, neutrophil depletion enhanced anti-nuclear antibody development, which correlated with heightened IFN-γ production by natural killer (NK) cells. IFN-α/β produced by pDCs activated NK cells via IL-15 induction. Neutrophils released reactive oxygen species (ROS), which negatively modulated the levels of IL-15, thereby inhibiting IFN-γ production. Mice deficient in NADPH oxidase 2 produced increased amounts of IFN-γ and developed augmented titers of autoantibodies. Both the pDC-IFN-α/β pathway and IFN-γ were indispensable in stimulating humoral autoimmunity. Male NZB/W F1 mice expressed higher levels of superoxide than their female lupus-prone siblings, and depletion of neutrophils resulted in spontaneous NK cell and autoimmune B cell activation. Our findings suggest a regulatory role for neutrophils in vivo and highlight the importance of an NK-IFN-γ axis downstream of the pDC-IFN-α/β pathway in systemic autoimmunity. Graphical abstract Teaser Huang et al. find that IFN-α/β produced by plasmacytoid dendritic cells (pDCs) stimulates NK cells to secrete IFN-γ, which is essential for the development of autoantibodies. ROS-producing neutrophils negatively regulate this NK-IFN-γ pathway and control autoimmune progression in lupus-prone mice.

Description: Publication date: Available online 6 August 2015 Source: Geoscience Frontiers Author(s): Afshin Hashmie, Ali Rostamnejad, Fariba Nikbakht, Mansour Ghorbanie, Peyman Rezaie, Hossien Gholamalian This study is focused on sedimentary environments, facies distribution, and sequence stratigraphy. The facies and sequence stratigraphic analyses of the Bahram Formation (middle–late Devonian) in south-central Iran are based on two measured stratigraphic sections in the southern Tabas block. The Bahram Formation overlies red sandstones Padeha Formation in sections Hutk and Sardar and is overlain by Carboniferous carbonate deposits of Hutk Formation paraconformably, with a thickness of 354 and 386 m respectively. Mixed siliciclastic and carbonate sediments are present in this succession. The field observations and laboratory studies were used to identify 14 micro/petrofacies, which can be grouped into 5 depositional environments: shore, tidal flat, lagoon, shoal and shallow open marine. A mixed carbonate-detrital shallow shelf is suggested for the depositional environment of the Bahram Formation which deepens to the east (Sardar section) and thins in southern locations (Hutk section). Three 3rd-order cyclic siliciclastic and carbonate sequences in the Bahram Formation and one sequence shared with the overlying joint with Hutk Formation are identified, on the basis of shallowing upward patterns in the micro/pertofacies. Graphical abstract

Description: Publication date: Available online 3 June 2015 Source: Journal of Rock Mechanics and Geotechnical Engineering Author(s): Foad Changizi , Abdolhosein Haddad This paper investigates the effect of recycled polyester fiber, produced from polyethylene (PET) bottles, in combination with nano-SiO 2 as a new stabilizer to improve the mechanical properties of soils. We intend to study the effect of adding nano-SiO 2 and recycled polyester fiber on soil engineering properties, especially the shear strength and unconfined compressive strength (UCS), using clayey soil with low liquid limit. Three different combinations of fiber-soil ratios ranging between 0.1% and 0.5% as well as three different combinations of nano-soil ratios ranging between 0.5% and 1% are used. The shear strength and UCS of treated specimens are obtained from direct shear test and unconfined compression test, respectively. Results of this study show that the addition of recycled polyester fiber and nano-SiO 2 increases the strength of soil specimens. Both the shear strength and UCS are improved by increasing the contents of recycled polyester fiber and nano-SiO 2 in the soil mixture. The increase in the nano-SiO 2 content leads to a reduction in failure strain, but the increase in the content of recycled polyester fiber leads to an increase in failure strain. The increase in the contents of recycled polyester fiber and nano-SiO 2 leads to an increase in elastic modulus of soils. Based on the test results, the addition of recycled polyester fiber improves the mechanical properties of soils stabilized with nano-SiO 2 as well as the recycled polyester fiber has a positive effect on soil behaviors.

Description: Publication date: Available online 3 June 2015 Source: Journal of Rock Mechanics and Geotechnical Engineering Author(s): Xingzhang Chen , Hui Chen , Yong You , Jinfeng Liu Many debris flows have occurred in the areas surrounding the epicenter of the Wenchuan earthquake. Susceptibility assessment of debris flows in this area is especially important for disaster prevention and mitigation. This paper studies one of the worst hit areas, the Subao river valley, and the susceptibility assessment of debris flows is performed based on field surveys and remote sensing interpretation. By investigating the formation conditions of debris flows in the valley, the following assessment factors are selected: mixture density of landslides and rock avalanches, distance to the seismogenic fault, stratum lithology, ground roughness, and hillside angle. The weights of the assessment factors are determined by the analytic hierarchy process (AHP) method. Each of the assessment factors is further divided into five grades. Then, the assessment model is built using the multifactor superposition method to assess the debris flow susceptibility. Based on the assessment results, the Subao river valley is divided into three areas: high susceptibility areas, medium susceptibility areas, and low susceptibility areas. The high susceptibility areas are concentrated in the middle of the valley, accounting for 17.6% of the valley area. The medium susceptibility areas are in the middle and lower reaches, most of which are located on both sides of the high susceptibility areas and account for 45.3% of the valley area. The remainders are classified as low susceptibility areas. The results of the model are in accordance with the actual debris flow events that occurred after the earthquake in the valley, confirming that the proposed model is capable of assessing the debris flow susceptibility. The results can also provide guidance for reconstruction planning and debris flow prevention in the Subao river valley.

Description: Publication date: Available online 3 June 2015 Source: Journal of Asian Ceramic Societies Author(s): Taishi Yokoi , Kei Tsukada , Sota Terasaka , Masanobu Kamitakahara , Hideaki Matsubara Layered double hydroxides (LDHs) have intercalation properties and are used in various applications. The performances of the LDH materials can be improved by controlling crystal morphology. Morphology of inorganic crystals is controlled by organic molecules in biomineralization. Inspired by biomineralization, we investigated the effect of the addition of mono, di and triacids as morphological control agents on crystal morphology of LDH synthesized by the homogeneous precipitation method. Morphology of LDH was changed from hexagonal plate to stacked disc by addition of monoacids, namely acetic acid and methanesulfonic acid, in the reaction solution. Flower-shaped LDH crystals were formed in the presence of diacids and a triacid, namely succinic acid, 1,2-ethanedisulfonic acid and 1,2,3-propanetricarboxylic acid. We found that the morphology of the LDH crystals was controlled by the number of functional group on the morphological control agent rather than the type of functional group. These findings can contribute for the development of novel and functional LDH materials with precisely controlled morphology.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 26 Author(s): Jed A. Long New tracking technologies are allowing researchers to study wildlife movements at unprecedented spatial and temporal resolutions. Researchers now routinely deploy tracking sensors on multiple individual animals simultaneously, offering new opportunities to study the spatial-temporal interactions (often termed dynamic interaction) in the movements of these animals. The objective of this paper is to examine the statistical properties of a suite of currently available methods aimed at measuring spatial-temporal interactions and the ability of each method to characterize and capture different patterns of spatial-temporal interaction encountered in practice. Specifically, this paper examines issues relating to the spatial arrangement of interactions across a study area, temporal patterns in interactions over a tracking period, and the effectiveness of different statistical testing procedures used to identify significant spatial-temporal interaction. Simulations using biased correlated random walks are used to emulate different patterns of spatial-temporal interaction encountered in empirical data. The results demonstrate the challenges of statistical testing of interaction patterns with several methods having high rates of type I and/or type II error. More problematic is that, in practice, spatial-temporal interactions exhibit underlying spatial and/or temporal patterns, for example with key watering holes revisited daily, which can cause problems for statistics that use permutation tests from the original data to test for significance. The need to consider statistical significance in the context of biological significance, which relates to quantifying the spatial locations and temporal patterns of interaction events and types of interactions, is emphasized. Methods that can be adapted to facilitate spatial and temporally ‘local’ analysis are advantageous with high resolution tracking data currently being collected. An R package–wildlifeDI–provides the computational tools for performing the analysis described herein and is made openly available to other researchers.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 26 Author(s): Y. Li , K.S. Kim , J. Deschamps , R. Briandet , A. Trubuil The biofilm ubiquitously exists on most wet surfaces. It is a protective shield of the bacteria and causes the difficulty in the disinfection. The irrigation of the biofilm by the specific swimmer bacteria can exacerbate killing of biofilm bacteria. Therefore, we precisely investigate the tunneling of swimmers bacteria within biofilms. These bacterial stealth swimmers create transient opened spaces in the biofilm. We found that these opened spaced in the biofilm is the obvious indication of the motion of the swimmers. We exploit both detected swimmer in one swimmer channel and the opened space in the other biofilm channel of confocal microscope video, in order to interactively improve the tracking of the swimmer's motion in the biofilm, which is implemented by improving a successful algorithm of single particle tracking. Moreover, we quantitatively study the swimmer trajectory, the opened space and their relation in the large-scale microscope video when the biofilm is separately irrigated by many different species of bacteria. We try to discover the influence of the irrigated bacteria on the biofilm.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 26 Author(s): Sylvain Coly , Myriam Charras-Garrido , David Abrial , Anne-Françoise Yao-Lafourcade Disease mapping aims to determine the underlying disease risk scattered from health data. This methodology enables to represent this disease risk by a gradation of colours on a map. Our aim is to apply disease mapping to infectious diseases, when a primary case can result in secondary cases, by direct or vector transmission. Contagion can lead to overdispersion and strengthen spatial and temporal structures. This study highlighted the relevance of using the negative binomial distribution to model such data. It also showed the need to take into account both spatial and temporal dimensions in this type of epidemiological study.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 26 Author(s): Manuel Castro Ribeiro , António Jorge Sousa , Maria João Pereira Geographical distribution of health outcomes are influenced by socio-economic and environmental factors operating at different spatial scales. Geographical variations in relationships between them can be revealed with a semi-parametric geographically weighted poisson regression (sGWPR), which is a mixed model than can combine geographically varying and geographically constant parameters. To decide if a parameter associated with a variable should vary geographically or not, two models can be compared: a model where all parameters are allowed to vary geographically and a mixed model, where all but one (the parameter under evaluation) parameters are allowed to vary geographically. If the difference between Aikaike's Information Criteria (AICc) is larger than 2, the model with lower AICc is selected. However, delivering model selection exclusively to AICc measure might hide important details in spatial variations of ecological associations, especially in situations where the difference between models is marginal. We propose to assist the decision by using a linear model of coregionalization (LMC), a geostatistical tool originally developed for geosciences. Here we show how the LMC can refine sGWPR analysis on ecological associations between socio-economic and environmental variables and low birth weight outcomes in the west north central region of Portugal.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 26 Author(s): Sara Fontanella , Lara Fontanella , Luigi Ippoliti , Pasquale Valentini Nowadays, one of the most changeling points in statistics is the analysis of high dimensional data. In such cases, it is commonly assumed that the dimensionality of the data is only artificially high: although each data point is described by thousands of features, it is assumed that it can be modeled as a function of only a few underlying parameters. Formally, it is assumed that the data points are samples from a low-dimensional manifold embedded in a high-dimensional space. In this paper, we discuss a recently proposed method, known as Maximum Entropy Unfolding (MEU), for learning non-linear structures that characterize high dimensional data. This method represents a new perspective on spectral dimensionality reduction and, joined with the theory of Gaussian Markov random fields, provides a unifying probabilistic approach to spectral dimensionality reduction techniques. Parameter estimation as well as approaches to learning the structure of the GMRF are discussed

