ALBERT

Description: Connections between vegetation and soil thermal dynamics are critical for estimating the vulnerability of permafrost to thaw with continued climate warming and vegetation changes. The interplay of complex biophysical processes results in a highly heterogeneous soil temperature distribution on small spatial scales. Moreover, the link between topsoil temperature and active layer thickness remains poorly constrained. Sixty-eight temperature loggers were installed at 1–3 cm depth to record the distribution of topsoil temperatures at the Trail Valley Creek study site in the northwestern Canadian Arctic. The measurements were distributed across six different vegetation types characteristic for this landscape. Two years of topsoil temperature data were analysed statistically to identify temporal and spatial characteristics and their relationship to vegetation, snow cover, and active layer thickness. The mean annual topsoil temperature varied between −3.7 and 0.1 ∘C within 0.5 km2. The observed variation can, to a large degree, be explained by variation in snow cover. Differences in snow depth are strongly related with vegetation type and show complex associations with late-summer thaw depth. While cold winter soil temperature is associated with deep active layers in the following summer for lichen and dwarf shrub tundra, we observed the opposite beneath tall shrubs and tussocks. In contrast to winter observations, summer topsoil temperature is similar below all vegetation types with an average summer topsoil temperature difference of less than 1 ∘C. Moreover, there is no significant relationship between summer soil temperature or cumulative positive degree days and active layer thickness. Altogether, our results demonstrate the high spatial variability of topsoil temperature and active layer thickness even within specific vegetation types. Given that vegetation type defines the direction of the relationship between topsoil temperature and active layer thickness in winter and summer, estimates of permafrost vulnerability based on remote sensing or model results will need to incorporate complex local feedback mechanisms of vegetation change and permafrost thaw.

Description: In this paper, we quantify the CO2 and N2O emissions from denitrification over the Amazonian wetlands. The study concerns the entire Amazonian wetland ecosystem with a specific focus on three floodplain (FP) locations: the Branco FP, the Madeira FP and the FP alongside the Amazon River. We adapted a simple denitrification model to the case of tropical wetlands and forced it by open water surface extent products from the Soil Moisture and Ocean Salinity (SMOS) satellite. A priori model parameters were provided by in situ observations and gauging stations from the HYBAM Observatory. Our results show that the denitrification and the trace gas emissions present a strong cyclic pattern linked to the inundation processes that can be divided into three distinct phases: activation, stabilization and deactivation. We quantify the average yearly denitrification and associated emissions of CO2 and N2O over the entire watershed at 17.8 kgN ha−1 yr−1, 0.37 gC-CO2 m−2 yr−1 and 0.18 gN-N2O m−2 yr−1 respectively for the period 2011–2015. When compared to local observations, it was found that the CO2 emissions accounted for 0.01 % of the integrated ecosystem, which emphasizes the fact that minor changes to the land cover may induce strong impacts on the Amazonian carbon budget. Our results are consistent with the state of the art of global nitrogen models with a positive bias of 28 %. When compared to other wetlands in different pedoclimatic environments we found that the Amazonian wetlands have similar emissions of N2O with the Congo tropical wetlands and lower emissions than the temperate and tropical anthropogenic wetlands of the Garonne (France), the Rhine (Europe) and south-eastern Asia rice paddies. In summary our paper shows that a data-model-based approach can be successfully applied to quantify N2O and CO2 fluxes associated with denitrification over the Amazon basin. In the future, the use of higher-resolution remote sensing products from sensor fusion or new sensors like the Surface Water and Ocean Topography (SWOT) mission will permit the transposition of the approach to other large-scale watersheds in tropical environments.

Description: Anaerobic nitrate-dependent Fe(II) oxidation (NDFeO) is widespread in various aquatic environments and plays a major role in iron and nitrogen redox dynamics. However, evidence for truly enzymatic, autotrophic NDFeO remains limited, with alternative explanations involving the coupling of heterotrophic denitrification with the abiotic oxidation of structurally bound or aqueous Fe(II) by reactive intermediate nitrogen (N) species (chemodenitrification). The extent to which chemodenitrification is caused (or enhanced) by ex vivo surface catalytic effects has not been directly tested to date. To determine whether the presence of either an Fe(II)-bearing mineral or dead biomass (DB) catalyses chemodenitrification, two different sets of anoxic batch experiments were conducted: 2 mM Fe(II) was added to a low-phosphate medium, resulting in the precipitation of vivianite (Fe3(PO4)2), to which 2 mM nitrite (NO2-) was later added, with or without an autoclaved cell suspension (∼1.96×108 cells mL−1) of Shewanella oneidensis MR-1. Concentrations of nitrite (NO2-), nitrous oxide (N2O), and iron (Fe2+, Fetot) were monitored over time in both set-ups to assess the impact of Fe(II) minerals and/or DB as catalysts of chemodenitrification. In addition, the natural-abundance isotope ratios of NO2- and N2O (δ15N and δ18O) were analysed to constrain the associated isotope effects. Up to 90 % of the Fe(II) was oxidized in the presence of DB, whereas only ∼65 % of the Fe(II) was oxidized under mineral-only conditions, suggesting an overall lower reactivity of the mineral-only set-up. Similarly, the average NO2- reduction rate in the mineral-only experiments (0.004±0.003 mmol L−1 d−1) was much lower than in the experiments with both mineral and DB (0.053±0.013 mmol L−1 d−1), as was N2O production (204.02±60.29 nmol L−1 d−1). The N2O yield per mole NO2- reduced was higher in the mineral-only set-ups (4 %) than in the experiments with DB (1 %), suggesting the catalysis-dependent differential formation of NO. N-NO2- isotope ratio measurements indicated a clear difference between both experimental conditions: in contrast to the marked 15N isotope enrichment during active NO2- reduction (15εNO2=+10.3 ‰) observed in the presence of DB, NO2- loss in the mineral-only experiments exhibited only a small N isotope effect (

