ALBERT

Description: Seasonal measurements of total OH reactivity fluxes, total ozone loss rates and missing emissions from Norway spruce in 2011 Biogeosciences Discussions, 9, 13497-13536, 2012 Author(s): A.C. Nölscher, E. Bourtsoukidis, B. Bonn, J. Kesselmeier, J. Lelieveld, and J. Williams Numerous reactive volatile organic compounds (VOCs) are emitted into the atmosphere by vegetation. Most biogenic VOCs are highly reactive towards the atmosphere's most important oxidant, the hydroxyl (OH) radical. One way to investigate the chemical interplay between biosphere and atmosphere is through the measurement of total OH reactivity, the total loss rate of OH radicals. This study presents the first determination of total OH reactivity emission rates (measurements via the Comparative Reactivity Method) based on a branch cuvette enclosure system mounted on a Norway spruce (Picea abies) throughout spring, summer and autumn 2011. In parallel separate VOC emission rates were monitored by a Proton Transfer Reaction-Mass Spectrometer (PTR-MS), and total ozone (O 3 ) loss rates were obtained inside the cuvette. Total OH reactivity emission rates were in general temperature and light dependent, showing strong diel cycles with highest values during daytime. Monoterpene emissions contributed most, accounting for 56–69% of the measured total OH reactivity flux in spring and early summer. However, during late summer and autumn the monoterpene contribution decreased to 11–16%. At this time, a large missing fraction of the total OH reactivity emission rate (70–84%) was found when compared to the VOC budget measured by PTR-MS. Total OH reactivity and missing total OH reactivity emission rates reached maximum values in late summer corresponding to the period of highest temperature. Total O 3 loss rates within the closed cuvette showed similar diel profiles and comparable seasonality to the total OH reactivity fluxes. Total OH reactivity fluxes were also compared to emissions from needle storage pools predicted by a temperature-only dependent algorithm. Deviations of total OH reactivity fluxes from the temperature-only dependent emission algorithm were observed for occasions of mechanical and heat stress. While for mechanical stress, induced by strong wind, measured VOCs could explain total OH reactivity emissions, during heat stress they could not. The temperature driven algorithm matched the diel course much better in spring than in summer, indicating a different production and emission scheme for summer and early autumn. During these times, unmeasured and possibly unknown primary biogenic emissions contributed significantly to the observed total OH reactivity flux.

Description: Publication year: 2012 Source: Cell Reports Aurélie Jory, Carlos Estella, Matt W. Giorgianni, Matthew Slattery, Todd R. Laverty, Gerald M. Rubin, Richard S. Mann Over 6,000 fragments from the genome of Drosophila melanogaster were analyzed for their ability to drive expression of GAL4 reporter genes in the third-instar larval imaginal discs. About 1,200 reporter genes drove expression in the eye, antenna, leg, wing, haltere, or genital imaginal discs. The patterns ranged from large regions to individual cells. About 75% of the active fragments drove expression in multiple discs; 20% were expressed in ventral, but not dorsal, discs (legs, genital, and antenna), whereas ∼23% were expressed in dorsal but not ventral discs (wing, haltere, and eye). Several patterns, for example, within the leg chordotonal organ, appeared a surprisingly large number of times. Unbiased searches for DNA sequence motifs suggest candidate transcription factors that may regulate enhancers with shared activities. Together, these expression patterns provide a valuable resource to the community and offer a broad overview of how transcriptional regulatory information is distributed in the Drosophila genome. Graphical abstract Graphical Abstract Highlights ► Over 6,000 fragments from the Drosophila genome were analyzed for enhancer ► About 1,200 fragments drove expression of GAL4 in at least one of six imaginal discs ► The lines greatly expand the number of GAL4 drivers available to the community

Description: Increasing cloudiness in Arctic damps the increase in phytoplankton primary production due to sea ice receding Biogeosciences Discussions, 9, 13987-14012, 2012 Author(s): S. Bélanger, M. Babin, and J.-E. Tremblay The Arctic Ocean and its marginal seas are among the marine regions most affected by climate change. Here we present the results of a diagnostic model used to elucidate the main drivers of primary production (PP) trends over the 1998–2010 period at pan-Arctic and local (i.e. 9.28 km resolution) scales. Photosynthetically active radiation (PAR) above and below the sea surface was estimated using precomputed look-up tables of spectral irradiance and satellite-derived cloud optical thickness and cloud fraction parameters from the International Satellite Cloud Climatology Project (ISCCP) and sea ice concentration from passive microwaves data. A spectrally resolved PP model, designed for optically complex waters, was then used to produce maps of PP trends. Results show that incident PAR above the sea surface (PAR(0+)) has significantly decreased over the whole Arctic and sub-Arctic Seas, except over the perrennially sea ice covered waters of the Central Arctic Ocean. This fading of PAR(0+) (+8% decade –1 ) was caused by increasing cloudiness May and June. Meanwhile PAR penetrating the ocean (PAR(0–)) increased only along the sea ice margin over the large Arctic continental shelf where sea ice concentration declined sharply since 1998. Overall, PAR(0–) slightly increased in the Circum Arctic (+3.4% decade –1 ), while it decreased when considering both Arctic and sub-Arctic Seas (–3% decade –1 ). We showed that rising phytoplankton biomass (i.e. chlorophyll a ) normalized by the diffuse attenuation of photosynthetically usable radiation (PUR) by phytoplankton accounted for a larger proportion of the rise in PP than did the increase in light availability due to sea-ice loss in several sectors and particularly in perrennially and seasonally open waters. Against a general backdrop of rising productivity over Arctic shelves, significant negative trends were observed in regions known for their great biological importance such as the coastal polynyas of Northern Greenland.

Description: Storage and stability of organic carbon in soils as related to depth, occlusion within aggregates, and attachment to minerals Biogeosciences Discussions, 9, 13085-13133, 2012 Author(s): M. Schrumpf, K. Kaiser, G. Guggenberger, T. Persson, I. Kögel-Knabner, and E.-D. Schulze Conceptual models suggest that stability and age of organic carbon (OC) in soil depends on the source of plant litter, occlusion within aggregates, incorporation in organo-mineral complexes, and location within the soil profile. Various tools like density fractionation, mineralization experiments, and radiocarbon analyses have been used to study the importance of these mechanisms. We systematically apply them to a range of European soils to test whether general controls emerge even for soils that vary in vegetation, soil types, parent material, and land use. At each of the 12 study sites, 10 soil cores were sampled in 10 cm depth intervals to 60 cm depth and subjected to density separation. Bulk soil samples and density fractions (free light fractions – fLF, occluded light fractions – oLF, heavy fractions – HF) were analysed for OC, total nitrogen (TN), δ 13 C, and Δ 14 C. Bulk samples were also incubated to determine mineralizable OC. Declining OC-normalized CO 2 release and increasing age with soil depth confirm greater stability of OC in subsoils across sites. Depth profiles of LF-OC matched those of roots, which in turn reflect plant functional types in soil profiles not subject to ploughing. Modern Δ 14 C signatures and positive correlation between mineralizable C and fLF-OC indicate the fLF is an easily available energy and nutrient source for subsurface microbes. Fossil C derived from the geogenic parent material affected the age of OC especially in the LF at three study sites. The overall importance of OC stabilization by binding to minerals was demonstrated by declining OC-normalized CO 2 release rates with increasing contributions of HF-OC to bulk soil OC and the low Δ 14 C values of HF-OC. The stability of HF-OC was greater in subsoils than in topsoils; nevertheless, a portion of HF-OC was active throughout the profile. The decrease in Δ 14 C (increase in age) of HF-OC with soil depth was related to soil pH as well as to dissolved OC fluxes. This indicates that dissolved OC translocation contributes to the formation of subsoil HF-OC and shapes the Δ 14 C profiles. While quantitatively less important than OC in the HF, consistent older ages of oLF-OC than fLF-OC indicate that occlusion of LF-OC in aggregates also contributes to OC stability in subsoils. Overall, our results showed that association with minerals is the most important factor in stabilization of OC in soils.

Description: The non-steady-state oceanic CO 2 signal: its importance, magnitude and a novel way to detect it Biogeosciences Discussions, 9, 13161-13186, 2012 Author(s): B. I. McNeil and R. J. Matear The ocean's role has been pivotal in modulating rising atmospheric CO 2 levels since the industrial revolution, sequestering over a quarter of all fossil-fuel derived CO 2 emissions. Net oceanic uptake of CO 2 has roughly doubled between the 1960's (~1 Pg C yr −1 ) and 2000's (~2 Pg C yr −1 ), with expectations it will continue to absorb even more CO 2 with rising future atmospheric CO 2 levels. However, recent CO 2 observational analyses along with numerous model predictions suggest the rate of oceanic CO 2 uptake is already slowing, largely as a result of a natural decadal-scale outgassing signal. This recent and unexpected CO 2 outgassing signal represents a paradigm-shift in our understanding of the oceans role in modulating atmospheric CO 2 . Current tracer-based estimates for the ocean storage of anthropogenic CO 2 assume the ocean circulation and biology is in steady state, thereby missing the new and potentially important "non-steady-state" CO 2 outgassing signal. By combining data-based techniques that assume the ocean is in steady-state, with techniques that constrain the net oceanic CO 2 uptake signal, we show how to extract the non-steady-state CO 2 signal from observations. Over the entire industrial era, the non-steady-state CO 2 outgassing signal (~13 ± 10 Pg C) is estimated to represent about 9% of the total net CO 2 inventory change (~142 Pg C). However between 1989 and 2007, the non-steady-state CO 2 outgassing signal (~6.3 Pg C) has likely increased to be ~18% of net oceanic CO 2 storage over that period (~36 Pg C), a level which cannot be ignored. The present uncertainty of our data-based techniques for oceanic CO 2 uptake limit our capacity to quantify the non-steady-state CO 2 signal, however with more data and better certainty estimates across a~range of diverse methods, this important and growing CO 2 signal could be better constrained in the future.

Description: Diversity pattern of nitrogen fixing microbes in nodules of Trifolium arvense (L.) at different initial stages of ecosystem development Biogeosciences Discussions, 9, 13135-13160, 2012 Author(s): S. Schulz, M. Engel, D. Fischer, F. Buegger, M. Elmer, G. Welzl, and M. Schloter Legumes can be considered as pioneer plants during ecosystem development, as they form a symbiosis with different nitrogen fixing rhizobia species, which enable the plants to grow on soils with low available nitrogen content. In this study we compared the abundance and diversity of nitrogen fixing microbes based on the functional marker gene nifH , which codes for a subunit of the Fe-protein of the dinitrogenase reductase, in nodules of different size classes of Trifolium arvense (L.). Additionally, carbon and nitrogen contents of the bulk soil and plant material were measured. Plants were harvested from different sites, reflecting 2 (2a) and 5 (5a) yr of ecosystem development, of an opencast lignite mining area in the south of Cottbus, Lower Lusatia (Germany) where the artificial catchment "Chicken Creek" was constructed to study the development of terrestrial ecosystems. Plants from the 5a site revealed higher amounts of carbon and nitrogen, although nifH gene abundances in the nodules and carbon and nitrogen contents between the two soils did not differ significantly. Analysis of the nifH clone libraries showed a significant effect of the nodule size on the community composition of nitrogen fixing microbes. Medium sized nodules (2–5 mm) contained a uniform community composed of Rhizobium leguminosarum bv. trifolii , whereas the small nodules ( 〈 2 mm) consisted of a diverse community including clones with non- Rhizobium nifH gene sequences. Regarding the impact of the soil age on the community composition a clear distinction between the small and the medium nodules can be made. While clone libraries from the medium nodules were pretty similar at both soil ages, soil age had a significant effect on the community compositions of the small nodules, where the proportion of R. leguminosarum bv. trifolii increased with soil age.

Description: Publication year: 2012 Source: FEBS Open Bio Ambuj Kumar, Vidya Rajendran, Rao Sethumadhavan, R. Purohit Human STIL (SCL/TAL1 interrupting locus) protein maintains centriole stability and spindle pole localization. It helps in recruitment of CENPJ (Centromere protein J)/CPAP (centrosomal P4.1-associated protein) and other centrosomal proteins. Mutations in STIL protein are reported in several disorders, especially in deregulation of cell cycle cascades. In this work, we examined the non-synonymous single nucleotide polymorphisms (nsSNPs) reported in STIL protein for their disease association. Different SNP prediction tools were used to predict disease-associated nsSNPs. Our evaluation technique predicted rs147744459 (R242C) as a highly deleterious disease-associated nsSNP and its interaction behavior with CENPJ protein. Molecular modelling, docking and molecular dynamics simulation were conducted to examine the structural consequences of the predicted disease-associated mutation. By molecular dynamic simulation we observed structural consequences of R242C mutation which affects interaction of STIL and CENPJ functional domains. The result obtained in this study will provide a biophysical insight into future investigations of pathological nsSNPs using a computational platform.

Description: Publication year: 2012 Source: Cell Reports Rachel Spokoini, Ofer Moldavski, Yaakov Nahmias, Jeremy L. England, Maya Schuldiner, Daniel Kaganovich The division of the S. cerevisiae budding yeast, which produces one mother cell and one daughter cell, is asymmetric with respect to aging. Remarkably, the asymmetry of yeast aging coincides with asymmetric inheritance of damaged and aggregated proteins by the mother cell. Here, we show that misfolded proteins are retained in the mother cell by being sequestered in juxtanuclear quality control compartment (JUNQ) and insoluble protein deposit (IPOD) inclusions, which are attached to organelles. Upon exposure to stress, misfolded proteins accumulate in stress foci that must be disaggregated by Hsp104 in order to be degraded or processed to JUNQ and IPOD. Cells that fail to deliver aggregates to an inclusion pass on aggregates to subsequent generations. Graphical abstract Graphical Abstract Highlights ► Misfolded proteins form stress foci, JUNQ inclusions, or IPOD inclusions ► JUNQs and IPODs are attached to organelles ► JUNQ and IPOD inclusions are asymmetrically inherited during cell division ► Hsp104 is required for disaggregation of stress foci

Description: Publication year: 2012 Source: Cell Reports Ellen M. van Beek, Julian Alvarez Zarate, Robin van Bruggen, Karin Schornagel, Anton T.J. Tool, Takashi Matozaki, Georg Kraal, Dirk Roos, Timo K. van den Berg The phagocyte NADPH oxidase mediates oxidative microbial killing in granulocytes and macrophages. However, because the reactive oxygen species produced by the NADPH oxidase can also be toxic to the host, it is essential to control its activity. Little is known about the endogenous mechanism(s) that limits NADPH oxidase activity. Here, we demonstrate that the myeloid-inhibitory receptor SIRPα acts as a negative regulator of the phagocyte NADPH oxidase. Phagocytes isolated from SIRPα mutant mice were shown to have an enhanced respiratory burst. Furthermore, overexpression of SIRPα in human myeloid cells prevented respiratory burst activation. The inhibitory effect required interactions between SIRPα and its natural ligand, CD47, as well as signaling through the SIRPα cytoplasmic immunoreceptor tyrosine-based inhibitory motifs. Suppression of the respiratory burst by SIRPα was caused by a selective repression of gp91 phox expression, the catalytic component of the phagocyte NADPH oxidase complex. Thus, SIRPα can limit gp91 phox expression during myeloid development, thereby controlling the magnitude of the respiratory burst in phagocytes. Graphical abstract Graphical Abstract Highlights ► Activity of the phagocyte NADPH oxidase is restricted by SIRPα ► This involves SIRP-CD47 interactions and signaling through the SIRPα immunoreceptor tyrosine-based inhibitory motifs ► SIRPα signaling represses expression of the catalytic NADPH oxidase subunit gp91 phox

Description: Publication year: 2012 Source: Cell Reports Ping Yin, Dong Deng, Chuangye Yan, Xiaojing Pan, Jianzhong Jeff Xi, Nieng Yan, Yigong Shi The transcription activator-like (TAL) effector targets specific host promoter through its central DNA-binding domain, which comprises multiple tandem repeats (TALE repeats). Recent structural analyses revealed that the TALE repeats form a superhelical structure that tracks along the forward strand of the DNA duplex. Here, we demonstrate that TALE repeats specifically recognize a DNA-RNA hybrid where the DNA strand determines the binding specificity. The crystal structure of a designed TALE in complex with the DNA-RNA hybrid was determined at a resolution of 2.5 Å. Although TALE repeats are in direct contact with only the DNA strand, the phosphodiester backbone of the RNA strand is inaccessible by macromolecules such as RNases. Consistent with this observation, sequence-specific recognition of an HIV-derived DNA-RNA hybrid by an engineered TALE efficiently blocked RNase H-mediated degradation of the RNA strand. Our study broadens the utility of TALE repeats and suggests potential applications in processes involving DNA replication and retroviral infections. Graphical abstract Graphical Abstract Highlights ► TALE repeats specifically bind to DNA-RNA hybrids ► The sequence of DNA determines binding specificity by TALE repeats ► TALE repeats protect DNA-RNA hybrids from RNase H degradation ► TALEs may be used to fight retroviral infection and modulate transcription

Description: Publication year: 2012 Source: Cell Reports Michael Hiller, Bruce T. Schaar, Vahan B. Indjeian, David M. Kingsley, Lee R. Hagey, Gill Bejerano Genotype-phenotype mapping is hampered by countless genomic changes between species. We introduce a computational “forward genomics” strategy that—given only an independently lost phenotype and whole genomes—matches genomic and phenotypic loss patterns to associate specific genomic regions with this phenotype. We conducted genome-wide screens for two metabolic phenotypes. First, our approach correctly matches the inactivated Gulo gene exactly with the species that lost the ability to synthesize vitamin C. Second, we attribute naturally low biliary phospholipid levels in guinea pigs and horses to the inactivated phospholipid transporter Abcb4. Human ABCB4 mutations also result in low phospholipid levels but lead to severe liver disease, suggesting compensatory mechanisms in guinea pig and horse. Our simulation studies, counts of independent changes in existing phenotype surveys, and the forthcoming availability of many new genomes all suggest that forward genomics can be applied to many phenotypes, including those relevant for human evolution and disease. Graphical abstract Graphical Abstract Highlights ► Matching independent phenotypic losses with ancestral genomic information erosion ► Gulo gene loss uniquely matches to “loss of vitamin C synthesis” in mammals ► Abcb4 gene loss matches “low biliary phospholipid levels” in guinea pig & horse ► Broad applicability of the approach from simulation and phenotype measurements

Description: Publication year: 2012 Source: FEBS Open Bio Meng-Chun Chi, Yi-Yu Chen, Huei-Fen Lo, Long-Liu Lin The role of glutamate 398 in the autocatalytic processing of Bacillus licheniformis γ-glutamyltranspeptidase ( Bl GGT) was explored by site-directed mutagenesis. This glutamate was substituted by either alanine, aspartate, arginine or glutamine and the expressed mutant enzymes were purified to apparent homogeneity with metal-affinity chromatography. SDS–PAGE analysis showed that E398A, E398D and E398K were unable to process themselves into a large and a small subunit. However, E398Q was not only able to process itself, but also had a catalytic activity comparable to that of Bl GGT. As compared with the wild-type enzyme, no significant change in circular dichroism spectra was observed for the mutant proteins. Thermal unfolding of Bl GGT, E398A, E398D, E398K and E398Q followed the two-state unfolding process with a transition point ( T m ) of 47.7–69.4°C. Tryptophan fluorescence spectra of the mutant enzymes were different from the wild-type protein in terms of fluorescence intensity. Native Bl GGT started to unfold beyond ∼ 1.92 M guanidine hydrochloride (GdnHCl) and reached an unfolded intermediate, [GdnHCl] 0.5, N-U , at 3.07 M equivalent to free energy change ( Δ G N − U H 2 O ) of 14.53 kcal/mol for the N → U process, whereas the denaturation midpoints for the mutant enzymes were 1.31–2.99 M equivalent to Δ G N − U H 2 O of 3.29–12.05 kcal/mol. Taken together, these results strongly suggest that the explored glutamate residue is indeed important for the autocatalytic processing of Bl GGT. Highlights ▸ Bioinformatics was used to identify a key residue required for autocatalytic processing. ▸ Substitution of Glu398 with Ala, Asp or Lys blocked maturation of the enzyme. ▸ Wild-type and mutant enzymes exhibited different sensitivities towards thermal and GdnHCl-induced denaturation.

