ALBERT

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.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Puji Harsanto Mt.Merapi is one of the most active volcanoes in Indonesia. Some of the rivers that the origin is located at Mt.Merapi have a large amount of sediment resources after eruption in October-November 2010. The total volume of sediment is estimated at 130 million m 3 .The deposited sediment flows to the downstream area as a debris or bed load transport in high density. Few studies considered downstream change along volcanic rivers due to a high density of bed load transport. Using numerical simulation, the impact of high concentration of bed-load transport is applied in Progo River, Yogyakarta, Indonesia. The results show that the high bed-load transport rate increases the mid-channel bar grow rate and the bed degradation near the bank toe. The increase of bed degradation is an important parameter of bank erosion process. Furthermore, the bed morphology on the downstream after 2010 eruption of Mt. Merapi should be considered intensively.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Dwi Astiani, Mujiman, Muhammad Hatta, Hanisah, Firda Fifian Kalimantan peatland spans ∼5.9million ha (∼11% of Kalimantan's total terrestrial land area) as a part ofIndonesian peatlands, covers∼21 million ha, contains∼57.8 Gtof terrestrial carbon. Land cover change of peatland forest results in significant sources CO 2 emissions. Thus, we identified to estimate carbon emissions generated by crop land and ex burnt activities in Kalimantan's peatlands degraded forest.Soil CO 2 respiration was measured under four of the most prominent land cover and annual agricultural crops on 4-5 year post fire (fern, corn, pineapple) and newly burnt areas in West Kalimantan peatlands. Measurements were obtained from Licor 8100 and gatheredby monthly assessments. Among the land cover types showed different meanmonthly CO 2 fluxes.Soil CO 2 respiration on newly burnt peatland, pineapple plantation and fern covered showed the highest and not significantly different among them. Cornsmall-scale plantation soil respired the lowest and significantly different from the other three land covers. Dry vs. rainy month comparisons show huge different (>50%) monthly CO 2 fluxes rate. Each land cover type has distinctive peat environmental factors that significantly affect CO 2 respiration. Theresult indicates that each crop/cover types generate different level site factors, which affect different level of peat CO 2 rates. The regression models of site factors measured for each specific land cover can be applied to obtain better estimate CO 2 respiration rates of degraded peatland and agricultural crop cover types. Moreover, it is able to be applied as a baseline for degraded peatland management and CO 2 emission mitigation.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Dina Oktavia, Yadi Setiadi, Iwan Hilwan Heath forest is a restricted forest ecosystem in the world. In Indonesia, heath forest degradation caused by tin mining activity on Belitung Island emerges biodiversity lost and soil properties lost. In fact, they play important role as main aspect for rehabilitiation. This study aims to describe soil properties and vegetation in heath forest and two different ages of tin mined land. The result shows thatin 3 year tailing contains very high amount of sand, low organic matter, low CEC which effect to desertification that hindered plant to grow. Indeed, low organic matter affects low water absorbtion. Meanwhile, 130 year tailing results lower amount of sand than 3 year tailing. Adequate organic matter closes to organic matter in the forest and appropriate CEC. Soil development in tin tailing soil takeshundreds years to slightly improve naturally. Several soil amendments could be implemented to improve sandy soil, such by adding organic matterial, following with polymer fertilizer. Heath forest restorationby natural succession approach should select local species which well adapted as pioneer and apply seedbank from forest floor as seed source of native species.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Wiwik Ekyastuti, Tri Rima Setyawati Bioaccumulation of mercury is one of the reclamation methods in ex-gold mining areas. Mercury-resistant bacteria canbe used as a mercury bioaccumulation agent. The previous study in Mandor District West Kalimantan has collected four mercury-resistant bacteria from 62 samples with isolates code: HgTA1, HgTL2, HgRL and HgRA. The purpose of this study is to identify and verify the in vitro effectiveness ofthese four mercury-resistant bacteria. Identification of the bacteria is performed using16SrRNAsequencinganalysis, while the in vitro effectiveness test of the bacteriais done by using Canstein's selective media.The results show that the identification of bacterial isolates finds that HgTA1 and HgTL2 are Bacillus subtilis , HgRL is Burkholderia cepacia , and HgRA is Burkholderia cenosepacia . These three species of bacteria belong to the class of bacteria that are resistant to extreme conditions. Thus, these bacteria have anability toaccumulatemercury. Meanwhile, based on the test results of colony growth, detoxification abilities, mercury accumulation and bioaccumulation levels,three out of the four bacterial isolates are proven to be effective and superior to accumulate mercury i.e. HgRA, HgTA1 and HgTL2 isolates. Furthermore, these three isolates can be used as bioacculation agents of mercury-contaminated soil.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Aisyah Abu Bakar, Mariana Mohamed Osman, Syahriah Bachok, Mansor Ibrahim, Mohd Zin Mohamed The purpose of this paper is to explore relation between wellbeing and sustainability in an attempt to establish theoretical concept for sustainable wellbeing. Over the years, growing number of researches seek to understand and reason with factors that influence and constitute wellbeing and its potential synergy with sustainability. Recent studies have highlighted that factors constituting wellbeing do not necessarily indicate sustainability. Despite sustainability, studies share the same aim that is to improve wellbeing. The distinction between sustainability and wellbeing is clear. Sustainability is more of a future-oriented concept, while wellbeing accounts for present condition. Consequently, wellbeing indicators fail to capture issues, such as inequalities, climate change, scarcity of natural resources and many others. Malaysia Wellbeing Report 2014 established 14 components of wellbeing that constituted under economic and social wellbeing. In Malaysia Wellbeing Report 2014, environment and family institutions indexes correlated negatively with national economic growth. Social participation, public safety and health indexes also had weak positive correlation with the national economic growth. Two important components in sustainability are awareness and participation. Ethical and moral knowledge, as well as environmental responsibilities, are among obligations owed to as far as distant strangers at a distant time and space. Thus, sustainable wellbeing encompasses interconnectedness with people and interconnectedness with nature. Therefore, the discovery of synergy between wellbeing and sustainability involve not only measuring human capital but also the contribution of their conscious decisions to the wellbeing of the future. The paper summarized how reconciling wellbeing and sustainability unlocks opportunities for better and all-inclusive indicators for sustainable wellbeing.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Vevin S. Ardiwijaya, Tresna P. Sumardi, Emirhadi Suganda, Yuswanda A. Temenggung In the urban sustainability context, there is a growing concern about social, economic, and environmental costs of sprawling urban development patterns.Idle landis one indicator of that sprawl. This paper aims to investigate the relation of urban physical growth to the expansion of idle land and its effects to the urban environment sustainability. This paper also examines the land rejuvenation as the method to manage the growth of idle lands in urban areas. This paper takes Bandung Metropolitan Area (BMA), one of the metropolitan areas in Indonesia that has basin shape restricted to the urban physical expansion, as a case study. This paper uses system dynamic approach in simulating the behaviour of urban physical growth, the idle land expansions, and their effects to the urban carrying capacity. This research finds that the urban achieved more sustainable from the potential management of physically vacant lands, abandoned buildings, critical land management, increasing revenue, and reduced conflict. The simulation result also finds that BMA will not be sustainedwhen the population grows and continuously occupies the preservation and conservation lands (PCL) in outskirt as urban carrying capacity. It is especially in 2051 when PCLwill be reduced and continuously degrade under 30% of green area as spatial planning requirement, unless the rejuvenation of the idle lands is implemented as the interventions to manage this sprawl urban areas.By using idle land rejuvenation, urban will be more sustainable andpeople could live in high quality of urban environment.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Lina Tri M. Astuti, Prijono Tjiptoherijanto, Herman Haeruman, Raldi Koestoer The core goal of the SDGs is to achieve public welfare through holistic approaches and processes (UN, 2012). One of the objectives of SDGs is cities and human settlements inclusive safe, resilient and sustainable. The ability of individuals and government in providing a decent housing could be considered as an important factor for sustainable housing environment. On the other hand, economic growth in urban areas could lead to the urbanization in urban area and migration in the hinterland area to find a shelter location. It maytrigger the improper land utilizations.Urbanization puts a pressure on limited land resources, and, in turn, may have a negative impact on well-being sustainability. House quality could form the housing profile. The adequate housing profile reflects a quality of life, and quality of life itself reflects the well-being as well. This study proposes an estimated model of sustainability to find the housing sustainable indices to the built environment which can be used as one of measurements for a household welfare. This study was conducted in Bekasi City of Indonesia as an emerging urban development in the hinterland area of Jakarta Metropolitan. This research methods combined sampling techniques of stratified and cluster treatments. From the research methods and spatial analysis, the model to measure the well-being referring to the built environment was obtained. The result shows that the sustainable housing environment quality is the core aspect of well-being. However, it is triggered by human quality.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Haula Rosdiana, Inayati, Machfud Sidik In 2010, Indonesia implemented regulation consisting of a new concept on cost recovery replacing assume and discharge. Under cost recovery, all contractors are requested to meet obligation on property tax in the first pace, meanwhile assume and discharge stipulate that government will bear LBT expense. LBT expense is also treated as operating cost that willrecover after the work area has reached commercial production. This new policy invited pros and cons particularly since the release of Notice of LBT Payable from Directorate General of Tax for 16 Production Sharing Contractors with a huge amount of IDR 2,6 trillion. This amount was higher than three years firm commitment and the base of LBT imposed was offshore work area in a whole as stated in a signed contract document.The imposition of LBT in the upstream oil and gas business activity has become a determinant variable for investors either existing or candidate in business forecasting and decision making on oil and gas investment. It can be seen from the decrease of candidate of investors’ participation in the tender of exploration work area in the first pace of 2013. This tender was only followed by 37,5% applicants,compared to the preceding ones that participations reached 90%. In addition, there was a propensity of investors to resign from the existing exploration projects due to the high burden of fiscal expenses. We analysed the impact of new policy concerning the upstream oil and gas business tax property on the Indonesia program of national energy security.Based on comprehensive analysis, we recommend government to amend related policy and law in order to connect with current development as well as to protect Indonesia economy and state budget. Besides, it is necessary to protect oil and gas investors and to mend the investment climate as well.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Bounhieng Vilaysane, Kaoru Takara, Pingping Luo, Inthavy Akkharath, Weili Duan The hydrological stream flow modeling is applied by the Soil for Water Assessment Tool (SWAT) model in the Xedone River basin, covering an area of 7,224.61 km 2 , in the southern part of Laos. The main objective of this research is to test the performance and feasibility of the SWAT model for predicting stream flow in the river basin. The model is calibrated and validated for two periods: 1993-2000 and 2001-2008, respectively, by using the SUFI-2 technique in this analysis. The SUFI-2 gives good results with the high value of R 2 and NSE larger than 0.70 respectively, for daily simulation. Monthly simulation results during calibration and validation are also good with R 2 > 0.80 and NSE > 0.80. The sensitivity analysis results of the model to each sub-basin delineation and hydrological response unit (HRU) in this basin are 230 HRUs in the whole basin. For uncertainty results, the 95% prediction uncertainty (95PPU) brackets very well with the observed discharge. All of sources uncertainty results are captured by bracketing value, higher than 65% of the observed river discharge. All of the results in this study are important to water discharge. The calibrated model can be used for further analysis of the effects of the climate and land use change, water quality analysis and sediment yield analysis; furthermore, the modelling can be applied for planning dam construction in the future and flood disaster risk management and thereby is useful for the sustainable development of the country.