Description: Temperature appears to be the best predictor of species composition of planktonic foraminifera communities, making it possible to use their fossil assemblages to reconstruct sea surface temperature (SST) variation in the past. However, the role of other environmental factors potentially modulating the spatial and vertical distribution of planktonic foraminifera species is poorly understood. This is especially relevant for environmental factors affecting the subsurface habitat. If such factors play a role, changes in the abundance of subsurface-dwelling species may not solely reflect SST variation. In order to constrain the effect of subsurface parameters on species composition, we here characterize the vertical distribution of living planktonic foraminifera community across an east–west transect through the subtropical South Atlantic Ocean, where SST variability was small, but the subsurface water mass structure changed dramatically. Four planktonic foraminifera communities could be identified across the top 700 m of the transect. Gyre and Agulhas Leakage surface faunas were predominantly composed of Globigerinoides ruber, Globigerinoides tenellus, Trilobatus sacculifer, Globoturborotalita rubescens, Globigerinella calida, Tenuitella iota, and Globigerinita glutinata, and these only differed in terms of relative abundances (community composition). Upwelling fauna was dominated by Neogloboquadrina pachyderma, Neogloboquadrina incompta, Globorotalia crassaformis, and Globorotalia inflata. Thermocline fauna was dominated by Tenuitella fleisheri, Globorotalia truncatulinoides, and Globorotalia scitula in the west and by G. scitula only in the east. The largest part of the standing stock was consistently found in the surface layer, but SST was not the main predictor of species composition either for the depth-integrated fauna across the stations or at individual depth layers. Instead, we identified a pattern of vertical stacking of different parameters controlling species composition, reflecting different aspects of the pelagic habitat. Whereas productivity appears to dominate in the mixed layer (0–60 m), physical properties (temperature, salinity) become important at intermediate depths and in the subsurface, a complex combination of factors including oxygen concentration is required to explain the assemblage composition. These results indicate that the seemingly straightforward relationship between assemblage composition and SST in sedimentary assemblages reflects vertically and seasonally integrated processes that are only indirectly linked to SST. It also implies that fossil assemblages of planktonic foraminifera should also contain a signature of subsurface processes, which could be used for paleoceanographic reconstructions.

Description: Light-use efficiency defines the ability of primary producers to convert sunlight energy to primary production and is computed as the ratio between the gross primary production and the intercepted photosynthetic active radiation. While this measure has been applied broadly within terrestrial ecology to investigate habitat resource-use efficiency, it remains underused within the aquatic realm. This report provides a conceptual framework to compute hourly and daily light-use efficiency using underwater O2 eddy covariance, a recent technological development that produces habitat-scale rates of primary production under unaltered in situ conditions. The analysis, tested on two benthic flux datasets, documents that hourly light-use efficiency may approach the theoretical limit of 0.125 O2 per photon under low-light conditions, but it decreases rapidly towards the middle of the day and is typically 10-fold lower on a 24 h basis. Overall, light-use efficiency provides a useful measure of habitat functioning and facilitates site comparison in time and space.