Description: The climate dependence of the terrestrial carbon cycle; including parameter and structural uncertainties Biogeosciences Discussions, 9, 13439-13496, 2012 Author(s): M. J. Smith, M. C. Vanderwel, V. Lyutsarev, S. Emmott, and D. W. Purves The feedback between climate and the terrestrial carbon cycle will be a key determinant of the dynamics of the Earth System over the coming decades and centuries. However Earth System Model projections of the terrestrial carbon-balance vary widely over these timescales. This is largely due to differences in their carbon cycle models. A major goal in biogeosciences is therefore to improve understanding of the terrestrial carbon cycle to enable better constrained projections. Essential to achieving this goal will be assessing the empirical support for alternative models of component processes, identifying key uncertainties and inconsistencies, and ultimately identifying the models that are most consistent with empirical evidence. To begin meeting these requirements we data-constrained all parameters of all component processes within a global terrestrial carbon model. Our goals were to assess the climate dependencies obtained for different component processes when all parameters have been inferred from empirical data, assess whether these were consistent with current knowledge and understanding, assess the importance of different data sets and the model structure for inferring those dependencies, assess the predictive accuracy of the model, and to identify a methodology by which alternative component models could be compared within the same framework in future. Although formulated as differential equations describing carbon fluxes through plant and soil pools, the model was fitted assuming the carbon pools were in states of dynamic equilibrium (input rates equal output rates). Thus, the parameterised model is of the equilibrium terrestrial carbon cycle. All but 2 of the 12 component processes to the model were inferred to have strong climate dependencies although it was not possible to data-constrain all parameters indicating some potentially redundant details. Similar climate dependencies were obtained for most processes whether inferred individually from their corresponding data sets or using the full terrestrial carbon model and all available data sets, indicating a strong overall consistency in the information provided by different data sets under the assumed model formulation. A notable exception was plant mortality, in which qualitatively different climate dependencies were inferred depending on the model formulation and data sets used, highlighting this component as the major structural uncertainty in the model. All but two component processes predicted empirical data better than a null model in which no climate dependency was assumed. Equilibrium plant carbon was predicted especially well (explaining around 70% of the variation in the withheld evaluation data). We discuss the advantages of our approach in relation to advancing our understanding of the carbon cycle and enabling Earth System Models make better constrained projections.

Description: Publication year: 2012 Source: Cell Reports Jian Zhu, Gaurav D. Gaiha, Sinu P. John, Thomas Pertel, Christopher R. Chin, Geng Gao, Hongjing Qu, Bruce D. Walker, Stephen J. Elledge, Abraham L. Brass HIV-1 depends on many host factors for propagation. Other host factors, however, antagonize HIV-1 and may have profound effects on viral activation. Curing HIV-1 requires the reduction of latent viral reservoirs that remain in the face of antiretroviral therapy. Using orthologous genetic screens, we identified bromodomain containing 4 (BRD4) as a negative regulator of HIV-1 replication. Antagonism of BRD4, via RNA interference or with a small molecule inhibitor, JQ1, both increased proviral transcriptional elongation and alleviated HIV-1 latency in cell-line models. In multiple instances, JQ1, when used in combination with the NF-κB activators Prostratin or PHA, enhanced the in vitro reactivation of latent HIV-1 in primary T cells. These data are consistent with a model wherein BRD4 competes with the virus for HIV-1 dependency factors (HDFs) and suggests that combinatorial therapies that activate HDFs and antagonize HIV-1 competitive factors may be useful for curing HIV-1 infection. Graphical abstract Graphical Abstract Highlights ► BRD4 depletion or inhibition with JQ1 increases HIV-1 replication and gene expression ► BRD4 inhibition increases Tat-dependent transcriptional elongation and Tat–PTEF-b association ► BRD4 inhibition alleviates HIV-1 latency in cell-line models ► JQ1 with HDF activators enhances HIV-1 replication in primary and latently infected T cells

Description: Publication year: 2012 Source: Cell Reports Stefanie Reissmann, Lukasz A. Joachimiak, Bryan Chen, Anne S. Meyer, Anthony Nguyen, Judith Frydman The eukaryotic chaperonin TRiC/CCT uses ATP cycling to fold many essential proteins that other chaperones cannot fold. This 1 MDa hetero-oligomer consists of two identical stacked rings assembled from eight paralogous subunits, each containing a conserved ATP-binding domain. Here, we report a dramatic asymmetry in the ATP utilization cycle of this ring-shaped chaperonin, despite its apparently symmetric architecture. Only four of the eight different subunits bind ATP at physiological concentrations. ATP binding and hydrolysis by the low-affinity subunits is fully dispensable for TRiC function in vivo . The conserved nucleotide-binding hierarchy among TRiC subunits is evolutionarily modulated through differential nucleoside contacts. Strikingly, high- and low-affinity subunits are spatially segregated within two contiguous hemispheres in the ring, generating an asymmetric power stroke that drives the folding cycle. This unusual mode of ATP utilization likely serves to orchestrate a directional mechanism underlying TRiC/CCT's unique ability to fold complex eukaryotic proteins. Graphical abstract Graphical Abstract Highlights ► The eight paralogous TRiC subunits display hierarchical ATP occupancy ► Conservation of nucleoside contacts among TRiC orthologs mirrors ATP affinity ► ATP binding and hydrolysis in the low-affinity subunits are dispensable for life ► ATP usage segregates asymmetrically into two hemispheres of the chaperonin ring

Description: Publication year: 2012 Source: Cell Reports Gil Diamant, Liat Amir-Zilberstein, Yuki Yamaguchi, Hiroshi Handa, Rivka Dikstein NF-κB is central for immune response and cell survival, and its deregulation is linked to chronic inflammation and cancer through poorly defined mechanisms. IκBα and A20 are NF-κB target genes and negative feedback regulators. Upon their activation by NF-κB, DSIF is recruited, P-TEFb is released, and their elongating polymerase II (Pol II) C-terminal domain (CTD) remains hypophosphorylated. We show that upon DSIF knockdown, mRNA levels of a subset of NF-κB targets are not diminished; yet much less IκBα and A20 protein are synthesized, and NF-κB activation is abnormally prolonged. Further analysis of IκBα and A20 mRNA revealed that a significant portion is uncapped, unspliced, and retained in the nucleus. Interestingly, the Spt5 C-terminal repeat (CTR) domain involved in elongation stimulation through P-TEFb is dispensable for IκBα and A20 regulation. These findings assign a function for DSIF in cotranscriptional mRNA processing when elongating Pol II is hypophosphorylated and define DSIF as part of the negative feedback regulation of NF-κB. Graphical abstract Graphical Abstract Highlights ► IκBα and A20, negative feedback regulators of NF-κB, have unusual elongation control ► Upon activation of IκBα and A20, DSIF is recruited, and the Pol II CTD remains hypophosphorylated ► DSIF is selectively required for IκBα and A20 mRNA processing and proper NF-κ B signaling ► DSIF’s CTR domain involved in elongation stimulation is dispensable for this function

Description: Publication year: 2012 Source: Cell Reports Samantha A. Morris, Yu Guo, Magdalena Zernicka-Goetz Plasticity is a well-known feature of mammalian development, and yet very little is known about its underlying mechanism. Here, we establish a model system to examine the extent and limitations of developmental plasticity in living mouse embryos. We show that halved embryos follow the same strict clock of developmental transitions as intact embryos, but their potential is not equal. We have determine that unless a minimum of four pluripotent cells are established before implantation, development will arrest. This failure can be rescued by modulating Fgf and Wnt signaling to enhance the pluripotent cell number, allowing the generation of monozygotic twins, which is an otherwise rare phenomenon. Knowledge of the minimum pluripotent-cell number required for development to birth, as well as the different potentials of blastomeres, allowed us to establish a protocol for splitting an embryo into one part that develops to adulthood and another that provides embryonic stem cells for that individual. Graphical abstract Graphical Abstract Highlights ► Half embryos follow the same clock as intact embryos, but their potential is not equal ► To support development, four pluripotent cells must be generated before implantation ► Fgf/Wnt signal modulation enhances pluripotency to rescue half-embryo development ► ESCs and a viable mouse can be derived from a single embryo with high efficiency

Description: Publication year: 2012 Source: Cell Reports Pol Margalef, Vanessa Fernández-Majada, Alberto Villanueva, Ricard Garcia-Carbonell, Mar Iglesias, Laura López, María Martínez-Iniesta, Jordi Villà-Freixa, Mari Carmen Mulero, Montserrat Andreu, Ferran Torres, Marty W. Mayo, Anna Bigas, Lluis Espinosa Nuclear IKKα regulates gene transcription by phosphorylating specific substrates and has been linked to cancer progression and metastasis. However, the mechanistic connection between tumorigenesis and IKKα activity remains poorly understood. We have now analyzed 288 human colorectal cancer samples and found a significant association between the presence of nuclear IKK and malignancy. Importantly, the nucleus of tumor cells contains an active IKKα isoform with a predicted molecular weight of 45 kDa (p45-IKKα) that includes the kinase domain but lacks several regulatory regions. Active nuclear p45-IKKα forms a complex with nonactive IKKα and NEMO that mediates phosphorylation of SMRT and histone H3. Proteolytic cleavage of FL-IKKα into p45-IKKα is required for preventing the apoptosis of CRC cells in vitro and sustaining tumor growth in vivo. Our findings identify a potentially druggable target for treating patients with advance refractory CRC. Graphical abstract Graphical Abstract Highlights ► A truncated active form of IKKα is found in colorectal cancer cells ► Nuclear complex containing p45-IKKα phosphorylates SMRT and histone H3 ► Cleavage of IKK(alpha) into p45-IKKα is required for cancer cell growth

Description: Nitrogen cycling in the Central Arabian Sea: a model study Biogeosciences Discussions, 9, 13581-13625, 2012 Author(s): A. Beckmann and I. Hense We present a biogeochemical model that couples the marine nitrogen and oxygen cycles and includes euphotic, aphotic, aerobic and anaerobic processes. The model is used to investigate the mechanisms affecting nitrite and nitrogen losses in the suboxic layer of the Central Arabian Sea. In an idealized two-dimensional physical environment the model is able to reproduce the observed meridional-vertical structure of suboxic zone, secondary nitrite maximum, nitrate and oxygen. Characteristic features of vertical profiles are well represented and the modelled nitrogen transformation rates are in good agreement with observed values. The model results show that the oxygen minimum zone is not vertically homogeneous, as all suboxic processes are confined to the top 100 m of this zone. Minute differences in oxygen concentration determine the thickness of the nitrite layer. The modelled average N-loss rate in the suboxic region of the Arabian Sea is about 50 mmol N m −2 yr −1 (about 30 times smaller than most previous estimates). The system response time scale is about 50 yr, much larger than usually assumed.

Description: The carbon budget of South Asia Biogeosciences Discussions, 9, 13537-13580, 2012 Author(s): P. K. Patra, J. G. Canadell, R. A. Houghton, S. L. Piao, N.-H. Oh, P. Ciais, K. R. Manjunath, A. Chhabra, T. Wang, T. Bhattacharya, P. Bousquet, J. Hartman, A. Ito, E. Mayorga, Y. Niwa, P. Raymond, V. V. S. S. Sarma, and R. Lasco The source and sinks of carbon dioxide (CO 2 ) and methane (CH 4 ) due to anthropogenic and natural biospheric activities were estimated for the South Asia region (Bangladesh, Bhutan, India, Nepal, Pakistan and Sri Lanka). Flux estimates were based on top-down methods that use inversions of atmospheric data, and bottom-up methods that use field observations, satellite data, and terrestrial ecosystem models. Based on atmospheric CO 2 inversions, the net biospheric CO 2 flux in South Asia (equivalent to the Net Biome Productivity, NBP) was a sink, estimated at −104 ± 150 Tg C yr −1 during 2007–2008. Based on the bottom-up approach, the net biospheric CO 2 flux is estimated to be −191 ± 193 Tg C yr −1 during the period of 2000–2009. This last net flux results from the following flux components: (1) the Net Ecosystem Productivity, NEP (net primary production minus heterotrophic respiration) of −220 ± 186 Tg C yr −1 (2) the annual net carbon flux from land-use change of −14 ± 50 Tg C yr −1 , which resulted from a sink of −16 Tg C yr −1 due to the establishment of tree plantations and wood harvest, and a source of 2 Tg C yr −1 due to the expansion of croplands; (3) the riverine export flux from terrestrial ecosystems to the coastal oceans of +42.9 Tg C yr −1 ; and (4) the net CO 2 emission due to biomass burning of +44.1 ± 13.7 Tg C yr −1 . Including the emissions from the combustion of fossil fuels of 444 Tg C yr −1 for the decades of 2000s, we estimate a net CO 2 land-to-atmosphere flux of 297 Tg C yr −1 . In addition to CO 2 , a fraction of the sequestered carbon in terrestrial ecosystems is released to the atmosphere as CH 4 . Based on bottom-up and top-down estimates, and chemistry-transport modeling, we estimate that 37 ± 3.7 Tg C-CH 4 yr −1 were released to atmosphere from South Asia during the 2000s. Taking all CO 2 and CH 4 fluxes together, our best estimate of the net land-to-atmosphere CO 2 -equivalent flux is a net source of 334 Tg C yr −1 for the South Asia region during the 2000s. If CH 4 emissions are weighted by radiative forcing of molecular CH 4 , the total CO 2 -equivalent flux increases to 1148 Tg C yr −1 suggesting there is great potential of reducing CH 4 emissions for stabilizing greenhouse gases concentrations.

Description: Interactions between leaf nitrogen status and longevity in relation to N cycling in three contrasting European forest canopies Biogeosciences Discussions, 9, 9759-9790, 2012 Author(s): L. Wang, A. Ibrom, J. F. J. Korhonen, K. F. Arnoud Frumau, J. Wu, M. Pihlatie, and J. K. Schjoerring Seasonal and spatial variations in foliar nitrogen (N) parameters were investigated in three European forests with different tree species, viz. beech ( Fagus sylvatica L.), Douglas fir ( Pseudotsuga menziesii , Mirb., Franco) and Scots pine ( Pinus sylvestris L.) in Denmark, The Netherlands and Finland, respectively. This was done in order to obtain information about functional acclimation, tree internal N conservation and its relevance for both ecosystem internal N cycling and foliar N exchange with the atmosphere. Leaf N pools generally showed much higher seasonal variability in beech trees than in the coniferous canopies. The concentrations of N and chlorophyll in the beech leaves were synchronized with the seasonal course of solar radiation implying close physiological acclimation, which was not observed in the coniferous needles. During phases of intensive N metabolism in the beech leaves, the NH 4 + concentration rose considerably. This was compensated for by a strong pH decrease resulting in relatively low Γ values (ratio between tissue NH 4 + and H + ). The Γ values in the coniferous were even smaller than in beech, indicating low probability of NH 3 emissions from the foliage to the atmosphere as an N conserving mechanism. The reduction in foliage N content during senescence was interpreted as N re-translocation from the senescing leaves into the rest of the trees. The N re-translocation efficiency (η r ) ranged from 37 to 70% and decreased with the time necessary for full renewal of the canopy foliage. Comparison with literature data from in total 23 tree species showed a general tendency for η r to on average be reduced by 8% per year the canopy stays longer, i.e. with each additional year it takes for canopy renewal. The boreal pine site returned the lowest amount of N via foliage litter to the soil, while the temperate Douglas fir stand which had the largest peak canopy N content and the lowestη r returned the highest amount of N to the soil. These results support the hypothesis that a high N status, e.g. as a consequence of chronically high atmospheric N inputs, increases ecosystem internal over tree-bulk-tissue internal N cycling in conifer stands. The two evergreen tree species investigated in the present study behaved very differently in all relevant parameters, i.e. needle longevity, N c and η r , showing that generalisations on tree internal vs. ecosystem internal N cycling cannot be made on the basis of the leaf habit alone.

Description: Net sea-air CO 2 flux uncertainties in the Bay of Biscay based on the choice of wind speed products and gas transfer parameterizations Biogeosciences Discussions, 9, 9993-10017, 2012 Author(s): P. Otero, X. A. Padín, M. Ruiz-Villarreal, L. M. García-García, A. F. Ríos, and F. F. Pérez The estimation of sea-air CO 2 fluxes are largely dependent on wind speed through the gas transfer velocity parameterization. In this paper, we quantify uncertainties in the estimation of the CO 2 uptake in the Bay of Biscay resulting from using different sources of wind speed such as three different global reanalysis meteorological models (NCEP/NCAR 1, NCEP/DOE 2 and ERA-Interim), one regional high-resolution forecast model (HIRLAM-AEMet) and QuikSCAT winds, in combination with some of the most widely used gas transfer velocity parameterizations. Results show that net CO 2 flux estimations during an entire seasonal cycle may differ up to 240% depending on the wind speed product and the gas exchange parameterization. The comparison of satellite and model derived winds with observations at buoys advises against the systematic overestimation of NCEP-2 and the underestimation of NCEP-1. In this region, QuikSCAT has the best performing, although ERA-Interim becomes the best choice in areas near the coastline or when the time resolution is the constraint.

Description: Carbon dioxide balance of subarctic tundra from plot to regional scales Biogeosciences Discussions, 9, 9945-9991, 2012 Author(s): M. E. Marushchak, I. Kiepe, C. Biasi, V. Elsakov, T. Friborg, T. Johansson, H. Soegaard, T. Virtanen, and P. J. Martikainen We report here the carbon dioxide (CO 2 ) budget of a 98.6-km 2 subarctic tundra area in Northeast European Russia based on measurements at two different scales and two independent up-scaling approaches. Plot scale measurements (chambers on terrestrial surfaces, gas gradient method and bubble collectors on lakes) were carried out from July 2007 to October 2008. The landscape scale eddy covariance (EC) measurements covered the snow-free period 2008. The annual net ecosystem exchange (NEE) of different land cover types ranged from −251 to 84 g C m −2 . Leaf area index (LAI) was an excellent predictor of the spatial variability in gross photosynthesis (GP), NEE and ecosystem respiration (ER). The plot scale CO 2 fluxes were first scaled up to the EC source area and then to the whole study area using two data sets: a land cover classification and a LAI map, both based on field data and 2.4 m pixel-sized Quickbird satellite image. The good agreement of the CO 2 balances for the EC footprint based on the different methods (−105 to −81 g C m −2 vs. −79 g C m −2 ; growing season 2008) justified the integration of the plot scale measurements over the larger area. The annual CO 2 balance for the study region was −67 to −41 g C m −2 . Due to the heterogeneity of tundra, the effect of climate change on CO 2 uptake will vary strongly according to the land cover type and, moreover, likely changes in their relative coverage in future will have great impact on the regional CO 2 balance.

