ALBERT

Description: Effects of seawater p CO 2 changes on the calcifying fluid of scleractinian corals Biogeosciences Discussions, 9, 2655-2689, 2012 Author(s): S. Hohn and A. Merico Rising atmospheric CO 2 concentrations due to anthropogenic emissions induce changes in the ocean carbonate chemistry and a drop in ocean pH. This acidification process is expected to harm calcifying organisms like coccolithophores, molluscs, echinoderms, and corals. A severe decline in coral abundance is, for example, expected by the end of this century with associated disastrous effects on reef ecosystems. Despite the growing importance of the topic, little progress has been made with respect to modelling the impact of acidification on coral calcification. Here we present a model for a coral polyp that simulates the carbonate system in four different compartments: the seawater, the polyp tissue, the coelenteron, and the calicoblastic layer. Precipitation of calcium carbonate takes place in the metabolically controlled calicoblastic layer beneath the polyp tissue. The model is adjusted to a state of activity as observed by direct microsensor measurements in the calcifying fluid. Simulated CO 2 perturbation experiments reveal decreasing calcification rates under elevated p CO 2 despite strong metabolic control of the calcifying fluid. Diffusion of CO 2 through the tissue into the calicoblastic layer increases with increasing seawater p CO 2 leading to decreased aragonite saturation in the calcifying fluid of the coral polyp. Our modelling study provides important insights into the complexity of the calcification process at the organism level and helps to quantify the effect of ocean acidification on corals.

Description: The role of the seagrass Posidonia oceanica in the cycling of trace elements Biogeosciences Discussions, 9, 2623-2653, 2012 Author(s): C. Sanz-Lázaro, P. Malea, E. T. Apostolaki, I. Kalantzi, A. Marín, and I. Karakassis The aim of this work was to study the role of the seagrass Posidonia oceanica on the cycling of a wide set of trace elements (Ag, As, Ba, Bi, Cd, Co, Cr, Cs, Cu, Fe, Ga, Li, Mn, Ni, Pb, Rb, Sr, Tl, V and Zn). We measured the concentration of these trace elements in the different compartments of P. oceanica (leaves, rhizomes, roots and epibiota) in a non-polluted seagrass meadow representative of the Mediterranean and calculated the annual budget from a mass balance. We provide novel data on accumulation dynamics of many trace elements in P. oceanica compartments and demonstrate that trace element accumulation patterns are mainly determined by plant compartment rather than by temporal variability. Epibiota was the compartment which showed the greatest concentrations for most trace elements. Thus, they constitute a key compartment when estimating trace element transfer to higher trophic levels by P. oceanica . For most trace elements, translocation seemed to be low and acropetal. Zn, Cd, Sr and Rb were the trace elements that showed the highest release rate through decomposition of plant detritus, while Cs, Tl and Bi the lowest. P. oceanica acts as a sink of potentially toxic trace elements (Ni, Cr, As and Ag), which can be sequestered, decreasing their bioavailability. P. oceanica may have a relevant role in the cycling of trace elements in the Mediterranean.

Description: Direct observations of diel biological CO 2 fixation in the oceans Biogeosciences Discussions, 9, 2153-2168, 2012 Author(s): H. Thomas, S. E. Craig, B. J. W. Greenan, W. Burt, G. J. Herndl, S. Higginson, L. Salt, E. H. Shadwick, and J. Urrego-Blanco Much of the variability in the surface ocean's carbon cycle can be attributed to the availability of sunlight, through processes such as heat fluxes and photosynthesis, which regulate over a wide range of time scales. The critical processes occurring on timescales of a day or less, however, have undergone few investigations, and most of these have been limited to a time span of several days to months, or exceptionally, for longer periods. Optical methods have helped to infer short-term biological variability, however corresponding investigations of the oceanic CO 2 system are lacking. We employ high-frequency CO 2 and optical observations covering the full seasonal cycle on the Scotian Shelf, Northwestern Atlantic Ocean, in order to unravel diel periodicity of the surface ocean carbon cycle and its effects on annual budgets. Significant diel periodicity occurs only if the water column is sufficiently stable as observed during seasonal warming. During that time biological CO 2 drawdown, or net community production (NCP), is delayed for several hours relative to the onset of photosynthetically available radiation (PAR), due to diel cycles in chlorophyll- a concentration and to grazing, both of which, we suggest, inhibit NCP in the early morning hours. In summer, NCP decreases by more than 90 %, coinciding with the seasonal minimum of the mixed layer depth and resulting in the disappearance of the diel CO 2 periodicity in the surface waters.

Description: Contribution of flowering trees to urban atmospheric biogenic volatile organic compound emissions Biogeosciences Discussions, 9, 3145-3172, 2012 Author(s): R. Baghi, D. Helmig, A. Guenther, T. Duhl, and R. Daly Emissions of biogenic volatile organic compounds (BVOC) from urban trees during and after blooming were measured during spring and early summer 2009 in Boulder, Colorado. Air samples were collected onto solid adsorbent cartridges from branch enclosures on the tree species crabapple, horse chestnut, honey locust, and hawthorn. These species constitute ~65 % of the insect-pollinated fraction of the flowering tree canopy (excluding catkin-producing trees) from the street area managed by the City of Boulder. Samples were analyzed for C 10 –C 15 BVOC by thermal desorption and gas chromatography coupled to a flame ionization detector and a mass spectrometer (GC/FID/MS). Identified emissions and emission rates from these four tree species during the flowering phase were found to vary over a wide range. Monoterpene emissions were identified for honey locust, horse chestnut and hawthorn. Sesquiterpene emissions were observed in horse chestnut and hawthorn samples. Crabapple flowers were found to emit significant amounts of benzyl alcohol and benzaldehyde. Floral BVOC emissions increased with temperature, generally exhibiting exponential temperature dependence. Changes in BVOC speciation during and after the flowering period were observed for every tree studied. Emission rates were significantly higher during the blooming compared to the vegetative state for crabapple and honey locust. Total normalized (30 °C) monoterpene emissions from honey locust were higher during flowering (5.26 μg Cg −1 h −1 ) than after flowering (1.23 μg Cg −1 h −1 ). The total normalized BVOC emission rate from crabapple (93 μg Cg −1 h −1 ) during the flowering period is of the same order as isoprene emissions from oak trees, which are among the highest BVOC emissions observed from plants to date. These findings illustrate that during the relatively brief springtime flowering period, floral emissions constitute by far the most significant contribution to the BVOC flux from these tree species, some of which are leafless at this time. Experimental results were integrated into the MEGAN biogenic emission model and simulations were performed to estimate the contribution of floral BVOC emissions to the total urban BVOC flux during the spring flowering period. The floral BVOC emitted during this three-month simulation are equivalent to 11 % of the cumulative monoterpene flux for the Boulder urban area.

Description: Contributions of ectomycorrhizal fungal mats to forest soil respiration Biogeosciences Discussions, 9, 1635-1666, 2012 Author(s): C. L. Phillips, L. A. Kluber, J. P. Martin, B. A. Caldwell, and B. J. Bond Distinct aggregations of fungal hyphae and rhizomorphs, or "mats" formed by some genera of ectomycorrhizal (EcM) fungi are common features of soils in coniferous forests of the Pacific Northwest. We measured in situ respiration rates of Piloderma mats and neighboring non-mat soils in an old-growth Douglas-fir forest in Western Oregon to investigate whether there was an incremental increase in respiration from mat soils, and to estimate mat contributions to total soil respiration. We found that areas where Piloderma mats colonized the organic horizon often had higher soil surface flux than non-mats, with the incremental increase in respiration averaging 16 % across two growing seasons. Both soil physical factors and biochemistry were related to the higher surface flux of mat soils. When air-filled pore space was low (high soil moisture), soil CO 2 production was concentrated into near-surface soil horizons where mats tend to colonize, resulting in greater apparent differences in respiration between mat and non-mat soils. Respiration rates were also correlated with the activity of chitin-degrading soil enzymes. This suggests that the elevated activity of fungal mats may be related to consumption or turnover of chitinous fungal cell-wall materials. We found Piloderma mats present across 57 % of the soil surface in the study area, and use this value to estimate a respiratory contribution from mats at the stand-scale of about 9 % of total soil respiration. The activity of EcM mats, which includes both EcM fungi and microbial associates, was estimated to constitute a substantial portion of total soil respiration in this old-growth Douglas-fir forest.

Description: Remote sensing-based estimation of gross primary production in a subalpine grassland Biogeosciences Discussions, 9, 1711-1758, 2012 Author(s): M. Rossini, S. Cogliati, M. Meroni, M. Migliavacca, M. Galvagno, L. Busetto, E. Cremonese, T. Julitta, C. Siniscalco, U. Morra di Cella, and R. Colombo This study investigates the performances in a terrestrial ecosystem of gross primary production (GPP) estimation of a suite of spectral vegetation indexes (VIs) that can be computed from currently orbiting platforms. Vegetation indexes were computed from near-surface field spectroscopy measurements collected using an automatic system designed for high temporal frequency acquisition of spectral measurements in the visible near-infrared region. Spectral observations were collected for two consecutive years in Italy in a subalpine grassland equipped with an Eddy Covariance (EC) flux tower which provides continuous measurements of net ecosystem carbon dioxide (CO 2 ) exchange (NEE) and the derived GPP. Different VIs were calculated based on ESA-MERIS and NASA-MODIS spectral bands and correlated with biophysical (Leaf Area Index, LAI; fraction of photosynthetically active radiation intercepted by green vegetation, f IPAR g ), biochemical (chlorophyll concentration) and ecophysiological (green light-use efficiency, LUE g ) canopy variables. In this study, the normalized difference vegetation index (NDVI) showed better correlations with LAI and f PAR g ( r = 0.90 and 0.95, respectively), the MERIS terrestrial chlorophyll index (MTCI) with leaf chlorophyll content ( r = 0.91) and the Photochemical Reflectance Index (PRI 551 ), computed as ( R 531 − R 551 )/( R 531 + R 551 ) with LUE g ( r = 0.64). Subsequently, these VIs were used to estimate GPP using different modelling solutions based on the light-use efficiency model describing the GPP as driven by the photosynthetically active radiation absorbed by green vegetation (APAR g ) and by the efficiency (ε) with which plants use the absorbed radiation to fix carbon via photosynthesis. Results show that GPP can be successfully modelled with a combination of VIs and meteorological data or VIs only. Vegetation indexes designed to be more sensitive to chlorophyll content explained most of the variability in GPP in the ecosystem investigated, characterized by a strong seasonal dynamic of GPP. Accuracy in GPP estimation slightly improves when taking into account high frequency modulations of GPP driven by incident PAR or modelling LUE g with the PRI in model formulation. Similar results were obtained for both measured daily VIs and VIs obtained as 16-day composite time series and then downscaled from the compositing period to daily scale (resampled data). However, the use of resampled data rather than measured daily input data decreases the accuracy of the total GPP estimation on an annual basis.

Description: Soil organic carbon storage changes in coastal wetlands of the modern Yellow River Delta from 2000 to 2009 Biogeosciences Discussions, 9, 1759-1779, 2012 Author(s): J. Yu, Y. Wang, Y. Li, H. Dong, D. Zhou, G. Han, H. Wu, G. Wang, P. Mao, and Y. Gao Soil carbon sequestration plays an essential role in mitigating CO 2 increases and the subsequently global greenhouse effect. The storages and dynamics of soil organic carbon (SOC) of 0–30 cm soil depth in different landscape types including beaches, reservoir and pond, reed wetland, forest wetland, bush wetland, farmland, building land, bare land (severe saline land) and salt field in the modern Yellow River Delta (YRD), were studied based on the data of the regional survey and laboratory analysis. The landscape types were classified by the interpretation of remote sensing images of 2000 and 2009, which was calibrated by field survey results. The results revealed an increase of 10.59 km 2 in the modem YRD area from 2000 to 2009. The SOC density varied ranging from 0.73 kg m −2 to 21.60 kg m −2 at depth of 30 cm. There were ~3.97 × 10 6 t and 3.98 × 10 6 t SOC stored in the YRD in 2000 and 2009, respectively. The SOC storages changed greatly in beaches, bush wetland, farm land and salt field which were affected dominantly by anthropogenic activities. The area of the YRD increased greatly within 10 yr, however, the small increase of SOC storage in the region was observed due to landscape changes, indicating that the modern YRD was a potential carbon sink and anthropogenic activity was a key factor for SOC change.

Description: Micro-relief heterogeneity can lead to substantial variability in microclimate and hence niche opportunities on a small scale. We explored the relationship between plant species richness and small-scale heterogeneity of micro-relief on the subtropical island of La Palma, Canary Islands. Overall, we sampled 40 plots in laurel and pine forests at four altitudinal bands. Species richness was recorded separately for various growth forms (i.e., mosses, herbaceous and woody plants). Site conditions such as altitude, slope, aspect, and tree density were measured. Micro-relief heterogeneity was characterized by surface structure and a subsequently derived surface heterogeneity index. The effect of micro-relief heterogeneity on species richness was analysed by means of linear mixed effect models and variance partitioning. Effects of micro-relief heterogeneity on species richness varied considerably between growth forms. While moss richness was affected significantly by micro-relief heterogeneity, herbaceous and woody plants richness responded mainly to larger-scale site conditions such as aspect and tree density. Our results stress the importance of small-scale relief heterogeneity for the explanation of spatial patterns of species richness. This poses new challenges as small-scale heterogeneity is largely underrepresented, e.g. with regard to its application in species distribution models.

Description: Implications of observed inconsistencies in carbonate chemistry measurements for ocean acidification studies Biogeosciences Discussions, 9, 1781-1792, 2012 Author(s): C. J. M. Hoppe, G. Langer, S. D. Rokitta, D. A. Wolf-Gladrow, and B. Rost The growing field of ocean acidification research is concerned with the investigation of organisms' responses to increasing p CO 2 values. One important approach in this context is culture work using seawater with adjusted CO 2 levels. As aqueous p CO 2 is difficult to measure directly in small scale experiments, it is generally calculated from two other measured parameters of the carbonate system (often A T , C T or pH). Unfortunately, the overall uncertainties of measured and subsequently calculated values are often unknown. Especially under high p CO 2 , this can become a severe problem with respect to the interpretation of physiological and ecological data. In the few datasets from ocean acidification research where all three of these parameters were measured, p CO 2 values calculated from A T and C T are typically about 30 % lower (i.e. ~300 μatm at a target p CO 2 of 1000 μatm) than those calculated from A T and pH or C T and pH. This study presents and discusses these discrepancies as well as likely consequences for the ocean acidification community. Until this problem is solved, one has to consider that calculated parameters of the carbonate system (e.g. p CO 2 , calcite saturation state) may not be comparable between studies, and that this may have important implications for the interpretation of CO 2 perturbation experiments.

Description: Riverine influence on the tropical Atlantic Ocean biogeochemistry Biogeosciences Discussions, 9, 1945-1969, 2012 Author(s): L. Cotrim da Cunha and E. T. Buitenhuis We assess the role of riverine inputs of N, Si, Fe, organic and inorganic C in the tropical Atlantic Ocean using a global ocean biogeochemistry model. We use two sensitivity tests to investigate the role of the western (South American Rivers) and eastern (African Rivers) riverine nutrient inputs on the tropical Atlantic Ocean biogeochemistry (between 20° S–20° N and 70° W–20°). Increased nutrient availability from river inputs in this area (compared to an extreme scenario with no river nutrients) leads to an increase in 14 % (0.7 Pg C a −1 ) in open ocean primary production (PP), and 21 % (0.2 Pg C a −1 ) in coastal ocean PP. We estimate very modest increases in open and coastal ocean export production and sea-air CO 2 fluxes. Results suggest that in the tropical Atlantic Ocean, the large riverine nutrient inputs on the western side have a larger impact on primary production and sea-air CO 2 exchanges. On the other hand, African river inputs, although smaller than South American inputs, have larger impact on the coastal and open tropical Atlantic Ocean export production. This is probably due to a combination of nutrient trapping in upwelling areas off the Congo River outflow, and differences in delivered nutrient ratios leading to alleviation in limitation conditions mainly for diatoms.

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 Insulin stimulates glucose uptake through the membrane translocation of GLUT4 and GLUT1. Peroxisome proliferator-activated receptor γ (PPARγ) enhances insulin sensitivity. Here, we demonstrate that insulin stimulates GLUT4 and GLUT1 translocation, and glucose uptake, by activating the signaling pathway involving nicotinic acid adenine dinucleotide phosphate (NAADP), a calcium mobilizer, in adipocytes. We also demonstrate that PPARγ mediates insulin sensitization by enhancing NAADP production through upregulation of CD38, the only enzyme identified for NAADP synthesis. Insulin produced NAADP by both CD38-dependent and -independent pathways, whereas PPARγ produced NAADP by CD38-dependent pathway. Blocking the NAADP signaling pathway abrogated both insulin-stimulated and PPARγ-induced GLUT4 and GLUT1 translocation, thereby inhibiting glucose uptake. CD38 knockout partially inhibited insulin-stimulated glucose uptake. However, CD38 knockout completely blocked PPARγ-induced glucose uptake in adipocytes and PPARγ-mediated amelioration of glucose tolerance in diabetic mice. These results demonstrated that the NAADP signaling pathway is a critical molecular target for PPARγ-mediated insulin sensitization. Graphical abstract Highlights ► Insulin induces glucose uptake via NAADP-mediated calcium increase ► PPARγ mediates insulin sensitization by upregulating the NAADP-producing enzyme CD38 ► PPARγ agonists ameliorate glucose tolerance by CD38 upregulation

Description: Available online 27 December 2012 Publication year: 2012 Source: Cell Reports Enveloped viruses have developed various adroit mechanisms to invade their host cells. This process requires one or more viral envelope glycoprotein to achieve cell attachment and membrane fusion. Members of the Flaviviridae such as flaviviruses possess only one envelope glycoprotein, E, whereas pestiviruses and hepacivirus encode two glycoproteins, E1 and E2. Although E2 is involved in cell attachment, it has been unclear which protein is responsible for membrane fusion. We report the crystal structures of the homodimeric glycoprotein E2 from the pestivirus bovine viral diarrhea virus 1 (BVDV1) at both neutral and low pH. Unexpectedly, BVDV1 E2 does not have a class II fusion protein fold, and at low pH the N-terminal domain is disordered, similarly to the intermediate postfusion state of E2 from sindbis virus, an alphavirus. Our results suggest that the pestivirus and possibly the hepacivirus fusion machinery are unlike any previously observed. Graphical abstract Highlights ► Structure of the major antigenically dominant protein of BVDV ► The overall fold of BVDV E2 shows no similarity to the class II fusion proteins ► At low pH, BVDV E2 N-terminal domain is disordered ► Entry mechanism of BVDV is probably applicable to hepatitis C virus

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 Controversy has recently arisen over the role of sirtuins in metazoan aging. In this issue of Cell Reports , Banerjee et al. demonstrate that Drosophila Sir2 is necessary for life span extension in response to dietary restriction and that its overexpression in the fat body increases the life span.