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 26 Author(s): A.D. Maldonado , R.F. Ropero , P.A. Aguilera , A. Fernández , R. Rumí , A. Salmerón Several algorithms have been developed in the literature to solve regression problems. We propose a novel methodology based on Bayesian networks (BNs) to deal with regression problems in environmental research. To demonstrate its capabilities and strength, we compare a BN model with 3 other methods commonly used to solve regression tasks, in terms of their root mean squared error (RMSE). The errors were depicted on error maps, providing information about the reliability of the predictions in each observation. The results show that BNs are competitive with other popular methods.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 26 Author(s): XiWei Chen , ZhiYuan Pei , Ai Lian Chen , Fei Wang , KeJian Shen , QiaoFu Zhou , Li Sun Poverty is one of the worldwide and key issues concerned by governments and international organizations. Chinese rural poverty was massive poverty caused by universal factors such as underdeveloped national economy and lack of related institution and policy in the past, instead, now has shown “point-scatted” distribution due to special regional environment, backward production conditions and low population quality with the long-term efforts. In addition to the impact of economic and social factors, natural condition is also one of the main factors restricting the incidence of poverty in rural areas. In this paper, spatial statistical analysis and GIS are combined to analyze the patterns and factors of spatial poverty distribution of Xianfeng County, a key country from national contiguous special poverty-stricken areas in China. Two indexes representing extend and depth of poverty, poverty headcount ratio and the per capita net income of poverty population, were used to analyze spatial poverty distribution based on the spatial autocorrelation method.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 26 Author(s): Kejian Shen , Weifang Li , Zhiyuan Pei , Wang Fei , Guannan Sun , Xiaoqian Zhang , Xiwei Chen , Shangjie Ma Using remote sensing data to estimate crop area is efficient to a wide range of end-users, including government agencies, farmers and researchers. Moderate spatial resolution (MSR) image data are widely used to estimate crop area. But its accuracy can’t meet the demands of precision. Spatial sampling techniques integrated the strengths of remote sensing and sampling survey are being widely used. This method need large sample size which is cannot be guaranteed by remote sensing due to weather. The Unmanned Aerial Vehicle (UAV) can be used as an effective way to guarantee enough sample size. This paper proposed a spatial sampling method using MSR image classification results and UAV transects, a stratified random sampling method was proposed, area-scale (from MSR image classification) was used as auxiliary variable to guide the distribution of UAV transects, which had proved that 2% sampling ratio can make the crop area estimation accuracy more than 95% with a 95% confidence interval.

Description: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Laura W. Dillon , Pankaj Kumar , Yoshiyuki Shibata , Yuh-Hwa Wang , Smaranda Willcox , Jack D. Griffith , Yves Pommier , Shunichi Takeda , Anindya Dutta MicroDNAs are 〈400-base extrachromosomal circles found in mammalian cells. Tens of thousands of microDNAs have been found in all tissue types, including sperm. MicroDNAs arise preferentially from areas with high gene density, GC content, and exon density from promoters with activating chromatin modifications and in sperm from the 5′-UTR of full-length LINE-1 elements, but are depleted from lamin-associated heterochromatin. Analysis of microDNAs from a set of human cancer cell lines revealed lineage-specific patterns of microDNA origins. A survey of microDNAs from chicken cells defective in various DNA repair proteins reveals that homologous recombination and non-homologous end joining repair pathways are not required for microDNA production. Deletion of the MSH3 DNA mismatch repair protein results in a significant decrease in microDNA abundance, specifically from non-CpG genomic regions. Thus, microDNAs arise as part of normal cellular physiology—either from DNA breaks associated with RNA metabolism or from replication slippage followed by mismatch repair. Graphical abstract Teaser Through isolating and sequencing small extrachromosomal circular microDNAs across multiple species and cell types, Dillon et al. identify specific genomic features associated with the generation of microDNAs and link the DNA mismatch repair pathway to this process.

Description: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Caroline Ramspacher , Emily Steed , Francesco Boselli , Rita Ferreira , Nathalie Faggianelli , Stéphane Roth , Coralie Spiegelhalter , Nadia Messaddeq , Le Trinh , Michael Liebling , Nikhil Chacko , Federico Tessadori , Jeroen Bakkers , Jocelyn Laporte , Karim Hnia , Julien Vermot Desminopathies belong to a family of muscle disorders called myofibrillar myopathies that are caused by Desmin mutations and lead to protein aggregates in muscle fibers. To date, the initial pathological steps of desminopathies and the impact of desmin aggregates in the genesis of the disease are unclear. Using live, high-resolution microscopy, we show that Desmin loss of function and Desmin aggregates promote skeletal muscle defects and alter heart biomechanics. In addition, we show that the calcium dynamics associated with heart contraction are impaired and are associated with sarcoplasmic reticulum dilatation as well as abnormal subcellular distribution of Ryanodine receptors. Our results demonstrate that desminopathies are associated with perturbed excitation-contraction coupling machinery and that aggregates are more detrimental than Desmin loss of function. Additionally, we show that pharmacological inhibition of aggregate formation and Desmin knockdown revert these phenotypes. Our data suggest alternative therapeutic approaches and further our understanding of the molecular determinants modulating Desmin aggregate formation. Graphical abstract Teaser Desminopathies are myopathies and cardiomyopathies associated with Desmin mutations leading to protein aggregates. Ramspacher et al. demonstrate that altered Desmin function or expression affect the EC coupling machinery and calcium dynamics. They show that aggregates are more toxic than the loss of function and can be rescued by knockdown and pharmacological treatment.