Description: Publication date: Available online 14 August 2015 Source: Journal of Hydrology: Regional Studies Author(s): Mayank Shekhar, Amalava Bhattacharyya Study region Zemu Chuu (river), Lachen, North Sikkim, Eastern Himalaya India. Study focus Using tree-ring data of fir ( Abies densa ) the temporal variation of 222 years January–April mean discharge of Zemu Chuu, upper reaches of the Teesta River at Lachen, North Sikkim Eastern Himalaya was investigated. This was based on linear regression reconstruction model which explained variance of 50.1% during calibration period (AD 1976–1996). The model was verified by reduction of error (RE), sign test (ST), product mean test (Pmt), root mean square error (RMSE) and Durbin–Watson test (DW). The RE never falls below zero suggesting the model had explanatory power over the entire period of reconstruction. New hydrological insights for the region The explored strong relationship between tree ring records and instrumental data enable to develop mean January–April months (premonsoon) river discharge of Zemu Chuu from remote area of Sikkim. Reconstructed data reveals high stream-flow when it is more than the mean plus one standard deviation and as low when flow is less than the mean minus one standard deviation. There were such 23 high discharge and 21 extremely low years over the past AD 1775–1996. This premonsoon reconstruction of river flow would be of great significance when scarcity of water is acute in the North East Himalaya.

Description: Publication date: Available online 11 August 2015 Source: FEBS Open Bio Author(s): Charlotte Harrison, K. Ravi Acharya Angiotensin converting enzyme (ACE) is a zinc-dependent dipeptidyl carboxypeptidase with an essential role in blood pressure homeostasis in mammals. ACE has long been targeted in the treatment of hypertension through ACE inhibitors, however current inhibitors are known to cause severe side effects. Therefore, there is a requirement for a new generation of ACE inhibitors and structural information will be invaluable in their development. ACE is a challenging enzyme to work with due to its extensive glycosylation. As such, the Drosophila melanogaster ACE homologue, AnCE, which shares ∼ 60% sequence similarity with human ACE, can be used as a model for studying inhibitor binding. The presence of ligands originating from the crystallisation condition at the AnCE active site has proved an obstacle to studying the binding of new inhibitor precursors. Here we present the crystal structure of AnCE (in a new crystal form) at 1.85 Å resolution, using crystals grown under different conditions. This new structure may be more suitable for studying the binding of new compounds, with the potential of developing a new generation of improved ACE inhibitors. Graphical abstract

Description: Publication date: July 2015 Source: Global Ecology and Conservation, Volume 4 Author(s): K.L. Parkins, J.A. Clark Understanding bat use of human-altered habitat is critical for developing effective conservation plans for this ecologically important taxon. Green roofs, building rooftops covered in growing medium and vegetation, are increasingly important conservation tools that make use of underutilized space to provide breeding and foraging grounds for urban wildlife. Green roofs are especially important in highly urbanized areas such as New York City (NYC), which has more rooftops (34%) than green space (13%). To date, no studies have examined the extent to which North American bats utilize urban green roofs. To investigate the role of green roofs in supporting urban bats, we monitored bat activity using ultrasonic recorders on four green and four conventional roofs located in highly developed areas of NYC, which were paired to control for location, height, and local variability in surrounding habitat and species diversity. We then identified bat vocalizations on these recordings to the species level. We documented the presence of five of nine possible bat species over both roof types: Lasiurus borealis, L. cinereus, L. noctivagans, P. subflavus, and E. fuscus. Of the bat calls that could be identified to the species level, 66% were from L. borealis . Overall levels of bat activity were higher over green roofs than over conventional roofs. This study provides evidence that, in addition to well documented ecosystem benefits, urban green roofs contribute to urban habitat availability for several North American bat species.

Description: Publication date: Available online 12 August 2015 Source: Geoscience Frontiers Author(s): David J. Lary, Amir H. Alavi, Amir H. Gandomi, Annette L. Walker Learning incorporates a broad range of complex procedures. Machine learning (ML) is a subdivision of artificial intelligence based on the biological learning process. The ML approach deals with the design of algorithms to learn from machine readable data. ML covers main domains such as data mining, difficult-to-program applications, and software applications. It is a collection of a variety of algorithms (e.g. neural networks, support vector machines, self-organizing map, decision trees, random forests, case-based reasoning, genetic programming, etc.) that can provide multivariate, nonlinear, nonparametric regression or classification. The modeling capabilities of the ML-based methods have resulted in their extensive applications in science and engineering. Herein, the role of ML as an effective approach for solving problems in geosciences and remote sensing will be highlighted. The unique features of some of the ML techniques will be outlined with a specific attention to genetic programming paradigm. Furthermore, nonparametric regression and classification illustrative examples are presented to demonstrate the efficiency of ML for tackling the geosciences and remote sensing problems. Graphical abstract

Description: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Casandra Panea, Adam M. Farkas, Yoshiyuki Goto, Shahla Abdollahi-Roodsaz, Carolyn Lee, Balázs Koscsó, Kavitha Gowda, Tobias M. Hohl, Milena Bogunovic, Ivaylo I. Ivanov Generation of different CD4 T cell responses to commensal and pathogenic bacteria is crucial for maintaining a healthy gut environment, but the associated cellular mechanisms are poorly understood. Dendritic cells (DCs) and macrophages (Mfs) integrate microbial signals and direct adaptive immunity. Although the role of DCs in initiating T cell responses is well appreciated, how Mfs contribute to the generation of CD4 T cell responses to intestinal microbes is unclear. Th17 cells are critical for mucosal immune protection and at steady state are induced by commensal bacteria, such as segmented filamentous bacteria (SFB). Here, we examined the roles of mucosal DCs and Mfs in Th17 induction by SFB in vivo. We show that Mfs, and not conventional CD103 + DCs, are essential for the generation of SFB-specific Th17 responses. Thus, Mfs drive mucosal T cell responses to certain commensal bacteria. Graphical abstract Teaser How various mucosal mononuclear phagocyte subsets orchestrate immune responses to intestinal bacteria in vivo is poorly understood. Panea et al. identify intestinal macrophages as essential drivers of Th17 cell responses to certain commensal bacteria.

Description: Publication date: Available online 13 August 2015 Source: Geoscience Frontiers Author(s): H.N. Sinha, Jacques Verniers Belonechitina capitata , a typically middle to late Ordovician chitinozoan index taxon was for the first time recovered from the northeastern Kumaon region, a part of Garhwal-Kumaon Tethys basin of the Himalaya, India. This species is of great biostratigraphic importance and has already been reported from Avalonia, Baltica and northern Gondwana. The study area was during Ordovician, part of a low-palaeolatitudinal Gondwana region. The vesicles of recovered forms are black and fragmentary. This is principally attributed to intense tectonic activity during the Himalayan orogenic movement which resulted into high thermal alteration. The chitinozoans are found along with melanosclerites. Graphical abstract