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 Inhibition of sirtuin 2 (SIRT2) deacetylase mediates protective effects in cell and invertebrate models of Parkinson’s disease and Huntington’s disease (HD). Here we report the in vivo efficacy of a brain-permeable SIRT2 inhibitor in two genetic mouse models of HD. Compound treatment resulted in improved motor function, extended survival, and reduced brain atrophy and is associated with marked reduction of aggregated mutant huntingtin, a hallmark of HD pathology. Our results provide preclinical validation of SIRT2 inhibition as a potential therapeutic target for HD and support the further development of SIRT2 inhibitors for testing in humans. Graphical abstract Highlights ► Sirtuin 2 (SIRT2) inhibition is neuroprotective in two HD mouse models ► SIRT2 inhibitor treatment markedly reduces huntingtin aggregates in HD mouse brain ► SIRT2 is a promising therapeutic target for neurological protein aggregation disorders

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 Planar cell polarity (PCP) refers to the collective orientation of cells within the epithelial plane. We show that progenitor cells forming the ducts of the embryonic pancreas express PCP proteins and exhibit an active PCP pathway. Planar polarity proteins are acquired at embryonic day 11.5 synchronously to apicobasal polarization of pancreas progenitors. Loss of function of the two PCP core components Celsr2 and Celsr3 shows that they control the differentiation of endocrine cells from polarized progenitors, with a prevalent effect on insulin-producing beta cells. This results in a decreased glucose clearance. Loss of Celsr2 and 3 leads to a reduction of Jun phosphorylation in progenitors, which, in turn, reduces beta cell differentiation from endocrine progenitors. These results highlight the importance of the PCP pathway in cell differentiation in vertebrates. In addition, they reveal that tridimensional organization and collective communication of cells are needed in the pancreatic epithelium in order to generate appropriate numbers of endocrine cells. Graphical abstract Highlights ► PCP proteins are restricted to progenitor cells in the embryonic pancreas ► The PCP core components Celsr2 and Celsr3 control endocrine cell differentiation ► This effect is mediated by the JNK pathway

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 MicroRNAs (miRNAs) are small, noncoding RNAs that inhibit translation and promote mRNA decay. The levels of mature miRNAs are the result of different rates of transcription, processing, and turnover. The noncanonical polymerase Gld2 has been implicated in the stabilization of miR-122, possibly through catalyzing 3′ monoadenylation; however, there is little evidence that this relationship is one of cause and effect. Here, we biochemically characterize Gld2’s involvement in miRNA monoadenylation and its effect on miRNA stability. We find that Gld2 directly monoadenylates and stabilizes specific miRNA populations in human fibroblasts and that sensitivity to monoadenylation-induced stability depends on nucleotides in the miRNA 3′ end. These results establish a mechanism of miRNA stability and resulting posttranscriptional gene regulation. Graphical abstract Highlights ► Gld2 monoadenylates specific microRNAs (miRNAs) ► Monoadenylation stabilizes miRNA subpopulations and prolongs their activity ► Sensitivity to monoadenylation and stability depends on nucleotides in the miRNA 3′ end

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 In the cytoplasm, the correct delivery of membrane proteins is an essential and highly regulated process. The posttranslational targeting of the important tail-anchor membrane (TA) proteins has recently been under intense investigation. A specialized pathway, called the guided entry of TA proteins (GET) pathway in yeast and the transmembrane domain recognition complex (TRC) pathway in vertebrates, recognizes endoplasmic-reticulum-targeted TA proteins and delivers them through a complex series of handoffs. An early step is the formation of a complex between Sgt2/SGTA, a cochaperone with a presumed ubiquitin-like-binding domain (UBD), and Get5/UBL4A, a ubiquitin-like domain (UBL)-containing protein. We structurally characterize this UBD/UBL interaction for both yeast and human proteins. This characterization is supported by biophysical studies that demonstrate that complex formation is mediated by electrostatics, generating an interface that has high-affinity with rapid kinetics. In total, this work provides a refined model of the interplay of Sgt2 homologs in TA targeting. Graphical abstract Highlights ► Sgt2 homologs contain dimerization motifs that are novel UBDs ► The UBL of Get5 homologs has features that distinguish it from other UBLs ► Complex formation of Sgt2 and Get5 includes a conserved and dynamic interface ► The system can rapidly discriminate between other UBL pathways

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 Chimera formation after blastocyst injection or morula aggregation is the principal functional assay of the developmental potential of mouse embryonic stem cells (ESCs). This property, which demonstrates functional equivalence between ESCs and the preimplantation epiblast, is not shared by epiblast stem cell (EpiSC) lines. Here, we show that EpiSCs derived either from postimplantation embryos or from ESCs in vitro readily generate chimeras when grafted to postimplantation embryos in whole embryo culture. EpiSC derivatives integrate and differentiate to derivatives of all three embryonic germ layers and primordial germ cells. In contrast, grafted ESCs seldom proliferate in postimplantation embryos, and fail to acquire the identity of their host-derived neighbors. EpiSCs do not incorporate efficiently into embryonic day 8.5 embryos, a stage by which pluripotency has been lost. Thus, chimera formation by EpiSCs requires a permissive environment, the postimplantation epiblast, and demonstrates functional equivalence between this cell type and EpiSCs. Graphical abstract Highlights ► Epiblast stem cells (EpiSCs) form chimeras when injected into postimplantation epiblast ► Embryonic stem cells do not form postimplantation chimeras ► EpiSCs do not integrate if they are injected after gastrulation

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 An increased understanding of antitumor immunity is necessary for improving cell-based immunotherapies against human cancers. Here, we investigated the roles of two immune system-expressed microRNAs (miRNAs), miR-155 and miR-146a, in the regulation of antitumor immune responses. Our results indicate that miR-155 promotes and miR-146a inhibits interferon γ (IFNγ) responses by T cells and reduces solid tumor growth in vivo. Using a double-knockout (DKO) mouse strain deficient in both miR-155 and miR-146a, we have also identified an epistatic relationship between these two miRNAs. DKO mice had defective T cell responses and tumor growth phenotypes similar to miR-155 −/− mice. Further analysis of the T cell compartment revealed that miR-155 modulates IFNγ expression through a mechanism involving repression of Ship1. Our work reveals critical roles for miRNAs in the reciprocal regulation of CD4 + and CD8 + T cell-mediated antitumor immunity and demonstrates the dominant nature of miR-155 during its promotion of immune responses. Graphical abstract Highlights ► miR-155 promotes and miR-146a inhibits both CD4+ and CD8+ T cell antitumor responses ► DKO mice reveal epistasis between miR-155 and miR-146a during tumor immunity ► miR-155 regulation of IFNγ involves repression of its target Ship1 in T cells

Description: Available online 29 December 2012 Publication year: 2012 Source: FEBS Open Bio A water-soluble selenoxide (DHS ox ) having a five-membered ring structure enables rapid and selective conversion of cysteinyl SH groups in a polypeptide chain into SS bonds in a wide pH and temperature range. It was previously demonstrated that the second-order rate constants for the SS formation with DHS ox would be proportional to the number of the free SH groups present in the substrate if there is no steric congestion around the SH groups. In the present study, kinetics of the SS formation with DHS ox was extensively studied at pH 4–10 and 25°C by using reduced ribonuclease A, recombinant hirudin variant (CX-397), insulin A- and B-chains, and relaxin A-chain, which have two to eight cysteine residues, as polythiol substrates. The obtained rate constants showed stochastic SS formation behaviors under most conditions. However, the rate constants for CX-397 at pH 8.0 and 10.0 were not proportional to the number of the free SH groups, suggesting that the SS intermediate ensembles possess densely packed structures under weakly basic conditions. The high two-electron redox potential of DHS ox (375 mV at 25°C) compared to L-cystine supported the high ability of DHS ox for SS formation in a polypeptide chain. Interestingly, the rate constants of the SS formation jumped up at a pH around the p K a value of the cysteinyl SH groups. The SS formation velocity was slightly decreased by addition of a denaturant due probably to the interaction between the denaturant and the peptide. The stochastic behaviors as well as the absolute values of the second-order rate constants in comparison to dithiothreitol (DTT red ) are useful to probe the chemical reactivity and conformation, hence the folding, of polypeptide chains. Graphical abstract Highlights ▸ DHS ox was applied as a SS-forming reagent for five polythiol peptides and DTT red . ▸ The SS formation velocities depend on the kind of substrate and solvent conditions. ▸ The SS-formation rate constants are proportional to the number of free SH groups. ▸ Folded structures and SH p K a modify the stochastic nature and absolute values of the rate constants. ▸ DHS ox is a useful probe of chemical reactivity and intermediate structures in oxidative protein folding.

Description: Coral Patch seamount (NE Atlantic) – a sedimentological and macrofaunal reconnaissance based on video and hydroacoustic surveys Biogeosciences Discussions, 9, 18707-18753, 2012 Author(s): C. Wienberg, P. Wintersteller, L. Beuck, and D. Hebbeln The present study provides new knowledge about the so far largely unexplored Coral Patch seamount which is located in the NE Atlantic Ocean half-way between the Iberian Peninsula and Madeira. For the first time a detailed hydroacoustic mapping (MBES) in conjunction with video surveys (ROV, camera sled) were performed to describe the sedimentological and biological characteristics of this sub-elliptical ENE-WSW elongated seamount. Video observations were restricted to the south-western summit area of Coral Patch seamount (area: ~ 8 km 2 , water depth: 560–760 m) and revealed that this part of the summit is dominated by exposed hard substrate, whereas soft sediment is just a minor substrate component. Although exposed hardgrounds are dominant for this summit area, and thus, offer suitable habitat for settlement by benthic organisms, the macrofauna shows rather low abundance and diversity. In particular, scleractinian framework-building cold-water corals are apparently rare with very few isolated and small-sized live occurrences of the species Lophelia pertusa and Madrepora oculata . In contrast, dead coral framework and coral rubble are more frequent pointing to a higher abundance of cold-water corals on Coral Patch during the recent past. This is even supported by the observation of fishing lines that got entangled with rather fresh-looking coral frameworks. Overall, long lines and various species of commercially important fish were frequently observed emphasising the potential of Coral Patch as an important target for fisheries that may have impacted the entire benthic community. Hydroacoustic seabed classification covered the entire summit of Coral Patch and its northern and southern flanks (area: 560 km 2 ; water depth: 560–2660 m) and revealed extended areas dominated by mixed and soft sediments at the northern flank and to a minor degree at its easternmost summit and southern flank. Nevertheless, also these data predict most of the summit area to be dominated by exposed bedrock which would offer suitable habitat for benthic organisms. By comparing the locally restricted video observations and the broad-scale monitoring of a much larger and deeper seafloor area as derived by hydroacoustic seabed classification, it becomes obvious that habitat information obtained by in situ sampling may provide a rather scattered pattern about the entire seamount ecosystem. Solely with a combination of both methods, a satisfactory approach to describe the diverse characteristics of a seamount ecosystem can be derived which is in turn indispensable for future scientific monitoring campaigns as well as management and conservation purposes.

Description: High-resolution measurements of atmospheric molecular hydrogen and its isotopic composition at the West African coast of Mauritania Biogeosciences Discussions, 9, 18799-18829, 2012 Author(s): S. Walter, A. Kock, and T. Röckmann Oceans are a net source of molecular hydrogen (N 2 ) to the atmosphere, where nitrogen (N 2 ) fixation is assumed to be the main biological production pathway besides photochemical production from organic material. The sources can be distinguished using isotope measurements because of clearly differing isotopic signatures of the produced hydrogen. Here we present the first ship-borne measurements of atmospheric molecular H 2 mixing ratio and isotopic composition at the West African coast of Mauritania (16–25° W, 17–24° N). This area is one of the biologically most active regions of the world's oceans with seasonal upwelling events and characterized by strongly differing hydrographical/biological properties and phytoplankton community structures. The aim of this study was to identify areas of H 2 production and distinguish H 2 sources by isotopic signatures of atmospheric H 2 . Besides this a diurnal cycle of atmospheric H 2 was investigated. For this more than 100 air samples were taken during two cruises in February 2007 and 2008, respectively. During both cruises a transect from the Cape Verde Island towards the Mauritanian Coast was sampled. In 2007 additionally four days were sampled with a high resolution of one sample per hour. Our results clearly indicate the influence of local sources and suggest the Banc d'Arguin as a pool for precursors for photochemical H 2 production, whereas N 2 fixation could not be identified as a H 2 source during these two cruises. With our experimental setup we could demonstrate that variability in diurnal cycles is probably influenced and biased by released precursors for photochemical H 2 production and the origin of air masses. This means for further investigations that just measuring the mixing ratio of H 2 is insufficient to explain the variability of a diurnal cycle and support is needed, e.g. by isotopic measurements. However, measurements of H 2 mixing ratios, which are easy to conduct online during ship cruises could be a helpful tool to easily identify production areas of biological precursors such as VOC's for further investigations.

Description: Physical transport properties of marine microplastic pollution Biogeosciences Discussions, 9, 18755-18798, 2012 Author(s): A. Ballent, A. Purser, P. de Jesus Mendes, S. Pando, and L. Thomsen Given the complexity of quantitative collection, knowledge of the distribution of microplastic pollution in many regions of the world ocean is patchy, both spatially and temporally, especially for the subsurface environment. However, with knowledge of typical hydrodynamic behavior of waste plastic material, models predicting the dispersal of pelagic and benthic plastics from land sources into the ocean are possible. Here we investigate three aspects of plastic distribution and transport in European waters. Firstly, we assess patterns in the distribution of plastics found in fluvial strandlines of the North Sea and how distribution may be related to flow velocities and distance from source. Second, we model transport of non-buoyant preproduction pellets in the Nazaré Canyon of Portugal using the MOHID system after assessing the density, settling velocity, critical and depositional shear stress characteristics of such waste plastics. Thirdly, we investigate the effect of surface turbulences and high pressures on a range of marine plastic debris categories (various densities, degradation states and shapes tested) in an experimental water column simulator tank and pressure laboratory. Plastics deposited on North Sea strandlines varied greatly spatially, as a function of material composition and distance from source. Model outputs indicated that such dense production pellets are likely transported up and down canyon as a function of tidal forces, with only very minor net down canyon movement. Behaviour of plastic fragments under turbulence varied greatly, with the dimensions of the material, as well as density, playing major determining roles. Pressure was shown to affect hydrodynamic behaviours of only low density foam plastics at pressures ≥ 60 bar.

Description: Available online 19 December 2012 Publication year: 2012 Source: FEBS Open Bio The green fluorescent protein (GFP) is the most commonly used reporter protein for monitoring gene expression and protein localization in a variety of living and fixed cells, including not only prokaryotes, but also eukaryotes, e.g., yeasts, mammals, plants and fish. In general, it is thought that GFP is nontoxic to cells, although there are some reports on the side effect of GFP. However, details of the molecular mechanism concerning the side effect of GFP remain unclear. Here we show that Ku80, but not XRCC4, plays an important role in the mechanism of the resistance to cytotoxicity induced by enhanced GFP (EGFP). EGFP inhibited both cell proliferation and colony formation, and induced cell death in Ku80-deficient hamster cells, i.e., xrs-6 cells. In addition, Ku80 attenuated EGFP-induced cytotoxicity in the xrs-6 cells. No EGFP-induced cytotoxicity was observed in the NHEJ core protein XRCC4-deficient hamster cells, i.e., XR-1 cells. Furthermore, EGFP markedly enhanced X-ray-induced cytotoxicity in the xrs-6 cells. These results suggest that Ku80 plays a key role in the novel NHEJ-independent defense mechanism against EGFP-induced cytotoxicity. Caution should be taken in considering of the potential influence by the stress response mechanism, namely, the Ku80-dependent elimination mechanism of EGFP-induced cytotoxicity, being activated, even when using EGFP-expressing cells in which Ku80 functions normally.