Description: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Peng Liu , Miranda N. Reed , Linda A. Kotilinek , Marianne K.O. Grant , Colleen L. Forster , Wei Qiang , Samantha L. Shapiro , John H. Reichl , Angie C.A. Chiang , Joanna L. Jankowsky , Carrie M. Wilmot , James P. Cleary , Kathleen R. Zahs , Karen H. Ashe The accumulation of amyloid-β (Aβ) as amyloid fibrils and toxic oligomers is an important step in the development of Alzheimer’s disease (AD). However, there are numerous potentially toxic oligomers and little is known about their neurological effects when generated in the living brain. Here we show that Aβ oligomers can be assigned to one of at least two classes (type 1 and type 2) based on their temporal, spatial, and structural relationships to amyloid fibrils. The type 2 oligomers are related to amyloid fibrils and represent the majority of oligomers generated in vivo, but they remain confined to the vicinity of amyloid plaques and do not impair cognition at levels relevant to AD. Type 1 oligomers are unrelated to amyloid fibrils and may have greater potential to cause global neural dysfunction in AD because they are dispersed. These results refine our understanding of the pathogenicity of Aβ oligomers in vivo. Graphical abstract Teaser Liu et al. classify brain-derived amyloid-β oligomers into type 1 and type 2. Type 2, but not type 1, oligomers have a spatiotemporal and structural relationship with amyloid plaques. Highly abundant type 2 oligomers do not impair cognition in situ, possibly due to spatial sequestration around plaques.

Description: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Alessandro Fantin , Anastasia Lampropoulou , Gaia Gestri , Claudio Raimondi , Valentina Senatore , Ian Zachary , Christiana Ruhrberg Sprouting blood vessels are led by filopodia-studded endothelial tip cells that respond to angiogenic signals. Mosaic lineage tracing previously revealed that NRP1 is essential for tip cell function, although its mechanistic role in tip cells remains poorly defined. Here, we show that NRP1 is dispensable for genetic tip cell identity. Instead, we find that NRP1 is essential to form the filopodial bursts that distinguish tip cells morphologically from neighboring stalk cells, because it enables the extracellular matrix (ECM)-induced activation of CDC42, a key regulator of filopodia formation. Accordingly, NRP1 knockdown and pharmacological CDC42 inhibition similarly impaired filopodia formation in vitro and in developing zebrafish in vivo. During mouse retinal angiogenesis, CDC42 inhibition impaired tip cell and vascular network formation, causing defects that resembled those due to loss of ECM-induced, but not VEGF-induced, NRP1 signaling. We conclude that NRP1 enables ECM-induced filopodia formation for tip cell function during sprouting angiogenesis. Graphical abstract Teaser During angiogenesis, new blood vessel sprouts are led by filopodia-studded tip cells to sense environmental signals and enable directional migration. NRP1 is a tip cell protein that senses angiogenic cues. Fantin et al. now show that NRP1 promotes tip cell function by enabling CDC42 activation for filopodia formation and actin remodeling.

Description: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Chien-Der Lee , Benjamin P. Tu PUF proteins are post-transcriptional regulators that bind to the 3′ UTRs of mRNA transcripts. Herein, we show how a yeast PUF protein, Puf3p, responds to glucose availability to switch the fate of its bound transcripts that encode proteins required for mitochondrial biogenesis. Upon glucose depletion, Puf3p becomes heavily phosphorylated within its N-terminal region of low complexity, associates with polysomes, and promotes translation of its target mRNAs. Such nutrient-responsive phosphorylation toggles the activity of Puf3p to promote either degradation or translation of these mRNAs according to the needs of the cell. Moreover, activation of translation of pre-existing mRNAs might enable rapid adjustment to environmental changes without the need for de novo transcription. Strikingly, a Puf3p phosphomutant no longer promotes translation but becomes trapped in intracellular foci in an mRNA-dependent manner. Our findings suggest that the inability to properly resolve Puf3p-containing RNA-protein granules via a phosphorylation-based mechanism might be toxic to a cell. Graphical abstract Teaser Lee and Tu report that the PUF protein Puf3 becomes phosphorylated in its low-complexity region upon glucose depletion to promote the translation of its bound mRNAs that are important for mitochondrial biogenesis. A Puf3 phosphomutant becomes trapped in punctate foci, providing insights into the dynamic nature of RNA granules.

Description: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Takashi Izawa , Nidhi Rohatgi , Tomohiro Fukunaga , Qun-Tian Wang , Matthew J. Silva , Michael J. Gardner , Michael L. McDaniel , Nada A. Abumrad , Clay F. Semenkovich , Steven L. Teitelbaum , Wei Zou ASXL2 is an ETP family protein that interacts with PPARγ. We find that ASXL2−/− mice are insulin resistant, lipodystrophic, and fail to respond to a high-fat diet. Consistent with genetic variation at the ASXL2 locus and human bone mineral density, ASXL2−/− mice are also severely osteopetrotic because of failed osteoclast differentiation attended by normal bone formation. ASXL2 regulates the osteoclast via two distinct signaling pathways. It induces osteoclast formation in a PPARγ/c-Fos-dependent manner and is required for RANK ligand- and thiazolidinedione-induced bone resorption independent of PGC-1β. ASXL2 also promotes osteoclast mitochondrial biogenesis in a process mediated by PGC-1β but independent of c-Fos. Thus, ASXL2 is a master regulator of skeletal, lipid, and glucose homeostasis. Graphical abstract Teaser ASXL2 regulates glucose homeostasis, adipogenesis, and osteoclast differentiation by activating PPARγ. Izawa et al. find that ASXL2-deficient mice are insulin resistant, lipodystrophic, and osteopetrotic. ASXL2 promotes osteoclast formation in a Fos-dependent manner independent of PGC-1β. ASXL2 enhances osteoclast mitochondrial biogenesis in a process mediated by PGC-1β but independent of c-Fos.

Description: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Jan-Philipp Mallm , Karsten Rippe Non-coding RNAs can modulate histone modifications that, at the same time, affect transcript expression levels. Here, we dissect such a network in mouse embryonic stem cells (ESCs). It regulates the activity of the reverse transcriptase telomerase, which synthesizes telomeric repeats at the chromosome ends. We find that histone H3 serine 10 phosphorylation set by Aurora kinase B (AURKB) in ESCs during the S phase of the cell cycle at centromeric and (sub)telomeric loci promotes the expression of non-coding minor satellite RNA ( cen RNA). Inhibition of AURKB induces silencing of cen RNA transcription and establishment of a repressive chromatin state with histone H3 lysine 9 trimethylation and heterochromatin protein 1 accumulation. This process results in a continuous shortening of telomeres. We further show that AURKB interacts with both telomerase and cen RNA and activates telomerase in trans . Thus, in mouse ESCs, telomere maintenance is regulated via expression of cen RNA in a cell-cycle-dependent manner. Graphical abstract Teaser Mallm and Rippe find that AURKB kinase and centromeric RNA regulate telomerase activity. AURKB phosphorylates serine 10 of histone H3 at chromosome p-arms during S phase in embryonic stem cells to induce centromere repeat transcription. Together, AURKB and centromere transcripts activate telomerase and ensure telomere maintenance.

Description: Publication date: September 2015 Source: Journal of Hydrology: Regional Studies, Volume 4, Part B Author(s): Z. Zomlot, B. Verbeiren, M. Huysmans, O. Batelaan Study focus Groundwater is of strategic importance. The accurate estimation of groundwater recharge and assessing the fundamental controlling factors are therefore of utmost importance to protect groundwater systems. We used the spatially-distributed water-balance model WetSpass to estimate long-term average recharge in Flanders. We validated recharge rates with base flow estimates of 67 daily stream flow records using the hydrograph analyses. To this end we performed principal component analysis, multiple linear regression analysis and relative importance analysis to assess the controlling factors of the spatial variation of recharge and base flow with the influencing watershed characteristics. New hydrological insights for the region The average resulting recharge is 235 mm/year and occurs mainly in winter. The overall moderate correlation between base flow estimates and modeled recharge rates indicates that base flow is a reasonable proxy of recharge. Groundwater recharge variation was explained in order of importance by precipitation, soil texture and vegetation cover; while base flow variation was strongly controlled by vegetation cover and groundwater depth. The results of this study highlight the important role of spatial variables in estimation of recharge and base flow. In addition, the prominent role of vegetation makes clear the potential importance of land-use changes on recharge and hence the need to include a proper strategy for land-use change in sustainable management of groundwater resources.

Description: Publication date: Available online 1 August 2015 Source: Journal of Asian Ceramic Societies Author(s): C.J. Ngally Sabouang, J.A. Mbey, F. Hatert, D. Njopwouo This study reports the use of calcined talc for cementitious products making. The calcination is used to enhance the availability of magnesium from talc to react with phosphate for cement phase formation. It is shown that previous calcination of talc leads to products having enhanced mechanical performance due to the formation of more cement phase than in products based on raw talc. Talc fired at 900 °C was found to be the one in which magnesium release was maximal. Firing at temperature higher than 900 °C leads to the stabilization of enstatite, which decreased the magnesium availability. The cement phase is struvite, which was better detected on the X-ray patterns of the products involving fired talc. All the products have very rapid setting time and low shrinkage.