Description: The CloudRoots field experiment was designed to obtain a comprehensive observational dataset that includes soil, plant, and atmospheric variables to investigate the interaction between a heterogeneous land surface and its overlying atmospheric boundary layer at the sub-hourly and sub-kilometre scale. Our findings demonstrate the need to include measurements at leaf level to better understand the relations between stomatal aperture and evapotranspiration (ET) during the growing season at the diurnal scale. Based on these observations, we obtain accurate parameters for the mechanistic representation of photosynthesis and stomatal aperture. Once the new parameters are implemented, the model reproduces the stomatal leaf conductance and the leaf-level photosynthesis satisfactorily. At the canopy scale, we find a consistent diurnal pattern on the contributions of plant transpiration and soil evaporation using different measurement techniques. From highly resolved vertical profile measurements of carbon dioxide (CO2) and other state variables, we infer a profile of the CO2 assimilation in the canopy with non-linear variations with height. Observations taken with a laser scintillometer allow us to quantify the non-steadiness of the surface turbulent fluxes during the rapid changes driven by perturbation of photosynthetically active radiation by cloud flecks. More specifically, we find 2 min delays between the cloud radiation perturbation and ET. To study the relevance of advection and surface heterogeneity for the land–atmosphere interaction, we employ a coupled surface–atmospheric conceptual model that integrates the surface and upper-air observations made at different scales from leaf to the landscape. At the landscape scale, we calculate a composite sensible heat flux by weighting measured fluxes with two different land use categories, which is consistent with the diurnal evolution of the boundary layer depth. Using sun-induced fluorescence measurements, we also quantify the spatial variability of ET and find large variations at the sub-kilometre scale around the CloudRoots site. Our study shows that throughout the entire growing season, the wide variations in stomatal opening and photosynthesis lead to large diurnal variations of plant transpiration at the leaf, plant, canopy, and landscape scales. Integrating different advanced instrumental techniques with modelling also enables us to determine variations of ET that depend on the scale where the measurement were taken and on the plant growing stage.

Description: Background HMGCR, SCAP, SREBF1, SREBF2 and TBL2 are well-known genes that are involved in the process of lipid metabolism. However, it is not known whether epigenetic changes of these genes are associated with lipid metabolism. In this study, the methylation levels of the HMGCR, SCAP, SREBF1, SREBF2 and TBL2 genes were analyzed between samples from a hyper-low-density lipoprotein cholesterolemia (hyper-LDL) group and a control group to examine the association between the methylation levels of these genes and the risk of hyper-LDL. Methods In this study, a case-control approach was used to explore the association between DNA methylation and hyper-LDL. The DNA methylation levels of HMGCR, SCAP, SREBF1, SREBF2 and TBL2 genes and 231 CpG sites in the promoter regions of these genes were measured in 98 hyper-LDL participants and 89 participants without hypo-LDL. Results Compared with participants without hyper-LDL, patients with hyper-LDL TBL2 gene had lower methylation levels (11.93 vs. 12.02, P = 0.004). The methylation haplotypes with significant abundance in the TBL2 gene are tcttttttttt (P = 0.034), ctttttttcct (P = 0.025), ctctttctttt (P = 0.040), ccttttttttt (P = 0.028), and tctttttttttttttt. Conclusion The study demonstrates that participants with hyper-LDL have lower methylation of TBL2. The results suggest that DNA methylation of TBL2 can decrease the risk for hyper-LDL in humans.

Description: In the western Mediterranean Sea, Levantine intermediate waters (LIW), which circulate below the surface productive zone, progressively accumulate nutrients along their pathway from the Tyrrhenian Sea to the Algerian Basin. This study addresses the role played by diffusion in the nutrient enrichment of the LIW, a process particularly relevant inside step-layer structures extending down to deep waters – structures known as thermohaline staircases. Profiling float observations confirmed that staircases develop over epicentral regions confined in large-scale circulation features and maintained by saltier LIW inflows on the periphery. Thanks to a high profiling frequency over the 4-year period 2013–2017, float observations reveal the temporal continuity of the layering patterns encountered during the cruise PEACETIME and document the evolution of layer properties by about +0.06 ∘C in temperature and +0.02 in salinity. In the Algerian Basin, the analysis of in situ lateral density ratios untangled double-diffusive convection as a driver of thermohaline changes inside epicentral regions and isopycnal diffusion as a driver of heat and salt exchanges with the surrounding sources. In the Tyrrhenian Sea, the nitrate flux across thermohaline staircases, as opposed to the downward salt flux, contributes up to 25 % of the total nitrate pool supplied to the LIW by vertical transfer. Overall, however, the nutrient enrichment of the LIW is driven mostly by other sources, coastal or atmospheric, as well as by inputs advected from the Algerian Basin.

Description: Peatlands store ∼ 20 %–30 % of the global soil organic carbon stock and are an important source of dissolved organic carbon (DOC) for inland waters. Recent improvements for in situ optical monitoring revealed that the DOC concentration in streams draining peatlands is highly variable, showing seasonal variation and short and intense DOC concentration peaks. This study aimed to statistically determine the variables driving stream DOC concentration variations at seasonal and event scales. Two mountainous peatlands (one fen and one bog) were monitored in the French Pyrenees to capture their outlet DOC concentration variability at a high-frequency rate (30 min). Abiotic variables including precipitation, stream temperature and water level, water table depth, and peat water temperature were also monitored at high frequency and used as potential predictors to explain DOC concentration variability. Results show that at both sites DOC concentration time series can be decomposed into a seasonal baseline interrupted by many short and intense peaks of higher concentrations. The DOC concentration baseline is driven, at the seasonal scale, by peat water temperature. At the event scale, DOC concentration increases are mostly driven by a rise in the water table within the peat at both sites. Univariate linear models between DOC concentration and peat water temperature or water table increases show greater efficiency at the fen site. Water recession times were derived from water level time series using master recession curve coefficients. They vary greatly between the two sites but also within one peatland site. They partly explain the differences between DOC dynamics in the studied peatlands, including peat porewater DOC concentrations and the links between stream DOC concentration and water table rise within the peatlands. This highlights that peatland complexes are composed of a mosaic of heterogeneous peat units distinctively producing or transferring DOC to streams.