Description: Available online 20 December 2012 Publication year: 2012 Source: Cell Reports In the fission yeast Schizosaccharomyces pombe , a chromosomal imprinting event controls the asymmetric pattern of mating-type switching. The orientation of DNA replication at the mating-type locus is instrumental in this process. However, the factors leading to imprinting are not fully identified and the mechanism is poorly understood. Here, we show that the replication fork pause at the mat1 locus ( MPS1 ), essential for imprint formation, depends on the lysine-specific demethylase Lsd1. We demonstrate that either Lsd1 or Lsd2 amine oxidase activity is required for these processes, working upstream of the imprinting factors Swi1 and Swi3 (homologs of mammalian Timeless and Tipin, respectively). We also show that the Lsd1/2 complex controls the replication fork terminators, within the rDNA repeats. These findings reveal a role for the Lsd1/2 demethylases in controlling polar replication fork progression, imprint formation, and subsequent asymmetric cell divisions. Graphical abstract Highlights ► The lysine-specific demethylase, Lsd1, is a mating-type switching mutant ► Lsd1 is essential for replication fork pausing at the mat1 locus ► Lsd1 is essential for replication fork arrest at the replication fork block at rDNA loci ► Lsd1 and Lsd2 act in a redundant manner for replication fork pausing

Description: Available online 21 December 2012 Publication year: 2012 Source: Cell Reports Chromatin dynamics play a central role in maintaining genome integrity, but how this is achieved remains largely unknown. Here, we report that microrchidia CW-type zinc finger 2 (MORC2), an uncharacterized protein with a derived PHD finger domain and a conserved GHKL-type ATPase module, is a physiological substrate of p21-activated kinase 1 (PAK1), an important integrator of extracellular signals and nuclear processes. Following DNA damage, MORC2 is phosphorylated on serine 739 in a PAK1-dependent manner, and phosphorylated MORC2 regulates its DNA-dependent ATPase activity to facilitate chromatin remodeling. Moreover, MORC2 associates with chromatin and promotes gamma-H2AX induction in a PAK1 phosphorylation-dependent manner. Consequently, cells expressing MORC2-S739A mutation displayed a reduction in DNA repair efficiency and were hypersensitive to DNA-damaging agent. These findings suggest that the PAK1-MORC2 axis is critical for orchestrating the interplay between chromatin dynamics and the maintenance of genomic integrity through sequentially integrating multiple essential enzymatic processes. Graphical abstract Highlights ► MORC2 is a DNA damage-responsive phosphoprotein activated by PAK1 kinase ► MORC2 regulates phosphorylation-coupled, ATPase-dependent chromatin remodeling ► MORC2 facilitates gamma-H2AX induction independently of PIKK kinases ► MORC2 promotes DSB repair in a PAK1 phosphorylation-dependent manner

Description: Effects of precipitation on soil respiration and its temperature/moisture sensitivity in three subtropical forests in Southern China Biogeosciences Discussions, 9, 15667-15698, 2012 Author(s): H. Jiang, Q. Deng, G. Zhou, D. Hui, D. Zhang, S. Liu, G. Chu, and J. Li Both long-term observation data and model simulations suggest an increasing chance of serious drought in the dry season and extreme flood in the wet season in Southern China, yet little is known about how changes in precipitation pattern will affect soil respiration in the region. We conducted a field experiment to study the responses of soil respiration to precipitation manipulations – precipitation exclusion to mimic drought, double precipitation to simulate flood, and ambient precipitation (Abbr. EP, DP and AP, respectively) – in three subtropical forests in Southern China. The three forests include Masson pine forest (PF), coniferous and broadleaved mixed forest (MF) and monsoon evergreen broadleaved forest (BF). Our observations showed that altered precipitation can strongly influence soil respiration, not only through the well-known direct effects of soil moisture, but also by modification on both moisture and temperature sensitivity of soil respiration. In the dry season, soil respiration and its temperature sensitivity in the three forests showed rising trends with precipitation increase, and its moisture sensitivity showed an opposite trend. In the wet season, the EP treatment also decreased soil respiration and its temperature sensitivity, and enhanced moisture sensitivity in all three forests. Soil respiration under the DP treatment increased significantly in the PF only, and no significant change was found for either moisture or temperature sensitivity. However, the DP treatment in the MF and BF reduced temperature sensitivity significantly. Our results indicated that soil respiration would decrease in the three subtropical forests if soil moisture continues to decrease in the future. More rainfall in the wet season could have limited effect on the response of soil respiration to the rising of temperature in the BF and MF.

Description: Publication year: 2012 Source: Cell Reports Hong Zan, Clayton A. White, Lisa M. Thomas, Thach Mai, Guideng Li, Zhenming Xu, Jinsong Zhang, Paolo Casali By diversifying the biological effector functions of antibodies, class switch DNA recombination (CSR) plays a critical role in the maturation of the immune response. It is initiated by activation-induced cytidine deaminase (AID)-mediated deoxycytosine deamination, yielding deoxyuridine (dU), and dU glycosylation by uracil DNA glycosylase (Ung) in antibody switch (S) region DNA. Here we showed that the translesion DNA synthesis polymerase Rev1 directly interacted with Ung and targeted in an AID-dependent and Ung-independent fashion the S regions undergoing CSR. Rev1 −/− Ung +/+ B cells reduced Ung recruitment to S regions, DNA-dU glycosylation, and CSR. Together with an S region spectrum of mutations similar to that of Rev1 +/+ Ung −/− B cells, this suggests that Rev1 operates in the same pathway as Ung, as emphasized by further decreased CSR in Rev1 −/− Msh2 −/− B cells. Rescue of CSR in Rev1 −/− B cells by a catalytically inactive Rev1 mutant shows that the important role of Rev1 in CSR is mediated by Rev1’s scaffolding function, not its enzymatic function. Graphical abstract Graphical Abstract Highlights ► Rev1 DNA polymerase plays an important role in class switch DNA recombination ► This role is mediated by Rev1’s scaffolding function, not its enzymatic function ► Rev1 interacts with Ung and recruits it to switch region DNA ► Rev1 enhances Ung-mediated dU glycosylation in DNA

Description: Publication year: 2012 Source: Cell Reports Michihiko Sugimoto, Masayo Kondo, Michiko Hirose, Misao Suzuki, Kazuyuki Mekada, Takaya Abe, Hiroshi Kiyonari, Atsuo Ogura, Nobuo Takagi, Karen Artzt, Kuniya Abe After implantation, pluripotent epiblasts are converted to embryonic ectoderm through cell–cell interactions that significantly change the transcriptional and epigenetic networks. An entrée to understanding this vital developmental transition is the t w5 mutation of the mouse t complex. This mutation produces highly specific defects in the embryonic ectoderm before gastrulation, leading to death of the embryonic ectoderm. Using a positional cloning approach, we have now identified the mutated gene, completing a decades-long search. The gene, vacuolar protein sorting 52 ( Vps52 ), is a mouse homolog of yeast VPS52 that is involved in the retrograde trafficking of endosomes. Our data suggest that Vps52 acts in extraembryonic tissues to support the growth and differentiation of embryonic ectoderm via cell–cell interactions. It is also required in the formation of embryonic structures at a later stage of development, revealing hitherto unknown functions of Vps52 in the development of a multicellular organism. Graphical abstract Graphical Abstract Highlights ► Vps52 , part of retrograde transport to the Golgi, causes the t w5 lethal phenotype ► Vps52 acts in extraembryonic tissues to dictate embryonic ectoderm differentiation ► VPS52’s essential function in the embryo involves cell–cell interactions ► VPS52 also has an indispensable function later in development

Description: Publication year: 2012 Source: Cell Reports Myrto Denaxa, Melanie Kalaitzidou, Anna Garefalaki, Angeliki Achimastou, Reena Lasrado, Tamara Maes, Vassilis Pachnis The generation of cortical interneuron subtypes is controlled by genetic programs that are activated in the ventral forebrain and unfold during the prolonged period of inhibitory neuron development. The LIM-homeodomain protein LHX6 is critical for the development of all cortical interneurons originating in the medial ganglionic eminence, but the molecular mechanisms that operate downstream of LHX6 to control the terminal differentiation of somatostatin- and parvalbumin-expressing interneurons within the cortex remain unknown. Here, we provide evidence that the nuclear matrix and genome organizer protein SATB1 is induced by neuronal activity and functions downstream of Lhx6 to control the transition of tangentially migrating immature interneurons into the terminally differentiated Somatostatin (SST)-expressing subtype. Our experiments provide a molecular framework for understanding the genetic and epigenetic mechanisms by which specified but immature cortical interneurons acquire the subtype-defining molecular and morphophysiological characteristics that allow them to integrate and function within cortical circuits. Graphical abstract Graphical Abstract Highlights ► Satb1 is specifically expressed in MGE-derived cortical interneurons ► Satb1 is required for the maturation of MGE-derived cortical interneurons in vivo ► Satb1 promotes the maturation of SST+ cortical interneurons downstream of Lhx6 ► Neuronal activity induces expression of Satb1 in immature cortical interneurons

Description: Publication year: 2012 Source: FEBS Open Bio Yusuke Ito, Suguru Shigemori, Takashi Sato, Tomoyuki Shimazu, Konomi Hatano, Hajime Otani, Haruki Kitazawa, Takeshi Shimosato We designed class I/II hybrid inhibitory oligodeoxynucleotides (iODNs), called iSG, and found that the sequence 5′-TTAGGG-3′, which has a six-base loop head structure, and a 3′-oligo (dG) 3–5 tail sequence are important for potent immunosuppressive activity. Interestingly, splenocytes isolated from ovalbumin (OVA)-immunized mice and treated with iSG3 showed suppression of not only interleukin (IL)-6, IL-12p35, IL-12p40, and interferon (IFN) γ mRNA expression, but also IL-4 and IL-13 mRNA expression. Thus, both Th2 and Th1 immune responses can be strongly suppressed by iODNs in splenocytes from allergen-immunized mice, suggesting usefulness in the treatment of diseases induced by over-active immune activation.

Description: Publication year: 2012 Source: FEBS Open Bio Katsuhiro Tanaka, Maiko Soeda, Yoichiro Hashimoto, Shigeo Takenaka, Masayuki Komori Pex14p is a peroxisomal membrane protein that is involved in both peroxisome biogenesis and selective peroxisome degradation. Previously, we showed that Hansenula polymorpha Pex14p was phosphorylated in vivo . In this study, we identified its phosphorylation site by mass spectrometry. Recombinant His-tagged Pex14p (H6-Pex14p) was overexpressed and purified from the yeast. The protein band corresponding to H6-Pex14p was in-gel digested with trypsin and subjected to LC/MS. As a result of LC/MS, Thr 248 and Ser 258 were identified as the phosphorylated sites. To confirm the phosphorylation sites and explore its functions, we made Ala mutants of the candidate amino acids. In the western blot analysis with anti-Pex14p, S258A mutant gave doublet bands while wild type (WT) and T248A mutants gave triplet bands. Moreover, the double mutant (T248A/S258A) gave a single band. WT and all mutant Pex14p labeled with [ 32 P] orthophosphate were immunoprecipitated and analyzed by autoradiography. The phosphorylation of Pex14p was suppressed in S258A mutant, but enhanced in T248A mutant compared to WT. Moreover, the phosphorylated Pex14p was not detected in the T248A/S258A double mutant. All mutants were able to grow on methanol and their matrix proteins (alcohol oxidase and amine oxidase) were mostly localized in peroxisomes. Furthermore all mutants showed selective degradation of peroxisome like WT during the glucose-induced macropexophagy.

Description: Revisiting factors controlling methane emissions from high-arctic tundra Biogeosciences Discussions, 9, 15853-15900, 2012 Author(s): M. Mastepanov, C. Sigsgaard, T. Tagesson, L. Ström, M. P. Tamstorf, M. Lund, and T. R. Christensen Among the numerous studies of methane emission from northern wetlands the number of measurements carried on at high latitudes (north of the Arctic Circle) is very limited, and within these there is a bias towards studies of the growing season. Here we present results of five years of automatic chamber measurements at a high-arctic location in Zackenberg, NE Greenland covering both the growing seasons and two months of the following freeze-in period. The measurements show clear seasonal dynamics in methane emission. The start of the growing season increase in CH 4 fluxes were strongly related to the date of snow melt. The greatest variation in fluxes between the study years were observed during the first part of the growing season. Somewhat surprisingly this variability could not be explained by commonly known factors controlling methane emission, i.e. temperature and water table position. Late in the growing season CH 4 emissions were found to be very similar between the study years (except the extremely dry 2010) despite large differences in climatic factors (temperature and water table). Late-season bursts of CH 4 coinciding with soil freezing in the autumn were observed at least during three years between 2006 and 2010. The accumulated emission during the freeze-in CH 4 bursts was comparable in size with the growing season emission for the year 2007, and about one third of the growing season emissions for the years 2009 and 2010. In all three cases the CH 4 burst was accompanied by a~corresponding episodic increase in CO 2 emission, which can compose a significant contribution to the annual CO 2 flux budget. The most probable mechanism of the late season CH 4 and CO 2 bursts is physical release of gases, accumulated in the soil during the growing season. In this study we investigate the drivers and links between growing season and late season fluxes. The reported surprising seasonal dynamics of CH 4 emissions at this site show that there are important occasions where conventional knowledge on factors controlling methane emissions is overruled by other processes, acting in longer than seasonal time scales. Our findings suggest the importance of multiyear studies with continued focus on shoulder seasons.

Description: Distribution of methane in the Lena Delta and Buor Khaya Bay, Russia Biogeosciences Discussions, 9, 16213-16237, 2012 Author(s): I. Bussmann The Lena River is one of the largest Russian rivers draining into the Laptev Sea. The permafrost areas surrounding the Lena are predicted to melt at increasing rates due to global temperature increases. With this melting, large amounts of carbon – either organic or as methane – will reach the waters of the Lena and the adjacent Buor Khaya Bay (Laptev Sea). Methane concentrations and the isotopic signal of methane in the waters of the Lena Delta and estuary were monitored from 2008 to 2010. Meltwater run-off of permafrost soils produced hotspots for methane input into the river system (median concentration 1500 nM) compared with concentrations of around 100 nM observed in the main channels of the Lena. Within the river, especially at sites with meltwater input, microbiological experiments indicated strong in situ methane production but a very low methane oxidation potential. In the estuary of Buor Khaya Bay, methane concentrations decreased towards background levels of 20 nM. Here, the strong stratification of the water column permits the dilution of methane with seawater, and methane is released mainly by diffusion into the atmosphere.

Description: Spectrally resolved efficiencies of carbon monoxide (CO) photoproduction in the Western Canadian Arctic: particles versus solutes Biogeosciences Discussions, 9, 16161-16211, 2012 Author(s): G. Song, H. Xie, S. Bélanger, and M. Babin Spectrally resolved efficiency (i.e. apparent quantum yield, AQY) of carbon monoxide (CO) photoproduction is a useful indicator of substrate photoreactivity and a crucial parameter for modeling CO photoproduction rates in the water column. Recent evidence has suggested that CO photoproduction from particles in marine waters is significant compared to the well-known CO production from chromophoric dissolved organic matter (CDOM) photodegradation. Although CDOM-based CO AQY spectra have been extensively determined, little is known of this information on the particulate phase. Using water samples collected from the Mackenzie estuary, shelf, and Canada Basin in the Southeastern Beaufort Sea, the present study for the first time quantified the AQY spectra of particle-based CO photoproduction and compared them with the concomitantly determined CDOM-based CO AQY spectra. CO AQYs of both particles and CDOM decreased with wavelength but the spectral shape of the particulate AQY was flatter in the visible regime. This feature resulted in a disproportionally higher visible light-driven CO production by particles, thereby increasing the ratio of particle- to CDOM-based CO photoproduction with depth in the euphotic zone. In terms of depth-integrated production in the euphotic zone, CO formation from CDOM was dominated by the ultraviolet (UV, 290–400 nm) radiation whereas UV and visible light played roughly equal roles in CO production from particles. Spatially, CO AQY of bulk particulate matter (i.e. the sum of organics and inorganics) augmented from the estuary to shelf to basin while CO AQY of CDOM trended inversely. Water from the deep chlorophyll maximum layer revealed higher CO AQYs than did surface water for both particles and CDOM. CO AQY of bulk particulate matter exceeded that of CDOM on the shelf and in the basin but the sequence reversed in the estuary. Mineral absorption-corrected CO AQY of particulate organic matter (POM) was, however, greater than its CDOM counterpart in all three sub-regions and displayed magnitudes in the estuary that were no inferior to those in shelf and offshore waters. In terms of CO photoproduction, POM was thus more photoreactive than CDOM, irrespective of the organic matter's origins (i.e. terrigenous or marine). Riverine CDOM exhibited higher photoreactivity than marine CDOM and land-derived POM appeared similarly or more photoreactive than marine POM. AQY-based modeling indicates that CO photoproduction in the study area is underestimated by 13–48 % if the particulate term is ignored.

Description: Radium-based estimates of cesium isotope transport and total direct ocean discharges from the Fukushima Nuclear Power Plant accident Biogeosciences Discussions, 9, 16139-16160, 2012 Author(s): M. A. Charette, C. F. Breier, P. B. Henderson, S. M. Pike, I. I. Rypina, S. R. Jayne, and K. O. Buesseler Radium has four naturally occurring isotopes that have proven useful in constraining water mass source, age, and mixing rates in the coastal and open ocean. In this study, we used radium isotopes to determine the fate and flux of runoff-derived cesium from the Fukushima Nuclear Power Plant (NPP). During a June 2011 cruise, the highest Cs concentrations were found along the eastern shelf of northern Japan, from Fukushima south, to the edge of the Kuroshio current, and in an eddy ∼ 130 km from the NPP site. Locations with the highest cesium also had some of the highest radium activities, suggesting much of the direct ocean discharges of Cs remained in the coastal zone 2–3 months after the accident. We used a short-lived Ra isotope ( 223 Ra, t 1/2 = 11.4 d) to derive an average water mass age ( T r ) in the coastal zone of 32 days. To ground-truth the Ra age model, we conducted a direct, station-by-station comparison of water mass ages with a numerical oceanographic model and found them to be in excellent agreement (model avg. T r = 27 days). From these independent T r values and the inventory of Cs within the water column at the time of our cruise, we were able to calculate an offshore 134 Cs flux of 3.9–4.6 × 10 13 Bq d −1 . Radium-228 ( t 1/2 = 5.75 yr) was used to derive a vertical eddy diffusivity ( K z ) of 0.7 m 2 d −1 (0.1 cm 2 s −1 ); from this K z and 134 Cs inventory, we estimated a 134 Cs flux across the pycnocline of 1.8 × 10 4 Bq d −1 for the same time period. On average, our results show that horizontal mixing loss of Cs from the coastal zone was ∼ 10 9 greater than vertical exchange below the surface mixed layer. Finally, a mixing/dilution model that utilized our Ra-based and oceanographic model water mass ages produced a direct ocean discharge of 134 Cs from the FNPP of 11–16 PBq at the time of the peak release in early April 2011. Our results can be used to calculate discharge of other water-soluble radionuclides that were released to the ocean directly from the Fukushima NPP.