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Hatma Suryatmojo Vegetation cover change has a profound influence on the hydrological cycle. A reduction in vegetative cover from forest harvesting generally increases the average surface runoff volume and total water yield for a given area of land. The differences of structure and land cover type are the main baseline in this research to understand the hydrological response of catchment. This research is using two catchment experiments, pine forest and mix-plant forest catchments. Plantation forest with clear cutting system in the mountain area is very sensitive with the changes of runoff and soil erosion. This study investigated the impact of vegetation changes on rainfall-runoff response in different type and periods of Pine forest plantation from their respective forestry treatments. The result shown that in the 7-year old mix-plant forest, direct runoff, peak discharge and runoff coefficient are dramatically increased than that in the 37-year old pine forest. 15 years after planting, direct runoff, peak discharge and runoff coefficient are decreased and reaching to the 37-year old pine forest responses. Implementation of a mix-plant forest method is effective in controlling the hydrological responses of direct runoff, peak discharge and runoff coefficient. The results showed that the magnitude of runoff during different forest treatments depend on interactions among rainfall, forest cover changes and surface disturbance. Forest management practices should consider and attempt to minimize disturbance during each plantation stage to control runoff response.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Ridwan Sutriadi, Astri Aulia Safrianty, Afrizal Ramadhan This paper discusses how important to describe cities and regencies (kotadankabupaten) by using official statistical data in such a way to understand their position in the context of regional rating system within regional autonomy policy in Indonesia. Regional rating system can be seen as a creative method towards sustainable growth by accelerating or decelerating down the growth in the regional context. The global competitiveness index is adapted as a method to formulate regional rating system. Furthermore, the simplification is made to facilitate probable planning prescription with the category to accelerate, continue, or decelerate by modifying particular variables which are presented by related statistical data. In terms of performing planning prescription, it is important to understand the existing and future role of cities and regencies especially in performing development equity, reducing the dominant role of large size cities, facilitating medium sized cities, and envisioning small sized cities. Note that rating system method in terms of planning prescriptions formulation can be seen as a progress of communicative city concept, by sharing information, promoting communication, providing option, and promotingparticipation.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Edy Hartulistiyoso, Febri A.P.A.G. Sigiro, Muhamad Yulianto This paper aims to investigate the temperature distribution in the reactor of a plastics pyrolysis process from waste bottles of beverage to produce fuel. This process is considered an alternative technology to replace fossil fuel. This experiment was conducted using a cylindrical reactor, which has dimension of 0.31 m in diameter and 1 m high. In order to understand the temperature distribution in the reactor, five thermocouples were placed to measure temperature at the bottom and the top of the reactor as well as in the middle, with the different position of each thermocouple of 0.19 m respectively. The temperature outside the reactor and outside the condenser was also measured. Data Acquisition recorded all temperature data. The reactor was used to process 1,500 g plastics. The Computational Fluid Dynamic (CFD) was also used to know the contour of temperature inside the reactor. The result showed that to increase temperature from the ambient temperature to 450 o C, 72 minutes of time were needed. The lowest temperature of 310 °C was measured at the top of the reactor, whereas different temperature in the middle of the reactor was found to be 46 °C respectively. The pyrolysis process of 1,500 g plastics was completed in 110 minutes to produce 21 g of fuel. This fact shows that the pyrolysis process of plastics can produce fuel at 450 o C in the reactor and 75 o C outside the reactor.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Wawan Rusiawan, Prijono Tjiptoherijanto, Emirhadi Suganda, Linda Darmajanti In 2008, the economic growth of Jakarta, the capital of Indonesia, reached 6,44% with the GDP amount of IDR 501,771,735 million (Central Statistic Bureau, 2008). The high growth of economic contributes to the rapid growth of the number of motorcycle vehicles around 8% or up to 5.798.000 units(Central Statistic Bureau, 2011). This model is expected to reduce CO 2 emissions without affecting the growth of GDP or economic growth. High economic growth is still needed by Jakarta to improve the welfare of the population. First, a BAU scenario (business as usual scenario) has been defined, in which the variables of the model were parameterized according to the observed tendency during the period 2008-2012, assuming a geometric growth rate during the period 2009–2029. The second scenario, called EGCO 2 -1 is characterized by reducing CO 2 emission intervention by the developed green open space during the period 2009-2014.In the third scenario, called EGCO 2 -2 scenario, besides assuming the renewable energy share increased, we imposed the decreasing of the fossil energy share up to 15%. The result of this study is the estimation of economic growth and CO 2 emissions in 2029 in each scenario. In the BAU scenario, CO 2 emission is 11.492 million tons. In the second scenario, CO 2 emission is 0.529 million tons, and in the third scenario, CO 2 emission is 7.250 million tons. GDRP is relatively stable at IDR 1,544,570,856 million and economic growth is 5.49%. Finally, main outcome of this work can be role model to Jakarta sustainable urban development policy. These are most important to environmentally aspect and enhancing economic growth for a better future.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): NiLuh Widyaningsih, Prijono Tjiptoherijanto, Sulistyoweni Widanarko, Francisia SSE Seda The growth of population increases not only the basic needs of human but also the use of natural resources. Household consumption pattern gives impact to economic growth, social condition, and environmental quality. Jakarta as the capital of Indonesia (the 4 th biggest most populous country in the world) still has waste management problems. East Jakarta area has the biggest issue of unmanaged waste (2,430 m 3 /day) and Duren Sawit District has the biggest number of households or families (94,862 KK). This paper analyzed how the household consumption pattern links to the household waste management. The Spearman's Rho Correlation analysis showed that there are correlations between household consumption (for food and non-food) with the application of the 3R principles (Reduce, Reuse, and Recycle). To build the linkage model between sustainable consumption and household waste management, this research used the system dynamics analysis. The result shows that the waste management system now in Jakarta is not sustainable, and it increases the unmanaged waste. To reduce the unmanaged waste, the model of inside (functional intervention through green motivation and green lifestyle) and outside (3R-structural intervention) could be applied.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Ambar Kusumandari, Prasetyo Nugroho The growing population in Indonesia impacts on increasing of human needs which influences on the larger area of land degradation. To reduce area of land degradation, land rehabilitation is a key to achieve sustainable development.In identifying area to be rehabilitated, land capability analysis is required. The objectives of this research are: a) to examine soil characteristics as a data base for rehabilitating critical area, b) to study water balance, and c) to analyze land capability. Moreover, this study applies data collection, both primary and secondary for its method. Primary data includes soil characteristics were collected by taking several soil samples at several types of land uses to be analyzed in laboratory includes: soil pH or acidity, organic matter, NPK contents and soil permeability. Secondary data such as, rainfall and temperature data were collected for evapotranspiration and total available water for runoff analysis. This research results that soil pH mostly is very low (〈 4.5) and 3 areas have the low soil pH of 4.5 – 5.5. Major soil organic matters are classified as high (3.1 – 5%) to very high (> 5.5%). Nitrogen content varies from low to very low, whereas the Phosphor content is very low at all location. Furthermore, K contents of soil ranges from low to moderate, whereas the CEC is classified as moderate. The soil permeability varies from very slow, slow, moderate to very fast. The water balance analysis shows that along the year there is surplus of the water, except during July to September.The study area has 4 land capability types. Based on the research result, it can be concluded that the critical land that capable to be rehabilitated includes: open area, shrubs and grassland, with an area of 612.03 ha; 117.75 ha and 27.57 ha, respectively. The soil fertility level is low; the deficit period is July to September. It was recommended that to rehabilitate the area, the lime and fertilizer should be applied. Regarding the climatologically analysis, the best time to plant the trees for rehabilitation is in the period of September to June.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Andi Kurniawan, Guntur, Ayami Hiraki, Yasuaki Fukuda, Tatsuya Yamamoto Microbial biofilms plays important roles in aquatic environments such as nutrient cycling and purification of pollutants. Such important function will be greatly influenced by the forming process of the biofilm. In this study, the nutrient ions inside the biofilms in relation to biofilm properties during biofilm formation were investigated. The result showed that the formation of biofilm was fast process taking just a week to reach the biomass (measured as wet weight) found for the mature biofilm. The nutrient-rich environment in the biofilm was established from a very early stage. These particular environmental conditions might promote the growth of microbial cells in the biofilm, resulting in a microbial community different from that of the lake water. The electrostatic interaction between ions in the lake water and the charged sites of polymers in the biofilm seemed to be the driving force for the accumulation of ions inside the biofilm. The result of this study suggested that microbial biofilm might play important function in the ecosystems because of the early stage of biofilm forming process.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Sartika Laban, Hiroki Oue, Agnes Rampisela Irrigation in Renggang Water Users’ Association region in the first dry season, 2012 and 2013 was characterized by the reused water irrigation of drainage and the groundwater irrigation from wells. The shortage of the canal irrigation in 2012 was improved mainly by the renovation of the secondary canal by farmers’ “ gotongroyong ”. The fluctuation of groundwater level was highly correspondedbythe timely change of stored water in the ground (ΔS).The positive ΔScaused by the gross water supply in the first half period of the rice cultivation, was evaluated to keep the groundwater at some level.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Joji Sato, Mamoru Wakayama, Kazuyoshi Takagi Acetobacterpasteurianus which is widely used for commercial brewing of vinegar can grow well with lactate as an energy source. In the utilization processes of lactate in A. pasteurianus , it is first converted to pyruvate, and then converted to final product; acetate via acetaldehyde. In the other pathway, pyruvate, formed from lactate is metabolized through the tricarboxylic acid (TCA) cycle. The enzymes catalyzing reaction from pyruvate to acetaldehyde had been identified, however, the enzyme responsible for the oxidation of lactate to pyruvate in A. pasteurianus have not been identified. In this study, we focused on the enzymes involved in the process and aimed at their characterization. This study will contribute to quality improvement of vinegar which provides human health with a good effect. A. pasteurianus assimilated D-lactate as well as L-lactate, indicating that the enzymes catalyzing the oxidation of D- and L-lactate to pyruvate could be produced in the cell. The presence of the enzyme which catalyzes the oxidation of lactate to pyruvate in A. pasteurianus was confirmed by enzymatic assays using dichloropenol-indophenol as redox dye, phenazinemethosulfate as electron acceptor, and lactate as substrate.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Takeshi Kuwabara, Asep A. Prihanto, Mamoru Wakayama, Kazuyoshi Takagi The prevalence of bacterial infection has been gradually increased for the last decades. This phenomenon is predicted as one of serious problems to human security in the next decades. Helicobactorpylori has been clarified to be related to gastric inflammation and a variety of diseases including gastric cancer. Recently, it has been known that H. pylori asparaginase is necessary for the growth in host infection and might be involved in inhibition of lymphocyte function at gastric niche. On the other hand, Pseudomonas aeruginosa is known to cause a fence-sitting infectious disease. However, no studies on a physiological role of asparaginase in relation to pathogenicity of P. aeruginosa have been found. Also, there are no studies on its physiological role in relation to pathogenicity of P. aeruginosa have been found. Therefore, we focused on purification and characterization of P. aeruginosa PAO1 asparaginase in order to clarify its physiological roles in this study. Intracellular asparaginase was highly purified and characterized from P. aeruginosa PAO1. The profile of DEAE-cellufine A 500 column chromatography suggested that two types of asparaginases were produced in P. aeruginosa PAO1. The optimum pH and temperature of the one enzyme was 9.5 and 40 °C, respectively while those of the another was 9.5 and 65 °C, respectively. Those results indicated that P. aeruginosa PAO1 had two different types of asparaginases.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Wahyu Sujatmiko, Hermawan K. Dipojono, F.X. Nugroho Soelami, Soegijanto The effect of increasing RUSUNAMI high-rise and low cost building flats construction has brought about some problems. One of them is the use of air conditioning in many building flats. It shows that the objective of the RUSUNAMI is not fulfilled because it needs additional operational cost for air conditioning. Two RUSUNAMIs in Bandung and three RUSUNAMIs in Jakarta were selected and measured related to ventilation and indoor air temperature. This paper examines the performance of natural ventilation and indoor air temperature and their ability in thermal comfort with the adaptive approach. In general, all RUSUNAMI is not effective in utilizing the wind because it is designed for air conditioning. On this occasion, it is discussed the opportunities of natural ventilation associated with utilization approach of adaptive thermal comfort.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Eko Agus Suyono, Aminin, Listia Pradani, Umi Mu’avatun, Ratri Nisfi Habiba, Ramdaniyah, Eva Fatihatur Rohma Microalga Haematococcus pluvialis is reported as a large producer of carotenoid. One of the carotenoids produced by the microalgae is astaxanthin that can be used as antioxidant. The astaxanthin is known as “the king of antioxidant”, reportedly 800 times stronger than Coenzyme Q10 (CoQ10), 75 times stronger than Alpha Lipoic Acid (ALA) and 6000 times stronger than Vitamin C. Research has discovered that astaxanthin absorbs more free radicals than any other antioxidants. It is also indicated for sun protection, exercising recovery and eye health. However, under normal condition, carotenoid and biomass of the microalgae are very low. Light stress treatment is reportedly able to enhance carotenoids in plants and presumably in microalgae. Therefore, this research aims to increase carotenoid and biomass of the microalga by using the combination of blue, red, and white with ultraviolet lights. The microalga H.pluvialis was cultured in Bold Basal medium for 14 days under irradiation of blue, red and white lamp (1500 lux) for 21 hours and irradiation of ultraviolet light (500 lux) for 3 hours. As a control, the microalga wascultured in Bold Basal medium under irradiation of white lamp (1500 lux) for 12:12 hours (dark and light cycle). Each treatment and control was repeated for three times. Its parameters were cell number, chlorophyll and carotenoid content. The number of cells was counted by Haemacytometer Neubauer 1 mm and chlorophyll, and carotenoids content were analyzed by spectrophotometry at absorbance of 700, 663, 645, and 478 nm. The combination of ultraviolet and blue light was the best treatment for increasing the total carotenoid and chlorophyll content since the total carotenoid content increased about 8 times of the control and the total chlorophyll content increased about 2 times of the control, they accounted for 5,1 mg / L and 6,55 mg / L, respectively. Meanwhile, the combination of ultraviolet and red light increased its biomass up to 1.4 x 10 4 cell /ml which was about 2 times of the control.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Haza Hanurhaza Md Jani, Nor Zalina Harun, Mazlina Mansor, Ismawi Zen Malaysia is a Muslim country which comprises of a heterogeneous society. Through the efforts of the current and previous government, Malaysia has beenattempting to include the Islamic principles into its governance. Firstly, it starts with the concept of the Asian values, moving on to Islam Hadhari , and the recent one is the idea of One Malaysia. These gestures speculate that Malaysia is in the process of bringing and applying back the Islamic way of governance system with reference to the first Islamic law, the Medina charter. Based on the Islamic history, the Medina charter was the first constitution drafted and documented in Islam providing the basis of the city-state between Muslim and non-Muslim in the medieval Muslim city of Medina. The content of the charter manages to unite a multi-religious and multi-ethnicity (heterogeneous) in the city. Therefore, this study is conducted to enlighten people's understanding on the success of the Medina charter, in relation to the heterogeneous society in Malaysia. The charter is applicable to be adapted into the Malaysian government in which the citizens are heterogeneous society. Hence, the aim of this study is to learn the reasons behind the success of the Medina charter in response to the heterogeneous society in Malaysia. In order to achieve the aim of this study, several objectives are highlighted to identify the purpose and function of the charter as well as to analyze the success of the charter to heterogeneous society in Malaysia. This study is based on the qualitative research methodology; thus, the document analysis is adopted to define and understand the Medina charter. The findings of this study emphasize three main aspects, namely, i) the condition of the Medina city before and after the establishment of the charter, and ii) the relationship of the charter with heterogeneous society, and iii) the importance of the charter to the Islamic city-state, especially in Malaysia. The outcomes of this study will assist to strengthen the understanding towards the importance of Medina charter and the significance of upholding the Islamic principles and values in heterogeneous.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Diananta Pramitasari, Ahmad Sarwadi This study aims to identify the going out activities conducted by senior residents during their daily lives and how the built environment especially in the high densely settlement of the city center support these activities. The observations were conducted in one high-densely populated neighborhood in Yogyakarta City Center and personal interviews were carried out to 48 elderly who lives in the neighborhood. This study finally clarified that the going out activity of the elderly is basically divided into four types based on the motivation: economy, health, recreation and social. Economic motivation-based activity was learned as the most frequent going out and it employed the shortest distance of travelling range. The spots within a walkable distance inside the neighborhood were relied on by the elderly therefore the sufficient facilities inside the neighborhood should be provided appropriately. As the elderly stayed for long time in the commune as well involved personally in the community, the development or growth of the living environment constitutes the social and physical challenges among themselves.