Description: Anoxic sediments, as compared to oxic settings, encompass a much higher proportion of relatively labile and thus more reactive organic matter, naturally giving rise to structural changes of the organic molecules themselves, as well as cross-linking between them (e.g., through reactive sulfur species). Both processes transform the original biomolecules into geomolecules. For the oxic environment, these intermolecular and intramolecular transformations also operate, but cross-linking may be less important since the labile, reactive component is rapidly removed. As such, one may expect a structurally better preservation of the more refractory initial biomolecules in the oxic environment. To test this hypothesis, initially identical biomolecules need to be compared between different preservational environments. Here, we use the species-specific morphology of organic microfossils to assure a single initial biosynthetic product (the cysts of the fossil dinoflagellate species Thalassiphora pelagica) for comparison. We assess the macromolecular structures of cysts from the Eocene (∼40 Ma) sulfidic Rhine Graben and the oxic Kerguelen Plateau and compare them with each other and the structures of recent cysts. While between the sites the T. pelagica cysts are morphologically identical and show no signs of morphological modification, pyrolysis gas chromatography mass spectroscopy and micro Fourier transform infrared analyses show that their macromolecular characteristics are strongly different. Comparison with recent cysts shows that the cysts deposited in the sulfidic Rhine Graben show a strong additional contribution of long-chain aliphatic moieties and thus less diagenetic intermolecular cross-linking. The presence of organic sulfur identifies natural volcanization as one of the diagenetic processes. Furthermore, we observe a loss of bound oxygen and no trace of the original carbohydrate signature of the cyst wall biomacromolecule. The material deposited in the oxic sediments of the Kerguelen Plateau shows no traces of sulfurization. It shows a minor contribution of short carbon chains only and thus less diagenetic intermolecular cross-linking. Furthermore, a carbohydrate signature was still preserved evidencing a better molecular preservation of the initial biomacromolecule, supporting our initial hypothesis. This shows that excellent morphological preservation does not imply excellent chemical preservation. It also leads to the conclusion that the best preservation of molecular structure is not necessarily where most organic matter gets preserved, which, in turn, is important for understanding the nature and fate of sedimentary organic matter and its isotopic signature.

Description: The most prolific acacias in southern Europe (Acacia dealbata, A. melanoxylon and A. longifolia) are rapidly spreading in its westernmost area: Portugal and NW Spain, where congeners with invasion potential are already established. We performed a bibliographic search of acacia invasions in southern Europe and used spatial data on acacia distribution and abiotic parameters in Iberia to check the influence of abiotic factors on acacia invasion. According to our results, in Iberia A. dealbata and A. melanoxylon seem limited by high soil pH (pHCaCl2〉5.5), frequent frosts (〉21 to 40 d yr−1) and low annual precipitation (

Description: Boron isotope systematics of planktonic foraminifera from core-top sediments and culture experiments have been studied to investigate the sensitivity of δ11B of calcite tests to seawater pH. However, our knowledge of the relationship between δ11B and pH remains incomplete for many taxa. Thus, to expand the potential scope of application of this proxy, we report δ11B data for seven different species of planktonic foraminifera from sediment core tops. We utilize a method for the measurement of small samples of foraminifera and calculate the δ11B-calcite sensitivity to pH for Globigerinoides ruber, Trilobus sacculifer (sacc or without sacc), Orbulina universa, Pulleniatina obliquiloculata, Neogloboquadrina dutertrei, Globorotalia menardii, and Globorotalia tumida, including for unstudied core tops and species. These taxa have diverse ecological preferences and are from sites that span a range of oceanographic regimes, including some that are in regions of air–sea equilibrium and others that are out of equilibrium with the atmosphere. The sensitivity of δ11Bcarbonate to δ11Bborate (e.g., Δδ11Bcarbonate∕Δδ11Bborate) in core tops is consistent with previous studies for T. sacculifer and G. ruber and close to unity for N. dutertrei, O. universa, and combined deep-dwelling species. Deep-dwelling species closely follow the core-top calibration for O. universa, which is attributed to respiration-driven microenvironments likely caused by light limitation and/or symbiont–host interactions. Our data support the premise that utilizing boron isotope measurements of multiple species within a sediment core can be utilized to constrain vertical profiles of pH and pCO2 at sites spanning different oceanic regimes, thereby constraining changes in vertical pH gradients and yielding insights into the past behavior of the oceanic carbon pumps.