Description: Nitrous oxide dynamics in low oxygen regions of the Pacific: insights from the MEMENTO database Biogeosciences Discussions, 9, 10019-10056, 2012 Author(s): L. M. Zamora, A. Oschlies, H. W. Bange, J. D. Craig, K. B. Huebert, A. Kock, and C. R. Löscher The Eastern Tropical Pacific (ETP) is believed to be one of the largest marine sources of the greenhouse gas nitrous oxide N 2 O). Future N 2 Oemissions from the ETP are highly uncertain because oxygen minimum zones are expected to expand, affecting both regional production and consumption of N 2 O. Here we assess three primary uncertainties in how N 2 O may respond to changing O 2 levels: (1) the relationship between N 2 O production and O 2 (is it linear or exponential at low O 2 concentrations?), (2) the cutoff point at which net N 2 O production switches to net N 2 O consumption (uncertainties in this parameterization can lead to differences in model ETP N 2 O concentrations of more than 20%), and (3) the rate of net N 2 O consumption at low O 2 . Based on the MEMENTO database, which is the largest N 2 O dataset currently available, we find that N 2 O production in the ETP increases linearly rather than exponentially with decreasing O 2 . Additionally, net N 2 O consumption switches to net N 2 O production at ~ 10 μM O 2 , a value in line with recent studies that suggest consumption occurs on a larger scale than previously thought. N 2 O consumption is on the order of 0.129 mmol N 2 O m −3 yr −1 in the Peru–Chile Undercurrent. Based on these findings, it appears that recent studies substantially overestimated N 2 O production in the ETP. In light of expected deoxygenation, future N 2 O production is still uncertain, but due to higher-than-expected consumption levels, it is possible that N 2 Oconcentrations may decrease rather than increase as oxygen minimum zones expand.

Description: Reducing the model-data misfit in a marine ecosystem model using periodic parameters and Linear Quadratic Optimal Control Biogeosciences Discussions, 9, 10207-10239, 2012 Author(s): M. El Jarbi, J. Rückelt, T. Slawig, and A. Oschlies This paper presents the application of the Linear Quadratic Optimal Control (LQOC) method for a parameter optimization problem in a marine ecosystem model. The ecosystem model simulates the distribution of nitrogen, phytoplankton, zooplankton and detritus in a water column with temperature and turbulent diffusivity profiles taken from a three-dimensional ocean circulation model. We present the linearization method which is based on the available observations. The linearization is necessary to apply the LQOC method on the nonlinear system of state equations. We show the form of the linearized time-variant problems and the resulting two algebraic Riccati Equations. By using the LQOC method, we are able to introduce temporally varying periodic model parameters and to significantly improve – compared to the use of constant parameters – the fit of the model output to given observational data.

Description: Publication year: 2012 Source: Cell Reports Adrian W.R. Serohijos, Zilvinas Rimas, Eugene I. Shakhnovich The consistent observation across all kingdoms of life that highly abundant proteins evolve slowly demonstrates that cellular abundance is a key determinant of protein evolutionary rate. However, other empirical findings, such as the broad distribution of evolutionary rates, suggest that additional variables determine the rate of protein evolution. Here, we report that under the global selection against the cytotoxic effects of misfolded proteins, folding stability (Δ G ), simultaneous with abundance, is a causal variable of evolutionary rate. Using both theoretical analysis and multiscale simulations, we demonstrate that the anticorrelation between the premutation Δ G and the arising mutational effect (ΔΔ G ), purely biophysical in origin, is a necessary requirement for abundance–evolutionary rate covariation. Additionally, we predict and demonstrate in bacteria that the strength of abundance–evolutionary rate correlation depends on the divergence time separating reference genomes. Altogether, these results highlight the intrinsic role of protein biophysics in the emerging universal patterns of molecular evolution. Graphical abstract Graphical Abstract Highlights ► Protein stability and abundance mutually determine its evolutionary rate ► Coupling of stability changes with wild-type stability affects rate of evolution ► Abundance–evolutionary rate covariation depends on divergence time

Description: An eddy-stimulated hotspot for fixed nitrogen-loss from the Peru oxygen minimum zone Biogeosciences Discussions, 9, 8013-8038, 2012 Author(s): M. A. Altabet, E. Ryabenko, L. Stramma, D. W. R. Wallace, M. Frank, P. Grasse, and G. Lavik Fixed nitrogen (N) loss to biogenic N 2 in intense oceanic O 2 minimum zones (OMZ) accounts for a large fraction of the global N sink and is an essential control on the ocean's N budget. However, major uncertainties exist regarding microbial pathways as well as net impact on the magnitude of N-loss and the ocean's overall N budget. Here we report the discovery of a N-loss hotspot in the Peru OMZ associated with a coastally trapped mesoscale eddy that is marked by an extreme N deficit matched by biogenic N 2 production, high NO 2 − levels, and the highest isotope enrichments observed so far in OMZ's for the residual NO 3 − . High sea surface chlorophyll (SSC) in seaward flowing streamers provides evidence for offshore eddy transport of highly productive, inshore water. Resulting pulses in the downward flux of particles likely stimulated heterotrophic dissimilatory NO 3 − reduction and subsequent production of biogenic N 2 . The associated temporal/spatial heterogeneity of N-loss, mediated by a local succession of microbial processes, may explain inconsistencies observed among prior studies. Similar transient enhancements of N-loss likely occur within all other major OMZ's exerting a major influence on global ocean N and N isotope budgets.

Description: Feedbacks of CO 2 dependent dissolved organic carbon production on atmospheric CO 2 in an ocean biogeochemical model Biogeosciences Discussions, 9, 7983-8011, 2012 Author(s): L. A. Bordelon-Katrynski and B. Schneider We use an ocean biogeochemical model to test whether a potential CO 2 dependence of dissolved organic carbon (DOC) production may have an influence on marine carbon sequestration via particle aggregation and so may represent a potentially larger ocean sink for anthropogenic CO 2 . The hypothesis is based on mesocosm experiments that have shown enhanced carbon uptake by phytoplankton when more CO 2 is available, and where the extra carbon was probably directly routed into DOC instead of the particulate phase. Sensitivity experiments are carried out where phytoplankton exudation of DOC is systematically increased with and without a parallel rise in atmospheric CO 2 . We find that under a fourfold increase of the DOC formation rate, there is a slight reduction of global particle export, which results in a shallower turnover of nutrients and carbon. As a consequence, a positive feedback loop develops, such that the ocean becomes a weak source of CO 2 to the atmosphere. The effect is amplified under high CO 2 conditions due to the decreased CO 2 buffer capacity of the ocean, however, it is rather low compared to the total anthropogenic perturbation. The positive feedback is in contrast to a very similar study, where a slight stimulation of particle export was found. Therefore, we conclude that the sign of the feedback depends on the actual pathway the extra carbon is taking and on the overall background conditions of marine primary production and ocean circulation.

Description: Technical Note: n -Alkane lipid biomarkers in loess: post-sedimentary or syn-sedimentary? Biogeosciences Discussions, 9, 9875-9896, 2012 Author(s): M. Zech, S. Kreutzer, T. Goslar, S. Meszner, T. Krause, D. Faust, and M. Fuchs There is an ongoing discussion whether n -alkane biomarkers – and organic matter (OM) from loess in general – reflect a syn-sedimentary paleoenvironmental and paleoclimate signal or whether they are significantly a post-sedimentary feature contaminated by root-derived OM. We present first radiocarbon data for the n -alkane fraction of lipid extracts and for the first time luminescence ages for the Middle to Late Weichselian loess-paleosol sequence of Gleina in Saxony, Germany. Comparison of these biomarker ages with sedimentation ages as assessed by optically stimulated luminescence (OSL) dating shows that one n -alkane sample features a syn-sedimentary age ( 14 C: 29.2 ± 1.4 kyr cal BP versus OSL: 27.3 ± 3.0 kyr). By contrast, the 14 C ages derived from the other n -alkane samples are clearly younger (20.3 ± 0.7 kyr cal BP, 22.1 ± 0.7 kyr cal BP and 29.8 ± 1.4 kyr cal BP) than the corresponding OSL ages (26.6 ± 3.1 kyr, 32.0 ± 3.5 kyr and 45.6 ± 5.3 kyr). This finding suggests that a post-sedimentary n -alkane contamination presumably by roots has occurred. In order to estimate the post-sedimentary n -alkane contamination more quantitatively, we applied a 14 C mass balance calculation based on the measured pMC (percent modern carbon) values, the calculated syn-sedimentary pMC values and pMC values suspected to reflect likely time points of post-sedimentary contamination (current, modern, 3 kyr, 6 kyr and 9 kyr). Accordingly, current and modern root-contamination would account for up to 7%, a 3 kyr old root-contamination for up to 10%, and an Early and Middle Holocene root-contamination for up to 20% of the total sedimentary n -alkane pool. We acknowledge and encourage that these first radiocarbon results need further confirmation both from other loess-paleosol sequences and for different biomarkers, e.g. carboxylic acids or alcohols as further lipid biomarkers.

Description: On the choice of the driving temperature for eddy-covariance carbon dioxide flux partitioning Biogeosciences Discussions, 9, 9829-9873, 2012 Author(s): G. Lasslop, M. Migliavacca, G. Bohrer, M. Reichstein, M. Bahn, A. Ibrom, C. Jacobs, P. Kolari, D. Papale, T. Vesala, G. Wohlfahrt, and A. Cescatti Networks that merge and harmonise eddy-covariance measurements from many different parts of the world have become an important observational resource for ecosystem science. Empirical algorithms have been developed which combine direct observations of the net ecosystem exchange of carbon dioxide with simple empirical models to disentangle photosynthetic (GPP) and respiratory fluxes ( R eco ). The increasing use of these estimates for the analysis of climate sensitivities, model evaluation, and calibration demands a thorough understanding of assumptions in the analysis process and the resulting uncertainties of the partitioned fluxes. The semi-empirical models used in flux partitioning algorithms require temperature observations as input, but as respiration takes place in many parts of an ecosystem, it is unclear which temperature input – air, surface, bole, or soil at a specific depth – should be used. This choice is a source of uncertainty and potential biases. In this study we analysed the correlation between different temperature observations and nighttime NEE (which equals nighttime respiration) across FLUXNET sites to understand the potential of the different temperature observations as input for the flux partitioning model. We found that the differences in the correlation between different temperature data streams and nighttime NEE are small and depend on the selection of sites. We investigated the effects of the choice of the temperature data by running two flux partitioning algorithms with air and soil temperature. We found the time lag (phase shift) between air and soil temperatures explains the differences in the GPP and R eco estimates when using either air or soil temperatures for flux partitioning. The impact of the source of temperature data on other derived ecosystem parameters was estimated, and the strongest impact was found for the temperature sensitivity. Overall, this study suggests that the choice between soil or air temperature must be made on site-by-site basis by analysing the correlation between temperature and nighttime NEE. We recommend using an ensemble of estimates based on different temperature observations to account for the uncertainty due to the choice of temperature and to assure the robustness of the temporal patterns of the derived variables.

Description: Interactive effects of vertical mixing, nutrients and ultraviolet radiation: in situ photosynthetic responses of phytoplankton from high mountain lakes of Southern Europe Biogeosciences Discussions, 9, 9791-9827, 2012 Author(s): E. W. Helbling, P. Carrillo, J. M. Medina-Sanchez, C. Durán, G. Herrera, M. Villar-Argaiz, and V. E. Villafañe Global change, together with human activities had resulted in increasing amounts of organic material (including nutrients) received by water bodies. This input further attenuates the penetration of solar radiation leading to the view that opaque lakes are more "protected" from solar ultraviolet radiation (UVR) than clear ones. Vertical mixing, however, complicates this view as cells are exposed to fluctuating radiation regimes, which effects have in general been neglected. Even more, the combined impacts of mixing, together with those of UVR and nutrients input are virtually unknown. In this study, we carried out in situ experiments in three high mountain lakes of Spain (Lake Enol in Asturias, and lakes Las Yeguas and La Caldera in Granada) to determine the combined effects of these three variables associated to global change on photosynthetic responses of natural phytoplankton communities. The experimentation consisted in all possible combinations of the following treatments: (a) solar radiation: UVR + PAR (280–700 nm) versus PAR alone (400–700 nm); (b) nutrient addition (phosphorus (P) and nitrogen (N)): ambient versus addition (P to reach to a final concentration of 30 μg P l −1 , and N to reach a N : P molar ratio of 31) and, (c) mixing: mixed (one rotation from surface to 3 m depth (speed of 1 m every 4 min, total of 10 cycles) versus static. Our findings suggest that under in situ nutrient conditions there is a synergistic effect between vertical mixing and UVR, increasing phytoplankton photosynthetic inhibition and EOC from opaque lakes as compared to algae that received constant mean irradiance within the epilimnion. The opposite occurs in clear lakes where antagonistic effects were determined, with mixing partially counteracting the negative effects of UVR. Nutrients input mimicking atmospheric pulses from Saharan dust, reversed this effect and clear lakes became more inhibited during mixing, while opaque lakes benefited from the fluctuating irradiance regime. These climate change-related nutrients input and increased mixing would not only affect photosynthesis and production of lakes, but might also further influence the microbial loop and trophic interactions via enhanced EOC under fluctuating UVR exposure.

Description: Tracing biogeochemical processes and pollution sources with stable isotopes in river systems: Kamniška Bistrica, North Slovenia Biogeosciences Discussions, 9, 9711-9757, 2012 Author(s): T. Kanduč, M. Šturm, S. Žigon, and J. McIntosh Biogeochemical processes were investigated in the Kamniška Bistrica River (Slovenia), which represents an ideal natural laboratory for studying pollution sources in catchments with high weathering capacity. The Kamniška Bistrica River water chemistry is dominated by HCO 3 − , Ca 2+ , and Mg 2+ and Ca 2+ /Mg 2+ molar ratios indicate that calcite weathering is the major source of solutes to the river system. The Kamniška Bistrica River and its tributaries are oversaturated with respect to calcite and dolomite. p CO 2 concentrations were on average up to 25 times over atmospheric values. δ 18 O values in river water ranged from −10.4 to −7.7‰ and plotted near the local meteoric water line, δ 13 C DIC values ranged from −12.7 to −2.7‰, controlled by biogeochemical processes in the catchment and within the stream; carbon dissolution is the most important biogeochemical process affecting carbon isotopes in the upstream portions of the catchment, while carbon dissolution and organic matter degradation control carbon isotope signatures downstream. Contributions of DIC from various biogeochemical processes were determined using steady state equations for different sampling seasons at the mouth of the Kamniška Bistrica River; results indicate that: (1) 1.9 to 2.2% of DIC came from exchange with atmospheric CO 2 , (2) 0 to 27.5% of DIC came from degradation of organic matter, (3) 25.4 to 41.5% of DIC came from dissolution of carbonates, and (4) 33 to 85% of DIC came from tributaries. δ 15 N values of nitrate ranged from −5.2‰ at the headwater spring to 9.8‰ in the lower reaches. Higher δ 15 N values in the lower reaches of the river suggest anthropogenic pollution from agricultural activity.

Description: Inter-annual variation of carbon uptake by a plantation oak woodland in south-eastern England Biogeosciences Discussions, 9, 9667-9710, 2012 Author(s): M. Wilkinson, E. L. Eaton, M. S. J. Broadmeadow, and J. I. L. Morison The carbon balance of an 80 yr old deciduous oak plantation in the temperate oceanic climate of the south-east of Britain was measured by eddy covariance over 12 yr (1999–2010). The mean annual net ecosystem productivity (NEP) was 486 g C m −2 y −1 (95% CI of ±73 g C m −2 y −1 ), and this was partitioned into a Gross Primary Productivity (GPP) of 2034 ± 145 g C m −2 y −1 , over a 165 (±6) day growing season, and an annual loss of carbon through respiration and decomposition (ecosystem respiration, R eco ) of 1548 ± 122 g C m −2 y −1 . The interannual variation of NEP was large (coefficient of variation (CV) 23%), although the variation for GPP and R eco was smaller (12%) and the ratio of R eco /GPP was relatively constant (0.76 ± 0.02 CI). Some anomalies in the annual patterns of the carbon balance could be linked to particular combinations of anomalous weather events, such as high summer air temperature and low soil moisture content. The Europe-wide heat-wave and drought of 2003 had little effect on the C balance of this woodland on a surface water gley soil. Annual variation in precipitation (CV 18%) was not a main factor in the variation in NEP. The inter-annual variation in estimated intercepted radiation only accounted for ~ 47% of the variation in GPP, although a significant relationship ( p

Description: Root growth of Lotus corniculatus interacts with P distribution in young sandy soil Biogeosciences Discussions, 9, 9637-9665, 2012 Author(s): B. Felderer, K. M. Boldt-Burisch, B. U. Schneider, R. F. J. Hüttl, and R. Schulin Large areas of land are restored with un-weathered soil substrates following mining activities in eastern Germany and elsewhere. In the initial stages of colonization of such land by vegetation, plant roots may become key agents in generating soil formation patterns by introducing gradients in chemical and physical soil properties. On the other hand, such patterns may be influenced by root growth responses to pre-existing substrate heterogeneities. In particular, the roots of many plants were found to preferentially proliferate into nutrient-rich patches. Phosphorus (P) is of primary interest in this respect because its availability is often low in unweathered soils, limiting especially the growth of leguminous plants. However, leguminous plants occur frequently among the pioneer plant species on such soils as they only depend on atmospheric nitrogen (N) fixation as N source. In this study we investigated the relationship between root growth allocation of the legume Lotus corniculatus and soil P distribution on recently restored land. As test sites the experimental Chicken Creek Catchment (CCC) in eastern Germany and a nearby experimental site (ES) with the same soil substrate were used. We established two experiments with constructed heterogeneity, one in the field on the experimental site and the other in a climate chamber. In addition we conducted high-density samplings on undisturbed soil plots colonized by L. corniculatus on the ES and on the CCC. In the field experiment, we installed cylindrical ingrowth soil cores (4.5×10 cm) with and without P fertilization around single two-month-old L. corniculatus plants. Roots showed preferential growth into the P-fertilized ingrowth-cores. Preferential root allocation was also found in the climate chamber experiment, where single L. corniculatus plants were grown in containers filled with ES soil and where a lateral portion of the containers was additionally supplied with a range of different P concentrations. In the high-density samplings, we excavated soil-cubes of 10×10×10 cm size from the topsoil of 3 mini-plot areas (50×50 cm) each on the ES and the CCC on which L. corniculatus had been planted (ES) or occurred spontaneously (CCC) and for each cube separated the soil attached to the roots (root-adjacent soil) from the remaining soil (root-distant soil). Root length density was negatively correlated with labile P (resin-extractable P) in the root-distant soil of the CCC plots and with water-soluble P in the root-distant soil of the ES plots. The results suggest that P depletion by root uptake during plant growth soon overrode the effect of preferential root allocation in the relationship between root density and plant-available soil P heterogeneity.