Description: Soil respiration compartments on an aging managed heathland: can model selection procedures contribute to our understanding of ecosystem processes? Biogeosciences Discussions, 9, 16239-16301, 2012 Author(s): G. R. Kopittke, E. E. van Loon, A. Tietema, and D. Asscheman Soil respiration studies are increasingly undertaken with the aim of quantifying C fluxes and predicting changes for the future. The interpretation of field data into annual C loss predictions requires the use of modeling tools which generally include model variables related to the underlying drivers of soil respiration, such as soil temperature, soil moisture and plant activity. Very few studies have reported using model selection procedures in which structurally different models are calibrated, then validated on separate observation datasets and the outcomes critically compared. This study utilized thorough model selection procedures to determine soil heterotrophic (microbial) and autotrophic (root) respiration for a heathland chronosequence. The model validation process identified that none of the six measured plant variables explained any data variation when included in models with soil temperature, which contradicts many current studies. The best predictive model used a generalized linear mixed effect model format with soil temperature as the only variable. There were no heterotrophic respiration differences between the community ages. In contrast, autotrophic respiration was significantly greater on the youngest vegetation (55 % of total soil respiration in summer) and decreased as the plants aged (oldest vegetation: 37 % of total soil respiration in summer). Total annual soil C loss from the youngest and oldest communities was estimated to be 650 and 435 g C m −2 yr −1 respectively. Heathlands are cultural landscapes which are managed through cyclical cutting, burning or grazing practices. Understanding the C fluxes from these ecosystems provides information on the optimal management cycle-time to maximize C uptake and minimize C output. Inclusion of the predicted soil fluxes into a preliminary ecosystem C balance suggested that the youngest vegetation is a C sink while the oldest vegetation is a C source, indicating that shorter management cycles could reduce C emissions.

Description: Biological production in the Bellingshausen Sea from oxygen-to-argon ratios and oxygen triple isotopes Biogeosciences Discussions, 9, 16033-16085, 2012 Author(s): K. Castro-Morales, N. Cassar, and J. Kaiser We present estimates of mixed layer net community oxygen production ( N ) and gross oxygen production ( G ) of the Bellingshausen Sea in March and April 2007. N was derived from oxygen-to-argon (O 2 / Ar) ratios; G was derived using the dual-delta method from triple oxygen isotope measurements. In addition, O 2 profiles were collected at 253 CTD stations. N is often approximated by the biological oxygen air-sea exchange flux ( F bio ) based on the O 2 / Ar supersaturation, assuming that significant horizontal or vertical fluxes are absent. Here, we show that the effect of vertical fluxes alone can account for F bio values 〈 0 in large parts of the Bellingshausen Sea towards the end of the productive season, which could be mistaken to represent net heterotrophy. Thus, improved estimates of mixed-layer N can be derived from the sum of F bio , F e (entrainment from the upper thermocline during mixed-layer deepening) and F v (diapycnal eddy diffusion across the base of the mixed layer). In the Winter Sea Ice Zone (WSIZ), the corresponding correction results in a small change of F bio = (30 ± 17) mmol m −2 d −1 to N = (34 ± 17) mmol m −2 d −1 . However, in the permanent open ocean zone (POOZ), the original F bio value of (−17 ± 10) mmol m −2 d −1 gives a corrected value for N of (−2 ± 18) mmol m −2 d −1 . We hypothesize that in the WSIZ enhanced water column stability due to the release of freshwater and nutrients from sea-ice melt may account for the higher N-value. These results stress the importance of accounting for physical biases when estimating mixed layer-marine productivity from in situ O 2 / Ar ratios.

Description: Constraints from atmospheric CO 2 and satellite-based vegetation activity observations on current land carbon cycle trends Biogeosciences Discussions, 9, 16087-16138, 2012 Author(s): D. Dalmonech and S. Zaehle Terrestrial ecosystem models used for Earth system modelling show a significant divergence in future patterns of ecosystem processes, in particular carbon exchanges, despite a seemingly common behaviour for the contemporary period. An in-depth evaluation of these models is hence of high importance to achieve a better understanding of the reasons for this disagreement. Here, we develop an extension for existing benchmarking systems by making use of the complementary information contained in the observational records of atmospheric CO 2 and remotely-sensed vegetation activity to provide a firm set of diagnostics of ecosystem responses to climate variability in the last 30 yr at different temporal and spatial scales. The selection of observational characteristics (traits) specifically considers the robustness of information given the uncertainties in both data and evaluation analysis. In addition, we provide a baseline benchmark, a minimum test that the model under consideration has to pass, to provide a more objective, quantitative evaluation framework. The benchmarking strategy can be used for any land surface model, either driven by observed meteorology or coupled to a climate model. We apply this framework to evaluate the offline version of the MPI-Earth system model's land surface scheme JSBACH. We demonstrate that the complementary use of atmospheric CO 2 and satellite based vegetation activity data allows to pinpoint specific model failures that would not be possible by the sole use of atmospheric CO 2 observations.

Description: Seasonal and spatial comparisons of phytoplankton growth and mortality rates due to microzooplankton grazing in the northern South China Sea Biogeosciences Discussions, 9, 16005-16032, 2012 Author(s): B. Chen, L. Zheng, B. Huang, S. Song, and H. Liu We conducted a comprehensive investigation on the microzooplankton herbivory effect on phytoplankton in the northern South China Sea (SCS) using the seawater dilution technique at surface and deep chlorophyll maximum (DCM) layers in two cruises (July–August of 2009 and January of 2010). We compared vertical (surface vs. DCM), spatial (onshore vs. offshore), and seasonal (summer vs. winter) differences of phytoplankton growth (μ 0 ) and microzooplankton grazing rates ( m ). During summer, both μ 0 and m were significantly higher at the surface than at the layer of DCM, which was below the mixed layer. During winter, surface μ 0 was significantly higher than at DCM, while m was not significantly different between the two layers, both of which were contained within the mixed layer. Surface μ 0 was, on average, significantly higher in summer than in winter; while average surface m was not different between the two seasons. There were no significant cross-shelf trends of μ 0 in summer or winter surface waters. In surface waters, μ 0 was not correlated with ambient nitrate concentrations and the effect of nutrient enrichment on phytoplankton growth was not pronounced. There was a decreasing trend of m from shelf to basin surface waters in summer, but not in winter. Microzooplankton grazing effect on phytoplankton ( m /μ 0 ) did not increase with distance offshore, suggesting that the importance of microzooplankton as grazers of phytoplankton may not decrease in onshore waters. On average, microzooplankton grazed 73% and 65% of the daily primary production in summer and winter, respectively.

Description: Interconnectivity vs. isolation of prokaryotic communities in European deep-sea mud volcanoes Biogeosciences Discussions, 9, 17377-17400, 2012 Author(s): M. G. Pachiadaki and K. A. Kormas By exploiting the available data on 16S rRNA gene sequences – spanning over a sampling period of more than 10 yr – retrieved from sediments of the Haakon Mosby mud volcano (HMMV), Gulf of Cadiz (GoC) and eastern Mediterranean (Amsterdam and Kazan mud volcanoes; AMSMV, KZNMV) mud volcanoes/pockmarks, we investigated whether these systems are characterized by high (interconnectivity) or low (isolation) connection degree based on shared bacterial and archaeal phylotypes. We found only two archaeal and two bacterial phylotypes to occur in all three sites and a few more that were found in two of the three sites. Although the number of shared species depends a lot on the analysis depth of each sample, the majority of the common phylotypes were related mostly to cold seep deep-sea habitats, while for some of them their relative abundance was high enough to be considered as key-species for the habitat they were found. As new tools, like next generation sequencing platforms, are more appropriate for revealing greater depth of diversity but also allow sample replication and uniform sampling protocols, and gain wider recognition and usage, future attempts are more realistic now for fully elucidating the degree of specificity in deep-sea mud volcanoes and pockmarks microbial communities.

Description: Available online 7 December 2012 Publication year: 2012 Source: Cell Reports Periodic somite segmentation is controlled by the cyclic gene Hes7 , whose oscillatory expression depends upon negative feedback with a delayed timing. The mechanism that regulates the pace of segmentation remains to be determined, but mathematical modeling has predicted that negative feedback with shorter delays would give rise to dampened but more rapid oscillations. Here, we show that reducing the number of introns within the Hes7 gene shortens the delay and results in a more rapid tempo of both Hes7 oscillation and somite segmentation, increasing the number of somites and vertebrae in the cervical and upper thoracic region. These results suggest that the number of introns is important for the appropriate tempo of oscillatory expression and that Hes7 is a key regulator of the pace of the segmentation clock. Graphical abstract Highlights ► Reduction of Hes7 intron number accelerates the tempo of Hes7 oscillation ► Reduction of Hes7 intron number accelerates the tempo of somite segmentation ► Hes7 is a key segmentation pacemaker ► The number of introns may be important for normal timing of gene expression

Description: Density and distribution of megafauna at the Håkon Mosby Mud Volcano (the Barents Sea) based on image analysis Biogeosciences Discussions, 9, 17475-17517, 2012 Author(s): E. Rybakova (Goroslavskaya), S. Galkin, M. Bergmann, T. Soltwedel, and A. Gebruk During a survey of the Håkon Mosby Mud Volcano (HMMV), located on the Bear Island Fan in the southwest Barents Sea at ~ 1250 m water depth, different habitats inside the volcano caldera and outside it were photographed using a towed camera platform, an Ocean Floor Observation System (OFOS). Three transects were performed across the caldera and one outside, in the background area, each transect was ~ 2 km in length. We compared the density, taxa richness and diversity of non-symbiotrophic megafauna in areas inside the volcano caldera with different bacterial mat and pogonophoran tubeworm cover. Significant variations in megafaunal composition, density and distribution were found between considered areas. Total megafaunal density was highest in areas of dense pogonophoran populations (mean 52.9 ind. m −2 ) followed by areas of plain light-coloured sediment that were devoid of bacterial mats and tubeworms (mean 37.7 ind. m −2 ). The lowest densities were recorded in areas of dense bacterial mats (mean ≤ 1.4 ind. m −2 ). Five taxa contributed to most of the observed variation: the ophiuroid Ophiocten gracilis , lysianassid amphipods, the pycnogonid Nymphon macronix , the caprellid Metacaprella horrida and the fish Lycodes squamiventer . In agreement with previous studies, three zones within the HMMV caldera were distinguished, based on different habitats and megafaunal composition: "bacterial mats", "pogonophoran fields" and "plain light-coloured sediments". The zones were arranged almost concentrically around the central part of the caldera that was devoid of visible megafauna. The total number of taxa showed little variation inside (24 spp.) and outside the caldera (26 spp.). The density, diversity and composition of megafauna varied substantially between plain light-coloured sediment areas inside the caldera and the HMMV background. Megafaunal density was lower in the background (mean 25.3 ind. m −2 ) compared to areas of plain light-coloured sediments inside the caldera.

Description: Phosphorus sorption and buffering mechanisms in suspended sediments from the Yangtze Estuary and Hangzhou Bay, China Biogeosciences Discussions, 9, 17519-17538, 2012 Author(s): M. Li, M. J. Whelan, G. Wang, and S. M. White The adsorption isotherm and the mechanism of the buffering effect are important controls on phosphorus behaviors in estuaries and are important for estimating phosphate concentrations in aquatic environments. In this paper, we derive phosphate adsorption isotherms in order to investigate sediment adsorption and buffering capacity for phosphorus discharged from sewage outfalls in the Yangtze Estuary and Hangzhou Bay near Shanghai, China. Experiments were also carried out at different temperatures in order to explore the buffering effects for phosphate. The results show that P sorption in sediments with low fine particle fractions was best described using exponential equations. Some P interactions between water and sediment may be caused by the precipitation of CaHPO 4 from Ca 2+ and HPO 4 2− when the phosphate concentration in the liquid phase is high. Results from the buffering experiments suggest that the Zero Equilibrium Phosphate Concentrations (EPC 0 ) vary from 0.014 mg l −1 to 0.061 mg l −1 , which are consistent with measured phosphate concentrations in water samples collected at the same time as sediment sampling. Values of EPC 0 and linear sorption coefficients ( K ) in sediments with high fine particle and organic matter contents are relatively high, which implies that they have high buffering capacity. Both EPC 0 and K increase with increasing temperature, indicating a higher P buffering capacity at high temperatures.

Description: Seasonal, daily and diel N 2 effluxes in permeable carbonate sediments Biogeosciences Discussions, 9, 17437-17473, 2012 Author(s): B. D. Eyre, I. R. Santos, and D. T. Maher Benthic metabolism and inorganic nitrogen and N 2 flux rates (denitrification) were measured in permeable carbonate sands from Heron Island (Great Barrier Reef). Some of the N 2 flux rates were among the highest measured in sediments. All benthic fluxes showed a significant difference between seasons with higher rates in summer and late summer. There was no distinct response of the benthic system to mass coral spawning. Instead, changes in benthic fluxes over 12 days in summer appears to be driven by tidal changes in water depth and associated changes in phytosynthetically active radiation reaching the sediments. Dark N 2 fluxes were strongly correlated to benthic oxygen consumption across all sites and seasons ( r 2 = 0.64; p 〈 0.005; slope = 0.036). However, there were seasonal differences with a steeper slope in summer than winter reflecting either more efficient coupling between respiration and nitrification-denitrification at higher temperatures or different sources of organic matter. Adding data from published studies on carbonate sands revealed two slopes in the dark N 2 flux versus benthic oxygen consumption relationship. The lower slope (0.035) was most likely due to high carbon : nitrogen (C : N) organic matter from coral reefs, but competition by benthic microalgae for nitrogen, N-fixation or inefficient coupling between respiration and nitrification-denitrification can not be excluded. The steeper slope (0.089) was most likely due to respiration being driven by low C : N phyto-detritus. If the different slopes were driven by the sources of organic matter then global estimates of continental shelf denitrification are probably about right. In contrast, global estimates of continental shelf may be over-estimated if the low slope was due to inefficient coupling between respiration and nitrification-denitrification and also due to reduced N 2 effluxes in the light associated with competition by benthic microalgae for nitrogen and N-fixation.

Description: Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic) Biogeosciences Discussions, 9, 17401-17435, 2012 Author(s): E. Ortega-Retuerta, F. Joux, W. H. Jeffrey, and J.-F. Ghiglione We explored the patterns of total and active bacterial community structure in a gradient covering surface waters from the Mackenzie River to the coastal Beaufort Sea, Canadian Arctic Ocean, with a particular focus on free-living vs. particle-attached communities. Capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) showed significant differences when comparing river, coast and open sea bacterial community structures. In contrast to the river and coastal waters, total (16S rDNA-based) and active (16S rRNA-based) communities in the open sea samples were not significantly different, suggesting that most present bacterial groups were equally active in this area. Additionally, we observed significant differences between particle-attached (PA) and free-living (FL) bacterial communities in the open sea, but similar structure in the two fractions for coastal and river samples. Direct multivariate statistical analyses showed that total community structure was mainly driven by salinity (proxy of DOC and CDOM), suspended particles, amino acids and chlorophyll a . 16S rRNA genes pyrosequencing of selected samples confirmed these significant differences from river to sea and also between PA and FL fractions only in open sea samples, and PA samples generally showed higher diversity (Shannon, Simpson and Chao indices) than FL samples. At the class level, Opitutae was most abundant in the PA fraction of the sea sample, followed by Flavobacteria and Gammaproteobacteria , while the FL sea sample was dominated by Alphaproteobacteria . Finally, the coast and river samples, both PA and FL fractions, were dominated by Betaproteobacteria , Alphaproteobacteria and Actinobacteria . These results highlight the coexistence of particle specialists and generalists and the role of particle quality in structuring bacterial communities in the area. These results may also serve as a~basis to predict further changes in bacterial communities should climate change lead to further increases in river discharge and related particles load.

Description: Unicellular saprobic fungi (yeasts) inhabit soils worldwide. Although yeast species typically occupy defined areas on the biome scale, their distribution patterns within a single type of vegetation, such as forests, are more complex. In order to understand factors that shape soil yeast communities, soils collected underneath decaying wood logs and under forest litter were analyzed. We isolated and identified molecularly a total of 25 yeast species, including three new species. Occurrence and distribution of yeasts isolated from these soils provide new insights into ecology and niche specialization of several soil-borne species. Although abundance of typical soil yeast species varied among experimental plots, the analysis of species abundance and community composition revealed a strong influence of wood log deposition and leakage of organic carbon. Unlike soils underneath logs, yeast communities in adjacent areas harbored a considerable number of transient (phylloplane-related) yeasts reaching 30% of the total yeast quantity. We showed that distinguishing autochthonous community members and species transient in soils is essential to estimate appropriate effects of environmental factors on soil fungi. Furthermore, a better understanding of species niches is crucial for analyses of culture-independent data, and may hint to the discovery of unifying patterns of microbial species distribution.

Description: Physical and biogeochemical forcing of oxygen changes in the tropical eastern South Pacific along 86° W: 1993 versus 2009 Biogeosciences Discussions, 9, 17583-17618, 2012 Author(s): P. J. Llanillo, J. Karstensen, J. L. Pelegrí, and L. Stramma Temporal changes of the water mass distribution and biogeochemical cycling in the tropical eastern South Pacific are investigated based on the extended Optimum Multi-Parameter (OMP) method. Two ship occupations of a meridional section along 85°50´ W, from 14° S to 1° N, are analysed, one during a relatively warm (El Niño/El Viejo, March 1993) and the other during a cold (La Niña/La Vieja, February 2009) upper-ocean phase. The largest El Niño – Southern Oscillation (ENSO) impact was found in the water properties and water mass distribution in the upper 250 m. The most prominent change is the vertical motion of the Oxygen Minimum Zone (OMZ) associated to the hypoxic Equatorial Subsurface Water (ESSW). During a cold phase the core of the ESSW is found at shallower layers, replacing the shallow (top 250 m) Subtropical Surface Water (STW) and allowing an intrusion of oxygen-rich and nutrient-poor Antarctic Intermediate Water (AAIW) in the depth range of 300 to 600 m. The shift in the vertical location of the intrusion of AAIW in the OMZ induces changes in oxygen advection and respiration, the largest the oxygen supply the greatest the respiration and the lowest the nitrate loss by denitrification. Changes in the intensity of the zonal currents in the Equatorial Current System, that ventilate the OMZ from the west, are used to explain the patchy latitudinal changes of seawater properties observed along the repeated section. Given that changes down to 800 m depth are observed, not only interannual (ENSO) but also decadal variability (Pacific Decadal Oscillation) is a potential driver for the observed changes.