Description: Carbon–nitrogen (C–N) interactions regulate N availability for plant growth and for emissions of nitrous oxide (N2O) and the uptake of carbon dioxide. Future projections of these terrestrial greenhouse gas fluxes are strikingly divergent, leading to major uncertainties in projected global warming. Here we analyse the large increase in terrestrial N2O emissions over the past 21 000 years as reconstructed from ice-core isotopic data and presented in part 1 of this study. Remarkably, the increase occurred in two steps, each realized over decades and within a maximum of 2 centuries, at the onsets of the major deglacial Northern Hemisphere warming events. The data suggest a highly dynamic and responsive global N cycle. The increase may be explained by an increase in the flux of reactive N entering and leaving ecosystems or by an increase in N2O yield per unit N converted. We applied the LPX-Bern dynamic global vegetation model in deglacial simulations forced with Earth system model climate data to investigate N2O emission patterns, mechanisms, and C–N coupling. The N2O emission changes are mainly attributed to changes in temperature and precipitation and the loss of land due to sea-level rise. LPX-Bern simulates a deglacial increase in N2O emissions but underestimates the reconstructed increase by 47 %. Assuming time-independent N sources in the model to mimic progressive N limitation of plant growth results in a decrease in N2O emissions in contrast to the reconstruction. Our results appear consistent with suggestions of (a) biological controls on ecosystem N acquisition and (b) flexibility in the coupling of the C and N cycles during periods of rapid environmental change. A dominant uncertainty in the explanation of the reconstructed N2O emissions is the poorly known N2O yield per N lost through gaseous pathways and its sensitivity to soil conditions. The deglacial N2O record provides a constraint for future studies.

Description: Seamounts represent ideal systems to study the influence and interdependency of environmental gradients at a single geographic location. These topographic features represent a prominent habitat for various forms of life, including microbiota and macrobiota, spanning benthic as well as pelagic organisms. While it is known that seamounts are globally abundant structures, it still remains unclear how and to which extent the complexity of the sea floor is intertwined with the local oceanographic mosaic, biogeochemistry, and microbiology of a seamount ecosystem. Along these lines, the present study aimed to explore whether and to what extent seamounts can have an imprint on the microbial community composition of seawater and of sessile benthic invertebrates, sponges. For our high-resolution sampling approach of microbial diversity (16S rRNA gene amplicon sequencing) along with measurements of inorganic nutrients and other biogeochemical parameters, we focused on the Schulz Bank seamount ecosystem, a sponge ground ecosystem which is located on the Arctic Mid-Ocean Ridge. Seawater samples were collected at two sampling depths (mid-water, MW, and near-bed water, BW) from a total of 19 sampling sites. With a clustering approach we defined microbial microhabitats within the pelagic realm at Schulz Bank, which were mapped onto the seamount's topography and related to various environmental parameters (such as suspended particulate matter, SPM; dissolved inorganic carbon, DIC; silicate, SiO4-; phosphate, PO43-; ammonia, NH4+; nitrate, NO32-; nitrite, NO2-; depth; and dissolved oxygen, O2). The results of our study reveal a “seamount effect” (sensu stricto) on the microbial mid-water pelagic community at least 200 m above the sea floor. Further, we observed a strong spatial heterogeneity in the pelagic microbial landscape across the seamount, with planktonic microbial communities reflecting oscillatory and circulatory water movements, as well as processes of bentho-pelagic coupling. Depth, NO32-, SiO4-, and O2 concentrations differed significantly between the determined pelagic microbial clusters close to the sea floor (BW), suggesting that these parameters were presumably linked to changes in microbial community structures. Secondly, we assessed the associated microbial community compositions of three sponge species along a depth gradient of the seamount. While sponge-associated microbial communities were found to be mainly species-specific, we also detected significant intra-specific differences between individuals, depending on the pelagic near-bed cluster they originated from. The variable microbial phyla (i.e. phyla which showed significant differences across varying depth, NO32-, SiO4-, O2 concentrations, and different from local seawater communities) were distinct for every sponge species when considering average abundances per species. Variable microbial phyla included representatives of both those taxa traditionally counted for the variable community fraction and taxa counted traditionally for the core community fraction. Microbial co-occurrence patterns for the three examined sponge species Geodia hentscheli, Lissodendoryx complicata, and Schaudinnia rosea were distinct from each other. Over all, this study shows that topographic structures such as the Schulz Bank seamount can have an imprint (seamount effect sensu lato) on both the microbial community composition of seawater and sessile benthic invertebrates such as sponges by an interplay between the geology, physical oceanography, biogeochemistry, and microbiology of seamounts.