Description: Towards adaptable, interactive and quantitative paleogeographic maps Biogeosciences Discussions, 9, 9603-9636, 2012 Author(s): N. Wright, S. Zahirovic, R. D. Müller, and M. Seton A variety of paleogeographic atlases have been constructed, with applications from paleoclimate, ocean circulation and faunal radiation models to resource exploration; yet their uncertainties remain difficult to assess, as they are generally presented as low-resolution static maps. We present a methodology for ground-truthing paleogeographic maps, by linking the GPlates plate reconstruction tool to the global Paleobiology Database and a Phanerozoic plate motion model. We develop a spatio-temporal data mining workflow to compare a Phanerozoic Paleogeographic Atlas of Australia with biogeographic indicators. The agreement between fossil data and paleogeographic maps is quite good, but the methodology also highlights key inconsistencies. The Early Devonian paleogeography of southeastern Australia insufficiently describes the Emsian inundation that is supported by biogeography. Additionally, the Cretaceous inundation of eastern Australia retreats by 110 Ma according to the paleogeography, but the biogeography indicates that inundation prevailed until at least 100 Ma. Paleobiogeography can also be used to refine Gondwana breakup and the extent of pre-breakup Greater India can be inferred from the southward limit of inundation along western Australia. Although paleobiology data provide constraints only for paleoenvironments with high preservation potential of organisms, our approach enables the use of additional proxy data to generate improved paleogeographic reconstructions.

Description: Modeling the vertical soil organic matter profile using Bayesian parameter estimation Biogeosciences Discussions, 9, 11239-11292, 2012 Author(s): M. C. Braakhekke, T. Wutzler, C. Beer, J. Kattge, M. Schrumpf, I. Schöning, M. R. Hoosbeek, B. Kruijt, P. Kabat, and M. Reichstein The vertical distribution of soil organic matter (SOM) in the profile may constitute a significant factor for soil carbon cycling. However, the formation of the SOM profile is currently poorly understood due to equifinality, caused by the entanglement of several processes: input from roots, mixing due to bioturbation, and organic matter leaching. In this study we quantified the contribution of these three processes using Bayesian parameter estimation for the mechanistic SOM profile model SOMPROF. Based on organic carbon measurements, 13 parameters related to decomposition and transport of organic matter were estimated for two temperature forest soils: an Arenosol with a mor humus form (Loobos, The Netherlands), and a Cambisol with mull type humus (Hainich, Germany). Furthermore, the use of the radioisotope 210 Pb ex as tracer for vertical SOM transport was studied. For Loobos the calibration results demonstrate the importance of liquid phase transport for shaping the vertical SOM profile, while the effects of bioturbation are generally negligible. These results are in good agreement with expectations given in situ conditions. For Hainich the calibration offered three distinct explanations for the observations (three modes in the posterior distribution). With the addition of 210 Pb ex data and prior knowledge, as well as additional information about in situ conditions, we were able to identify the most likely explanation, which identified root litter input as the dominant process for the SOM profile. For both sites the organic matter appears to comprise mainly adsorbed but potentially leachable material, pointing to the importance of organo-mineral interactions. Furthermore, organic matter in the mineral soil appears to be mainly derived from root litter, supporting previous studies that highlighted the importance of root input for soil carbon sequestration. The 210 Pb ex measurements added only slight additional constraint on the estimated parameters. However, with sufficient replicate measurements and possibly in combination with other tracers, this isotope may still hold value as tracer for a SOM transport.

Description: Warming increases carbon-nutrient fluxes from sediments in streams across land use Biogeosciences Discussions, 9, 11293-11330, 2012 Author(s): S.-W. Duan and S. S. Kaushal Rising water temperatures due to climate and land-use change can accelerate biogeochemical fluxes from sediments to streams. We investigated impacts of increased streamwater temperatures on sediment fluxes of dissolved organic carbon (DOC), nitrate, soluble reactive phosphorus (SRP) and sulfate. Experiments were conducted at 8 long-term monitoring sites across land use (forest, agricultural, suburban, and urban) at the Baltimore Ecosystem Study Long-Term Ecological Research (LTER) site in the Chesapeake Bay watershed. Over 20 yr of routine water temperature data showed substantial variation across seasons and years, and lab incubations were conducted at 4 temperatures (4 °C, 15 °C, 25 °C and 35 °C) for 48 h. Results indicated: (1) warming consistently increased sediment DOC fluxes to overlying water across land use but decreased DOC quality via increases in the humic-like to protein-like fractions (2) warming consistently increased SRP fluxes from sediments to overlying water across land use (3) warming increased sulfate fluxes from sediments to overlying water at rural/suburban sites but decreased sulfate fluxes at urban sites likely due to sulfate reduction (4) nitrate fluxes showed an increasing trend with temperature but with larger variability than SRP. Sediment fluxes of nitrate, SRP and sulfate were strongly related to watershed urbanization and organic matter content. Using relationships of sediment fluxes with temperature, we estimate a 5 °C warming would increase the annual sediment release by 1.0–3.9 times. In addition to hydrologic variability, understanding warming impacts on coupled biogeochemical cycles in streams (e.g., organic matter mineralization, P sorption, nitrification, denitrification, and sulfate reduction) is critical for forecasting changes in carbon and nutrient exports across watershed land use.

Description: Food quality determines sediment community responses to marine vs. terrigenous organic matter in a submarine canyon Biogeosciences Discussions, 9, 11331-11374, 2012 Author(s): W. R. Hunter, A. Jamieson, V. A. I. Huvenne, and U. Witte The Whittard canyon is a branching submarine canyon on the Celtic continental margin, which may act as a conduit for sediment and organic matter (OM) transport from the European continental slope to the abyssal sea floor. In situ stable-isotope labelling experiments were conducted in the eastern and western branches of the Whittard canyon testing short term (3–7 day) responses of sediment communities to deposition of nitrogen-rich marine ( Thallassiosira weissflogii ) and nitrogen-poor terrigenous ( Triticum aestivum ) phytodetritus. 13 C and 15 N labels were traced into faunal biomass and bulk sediments, and the 13 C label traced into bacterial polar lipid fatty acids (PLFAs). Isotopic labels penetrated to 5 cm sediment depth, with no differences between stations or experimental treatments (substrate or time). Macrofaunal assemblage structure differed between the eastern and western canyon branches. Following deposition of marine phytodetritus, no changes in macrofaunal feeding activity were observed between the eastern and western branches, with little change between 3 and 7 days. Macrofaunal C and N uptake was substantially lower following deposition of terrigenous phytodetritus with feeding activity governed by a strong N demand. Bacterial C uptake was greatest, in the western branch of the Whittard canyon, but feeding activity decreased between 3 and 7 days. Bacterial processing of marine and terrigenous OM were similar to the macrofauna in surficial (0–1 cm) sediments. However, in deeper sediments bacteria utilised greater proportions of terrigenous OM. Bacterial biomass decreased following phytodetritus deposition and was negatively correlated to macrofaunal feeding activity. Consequently, this study suggests that macrofaunal-bacterial interactions influence benthic C cycling in the Whittard canyon, resulting in differential fates for marine and terrigenous OM.

Description: Nitrogen balance of a boreal Scots pine forest Biogeosciences Discussions, 9, 11201-11237, 2012 Author(s): J. F. J. Korhonen, M. Pihlatie, J. Pumpanen, H. Aaltonen, P. Hari, J. Levula, A.-J. Kieloaho, E. Nikinmaa, T. Vesala, and H. Ilvesniemi The productivity of boreal forests is considered to be limited by low nitrogen (N) availability. Increased atmospheric N deposition has altered the functioning and N cycling of these N-sensitive ecosystems. The most important components of N pools and fluxes were measured in a boreal Scots pine stand in Hyytiälä, Southern Finland. The measurement at the site allowed direct estimations of nutrient pools in the soil and biomass, inputs from the atmosphere and outputs as drainage flow and gaseous losses from two micro-catchments. N was accumulating to the system with a rate of 7 kg N ha −1 yr −1 . Nitrogen input as atmospheric deposition was 7.4 kg N ha −1 yr −1 . Dry deposition and organic N in wet deposition contributed over half of the input in deposition. Total outputs were 0.4 kg N ha −1 yr −1 , the most important outputs being N 2 O emission to the atmosphere and organic N flux in drainage flow. Nitrogen uptake and retranslocation were as important sources of N for plant growth. Most of the uptaken N originated from decomposition of organic matter, and the fraction of N that could originate directly from deposition was about 30%. In conclusion, atmospheric N deposition fertilizes the site considerably.

Description: A~probe into the different fates of locust swarms in the plains of North America and East Asia Biogeosciences Discussions, 9, 11179-11200, 2012 Author(s): G. Yu, D. Johnson, X. Ke, and Y. Li Locust swarms had periodically raged in both North American Plains (NAP) and East Asian Plains (EAP) before 1880 AD. After this period, the locust outbreaks almost never recurred in NAP but have continued to occur in EAP. Since large quantities of pesticides were used in the major agriculture regions of NAP in the late 1870s; this has been suggested as a possible major cause of the disappearing of locust outbreaks. Extensive applications of more effective chemical pesticides were also used in the granary regions of EAP in the 1950s in an effort to kill the pests at a much higher intensity. However, locust swarms came back again in many areas of China in the 1960s. Therefore, NAP locust extinction still remains a puzzle. Frequent locust outbreaks in EAP over the past 130 yr may offer clues to probe key control elements in the disappearing of locust outbreaks in NAP. This paper analyzes the climate extremes and monthly temperature-precipitation combines of NAP and EAP, and found the differences in their frequencies of these climate combines caused different locust fates in the two regions: restrained the locust outbreak in NAP but induced such events in EAP. Validation shows that severer EAP locust outbreak years were coincided with the climate extreme combines years. Thus we suggest that climate changes in frequency, extremes and trends can explain why the fate of the locust plague in EAP was different from that in NAP. The study also points out that, under the present global warming, cautions should be taken to make sure the pest hazard being nipped in the-bud.

Description: Bioerosion by microbial euendoliths in benthic foraminifera from heavy metal-polluted coastal environments of Portovesme (South-Western Sardinia, Italy) Biogeosciences Discussions, 9, 11103-11137, 2012 Author(s): A. Cherchi, C. Buosi, P. Zuddas, and G. De Giudici A monitoring survey of the coastal area facing the industrial area of Portoscuso-Portovesme (South-Western Sardinia, Italy) revealed intense bioerosional processes. Benthic foraminifera collected at the same depth (about 2 m) but at different distances from the pollution source show extensive microbial infestation, anomalous Mg/Ca molar ratios and high levels of heavy metals in the shell associated with a decrease in foraminifera richness, population density and biodiversity with the presence of morphologically abnormal specimens. We found that carbonate dissolution induced by euendoliths is selective, depending on the Mg content and morpho-structural types of foraminiferal taxa. This study provides evidences for a connection between heavy metal dispersion, decrease in pH of the sea-water and bioerosional processes on foraminifera.

Description: Black carbon contributes to organic matter in young soils in the Morteratsch proglacial area (Switzerland) Biogeosciences Discussions, 9, 13899-13923, 2012 Author(s): E. Eckmeier, C. Mavris, R. Krebs, B. Pichler, and M. Egli Most glacier forefields of the European Alps are progressively exposed since the glaciers reached their maximum expansion in the 1850s. Global warming and climate changes additionally promote the exposure of sediments in previously glaciated areas. In these proglacial areas, initial soils have started to develop so that they may offer a continuous chronosequence from 0 to 150 yr-old soils. The build-up of organic matter is an important factor of soil formation, and not only autochthonous but also distant sources might contribute to its accumulation in young soils and surfaces of glacier forefields. Only little is known about black carbon in soils that develop in glacier forefields, although charred organic matter could be an important component of organic carbon in Alpine soils. The aim of our study was to examine whether black carbon is present in the initial soils of a proglacial area, and to estimate its relative contribution to soil organic matter. We investigated soil samples from 35 sites distributed over the whole proglacial area of Morteratsch, covering a chronosequence from 0 to 150 yr. BC concentrations were determined in fine-earth using the benzene polycarboxylic acid (BPCA) marker method. We found that the proportion of BC to total C org was related to the time since the surface was exposed. Soils on surfaces exposed less than 40 yr ago contained the highest proportion of BC. The absolute concentrations of BC in fine-earth were generally low but increased in soils that had been exposed for more than 40 yr. Charred organic matter occurred in the whole area, and it was a main component of soil organic matter in young soils, where total C org concentrations were very low. Specific initial microbial communities consequently may profit from this additional C source during the first years of soil evolution and potentially promote soil development in its early stage.

Description: Impacts of dust deposition on dissolved trace metal concentrations (Mn, Al and Fe) during a mesocosm experiment Biogeosciences Discussions, 9, 13857-13897, 2012 Author(s): K. Wuttig, T. Wagener, M. Bressac, A. Dammshäuser, P. Streu, C. Guieu, and P. L. Croot The deposition of atmospheric dust is the primary process supplying trace elements abundant in crustal rocks (e.g. Al, Mn and Fe) to the surface ocean. Upon deposition, the residence time in surface waters for each of these elements differs according to their chemical speciation and biological utilization. Presently however their behavior after atmospheric deposition is poorly constrained, principally because of the difficulty in following natural dust events in-situ. In the present work we examined the temporal changes in the biogeochemistry of crustal metals (in particular Al, Mn and Fe) after an artificial dust deposition event. The experiment was contained inside trace metal clean mesocosms (0–12.5 m depths) deployed in the surface waters of the Northwestern Mediterranean, close to the coast of Corsica in the frame of the DUNE project (a DUst experiment in a low Nutrient low chlorophyll Ecosystem). Two consecutive artificial dust deposition events, each mimicking a wet deposition of 10 g m −2 of dust, were performed during the course of this DUNE-2 experiment. The changes in dissolved manganese (dMn), iron (dFe) and aluminium (dAl) concentrations were followed immediately and over the following week and their inventories and loss or dissolution rates were determined. The evolution of the inventories after the two consecutive additions of dust showed distinct behaviors for dMn, dAl and dFe. Even though the mixing conditions differed from one seeding to the other, dMn and dAl showed clear increases directly after both seedings due to dissolution processes. Three days after the dust additions, dAl concentrations decreased as a consequence of scavenging on sinking particles. dAl appeared to be highly affected by the concentrations of biogenic particles, with an order of magnitude difference in its loss rates related to the increase of biomass after the addition of dust. For dFe concentrations, the first dust addition decreased the concentrations through scavenging of the dust particles, whereas the second seeding induced dissolution of Fe from the dust particles. This difference, which might be related to a change in Fe-binding ligand concentration in the mesocosms, highlights the complex processes that control the solubility of Fe. Based on the inventories at the mesocosm scale, the estimations of solubility of metals from dust particles in seawater were 1% for Al and 40% for Mn which were in good agreement with laboratory based estimates. Overall, the trace metal dataset presented here makes a significant contribution to enhancing our knowledge on the processes influencing trace metals release from Saharan dust and the subsequent processes of bio-uptake and scavenging in a low nutrient low chlorophyll area.

Description: Publication year: 2012 Source: Cell Reports Byung Ouk Park, Robert Ahrends, Mary N. Teruel Adipogenesis, or the conversion of proliferating preadipocytes into nondividing adipocytes, is an important part of the vertebrate weight-maintenance program. It is not yet understood how and when an irreversible transition occurs into a distinct state capable of accumulating lipid. Here, we use single-cell fluorescence imaging to show that an all-or-none switch is induced before lipid accumulation occurs. Conversion begins by glucocorticoid and cAMP signals raising C/EBPβ levels above a critical threshold, triggering three consecutive positive feedback loops: from PPARγ to C/EBPα, then to C/EBPβ, and last to the insulin receptor. Experiments and modeling show that these feedbacks create a robust, irreversible transition to a terminally differentiated state by rejecting short- and low-amplitude stimuli. After the differentiation switch is triggered, insulin controls fat accumulation in a graded fashion. Altogether, our study introduces a regulatory motif that locks cells in a differentiated state by engaging a sequence of positive feedback loops. Graphical abstract Graphical Abstract Highlights ► A quantitative molecular model of adipogenesis is developed ► Multiple, consecutive feedback loops from PPARγ drive adipogenesis ► The circuit design with sequential, delayed loops prevents accidental triggering ► Insulin-regulated fat accumulation is graded and occurs only after the switch is made

Description: Marine denitrification rates determined from a global 3-dimensional inverse model Biogeosciences Discussions, 9, 14013-14052, 2012 Author(s): T. DeVries, C. Deutsch, P. A. Rafter, and F. Primeau A major impediment to understanding long-term changes in the marine nitrogen (N) cycle is the persistent uncertainty about the rates, distribution, and sensitivity of its largest fluxes in the modern ocean. We use a global 3-dimensional ocean circulation model to obtain the first estimate of marine denitrification rates that is maximally consistent with available observations of nitrate deficits and the nitrogen isotopic ratio of ocean nitrate. We find a global rate of marine denitrification in suboxic waters and sediments of 120–240 Tg N yr −1 , which is lower than most other recent estimates. The difference stems from the ability to represent the 3-D spatial structure of suboxic zones, where denitrification rates of 50–77 Tg N yr −1 result in up to 50% depletion of nitrate. This depletion reduces the effect of local isotopic enrichment on the rest of the ocean, allowing the N isotope ratio of oceanic nitrate to be achieved with a sedimentary denitrification rate about 1.3–2.3 times that of suboxic zones. This balance of N losses between sediments and suboxic zones is shown to obey a simple relationship between isotope fractionation and the degree of nitrate consumption in the core of the suboxic zones. The global denitrification rates derived here suggest that the marine nitrogen budget is likely close to balanced.

Description: Carbon sources in the Beaufort Sea revealed by molecular lipid biomarkers and compound specific isotope analysis Biogeosciences Discussions, 9, 13925-13985, 2012 Author(s): I. Tolosa, S. Fiorini, B. Gasser, J. Martín, and J. C. Miquel Molecular lipid biomarkers (hydrocarbons, alcohols, sterols and fatty acids) and compound specific isotope analysis of suspended particulate organic matter (SPM) and surface sediments of the Mackenzie Shelf and slope (Southeast Beaufort Sea, Arctic Ocean), were studied in summer 2009. The concentrations of the molecular lipid markers, characteristic of known organic matter sources, were grouped and used as proxies to evaluate the relative importance of fresh algal, detrital algal, fossil, C 3 terrestrial plants, bacterial and zooplankton material in the sedimentary organic matter (OM). Fossil and detrital algal contributions were the major fractions of the freshwater SPM from the Mackenzie River with ~34% each of the total molecular biomarkers. Fresh algal, C 3 terrestrial, bacterial and zooplanktonic components represented much lower percentages, 17, 10, 4 and 〈 1%, respectively. In marine SPM from the Mackenzie slope, the major contributions were fresh and detrital algal components (〉 80%) with a minor contribution of fossil and C 3 terrestrial biomarkers. Characterization of the sediments revealed a major sink of refractory algal material mixed with some fresh algal material, fossil hydrocarbons and a small input of C 3 terrestrial sources. In particular, the sediments from the shelf and at the mouth of the Amundsen Gulf presented the highest contribution of detrital algal material (60–75%) whereas those from the slope contained the highest proportion of fossil (40%) and C 3 terrestrial plant material (10%). Overall, considering that the detrital algal material is marine derived, autochthonous sources contributed more than allochthonous sources to the OM lipid pool. Using the ratio of an allochthonous biomarker (normalized to total organic carbon, TOC) found in the sediments to those measured at the river mouth water, we estimated that the fraction of terrestrial material preserved in the sediments accounted for 30–40% of the total carbon in the inner shelf sediments, 17% in the outer shelf and Amundsen Gulf and up to 25% in the slope sediments.