Description: Publication date: Available online 1 August 2015 Source: Journal of Asian Ceramic Societies Author(s): Pardeep Sharma, Satpal Sharma, Dinesh Khanduja The present research work focuses on the production of aluminium (AA6082-T6) matrix composites reinforced with various weight percentage of silicon nitride particles by conventional stir casting route. The percentage of reinforcement is varied from 0 wt.% to 12 wt.% in a stage of 3%. The microstructures and mechanical properties of the fabricated aluminium matrix composites are investigated. The scanning electron microstructure images reveal the presence of Si 3 N 4 particles in the aluminium matrix. The distribution of Si 3 N 4 particles has also been recognized with X-ray diffraction technique. The mechanical properties such as ultimate tensile strength and hardness have improved at the cost of reduction in ductility with increase in weight percentage of silicon nitride particulates in the aluminium metal matrix. The density and porosity of the composites also show an increasing trend with increase in volume fraction of Si 3 N 4 particles in the aluminium matrix.

Description: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Jenea M. Bin, Dong Han, Karen Lai Wing Sun, Louis-Philippe Croteau, Emilie Dumontier, Jean-Francois Cloutier, Artur Kania, Timothy E. Kennedy Netrin-1 regulates cell migration and adhesion during the development of the nervous system, vasculature, lung, pancreas, muscle, and mammary gland. It is also proposed to function as a dependence ligand that inhibits apoptosis; however, studies disagree regarding whether netrin-1 loss-of-function mice exhibit increased cell death. Furthermore, previously studied netrin-1 loss-of-function gene-trap mice express a netrin-1-β-galactosidase protein chimera with potential for toxic gain-of-function effects, as well as a small amount of wild-type netrin-1 protein. To unambiguously assess loss of function, we generated netrin-1 floxed and netrin-1 null mouse lines. Netrin-1 −/− mice die earlier and exhibit more severe axon guidance defects than netrin-1 gene-trap mice, revealing that complete loss of function is more severe than previously reported. Netrin-1 −/− embryos also exhibit increased expression of the netrin receptors DCC and neogenin that are proposed dependence receptors; however, increased apoptosis was not detected, inconsistent with netrin-1 being an essential dependence receptor ligand in the embryonic spinal cord. Graphical abstract Teaser Bin et al. have generated a netrin-1 null mouse that displays phenotypes more severe than those of the reported netrin-1 gene-trap mouse, including embryonic lethality and exacerbated axon guidance defects. No increased apoptosis was detected, indicating that netrin-1 is not an essential dependence ligand, despite increased DCC and neogenin in netrin-1 nulls.

Description: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Michael S. Werner, Alexander J. Ruthenburg A number of long noncoding RNAs (lncRNAs) have been reported to regulate transcription via recruitment of chromatin modifiers or bridging distal enhancer elements to gene promoters. However, the generality of these modes of regulation and the mechanisms of chromatin attachment for thousands of unstudied human lncRNAs remain unclear. To address these questions, we performed stringent nuclear fractionation coupled to RNA sequencing. We provide genome-wide identification of human chromatin-associated lncRNAs and demonstrate tethering of RNA to chromatin by RNAPII is a pervasive mechanism of attachment. We also uncovered thousands of chromatin-enriched RNAs (cheRNAs) that share molecular properties with known lncRNAs. Although distinct from eRNAs derived from active prototypical enhancers, the production of cheRNAs is strongly correlated with the expression of neighboring protein-coding genes. This work provides an updated framework for nuclear RNA organization that includes a large chromatin-associated transcript population correlated with active genes and may prove useful in de novo enhancer annotation. Graphical abstract Teaser Werner and Ruthenburg report a compendium of tightly chromatin-associated human lncRNAs, which is substantially larger than previously appreciated and also encompasses thousands of chromatin-enriched RNAs (cheRNAs) largely attached to chromatin via RNAPII. CheRNAs may provide a way to annotate enhancers de novo.

Description: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Tony DeFalco, Sarah J. Potter, Alyna V. Williams, Brittain Waller, Matthew J. Kan, Blanche Capel The testis produces sperm throughout the male reproductive lifespan by balancing self-renewal and differentiation of spermatogonial stem cells (SSCs). Part of the SSC niche is thought to lie outside the seminiferous tubules of the testis; however, specific interstitial components of the niche that regulate spermatogonial divisions and differentiation remain undefined. We identified distinct populations of testicular macrophages, one of which lies on the surface of seminiferous tubules, in close apposition to areas of tubules enriched for undifferentiated spermatogonia. These macrophages express spermatogonial proliferation- and differentiation-inducing factors, such as colony-stimulating factor 1 (CSF1) and enzymes involved in retinoic acid (RA) biosynthesis. We show that transient depletion of macrophages leads to a disruption in spermatogonial differentiation. These findings reveal an unexpected role for macrophages in the spermatogonial niche in the testis and raise the possibility that macrophages play previously unappreciated roles in stem/progenitor cell regulation in other tissues. Graphical abstract Teaser Macrophages are abundant in the adult mammalian testis, but not much is known about how they directly affect spermatogenesis. DeFalco et al. describe a role for testicular macrophages, showing that they are enriched near spermatogonial precursors and are required for spermatogonial differentiation, potentially acting through CSF1 and retinoic acid pathways.

Description: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Evgeny Ivashkin, Marina Yu. Khabarova, Victoria Melnikova, Leonid P. Nezlin, Olga Kharchenko, Elena E. Voronezhskaya, Igor Adameyko Many organisms survive in constantly changing environments, including cycling seasons. Developing embryos show remarkable instant adaptations to the variable environmental challenges they encounter during their adult life, despite having no direct contact with the changing environment until after birth or hatching. The mechanisms by which such non-genetic information is transferred to the developing embryos are largely unknown. Here, we address this question by using a freshwater pond snail ( Lymnaea stagnalis ) as a model system. This snail normally lives in a seasonal climate, and the seasons define its locomotion, feeding, and reproductive behavior. We discovered that the serotonergic system plays a crucial role in transmitting a non-genetic instructive signal from mother to progeny. This maternal serotonin-based signal functions in embryos during a short time window at exclusively early pre-neural developmental stages and modulates the dynamics of embryonic and juvenile growth, feeding behavior, and locomotion. Graphical abstract Teaser Ivashkin et al. reveal that maternally derived serotonin tunes the developmental dynamics and behavior of snail offspring under changing environmental conditions. The balance of intra- and extracellular serotonin exclusively during the non-neural stage of development, as well as serotonylation of proteins, is crucial for the transmission of a serotonin-based non-genetic signal.

Description: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Cheng Li, Yahui Lan, Lianna Schwartz-Orbach, Evgenia Korol, Mamta Tahiliani, Todd Evans, Mary G. Goll The Tet family of methylcytosine dioxygenases (Tet1, Tet2, and Tet3) convert 5-methylcytosine to 5-hydroxymethylcytosine. To date, functional overlap among Tet family members has not been examined systematically in the context of embryonic development. To clarify the potential for overlap among Tet enzymes during development, we mutated the zebrafish orthologs of Tet1 , Tet2 , and Tet3 and examined single-, double-, and triple-mutant genotypes. Here, we identify Tet2 and Tet3 as the major 5-methylcytosine dioxygenases in the zebrafish embryo and uncover a combined requirement for Tet2 and Tet3 in hematopoietic stem cell (HSC) emergence. We demonstrate that Notch signaling in the hemogenic endothelium is regulated by Tet2/3 prior to HSC emergence and show that restoring expression of the downstream gata2b/scl/runx1 transcriptional network can rescue HSCs in tet2/3 double mutant larvae. Our results reveal essential, overlapping functions for tet genes during embryonic development and uncover a requirement for 5hmC in regulating HSC production. Graphical abstract Teaser The Tet proteins comprise a family of dioxygenases that convert 5-methylcytosine to 5-hydroxymethylcytosine. Li et al. identify Tet2 and Tet3 as the major 5-methylcytosine dioxygenases in the zebrafish embryo and uncover an overlapping requirement for Tet2 and Tet3 in hematopoietic stem cell emergence.

Description: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Ann V. Griffith, Thomas Venables, Jianjun Shi, Andrew Farr, Holly van Remmen, Luke Szweda, Mohammad Fallahi, Peter Rabinovitch, Howard T. Petrie T lymphocytes are essential mediators of immunity that are produced by the thymus in proportion to its size. The thymus atrophies rapidly with age, resulting in progressive diminution of new T cell production. This decreased output is compensated by duplication of existing T cells, but it results in gradual dominance by memory T cells and decreased ability to respond to new pathogens or vaccines. Here, we show that accelerated and irreversible thymic atrophy results from stromal deficiency in the reducing enzyme catalase, leading to increased damage by hydrogen peroxide generated by aerobic metabolism. Genetic complementation of catalase in stromal cells diminished atrophy, as did chemical antioxidants, thus providing a mechanistic link between antioxidants, metabolism, and normal immune function. We propose that irreversible thymic atrophy represents a conventional aging process that is accelerated by stromal catalase deficiency in the context of an intensely anabolic (lymphoid) environment. Graphical abstract Teaser Thymic function is essential for maintenance of immunity but decreases with age. Griffith et al. show that stromal deficiency in catalase leads to mitochondrial dysfunction and DNA damage in stromal cells and that atrophy is ameliorated by genetic complementation of catalase or biochemical antioxidants.