Description: Benthic communities in the deep Mediterranean Sea: exploring microbial and meiofaunal patterns in slope and basin ecosystems Biogeosciences Discussions, 9, 17539-17581, 2012 Author(s): K. Sevastou, N. Lampadariou, P. N. Polymenakou, and A. Tselepides The long held perception of the deep sea consisting of monotonous slopes and uniform oceanic basins has over the decades given way to the idea of a complex system with wide habitat heterogeneity. Under the prism of a highly diverse environment, a large dataset was used to describe and compare spatial patterns of the dominant small-size components of deep-sea benthos, metazoan meiofauna and bacteria, from Mediterranean basins and slopes. A grid of 73 stations sampled at five geographical areas along the central-eastern Mediterranean basin (central Mediterranean, northern Aegean Sea, Cretan Sea, Libyan Sea, eastern Levantine) spanning over 4 km in depth revealed a high diversity in terms of both metazoan meiofauna and microbial communities. The higher meiofaunal abundance and richness observed in the northern Aegean Sea highlights the effect of productivity on benthic patterns. Non parametric analyses detected no differences for meiobenthic standing stocks and major taxa diversity ( α , β , γ and δ components) between the two habitats (basin vs. slope) for the whole investigated area and within each region, but revealed significant bathymetric trends: abundance and richness follow the well-known gradient of decreasing values with increasing depth, whereas differentiation diversity ( β - and δ -diversity) increases with depth. In spite of a similar bathymetric trend observed for nematode genera richness, no clear pattern was detected with regard to habitat type; the observed number of nematode genera suggests higher diversity in slopes, whereas richness estimator Jack1 found no differences between habitats. On the other hand, δ -diversity was higher at the basin habitat, but no differences were found among depth ranges, though turnover values were high in all pairwise comparisons of the different depth categories. Results of multivariate analysis are in line with the above findings, indicating high within habitat variability of meiofaunal communities and a gradual change of meiofaunal structure towards the abyssal stations. In contrast to meiobenthic results, microbial richness is significantly higher at the basin ecosystem and tends to increase with depth, while community structure varies greatly among samples regardless of the type of habitat, depth or area. The results presented here suggest that differences in benthic parameters between the two habitats are neither strong nor consistent; it appears that within habitat variability is high and differences among depth ranges are more important.

Description: Air-sea exchange of CO 2 at a Northern California coastal site along the California Current upwelling system Biogeosciences Discussions, 9, 17707-17741, 2012 Author(s): H. Ikawa, I. Faloona, J. Kochendorfer, K. T. Paw U, and W. C. Oechel Uncertainty in the air-sea CO 2 exchange (CO 2 flux) in coastal upwelling zones is attributed to high temporal variability, which is caused by changes in ocean currents. Upwelling transports heterotrophic, CO 2 enriched water to the surface and releases CO 2 to the atmosphere, whereas the presence of nutrient-rich water at the surface supports high primary production and atmospheric CO 2 uptake. To quantify the effects of upwelling on CO 2 fluxes, we measured CO 2 flux at a coastal upwelling site off of Bodega Bay, California, during the summer of 2007 and the fall of 2008 using the eddy covariance technique and the bulk method with p CO 2 measurements from November 2010 to July 2011. Variations in sea surface temperatures (SST) and alongshore wind speeds suggest that the measurement period in 2007 coincided with a typical early-summer upwelling period and the measurement period in 2008 was during a typical fall relaxation period. A strong source of CO 2 (~1.5 ± 7 SD (standard deviation) g C m −2 day −1 ) from the ocean to the atmosphere during the upwelling period was concurrent with high salinity, low SST, and low chlorophyll density. In contrast, a weak source of CO 2 flux (~0.2 ± 3 SD g C m −2 day −1 ) was observed with low salinity, high SST and high chlorophyll density during the relaxation period. Similarly, the sink and source balance of CO 2 flux was highly related to salinity and SST during the p CO 2 measurement periods; high salinity and low SST corresponded to high p CO 2 , and vice versa. We estimated that the coastal area off Bodega Bay was likely a source of CO 2 to the atmosphere based on the following conclusions: (1) the overall CO 2 flux estimated from both eddy covariance and p CO 2 measurements showed a source of CO 2 ; (2) although the relaxation period during the 2008 measurements were favorable to CO 2 uptake, CO 2 flux during this period was still a slight source, (3) salinity and SST were found to be good predictors of the CO 2 flux for both eddy covariance and p CO 2 measurements, and historical data of daily averaged SST and salinity between 1988 to 2011 show that 99% of the data falls within the range of our observation in May–June 2007, August–September 2008 and November 2010–July 2011 indicating that our data set was representative of the annual variations in the sea state. Based on the developed relationship between p CO 2 and SST and salinity, the average annual CO 2 flux between 1988 and 2011 was estimated to be ~35 mol C m −2 yr −1 . The peak monthly CO 2 flux of ~7 mol C m −2 month −1 accounted for about 30% of the dissolved inorganic carbon in the surface mixed-layer.

Description: Trophic state of sediments from two deep continental margins off Iberia: a biomimetic approach Biogeosciences Discussions, 9, 17619-17650, 2012 Author(s): A. Dell'Anno, A. Pusceddu, C. Corinaldesi, M. Canals, S. Heussner, L. Thomsen, and R. Danovaro The trophic state of benthic deep-sea ecosystems can greatly influence key ecological processes (e.g. biomass production and nutrient cycling). Thus, assessing the trophic state of the sediment at different spatial and temporal scales is crucial for a better understanding of deep-sea ecosystem functioning. Here, using a biomimetic approach based on enzymatic digestion of protein and carbohydrate pools, we assess the bioavailability of organic detritus and its nutritional value in the uppermost layer of deep-sea sediments from open slopes and canyons of the Catalan (NW Mediterranean) and Portuguese (NE Atlantic) continental margins, offshore east and west Iberia, respectively. Patterns of sediment trophic state were analyzed in relation to increasing water depth, including repeated samplings over a 3 yr period in the Catalan margin. Bioavailable organic matter and its nutritional value were significantly higher in the Portuguese margin than in the Catalan margin, thus reflecting differences in primary productivity of surface waters reported for the two regions. Similarly, sediments of the Catalan margin were characterized by significantly higher food quantity and quality in spring, when higher primary production processes occur in surface waters, than in summer and autumn. In both continental margins, bioavailable organic C concentrations did not vary or increase with increasing water depth. Differences in the benthic trophic state of canyons against open slopes were more evident in the Portuguese than in the Catalan margin. Overall our findings indicate that deep-sea sediments are characterized by relatively high amounts of bioavailable organic matter. We suggest that the interactions between biological-related processes in surface waters and particle transport and deposition dynamics can play a crucial role in shaping the quantity and distribution of bioavailable organic detritus and its nutritional value along deep continental margins.

Description: Effects of increased p CO 2 and geographic origin on purple sea urchin ( Strongylocentrotus purpuratus ) calcite elemental composition Biogeosciences Discussions, 9, 17939-17973, 2012 Author(s): M. LaVigne, T. M. Hill, E. Sanford, B. Gaylord, A. D. Russell, E. A. Lenz, J. D. Hosfelt, and M. K. Young Ocean acidification will likely have negative impacts on invertebrates producing skeletons composed of calcium carbonate. Skeletal solubility is partly controlled by the incorporation of "foreign" ions (such as Mg and Sr) into the crystal lattice of these skeletal structures, a process that is sensitive to a variety of biological and environmental factors. Here we explore the effects of life stage, oceanographic region of origin, and changes in the partial pressure of carbon dioxide in seawater ( p CO 2 ) on trace elemental composition in the purple sea urchin ( Strongylocentrotus purpuratus ). We show that, similar to other urchin taxa, adult purple sea urchins have the ability to precipitate skeleton composed of a range of biominerals spanning low to high magnesium calcites. Mg/Ca and Sr/Ca ratios were substantially lower in adult spines compared to adult tests. On the other hand, trace elemental composition was invariant among adults collected from four oceanographically distinct regions along the US west coast (Oregon, Northern California, Central California, and Southern California). Skeletons of newly settled juvenile urchins that originated from adults from the four regions exhibited intermediate Mg/Ca and Sr/Ca between adult spine and test endmembers, indicating that skeleton precipitated during early life stages is more soluble than adult spines and less soluble than adult tests. Mean skeletal Mg/Ca or Sr/Ca of juvenile skeleton did not vary with source region when larvae were reared under present-day, global-average seawater carbonate conditions (400 ppm; pH = 8.02 ± 0.03 1 SD; Ω calcite = 3.3 ± 0.2 1 SD). However, when reared under elevated CO 2 (900 ppm; pH = 7.72 ± 0.03; Ω calcite = 1.8 ± 0.1), skeletal Sr/Ca in juveniles exhibited increased variance across the four regions. Although larvae from the northern populations (Oregon, Northern California, Central California) did not exhibit differences in Mg or Sr incorporation under elevated CO 2 (Sr/Ca = 2.09 ± 0.06 mmol mol −1 ; Mg/Ca = 66.9 ± 4.1 mmol mol −1 ), juveniles of Southern California origin partitioned ∼ 8% more Sr into their skeletons when exposed to higher CO 2 (Sr/Ca = 2.26 ± 0.05 vs. 2.10 ± 0.03 mmol mol −1 1 SD). Together these results suggest that the diversity of carbonate minerologies present across different skeletal structures and life stages in purple sea urchins does not translate into an equivalent plasticity of response associated with geographic variation or temporal shifts in seawater properties. Rather, composition of S. purpuratus skeleton precipitated during both early and adult life history stages appears relatively robust to spatial gradients and predicted changes in seawater carbonate chemistry for 2100. An exception to this trend may arise during early life stages, where certain populations of purple sea urchins may alter skeletal mineral precipitation rates and composition beyond a given CO 2 threshold. The degree to which this latter geochemical plasticity might affect mineral stability and solubility in a future, altered ocean requires additional study.

Description: Available online 13 December 2012 Publication year: 2012 Source: Cell Reports Dopamine contributes to corticostriatal plasticity and motor learning. Dopamine denervation profoundly alters motor performance, as in Parkinson’s disease (PD); however, the extent to which these symptoms reflect impaired motor learning is unknown. Here, we demonstrate a D2 receptor blockade-induced aberrant learning that impedes future motor performance when dopamine signaling is restored, an effect diminished by coadministration of adenosine antagonists during blockade. We hypothesize that an inappropriate corticostriatal potentiation in striatopallidal cells of the indirect pathway underlies aberrant learning. We demonstrate synaptic potentiation in striatopallidal neurons induced by D2 blockade and diminished by application of an adenosine antagonist, consistent with behavioral observations. A neurocomputational model of the basal ganglia recapitulates the behavioral pattern and further links aberrant learning to plasticity in the indirect pathway. Thus, D2-mediated aberrant learning may contribute to motor deficits in PD, suggesting new avenues for the development of therapeutics. Graphical abstract Highlights ► Dopamine blockade induces aberrant learning that impairs future motor performance ► Aberrant learning is mediated by the D2-expressing striatopallidal pathway ► A2A antagonism protects against aberrant learning but impairs recovery ► D2 blockade induces potentiation at striatopallidal corticostriatal synapses

Description: Available online 13 December 2012 Publication year: 2012 Source: Cell Reports Elimination of aberrantly folded polypeptides from the endoplasmic reticulum (ER) by the ER - a ssociated d egradation (ERAD) system promotes cell survival under stress conditions. This quality control mechanism requires movement of misfolded proteins across the ER membrane for targeting to the cytosolic proteasome, a process facilitated by a “holdase” complex, consisting of Bag6 and the cofactors Ubl4A and Trc35. This multiprotein complex also participates in several other protein quality control processes. Here, we report SGTA as a component of the Bag6 system, which cooperates with Bag6 to channel dislocated ERAD substrates that are prone to aggregation. Using nuclear magnetic resonance spectroscopy and biochemical assays, we demonstrate that SGTA contains a noncanonical ubiquitin-like-binding domain that interacts specifically with an unconventional ubiquitin-like protein/domain in Ubl4A at least in part via electrostatics. This interaction helps recruit SGTA to Bag6, enhances substrate loading to Bag6, and thus prevents the formation of nondegradable protein aggregates in ERAD. Graphical abstract Highlights ► The two UBLs in the Bag6 complex have distinct features that specify their interactors ► The Ubl4A UBL interacts with SGTA to enhance its binding to Bag6 ► The Ubl4A UBL binds SGTA-N via an unconventional means of UBL recognition ► SGTA assists Bag6 in maintaining the solubility of ERAD substrates and promoting ERAD

Description: Available online 13 December 2012 Publication year: 2012 Source: Cell Reports The formation of the mammalian cortex requires the generation, migration, and differentiation of neurons. The vital role that the microtubule cytoskeleton plays in these cellular processes is reflected by the discovery that mutations in various tubulin isotypes cause different neurodevelopmental diseases, including lissencephaly ( TUBA1A ), polymicrogyria ( TUBA1A , TUBB2B , TUBB3 ), and an ocular motility disorder ( TUBB3 ). Here, we show that Tubb5 is expressed in neurogenic progenitors in the mouse and that its depletion in vivo perturbs the cell cycle of progenitors and alters the position of migrating neurons. We report the occurrence of three microcephalic patients with structural brain abnormalities harboring de novo mutations in TUBB5 (M299V, V353I, and E401K). These mutant proteins, which affect the chaperone-dependent assembly of tubulin heterodimers in different ways, disrupt neurogenic division and/or migration in vivo. Our results provide insight into the functional repertoire of the tubulin gene family, specifically implicating TUBB5 in embryonic neurogenesis and microcephaly. Graphical abstract Highlights ► The β-tubulin Tubb5 is highly expressed in the developing mouse and human cortex ► In vivo knockdown of Tubb5 perturbs the cell cycle and alters neuronal positioning ► Mutations in TUBB5 cause microcephaly with dysmorphic basal ganglia in humans ► TUBB5 mutations affect chaperone-mediated tubulin folding in different ways

Description: The practice of adding organic amendments to crop soils is undergoing resurgence as an efficient way to restore soil organic matter content and to improve soil quality. The quantity and quality of the organic matter inputs affect soil physicochemical properties and soil microbiota, influencing different parameters such as microbial biomass and diversity, community structure and microbial activities or functions. The influence of organic amendments on soil quality has also effects on crop production and plant health. The enhancement of soil suppressiveness using organic amendments has been widely described, especially for soil-borne diseases. However, there is great variability in the effectiveness of suppression depending on the nature of the amendment, the crop, the pathogen, and the environmental conditions. Although the effects of organic amendments on soil properties have been widely studied, relationships between these properties and soil suppressiveness are not still well understood. Changes in soil physicochemical parameters may modulate the efficacy of suppression. However, the parameters more frequently associated to disease suppression appear to be related to soil microbiota, such as microbial biomass and activity, the abundance of specific microbial groups and some hydrolytic activities. This review focuses on the effect of organic amendments on soil microbial populations, diversity and activities; their ability to enhance plant health through disease suppression; and which of the parameters affected by the organic amendments are potentially involved in soil suppressiveness.