Description: Publication date: 2015 Source: Procedia Environmental Sciences, Volume 28 Author(s): Suharman Hamzah, Sakti Adji Adisasmita The purpose in this study is to analyze the optimization of aircraft parking stands, and proposed model for apron development in near future at Sultan HasanuddinInternational Airport (SHIA) to achieve safety on airport operation activities.The study was conducted by collecting and analyzing data. The data were based on field survey, interviews, discussion with airport authority, official government, etc. and also from various agencies. Analytical tools applied were: regression analysis, to forecasts passenger and aircraft movements; and JICA formulas, to analyze the aircraft movement at peak hours, and number of aircraft parking stands for short, medium, and long terms period.The conclusion are: (a) the optimizing level on the apron area, especially at peak hours at SHIA depends on the aircraft service time, (b) the ability to serve the aircrafts on the apron area at peak hours as many as 17 to 22 aircraft parking stands, and need additional space as much as 24,431m 2 , 39,216 m 2 , and 52,354 m 2 in 2015, 2020 and 2025 respectively, (c) requirement to develop/introduceother aircraft parking stands model, (d) proposed the new apron or aircraft parking stands model as known as pier or satellite models to anticipate the increasing number of passenger and aircraft movements in the near future; while the recommendation can be included that the use of service time as effectively and efficiently at the apron area could provide better service for passengers, aircrafts.

Description: Publication date: Available online 13 August 2015 Source: Water Science Author(s): C.M. Pilgrim, E.A. Mikhailova, C.J. Post, J.J. Hains, S.K. Cox Spatial and temporal land cover changes can reduce or accelerate lake sedimentation. This study was conducted to examine morphometry and bathymetry, and the long-term changes (over 75 years) in sedimentation in the Lake Issaqueena reservoir, South Carolina. The watershed and catchment areas were delineated using Light Detection and Ranging (LiDAR) based data. Trends in lake surface area and riparian buffer condition (vegetated or unvegetated) were determined from historical aerial photography. From 1938 to 2009, the lake experienced a decrease in surface area of approximately 11.33 ha while catchment area increased by 6.99 ha, and lake volume decreased by 320,800.00 m 3 . Lake surface area decreased in years corresponding to equal coverage or largely unvegetated riparian buffers. Surface area and average annual precipitation were not correlated; therefore other factors such as soil type, riparian buffer condition and changes in land use likely contributed to sedimentation. Shift from agricultural land to forestland in this watershed resulted in a decrease in sedimentation rates by 88.28%.

Description: Publication date: Available online 9 September 2015 Source: Dendrochronologia Author(s): Stefan Krottenthaler, Philipp Pitsch, Gerd Helle, Giuliano Maselli Locosselli, Gregório Ceccantini, Jan Altman, Miroslav Svoboda, Jiri Dolezal, Gerhard Schleser, Dieter Anhuf High-density hardwood trees with large diameters have been found to damage manually operated increment borers, thus limiting their use in the tropics. Therefore, we herein report a new, low-cost gasoline-powered sampling system for high-density tropical hardwood trees with large diameters. This system provides increment cores 15 mm in diameter and up to 1.35 m in length, allowing minimally invasive sampling of tropical hardwood tree species, which, up to the present, could not be collected by conventional 5 or 10 mm increment borers. This system provides a single core sample with ample amount of wood for multidisciplinary analyses, including ring width, stable isotope and wood anatomical measurements. The borer never gets stuck inside stems, even in hollowed trees, cores will never twist during coring, and the gasoline drill gives ample flexibility in the field. It is anticipated that the dendrochronological community will find our technique very useful in the pursuit of tropical tree ring research.