Description: Publication date: Available online 6 August 2015 Source: Geoscience Frontiers Author(s): Luca Cocchi, Giuseppe Masetti, Filippo Muccini, Cosmo Carmisciano Since the Tortonian, the geodynamic evolution of the Tyrrhenian Sea has been driven by an eastward roll-back of the entire Apennine subduction system, triggering distinct episodes of back-arc basin formation with spots of oceanic crust. Major structural differences are observed between northern and southern portions of the Tyrrhenian Sea, reflecting two distinct evolution stages of the Ionian slab retreat. In the central portion of the Tyrrhenian Sea, the seafloor morphology is characterised by a set of magmatic intrusions and structural highs associated to an E–W magnetic lineament along the 41st geographical parallel. The Vercelli seamount represents one example of structural highs correlated to Miocene magmatic episodes along the 41st parallel zone. In this study, we discuss the results of new high resolution magnetic data and morphological mapping of the Vercelli seamount acquired during the VER2010 cruise. The seamount represents the relict part of a granitic intrusion emplaced during the Tortonian phase of Tyrrhenian rifting. Tectonic and deep-sea erosive processes have jointly modified the seamount structure that can observed nowadays. Cumulative gradient analysis highlights an asymmetric morphology of the flanks as a result of erosive action of opposite water mass gyres which modelled the southern portion of the seamount. The joint interpretation of magnetic and bathymetric datasets identifies a high magnetized source laying close to the base of the seamount and located in correspondence to a small basin. This structure has been modelled as a post-Tortonian lava sequence emplaced between structural highs in correspondence of N–S elongated flat sedimentary basin. Modelling of new geophysical data highlights the relationship between crustal setting and magnetic evidences of the central Tyrrhenian Sea, providing a new interpretation of the 41st magnetic lineament. Graphical abstract

Description: Publication date: September 2015 Source: Journal of Hydrology: Regional Studies, Volume 4, Part B Author(s): B. Ibrahim, D. Wisser, B. Barry, T. Fowe, A. Aduna Study region Hydrological observation networks in the West African region are not dense and reliable. Furthermore, the few available discharge data often present significant gaps. The Volta basin, the second largest transboundary basin in the region, is a typical example of a basin with inadequate hydrological networks. Study focus In this study, a prediction approach to determine monthly discharge in ungauged watersheds is developed. The approach is based on the calibration of two conceptual models for gauged watersheds and an estimation of models’ parameters from the physical and climatic characteristics of the watersheds. The models’ parameters were determined for each ungauged watershed through two different methods: the multiple linear regressions and the kriging method. The two methods were first validated on five gauged watersheds and then applied to the three ungauged watersheds. New hydrological insights for the region The application of the two hydrological models on the eight watersheds helped to produce relevant monthly runoff and to establish the annual hydrological balances from 1970 to 2000 for both gauged and ungauged watersheds. The developed method in this study could therefore help estimate runoff time series, which are of crucial importance when it comes to design hydraulic structures such as small reservoirs.

Description: Publication date: Available online 6 August 2015 Source: Journal of Rock Mechanics and Geotechnical Engineering Author(s): Manchao He, Guolong Zhu, Zhibiao Guo With the third innovation in science and technology worldwide, China has also experienced this marvelous progress. Concerning the longwall mining in China, the “masonry beam theory” (MBT) was first proposed in the 1960s, illustrating that the transmission and equilibrium method of overburden pressure using reserved coal pillar in mined-out areas can be realized. This forms the so-called “121 mining method”, which lays a solid foundation for development of mining science and technology in China. The “transfer rock beam theory” (TRBT) proposed in the 1980s gives a further understanding for the transmission path of stope overburden pressure and pressure distribution in high-stress areas. In this regard, the advanced 121 mining method was proposed with smaller coal pillar for excavation design, making significant contributions to improvement of the coal recovery rate in that era. In the 21st century, the traditional mining technologies faced great challenges and, under the theoretical developments pioneered by Profs. Minggao Qian and Zhenqi Song, the “cutting cantilever beam theory” (CCBT) was proposed in 2008. After that the 110 mining method is formulated subsequently, namely one stope face, after the first mining cycle, needs one advanced gateway excavation, while the other one is automatically formed during the last mining cycle without coal pillars left in the mining area. This method can be implemented using the CCBT by incorporating the key technologies, including the directional pre-splitting roof cutting, constant resistance and large deformation (CRLD) bolt/anchor supporting system with negative Poisson’s ratio (NPR) effect material, and remote real-time monitoring technology. The CCBT and 110 mining method will provide the theoretical and technical basis for the development of mining industry in China.

Description: Publication date: Available online 6 August 2015 Source: Journal of Rock Mechanics and Geotechnical Engineering Author(s): Chun’an Tang, Lianchong Li, Nuwen Xu, Ke Ma For high-steep slopes in hydropower engineering, damage can be induced or accumulated due to a series of human or natural activities, including excavation, dam construction, earthquake, rainstorm, rapid rise or drop of water level in the service lifetime of slopes. According to the concept that the progressive damage (microseismicity) of rock slope is the essence of the precursor of slope instability, a microseismic monitoring system for high-steep rock slopes is established. Positioning accuracy of the monitoring system is tested by fixed-position blasting method. Based on waveform and cluster analyses of microseismic events recorded during test, the tempo-spatial distribution of microseismic events is analyzed. The deformation zone in the deep rock masses induced by the microseismic events is preliminarily delimited. Based on the physical information measured by in situ microseismic monitoring, an evaluation method for the dynamic stability of rock slopes is proposed and preliminarily implemented by combining microseismic monitoring and numerical modeling. Based on the rock mass damage model obtained by back analysis of microseismic information, the rock mass elements within the microseismic damage zone are automatically searched by finite element program. Then the stiffness and strength reductions are performed on these damaged elements accordingly. Attempts are made to establish the correlation between microseismic event, strength deterioration and slope dynamic instability, so as to quantitatively evaluate the dynamic stability of slope. The case studies about two practical slopes indicate that the proposed method can reflect the factor of safety of rock slope more objectively. Numerical analysis can help to understand the characteristics and modes of the monitored microseismic events in rock slopes. Microseismic monitoring data and simulation results can be used to mutually modify the sensitive rock parameters and calibrate the model. Combination of microseismic monitoring and numerical simulation provides a more objective basis for the numerical model and parameters and a solid mechanical foundation for the microseismic monitoring.

Description: Publication date: Available online 8 August 2015 Source: FEBS Open Bio Author(s): Jonghwan Lee, Do Won Hwang, Seung U Kim, Dong Soo Lee, Yong Seung Lee, Hyejung Heo, Bahy A. Ali, Abdulaziz A. Al-Khedhairy, Soonhag Kim Evaluation of the function of microRNAs (miRNAs or miRs) through miRNA expression profiles during neuronal differentiation plays a critical role not only in identifying unique miRNAs relevant to cellular development but also in understanding regulatory functions of the cell-specific miRNAs in living organisms. Here, we examined the microarray-based miRNA expression profiles of G2 cells (recently developed human neural stem cells) and monitored the expression pattern of known neuron-specific miR-9 and miR-124a during neuronal differentiation of G2 cells in vitro and in vivo . Of 500 miRNAs analyzed by microarray of G2 cells, the expression of 90 miRNAs was significantly increased during doxycycline-dependent neuronal differentiation of G2 cells and about 60 miRNAs showed a gradual enhancement of gene expression as neuronal differentiation progressed. Real-time PCR showed that expression of endogenous mature miR-9 was continuously and gradually increased in a pattern dependent on the period of neuronal differentiation of G2 cells while the increased expression of neuron-specific mature miR-124a was barely observed during neurogenesis. Our recently developed miRNA reporter imaging vectors (CMV/Gluc/3×PT_miR-9 and CMV/Gluc/3×PT_miR-124a) containing Gaussia luciferase, CMV promoter and three copies of complementary nucleotides of each corresponding miRNA showed that luciferase activity from CMV/Gluc/3×PT_miR-9 was gradually decreased both in vitro and in vivo in G2 cells induced to differentiate into neurons. However, in vitro and in vivo bioluminescence signals for CMV/Gluc/3×PT_miR-124a were not significantly different between undifferentiated and differentiated G2 cells. Our results demonstrate that biogenesis of neuron-specific miR-124a is not necessary for doxycycline-dependent neurogenesis of G2 cells.