Description: The annual carbon and water dynamics of two eastern North American temperate forests were compared over a 6-year period from 2012 to 2017. The geographic location, forest age, soil, and climate were similar between the two stands; however, stand composition varied in terms of tree leaf-retention and shape strategy: one stand was a deciduous broadleaf forest, while the other was an evergreen needleleaf forest. The 6-year mean annual net ecosystem productivity (NEP) of the coniferous forest was slightly higher and more variable (218±109 g C m−2 yr−1) compared to that of the deciduous forest NEP (200±83 g C m−2 yr−1). Similarly, the 6-year mean annual evapotranspiration (ET) of the coniferous forest was higher (442±33 mm yr−1) than that of the deciduous forest (388±34 mm yr−1), but with similar interannual variability. Summer meteorology greatly impacted the carbon and water fluxes in both stands; however, the degree of response varied among the two stands. In general, warm temperatures caused higher ecosystem respiration (RE), resulting in reduced annual NEP values – an impact that was more pronounced at the deciduous broadleaf forest compared to the evergreen needleleaf forest. However, during warm and dry years, the evergreen forest had largely reduced annual NEP values compared to the deciduous forest. Variability in annual ET at both forests was related most to the variability in annual air temperature (Ta), with the largest annual ET observed in the warmest years in the deciduous forest. Additionally, ET was sensitive to prolonged dry periods that reduced ET at both stands, although the reduction at the coniferous forest was relatively larger than that of the deciduous forest. If prolonged periods (weeks to months) of increased Ta and reduced precipitation are to be expected under future climates during summer months in the study region, our findings suggest that the deciduous broadleaf forest will likely remain an annual carbon sink, while the carbon sink–source status of the coniferous forest remains uncertain.

Description: Aside from many well-known sources, the greenhouse gas methane (CH4) was recently discovered entrapped in the sediments of Swiss Alpine glacier forefields derived from calcareous bedrock. A first study performed in one glacial catchment indicated that CH4 was ubiquitous in sediments and rocks and was largely of thermogenic origin. Here, we present the results of a follow-up study that aimed at (1) determining the occurrence and origin of sediment-entrapped CH4 in other calcareous glacier forefields across Switzerland and (2) providing an inventory of this sediment-entrapped CH4, i.e., determining the contents and total mass of CH4 present, and its spatial distribution within and between five different Swiss glacier forefields situated on calcareous formations of the Helvetic nappes in the Central Alps. Sediment and bedrock samples were collected at high spatial resolution from the forefields of Im Griess, Griessfirn, Griessen, Wildstrubel, and Tsanfleuron glaciers, representing different geographic and geologic regions of the Helvetic nappes. We performed geochemical analyses on gas extracted from sediments and rocks, including the determination of CH4 contents, stable carbon-isotope analyses (δ13CCH4), and the determination of gas-wetness ratios (ratio of CH4 to ethane and propane contents). To estimate the total mass of CH4 entrapped in glacier-forefield sediments, the total volume of sediment was determined based on the measured forefield area and either literature values of mean sediment thickness or direct depth measurements using electrical resistivity tomography. Methane was found in all sediments (0.08–73.81 µg CH4 g−1 dry weight) and most rocks (0.06–108.58 µg CH4 g−1) collected from the five glacier forefields, confirming that entrapped CH4 is ubiquitous in these calcareous formations. Geochemical analyses further confirmed a thermogenic origin of the entrapped CH4 (average δ13CCH4 of sediment of −28.23 (± 3.42) ‰; average gas-wetness ratio of 75.2 (± 48.4)). Whereas sediment-entrapped CH4 contents varied moderately within individual forefields, we noted a large, significant difference in the CH4 content and total CH4 mass (range of 200–3881 t CH4) between glacier forefields at the regional scale. The lithology and tectonic setting within the Helvetic nappes appeared to be dominant factors determining rock and sediment CH4 contents. Overall, a substantial quantity of CH4 was found to be entrapped in Swiss calcareous glacier forefields. Its potential release and subsequent fate in this environment is the subject of ongoing studies.

Description: The dynamics of the physicochemical and biological parameters were followed during the decline of a Cymodocea nodosa meadow in the northern Adriatic Sea from July 2017 to October 2018. During the regular growth of C. nodosa from July 2017 to March 2018, the species successfully adapted to the changes in environmental conditions and prevented H2S accumulation by its reoxidation, supplying the sediment with O2 from the water column and/or leaf photosynthesis. The C. nodosa decline was most likely triggered in April 2018 when light availability to the plant was drastically reduced due to increased seawater turbidity that resulted from increased terrigenous input, indicated by a decrease in salinity accompanied with a substantial increase in particulate matter concentration, combined with resuspension of sediment and elevated autotrophic biomass. Light reduction impaired photosynthesis of C. nodosa and the oxidation capability of belowground tissue. Simultaneously, a depletion of oxygen due to intense oxidation of H2S occurred in the sediment, thus creating anoxic conditions in most of the rooted areas. These linked negative effects on the plant performance caused an accumulation of H2S in the sediments of the C. nodosa meadow. During the decay of aboveground and belowground tissues, culminating in August 2018, high concentrations of H2S were reached and accumulated in the sediment as well as in bottom waters. The influx of oxygenated waters in September 2018 led to the re-establishment of H2S oxidation in the sediment and remainder of the belowground tissue. Our results indicate that if disturbances of environmental conditions, particularly those compromising the light availability, take place during the recruitment phase of plant growth when metabolic needs are at a maximum and stored reserves minimal, a sudden and drastic decline of the seagrass meadow occurs.