Description: Publication date: September 2015 Source: GeoResJ, Volume 7

Description: Publication date: Available online 16 September 2015 Source: Advances in Climate Change Research Author(s): H.E. Jian-Kun Global climate change mitigation and CO 2 emission reduction have promoted the revolutionary transformation in energy system. The core content of energy system revolutionary transformation is to replace the high-carbon energy system dominated by fossil energy with low-carbon energy system dominated by new and renewable energy and finally realize the near-zero emission of CO 2 . The new energy system transformation has also led to a reform in global economic and social development patterns. Developing low-carbon economy becomes the fundamental strategy of sustainable development under climate risk management and the only solution to getting on the road from industrial civilization to ecological civilization. China intends to achieve the peaking of CO 2 emissions around 2030 and increase the share of non-fossil fuels in primary energy consumption to around 20% by 2030. Guided by the targets, China directs its economy development to a low-carbon pattern. Therefore, new and renewable power capacity need to reach 1300 GW, and the electricity generated should be 4 times of that in 2013 with a continuous increase rate of 6%－8% around 2030. The pace of energy substitution need to be accelerated and efficient, safe, clean, and low-carbon energy supply and consumption systems should be established besides strengthened energy conservation and improved energy efficient. Therefore, reform need be deepened, favorable policy system and market mechanism for energy revolution and low-carbon development need be established, energy pricing mechanism should be reformed, and national carbon market should be formed to provide a favorable policy and market environment for low-carbon technology innovation and industry development.

Description: Publication date: September 2015 Source: Journal of Hydrology: Regional Studies, Volume 4, Part B Author(s): Jonathan A. Warrick, John M. Melack, Blair M. Goodridge Study region Coastal watersheds of southern California, United States. Study focus We sought to better understand the rates and variability of suspended-sediment discharge from small coastal watersheds (〈100 km 2 ) of California. Suspended-sediment concentrations and stream discharge were measured with automated samplers near the mouths of four small watersheds (10–56 km 2 ). New hydrological insights for the region The watersheds were found to have suspended-sediment concentrations that extended over five orders of magnitude (1 to over 100,000 mg L −1 ). Sediment concentrations were weakly correlated with discharge ( r 2 = 0.10–0.25), and four types of hysteresis patterns were observed during high flow events (clockwise, counterclockwise, no hysteresis, and complex). Annual sediment yields varied by 400-fold across the four watersheds (e.g., 5–2100 t km −2 yr −1 during the 2003–2006 water years), and sediment discharge was measurably elevated in one watershed that was partially burned by a late summer wildfire. Dozens of high flow events provided evidence that suspended-sediment yields were generally related to peak stream discharge and event-based precipitation, although these relationships were not consistent across the watersheds. This suggests that watersheds smaller than 100 km 2 can provide large – and therefore important – fluxes of sediment to the coast, but that simple techniques to estimate sediment loads, such as sediment rating curves, hydrologic regressions, and extrapolation using global sediment yield relationships that include watershed area as a primary factor, may provide poor results. Graphical abstract

Description: Publication date: September 2015 Source: Journal of Hydrology: Regional Studies, Volume 4, Part B Author(s): Chris C. Gianfagna, Chris E. Johnson, David G. Chandler, Charlie Hofmann Study region The Catskills region of New York State is largely forested and dominated hydrologically by stream watersheds with few natural lakes. The area experiences intensive water resources management and ecosystem monitoring due to its strategic role as the principal water supply for New York City. Study focus We analyzed average daily flows in nested and non-nested pairs of gaged watersheds in the Catskills to assess whether daily flow in ungaged watersheds can be calculated based on watershed area ratios. New hydrological insights for the region Watershed area ratio was the most important basin parameter for estimating flow at upstream sites based on downstream flow. The area ratio alone explained 93% of the variance in the slopes of relationships between upstream and downstream flows. Regression analysis indicated that flow at any upstream point can be estimated by multiplying the flow at a downstream reference gage by the watershed area ratio. This method accurately predicted upstream flows at area ratios as low as 0.005. We also observed a very strong relationship ( R 2 = 0.79) between area ratio and flow–flow slopes in non-nested catchments. Our results indicate that a simple flow estimation method based on watershed area ratios is justifiable, and indeed preferred, for the estimation of daily streamflow in ungaged watersheds in the Catskills region.

Description: Publication date: July 2015 Source: Global Ecology and Conservation, Volume 4 Author(s): Jonathan Y.S. Leung Mangroves have been dwindling rapidly in the last few decades due to human activities, and thus restoration is commonly conducted to recover the ecological functions of degraded mangroves. However, afforestation (i.e. mangrove plantation in mudflats) can lead to habitat conversion and hence modify the ecosystem functions by increasing habitat heterogeneity. Mudflats are scarce in mangroves, but provide vital ecological functions by the macrobenthos. As such, the present study investigated how habitat heterogeneity affects the ecological functions of macrobenthic communities in a mangrove by analysing functional diversity, functional redundancy and biological trait patterns. Samples were collected from different habitats with increasing order of habitat heterogeneity (mudflat 〈seedling 〈 Kandelia 〈 Kandelia with algal mats 〈pneumatophore). Results showed that functional redundancy was generally high in the mangrove, indicating that most of the species performed similar functions. Functional diversity, however, generally decreased with increasing habitat heterogeneity primarily due to the dense root structure. Different habitats had different trait patterns where smaller body size, fewer carnivores and more direct developers were observed when habitat heterogeneity increased. Overall, moderate increase in habitat heterogeneity enhanced the functional diversity of macrobenthic communities, but negative effect was incurred when the habitat heterogeneity was too high. For the sake of conservation and management of mangroves, restoration should consider plant density and plant species to minimize the impact of dense root structures on macrobenthos. Given the lower functional redundancy and distinct trait pattern in the mudflat, afforestation is not recommended so that the integrity of the ecological functions of mangroves can be maintained.

Description: Publication date: November 2015 Source: Energy Reports, Volume 1 Author(s): Anjali Sandip, Val H. Smith, Terry N. Faddis The objective of this study was to investigate the microalgal dewatering efficiency of a belt filter system for feed concentrations below 10 g dry wt./L. A prototype belt filtration system designed for 50 g dry wt./L microalgal feed concentration was used for this investigation. The highest concentration of microalgal suspension available for testing on the prototype belt filtration system was 6 g dry wt./L obtained from biomass settling tanks at the Lawrence, Kansas domestic wastewater treatment plant. For preparation of feed suspension with concentrations below 10 g dry wt./L, microalgal cultivation was followed by flocculation. A mixed laboratory culture of freshwater species dominated by three eukaryotic green microalgae (Chlorella vulgaris, Scenedesmus sp., and Kirchneriella sp.) was cultivated in wastewater effluent. This was followed by flocculation which resulted in a microalgal feed suspension concentration of 4 g dry wt./L. Belt dewatering tests were conducted on microalgal suspensions with feed concentrations of 4 g dry wt./L and 6 g dry wt./L. The maximum microalgal recovery with the belt dewatering system was 46% from the 4 g dry wt./L, and 84% from the 6 g dry wt./L suspensions respectively. The results of this study indicate that microalgal suspension concentrations as low as 6 g dry wt./L can be recovered with a belt filter system improving the overall dewatering efficiency of the system.

Description: Publication date: Available online 21 September 2015 Source: FEBS Open Bio Author(s): William L. Coleman, Adam C. Kulp, Jennifer J. Venditti Proteins known to function during cell-cell communication and exocytosis in neurons and other secretory cells have recently been reported in human sperm. Synapsins are a group of proteins that have been very well characterized in neurons, but little is known about synapsin function in other cell types. Based upon previous findings and the known function of synapsin, we tested the hypothesis that synapsin I was present in human sperm. Washed, capacitated, and acrosome induced sperm preparations were used to evaluate the functional distribution of synapsin I using immunocytochemistry. Protein extracts from mouse brain, mouse testis/epididymis, and human semen were used for protein blotting techniques. Immunolocalization revealed synapsin I was enriched in the sperm equatorial segment. Protein extracts from mouse brain, mouse testis/epididymis, and human semen were positive for synapsin I using several different antibodies, and dot blot results were confirmed by Western blot analyses. Finally, treatment of capacitated and acrosome reaction induced samples with anti-synapsin antibodies significantly reduced sperm motility. Localization of synapsin I in human sperm is a novel finding. The association of synapsin I with the sperm equatorial segment and effects on motility are suggestive of a role associated with capacitation and/or acrosome reaction, processes that render sperm capable of fertilizing an oocyte.

Description: Publication date: Available online 21 September 2015 Source: Geoscience Frontiers Author(s): J.L.R. Touret, M. Santosh, J.M. Huizenga The formation of continents involves a combination of magmatic and metamorphic processes. These processes become indistinguishable at the crust-mantle interface, where the pressure-temperature ( P-T ) conditions of (ultra) high-temperature granulites and magmatic rocks are similar. Continents grow laterally, by magmatic activity above oceanic subduction zones (high-pressure metamorphic setting), and vertically by accumulation of mantle-derived magmas at the base of the crust (high-temperature metamorphic setting). Both events are separated from each other in time; the vertical accretion postdating lateral growth by several tens of millions of years. Fluid inclusion data indicate that during the high-temperature metamorphic episode the granulite lower crust is invaded by large volumes of low H 2 O-activity fluids including high-density CO 2 and concentrated saline solutions (brines).These fluids are expelled from the lower crust to higher crustal levels at the end of the high-grade metamorphic event. The final amalgamation of supercontinents corresponds to episodes of ultra-high temperature metamorphisminvolving large-scaleaccumulation of these low-water activity fluids in the lower crust. This accumulation causes tectonic instability, which together with the heat input from the sub-continental lithospheric mantle, leads to the disruption of supercontinents. Thus, the fragmentation of a supercontinent is already programmed at the time of its amalgamation. Graphical abstract

Description: Publication date: Available online 21 September 2015 Source: Journal of Rock Mechanics and Geotechnical Engineering Author(s): Mohsen S. Masoudian To reduce the emissions of carbon dioxide (CO 2 ) into the atmosphere, it is proposed to inject anthropogenic CO 2 into deep geological formations. Deep un-mineable coalbeds are considered to be possible CO 2 repositories because coal is able to adsorb a large amount of CO 2 inside its microporous structure. However, the response of coalbeds is complex because of coupled flow and mechanical processes. Injection of CO 2 causes coal to swell, which leads to reductions in permeability and hence makes injection more difficult, and at the same time leads to changes in the mechanical properties which can affect the stress state in the coal and overlying strata. The mechanical properties of coal under storage conditions are of importance when assessing the integrity and safety of the storage scheme. On the other hand, the geomechanical response of coalbed will also influence the reservoir performance of coalbed. This paper provides an overview of processes associated with coalbed geosequestration of CO 2 while the importance of geomechanical characteristics of coalbeds is highlighted. The most recent findings about the interactions between gas transport and geomechanical characteristics of coal will be discussed and the essence will be delivered. The author suggests areas for future research efforts to further improve the understanding of enhanced coalbed methane (ECBM) and coalbed geosequestration of CO 2 .