Description: Publication date: Available online 7 August 2015 Source: FEBS Open Bio Author(s): Tao Liu, Xuan-Cheng Fang, Zhen Ding, Ze-Gan Sun, Li-Ming Sun, Yi-Lian Wang Inflammatory markers have been proposed to predict clinical outcomes in many types of cancers. The purpose of this study was to explore the influence of the lymphocyte-to-monocyte ratio (LMR) on clinical prognosis of patients with osteosarcoma. This study collected 327 patients who underwent surgical treatment for osteosarcoma during the period 2006 2010. LMR was calculated from pre-operative peripheral blood cells counts. The optimal cut-off value of LMR was determined based on receiver operating characteristic curve analysis. Overall survival (OS) and event free survival (EFS) was plotted using the Kaplan–Meier method and evaluated by the log-rank test. A predictive model was established to predict clinical prognosis for OS, and the predictive accuracy of this model was determined by concordance index (c-index). Our results showed that young age, elevated alkaline phosphatase, metastasis at diagnosis, chemotherapy, lymphocyte and monocyte counts were significantly associated with LMR. Low LMR was associated with shorter OS and EFS ( P 〈 0.001), and was an independent predictor of both OS and EFS (HR=1.72, 95% CI=1.14-2.60, P = 0.010; HR=1.89, 95% CI=1.32-2.57, P = 0.009). The nomogram performed well in the prediction of overall survival in patients with osteosarcoma (c-index 0.630). In conclusion, low pre-operative LMR is associated with a poor prognosis in patients suffering from osteosarcoma. A prospective study is warranted for further validation of our results.

Description: Publication date: Available online 7 August 2015 Source: Geoscience Frontiers Author(s): R.M. Lobatskaya, I.P. Strelchenko The capabilities of GIS in modeling fault patterns are explored for Irkutsk city in East Siberia with implications for ground stability. The neotectonic structure of the area is visualized in three dimension (3D) taking into account fault dips, using the ArcGIS, GlobalMapper and Paradigm Geophysical packages. The study area is divided into blocks of different size classes according to the length-based ranks of the bounding faults, which are of five classes distinguished with the equal interval method. The blocks show different deformation patterns, with different densities and strikes of crossing and bounding faults. The data are statistically processed using GIS to estimate the deformation degrees of blocks in arbitrary units per square kilometer using the attributes of rank and crossing/bounding position of faults and the size of blocks. The deformation degrees are then compared with available estimates of ground stability measured as a score of points corresponding to destabilizing factors. Although the comparison generally confirms some linkage between the deformation degree of blocks and their ground stability, the correlation is intricate and ambiguous. In order to enhance the advantages of GIS in building and analyzing 3D models of fault patterns for estimating ground stability and mitigating geological hazards, it is expected in the future to proceed from the reported initial step of visualization to more advanced analysis. Graphical abstract

Description: Publication date: Available online 12 August 2015 Source: Journal of Rock Mechanics and Geotechnical Engineering Author(s): Levan Japaridze In this study, the interaction between cylindrical specimen made of homogeneous, isotropic, and linearly elastic material and loading jaws of any curvature is considered in the Brazilian test. It is assumed that the specimen is diametrically compressed by elliptic normal contact stresses. The frictional contact stresses between the specimen and platens are neglected. The analytical solution starts from the contact problem of the loading jaws of any curvature and cylindrical specimen. The contact width, corresponding loading angle (2 θ 0 ), and elliptical stresses obtained through solution of the contact problems are used as boundary conditions for a cylindrical specimen. The problem of the theory of elasticity for a cylinder is solved using Muskhelishvili’s method. In this method, the displacements and stresses are represented in terms of two analytical functions of a complex variable. In the main approaches, the nonlinear interaction between the loading bearing blocks and the specimen as well as the curvature of their surfaces and the elastic parameters of their materials are taken into account. Numerical examples are solved using MATLAB to demonstrate the influence of deformability, curvature of the specimen and platens on the distribution of the normal contact stresses as well as on the tensile and compressive stresses acting across the loaded diameter. Derived equations also allow calculating the modulus of elasticity, total deformation modulus and creep parameters of the specimen material based on the experimental data of radial contraction of the specimen.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Sergei A. Manakov, Dubravka Pezic, Georgi K. Marinov, William A. Pastor, Ravi Sachidanandam, Alexei A. Aravin In developing male germ cells, prospermatogonia, two Piwi proteins, MILI and MIWI2, use Piwi-interacting RNA (piRNA) guides to repress transposable element (TE) expression and ensure genome stability and proper gametogenesis. In addition to their roles in post-transcriptional TE repression, both proteins are required for DNA methylation of TE sequences. Here, we analyzed the effect of Miwi2 deficiency on piRNA biogenesis and transposon repression. Miwi2 deficiency had only a minor impact on piRNA biogenesis; however, the piRNA profile of Miwi2 -knockout mice indicated overexpression of several LINE1 TE families that led to activation of the ping-pong piRNA cycle. Furthermore, we found that MILI and MIWI2 have distinct functions in TE repression in the nucleus. MILI is responsible for DNA methylation of a larger subset of TE families than MIWI2 is, suggesting that the proteins have independent roles in establishing DNA methylation patterns. Graphical abstract Teaser Two components in the piRNA pathway, MILI and MIWI2, were proposed to work in a linear hierarchy to generate piRNAs and methylate transposon sequences. Manakov et al. now profile transcription and methylation patterns in Mili and Miwi2 mutants and demonstrate that these proteins are in part functionally independent.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Sang Woo Seo, Donghyuk Kim, Richard Szubin, Bernhard O. Palsson Three transcription factors (TFs), OxyR, SoxR, and SoxS, play a critical role in transcriptional regulation of the defense system for oxidative stress in bacteria. However, their full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OxyR, SoxR, and SoxS regulons in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 68 genes in 51 transcription units (TUs) belong to these regulons. Among them, 48 genes showed more than 2-fold changes in expression level under single-TF-knockout conditions. This reconstruction expands the genome-wide roles of these factors to include direct activation of genes related to amino acid biosynthesis (methionine and aromatic amino acids), cell wall synthesis (lipid A biosynthesis and peptidoglycan growth), and divalent metal ion transport (Mn 2+ , Zn 2+ , and Mg 2+ ). Investigating the co-regulation of these genes with other stress-response TFs reveals that they are independently regulated by stress-specific TFs. Graphical abstract Teaser Seo et al. reconstruct OxyR, SoxR, and SoxS transcriptional regulatory networks under oxidative stress in E. coli and expand their roles to include direct activation of amino acid biosynthesis, cell wall synthesis, and divalent metal ion transport. These processes are independently regulated by TFs specific to oxidative stress.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Anders S. Hansen, Erin K. O’Shea Although the relationship between DNA cis -regulatory sequences and gene expression has been extensively studied at steady state, how cis -regulatory sequences affect the dynamics of gene induction is not known. The dynamics of gene induction can be described by the promoter activation timescale (AcTime) and amplitude threshold (AmpThr). Combining high-throughput microfluidics with quantitative time-lapse microscopy, we control the activation dynamics of the budding yeast transcription factor, Msn2, and reveal how cis -regulatory motifs in 20 promoter variants of the Msn2-target-gene SIP18 affect AcTime and AmpThr. By modulating Msn2 binding sites, we can decouple AmpThr from AcTime and switch the SIP18 promoter class from high AmpThr and slow AcTime to low AmpThr and either fast or slow AcTime. We present a model that quantitatively explains gene-induction dynamics on the basis of the Msn2-binding-site number, TATA box location, and promoter nucleosome organization. Overall, we elucidate the cis- regulatory logic underlying promoter decoding of TF dynamics. Graphical abstract Teaser Cells control gene expression in part by regulating the dynamics of transcription-factor activity. Hansen and O’Shea investigate the cis -regulatory logic underlying promoter decoding of transcription-factor dynamics for 20 promoter variants and reveal that two properties characterizing the gene expression response—threshold and activation timescale—can be decoupled.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): David Lau, C. Peter Bengtson, Bettina Buchthal, Hilmar Bading The health of neurons is critically dependent on the relative signaling intensities of survival-promoting synaptic and death-inducing extrasynaptic NMDA receptors. Here, we show that BDNF is a regulator of this balance and promotes neuroprotection by reducing toxic NMDA receptor signaling. BDNF acts by initiating synaptic NMDA-receptor/nuclear-calcium-driven adaptogenomics, leading to increased expression of inhibin β- A ( inhba ). Inhibin β- A (its homodimer is known as activin A) in turn reduces neurotoxic extrasynaptic NMDA-receptor-mediated calcium influx, thereby shielding neurons against mitochondrial dysfunction, a major cause of excitotoxicity. Thus, BDNF induces acquired neuroprotection by enhancing synaptic activity and lowering extrasynaptic NMDA receptor death signaling through a nuclear calcium- inhibin β- A pathway. This process, which confers protection against ischemic brain damage in a mouse stroke model, may be compromised in Huntington’s disease, Alzheimer’s disease, or aging-related neurodegenerative conditions that are associated with reduced BDNF levels and/or enhanced extrasynaptic NMDA receptor signaling. Graphical abstract Teaser Lau et al. show that BDNF-induced neuroprotection is mediated by synaptic NMDA-receptor-dependent nuclear calcium signals activating transcription of inhibin β-A (activin A). Activin A in turn reduces toxic extrasynaptic NMDA-receptor-mediated calcium influx, shields neurons from mitochondrial dysfunction, and protects against stroke-induced brain damage.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Corina E. Antal, Julia A. Callender, Alexandr P. Kornev, Susan S. Taylor, Alexandra C. Newton The signaling output of protein kinase C (PKC) is exquisitely controlled, with its disruption resulting in pathophysiologies. Identifying the structural basis for autoinhibition is central to developing effective therapies for cancer, where PKC activity needs to be enhanced, or neurodegenerative diseases, where PKC activity should be inhibited. Here, we reinterpret a previously reported crystal structure of PKCβII and use docking and functional analysis to propose an alternative structure that is consistent with previous literature on PKC regulation. Mutagenesis of predicted contact residues establishes that the Ca 2+ -sensing C2 domain interacts intramolecularly with the kinase domain and the carboxyl-terminal tail, locking PKC in an inactive conformation. Ca 2+ -dependent bridging of the C2 domain to membranes provides the first step in activating PKC via conformational selection. Although the placement of the C1 domains remains to be determined, elucidation of the structural basis for autoinhibition of PKCβII unveils a unique direction for therapeutically targeting PKC. Graphical abstract Teaser Kinase autoinhibition is essential for suppressing signaling when appropriate signals are absent. Antal et al. reinterpret a protein kinase C βII crystal structure to show that its Ca 2+ -sensing C2 domain autoinhibits by binding over the kinase domain, unveiling an interface that can potentially be therapeutically targeted to enhance or restrain activity.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Yoosoo Yang, Jaewook Kim, Hye Yun Kim, Nayeon Ryoo, Sejin Lee, YoungSoo Kim, Hyewhon Rhim, Yeon-Kyun Shin Alzheimer’s disease (AD) is closely associated with synaptic dysfunction, and thus current treatments often aim to stimulate neurotransmission to improve cognitive impairment. Whereas the formation of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex is essential for synaptic transmission, the correlation between SNAREs and AD neuropathology is unknown. Here, we report that intracellular amyloid-β (Aβ) oligomers directly inhibit SNARE-mediated exocytosis by impairing SNARE complex formation. We observe abnormal reduction of SNARE complex levels in the brains of APP/PS1 transgenic (TG) mice compared to age-matched wild-types. We demonstrate that Aβ oligomers block SNARE complex assembly through the direct interaction with a target membrane (t)-SNARE syntaxin 1a in vitro. Furthermore, the results of the in vitro single-vesicle content-mixing assay reveal that Aβ oligomers inhibit SNARE-mediated fusion pores. Thus, our study identifies a potential molecular mechanism by which intracellular Aβ oligomers hamper SNARE-mediated exocytosis, likely leading to AD-associated synaptic dysfunctions. Graphical abstract Teaser The role of Aβ in cognitive impairment in Alzheimer’s disease still remains elusive. Yang et al. now show that Aβ oligomers bind to syntaxin 1a to impair SNARE complex formation to inhibit exocytosis. The resulting inhibition of neurotransmission could therefore lead to cognitive impairments.