Description: Many wetlands have been drained due to urbanization, agriculture, forestry or other purposes, which has resulted in a loss of their ecosystem services. To protect receiving waters and to achieve services such as flood control and storm water quality mitigation, new wetlands are created in urbanized areas. However, our knowledge of greenhouse gas exchange in newly created wetlands in urban areas is currently limited. In this paper we present measurements carried out at a created urban wetland in Southern Finland in the boreal climate. We conducted measurements of ecosystem CO2 flux and CH4 flux (FCH4) at the created storm water wetland Gateway in Nummela, Vihti, Southern Finland, using the eddy covariance (EC) technique. The measurements were commenced the fourth year after construction and lasted for 1 full year and two subsequent growing seasons. Besides ecosystem-scale fluxes measured by the EC tower, the diffusive CO2 and CH4 fluxes from the open-water areas (FwCO2 and FwCH4, respectively) were modelled based on measurements of CO2 and CH4 concentration in the water. Fluxes from the vegetated areas were estimated by applying a simple mixing model using the above-mentioned fluxes and the footprint-weighted fractional area. The half-hourly footprint-weighted contribution of diffusive fluxes from open water ranged from 0 % to 25.5 % in 2013. The annual net ecosystem exchange (NEE) of the studied wetland was 8.0 g C-CO2 m−2 yr−1, with the 95 % confidence interval between −18.9 and 34.9 g C-CO2 m−2 yr−1, and FCH4 was 3.9 g C-CH4 m−2 yr−1, with the 95 % confidence interval between 3.75 and 4.07 g C-CH4 m−2 yr−1. The ecosystem sequestered CO2 during summer months (June–August), while the rest of the year it was a CO2 source. CH4 displayed strong seasonal dynamics, higher in summer and lower in winter, with a sporadic emission episode in the end of May 2013. Both CH4 and CO2 fluxes, especially those obtained from vegetated areas, exhibited strong diurnal cycles during summer with synchronized peaks around noon. The annual FwCO2 was 297.5 g C-CO2 m−2 yr−1 and FwCH4 was 1.73 g C-CH4 m−2 yr−1. The peak diffusive CH4 flux was 137.6 nmol C-CH4 m−2 s−1, which was synchronized with the FCH4. Overall, during the monitored time period, the established storm water wetland had a climate-warming effect with 0.263 kg CO2-eq m−2 yr−1 of which 89 % was contributed by CH4. The radiative forcing of the open-water areas exceeded that of the vegetation areas (1.194 and 0.111 kg CO2-eq m−2 yr−1, respectively), which implies that, when considering solely the climate impact of a created wetland over a 100-year horizon, it would be more beneficial to design and establish wetlands with large patches of emergent vegetation and to limit the areas of open water to the minimum necessitated by other desired ecosystem services.

Description: Background: Despite their widespread use, the biological mechanisms underlying the efficacy of psychotropic drugs are still incompletely known; improved understanding of these is essential for development of novel more effective drugs and rational design of therapy. Given the large number of psychotropic drugs available and their differential pharmacological effects, it would be important to establish specific predictors of response to various classes of drugs. Results: To identify the molecular mechanisms that may initiate therapeutic effects, whole-genome expression profiling (using 324 Illumina Mouse WG-6 microarrays) of drug-induced alterations in the mouse brain was undertaken, with a focus on the time-course (1, 2, 4 and 8 h) of gene expression changes produced by eighteen major psychotropic drugs: antidepressants, antipsychotics, anxiolytics, psychostimulants and opioids. The resulting database is freely accessible at www.genes2mind.org. Bioinformatics approaches led to the identification of three main drug-responsive genomic networks and indicated neurobiological pathways that mediate the alterations in transcription. Each tested psychotropic drug was characterized by a unique gene network expression profile related to its neuropharmacological properties. Functional links that connect expression of the networks to the development of neuronal adaptations (MAPK signaling pathway), control of brain metabolism (adipocytokine pathway), and organization of cell projections (mTOR pathway) were found. Conclusions: The comparison of gene expression alterations between various drugs opened a new means to classify the different psychoactive compounds and to predict their cellular targets; this is well exemplified in the case of tianeptine, an antidepressant with unknown mechanisms of action. This work represents the first proof-of-concept study of a molecular classification of psychoactive drugs.