Description: Available online 13 December 2012 Publication year: 2012 Source: Cell Reports Elimination of aberrantly folded polypeptides from the endoplasmic reticulum (ER) by the ER - a ssociated d egradation (ERAD) system promotes cell survival under stress conditions. This quality control mechanism requires movement of misfolded proteins across the ER membrane for targeting to the cytosolic proteasome, a process facilitated by a “holdase” complex, consisting of Bag6 and the cofactors Ubl4A and Trc35. This multiprotein complex also participates in several other protein quality control processes. Here, we report SGTA as a component of the Bag6 system, which cooperates with Bag6 to channel dislocated ERAD substrates that are prone to aggregation. Using nuclear magnetic resonance spectroscopy and biochemical assays, we demonstrate that SGTA contains a noncanonical ubiquitin-like-binding domain that interacts specifically with an unconventional ubiquitin-like protein/domain in Ubl4A at least in part via electrostatics. This interaction helps recruit SGTA to Bag6, enhances substrate loading to Bag6, and thus prevents the formation of nondegradable protein aggregates in ERAD. Graphical abstract Highlights ► The two UBLs in the Bag6 complex have distinct features that specify their interactors ► The Ubl4A UBL interacts with SGTA to enhance its binding to Bag6 ► The Ubl4A UBL binds SGTA-N via an unconventional means of UBL recognition ► SGTA assists Bag6 in maintaining the solubility of ERAD substrates and promoting ERAD

Description: Available online 7 December 2012 Publication year: 2012 Source: Cell Reports The efficient generation of hematopoietic stem cells from human pluripotent stem cells is dependent on the appropriate specification of the definitive hematopoietic program during differentiation. In this study, we used T lymphocyte potential to track the onset of definitive hematopoiesis from human embryonic and induced pluripotent stem cells differentiated with specific morphogens in serum- and stromal-free cultures. We show that this program develops from a progenitor population with characteristics of hemogenic endothelium, including the expression of CD34, VE-cadherin, GATA2 , LMO2 , and RUNX1 . Along with T cells, these progenitors display the capacity to generate myeloid and erythroid cells. Manipulation of Activin/Nodal signaling during early stages of differentiation revealed that development of the definitive hematopoietic progenitor population is not dependent on this pathway, distinguishing it from primitive hematopoiesis. Collectively, these findings demonstrate that it is possible to generate T lymphoid progenitors from pluripotent stem cells and that this lineage develops from a population whose emergence marks the onset of human definitive hematopoiesis. Graphical abstract Highlights ► Activin/Nodal signaling distinguishes between primitive and definitive hematopoiesis ► T cell development identifies definitive hematopoiesis in human pluripotent cultures ► Primitive hematopoiesis can be distinguished by CD41a and CD235a coexpression ► Demonstration of human T cell development from hiPSCs

Description: Available online 7 December 2012 Publication year: 2012 Source: Cell Reports DNA ligase IV (LigIV) and Artemis are central components of the nonhomologous end-joining (NHEJ) machinery that is required for V(D)J recombination and the maintenance of genomic integrity in mammalian cells. We report here crystal structures of the LigIV DNA binding domain (DBD) in both its apo form and in complex with a peptide derived from the Artemis C-terminal region. We show that LigIV interacts with Artemis through an extended hydrophobic surface. In particular, we find that the helix α2 in LigIV-DBD is longer than in other mammalian ligases and presents residues that specifically interact with the Artemis peptide, which adopts a partially helical conformation on binding. Mutations of key residues on the LigIV-DBD hydrophobic surface abolish the interaction. Together, our results provide structural insights into the specificity of the LigIV-Artemis interaction and how the enzymatic activities of the two proteins may be coordinated during NHEJ. Graphical abstract Highlights ► Crystal structure of the Ligase-IV-Artemis complex ► Ligase IV DNA binding domain contains a unique hydrophobic cavity ► The structure shows why only Ligase IV can recruit Artemis ► Insights into how activities of Ligase IV and Artemis may be coordinated in NHEJ

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 A key feature of RNA polymerase II (Pol II) preinitiation complexes (PICs) is their ability to coordinate transcription initiation with chromatin modification and remodeling. To understand how this coordination is achieved, we employed extensive proteomic and mechanistic analyses to study the composition and assembly of PICs in HeLa cell and mouse embryonic stem cell (ESC) nuclear extracts. Strikingly, most of the machinery that is necessary for transcription initiation on chromatin is part of the PIC. The PIC is nearly identical between ESCs and HeLa cells and contains two major coactivator complexes: Mediator and SAGA. Genome-wide analysis of Mediator reveals that it has a close correlation with Pol II, TATA-binding protein, and messenger RNA levels and thus may play a major role in PIC assembly. Moreover, Mediator coordinates assembly of the Pol II initiation factors and chromatin machinery into a PIC in vitro, whereas SAGA acts after PIC assembly to allow transcription on chromatin. Graphical abstract Highlights ► The composition of mammalian PICs was determined by proteomic analysis ► A wide range of chromatin-modifying and -remodeling factors are recruited to PICs ► Mediator coordinates binding of Pol II initiation, elongation, and chromatin machineries ► SAGA acts after PIC assembly to make chromatin templates transcriptionally competent

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 In meiosis, two specialized cell divisions allow the separation of paired chromosomes first, then of sister chromatids. Separase removes the cohesin complex holding sister chromatids together in a stepwise manner from chromosome arms in meiosis I, then from the centromere region in meiosis II. Using mouse oocytes, our study reveals that cyclin A2 promotes entry into meiosis, as well as an additional unexpected role; namely, its requirement for separase-dependent sister chromatid separation in meiosis II. Untimely cyclin A2-associated kinase activity in meiosis I leads to precocious sister separation, whereas inhibition of cyclin A2 in meiosis II prevents it. Accordingly, endogenous cyclin A is localized to kinetochores throughout meiosis II, but not in anaphase I. Additionally, we found that cyclin B1, but not cyclin A2, inhibits separase in meiosis I. These findings indicate that separase-dependent cohesin removal is differentially regulated by cyclin B1 and A2 in mammalian meiosis. Graphical abstract Highlights ► Cyclin A2 is required for meiotic entry and sister chromatid separation in meiosis II ► Constitutive cyclin A2 activity in meiosis I leads to precocious sister separation ► Only cyclin B1, and not cyclin A2, can inhibit separase in mouse oocyte meiosis I ► Endogenous cyclin A is localized to centromeres throughout the second meiotic division

Description: Available online 6 December 2012 Publication year: 2012 Source: Cell Reports Pathogens that reside in the phagosomes of infected cells persist despite the presence of potent T cell responses. We addressed the mechanism of immune evasion by using a mouse model of Salmonella typhimurium (ST). Recombinants of ST were generated that translocated antigen to the cytosol or phagosomes of infected cells. We find that the kinetics of antigen presentation and CD8 + T cell priming is accelerated by cytosolic antigen delivery, although the magnitude of CD8 + T cell response is not influenced by antigenic location. More importantly, only those targets that readily display antigen on the cell surface, owing to antigenic translocation to the cytosol, are recognized and killed by CD8 + T cells. Thus, vaccination approaches developed to control phagosomal pathogens should incorporate methods for modulating antigen presentation such that infected target cells can be readily recognized by CD8 + T cells. Graphical abstract Highlights ► Intracellular location of antigen governs the duration of infection ► Forcing the recognition of infected cells by CD8 T cells controls infection ► CD8 T cells can convert a chronic infection to an acute infection ► Suppression is not the cause, but the end result, of a chronic infection

Description: Available online 13 December 2012 Publication year: 2012 Source: Cell Reports Trafficking of proteins specifically to the axonal or somatodendritic membrane allows neurons to establish and maintain polarized compartments with distinct morphology and function. Diverse evidence suggests that an actin-dependent vesicle filter within the axon initial segment (AIS) plays a critical role in polarized trafficking; however, no distinctive actin-based structures capable of comprising such a filter have been found within the AIS. Here, using correlative light and scanning electron microscopy, we visualized networks of actin filaments several microns wide within the AIS of cortical neurons in culture. Individual filaments within these patches are predominantly oriented with their plus ends facing toward the cell body, consistent with models of filter selectivity. Vesicles carrying dendritic proteins are much more likely to stop in regions occupied by the actin patches than in other regions, indicating that the patches likely prevent movement of dendritic proteins to the axon and thereby act as a vesicle filter. Graphical abstract Highlights ► 2 μm diameter actin networks are visualized by SEM and light microscopy in the AIS ► Actin filaments within networks are oriented with their plus ends facing proximally ► Actin network structure suggests a mechanism for selectively halting vesicles ► Vesicles carrying dendritic proteins halt and reverse in actin networks

Description: Available online 13 December 2012 Publication year: 2012 Source: Cell Reports Dopamine contributes to corticostriatal plasticity and motor learning. Dopamine denervation profoundly alters motor performance, as in Parkinson’s disease (PD); however, the extent to which these symptoms reflect impaired motor learning is unknown. Here, we demonstrate a D2 receptor blockade-induced aberrant learning that impedes future motor performance when dopamine signaling is restored, an effect diminished by coadministration of adenosine antagonists during blockade. We hypothesize that an inappropriate corticostriatal potentiation in striatopallidal cells of the indirect pathway underlies aberrant learning. We demonstrate synaptic potentiation in striatopallidal neurons induced by D2 blockade and diminished by application of an adenosine antagonist, consistent with behavioral observations. A neurocomputational model of the basal ganglia recapitulates the behavioral pattern and further links aberrant learning to plasticity in the indirect pathway. Thus, D2-mediated aberrant learning may contribute to motor deficits in PD, suggesting new avenues for the development of therapeutics. Graphical abstract Highlights ► Dopamine blockade induces aberrant learning that impairs future motor performance ► Aberrant learning is mediated by the D2-expressing striatopallidal pathway ► A2A antagonism protects against aberrant learning but impairs recovery ► D2 blockade induces potentiation at striatopallidal corticostriatal synapses

Description: Available online 13 December 2012 Publication year: 2012 Source: Cell Reports Sir2, an evolutionarily conserved NAD + -dependent deacetylase, has been implicated as a key factor in mediating organismal life span. However, recent contradictory findings have brought into question the role of Sir2 and its orthologs in regulating organismal longevity. In this study, we report that Drosophila Sir2 (dSir2) in the adult fat body regulates longevity in a diet-dependent manner. We used inducible Gal4 drivers to knock down and overexpress dSir2 in a tissue-specific manner. A diet-dependent life span phenotype of dSir2 perturbations (both knockdown and overexpression) in the fat body, but not muscles, negates the effects of background genetic mutations. In addition to providing clarity to the field, our study contrasts the ability of dSir2 in two metabolic tissues to affect longevity. We also show that dSir2 knockdown abrogates fat-body dFOXO-dependent life span extension. This report highlights the importance of the interplay between genetic factors and dietary inputs in determining organismal life spans. Graphical abstract Highlights ► The dSir2-dependent longevity phenotype is diet specific ► DR-dependent effects are associated with increased dSir2 expression and NAD + levels ► dSir2 in the fat body, but not in muscles, regulates longevity ► dSir2-dFOXO interaction in the fat body affects life-span extension

Description: Available online 6 December 2012 Publication year: 2012 Source: Cell Reports Deubiquitinating enzymes (DUBs) constitute a large family of cysteine proteases that have a broad impact on numerous biological and pathological processes, including the regulation of genomic stability. DUBs are often assembled onto multiprotein complexes to assist in their localization and substrate selection, yet it remains unclear how the enzymatic activity of DUBs is modulated by intracellular signals. Herein, we show that bursts of reactive oxygen species (ROS) reversibly inactivate DUBs through the oxidation of the catalytic cysteine residue. Importantly, USP1, a key regulator of genomic stability, is reversibly inactivated upon oxidative stress. This, in part, explains the rapid nature of PCNA monoubiquitination-dependent DNA damage tolerance in response to oxidative DNA damage in replicating cells. We propose that DUBs of the cysteine protease family act as ROS sensors in human cells and that ROS-mediated DUB inactivation is a critical mechanism for fine-tuning stress-activated signaling pathways. Graphical abstract Highlights ► USP1 is inactivated upon oxidative stress to fine-tune PCNA monoubiquitination ► The Cys protease family of DUBs are reversibly inactivated by ROS ► The AMSH metalloprotease DUB is refractory to ROS-mediated catalytic inactivation

Description: Available online 13 December 2012 Publication year: 2012 Source: Cell Reports Genome information, which is three-dimensionally organized within cells as chromatin, is searched and read by various proteins for diverse cell functions. Although how the protein factors find their targets remains unclear, the dynamic and flexible nature of chromatin is likely crucial. Using a combined approach of fluorescence correlation spectroscopy, single-nucleosome imaging, and Monte Carlo computer simulations, we demonstrate local chromatin dynamics in living mammalian cells. We show that similar to interphase chromatin, dense mitotic chromosomes also have considerable chromatin accessibility. For both interphase and mitotic chromatin, we observed local fluctuation of individual nucleosomes (∼50 nm movement/30 ms), which is caused by confined Brownian motion. Inhibition of these local dynamics by crosslinking impaired accessibility in the dense chromatin regions. Our findings show that local nucleosome dynamics drive chromatin accessibility. We propose that this local nucleosome fluctuation is the basis for scanning genome information. Graphical abstract Highlights ► Dense chromatin regions have considerable chromatin accessibility ► Observed local fluctuation of individual nucleosomes in interphase and mitotic chromatin ► Inhibition of nucleoome fluctuation impaired the chromatin accessibility ► Local fluctuation of nucleosomes is the basis for scanning genome information

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 Expansions of simple DNA repeats cause numerous hereditary diseases in humans. We analyzed the role of DNA polymerases in the instability of Friedreich’s ataxia (GAA) n repeats in a yeast experimental system. The elementary step of expansion corresponded to ∼160 bp in the wild-type strain, matching the size of Okazaki fragments in yeast. This step increased when DNA polymerase α was mutated, suggesting a link between the scale of expansions and Okazaki fragment size. Expandable repeats strongly elevated the rate of mutations at substantial distances around them, a phenomenon we call repeat-induced mutagenesis (RIM). Notably, defects in the replicative DNA polymerases δ and ε strongly increased rates for both repeat expansions and RIM. The increases in repeat-mediated instability observed in DNA polymerase δ mutants depended on translesion DNA polymerases. We conclude that repeat expansions and RIM are two sides of the same replicative mechanism. Graphical abstract Highlights ► Elementary step of repeat expansion corresponds to size of an Okazaki fragment ► Mutated DNA polymerase α leads to an increase in expansion step ► Mutated DNA polymerases δ and ε lead to elevated expansion rates ► Repeats induce mutagenesis, which is further elevated in polymerase mutants

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 Plasma sphingosine-1-phosphate (S1P) regulates vascular permeability, and plasma and lymph S1P guide lymphocyte egress from lymphoid organs. S1P is made intracellularly, and little is known about how S1P is delivered into circulatory fluids. Here, we find that mice without the major facilitator superfamily transporter Spns2 have a profound reduction in lymph S1P, but only a minor decrease in plasma S1P. Spns2-deficient mice have a redistribution of lymphocytes from the spleen to lymph nodes and a loss of circulating lymphocytes, consistent with normal egress from the spleen directed by plasma S1P and blocked egress from lymph nodes directed by lymph S1P. Spns2 is needed in endothelial cells to supply lymph S1P and support lymphocyte circulation. As a differential requirement for lymph and blood S1P, Spns2 may be an attractive target for immune suppressive drugs. Graphical abstract Highlights ► The transporter Spns2 is required to supply lymph, but not plasma, S1P ► Spns2-deficient mice have disrupted peripheral lymphocyte circulation ► Spns2 is required in endothelial cells to secrete lymph S1P and support trafficking

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 Elongin A increases the rate of RNA polymerase II (pol II) transcript elongation by suppressing transient pausing by the enzyme. Elongin A also acts as a component of a cullin-RING ligase that can target stalled pol II for ubiquitylation and proteasome-dependent degradation. It is not known whether these activities of Elongin A are functionally interdependent in vivo. Here, we demonstrate that Elongin A-deficient (Elongin A −/− ) embryos exhibit abnormalities in the formation of both cranial and spinal nerves and that Elongin A −/− embryonic stem cells (ESCs) show a markedly decreased capacity to differentiate into neurons. Moreover, we identify Elongin A mutations that selectively inactivate one or the other of the aforementioned activities and show that mutants that retain the elongation stimulatory, but not pol II ubiquitylation, activity of Elongin A rescue neuronal differentiation and support retinoic acid-induced upregulation of a subset of neurogenesis-related genes in Elongin A −/− ESCs. Graphical abstract Highlights ► RA-induced neuronal differentiation is markedly impaired in Elongin A −/− ESCs ► Formation of cranial ganglia and DRG is severely impaired in Elongin A −/− embryos ► Mutations that differentially affect the two activities of Elongin A were identified ► Elongin A’s elongation stimulatory activity is required for a subset of RA-induced genes

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 The large Mediator (L-Mediator) is a general coactivator of RNA polymerase II transcription and is formed by the reversible association of the small Mediator (S-Mediator) and the kinase-module-harboring Cdk8. It is not known how the kinase module association/dissociation is regulated. We describe the fission yeast Cdk11-L-type cyclin pombe (Lcp1) complex and show that its inactivation alters the global expression profile in a manner very similar to that of mutations of the kinase module. Cdk11 is broadly distributed onto chromatin and phosphorylates the Med27 and Med4 Mediator subunits on conserved residues. The association of the kinase module and the S-Mediator is strongly decreased by the inactivation of either Cdk11 or the mutation of its target residues on the Mediator. These results show that Cdk11-Lcp1 regulates the association of the kinase module and the S-Mediator to form the L-Mediator complex. Graphical abstract Highlights ► A complex related to metazoan Cdk11-CyclinL is conserved in fission yeast ► Loss of either Cdk8 or Cdk11 similarly affects global expression profile ► Cdk11 phosphorylates two Mediator subunits ► Association of the Cdk8 module with the S-Mediator requires phosphorylation by Cdk11

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in the elderly population worldwide. Although recent studies have demonstrated strong genetic associations between AMD and SNPs in a number of genes, other modes of regulation are also likely to play a role in the etiology of this disease. We identified a significantly decreased level of methylation on the IL17RC promoter in AMD patients. Furthermore, we showed that hypomethylation of the IL17RC promoter in AMD patients led to an elevated expression of its protein and messenger RNA in peripheral blood as well as in the affected retina and choroid, suggesting that the DNA methylation pattern and expression of IL17RC may potentially serve as a biomarker for the diagnosis of AMD and likely plays a role in disease pathogenesis. Graphical abstract Highlights ► ∼1.5% of CpG sites are differentially methylated between twins with discordant AMD ► Hypomethylated IL17RC promoter and elevated IL17RC expression are associated with AMD ► IL-17-mediated inflammatory responses contribute to AMD pathogenesis

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 RIG-I and MDA5 are cytosolic RNA sensors that play a critical role in innate antiviral responses. Major advances have been made in identifying RIG-I ligands, but our knowledge of the ligands for MDA5 remains restricted to data from transfection experiments mostly using poly(I:C), a synthetic dsRNA mimic. Here, we dissected the IFN-α/β-stimulatory activity of different viral RNA species produced during picornavirus infection, both by RNA transfection and in infected cells in which specific steps of viral RNA replication were inhibited. Our results show that the incoming genomic plus-strand RNA does not activate MDA5, but minus-strand RNA synthesis and production of the 7.5 kbp replicative form trigger a strong IFN-α/β response. IFN-α/β production does not rely on plus-strand RNA synthesis and thus generation of the partially double-stranded replicative intermediate. This study reports MDA5 activation by a natural RNA ligand under physiological conditions. Graphical abstract Highlights ► Viral ssRNA, with or without the 5′ VPg peptide, does not induce IFN-α/β ► Synthesis of minus-strand—but not plus-strand—RNA is crucial for MDA5 activation ► The picornavirus RF activates MDA5 both in vitro and in vivo ► MDA5 activation by viral replicative form is independent of the terminal groups of this RNA