Description: Publication date: Available online 24 September 2015 Source: Cell Reports Author(s): Jan Dudeck, Shanawaz Mohammed Ghouse, Christian H.K. Lehmann, Anja Hoppe, Nadja Schubert, Sergei A. Nedospasov, Diana Dudziak, Anne Dudeck Mast cells are critical promoters of adaptive immunity in the contact hypersensitivity model, but the mechanism of allergen sensitization is poorly understood. Using Mcpt5-CreTNF FL/FL mice, we show here that the absence of TNF exclusively in mast cells impaired the expansion of CD8 + T cells upon sensitization and the T-cell-driven adaptive immune response to elicitation. T cells primed in the absence of mast cell TNF exhibited a diminished efficiency to transfer sensitization to naive recipients. Specifically, mast cell TNF promotes CD8 + dendritic cell (DC) maturation and migration to draining lymph nodes. The peripherally released mast cell TNF further critically boosts the CD8 + T-cell-priming efficiency of CD8 + DCs, thereby linking mast cell effects on T cells to DC modulation. Collectively, our findings identify the distinct potential of mast cell TNF to amplify CD8 + DC functionality and CD8 + T-cell-dominated adaptive immunity, which may be of great importance for immunotherapy and vaccination approaches. Graphical abstract Teaser The impact of mast cells on T-cell-dominated adaptive immunity and diseases is poorly mechanistically defined. Dudeck et al. identify the distinct potential of mast-cell-derived TNF to amplify CD8 + T cell expansion and CD8 + T-cell-driven adaptive immune responses by modulating the CD8 + DC migration and priming efficiency.

Description: Publication date: Available online 24 September 2015 Source: Cell Reports Author(s): Vincent Sarrazy, Sophie Sore, Manon Viaud, Guylène Rignol, Marit Westerterp, Franck Ceppo, Jean-Francois Tanti, Rodolphe Guinamard, Emmanuel L. Gautier, Laurent Yvan-Charvet Enhanced glucose utilization can be visualized in atherosclerotic lesions and may reflect a high glycolytic rate in lesional macrophages, but its causative role in plaque progression remains unclear. We observe that the activity of the carbohydrate-responsive element binding protein ChREBP is rapidly downregulated upon TLR4 activation in macrophages. ChREBP inactivation refocuses cellular metabolism to a high redox state favoring enhanced inflammatory responses after TLR4 activation and increased cell death after TLR4 activation or oxidized LDL loading. Targeted deletion of ChREBP in bone marrow cells resulted in accelerated atherosclerosis progression in Ldlr −/− mice with increased monocytosis, lesional macrophage accumulation, and plaque necrosis. Thus, ChREBP-dependent macrophage metabolic reprogramming hinders plaque progression and establishes a causative role for leukocyte glucose metabolism in atherosclerosis. Graphical abstract Teaser Sarrazy et al. show that the carbohydrate-responsive element binding protein ChREBP is required for metabolic reprogramming in activated macrophages and provide evidence that changes in ChREBP-dependent macrophage redox status influence macrophage polarization and survival with physiopathological consequences on atherosclerosis.

Description: Publication date: Available online 25 September 2015 Source: Advances in Climate Change Research Author(s): Pitchai Sampathkumar, Srinivasan Balakrishnan, Krishnamoorthy Kamalakannan, Rethinavelu Sankar, Lakshmanan Ramkumar, Subramani Ramesh, Neelamegam Kabilan, Thambusamy Sureshkumar, Chellam Thenmozhi, Mookapillai Gopinath, Sekar Jayasudha, Amalanathan Arokiyasundram, Thiruvarasan Lenin, Thangavelu Balasubramanian Hydrographical parameters and phytoplankton assemblages were detremined along the Pondicherry, Parangipettai and Nagapattinam coastal waters, southeast coast of India. All the hydrographical parameters such as sea surface temperature, salinity, pH, total alkalinity, dissolved oxygen and nutrients like nitrate, nitrite, inorganic phosphate and reactive silicate, chlorophyll a and phytoplankton assemblages were studied for a period of five months (May, August, September 2010, March and November 2011). Over 121 species of phytoplankton represented by 93 species of diatoms, 16 species of dinoflagellates, 9 species of blue-green algae, 2 species of greens and 1 species of silicoflagellate were recorded. Higher phytoplankton species diversity was found in March 2011 when salinity and nitrate concentrations were low and reactive silicate and inorganic phosphates were moderate. Species diversity was low during May 2010 when increased sea surface temperature, salinity and low nutrients availability were observed. Coscinodiscus centralis , Diatoma vulgaris and Proboscia alata were dominant, especially Coscinodiscus sp. distributed in all stations whereas Skeletonema costatum , Odontella sinensis and Ditylum brightwellii were abundant in August and September 2010. From principal component analysis and multiple regression analysis, it is evident that variables like sea surface temperature and dissolved oxygen are the most important factors influencing the seasonal pattern of phytoplankton population.

Description: Publication date: July 2015 Source: Global Ecology and Conservation, Volume 4 Author(s): Kamaljit K. Sangha, Andrew Le Brocque, Robert Costanza, Yvonne Cadet-James The well-being of Indigenous people in Australia and throughout the world is linked to the use and value of natural resources. This research analyses the current well-being approach applied to measure well-being of Indigenous Australians. It reports findings from three case studies in Queensland on Indigenous people’s values and concerns and their capabilities in relation to natural systems. It applies a holistic approach based upon the Millennium Ecosystem Assessment and Sen’s capability approaches and proposes an integrated well-being model by incorporating intangible values such as cultural and identity values, that are linked to people’s capabilities involving natural systems. It provides a novel way of understanding the role of natural resources in Indigenous well-being by associating natural resources with people’s capabilities. The study suggests transforming the present concept of well-being and its measures for incorporating people’s capabilities that can effectively inform future policy decision making.

Description: Publication date: Available online 25 September 2015 Source: Geoscience Frontiers Author(s): Richard M. Palin, Owen M. Weller, David J. Waters, Brendan Dyck Pseudosection modelling is rapidly becoming an essential part of a petrologist’s toolkit and often forms the basis of interpreting the tectonothermal evolution of a rock sample, outcrop, or geological region. Of the several factors that can affect the accuracy and precision of such calculated phase diagrams, “geological” uncertainty related to natural petrographic variation at the hand sample- and/or thin section-scale is rarely considered. Such uncertainty influences the sample’s bulk composition, which is the primary control on its equilibrium phase relationships and thus the interpreted pressure–temperature ( P–T ) conditions of formation. Two case study examples—a garnet–cordierite granofels and a garnet–staurolite–kyanite schist—are used to compare the relative importance that geological uncertainty has on bulk compositions determined via (1) X-ray fluorescence (XRF) or (2) point counting techniques. We show that only minor mineralogical variation at the thin-section scale propagates through the phase equilibria modelling procedure and affects the absolute P–T conditions at which key assemblages are stable. Absolute displacements of equilibria can approach ±1 kbar for only a moderate degree of modal proportion uncertainty, thus being essentially similar to the magnitudes reported for analytical uncertainties in conventional thermobarometry. Bulk compositions determined from multiple thin sections of a heterogeneous garnet–staurolite–kyanite schist show a wide range in major-element oxides, owing to notable variation in mineral proportions. Pseudosections constructed for individual point count-derived bulks accurately reproduce this variability on a case-by-case basis, though averaged proportions do not correlate with those calculated at equivalent peak P–T conditions for a whole-rock XRF-derived bulk composition. The main discrepancies relate to varying proportions of matrix phases (primarily mica) relative to porphyroblasts (primarily staurolite and kyanite), indicating that point counting preserves small-scale petrographic features that are otherwise averaged out in XRF analysis of a larger sample. Careful consideration of the size of the equilibration volume, the constituents that comprise the effective bulk composition, and the best technique to employ for its determination based on rock type and petrographic character, offer the best chance to produce trustworthy data from pseudosection analysis. Graphical abstract

Description: Publication date: Available online 25 September 2015 Source: Journal of Asian Ceramic Societies Author(s): Akinori Takeyama, Akira Idesaki, Masaki Sugimoto, Masahito Yoshikawa Ceramic yield, density, volume change and pore size distribution were measured for radiation- and thermally cured PCS powder when they were pyrolyzed in the temperature range of 673–973 K. Higher ceramic yield was obtained for radiation-cured powder due to smaller amount of evolved gas. Temperature dependence of volume change and the total pore volume show that the formation and disappearance of pores in the powders were determined by the volume shrinkage and evolution of decomposed gases. Volume shrinkage narrowed the pore size distribution for radiation-cured powder. For thermally cured powder, the narrowing of size distribution was disturbed by aggregated pores. Smaller amount of evolved gas from radiation-cured powder relative to thermally cured powder prevented the aggregation of pores and provided the narrow size distribution.