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Behnam Nabet, Pilib Ó Broin, Jaime M. Reyes, Kevin Shieh, Charles Y. Lin, Christine M. Will, Relja Popovic, Teresa Ezponda, James E. Bradner, Aaron A. Golden, Jonathan D. Licht Unrestrained receptor tyrosine kinase (RTK) signaling and epigenetic deregulation are root causes of tumorigenesis. We establish linkage between these processes by demonstrating that aberrant RTK signaling unleashed by oncogenic HRas G12V or loss of negative feedback through Sprouty gene deletion remodels histone modifications associated with active typical and super-enhancers. However, although both lesions disrupt the Ras-Erk axis, the expression programs, enhancer signatures, and transcription factor networks modulated upon HRas G12V transformation or Sprouty deletion are largely distinct. Oncogenic HRas G12V elevates histone 3 lysine 27 acetylation (H3K27ac) levels at enhancers near the transcription factor Gata4 and the kinase Prkcb, as well as their expression levels. We show that Gata4 is necessary for the aberrant gene expression and H3K27ac marking at enhancers, and Prkcb is required for the oncogenic effects of HRas G12V -driven cells. Taken together, our findings demonstrate that dynamic reprogramming of the cellular enhancer landscape is a major effect of oncogenic RTK signaling. Graphical abstract Teaser Aberrant receptor tyrosine kinase signaling mediated by oncogenic Ras or loss of Sprouty promotes tumorigenesis. Nabet et al. find that unrestrained receptor tyrosine signaling driven by these lesions alters distinct super-enhancers, transcription factors, and target genes. Gata4 and Prkcb are identified as mediators of the oncogenic program upon Ras transformation.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Himawan Bayu Patriadi, Mohd. Zaini Abu Bakar, Zahri Hamat As a new concept, the definition of human security has been widely contested. It relates to the issues of human security ‘for whom’, ‘from what’ and by ‘what means’. Dealing with the first issue, scholars generally agree that the focus of it is protecting the individual rather than the state's security. But, dealing with two other central issues, scholars seem to hardly agree upon. This paper deals more with the third question focusing on pesantren (a traditional Islamic boarding school) that largely exists in Indonesia. One of the reasons is, as having religious-based local wisdoms, the pesantren has long time concerned with human security without necessarily trapped by either ‘for whom’ and ‘from what’ debates. The second reason refers to its social mission of securing people which seems to be valuable in balancing the continuing hegemonic discourse of putting the state as the ultimate reference of security. The last is related to the contemporary challenge for human security. As Acharya indicates, currently, securitization of religion is politically sensitive due to the fact that it closely related to or even being the basis of the new global politics identity. In this sense, I argue that the role of religious-based institution, particularly the pesantren , should not necessarily be seen as something incompatible with human security. Having its good practices, it may even suggest a new perspective of understanding human security by making use of religious-based local wisdom concept. This research used qualitative methodology supported by ethnography approach. Though some data from secondary sources were present, most supporting data were collected through various interviews to digging up first-hand perspectives.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): A. Trihartono, N. Viartasiwi This research investigates how civil society has contributed to human security, especially in the context of maintaining peace in the post-conflict society of Indonesia. Unlike former studies that have paid the most attention to the fundamental role of the state actors, this study emphasizes the importance of civil society as a non-state actor. This research pays attention, mainly but not exclusively, to the case of society in the post-conflict of Muslims and Christians in Poso, Central Sulawesi, Indonesia. The finding suggests that the role of civil society is evolving and essential in creating favorable conditions for maintaining peace, particularly in breaking the so-called cycle of violence. This study demonstrates that the emerging role of non-states actor, quietly but significantly, is supportive and cannot be overlooked in post-conflict society. Hence, providing space for further discussion of the role of non-states actors in backing up sustainable peace is indispensable. As a result, civil society has also been on the frontline in developing human security.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Tahra Talib Al-Rashdi, Hameed Sulaiman Water for irrigation and cultivable soil is very precious and more crucial for sustainable farming in arid environments. Sohar Industrial Area in Oman is the major industrial zone operating in a confined area closer to agriculture farms. This study aims to assess the physiochemical parameters in soils and the water used for irrigation in these farms. Samples were collected from 8 farms, 4 each from 2 sites (2 and 4 km from the industrial zone). Results show that the salinity of irrigation water varies from one farm to the other, where the closest farms are more affected. Most of the farm soils are saline in nature with Sodium adsorption ratio (SAR) of less than seven. The soil salinity is higher than water salinity with magnesium and chloride as predominant cation and anion respectively. In general, the vital water and soil parameters are within the prescribed limits for the existing crop cultivation.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Sanz Grifrio Limin, Hiroki Oue, Yoshinobu Sato, I Wayan Budiasa, Budi Indra setiawan Partitioning of gross rainfall into throughfall, stemflow, and rainfall interception were assessed in clove plantation during rainy season in Saba River Basin, Bali, Indonesia. Canopy openness did not appear to be the main factor that affected the amount of throughfall and stemflow. Rainfall partitioning showed that the throughfalltookmajor contribution in gross rainfall, while stemflow only took small portion in gross rainfall. Managed clove plantation gave slightly larger interception rate than natural forest in Saba River Basin. Cultivation method improvement is required to improve the hydrologic services of clove plantation.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Reny Nadlifatin, Mohammad Razif, Shu-Chiang Lin, Satria Fadil Persada, Prawira Fajarindra Belgiawan This paper explores citizens’ participation intention on environmental impact assessment (EIA) process through behavioral analysis perceptions. Perceived government support, subjective norms, and perceived environmental concern factors are used as the predictor model of behavior intention. The result shows that 40 percent of citizens intend to participate in the EIA process. Another finding reveals the subjective norms as a dominant factor to the participation intention. This situation can be used as a consideration to emphasize the role of social aspect to encourage the citizens on the EIA participation.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Kassahun Y. Kebede, Toshio Mitsufuji, Mohammad T. Islam The diffusion of renewable energy technologies (RETs) has been progressing very slowly in global scope, particularly in developing countries where the diffusion challenges for renewable are greater. Among potential actors in the promotion and diffusion of rural-based renewable energy innovations, NGOs and NPOs have been mentioned as promising actors. However, empirical studies that show the role of the actors and the way they can be system builders by diffusing existing technologies have been very rare. This paper discusses the practices of an NGO in Ethiopia (Solar Energy Foundation) and an NPO in Bangladesh (Grameen Shakti) and shows how local technological innovation systems can be built bykey actors in the context of developing countries. The studysheds light on the process of system building for accelerated diffusion of RETs in the context of developing countries. Using a theoretical framework, we compared the approach, technology adoption trend (solar home systems diffusion), and common challenges facing both actors in their respective countries. The two empirical cases which are in different geographical contexts provided lessons on thesimilarities and differences of system building practices and emerging innovation systems for diffusion of RETs in developing countries.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Jeffrey Kucharski, Hironobu Unesaki Modern energy systems are increasingly complex and face ever-changing demands. As energy markets become increasingly global and interdependent, the issues affecting energy systems have also increased in number and complexity. Geopolitical events, natural disasters, severe weather, public acceptance of energy activities, increasingly automated and integrated energy systems, and the impact of climate change are just some of the factors impacting on energy systems. Consequently, the assessment of risks, threats and vulnerabilities in energy systems has become more urgent and more challenging. Studies of energy security have been criticized on various grounds, including that they employ a narrow conception of energy security and rarely use a systematic approach. Various conceptual models have been proposed to evaluate energy security but are usually limited to the effect of supply disruptions. There are few examples of models that clearly define the broad range of risks faced by contemporary, complex energy systems. This paper seeks to address these issues by taking a broader, policy-oriented approach to the factors affecting modern energy systems. We employ a complex systems perspective in conceptualizing the energy system and a more comprehensive approach to identifying risks, threats and vulnerabilities for energy security assessment purposes.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Erni Johan, Toshio Yamada, Moses Wazingwa Munthali, Ponyadira Kabwadza-Corner, Hiromichi Aono, Naoto Matsue Adsorption experiments of Cs + were carried out by using two natural zeolites, namely mordenite and clinoptilolite. The same experiments were also conducted by using synthetic zeolite A, synthetic zeolite X, and artificial zeolite Na-P1 as references. The purpose of this study was to investigate the potential of natural zeolites on the adsorption of radioactiveCs + . The results indicated that although cation exchange capacity of the natural zeolites was much lower compared to the synthetic and artificial zeolites, the adsorption capacity of Cs + was much greater than the synthetic and artificial zeolites. The order of the adsorption capacity of Cs + was mordenite>clinoptilolite> Na-P1 >> zeolite A > zeolite X. It indicates that natural zeolites are promising materials in the removal of radioactive Cs + .