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 In mammals, each olfactory bulb (OB) contains a pair of mirror-symmetric glomerular maps organized to reflect odorant receptor identity. The functional implication of maintaining these symmetric medial-lateral maps within each OB remains unclear. Here, using in vivo multielectrode recordings to simultaneously detect odorant-induced activity across the entire OB, we reveal a timing difference in the odorant-evoked onset latencies between the medial and lateral halves. Interestingly, the latencies in the medial and lateral OB decreased at different rates as odorant concentration increased, causing the timing difference between them to also diminish. As a result, output neurons in the medial and lateral OB fired with greater synchrony at higher odorant concentrations. Thus, we propose that temporal differences in activity between the medial and lateral OB can dynamically code odorant concentration, which is subsequently decoded in the olfactory cortex through the integration of synchronous action potentials. Graphical abstract Highlights ► Odorants differentially activate the medial and lateral olfactory bulb (OB) ► An ∼60 ms time window is defined between medial and lateral mitral cell output ► The medial-lateral time window is dynamically modulated by odorant concentrations ► High odorant concentrations synchronize medial-lateral OB output

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 MicroRNAs (miRNAs) are essential regulators of development, physiology, and evolution, and their biogenesis is strictly controlled at multiple levels. Regulatory proteins, such as KSRP, modulate rates and timing of enzymatic reactions responsible for maturation of select miRNAs from their primary transcripts in response to specific stimuli. Here, we show that KSRP silencing in mesenchymal C2C12 cells produces a change in the transcriptome largely overlapping that induced by bone morphogenetic protein 2 (BMP2) signaling activation. This induces osteoblastic differentiation while preventing myogenic differentiation. KSRP silencing- and BMP2-dependent myogenic miRNA (myomiR) maturation blockade is required for osteoblastic differentiation of C2C12 cells. Our results demonstrate that phosphorylated R-SMAD proteins, the transducers of BMP2 signal, associate with phosphorylated KSRP and block its interaction with primary myomiRs. This abrogates KSRP-dependent myomiR maturation, with SMAD4, SMAD5, and SMAD9 silencing being able to rescue KSRP function. Thus, SMAD-induced blockade of KSRP-dependent myomiR maturation is critical for orienting C2C12 cell differentiation toward osteoblastic lineage. Graphical abstract Highlights ► KSRP silencing and BMP2 signaling activation block myomiR maturation ► myomiR maturation blockade is required for osteoblastic differentiation of C2C12 cells ► SMAD proteins interact with KSRP and block its ability to promote myomiR maturation

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 Senescence is a cellular response preventing tumorigenesis. The Ras oncogene is frequently activated or mutated in human cancers, but Ras activation is insufficient to transform primary cells. In a search for cooperating oncogenes, we identify the lysine demethylase JMJD2A/KDM4A. We show that JMJD2A functions as a negative regulator of Ras-induced senescence and collaborates with oncogenic Ras to promote cellular transformation by negatively regulating the p53 pathway. We find CHD5 , a known tumor suppressor regulating p53 activity, as a target of JMJD2A. The expression of JMJD2A inhibits Ras-mediated CHD5 induction leading to a reduced activity of the p53 pathway. In addition, we show that JMJD2A is overexpressed in mouse and human lung cancers. Depletion of JMJD2A in the human lung cancer cell line A549 bearing an activated K-Ras allele triggers senescence. We propose that JMJD2A is an oncogene that represents a target for Ras-expressing tumors. Graphical abstract Highlights ► JMJD2A contributes to the bypass of Ras-induced senescence ► Genome-wide search for gene promoters regulated by JMJD2A identifies CHD5 ► JMJD2A cooperates with Ras to transform primary cells ► JMJD2A depletion in human lung cancer cells leads to massive senescence

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 Mitochondria-originating reactive oxygen species (ROS) control T cell receptor (TCR)-induced gene expression. Here, we show that TCR-triggered activation of ADP-dependent glucokinase (ADPGK), an alternative, glycolytic enzyme typical for Archaea , mediates generation of the oxidative signal. We also show that ADPGK is localized in the endoplasmic reticulum and suggest that its active site protrudes toward the cytosol. The ADPGK-driven increase in glycolytic metabolism coincides with TCR-induced glucose uptake, downregulation of mitochondrial respiration, and deviation of glycolysis toward mitochondrial glycerol-3-phosphate dehydrogenase (GPD) shuttle; i.e., a metabolic shift to aerobic glycolysis similar to the Warburg effect. The activation of respiratory-chain-associated GPD2 results in hyperreduction of ubiquinone and ROS release from mitochondria. In parallel, mitochondrial bioenergetics and ultrastructure are altered. Downregulation of ADPGK or GPD2 abundance inhibits oxidative signal generation and induction of NF-κB-dependent gene expression, whereas overexpression of ADPGK potentiates them. Graphical abstract Highlights ► TCR triggering activates ADPGK, an ER-localized glycolytic enzyme ► TCR induction shifts metabolism toward glycolysis and activates mitochondrial GPD2 ► Activation of GPD2 leads to ubiquinol accumulation and ROS release from mitochondria ► ADPGK- and GPD2-dependent oxidative signal drives NF-κB-regulated gene expression

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 Alzheimer's disease (AD) is the most common cause of dementia among older people. There are no effective medications currently available to prevent and treat AD and halt disease progression. Monoacylglycerol lipase (MAGL) is the primary enzyme metabolizing the endocannabinoid 2-arachidonoylglycerol in the brain. We show here that inactivation of MAGL robustly suppressed production and accumulation of β-amyloid (Aβ) associated with reduced expression of β-site amyloid precursor protein cleaving enzyme 1 (BACE1) in a mouse model of AD. MAGL inhibition also prevented neuroinflammation, decreased neurodegeneration, maintained integrity of hippocampal synaptic structure and function, and improved long-term synaptic plasticity, spatial learning, and memory in AD animals. Although the molecular mechanisms underlying the beneficial effects produced by MAGL inhibition remain to be determined, our results suggest that MAGL, which regulates endocannabinoid and prostaglandin signaling, contributes to pathogenesis and neuropathology of AD, and thus is a promising therapeutic target for the prevention and treatment of AD. Graphical abstract Highlights ► Inactivation of MAGL reduces Aβ plaques and BACE1 expression in AD mice ► MAGL inhibition decreases neuroinflammation and neurodegeneration ► MAGL inhibition maintains integrity of hippocampal synaptic structure and function ► MAGL inhibition improves synaptic plasticity and learning and memory in AD mice

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 Antagonistic pleiotropy (AP), or genetic tradeoff, is an important concept that is frequently invoked in theories of aging, cancer, genetic disease, and other common phenomena. However, the prevalence of AP, which genes are subject to AP, and to what extent and how AP may be resolved remain unclear. By measuring the fitness difference between the wild-type and null alleles of ∼5,000 nonessential genes in yeast, we found that in any given environment, yeast expresses hundreds of genes that harm rather than benefit the organism, demonstrating widespread AP. Nonetheless, under sufficient selection, AP is often resolvable through regulatory evolution, primarily by trans -acting changes, although in one case we also detected a cis -acting change and localized its causal mutation. However, AP is resolved more slowly in smaller populations, predicting more unresolved AP in multicellular organisms than in yeast. These findings provide an empirical foundation for AP-dependent theories and have broad biomedical and evolutionary implications. Graphical abstract Highlights ► Under any conditions, yeast expresses many genes that are harmful to the cell ► Such problems can often be resolved by regulatory evolution under selection ► Such regulatory evolution tends to occur via trans -acting genetic changes ► Antagonistic pleiotropy is predicted to be more abundant in multicellular organisms

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 After implantation, pluripotent epiblasts are converted to embryonic ectoderm through cell–cell interactions that significantly change the transcriptional and epigenetic networks. An entrée to understanding this vital developmental transition is the t w5 mutation of the mouse t complex. This mutation produces highly specific defects in the embryonic ectoderm before gastrulation, leading to death of the embryonic ectoderm. Using a positional cloning approach, we have now identified the mutated gene, completing a decades-long search. The gene, vacuolar protein sorting 52 ( Vps52 ), is a mouse homolog of yeast VPS52 that is involved in the retrograde trafficking of endosomes. Our data suggest that Vps52 acts in extraembryonic tissues to support the growth and differentiation of embryonic ectoderm via cell–cell interactions. It is also required in the formation of embryonic structures at a later stage of development, revealing hitherto unknown functions of Vps52 in the development of a multicellular organism. Graphical abstract Highlights ► Vps52 , part of retrograde transport to the Golgi, causes the t w5 lethal phenotype ► Vps52 acts in extraembryonic tissues to dictate embryonic ectoderm differentiation ► VPS52’s essential function in the embryo involves cell–cell interactions ► VPS52 also has an indispensable function later in development

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 Human pluripotent stem cells (hPSCs), including embryonic stem cells and induced pluripotent stem cells, are potentially useful in regenerative therapies for heart disease. For medical applications, clinical-grade cardiac cells must be produced from hPSCs in a defined, cost-effective manner. Cell-based screening led to the discovery of KY02111, a small molecule that promotes differentiation of hPSCs to cardiomyocytes. Although the direct target of KY02111 remains unknown, results of the present study suggest that KY02111 promotes differentiation by inhibiting WNT signaling in hPSCs but in a manner that is distinct from that of previously studied WNT inhibitors. Combined use of KY02111 and WNT signaling modulators produced robust cardiac differentiation of hPSCs in a xeno-free, defined medium, devoid of serum and any kind of recombinant cytokines and hormones, such as BMP4, Activin A, or insulin. The methodology has potential as a means for the practical production of human cardiomyocytes for regeneration therapies. Graphical abstract Highlights ► KY02111 promotes the differentiation of hPSCs to functional cardiomyocytes ► KY02111 acts downstream of APC and GSK3β to inhibit WNT signaling ► KY02111 and WNT inhibitors cooperatively enhance hPSC cardiomyogenesis ► KY02111and WNT modulators permit cytokine and xeno-free hPSC cardiomyogenesis

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 Growing evidence suggests that aggregation-prone proteins are both harmful and functional for a cell. How do cellular systems balance the detrimental and beneficial effect of protein aggregation? We reveal that aggregation-prone proteins are subject to differential transcriptional, translational, and degradation control compared to nonaggregation-prone proteins, which leads to their decreased synthesis, low abundance, and high turnover. Genetic modulators that enhance the aggregation phenotype are enriched in genes that influence expression homeostasis. Moreover, genes encoding aggregation-prone proteins are more likely to be harmful when overexpressed. The trends are evolutionarily conserved and suggest a strategy whereby cellular mechanisms specifically modulate the availability of aggregation-prone proteins to (1) keep concentrations below the critical ones required for aggregation and (2) shift the equilibrium between the monomeric and oligomeric/aggregate form, as explained by Le Chatelier’s principle. This strategy may prevent formation of undesirable aggregates and keep functional assemblies/aggregates under control. Graphical abstract Highlights ► mRNA encoding aggregation-prone proteins is complex, suggesting greater translational regulation ► Aggregation-prone proteins are present in low abundance and for short periods of time ► Tight control is evolutionarily conserved and provides robustness against aggregation ► Aggregation-prone proteins are subject to tight regulation

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 Variability in signaling pathway activation between neighboring epithelial cells can arise from local differences in the microenvironment, noisy gene expression, or acquired genetic changes. To investigate the consequences of this cell-to-cell variability in signaling pathway activation on coordinated multicellular processes such as morphogenesis, we use DNA-programmed assembly to construct three-dimensional MCF10A microtissues that are mosaic for low-level expression of activated H-Ras. We find two emergent behaviors in mosaic microtissues: cells with activated H-Ras are basally extruded or lead motile multicellular protrusions that direct the collective motility of their wild-type neighbors. Remarkably, these behaviors are not observed in homogeneous microtissues in which all cells express the activated Ras protein, indicating that heterogeneity in Ras activity, rather than the total amount of Ras activity, is critical for these processes. Our results directly demonstrate that cell-to-cell variability in pathway activation within local populations of epithelial cells can drive emergent behaviors during epithelial morphogenesis. Graphical abstract Highlights ► Cell-to-cell variability in Ras activity triggers emergent behaviors ► Homogeneous and low-level Ras activation does not disrupt early morphogenesis ► Programmed assembly precisely controls the composition of mosaic epithelial tissues

Description: Bioavailability of sinking organic matter in the Blanes canyon and the adjacent open slope (NW Mediterranean Sea) Biogeosciences Discussions, 9, 18295-18330, 2012 Author(s): P. Lopez-Fernandez, S. Bianchelli, A. Pusceddu, A. Calafat, A. Sanchez-Vidal, and R. Danovaro Submarine canyons are sites of intense energy and material exchange between the shelf and the deep adjacent basins. To test the hypothesis that active submarine canyons represent preferential conduits of available food for the deep-sea benthos, two mooring lines were deployed at 1200 m depth from November 2008 to November 2009 inside the Blanes canyon and on the adjacent open slope (Catalan Margin, NW Mediterranean Sea). We investigated the fluxes, biochemical composition and food quality of sinking organic carbon (OC). OC fluxes in the canyon and the open slope varied among sampling periods, though not consistently in the two sites. In particular, while in the open slope the highest OC fluxes were observed in August 2009, in the canyon the highest OC fluxes occurred in April–May 2009. For almost the entire study period, the OC fluxes in the canyon were significantly higher than those in the open slope, whereas OC contents of sinking particles collected in the open slope were consistently higher than those in the canyon. This result confirms that submarine canyons are effective conveyors of OC to the deep sea, particles transferred are predominantly of inorganic origin, significantly higher than that reaching the open slope at a similar water depth. Using multivariate statistical tests, two major clusters of sampling periods were identified: one in the canyon that grouped trap samples collected in December 2008, concurrently with the occurrence of a major storm at the sea surface, and associated with increased fluxes of nutritionally available particles from the upper shelf. Another cluster grouped samples from both the canyon and the open slope collected in March 2009, concurrently with the occurrence of the seasonal phytoplankton bloom at the sea surface, and associated with increased fluxes of total phytopigments. Our results confirm the key ecological role of submarine canyons for the functioning of deep-sea ecosystems, and highlight the importance of canyons in linking episodic storms and primary production occurring at the sea surface to the deep sea floor.

Description: Influence of increasing dissolved inorganic carbon concentrations and decreasing pH on chemolithoautrophic bacteria from oxic-sulfidic interfaces Biogeosciences Discussions, 9, 18371-18395, 2012 Author(s): K. Mammitzsch, G. Jost, and K. Jürgens Increases in the dissolved inorganic carbon (DIC) concentration are expected to cause a decrease in the pH of ocean waters, a process known as ocean acidification. In oxygen-deficient zones this will add to already increased DIC and decreased pH values. It is not known how this might affect microbial communities and microbially mediated processes. In this study, the potential effects of ocean acidification on chemolithoautotrophic prokaryotes of marine oxic-anoxic transition zones were investigated, using the chemoautotrophic denitrifying ε -proteobacterium " Sulfurimonas gotlandica " strain GD1 as a model organism. This and related taxa use reduced sulfur compounds, e.g. sulfide and thiosulfate, as electron donors and were previously shown to be responsible for nitrate removal and sulfide detoxification in redox zones of the Baltic Sea water column but occur also in other oxygen-deficient marine systems. Bacterial cell growth within a broad range of DIC concentrations and pH values was monitored and substrate utilization was determined. The results showed that the DIC saturation concentration for growth was already reached at 800 μM, which is well below in situ DIC levels. The pH optimum was between 6.6 and 8.0. Within a pH range of 6.6–7.1 there was no significant difference in substrate utilization; however, at lower pH values cell growth decreased sharply and cell-specific substrate consumption increased. These findings suggest that a direct effect of ocean acidification, with the predicted changes in pH and DIC, on chemolithoautotrophic bacteria such as " S. gotlandica " str. GD1 is generally not very probable.

Description: Microbial bioavailability regulates organic matter preservation in marine sediments Biogeosciences Discussions, 9, 13187-13210, 2012 Author(s): K. A. Koho, K. G. J. Nierop, L. Moodley, J. J. Middelburg, L. Pozzato, K. Soetaert, J. van der Plicht, and G.-J. Reichart Burial of organic matter (OM) plays an important role in marine sediments, linking the short-term, biological carbon cycle with the long-term, geological subsurface cycle. It is well established that low-oxygen conditions promote organic carbon burial in marine sediments. However, the mechanism remains enigmatic. Here we report biochemical quality, microbial degradability, OM preservation and accumulation along an oxygen gradient in the Indian Ocean. Our results show that more OM, and of biochemically higher quality, accumulates under low oxygen conditions. Nevertheless, microbial degradability does not correlate with the biochemical quality of OM. This decoupling of OM biochemical quality and microbial degradability, or bioavailability, violates the ruling paradigm that higher quality implies higher microbial processing. The inhibition of bacterial OM remineralisation may play an important role in the burial of organic matter in marine sediments and formation of oil source rocks.

Description: Impact of an 8.2-kyr-like event on methane emissions in northern peatlands Biogeosciences Discussions, 9, 13243-13286, 2012 Author(s): S. Zürcher, R. Spahni, F. Joos, M. Steinacher, and H. Fischer Rapid changes in atmospheric methane (CH 4 ), temperature and precipitation are documented by Greenland ice core data both for glacial times (the so called Dangaard-Oeschger (DO) events) as well as for a cooling event in the early Holocene (the 8.2 kyr event). The onsets of DO warm events are paralleled by abrupt increases in CH 4 by up to 250 ppbv in a few decades. Vice versa, the 8.2 kyr event is accompanied by an intermittent decrease in CH 4 of about 80 ppbv over 150 yr. The abrupt CH 4 changes are thought to mainly originate from source emission variations in tropical and boreal wet ecosystems, but complex process oriented bottom-up model estimates of the changes in these ecosystems during rapid climate changes are still missing. Here we present simulations of CH 4 emissions from northern peatlands with the LPJ-Bern dynamic global vegetation model. The model represents CH 4 production and oxidation in soils and transport by ebullition, through plant aerenchyma, and by diffusion. Parameters are tuned to represent site emission data as well as inversion-based estimates of northern wetland emissions. The model is forced with climate input data from freshwater hosing experiments using the NCAR CSM1.4 climate model to simulate an abrupt cooling similar to the widespread 8.2 kyr event. As a main result we get a concentration reduction of ~10 ppbv per degree K change of mean northern hemispheric surface temperature in peatlands. This sensitivity comprises effects on peatland emissions of similar size by the temperature itself as well as by the accompanying change in precipitation rate, hence water table. Comparison with the ice core record reveals that a change in boreal peatland emissions alone could not completely account for the 80 ppbv methane decline during the 8.2 kyr event, pointing to a significant contribution from tropical wetlands to this event.