Description: Publication date: December 2015 Source: GeoResJ, Volume 8 Author(s): Wouter A. Marra, Ernst Hauber, Steven M. de Jong, Maarten G. Kleinhans Outflow channels on Mars reveal the past presence of water, possibly released from pressurized groundwater reservoirs. We aim to improve our understanding of such outflow systems in order to better constrain past hydrological conditions on Mars. We investigate the morphology of possible pressurized groundwater outflow systems on Mars and compare them to landscape evolution experiments. These experiments show that incised channels, like the classic outflow channels, form in a last, erosional, stage in morphological development. This is preceded by the formation of sedimentary lobes due to rapid water loss by infiltration. On Mars, we observe similar morphologies related to different stages of groundwater outflow in Lunae and Ophir Plana. In the experiments, pits formed by the pressure of the groundwater, whereas the pits in the source regions of the outflow channels relate to the regional tectonic structure and are not formed by groundwater alone. Faulting, subsidence and collapse likely triggered outflow from a pressurized aquifer. This scenario is consistent with the presence of one or several cryosphere-confined aquifers from the Early Hesperian to at least the middle Amazonian. A pronounced spatial trend of larger and further developed outflow systems at lower elevations suggests that features ranging from small lobes to large outflow channels were sourced from a common aquifer or from aquifers with similar pressures. The required cryosphere indicates a cold climate and enables groundwater outflow even under atmospheric conditions unfavorable for sustained presence of liquid water.

Description: Publication date: September 2015 Source: Journal of Hydrology: Regional Studies, Volume 4, Part B Author(s): Alfonso Rivera Study region Canada–USA border. Study focus Since 2005, Canada has followed international developments in transboundary groundwater issues in cooperation with its southern neighbor the United States (USA) within the Internationally Shared Aquifer Resources Management Initiative (ISARM) of UNESCO. As a result, 10 Transboundary Aquifer Systems (TAS) were identified along the border between Canada and the USA. This study is an extensive review of the current state of the 10 TAS. Documentation of scientifically-based knowledge on TAS is an important step in identifying potential issues in policies that might be adopted to address shared water-resource issues. New hydrological insights for the region This analysis emphasizes the need for more scientific data, widespread education and training, and a more clearly defined governments’ role to manage groundwater at the international level. The study reviews the current legal framework and summarises the current scientific knowledge for the TAS with respect to the hydrologic and geologic framework as well as some of the major drivers for supply and demand. It also describes the links, approach and relevance of studies on the TAS to the UN Law of Transboundary Aquifers and on how these might fit in the regional strategy for the assessment and management of the TAS. Clear communication, shared knowledge and common objectives in the management of TAS will prepare the countries for future negotiations and cooperative binational programs.

Description: Publication date: September 2015 Source: Journal of Hydrology: Regional Studies, Volume 4, Part B Author(s): Brioch Hemmings, Daren Gooddy, Fiona Whitaker, W. George Darling, Alia Jasim, Joachim Gottsmann Study region Montserrat, Lesser Antilles, Caribbean. Study focus Analysis of δ 2 H and δ 18 O isotopes, and chlorofluorocarbon (CFC) anthropogenic tracers in Montserrat groundwater provides insights into the age and provenance of the spring waters. New hydrological insights δ 2 H and δ 18 O analysis indicates uniform recharge elevations for groundwaters on Montserrat. CFC-11 and CFC-12 analysis reveals age differences between isotopically similar, high elevation springs and low elevation aquifer waters. Low CFC concentrations within a confined low elevation aquifer suggest water ages of ∼45 years. High CFC concentrations in the northern and western springs are explained by rapid infiltration of cool (high CFC concentration) rainfall into saturated compartments, with flow through the vadose zone to the phreatic zone dominated by compartment flow. Lower CFC concentrations in a number of aligned warmer springs suggest a contribution from older, warmer waters from depth. Temperatures and CFC concentrations indicate older component supply rates of up to 8 L/s to the highest yielding spring on Centre Hills, with contributions of up to 75% in the warmest spring waters.

Description: Publication date: Available online 19 November 2015 Source: Cell Reports Author(s): Samira Alliouachene, Benoit Bilanges, Gaëtan Chicanne, Karen E. Anderson, Wayne Pearce, Khaled Ali, Colin Valet, York Posor, Pei Ching Low, Claire Chaussade, Cheryl L. Scudamore, Rachel S. Salamon, Jonathan M. Backer, Len Stephens, Phill T. Hawkins, Bernard Payrastre, Bart Vanhaesebroeck In contrast to the class I phosphoinositide 3-kinases (PI3Ks), the organismal roles of the kinase activity of the class II PI3Ks are less clear. Here, we report that class II PI3K-C2β kinase-dead mice are viable and healthy but display an unanticipated enhanced insulin sensitivity and glucose tolerance, as well as protection against high-fat-diet-induced liver steatosis. Despite having a broad tissue distribution, systemic PI3K-C2β inhibition selectively enhances insulin signaling only in metabolic tissues. In a primary hepatocyte model, basal PI3P lipid levels are reduced by 60% upon PI3K-C2β inhibition. This results in an expansion of the very early APPL1-positive endosomal compartment and altered insulin receptor trafficking, correlating with an amplification of insulin-induced, class I PI3K-dependent Akt signaling, without impacting MAPK activity. These data reveal PI3K-C2β as a critical regulator of endosomal trafficking, specifically in insulin signaling, and identify PI3K-C2β as a potential drug target for insulin sensitization. Graphical abstract Teaser Organismal roles of class II PI3Ks are unclear. Alliouachene et al. show that inactivation of the class II PI3K-C2β in mice, by regulating insulin receptor trafficking, enhances insulin sensitivity and protects against high-fat-diet-induced liver steatosis. The results suggest that PI3K-C2β is a potential drug target for insulin sensitization.

Description: Publication date: Available online 19 November 2015 Source: Cell Reports Author(s): Ramanathan Narayanan, Mehdi Pirouz, Cemil Kerimoglu, Linh Pham, Robin J. Wagener, Kamila A. Kiszka, Joachim Rosenbusch, Rho H. Seong, Michael Kessel, Andre Fischer, Anastassia Stoykova, Jochen F. Staiger, Tran Tuoc BAF (Brg/Brm-associated factors) complexes play important roles in development and are linked to chromatin plasticity at selected genomic loci. Nevertheless, a full understanding of their role in development and chromatin remodeling has been hindered by the absence of mutants completely lacking BAF complexes. Here, we report that the loss of BAF155/BAF170 in double-conditional knockout (dcKO) mice eliminates all known BAF subunits, resulting in an overall reduction in active chromatin marks (H3K9Ac), a global increase in repressive marks (H3K27me2/3), and downregulation of gene expression. We demonstrate that BAF complexes interact with H3K27 demethylases (JMJD3 and UTX) and potentiate their activity. Importantly, BAF complexes are indispensable for forebrain development, including proliferation, differentiation, and cell survival of neural progenitor cells. Our findings reveal a molecular mechanism mediated by BAF complexes that controls the global transcriptional program and chromatin state in development. Graphical abstract Teaser Narayanan et al. show that elimination of both core BAF155 and BAF170 subunits causes degradation of the BAF complexes and impairment of gene expression program in forebrain development. Mechanistically, BAF complexes control key chromatin modifications (H3K27Me2/3) by modulating the activity of H3K27 demethylases JMJD3/UTX.

Description: Publication date: Available online 19 November 2015 Source: Cell Reports Author(s): Lena Seifert, Michael Deutsch, Sara Alothman, Dalia Alqunaibit, Gregor Werba, Mridul Pansari, Matthew Pergamo, Atsuo Ochi, Alejandro Torres-Hernandez, Elliot Levie, Daniel Tippens, Stephanie H. Greco, Shaun Tiwari, Nancy Ngoc Giao Ly, Andrew Eisenthal, Eliza van Heerden, Antonina Avanzi, Rocky Barilla, Constantinos P. Zambirinis, Mauricio Rendon, Donnele Daley, H. Leon Pachter, Cristina Hajdu, George Miller Dectin-1 is a C-type lectin receptor critical in anti-fungal immunity, but Dectin-1 has not been linked to regulation of sterile inflammation or oncogenesis. We found that Dectin-1 expression is upregulated in hepatic fibrosis and liver cancer. However, Dectin-1 deletion exacerbates liver fibro-inflammatory disease and accelerates hepatocarcinogenesis. Mechanistically, we found that Dectin-1 protects against chronic liver disease by suppressing TLR4 signaling in hepatic inflammatory and stellate cells. Accordingly, Dectin-1 –/– mice exhibited augmented cytokine production and reduced survival in lipopolysaccharide (LPS)-mediated sepsis, whereas Dectin-1 activation was protective. We showed that Dectin-1 inhibits TLR4 signaling by mitigating TLR4 and CD14 expression, which are regulated by Dectin-1-dependent macrophage colony stimulating factor (M-CSF) expression. Our study suggests that Dectin-1 is an attractive target for experimental therapeutics in hepatic fibrosis and neoplastic transformation. More broadly, our work deciphers critical cross-talk between pattern recognition receptors and implicates a role for Dectin-1 in suppression of sterile inflammation, inflammation-induced oncogenesis, and LPS-mediated sepsis. Graphical abstract Teaser Seifert et al. show Dectin-1 protects against chronic liver disease by suppressing TLR4 signaling via CD14 and M-CSF. This suggests that Dectin-1 is an attractive target for experimental therapeutics in hepatic fibrosis and transformation with implications for a role for Dectin-1 in suppression of sterile inflammation, inflammation-induced oncogenesis, and endotoxemia.