Description: Publication year: 2012 Source: FEBS Open Bio Masaharu Hazawa, Takeshi Yasuda, Katsuko Noshiro, Ai Saotome-Nakamura, Tomoko Fukuzaki, Yuichi Michikawa, Takaya Gotoh, Katsushi Tajima Vitronectin (VN) is a multi-functional protein involved in extracellular matrix (ECM)-cell binding through integrin receptors on the cell surface, which is an important environmental process for maintaining biological homeostasis. We investigated how VN affects the survival of endothelial cells after radiation damage. VN attenuated radiation-induced expression of p21, an inhibitor of cell cycle progression, and selectively inhibited Erk- and p38 MAPK-dependent p21 induction after radiation exposure through regulation of the activity of GSK-3β. VN also reduced the cleavage of caspase-3, thereby inhibiting radiation-induced apoptotic cell death. These results suggest that VN has important roles in cell survival after radiation damage.

Description: Spatial and temporal aspects of greenhouse gas emissions from Three Gorges Reservoir, China Biogeosciences Discussions, 9, 14503-14535, 2012 Author(s): Y. Zhao, B. F. Wu, and Y. Zeng Before completion of the Three Gorges Reservoir (TGR), China, there was growing apprehension that it would become a major emitter of greenhouse gases (GHG): Carbon Dioxide (CO 2 ), Methane (CH 4 ) and Nitrous Oxide (N 2 O). We report monthly measurements for one year of the fluxes of these gases at multiple sites within the TGR, Yangtze River, China, and from several major tributaries, and immediately downstream of the dam. The tributary areas have lower CO 2 fluxes than the main storage; CH 4 fluxes to the atmosphere after passage through the turbines are negligible. Overall, TGR showed significantly lower CH 4 emission rates than most new reservoirs in temperate and tropical regions. We attribute this to the well-oxygenated deep water and high water velocities which produce oxic mainstem conditions inimical to CH 4 emission. TGR's CO 2 fluxes were lower than most tropical reservoirs and higher than most temperate systems. This is due to the high load of metabolizable soil carbon delivered through erosion to the Yangtze River. Compared to fossil fuelled power plants of equivalent power output TGR is a very small GHG emitter, annual CO 2 -equivalent emissions are approximately 1.7% of a coal-fired generating plant of comparable power output.

Description: Publication year: 2012 Source: Cell Reports Yuchen Han, Gena Whitney, Jesse Donovan, Alexei Korennykh 2′,5′-linked oligoadenylates (2-5As) serve as conserved messengers of pathogen presence in the mammalian innate immune system. 2-5As induce self-association and activation of RNase L, which cleaves cytosolic RNA and promotes the production of interferons (IFNs) and cytokines driven by the transcription factors IRF-3 and NF-κB. We report that human RNase L is activated by forming high-order complexes, reminiscent of the mode of activation of the phylogenetically related transmembrane kinase/RNase Ire1 in the unfolded protein response. We describe crystal structures determined at 2.4 Å and 2.8 Å resolution, which show that two molecules of 2-5A at a time tether RNase L monomers via the ankyrin-repeat (ANK) domain. Each ANK domain harbors two distinct sites for 2-5A recognition that reside 50 Å apart. These data reveal a function for the ANK domain as a 2-5A-sensing homo-oligomerization device and describe a nonlinear, ultrasensitive regulation in the 2-5A/RNase L system poised for amplification of the IFN response. Graphical abstract Graphical Abstract Highlights ► Human RNase L undergoes a highly cooperative activation ► Two 2-5A molecules at a time tether RNase L into signaling complexes ► The ANK domain of RNase L is a homo-oligomerization device ► RNase L is poised for ultrasensitive amplification of the interferon response

Description: Publication year: 2012 Source: Cell Reports Anthony B. Mak, Allison M.L. Nixon, Saranya Kittanakom, Jocelyn M. Stewart, Ginny I. Chen, Jasna Curak, Anne-Claude Gingras, Ralph Mazitschek, Benjamin G. Neel, Igor Stagljar, Jason Moffat The pentaspan membrane glycoprotein CD133 marks lineage-specific cancer progenitor cells and is associated with poor prognosis in a number of tumor types. Despite its utility as a cancer progenitor cell marker, CD133 protein regulation and molecular function remain poorly understood. We find that the deacetylase HDAC6 physically associates with CD133 to negatively regulate CD133 trafficking down the endosomal-lysosomal pathway for degradation. We further demonstrate that CD133, HDAC6, and the central molecule of the canonical Wnt signaling pathway, β-catenin, can physically associate as a ternary complex. This association stabilizes β-catenin via HDAC6 deacetylase activity, which leads to activation of β-catenin signaling targets. Downregulation of either CD133 or HDAC6 results in increased β-catenin acetylation and degradation, which correlates with decreased proliferation in vitro and tumor xenograft growth in vivo. Given that CD133 marks progenitor cells in a wide range of cancers, targeting CD133 may be a means to treat multiple cancer types. Graphical abstract Graphical Abstract Highlights ► HDAC6 negatively regulates CD133 trafficking into endosomes ► CD133 knockdown suppresses colon and ovarian cancer cell differentiation ► CD133, HDAC6, and β-catenin physically associate to form a functional module ► CD133 regulates β-catenin stability through HDAC6 deacetylase activity

Description: The impact of sea-level rise on organic matter decay rates in Chesapeake Bay brackish tidal marshes Biogeosciences Discussions, 9, 14689-14708, 2012 Author(s): M. L. Kirwan, J. A. Langley, G. R. Guntenspergen, and J. P. Megonigal The balance between organic matter production and decay determines how fast coastal wetlands accumulate soil organic matter. Despite the importance of soil organic matter accumulation rates in influencing marsh elevation and resistance to sea-level rise, relatively little is known about how decomposition rates will respond to sea-level rise. Here, we estimate the sensitivity of decomposition to flooding by measuring rates of decay in 87 bags filled with milled sedge peat, including soil organic matter, roots and rhizomes. Experiments were located in field-based mesocosms along 3 mesohaline tributaries of the Chesapeake Bay. Mesocosm elevations were manipulated to influence the duration of tidal inundation. Although we found no significant influence of inundation on decay rate when bags from all study sites were analyzed together, decay rates at two of the sites increased with greater flooding. These findings suggest that flooding may enhance organic matter decay rates even in water-logged soils, but that the overall influence of flooding is minor. Our experiments suggest that sea-level rise will not accelerate rates of peat accumulation by slowing the rate of soil organic matter decay. Consequently, marshes will require enhanced organic matter productivity or mineral sediment deposition to survive accelerating sea-level rise.

Description: Plankton ecosystem functioning and nitrogen fluxes in the most oligotrophic waters of the Beaufort Sea, Arctic Ocean: a modeling study Biogeosciences Discussions, 9, 14751-14793, 2012 Author(s): V. Le Fouest, B. Zakardjian, H. Xie, P. Raimbault, F. Joux, and M. Babin The Arctic Ocean (AO) undergoes profound changes of its physical and biotic environments due to climate change. The greater light exposure and stratification alter its plankton ecosystem structure, functioning and productivity promoting oligotrophy in some areas as the Beaufort Sea. A one-dimension (1-D) physical-biological coupled model based on the large multiparametric database of the Malina project in the Beaufort Sea was used (i) to infer the functioning and nitrogen fluxes within the summer plankton ecosystem and (ii) to assess the model sensitivity to key light-associated processes involved in nutrient recycling and phytoplankton growth. The coupled model suggested that ammonium photochemically produced from photosensitive dissolved organic nitrogen (i.e. photoammonification process) was a necessary nitrogen source to achieve the observed levels of microbial biomass and production. It contributed to ca. two-thirds and one-third of the simulated surface (0–10 m) and depth-integrated primary and bacterial production, respectively. The model also suggested that carbon to chlorophyll ratios for small ( 〈 5 μm) phytoplankton (ca. 15–45 g g −1 ) lower than those commonly used in biogeochemical models applied to the AO were required to simulate the observed herbivorous versus microbial food web competition and realistic nitrogen fluxes in the Beaufort Sea oligotrophic waters. In face of accelerating Arctic warming, more attention should be paid in the future to the mechanistic processes involved in food webs and functional groups competition, nutrient recycling and primary production in poorly productive waters of the AO as they are expected to expand rapidly.

Description: Intra-aggregate CO 2 enrichment: a modelling approach for aerobic soils Biogeosciences Discussions, 9, 14795-14822, 2012 Author(s): D. Schlotter and H. Schack-Kirchner CO 2 concentration gradients inside soil aggregates, caused by the respiration of soil microorganisms and fungal hyphae, might lead to variations in the soil solution chemistry on a mm-scale, and to an underestimation of the CO 2 storage. But, up to now, there seems to be no feasible method for measuring CO 2 inside natural aggregates with sufficient spatial resolution. We combined a one-dimensional model for gas diffusion in the inter-aggregate pore-space with a cylinder diffusion model, simulating the consumption/production and diffusion of O 2 and CO 2 inside soil aggregates with air- and water-filled pores. Our model predicts that for aerobic respiration (respiratory quotient = 1) the intra-aggregate increase in the CO 2 partial pressure can never be higher than 0.9 kPa for siliceous, and 0.08 kPa for calcaric aggregates, independent of the level of water-saturation. This suggests that only for siliceous aggregates CO 2 produced by aerobic respiration might cause a high small-scale spatial variability in the soil solution chemistry. In calcaric aggregates, however, the contribution of carbonate species to the CO 2 transport should lead to secondary carbonates on the aggregate surfaces. As regards the total CO 2 storage in aerobic soils, both siliceous and calcaric, the effect of intra-aggregate CO 2 gradients seems to be negligible. To assess the effect of anaerobic respiration on the intra-aggregate CO 2 gradients, the development of a device for measuring CO 2 on a mm-scale in soils is indispensable.

Description: Tracing inputs of terrestrial high molecular weight dissolved organic matter within the Baltic Sea Ecosystem Biogeosciences Discussions, 9, 4483-4512, 2012 Author(s): B. Deutsch, V. Alling, C. Humborg, F. Korth, and C. M. Mörth To test the hypothesis whether dissolved organic matter (DOM) in a high latitude marginal sea is dominated by terrestrial derived matter 10 stations were sampled along the salinity gradient of the central and northern Baltic Sea and were analyzed for concentrations of dissolved organic carbon as well as δ 13 C values of high molecular weight DOM. Different end-member-mixing models were applied to quantify the influence of terrestrial DOM and to test for conservative versus non-conservative behavior of the terrestrial dissolved organic matter in the different Baltic Sea basins. The share of terrestrial DOM to the total DOM was calculated for each station, ranging from 43 to 83%. This shows the high influence of terrestrial DOM inputs for the Baltic Sea ecosystem. The data also suggest that terrestrial DOM that reaches the open Baltic Sea is not subject to substantial removal anymore. However compared to riverine DOM concentrations our results indicate that substantial amounts of DOM (〉50%) seems to be removed near the coastline during estuarine mixing. A budget approach yielded residence times for terrestrial DOM of 2.3, 2.7, and 4.1 yr for the Bothnian Bay, the Bothnian Sea and the Baltic Proper.

Description: Fine scale variability in methanol uptake and oxidation in the micro-layer and near-surface waters of the Atlantic Biogeosciences Discussions, 9, 4513-4542, 2012 Author(s): J. L. Dixon and P. D. Nightingale The aim of this research was to make the first depth profiles of the microbial assimilation of methanol carbon, and its oxidation to carbon dioxide and use as an energy source from the micro-layer to 1000 m. Some of the highest reported methanol oxidation rate constants of 0.5–0.6 d −1 were occasionally found in the micro-layer, and immediately underlying waters (10 cm depth), albeit these samples also showed the greatest heterogeneity compared to other depths down to 1000 m. Methanol uptake into the particulate phase was exceptionally low in micro-layer samples, suggesting that any methanol utilised by microbes in this environment is for energy generation. The sea surface micro-layer and 10 cm depth also showed a higher proportion of bacteria with a low DNA content, and bacterial leucine uptake rates in surface micro-layer samples were either less than, or the same as those in the underlying 10 cm layer. The average methanol oxidation and particulate rates were however statistically the same throughout the depths sampled, although the later were highly variable in the near surface 0.25–2 m compared to deeper depths. The statistically significant relationship demonstrated between uptake of methanol into particles and bacterial leucine incorporation suggests that heterotrophic bacteria use methanol carbon for cellular growth, but the lack of relationships observed with methanol oxidation, perhaps suggest that a wider group of marine microbes use methanol for energy generation. Whilst the statistically significant relationship observed between the uptake of methanol into cell particles and the numbers of Prochlorococcus during diel experiments could also suggest that this abundant group of marine cyanobacteria are capable of mixotrophy, using methanol as a carbon source for growth. We conclude that microbial methanol uptake rates, i.e., loss from seawater are highly variable, particularly close to the seawater surface, which could significantly impact upon seawater concentrations and hence the air-sea flux.

Description: Variations of net primary productivity and phytoplankton community composition in the Southern Ocean as estimated from ocean-color remote sensing data Biogeosciences Discussions, 9, 4361-4398, 2012 Author(s): S. Takao, T. Hirawake, S. W. Wright, and K. Suzuki Phytoplankton population dynamics play an important role in biogeochemical cycles in the Southern Ocean during austral summer. Recent environmental changes such as a rise in sea surface temperature (SST) are likely to impact on net primary productivity (NPP) and phytoplankton community composition. However, their spatiotemporal relationships are still unclear in the Southern Ocean. Here we assessed the relationships between NPP, dominant phytoplankton groups, and SST in the Indian sector of the Southern Ocean over the past decade (1997–2007) using satellite remote sensing data. As a result, we found a statistically significant reduction in NPP in the polar frontal zone over the past decade during austral summer. Moreover, the decrease in NPP positively correlated with the dominance of diatoms (Kendall's rank correlation τ = 0.60) estimated by a phytoplankton community composition model, but not correlated with SST. In the seasonal ice zone, NPP correlated with not only the dominance of diatoms positively (τ = 0.56), but also the dominance of haptophytes (τ = −0.54) and SST (τ = −0.54) negatively. Our results suggested that summer NPP values were strongly affected by the phytoplankton community composition in the Southern Ocean.

Description: Primary production in forests and grasslands of China: contrasting environmental responses of light- and water-use efficiency models Biogeosciences Discussions, 9, 4285-4321, 2012 Author(s): H. Wang, I. C. Prentice, and J. Ni An extensive data set on net primary production (NPP) in China's forests is analysed with two semi-empirical models based on the light use efficiency (LUE) and water use efficiency (WUE) concepts, respectively. Results are shown to be broadly consistent with other data sets (grassland above-ground NPP; globally extrapolated gross primary production, GPP) and published analyses. But although both models describe the data about equally well, they predict notably different responses to [CO 2 ] and temperature. These are illustrated by sensitivity tests in which [CO 2 ] is kept constant or doubled, temperatures are kept constant or increased by 3.5 K, and precipitation is changed by ±10%. Precipitation changes elicit similar responses in both models. The [CO 2 ] response of the WUE model is much larger but is probably an overestimate for dense vegetation as it assumes no increase in runoff; while the [CO 2 ] response of the LUE model is probably too small for sparse vegetation as it assumes no increase in vegetation cover. In the LUE model warming reduces total NPP with the strongest effect in South China, where the growing season cannot be further extended. In the WUE model warming increases total NPP, again with the strongest effect in South China, where abundant water supply precludes stomatal closure. The qualitative differences between the two formulations illustrate potential causes of the large differences (even in sign) in the global NPP response of dynamic global vegetation models to [CO 2 ] and climate change. As it is not clear which response is more realistic, the issue needs to be resolved by observation and experiment.

Description: Photoproduction of ammonium in the Southeastern Beaufort Sea and its biogeochemical implications Biogeosciences Discussions, 9, 4441-4482, 2012 Author(s): H. Xie, S. Bélanger, G. Song, R. Benner, A. Taalba, M. Blais, V. Lefouest, J.-É. Tremblay, and M. Babin Photochemistry of dissolved organic matter (DOM) plays an important role in marine biogeochemical cycles, including the regeneration of inorganic nutrients. DOM photochemistry affects nitrogen cycling by converting bio-refractory dissolved organic nitrogen to labile inorganic nitrogen, mainly ammonium (NH 4 + ). During the August 2009 Mackenzie Light and Carbon (MALINA) Program, the absorbed photon-based efficiency spectra of NH 4 + photoproduction (i.e. photoammonification) were determined using water samples from the SE Beaufort Sea, including the Mackenzie River estuary, shelf, and Canada Basin. The photoammonification efficiency decreased with increasing wavelength across the ultraviolet and visible regimes and was higher in offshore waters than in shelf and estuarine waters. The efficiency was positively correlated with the molar nitrogen : carbon ratio of DOM and negatively correlated with the absorption coefficient of chromophoric DOM (CDOM). Combined with collateral measurements of CO 2 and CO photoproduction, this study revealed a stoichiometry of DOM photochemistry with a CO 2 :CO:NH 4 + molar ratio of 165:11:1 in the estuary, 60:3:1 on the shelf, and 18:2:1 in the Canada Basin. The NH 4 + efficiency spectra, along with solar photon fluxes, CDOM absorption coefficients and sea ice concentrations, were used to model the monthly surface and depth-integrated photoammonification rates in 2009. The summertime (June–August) rates at the surface reached 6.6 nmol l −1 d −1 on the Mackenzie Shelf and 3.7 nmol l −1 d −1 further offshore; the depth-integrated rates were correspondingly 8.8 μmol m −2 d −1 and 11.3 μmol m −2 d −1 . The offshore depth-integrated rate in August (8.0 μmol m −2 d −1 ) was comparable to the missing dissolved inorganic nitrogen (DIN) source required to support the observed primary production in the upper 10-m layer of that area. The yearly NH 4 + photoproduction in the entire study area was estimated to be 1.4 × 10 8 moles, with 85 % of it being generated in summer when riverine DIN input is low. Photoammonification could mineralize 4 % of the annual dissolved organic nitrogen (DON) exported from the Mackenzie River and provide a~DIN source corresponding to 7 % of the riverine DIN discharge and 1400 times the riverine NH 4 + flux. Under a climate warming-induced ice-free scenario, these quantities would increase correspondingly to 6 %, 11 %, and 2100 times. Photoammonification is thus a significant nitrogen cycling term and may fuel previously unrecognized autotrophic and heterotrophic production pathways in the surface SE Beaufort Sea.