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Obie Farobie, Nur Hasanah, Yukihiko Matsumura Non-catalytic biodiesel production in supercritical methanol (SCM) and supercritical ethanol (SCE) was conducted using spiral reactor. The experimental data were used to create artificial neural network (ANN) model in order to predict biodiesel yield. The results showed that ANN was the powerful tool to estimate biodiesel yield that was proven by a high value (0.9980 and 0.9987 in SCM and SCE, respectively) of R and a low value (2.72×10 -5 , 1.68×10 -3 , and 2.30×10 -3 in SCM and 2.24×10 -4 , 4.49×10 -4 , and 5.03×10 -4 in SCE for training, validation, and testing, respectively) of mean squared error (MSE). For biodiesel production in SCM, the highest yield of biodiesel was determined of 1.01 mol/mol corresponding to the actual biodiesel yield of 1.00 mol/mol achieved at 350 °C, 20 MPa within 10 min; whereas, for SCE, the highest yield of biodiesel was observed of 0.97 mol/mol corresponding to the actual biodiesel yield of 0.96 mol/mol achieved at 400 °C, 20 MPa within 25 min.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Dewa Ayu Putu Eva Wishanti Energy security is positioned during the 21 st century as one of the worldwide development policy focal points, mainly The Millennium Development Goals, which timeline ends in 2015. Despite its rich energy resources, Indonesia has failed to provide equal access to energy as a mean to eradicate poverty. This implicates on the widening national developmental gaps among provinces, namely the agriculture and industrial sectors, the two of major sectors to provide the largest employment percentage in the country. Otherwise, the government still struggles to enforce the renewable energy policies into practices, and the policies of exporting oil and coal are still dominant as the major income of the country. It results in energy poverty when many poor Indonesian people have very limited access to energy.This article seeks to measure the Indonesian government concern upon energy crisis and its impact on poverty eradication, by focusing on the gaps of energy access as the main indicator to measure energy poverty in Indonesia. By utilizing the national gap analysis, this article urges the needs of investment in small-scale energy development. The investment may collaborate the role of government energy policies with the international private sectors to perform technology proliferation and access. This article also proposes the small-scale energy development as a focus of post-2015 development agenda.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Andi Dirpan, Yoshio Hikida This study investigated the effect of various sizes of citrus on their resistance ( R ) to gas diffusion. The purpose of the investigation was to compare the value of R in 3 different sizes of citrus. To measure the R to gas diffusion in citrus, the study applied ethane efflux method. This is the method which the evolution phenomenon of ethane was measured by applying Fick's Law. The results showed that R of ethane (C 2 H 6 ) gas was dependent on citrus size. It can be seen that the larger the size of the fruit, the greater the R value, i.e. M size had R =4.33x10 5 s.m -1 , L size had R =4.99 x10 5 s.m -1 and 3L size had R =6.84 x10 5 s.m -1 .This finding indicated that the fruit sizes can be considered as an important factor in designing storage control atmosphere (CA) condition for citrus.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Yuda Cahyoargo Hariadi, Arry Y. Nurhayati, Sigit Soeparjono, Idam Arif Salinity is a constraint to the sustainable agricultural production. Increasing salinity is found to inhibit growth, height, and total of leaf area ofrice from vegetative to generative stages. Electrophysiologically, increasing salinity and exposure duration reduce the PD of the plant leaves. The screening focuses on the response of six varieties of rice ( Oryza sativa ) grown in a glasshouse subjected to five different salinity levels [0 mM; 50 mM; 100 mM; 150 mM and 200 mM of NaCl]. Death occurred at 200 mM of NaCl though all six varieties were tolerant to 100mMofNaClduring 4 weeks of application, and four varieties of rice were found to be sensitive to salinity around 150 mM of NaCl during 3 weeks of application.In turn, this study will help increase the security of the major food demand consumed by around 90% of Indonesian and protect the livelihood sustainability of around 67% Indonesian farmers, and help reduce starvation risk of a community due to salinity effects.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): I. Nengah Suwastika, Muslimin, Rifka, Nurul Aisyah, Rahmansyah, Mutmainah, Yoko Ishizaki, Zainuddin Basri, Takashi Shiina Theobroma cacao L. is a commercial tree derivate chocolate, which is originally from tropical regions of Central and South America. Currently, cacao is distributed throughout warmer climates in South and Central America, Africa, and South East Asia including Indonesia. Sulawesi Island of Indonesia has contributed significantly on cacao bean production over more than a decade. Intensive and extensive developments of this plant have been progressively done. One of these steps is the introduction of various new superior cultivars/clones. In current status, due to introduction of numerous cultivars and clones, it raises the variability of cacao trees on the field and derivate products from it. However, screening based on genotype and phenotype properties is urgently elucidated. In this paper, we report the variation of distinguishable pot morphology and genetic variation based on SSR marker from several clones, collected from Central Sulawesi farms. Among the samples could be characterized based on pot performance including; shape, size, bean properties, etc. Genotyping was done by using SSR marker. The outcome clearly shows that the polymorphism among the samples indicates high evolution rate on cacao trees over Sulawesi Island.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Eky Yenita Ristanti, Wanglin Yan This study is aimed at synthesizing the social value-based model of Shimokawa, Hokkaido with economic value-based model of Hita, Oita to implement woody biomass renewable energy business in Japan. These two areas were chosen to highlight their contradictory economic and social situations in utilizing their abundant forest resources. The research uses an in-depth interview of stakeholders involved in the woody biomass project in both regions. The role of woody biomass in Hita and neighboring areas deals with renewable energy business, while in Shimokawa it handles an aging society issue and sustainability. By 2013, Hita has two woody biomass power plants operated, which utilized a total of 160,000 tons/year wood chips. Shimokawa promotes sustainable life by implementing Forest Future City model in which resources, society, and industry are integrated to achieve quality life.