Description: Publication date: Available online 19 November 2015 Source: Cell Reports Author(s): Elias Björnson, Bani Mukhopadhyay, Anna Asplund, Nusa Pristovsek, Resat Cinar, Stefano Romeo, Mathias Uhlen, George Kunos, Jens Nielsen, Adil Mardinoglu Hepatocellular carcinoma (HCC) is a deadly form of liver cancer that is increasingly prevalent. We analyzed global gene expression profiling of 361 HCC tumors and 49 adjacent noncancerous liver samples by means of combinatorial network-based analysis. We investigated the correlation between transcriptome and proteome of HCC and reconstructed a functional genome-scale metabolic model (GEM) for HCC. We identified fundamental metabolic processes required for cell proliferation using the network centric view provided by the GEM. Our analysis revealed tight regulation of fatty acid biosynthesis (FAB) and highly significant deregulation of fatty acid oxidation in HCC. We predicted mitochondrial acetate as an emerging substrate for FAB through upregulation of mitochondrial acetyl-CoA synthetase (ACSS1) in HCC. We analyzed heterogeneous expression of ACSS1 and ACSS2 between HCC patients stratified by high and low ACSS1 and ACSS2 expression and revealed that ACSS1 is associated with tumor growth and malignancy under hypoxic conditions in human HCC. Graphical abstract Teaser Stratification of HCC patients is vital for the development of effective treatment strategies. Björnson et al. stratify HCC patients based on acetate utilization and find that mitochondrial acetate is a metabolic fuel under hypoxic conditions. This is mediated by ACSS1, which may be a potential therapeutic target for treatment of HCC.

Description: Publication date: Available online 19 November 2015 Source: Cell Reports Author(s): Aiming Ren, Yi Xue, Alla Peselis, Alexander Serganov, Hashim M. Al-Hashimi, Dinshaw J. Patel Naturally occurring L-glutamine riboswitches occur in cyanobacteria and marine metagenomes, where they reside upstream of genes involved in nitrogen metabolism. By combining X-ray, NMR, and MD, we characterized an L-glutamine-dependent conformational transition in the Synechococcus elongatus glutamine riboswitch from tuning fork to L-shaped alignment of stem segments. This transition generates an open ligand-binding pocket with L-glutamine selectivity enforced by Mg 2+ -mediated intermolecular interactions. The transition also stabilizes the P1 helix through a long-range “linchpin” Watson-Crick G-C pair-capping interaction, while melting a short helix below P1 potentially capable of modulating downstream readout. NMR data establish that the ligand-free glutamine riboswitch in Mg 2+ solution exists in a slow equilibrium between flexible tuning fork and a minor conformation, similar, but not identical, to the L-shaped bound conformation. We propose that an open ligand-binding pocket combined with a high conformational penalty for forming the ligand-bound state provide mechanisms for reducing binding affinity while retaining high selectivity. Graphical abstract Teaser Ren et al. report on the structural and dynamic basis of low-affinity, high-selectivity binding of L-glutamine by the glutamine riboswitch. Molecular recognition of the bound L-glutamine in an open pocket is driven by a long-range linchpin G-C pairing capping interaction, resulting in a tuning fork to L-shaped conformational transition.

Description: Publication date: Available online 19 November 2015 Source: Cell Reports Author(s): Anne Teissier, Alexei Chemiakine, Benjamin Inbar, Sneha Bagchi, Russell S. Ray, Richard D. Palmiter, Susan M. Dymecki, Holly Moore, Mark S. Ansorge Despite the well-established role of serotonin signaling in mood regulation, causal relationships between serotonergic neuronal activity and behavior remain poorly understood. Using a pharmacogenetic approach, we find that selectively increasing serotonergic neuronal activity in wild-type mice is anxiogenic and reduces floating in the forced-swim test, whereas inhibition has no effect on the same measures. In a developmental mouse model of altered emotional behavior, increased anxiety and depression-like behaviors correlate with reduced dorsal raphé and increased median raphé serotonergic activity. These mice display blunted responses to serotonergic stimulation and behavioral rescues through serotonergic inhibition. Furthermore, we identify opposing consequences of dorsal versus median raphé serotonergic neuron inhibition on floating behavior, together suggesting that median raphé hyperactivity increases anxiety, whereas a low dorsal/median raphé serotonergic activity ratio increases depression-like behavior. Thus, we find a critical role of serotonergic neuronal activity in emotional regulation and uncover opposing roles of median and dorsal raphé function. Graphical abstract Teaser Teissier et al. report that acute activation of serotonergic neurons is anxiogenic. Inhibition has no effect in naive mice but restores normal behavior in a developmental model of anxiety and depression. Normalization of unbalanced serotonergic activity between the median and dorsal raphé nuclei likely underlies this beneficial effect.

Description: Publication date: Available online 25 November 2015 Source: Cell Reports Author(s): Isabel Siegert, Johannes Schödel, Manfred Nairz, Valentin Schatz, Katja Dettmer, Christopher Dick, Joanna Kalucka, Kristin Franke, Martin Ehrenschwender, Gunnar Schley, Angelika Beneke, Jörg Sutter, Matthias Moll, Claus Hellerbrand, Ben Wielockx, Dörthe M. Katschinski, Roland Lang, Bruno Galy, Matthias W. Hentze, Peppi Koivunen, Peter J. Oefner, Christian Bogdan, Günter Weiss, Carsten Willam, Jonathan Jantsch Both hypoxic and inflammatory conditions activate transcription factors such as hypoxia-inducible factor (HIF)-1α and nuclear factor (NF)-κB, which play a crucial role in adaptive responses to these challenges. In dendritic cells (DC), lipopolysaccharide (LPS)-induced HIF1α accumulation requires NF-κB signaling and promotes inflammatory DC function. The mechanisms that drive LPS-induced HIF1α accumulation under normoxia are unclear. Here, we demonstrate that LPS inhibits prolyl hydroxylase domain enzyme (PHD) activity and thereby blocks HIF1α degradation. Of note, LPS-induced PHD inhibition was neither due to cosubstrate depletion (oxygen or α-ketoglutarate) nor due to increased levels of reactive oxygen species, fumarate, and succinate. Instead, LPS inhibited PHD activity through NF-κB-mediated induction of the iron storage protein ferritin and subsequent decrease of intracellular available iron, a critical cofactor of PHD. Thus, hypoxia and LPS both induce HIF1α accumulation via PHD inhibition but deploy distinct molecular mechanisms (lack of cosubstrate oxygen versus deprivation of co-factor iron). Graphical abstract Teaser Siegert et al. find that the microbial cell wall component LPS reduces cytosolic free iron availability via induction of ferritin. Low free iron levels impair the prolyl hydroxylase domain enzyme (PHD) activity, thereby inhibiting hypoxia-inducible factor (HIF)-1α hydroxylation. This results in inflammatory HIF1α stabilization under normoxic conditions.

Description: Publication date: Available online 25 November 2015 Source: Cell Reports Author(s): Jeffrey M. Bhasin, Byron H. Lee, Lars Matkin, Margaret G. Taylor, Bo Hu, Yaomin Xu, Cristina Magi-Galluzzi, Eric A. Klein, Angela H. Ting A critical need in understanding the biology of prostate cancer is characterizing the molecular differences between indolent and aggressive cases. Because DNA methylation can capture the regulatory state of tumors, we analyzed differential methylation patterns genome-wide among benign prostatic tissue and low-grade and high-grade prostate cancer and found extensive, focal hypermethylation regions unique to high-grade disease. These hypermethylation regions occurred not only in the promoters of genes but also in gene bodies and at intergenic regions that are enriched for DNA-protein binding sites. Integration with existing RNA-sequencing (RNA-seq) and survival data revealed regions where DNA methylation correlates with reduced gene expression associated with poor outcome. Regions specific to aggressive disease are proximal to genes with distinct functions from regions shared by indolent and aggressive disease. Our compendium of methylation changes reveals crucial molecular distinctions between indolent and aggressive prostate cancer. Graphical abstract Teaser Bhasin et al. find that gains of DNA methylation at certain loci can distinguish indolent from aggressive forms of prostate cancer. These genomic regions of focal hypermethylation fall in diverse genomic contexts, are enriched for regulatory elements, and correlate with the expression of genes linked to poorer outcomes.

Description: Publication date: Available online 25 November 2015 Source: Cell Reports Author(s): Chong Yew Tan, Samuel Virtue, Guillaume Bidault, Martin Dale, Rachel Hagen, Julian L. Griffin, Antonio Vidal-Puig Although many transcriptional pathways regulating BAT have been identified, the role of lipid biosynthetic enzymes in thermogenesis has been less investigated. Whereas cold exposure causes changes in the fatty acid composition of BAT, the functional consequences of this remains relatively unexplored. In this study, we demonstrate that the enzyme Elongation of Very Long Chain fatty acids 6 (Elovl6) is necessary for the thermogenic action of BAT. Elovl6 is responsible for converting C16 non-essential fatty acids into C18 species. Loss of Elovl6 does not modulate traditional BAT markers; instead, it causes reduced expression of mitochondrial electron transport chain components and lower BAT thermogenic capacity. The reduction in BAT activity appears to be counteracted by increased beiging of scWAT. When beige fat is disabled by thermoneutrality or aging, Elovl6 KO mice gain weight and have increased scWAT mass and impaired carbohydrate metabolism. Overall, our study suggests fatty acid chain length is important for BAT function. Graphical abstract Teaser Tan et al. find that the elongation of non-essential C16 fatty acids to C18 species regulates mitochondrial function and is necessary for full recruitment of heat-generating brown adipose tissue.