Description: An isotopic (Δ 14 C, δ 13 C, and δ 15 N) investigation of particulate organic matter and zooplankton biomass in Lake Superior and across a size-gradient of aquatic systems Biogeosciences Discussions, 9, 4399-4439, 2012 Author(s): P. K. Zigah, E. C. Minor, J. P. Werne, and S. Leigh McCallister Food webs in aquatic systems can be supported both by carbon from recent local primary productivity and by carbon subsidies, such as material from terrestrial ecosystems or past in situ primary productivity. The importance of these subsidies to respiration and biomass production remains a topic of debate, but they may play major roles in determining the fate of organic carbon and in sustaining upper trophic levels, including those contributing to economically important fisheries. While some studies have reported that terrigenous organic carbon supports disproportionately high zooplankton production, others have suggested that phytoplankton preferentially supports zooplankton production in aquatic ecosystems. Here we apply natural abundance radiocarbon (Δ 14 C) and stable isotope (δ 13 C, δ 15 N) analyses to show that zooplankton in Lake Superior selectively incorporate recently-fixed, locally-produced (autochthonous) organic carbon even though other carbon sources are readily available. Estimates from Bayesian isotopic modeling based on Δ 14 C values show that the average lakewide median contributions of recent in situ algal, terrestrial, sedimentary, and bacterial organic carbon to the bulk POM in Lake Superior were 23%, 28%, 15%, and 25%, respectively. However, the isotopic modeling estimates show that recent in situ production (algae) contributed a disproportionately large amount (median, 40–89%) of the carbon in zooplankton biomass in Lake Superior. Although terrigenous organic carbon and old organic carbon from resuspended sediments were significant portions of the available basal food resources, these contributed only a small amount to zooplankton biomass (average lakewide median, 2% from sedimentary organic carbon and 9% from terrigenous organic carbon). Comparison of zooplankton food sources based on their radiocarbon composition showed that terrigenous organic carbon was relatively more important in rivers and small lakes, and the proportion of terrestrially-derived material used by zooplankton correlated with the hydrologic residence time and the ratio of basin area to water surface area.

Description: Predicting photosynthesis and transpiration responses to ozone: decoupling modeled photosynthesis and stomatal conductance Biogeosciences Discussions, 9, 4245-4283, 2012 Author(s): D. Lombardozzi, S. Levis, G. Bonan, and J. P. Sparks Plants exchange carbon dioxide and water, two key greenhouse gases, with the atmosphere through the processes of photosynthesis and transpiration, making them essential in climate regulation. Carbon dioxide and water exchange are typically coupled through the control of stomatal conductance, and the parameterization in many models often predict conductance based on photosynthesis values. Some environmental conditions, like exposure to high ozone (O 3 ) concentrations, alter photosynthesis independent of stomatal conductance, so models cannot accurately predict both. The goals of this study were to test direct and indirect photosynthesis and stomatal conductance modifications based on O 3 damage in a coupled Farquhar/Ball-Berry model. The same modifications were then tested in the Community Land Model (CLM) to determine the impacts on gross primary productivity (GPP) and transpiration. Modifying the V cmax parameter and directly modifying stomatal conductance best predicts photosynthesis and stomatal conductance responses to chronic O 3 over a range of environmental conditions. On a global scale, directly modifying conductance reduces the effect of O 3 on both transpiration and GPP compared to indirectly modifying conductance, particularly in the tropics. The results of this study suggest that independently modifying stomatal conductance can improve the ability of models to predict hydrologic cycling, and therefore improve future climate predictions.

Description: Mass, nutrients and oxygen budgets for the North Eastern Atlantic Ocean Biogeosciences Discussions, 9, 4323-4360, 2012 Author(s): G. Maze, H. Mercier, V. Thierry, L. Memery, P. Morin, and F. F. Perez A surface to bottom North-East Atlantic Ocean budget for mass, nutrients (nitrate and phosphate) and oxygen is determined using an optimization method based on climatological data from the World Ocean Atlas 2009 and three surveys of the OVIDE transect (from Greenland to Portugal). Budgets are derived for two communicating boxes representing the North Eastern European Basin (NEEB) and the Irminger Sea. For the NEEB (Irminger) box, it is found that 30% of the mass import (export) across the OVIDE section reach (originate from) the Nordic Seas while 70% is redistributed between both boxes through the Reykjanes Ridge (9.3±0.7×10 9 kg s −1 ). Net biological source/sink terms of nitrate point to both the Irminger and NEEB boxes as net organic matter production sites (consumming nitrate at a rate of −7.8±6.5 kmol s −1 and −8.4±6.6 kmol s −1 respectively). Using a standard Redfield ratio of C:N =106:16, nitrate consumption rates indicate that about 40 TgC yr −1 of carbon is fixed by organic matter production between the OVIDE transect and the Greenland-Scotland Ridge. Nutrients fluxes also induce a net biological production of oxygen of 73±60 kmol s −1 and 79±62 kmol s −1 in the Irminger and NEEB boxes which points to the region as being autotrophic. Air-sea oxygen fluxes show an oceanic oxygen uptake in the two regions (264±66 kmol s −1 in the north and 443±70 kmol s −1 in the south), dominated by the abiotic component. The abiotic flux is partitionned into a mixing and a thermal components. It is found that the Irminger Sea oceanic oxygen uptake is driven by an air-sea heat flux cooling increasing the ocean surface oxygen solubility. Over the North Eastern European Basin the mixing component is about half the thermal flux, presumably because of the oxygen minimum in the subtropical thermocline.

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 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 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 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: 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 How specific cell types can be directly converted into other distinct cell types is a matter of intense investigation with wide-ranging basic and biomedical implications. Here, we show that removal of the histone 3 lysine 27 (H3K27) methyltransferase Polycomb repressor complex 2 (PRC2) permits ectopically expressed, neuron-type-specific transcription factors (“terminal selectors”) to convert Caenorhabditis elegans germ cells directly into specific neuron types. Terminal-selector-induced germ-cell-to-neuron conversion can be observed not only upon genome-wide loss of H3K27 methylation in PRC2(−) animals but also upon genome-wide redistribution of H3K27 methylation patterns in animals that lack the H3K36 methyltransferase MES-4. Manipulation of the H3K27 methylation status not only permits conversion of germ cells into neurons but also permits hlh-1/MyoD -dependent conversion of germ cells into muscle cells, indicating that PRC2 protects the germline from the aberrant execution of multiple distinct somatic differentiation programs. Taken together, our findings demonstrate that the normally multistep process of development from a germ cell via a zygote to a terminally differentiated somatic cell type can be short-cut by providing an appropriate terminal selector transcription factor and manipulating histone methylation patterns. Graphical abstract Highlights ► Selector-type transcription factors cannot convert germ cells into neurons or muscle ► Loss of H3K27me3 allows direct, selector-driven germ cell conversion to neurons or muscle ► H3K27me3 redistribution in H3K36me(−) animals also permits germ cell conversion ► Mitotic cycling is not required for induced germ cell conversion

Description: 29 November 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 5 GATA transcription factors regulate transcription during development and differentiation by recognizing distinct GATA sites with a tandem of two conserved zinc fingers, and by mediating long-range DNA looping. However, the molecular basis of these processes is not well understood. Here, we determined three crystal structures of the full DNA-binding domain (DBD) of human GATA3 protein, which contains both zinc fingers, in complex with different DNA sites. In one structure, both zinc fingers wrap around a palindromic GATA site, cooperatively enhancing the binding affinity and kinetic stability. Strikingly, in the other two structures, the two fingers of GATA DBD bind GATA sites on different DNA molecules, thereby bridging two separate DNA fragments. This was confirmed in solution by an in-gel fluorescence resonance energy transfer analysis. These findings not only provide insights into the structure and function of GATA proteins but also shed light on the molecular basis of long-range gene regulation. Graphical abstract Highlights ► Crystal structures of the GATA3 DNA-binding domain are presented ► The two fingers of GATA3 can bridge two separate DNA fragments ► GATA protein may use this mechanism to mediate long-range DNA looping ► GATA3 uses a combination of base and shape readout to bind to its target sites

Description: 2012 Publication year: 2012 Source: FEBS Open Bio, Volume 2 Antimalarial chloroquine is also used for the treatment of immune-mediated diseases. The interference of chloroquine with interferon-γ-induced tryptophan breakdown and neopterin production has been investigated in human peripheral blood mononuclear cells (PBMC) in vitro . Micromolar concentrations (2–50 μM) of chloroquine dose-dependently suppressed mitogen-induced tryptophan breakdown in PBMC but not in the myelomonocytic THP-1-Blue cell line, after 48 h of treatment. In stimulated PBMC, neopterin production was super-induced by 10 μM chloroquine, while it was significantly suppressed at a concentration of 50 μM. These anti-inflammatory effects may relate to the therapeutic benefit of chloroquine in inflammatory conditions and may widen the spectrum of its clinical applications. Highlights ▸ 2–50 μM chloroquine suppresses mitogen-induced tryptophan breakdown in human PBMCs. ▸ The same effect was not seen in the myelomonocytic THP-1-Blue cell line. ▸ The anti-inflammatory property of chloroquine targets T cells more than monocytes. ▸ This anti-inflammatory effect may explain the drug's therapeutic benefit for malaria. ▸ Chloroquine treatment could be of benefit for other chronic inflammatory conditions.

Description: 2012 Publication year: 2012 Source: FEBS Open Bio, Volume 2 Tespa1 has been recently reported to be a critical molecule in T-cell development, however, the precise molecular mechanisms of Tespa1 remain elusive. Here, we demonstrate that Tespa1 shows amino-acid sequence homology to KRAS -induced actin-interacting protein (KRAP), an inositol 1,4,5-trisphosphate receptor (IP 3 R) binding protein, and that Tespa1 physically associates with IP 3 R in T and B lymphocytes. Two-consecutive phenylalanine residues (Phe185/Phe186) in Tespa1, which are conserved between Tespa1 and KRAP, are indispensable for the association between Tespa1 and IP 3 R. These findings suggest that Tespa1 plays critical roles in the immune system through the regulation of the IP 3 R. Highlights ▸ We identified Tespa1 as a novel IP 3 R-associated protein in lymphoid tissues. ▸ Tespa1 interacts with multiple subtypes of IP 3 R in T and B lymphocytes. ▸ Amino-terminal region of IP 3 R is sufficient for the association with Tespa1. ▸ Two consecutive phenylalanines in Tespa1 are critical for the interaction with IP 3 R. ▸ Tespa1 is structurally and functionally related to KRAP.

Description: 2012 Publication year: 2012 Source: FEBS Open Bio, Volume 2 Human STIL (SCL/TAL1 interrupting locus) protein maintains centriole stability and spindle pole localisation. It helps in recruitment of CENPJ (Centromere protein J)/CPAP (centrosomal P4.1-associated protein) and other centrosomal proteins. Mutations in STIL protein are reported in several disorders, especially in deregulation of cell cycle cascades. In this work, we examined the non-synonymous single nucleotide polymorphisms (nsSNPs) reported in STIL protein for their disease association. Different SNP prediction tools were used to predict disease-associated nsSNPs. Our evaluation technique predicted rs147744459 (R242C) as a highly deleterious disease-associated nsSNP and its interaction behaviour with CENPJ protein. Molecular modelling, docking and molecular dynamics simulation were conducted to examine the structural consequences of the predicted disease-associated mutation. By molecular dynamic simulation we observed structural consequences of R242C mutation which affects interaction of STIL and CENPJ functional domains. The result obtained in this study will provide a biophysical insight into future investigations of pathological nsSNPs using a computational platform.

Description: Bacteriohopanepolyols record stratification, nitrogen fixation and other biogeochemical perturbations in Holocene sediments of the Central Baltic Sea Biogeosciences Discussions, 9, 17139-17165, 2012 Author(s): M. Blumenberg, C. Berndmeyer, M. Moros, M. Muschalla, O. Schmale, and V. Thiel The Baltic Sea, one of the world's largest brackish-marine basins, established after deglaciation of Scandinavia about 17 000 to 15 000 yr ago. In the changeable history of the Baltic Sea, the initial freshwater system was connected to the North Sea about 8000 yr ago and the modern brackish-marine setting (Littorina Sea) was established. Today, a relatively stable stratification developed in the water column of the deep basins due to salinity differences. Stratification is only occasionally interrupted by mixing events, and controls nutrient availability and growth of specifically adapted microorganisms and algae. We studied bacteriohopanepolyols (BHPs), lipids of specific bacterial groups, in a sediment core from the Central Baltic Sea (Gotland Deep) and found considerable differences between the distinct stages of the Baltic Sea's history. Individual BHP structures indicate contributions from as yet unknown redoxcline-specific bacteria (bacteriohopanetetrol isomer), methanotrophic bacteria (35-aminobacteriohopanetetrol), cyanobacteria (bacteriohopanetetrol cyclitol ether isomer) and, through allochthonous input after the Littorina transgression, from soil bacteria (adenosylhopane), whereas the origin of other BHPs in the core has still to be identified. Notably high BHP abundances were observed in the deposits of the brackish-marine Littorina phase, particularly in laminated sediment layers. Because these sediments record periods of stable water column stratification, bacteria specifically adapted to these conditions may account for the high portions of BHPs. An additional and/or accompanying source may be nitrogen-fixing (cyano)bacteria, which is indicated by a good correlation of BHP abundances with C org and δ 15 N.

Description: Publication year: 2012 Source: Cell Reports Sang Mi Shim, Won Jae Lee, Youngdoo Kim, Jong Wook Chang, Sungmin Song, Yong-Keun Jung The ubiquitin-proteasome system is essential for maintaining protein homeostasis. However, proteasome dysregulation in chronic diseases is poorly understood. Through genome-wide cell-based screening using 5,500 cDNAs, a signaling pathway leading to NFκB activation was selected as an inhibitor of 26S proteasome. TNF-α increased S5b (HGNC symbol PSMD5; hereafter S5b/PSMD5) expression via NFκB, and the surplus S5b/PSMD5 directly inhibited 26S proteasome assembly and activity. Downregulation of S5b/PSMD5 abolished TNF-α-induced proteasome inhibition. TNF-α enhanced the interaction of S5b/PSMD5 with S7/PSMC2 in nonproteasome complexes, and interference of this interaction rescued TNF-α-induced proteasome inhibition. Transgenic mice expressing S5b/PSMD5 exhibited a reduced life span and premature onset of aging-related phenotypes, including reduced proteasome activity in their tissues. Conversely, S5b/PSMD5 deficiency in Drosophila melanogaster ameliorated the tau rough eye phenotype, enhanced proteasome activity, and extended the life span of tau flies. These results reveal the critical role of S5b/PSMD5 in negative regulation of proteasome by TNF-α/NFκB and provide insights into proteasome inhibition in human disease. Graphical abstract Graphical Abstract Highlights ► Proteasome-inhibitory TNF-α/NFκB was found by cell-based functional screening ► TNF-α-induced S5b reduces proteasome activity by interfering with assembly ► Interaction of S5b with S7 is critical for TNF-α-induced proteasome inhibition ► S5b deficiency rescues tauopathy and excess S5b inhibits proteasome in animal models

Description: Publication year: 2012 Source: Cell Reports Charles A. Easley, Bart T. Phillips, Megan M. McGuire, Jennifer M. Barringer, Hanna Valli, Brian P. Hermann, Calvin R. Simerly, Aleksander Rajkovic, Toshio Miki, Kyle E. Orwig, Gerald P. Schatten Human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) have been shown to differentiate into primordial germ cells (PGCs) but not into spermatogonia, haploid spermatocytes, or spermatids. Here, we show that hESCs and hiPSCs differentiate directly into advanced male germ cell lineages, including postmeiotic, spermatid-like cells, in vitro without genetic manipulation. Furthermore, our procedure mirrors spermatogenesis in vivo by differentiating PSCs into UTF1-, PLZF-, and CDH1-positive spermatogonia-like cells; HIWI- and HILI-positive spermatocyte-like cells; and haploid cells expressing acrosin, transition protein 1, and protamine 1 (proteins that are uniquely found in spermatids and/or sperm). These spermatids show uniparental genomic imprints similar to those of human sperm on two loci: H19 and IGF2 . These results demonstrate that male PSCs have the ability to differentiate directly into advanced germ cell lineages and may represent a novel strategy for studying spermatogenesis in vitro. Graphical abstract Graphical Abstract Highlights ► In vitro culture induces germ cell differentiation of hPSCs ► hPSCs differentiate into spermatogonia, spermatocytes, and haploid spermatids ► Haploid spermatids have uniparental imprints similar to fertile human sperm

Description: Publication year: 2012 Source: Cell Reports Xin Hui Derryn Chan, Srikanth Nama, Felicia Gopal, Pamela Rizk, Srinivas Ramasamy, Gopinath Sundaram, Ghim Siong Ow, Ivshina Anna Vladimirovna, Vivek Tanavde, Johannes Haybaeck, Vladimir Kuznetsov, Prabha Sampath Malignant gliomas are the most aggressive forms of brain tumors, associated with high rates of morbidity and mortality. Recurrence and tumorigenesis are attributed to a subpopulation of tumor-initiating glioma stem cells (GSCs) that are intrinsically resistant to therapy. Initiation and progression of gliomas have been linked to alterations in microRNA expression. Here, we report the identification of microRNA-138 (miR-138) as a molecular signature of GSCs and demonstrate a vital role for miR-138 in promoting growth and survival of bona fide tumor-initiating cells with self-renewal potential. Sequence-specific functional inhibition of miR-138 prevents tumorsphere formation in vitro and impedes tumorigenesis in vivo. We delineate the components of the miR-138 regulatory network by loss-of-function analysis to identify specific regulators of apoptosis. Finally, the higher expression of miR-138 in GSCs compared to non-neoplastic tissue and association with tumor recurrence and survival highlights the clinical significance of miR-138 as a prognostic biomarker and a therapeutic target for treatment of malignant gliomas. Graphical abstract Graphical Abstract Highlights ► MicroRNA-138 is a molecular signature of glioma stem cells ► Functional inhibition of miR-138 leads to apoptotic death of glioma stem cells ► MicroRNA-138 is a prosurvival oncomiR for glioma stem cells ► MicroRNA-138 is a prognostic biomarker for malignant gliomas

Description: Present state of global wetland extent and wetland methane modelling: conclusions from a model intercomparison project (WETCHIMP) Biogeosciences Discussions, 9, 11577-11654, 2012 Author(s): J. R. Melton, R. Wania, E. L. Hodson, B. Poulter, B. Ringeval, R. Spahni, T. Bohn, C. A. Avis, D. J. Beerling, G. Chen, A. V. Eliseev, S. N. Denisov, P. O. Hopcroft, D. P. Lettenmaier, W. J. Riley, J. S. Singarayer, Z. M. Subin, H. Tian, S. Zürcher, V. Brovkin, P. M. van Bodegom, T. Kleinen, Z. C. Yu, and J. O. Kaplan Global wetlands are believed to be climate sensitive, and are the largest natural emitters of methane (CH 4 ). Increased wetland CH 4 emissions could act as a positive feedback to future warming. The Wetland and Wetland CH 4 Inter-comparison of Models Project (WETCHIMP) investigated our present ability to simulate large scale wetland characteristics and corresponding CH 4 emissions. To ensure inter-comparability, we used a common experimental protocol driving all models with the same climate and carbon dioxide (CO 2 ) forcing datasets. The WETCHIMP experiments were conducted for model equilibrium states as well as transient simulations covering the last century. Sensitivity experiments investigated model response to changes in selected forcing inputs (precipitation, temperature, and atmospheric CO 2 concentration). Ten models participated, covering the spectrum from simple to relatively complex, including models tailored either for regional or global simulations. The models also varied in methods to calculate wetland size and location with some models simulating wetland area prognostically, while other models relied on remotely-sensed inundation datasets, or an approach intermediate between the two. Four major conclusions emerged from the project. First, the suite of models demonstrate extensive disagreement in their simulations of wetland areal extent and CH 4 emissions, in both space and time. Simple metrics of wetland area, such as the latitudinal gradient, show large variability, principally between models that use inundation dataset information and those that independently determine wetland area. Agreement between the models improves for zonally summed CH 4 emissions, but large variation between the models remains. For annual global CH 4 emissions, the models vary by ±40 % of the all model mean (190 Tg CH 4 yr −1 ). Second, all models show a strong positive response to increased atmospheric CO 2 concentrations (857 ppm) in both CH 4 emissions and wetland area. In response to increasing global temperatures (+3.4 % globally spatially uniform), on average, the models decreased wetland area and CH 4 fluxes, primarily in the tropics, but the magnitude and sign of the response varied greatly. Models were least sensitive to increased global precipitation (+3.9 % globally spatially uniform) with a consistent small positive response in CH 4 fluxes and wetland area. Results from the 20th century transient simulation show that interactions between climate forcings could have strong non-linear effects. Third, we presently do not have sufficient wetland methane observation datasets adequate to evaluate model fluxes at a spatial scale comparable to model grid cells (commonly 0.5°). This limitation severely restricts our ability to model global wetland CH 4 emissions with confidence. Our simulated wetland extents are also difficult to evaluate due to extensive disagreements between wetland mapping and remotely-sensed inundation datasets. And fourth, the large range in predicted CH 4 emission rates leads to the conclusion that there is both substantial parameter and structural uncertainty in large-scale CH 4 emission models, even after uncertainties in wetland areas are accounted for.