Description: Temporal variation of nitrate and phosphate transport in headwater catchments: the hydrological controls and landuse alteration Biogeosciences Discussions, 9, 13211-13241, 2012 Author(s): T.-Y. Lee, J.-C. Huang, S.-J. Kao, and C.-P. Tung Oceania Rivers are hotspots of high DIN (dissolved inorganic nitrogen) and DIP (dissolved inorganic phosphorus) transport. However, the effects of hydrologic controls and land use alternation on the temporal variations of DIN and DIP are rarely documented. In this study, we monitored the nitrate and phosphate concentrations from three headwater catchments with different cultivation gradients at a 3-day interval. This sampling scheme was supplemented with a 3-h interval monitoring during typhoon periods. The results showed that the DIN and DIP yields in the pristine, moderately cultivated, and intensively cultivated watersheds were 7.52/0.31, 31.17/0.30, and 40.96/0.52 kg ha −1 yr −1 , respectively. The high DIN yields are comparable to the intensively and extensively disturbed large rivers around the world. These N yields may be due to a high level of nitrogen deposition, rainfall-runoff, and fertilizer application. The importance of event sampling was indicated by the contribution of the three typhoons to the annual DIN and DIP fluxes, which were 30% and 60%, respectively. Both DIN and DIP fluxes significantly increased as the cultivation gradient increased. The DIN and DIP ratio varied from 54 to 230 depending on the decrease of the cultivation gradient. This value is higher than the global mean of ~18. Thus, we speculate that nitrogen saturation occurs in the headwater catchments of Oceania Rivers. The results obtained provide fundamental clues of DIN and DIP yield of Oceania Rivers, which are helpful in understanding the impact of human disturbance on headwater watersheds.

Description: Ammonia emissions from cattle urine and dung excreted on pasture Biogeosciences Discussions, 9, 13287-13318, 2012 Author(s): J. Laubach, A. Taghizadeh-Toosi, S. J. Gibbs, R. R. Sherlock, F. M. Kelliher, and S. P. P. Grover Twelve cattle were kept for three days in a circular area of 16 m radius on short pasture and fed with freshly-cut pasture. Ammonia (NH 3 ) emissions from the urine and dung excreted by the cattle were measured with a micrometeorological mass-balance method, during the cattle presence and for 10 subsequent days. Daily-integrated emission rates peaked on day 3 of the experiment (last day of cattle presence) and declined steadily for five days thereafter. Urine patches were the dominant sources for these emissions. On day 9, a secondary emissions peak occurred, with dung pats likely to be the main sources. This interpretation is based on simultaneous observations of the pH evolution in urine patches and dung pats created next to the circular plot. Feed and dung samples were analysed to estimate the amounts of nitrogen (N) ingested and excreted. Total N volatilised as NH 3 was 19.8 (±0.9) % of N intake and 22.4 (±1.3) % of N excreted. The bimodal shape of the emissions time series allowed to infer separate estimates for volatilisation from urine and dung, respectively, with the result that urine accounted for 88.6 (±2.6) % of the total NH 3 emissions. The emissions from urine represented 25.5 (±2.0) % of the excreted urine-N, while the emissions from dung amounted to 11.6 (±2.7) % of the deposited dung-N. Emissions from dung may have continued after day 13 but were not resolved by the measurement technique. A simple resistance model shows that the magnitude of the emissions from dung is controlled by the resistance of the dung crust.

Description: Publication year: 2012 Source: FEBS Open Bio Miki Hieda, Michiko Koizumi, Chiduru Higashi, Taro Tachibana, Tomohiko Taguchi, Shigeki Higashiyama Heparin-binding epidermal growth factor (EGF) – like growth factor (HB-EGF) is synthesized in the ER, transported along the exocytic pathway, and expressed on the plasma membrane as a type I transmembrane protein. Upon extracellular stimulation, HB-EGF, either proHB-EGF or the shed form HB-EGF-CTF, undergoes endocytosis and is then transported retrogradely to the ER. In this study, we showed the essential contribution of the short cytoplasmic tail of HB-EGF (HB-EGF-cyto) to the bidirectional intracellular trafficking between the ER and plasma membrane and revealed several critical amino acids residues that are responsible for internalization from the plasma membrane and ER targeting. We suggest that these anterograde and retrograde sorting signals within HB-EGF-cyto are strictly regulated by protein modification and conformation. Highlights ▸ The cytoplasmic tail of HB-EGF contributes to bidirectional intracellular trafficking. ▸ The carboxyl-terminal five amino acids are indispensable for internalization. ▸ Amino acids S207 and K201 play essential roles in retrograde transport to the ER. ▸ Sorting signals in HB-EGF are regulated by protein modification and conformation. ▸ The extracellular domain of proHB-EGF is not required for intracellular trafficking.

Description: Publication year: 2012 Source: Cell Reports Vadim Shchepachev, Harry Wischnewski, Edoardo Missiaglia, Charlotte Soneson, Claus M. Azzalin Clericuzio-type poikiloderma with neutropenia (PN) is a rare genodermatosis associated with mutations in the C16orf57 gene, which codes for the uncharacterized protein hMpn1. We show here that, in both fission yeasts and humans, Mpn1 processes the spliceosomal U6 small nuclear RNA (snRNA) posttranscriptionally. In Mpn1-deficient cells, U6 molecules carry 3′ end polyuridine tails that are longer than those in normal cells and lack a terminal 2′,3′ cyclic phosphate group. In mpn1 Δ yeast cells, U6 snRNA and U4/U6 di-small nuclear RNA protein complex levels are diminished, leading to precursor messenger RNA splicing defects, which are reverted by expression of either yeast or human Mpn1 and by overexpression of U6. Recombinant hMpn1 is a 3′-to-5′ RNA exonuclease that removes uridines from U6 3′ ends, generating terminal 2′,3′ cyclic phosphates in vitro. Finally, U6 degradation rates increase in mpn1 Δ yeasts and in lymphoblasts established from individuals affected by PN. Our data indicate that Mpn1 promotes U6 stability through 3′ end posttranscriptional processing and implicate altered U6 metabolism as a potential mechanism for PN pathogenesis. Graphical abstract Graphical Abstract Highlights ► Yeast and human cells deficient for Mpn1 fail to process U6 snRNA oligo(U) 3′ ends ► Cellular U6 levels and pre-mRNA splicing are compromised in mpn1 Δ yeasts ► Mpn1 is a 3′-to-5′ RNA exonuclease ► U6 degradation rates are accelerated in yeast and human cells deficient for Mpn1

Description: Publication year: 2012 Source: Cell Reports Agathe Valluet, Sabine Druillennec, Céline Barbotin, Coralie Dorard, Anne H. Monsoro-Burq, Magalie Larcher, Celio Pouponnot, Manuela Baccarini, Lionel Larue, Alain Eychène B-Raf and C-Raf kinases have emerged as critical players in melanoma. However, little is known about their role during development and homeostasis of the melanocyte lineage. Here, we report that knockout of B-raf and C-raf genes in this lineage results in normal pigmentation at birth with no defect in migration, proliferation, or differentiation of melanoblasts in mouse hair follicles. In contrast, the double raf knockout mice displayed hair graying resulting from a defect in cell-cycle entry of melanocyte stem cells (MSCs) and their subsequent depletion in the hair follicle bulge. Therefore, Raf signaling is dispensable for early melanocyte lineage development, but necessary for MSC maintenance. Graphical abstract Graphical Abstract Highlights ► Direct in vivo evidence of the involvement of Raf proteins in stemness ► B-Raf and C-Raf are required for melanocyte stem cell self-maintenance ► The Raf/MEK/ERK pathway is not essential for melanocyte lineage development ► SCF/Kit and Raf/ERK signaling pathways are uncoupled in the melanocyte lineage

Description: Publication year: 2012 Source: Cell Reports, Volume 2, Issue 3 Simone Prömel, Marie Frickenhaus, Samantha Hughes, Lamia Mestek, David Staunton, Alison Woollard, Ioannis Vakonakis, Torsten Schöneberg, Ralf Schnabel, Andreas P. Russ, Tobias Langenhan

Description: Publication year: 2012 Source: FEBS Open Bio Niege S. Mendes, Glauce L. Trevisan, Aline H.Silva Cruz, Rodrigo S. Santos, Nalu T.A. Peres, Nilce M. Martinez-Rossi, Antonio Rossi In fungi, ambient pH sensing involves the activation of the Pal/PacC signalling pathway. In the dermatophyte Trichophyton rubrum , pH-dependent secretion of keratinases, which are major virulence determinants, is affected by disruption of the pacC gene. Here, the transcription profiling of the genes coding for N- and O-linked mannosyltransferases, enzymes involved in protein glycosylation, was evaluated in T. rubrum in response to disruption of the pacC gene and growth in keratin, glucose, and glucose plus glycine. We show that transcription of these mannosyltransferase genes is affected by nutrients at acidic pH and by PacC.

Description: Publication year: 2012 Source: FEBS Open Bio Daisuke Sugimori, Kota Kano, Yusaku Matsumoto A novel metal ion-independent phospholipase A 1 of Streptpmyces albidoflavus isolated from Japanese soil has been purified and characterized. The enzyme consists of a 33-residue N-terminal signal secretion sequence and a 269-residue mature protein with a deduced molecular weight of 27,199. Efficient and extracellular production of the recombinant enzyme was successfully achieved using S. lividans cells and an expression vector. A large amount (25 mg protein, 14.7 kU) of recombinant enzyme with high specific activity (588 U/mg protein) was purified by simple purification steps. The maximum activity was found at pH 7.2 and 50°C. At pH 7.2, the enzyme preferably hydrolyzed phosphatidic acid and phosphatidylserine; however, the substrate specificity was dependent on the reaction pH. The enzyme hydrolyzed lysophosphatidylcholine and not triglyceride and the p -nitrophenyl ester of fatty acids. At the reaction equilibrium, the molar ratio of released free fatty acids ( sn -1: sn -2) was 65:35. The hydrolysis of phosphatidic acid at 50°C and pH 7.2 gave apparent V max and k cat values of 1389 μmol min −1 mg protein −1 and 630 s −1 , respectively. The apparent K m and k cat / K m values were 2.38 mM and 265 mM −1 s −1 , respectively. Mutagenesis analysis showed that Ser11 is essential for the catalytic function of the enzyme and the active site may include residues Ser216 and His218. Highlights ▸ A novel metal ion-independent phospholipase A 1 has been purified and characterized. ▸ We report the positional specific hydrolysis of glycerophospholipids. ▸ The enzyme preferably hydrolyzed phosphatidic acid and phosphatidylserine. ▸ The apparent K m , k cat , and K cat / K m values were 2.38 mM, 630 s −1 and 265 mM −1 s −1 . ▸ We demonstrate that the active site should be composed of Ser11, S216, and H218.

Description: Publication year: 2012 Source: FEBS Open Bio James A.L. Brown, John K. Eykelenboom, Noel F. Lowndes Under normal conditions histone H2AX is constitutively phosphorylated on tyrosine (Y) 142 by Williams-Beuren syndrome transcription factor kinase (WSTF). Following DNA double strand breaks (DSB), Y142 is de-phosphorylated and serine (S) 139 is phosphorylated. Here we explored DSB-dependent cross talk between H2AX residues S139 and Y142. H2axY142A mutation resulted in increased sensitivity to ionizing radiation (IR), compared to H2axS139A . Interestingly, co-mutation of S139A and Y142A rescued IR sensitivity. The DSB response proteins 53Bp1 and Rad51 were recruited to IR-induced foci (IRIF) in H2axS139A , H2axY142A and H2axS139A / Y142A cells. Our results suggest that H2axY142A IR sensitivity is dependent upon the C-terminal residue, S139.

Description: Isoprene emissions from a tundra ecosystem Biogeosciences Discussions, 9, 13351-13396, 2012 Author(s): M. J. Potosnak, B. M. Baker, L. LeStourgeon, S. M. Disher, K. L. Griffin, and M. S. Bret-Harte Whole-system fluxes of isoprene from a~moist acidic tundra ecosystem and leaf-level emission rates of isoprene from a common species ( Salix pulchra ) in that same ecosystem were measured during three separate field campaigns. The field campaigns were conducted during the summers of 2005, 2010 and 2011 and took place at the Toolik Field Station (68.6° N, 149.6° W) on the north slope of the Brooks Range in Alaska, USA. The maximum rate of whole-system isoprene flux measured was over 1.2 mg C m −2 h −1 with an air temperature of 22 ° C and a PAR level over 1500 μmol m −2 s −1 . Leaf-level isoprene emission rates for S. pulchra averaged 12.4 nmol m −2 s −1 (27.4 μg C gdw −1 h −1 ) extrapolated to standard conditions (PAR = 1000 μmol m −2 s −1 and leaf temperature = 30° C). Leaf-level isoprene emission rates were well characterized by the Guenther algorithm for temperature, but less so for light. Chamber measurements from a nearby moist acidic tundra ecosystem with less S. pulchra emitted significant amounts of isoprene, but at lower rates (0.45 mg C m −2 h −1 ). Comparison of our results to predictions from a global model found broad agreement, but a detailed analysis revealed some significant discrepancies. An atmospheric chemistry box model predicts that the observed isoprene emissions have a significant impact on Arctic atmospheric chemistry, including the hydroxyl radical (OH). Our results support the prediction that isoprene emissions from Arctic ecosystems will increase with global climate change.

Description: Publication year: 2012 Source: Cell Reports Andre L. Samson, Anja S. Knaupp, Maithili Sashindranath, Rachael J. Borg, Amanda E.-L. Au, Elisa J. Cops, Helen M. Saunders, Stephen H. Cody, Catriona A. McLean, Cameron J. Nowell, Victoria A. Hughes, Stephen P. Bottomley, Robert L. Medcalf Cellular injury causes a myriad of processes that affect proteostasis. We describe nucleocytoplasmic coagulation (NCC), an intracellular disulfide-dependent protein crosslinking event occurring upon late-stage cell death that orchestrates the proteolytic removal of misfolded proteins. In vitro and in vivo models of neuronal injury show that NCC involves conversion of soluble intracellular proteins, including tubulin, into insoluble oligomers. These oligomers, also seen in human brain tissue following neurotrauma, act as a cofactor and substrate for the plasminogen-activating system. In plasminogen −/− mice, levels of misfolded β-tubulin were elevated and its clearance delayed following neurotrauma, demonstrating a requirement for plasminogen in the removal of NCC constituents. While additional in vivo studies will further dissect this phenomenon, our study clearly shows that NCC, a process analogous to the formation of thrombi, generates an aggregated protein scaffold that limits release of cellular components and recruits clearance mechanisms to the site of injury. Graphical abstract Graphical Abstract Highlights ► Cell death triggers the process of nucleocytoplasmic coagulation (NCC) ► NCC is the abrupt misfolding and disulfide crosslinking of intracellular proteins ► NCC-aggregated proteins facilitate plasmin formation and subsequent proteolysis ► Thus, NCC limits release and promotes proteolytic clearance of dead cell debris

Description: Publication year: 2012 Source: Cell Reports Jennifer S. Liu, Justin T. Farlow, Amanda K. Paulson, Mark A. Labarge, Zev J. Gartner Variability in signaling pathway activation between neighboring epithelial cells can arise from local differences in the microenvironment, noisy gene expression, or acquired genetic changes. To investigate the consequences of this cell-to-cell variability in signaling pathway activation on coordinated multicellular processes such as morphogenesis, we use DNA-programmed assembly to construct three-dimensional MCF10A microtissues that are mosaic for low-level expression of activated H-Ras. We find two emergent behaviors in mosaic microtissues: cells with activated H-Ras are basally extruded or lead motile multicellular protrusions that direct the collective motility of their wild-type neighbors. Remarkably, these behaviors are not observed in homogeneous microtissues in which all cells express the activated Ras protein, indicating that heterogeneity in Ras activity, rather than the total amount of Ras activity, is critical for these processes. Our results directly demonstrate that cell-to-cell variability in pathway activation within local populations of epithelial cells can drive emergent behaviors during epithelial morphogenesis. Graphical abstract Graphical Abstract Highlights ► Cell-to-cell variability in Ras activity triggers emergent behaviors ► Homogeneous and low-level Ras activation does not disrupt early morphogenesis ► Programmed assembly precisely controls the composition of mosaic epithelial tissues

Description: Publication year: 2012 Source: Cell Reports Chandan Shee, Janet L. Gibson, Susan M. Rosenberg Mutation hotspots and showers occur across phylogeny and profoundly influence genome evolution, yet the mechanisms that produce hotspots remain obscure. We report that DNA double-strand breaks (DSBs) provoke mutation hotspots via stress-induced mutation in Escherichia coli . With tet reporters placed 2 kb to 2 Mb (half the genome) away from an I- Sce I site, RpoS/DinB-dependent mutations occur maximally within the first 2 kb and decrease logarithmically to ∼60 kb. A weak mutation tail extends to 1 Mb. Hotspotting occurs independently of I-site/ tet- reporter-pair position in the genome, upstream and downstream in the replication path. RecD, which allows RecBCD DSB-exonuclease activity, is required for strong local but not long-distance hotspotting, indicating that double-strand resection and gap-filling synthesis underlie local hotspotting, and newly illuminating DSB resection in vivo. Hotspotting near DSBs opens the possibility that specific genomic regions could be targeted for mutagenesis, and could also promote concerted evolution (coincident mutations) within genes/gene clusters, an important issue in the evolution of protein functions. Graphical abstract Graphical Abstract Highlights ► Spontaneous mutation pathway in Escherichia coli causes hotpots at double-strand breaks ► Strong local (2–60 kb) hotspot mechanism double-strand resection and gap-fill ► Weak long-distance (1 Mb) mutagenesis by break-induced replication ► Break-induced replication and length of DNA-end resection in natural repair with sister chromosomes