Description: Modeling benthic-pelagic nutrient exchange processes and porewater distributions in a seasonally-hypoxic sediment: evidence for massive phosphate release by Beggiatoa ? Biogeosciences Discussions, 9, 11517-11575, 2012 Author(s): A. W. Dale, V. J. Bertics, T. Treude, S. Sommer, and K. Wallmann This study presents benthic data from 12 samplings from February to December 2010 in a 2 m deep channel in the southwest Baltic Sea. In winter, the distribution of solutes in the porewater was strongly modulated by bioirrigation which efficiently flushed the upper 1 cm of sediment, leading to concentrations which varied little from bottom water values. Solute pumping by bioirrigation fell sharply in summer as the bottom waters became severely hypoxic (

Description: Belowground in situ redox dynamics and methanogenesis recovery in a degraded fen during dry-wet cycles and flooding Biogeosciences Discussions, 9, 11655-11704, 2012 Author(s): C. Estop-Aragonés, K.-H. Knorr, and C. Blodau Climate change induced drying and flooding may alter the redox conditions of organic matter decomposition in peat soils. The seasonal and intermittent changes in pore water solutes (NO 3 − , Fe 2+ , SO 4 2− , H 2 S, acetate) and dissolved soil gases (CO 2 , O 2 , CH 4 , H 2 ) under natural water table fluctuations were compared to the response under a reinforced drying and flooding in fen peats. Oxygen penetration during dryings led to CO 2 and CH 4 degassing and to a regeneration of dissolved electron acceptors (NO 3 − , Fe 3+ and SO 4 2− ). Drying intensity controlled the extent of the electron acceptor regeneration. Iron was rapidly reduced and sulfate pools ~ 1 mmol L −1 depleted upon rewetting and CH 4 did not substantially accumulate until sulfate levels declined to ~ 100 μmoll −1 . The post-rewetting recovery of soil methane concentrations to levels ~ 80 μmoll −1 needed 40–50 days after natural drought. This recovery was prolonged after experimentally reinforced drought. A greater regeneration of electron acceptors during drying was not related to prolonged methanogenesis suppression after rewetting. Peat compaction, solid phase content of reactive iron and total reduced inorganic sulfur and organic matter content controlled oxygen penetration, the regeneration of electron acceptors and the recovery of CH 4 production, respectively. Methane production was maintained despite moderate water table decline of 20 cm in denser peats. Flooding led to accumulation of acetate and H 2 , promoted CH 4 production and strengthened the co-occurrence of iron and sulfate reduction and methanogenesis. Mass balances during drying and flooding indicated that an important fraction of the electron flow must have been used for the generation and consumption of electron acceptors in the solid phase or other mechanisms. In contrast to flooding, dry-wet cycles negatively affect methane production on a seasonal scale but this impact might strongly depend on drying intensity and on the peat matrix, whose structure and physical properties influence moisture content.

Description: Publication year: 2012 Source: Cell Reports Tamar Hashimshony, Florian Wagner, Noa Sher, Itai Yanai High-throughput sequencing has allowed for unprecedented detail in gene expression analyses, yet its efficient application to single cells is challenged by the small starting amounts of RNA. We have developed CEL-Seq, a method for overcoming this limitation by barcoding and pooling samples before linearly amplifying mRNA with the use of one round of in vitro transcription. We show that CEL-Seq gives more reproducible, linear, and sensitive results than a PCR-based amplification method. We demonstrate the power of this method by studying early C. elegans embryonic development at single-cell resolution. Differential distribution of transcripts between sister cells is seen as early as the two-cell stage embryo, and zygotic expression in the somatic cell lineages is enriched for transcription factors. The robust transcriptome quantifications enabled by CEL-Seq will be useful for transcriptomic analyses of complex tissues containing populations of diverse cell types. Graphical abstract Graphical Abstract Highlights ► We present CEL-Seq, a single-cell transcriptomics method using in vitro transcription ► We show that CEL-Seq is linear, sensitive, and reproducible ► CEL-Seq is highly multiplexed, allowing for the parallel examination of hundreds of cells ► We describe early C. elegans embryology at the single-cell transcriptomic level

Description: Modeling the sensitivity of soil mercury storage to climate-induced changes in soil carbon pools Biogeosciences Discussions, 9, 11403-11441, 2012 Author(s): O. Hararuk, D. Obrist, and Y. Luo Substantial amounts of mercury (Hg) in the terrestrial environment reside in soils and are associated with soil organic carbon (C) pools, where they accumulated due to increased atmospheric deposition due to anthropogenic activities. The purpose of this study was to examine potential sensitivity of surface soil Hg pools to global change variables, particularly affected by predicted changes in soil C pools, in the contiguous US. To investigate, we included a soil Hg component in the Community Land Model based on empirical statistical relationships between soil Hg / C ratios and precipitation, latitude and clay; and subsequently explored the sensitivity of soil C and soil Hg densities (i.e. areal-mass) to climate scenarios in which we altered annual precipitation, carbon dioxide (CO 2 ) concentrations, and temperature. Our model simulations showed that current sequestration of Hg in the contiguous US accounted for 15 230 metric tons of Hg in the top 0–40 cm of soils. In the simulations, these soil Hg pools were most sensitive to changes in precipitation because of strong effects on soil C pools plus a direct effect of precipitation on soil Hg / C ratios. Soil Hg pools were predicted to increase beyond present-day values following an increase in precipitation amounts and decrease following a reduction in precipitation. We found pronounced regional differences in sensitivity of soil Hg to precipitation, which were particularly high along high-precipitation areas along the West and East Coasts. Modeled increases in CO 2 concentrations to 700 ppm stimulated soil C and Hg densities, while increased air temperatures had small negative effects on soil C and Hg. The combined effects of increased CO 2 , increased temperature, and increased or decreased precipitation were strongly governed by precipitation and CO 2 showing pronounced regional patterns. Based on these results, we conclude that the combination of precipitation and CO 2 should be emphasized when assessing how climate-induced changes in soil C may affect sequestration of Hg in soils.

Description: Publication year: 2012 Source: Cell Reports Chandrama Mukherjee, Deepak P. Patil, Brian A. Kennedy, Baskar Bakthavachalu, Ralf Bundschuh, Daniel R. Schoenberg The notion that decapping leads irreversibly to messenger RNA (mRNA) decay was contradicted by the identification of capped transcripts missing portions of their 5′ ends and a cytoplasmic complex that can restore the cap on uncapped mRNAs. In this study, we used accumulation of uncapped transcripts in cells inhibited for cytoplasmic capping to identify the targets of this pathway. Inhibition of cytoplasmic capping results in the destabilization of some transcripts and the redistribution of others from polysomes to nontranslating messenger ribonucleoproteins, where they accumulate in an uncapped state. Only a portion of the mRNA transcriptome is affected by cytoplasmic capping, and its targets encode proteins involved in nucleotide binding, RNA and protein localization, and the mitotic cell cycle. The 3′ untranslated regions of recapping targets are enriched for AU-rich elements and microRNA binding sites, both of which function in cap-dependent mRNA silencing. These findings identify a cyclical process of decapping and recapping that we term cap homeostasis . Graphical abstract Graphical Abstract Highlights ► mRNAs that undergo cyclical loss and restoration of the cap are identified ► Some recapping targets are destabilized when cytoplasmic capping is inhibited ► Cytoplasmic capping functions in cycling mRNA between polysomes and mRNPs ► In cells inhibited for cytoplasmic capping, nontranslating mRNA is stored uncapped

Description: Publication year: 2012 Source: Cell Reports Adrienne E. Dubin, Manuela Schmidt, Jayanti Mathur, Matthew J. Petrus, Bailong Xiao, Bertrand Coste, Ardem Patapoutian Heightened nociceptor function caused by inflammatory mediators such as bradykinin (BK) contributes to increased pain sensitivity (hyperalgesia) to noxious mechanical and thermal stimuli. Although it is known that sensitization of the heat transducer TRPV1 largely subserves thermal hyperalgesia, the cellular mechanisms underlying mechanical hyperalgesia have been elusive. The role of the mechanically activated (MA) channel piezo2 (known as FAM38B) present in mammalian sensory neurons is unknown. We test the hypothesis that piezo2 activity is enhanced by BK, an algogenic peptide that induces mechanical hyperalgesia within minutes. Piezo2 current amplitude is increased and inactivation is slowed by bradykinin receptor beta 2 (BDKRB2) activation in heterologous expression systems. Protein kinase A (PKA) and protein kinase C (PKC) agonists enhance piezo2 activity. BDKRB2-mediated effects are abolished by PKA and PKC inhibitors. Finally, piezo2-dependent MA currents in a class of native sensory neurons are enhanced 8-fold by BK via PKA and PKC. Thus, piezo2 sensitization may contribute to PKA- and PKC-mediated mechanical hyperalgesia. Graphical abstract Graphical Abstract Highlights ► Bradykinin (BK) enhances mechanically activated (MA) piezo2 currents ► B2 receptor activation increases piezo2 current amplitude and slows inactivation ► Protein kinase A and protein kinase C inhibition abrogates both BK-induced effects ► MA currents dependent on piezo2 in DRG neurons are similarly modulated by BK

Description: Internal respiration of Amazon tree stems greatly exceeds external CO 2 efflux Biogeosciences Discussions, 9, 11443-11477, 2012 Author(s): A. Angert, J. Muhr, R. Negron Juarez, W. Alegria Muñoz, G. Kraemer, J. Ramirez Santillan, E. Barkan, S. Mazeh, J. Q. Chambers, and S. E. Trumbore Respiration in tree stems is an important component of forest carbon balance. The rate of CO 2 efflux from the stem has often been assumed to be a measure of stem respiration. However, recent work in temperate forests has demonstrated that stem CO 2 efflux can either overestimate or underestimate respiration rate, because of emission or removal of CO 2 by transport in xylem water. Here we used the ratio between CO 2 efflux and O 2 influx in stems of tropical forest trees to better understand respiration in an ecosystem that plays a key role in the global carbon cycle. This ratio, which we defined here as apparent respiratory quotient (ARQ), is expected to equal 1.0 if carbohydrates are the substrate for respiration, and the net transport of CO 2 in the xylem water is negligible. However, using a stem chamber approach to quantifying ARQ we found values of 0.66 ± 0.18. These low ARQ values indicate that a large portion of respired CO 2 (~35%) is not emitted locally, and is probably transported upward in the stem. ARQ values of 0.21 ± 0.10 were found for the steady-state gas concentration within the tree, sampled by in-stem equilibration probes. These lower values may result from the proximity to the xylem water stream. In contrast, we found ARQ values of 1.00 ± 0.13 for soil respiration. Our results indicate, for the first time, the existence of a~considerable internal flux of CO 2 in the stem of tropical trees. If the transported CO 2 is used in the canopy as a substrate for photosynthesis, it could account for several percent of the C fixed by the tree, and perhaps serve as a mechanism that buffers the response of the tree to changing CO 2 levels. Our results also indicate, in agreement with previous work, that the widely used CO 2 efflux approach for determining stem respiration is unreliable. We demonstrate here a field applicable approach for measuring the O 2 uptake rate, which we suggest to be a more appropriate method to estimate stem respiration rates.

Description: Mesozooplankton community development at elevated CO 2 concentrations: results from a mesocosm experiment in an Arctic fjord Biogeosciences Discussions, 9, 11479-11515, 2012 Author(s): B. Niehoff, N. Knüppel, M. Daase, J. Czerny, and T. Boxhammer The increasing CO 2 concentration in the atmosphere caused by burning fossil fuels leads to increasing p CO 2 and decreasing pH in the world oceans. These changes may have severe consequences for marine biota, especially in cold-water ecosystems due to higher solubility of CO 2 . However, studies on the response of mesozooplankton communities to elevated p CO 2 are yet lacking. In order to test whether abundance and taxonomic composition change with p CO 2 , we have sampled nine mesocosms, which were deployed in Kongsfjorden, an Arctic fjord at Svalbard, and were adjusted to eight CO 2 concentrations, initially ranging from 185 μatm to 1420 μatm. Samples were taken weekly over a six-week period with an Apstein net (55 μm mesh size) in all mesocosms and the surrounding fjord. In addition, sediment trap samples, taken every second day in the mesocosms, were analyzed to account for losses due to vertical migration and mortality. The taxonomic analysis revealed that meroplanktonic larvae (cirripeds, polychaetes, bivalves, gastropod, and decapods) dominated in the mesocosms while copepods ( Calanus spp., Oithona similis , Acartia longiremis and Microsetella norvegica ) were found in lower abundances. In the fjord copepods prevailed for most of our study. With time, abundance and taxonomic composition developed similarly in all mesocosms; the p CO 2 had no significant effect on the overall community structure. However, single taxa responded to elevated CO 2 concentrations. The ratio of cirripedia nauplii to cypris larvae, the next developmental stage, in the sediment traps averaged over the entire experiment increased with p CO 2 and this suggests that increased p CO 2 may have delayed their development. Also, the number of bivalves, averaged over the experimental period, decreased significantly with increasing p CO 2 . The nature of the CO 2 effect, either direct or indirect, remains open and needs to be addressed in future.

Description: Net community production and stoichiometry of nutrient consumption in a pelagic ecosystem of a northern high latitude fjord: mesocosm CO 2 perturbation study Biogeosciences Discussions, 9, 11705-11737, 2012 Author(s): A. Silyakova, R. G. J. Bellerby, J. Czerny, K. G. Schulz, G. Nondal, T. Tanaka, A. Engel, T. De Lange, and U. Riebesell Net community production (NCP) and ratios of carbon to nutrient consumption were studied during a large-scale mesocosm experiment on ocean acidification in Kongsfjorden, West Spitsbergen, during June–July 2010. Nutrient-deplete fjord water with natural phyto- and bacteriaplankton assemblages, enclosed in nine mesocosms of ~ 50 m 3 volume, was exposed to p CO 2 levels ranging from 185 to 1420 μatm on initial state. Mean values of p CO 2 levels during experiment ranged from 175 to 1085 μatm in different mesocosms. Phytoplankton growth was stimulated by nutrient addition. In this study NCP is estimated as a cumulative change in dissolved inorganic carbon concentrations. Stoichiometric couping between inorganic carbon and nutrient is shown as a ratio of a cumulative NCP to a cumulative change in inorganic nutrients. Three peaks of chlorophyll a concentration occurred during the experiment. Accordingly the experiment was divided in three phases. Overall cumulative NCP was similar in all mesocosms by the final day of experiment. However, NCP varied among phases, showing variable response to CO 2 perturbation. Carbon to nitrogen (C : N) and carbon to phosphorus (C : P) uptake ratios were estimated only for the period after nutrient addition (post-nutrient period). For the total post-nutrient period ratios were close to Redfield proportions, however varied from it in different phases. The response of C : N and C : P uptake ratios to CO 2 perturbation was different for three phases of the experiment, reflecting variable NCP and dependence on changing microbial community. Through the variable NCP, C : N and C : P uptake ratios for 31 days of the experiment we show a flexibility of biogeochemical response establishing a strong microbial loop in Kongsfjorden under different CO 2 scenarios.

Description: Influences of tidal energy advection on the surface energy balance in a mangrove forest Biogeosciences Discussions, 9, 11739-11765, 2012 Author(s): J. G. Barr, J. D. Fuentes, M. S. DeLonge, T. L. O'Halloran, D. Barr, and J. C. Zieman Mangrove forests are ecosystems susceptible to changing water levels and temperatures due to climate change as well as perturbations resulting from tropical storms. Numerical models can be used to project mangrove forest responses to regional and global environmental changes, and the reliability of these models depends on surface energy balance closure. However, for tidal ecosystems, the surface energy balance is complex because the energy transport associated with tidal activity remains poorly understood. This study aimed to quantify impacts of tidal flows on energy dynamics within a mangrove ecosystem. To address the research objective, an intensive study was conducted in a mangrove forest located along the Shark River in the Everglades National Park, FL. Forest-atmosphere energy exchanges were quantified with an eddy covariance system deployed on a flux tower. The lateral energy transport associated with tidal activity was calculated based on a coupled mass and energy balance approach. The mass balance included tidal flows and accumulation of water on the forest floor. The energy balance included temporal changes in enthalpy, resulting from tidal flows and temperature changes in the water column. By serving as a net sink or a source of available energy, tidal flows reduced the impact of high radiational loads on the mangrove forest. Including tidal energy advection in the surface energy balance improved the 30-min daytime energy closure from 73% to 82% over the study period. Also, the cumulative sum of energy output improved from 79% to 91% of energy input during the study period. Results indicated that tidal inundation provides an important mechanism for heat removal and that tidal exchange should be considered in surface energy budgets of coastal ecosystems. Results also demonstrated the importance of including tidal energy advection in mangrove biophysical models that are used for predicting ecosystem response to changing climate and regional freshwater management practices.

Description: Publication year: 2012 Source: Cell Reports Eneda Toska, Hayley A. Campbell, Jayasha Shandilya, Sarah J. Goodfellow, Paul Shore, Kathryn F. Medler, Stefan G.E. Roberts The Wilms' tumor 1 protein WT1 is a transcriptional regulator that is involved in cell growth and differentiation. The transcriptional corepressor BASP1 interacts with WT1 and converts WT1 from a transcriptional activator to a repressor. Here, we demonstrate that the N-terminal myristoylation of BASP1 is required in order to elicit transcriptional repression at WT1 target genes. We show that myristoylated BASP1 binds to nuclear PIP2, which leads to the recruitment of PIP2 to the promoter regions of WT1-dependent target genes. BASP1's myristoylation and association with PIP2 are required for the interaction of BASP1 with HDAC1, which mediates the recruitment of HDAC1 to the promoter and elicits transcriptional repression. Our findings uncover a role for myristoylation in transcription, as well as a critical function for PIP2 in gene-specific transcriptional repression through the recruitment of histone deacetylase. Graphical abstract Graphical Abstract Highlights ► Myristoylation of BASP1 is required for its function as a transcriptional repressor ► BASP1 myristoylation facilitates its interaction with nuclear PIP2 ► Myristoylation of BASP1 recruits HDAC1 to gene promoters through PIP2

Description: Publication year: 2012 Source: Cell Reports Dirk Wohlleber, Hamid Kashkar, Katja Gärtner, Marianne K. Frings, Margarete Odenthal, Silke Hegenbarth, Carolin Börner, Bernd Arnold, Günter Hämmerling, Bernd Nieswandt, Nico van Rooijen, Andreas Limmer, Karin Cederbrant, Mathias Heikenwalder, Manolis Pasparakis, Ulrike Protzer, Hans-Peter Dienes, Christian Kurts, Martin Krönke, Percy A. Knolle Viruses can escape cytotoxic T cell (CTL) immunity by avoiding presentation of viral components via endogenous MHC class I antigen presentation in infected cells. Cross-priming of viral antigens circumvents such immune escape by allowing noninfected dendritic cells to activate virus-specific CTLs, but they remain ineffective against infected cells in which immune escape is functional. Here, we show that cross-presentation of antigen released from adenovirus-infected hepatocytes by liver sinusoidal endothelial cells stimulated cross-primed effector CTLs to release tumor necrosis factor (TNF), which killed virus-infected hepatocytes through caspase activation. TNF receptor signaling specifically eliminated infected hepatocytes that showed impaired anti-apoptotic defense. Thus, CTL immune surveillance against infection relies on two similarly important but distinct effector functions that are both MHC restricted, requiring either direct antigen recognition on target cells and canonical CTL effector function or cross-presentation and a noncanonical effector function mediated by TNF. Graphical abstract Graphical Abstract Highlights ► Endothelial cell cross-presentation in infected tissue facilitates CTL immunity ► A CTL effector function acts independently of MHC recognition on target cells ► Viral infection sensitizes hepatocytes toward TNF-induced death

Description: Evaluation of a regional air-quality model with bi-directional NH 3 exchange coupled to an agro-ecosystem model Biogeosciences Discussions, 9, 11375-11401, 2012 Author(s): J. O. Bash, E. J. Cooter, R. L. Dennis, J. T. Walker, and J. E. Pleim Atmospheric ammonia (NH 3 ) is the primary atmospheric base and an important precursor for inorganic particulate matter and when deposited NH 3 contributes to surface water eutrophication, soil acidification and decline in species biodiversity. Flux measurements indicate that the air-surface exchange of NH 3 is bi-directional. However, the effects of bi-directional exchange, soil biogeochemistry and human activity are not parameterized in air quality models. The US Environmental Protection Agency (EPA)'s Community Multiscale Air-Quality (CMAQ) model with bi-directional NH 3 exchange has been coupled with the United States Department of Agriculture (USDA)'s Environmental Policy Integrated Climate (EPIC) agro-ecosystem model's nitrogen geochemistry algorithms. CMAQ with bi-directional NH 3 exchange coupled to EPIC connects agricultural cropping management practices to emissions and atmospheric concentrations of reduced nitrogen and models the biogeochemical feedback on NH 3 air-surface exchange. This coupled modeling system reduced the biases and error in NH x (NH 3 + NH 4 + ) wet deposition and in ambient aerosol concentrations in an annual 2002 Continental US (CONUS) domain simulation when compared to a 2002 annual simulation of CMAQ without bi-directional exchange. Fertilizer emissions estimated in CMAQ 5.0 with bi-directional exchange exhibits markedly different seasonal dynamics than the US EPA's National Emissions Inventory (NEI), with lower emissions in the spring and fall and higher emissions in July.

Description: Publication year: 2012 Source: Cell Reports María J. Pérez-García, Steven J. Burden Amyotrophic lateral sclerosis (ALS) is a devastating disease that progresses from detachment of motor nerve terminals to complete muscle paralysis and lethal respiratory failure within 5 years of diagnosis. Genetic studies have linked mutations in several genes to ALS, and mice bearing mutations in SOD1 recapitulate hallmark features of the disease. We investigated whether disease symptoms can be ameliorated by co-opting the retrograde signaling pathway that promotes attachment of nerve terminals to muscle. We crossed SOD1G93A mice with transgenic mice that express MuSK, a receptor tyrosine kinase that is required for retrograde signaling, and we used histological and behavioral assays to assess motor innervation and behavior. A 3-fold increase in MuSK expression delayed the onset and reduced the extent of muscle denervation, improving motor function for more than a month without altering survival. These findings suggest that increasing MuSK activity by pharmacological means has the potential to improve motor function in ALS. Graphical abstract Graphical Abstract Highlights ► An increase in MuSK expression delays the onset of muscle denervation in ALS mice ► Increased MuSK expression reduces the extent of denervation in ALS mice ► Increased MuSK expression improves motor function and behavior in ALS mice ► MuSK agonists have the potential to improve motor function in ALS

Description: Accounting for spatial variation in vegetation properties improves simulations of Amazon forest biomass and productivity in a global vegetation model Biogeosciences Discussions, 9, 11767-11813, 2012 Author(s): A. D. de Almeida Castanho, M. T. Coe, M. Heil Costa, Y. Malhi, D. Galbraith, and C. A. Quesada Dynamic vegetation models forced with spatially homogeneous biophysical parameters are capable of producing average productivity and biomass values for the Amazon basin forest biome that are close to the observed estimates, but are unable to reproduce the observed spatial variability. Recent observational studies have shown substantial regional spatial variability of above-ground productivity and biomass across the Amazon basin, which is believed to be primarily driven by soil physical and chemical properties. In this study, spatial heterogeneity of vegetation properties is added to the IBIS land surface model, and the simulated productivity and biomass of the Amazon basin are compared to observations from undisturbed forest. The maximum Rubisco carboxylation capacity ( V cmax ) and the woody biomass residence time (τ w ) were found to be the most important properties determining the modeled spatial variation of above-ground woody net primary productivity and biomass, respectively. Spatial heterogeneity of these properties may lead to a spatial variability of 1.8 times in the simulated woody net primary productivity and 2.8 times in the woody above-ground biomass. The coefficient of correlation between the modeled and observed woody productivity improved from 0.10 with homogeneous parameters to 0.73 with spatially heterogeneous parameters, while the coefficient of correlation between the simulated and observed woody above-ground biomass improved from 0.33 to 0.88. The results from our analyses with the IBIS dynamic vegetation model demonstrate that using single values for key ecological parameters in the tropical forest biome severely limits simulation accuracy. We emphasize that our approach must be viewed as an important first step and that a clearer understanding of the biophysical mechanisms that drive the spatial variability of carbon allocation, τ w and V cmax are necessary.

Description: Controls on the spatial distribution of oceanic δ 13 C DIC Biogeosciences Discussions, 9, 11843-11883, 2012 Author(s): P. B. Holden, N. R. Edwards, S. A. Müller, K. I. C. Oliver, R. M. Death, and A. Ridgwell We describe the design and evaluation of a large ensemble of coupled climate-carbon cycle simulations with the Earth-system model of intermediate complexity GENIE. This ensemble has been designed for application to a range of carbon cycle questions including utilizing carbon isotope (δ 13 C) proxy records to help constrain the state at the last glacial. Here we evaluate the ensemble by applying it to a transient experiment over the recent industrial era (1858 to 2008 AD). We employ singular vector decomposition and principal component emulation to investigate the spatial modes of ensemble-variability of oceanic dissolved inorganic carbon (DIC) δ 13 C, considering both the spun-up pre-industrial state and the transient change due to the 13 C Suess Effect. These analyses allow us to separate the natural and anthropogenic controls on the δ 13 C DIC distribution. We apply the same dimensionally reduced emulation techniques to consider the drivers of the spatial uncertainty in anthropogenic DIC. We show that the sources of uncertainty governing the uptake of anthropogenic δ 13 C DIC and DIC are quite distinct. Uncertainty in anthropogenic δ 13 C uptake is dominated by uncertainties in air-sea gas exchange, which explains 63% of modelled variance. This mode of variability is absent from the ensemble variability in CO 2 uptake, which is rather driven by uncertainties in ocean parameters that control mixing of intermediate and surface waters. Although the need to account for air-sea gas exchange is well known, these results suggest that, to leading order, uncertainties in the 13 C Suess effect and anthropogenic CO 2 ocean-uptake are governed by different processes. This illustrates the difficulties in reconstructing one from the other and furthermore highlights the need for improved spatial coverage of both δ 13 C DIC and DIC observations to better constrain the ocean sink of anthropogenic CO 2 .

Description: A simple method for air/sea gas exchange measurement in mesocosms and its application in carbon budgeting Biogeosciences Discussions, 9, 11989-12017, 2012 Author(s): J. Czerny, K. G. Schulz, A. Ludwig, and U. Riebesell Mesocosms as large experimental vessels principally provide the opportunity of performing elemental budget calculations e.g. to derive net biological turnover rates. However, the system is in most cases not closed at the water surface and gases can exchange with the atmosphere. Previous attempts to budget carbon pools in mesocosms relied on educated guesses concerning the exchange of CO 2 with the atmosphere. Nevertheless, net primary production rates derived from these budget calculations were, despite large uncertainties in air/sea gas exchange, often more reasonable than cumulative extrapolations of bioassays. While bioassays have limitations representing the full spectrum of trophic levels and abiotic conditions inside the mesocosms, calculating dissolved inorganic carbon uptake inside the mesocosms has the potential to deliver net community production rates representative of the enclosed system. Here, we present a simple method for precise determination of air/sea gas exchange velocities in mesocosms using N 2 O as a deliberate tracer. Beside the application for carbon budgeting, exchange velocities can be used to calculate exchange rates of any gas of known concentration, e.g. to calculate aquatic production rates of climate relevant trace gases. Using an arctic (Kiel Off Shore Mesocosms for future Ocean Simulation) mesocosm experiment as an exemplary dataset, it is shown that application of the presented method largely improves accuracy of carbon budget estimates. Methodology of manipulation, measurement, data processing and conversion to CO 2 fluxes are explained. A theoretical discussion of prerequisites for precise gas exchange measurements provides a guideline for the applicability of the method under various experimental conditions.

Description: Publication year: 2012 Source: FEBS Open Bio Tadanobu Takahashi, Chairul A. Nidom, Mai thi QuynhLe, Takashi Suzuki, Yoshihiro Kawaoka Avian influenza A viruses (IAVs) and human 1918, 1957, and 1968 pandemic IAVs all have neuraminidases (NAs) that are stable at low pH sialidase activity, yet most human epidemic IAVs do not. We examined the pH stability of H5N1 highly pathogenic avian IAV (HPAI) NAs and identified amino acids responsible for conferring stability at low pH. We found that, unlike other avian viruses, most H5N1 IAVs isolated since 2003 had NAs that were unstable at low pH, similar to human epidemic IAVs. These H5N1 viruses are thus already human virus-like and, therefore, have the frequent infections of humans. Highlights ▸ All neuraminidases (NAs) of avian influenza A viruses (IAVs) are stable at low pH. ▸ Human 1918, 1957, and 1968 pandemic IAVs also have NAs that are stable at low pH. ▸ Most human epidemic IAVs have NAs that are unstable at low pH. ▸ The NAs of most H5N1 IAVs isolated since 2003 are unstable at low pH. ▸ Instability of H5N1 IAV NAs at low pH might explain frequent human infections.

Description: Element budgets in an Arctic mesocosm CO 2 perturbation study Biogeosciences Discussions, 9, 11885-11924, 2012 Author(s): J. Czerny, K. G. Schulz, T. Boxhammer, R. G. J. Bellerby, J. Büdenbender, A. Engel, S. A. Krug, A. Ludwig, K. Nachtigall, G. Nondal, B. Niehoff, A. Siljakova, and U. Riebesell Recent studies on the impacts of ocean acidification on pelagic communities have identified changes in carbon to nutrient dynamics with related shifts in elemental stoichiometry. In principle, mesocosm experiments provide the opportunity of determining the temporal dynamics of all relevant carbon and nutrient pools and, thus, calculating elemental budgets. In practice, attempts to budget mesocosm enclosures are often hampered by uncertainties in some of the measured pools and fluxes, in particular due to uncertainties in constraining air/sea gas exchange, particle sinking, and wall growth. In an Arctic mesocosm study on ocean acidification using KOSMOS ( K iel O ff- S hore M esocosms for future O cean S imulation) all relevant element pools and fluxes of carbon, nitrogen and phosphorus were measured, using an improved experimental design intended to narrow down some of the mentioned uncertainties. Water column concentrations of particulate and dissolved organic and inorganic constituents were determined daily. New approaches for quantitative estimates of material sinking to the bottom of the mesocosms and gas exchange in 48 h temporal resolution, as well as estimates of wall growth were developed to close the gaps in element budgets. Future elevated p CO 2 was found to enhance net autotrophic community carbon uptake in 2 of the 3 experimental phases but did not significantly affect particle elemental composition. Enhanced carbon consumption appears to result in accumulation of dissolved organic compounds under nutrient recycling summer conditions. This carbon over-consumption effect becomes evident from budget calculations, but was too small to be resolved by direct measurements of dissolved organics. The out-competing of large diatoms by comparatively small algae in nutrient uptake caused reduced production rates under future ocean CO 2 conditions in the end of the experiment. This CO 2 induced shift away from diatoms towards smaller phytoplankton and enhanced cycling of dissolved organics was pushing the system towards a retention type food chain with overall negative effects on export potential.

Description: Concentrations and fluxes of dissolved organic carbon in runoff from a forested catchment: insights from high frequency measurements Biogeosciences Discussions, 9, 11925-11959, 2012 Author(s): S. Strohmeier, K.-H. Knorr, M. Reichert, S. Frei, J. H. Fleckenstein, S. Peiffer, and E. Matzner Concentrations of dissolved organic carbon (DOC) in runoff from catchments are often subject to substantial short term variations. The aim of this study was to identify the spatial sources of DOC and the causes for short term variations in runoff from a forested catchment. Furthermore, we investigated the implication of short term variations for the calculation of annual runoff fluxes. High frequency measurements (30 min intervals) of DOC in runoff, of discharge and groundwater table were conducted for one year in the 4.2 km 2 forested Lehstenbach catchment, Germany. Riparian wetland soils represent about 30% of the catchment area. The quality of DOC was investigated by three dimensional fluorescence excitation-emission matrices in samples taken from runoff, deep groundwater and shallow groundwater from the riparian wetland soils. The concentrations of DOC in runoff were highly variable at an hourly to daily time scale, ranging from 2.6 mg l −1 to 34 mg l −1 with an annual average of 9.2 mg l −1 . The concentrations were positively related to discharge, with a pronounced, counter clockwise hysteresis. Relations of DOC to discharge were steeper in the summer/fall than in the winter/spring season. Dynamics of groundwater table, discharge, DOC concentrations and DOC quality parameters indicated that DOC in runoff originated mainly from the riparian wetland soils, both under low and high flow conditions. The annual export of DOC from the catchment was 84 kg C ha −1 yr −1 when calculated from the high frequency measurements. If the annual export was calculated by simulated random fortnightly samplings, the range was 47 to 124 kg C ha −1 yr −1 . Calculations of DOC export fluxes might result in significant errors when based on infrequent (e.g. fortnightly) sampling intervals. Future changes in the precipitation and discharge patterns will influence the DOC dynamics in this catchment, with largest effects in the summer season.

Description: Detection of large above ground biomass variability in lowland forest ecosystems by airborne LiDAR Biogeosciences Discussions, 9, 11815-11842, 2012 Author(s): J. Jubanski, U. Ballhorn, K. Kronseder, J. Franke, and F. Siegert Quantification of tropical forest Above Ground Biomass (AGB) over large areas as input for Reduced Emissions from Deforestation and forest Degradation (REDD+) projects and climate change models is challenging. This is the first study which attempts to estimate AGB and its variability across large areas of tropical lowland forests in Central Kalimantan (Indonesia) through correlating airborne Light Detection and Ranging (LiDAR) to forest inventory data. Two LiDAR height metrics were analysed and regression models could be improved through the use of LiDAR point densities as input ( R 2 = 0.88; n = 52). Surveying with a LiDAR point density per square meter of 2–4 resulted in the best cost-benefit ratio. We estimated AGB for 600 km of LiDAR tracks and showed that there exists a considerable variability of up to 140% within the same forest type due to varying environmental conditions. Impact from logging operations and the associated AGB losses dating back more than 10 yr could be assessed by LiDAR but not by multispectral satellite imagery. Comparison with a Landsat classification for a 1 million ha study area where AGB values were based on site specific field inventory data, regional literature estimates, and default values by the Intergovernmental Panel on Climate Change (IPCC) showed an overestimation of 46%, 102%, and 137%, respectively. The results show that AGB overestimation may lead to wrong GHG emission estimates due to deforestation in climate models. For REDD+ projects this leads to inaccurate carbon stock estimates and consequently to significantly wrong REDD+ based compensation payments.

Description: The distribution and species assembly of Japanese Protura collected from forest soils were examined using published databases and statistical analysis. We used records from 3110 sites where 71 taxa were found. The species richness of Protura ranged from one to 16 species, and TWINSPAN analysis of regional populations indicated that the northern and southern regions could be separated into distinct groups. Three major species assemblages were identified by cluster analysis from points containing more than six species. Three groups reflected historical migration from northern and western linkages to the Asian continent. The northern assemblage showed a negative correlation to winter minimum temperature and the other two assemblages exhibited relationships to precipitation and temperature. Vegetation was not responsible for proturan distribution. These results suggest that the history of Protura invasion explains the biogeography of these soil-based, small arthropods and also that climate change will induce a shift in the distribution of species irrespective of changes in vegetation type.

Description: Non-microbial methane formation in oxic soils Biogeosciences Discussions, 9, 11961-11987, 2012 Author(s): A. Jugold, F. Althoff, M. Hurkuck, M. Greule, J. Lelieveld, and F. Keppler Methane plays an important role as a radiatively and chemically active gas in our atmosphere. Until recently, sources of atmospheric methane in the biosphere have been attributed to strictly anaerobic microbial processes during degradation of organic matter. However, a large fraction of methane produced in the anoxic soil layers does not reach the atmosphere due to methanotrophic consumption in the overlaying oxic soil. Although methane fluxes from aerobic soils have been observed an alternative source other than methanogenesis has not been identified thus far. Here we provide evidence for non-microbial methane formation in soils under oxic conditions. We found that soils release methane upon heating and other environmental factors like ultraviolet irradiation, and drying-rewetting cycles. We suggest that chemical formation of methane during degradation of soil organic matter may represent the missing soil source that is needed to fully understand the complete methane cycle within the pedosphere. Although the emission fluxes are relatively low when compared to those from wetlands, they may be important in warm and wet regions subjected to ultraviolet radiation. We suggest that this methane source is highly sensitive to global change.