Description: Phage PhiC31 integrase integrates attB-containing plasmid into pseudo attP site in eukaryotic genomes in a unidirectional site-specific manner and maintains robust transgene expression. Few studies, however, explore its potential in livestock. This study aims to discover the molecular basis of PhiC31 integrase-mediated site-specific recombination in pig cells. We show that PhiC31 integrase can mediate site-specific transgene integration into the genome of pig kidney PK15 cells. Intramolecular recombination in pig PK15 cell line occurred at maximum frequency of 82% with transiently transfected attB- and attP-containing plasmids. An optimal molar ratio of pCMV-Int to pEGFP-N1-attB at 5:1 was observed for maximum number of cell clones under drug selection. Four candidate pseudo attP sites were identified by TAIL-PCR from those cell clones with single-copy transgene integration. Two of them gave rise to higher integration frequency occurred at 33%. 5[prime]and 3[prime]junction PCR showed that transgene integration mediated by PhiC31 integrase was mono-allelic. Micro- deletion and insertion were observed by sequencing the integration border, indicating that double strand break was induced by the recombination. We then constructed rescue reporter plasmids by ABI-REC cloning of the four pseudo attP sites into pBCPB + plasmid. Transfection of these rescue plasmids and pCMV-Int resulted in expected intramolecular recombination between attB and pseudo attP sites. This proved that the endogenous pseudo attP sites were functional substrates for PhiC31 integrase-mediated site-specific recombination. Two pseudo attP sites maintained robust extracellular and intracellular EGFP expression. Alamar blue assay showed that transgene integration into these specific sites had little effect on cell proliferation. This is the first report to document the potential use of PhiC31 integrase to mediate site-specific recombination in pig cells. Our work established an ideal model to study the position effect of identical transgene located in diverse chromosomal contexts. These findings also form the basis for targeted pig genome engineering and may be used to produce genetically modified pigs for agricultural and biomedical uses.

Description: Background: The molecular epidemiology of C. jejuni and C. coli clinical strains isolated from children with gastroenteritis, was investigated using the multilocus sequence typing method (MLST). This analysis establishes for the first time in Greece and constitutes an important tool for the epidemiological surveillance and control of Campylobacter infection in our country. Methods: The MLST genotypes were compared with those gained by other typing methods (HS-typing, PFGE and FlaA typing) and were also phylogenetically analyzed, in order to uncover genetic relationships. Results: Among 68 C. jejuni strains, 41 different MLST-Sequence Types (MLST-STs) were found. Fifty six strains or 34 MLST-STs could be sorted into 15 different MLST-Sequence Type Complexes (MLST-STCs), while twelve strains or seven MLST-STs did not match any of the MLST-STCs of the database. Twenty C. coli strains belonged to 14 different MLST-STs. Eleven MLST-STs were classified in the same MLST-STC (828), and three were unclassifiable. There was no significant association between the MLST-STs and the results of the other typing methods.Phylogenetic analysis revealed that some strains, classified to the species of C. jejuni, formed a separate, phylogenetically distinct group. In eight strains some alleles belonging to the taxonomic cluster of C. jejuni, were also detected in C. coli and vice versa, a phenomenon caused by the genetic mosaic encountered inside the genus Campylobacter. Conclusions: The MLST-ST determination proved to be a very useful tool for the typing as well as the identification of Campylobacter on the species level.

Description: Background: Opsins have been found in the majority of animals and their most apparent functions are related to vision and light-guided behaviour. As an increasing number of sequences have become available it has become clear that many opsin-like transcripts are expressed in tissues other than the eyes. Opsins can be divided into three main groups: rhabdomeric opsins (r-opsins), ciliary opsins (c-opsins) and group 4 opsins. In arthropods, the main focus has been on the r-opsins involved in vision. However, with increased sequencing it is becoming clear that arthropods also possess opsins of the c-type, group 4 opsins and the newly discovered arthropsins but the functions of these opsins are unknown in arthropods and data on their localisation is limited or absent. Results: We identified opsins from the spider Cupiennius salei and the onychophoran Euperipatoides kanangrensis and characterised the phylogeny and localisation of these transcripts. We recovered all known visual opsins in C. salei, and in addition found a peropsin, a c-opsin and an opsin resembling Daphnia pulex arthropsin. The peropsin was expressed in all eye types except the anterior median eyes. The arthropsin and the c-opsin were expressed in the central nervous system but not the eyes. In E. kanangrensis we found: a c-opsin; an opsin resembling D. pulex arthropsins; and an r-opsin with high sequence similarity to previously published onychophoran onychopsins. The E. kanangrensis c-opsin and onychopsin were expressed in both the eyes and the brain but the arthropsin only in the brain. Conclusion: Our novel finding that opsins of both the ciliary and rhabdomeric type are present in the onychophoran and a spider suggests that these two types of opsins were present in the last common ancestor of the Onychophora and Euarthropoda. The expression of the c-opsin in the eye of an onychophoran indicates that c-opsins may originally have been involved in vision in the arthropod clade. The lack of c-opsin expression in the spider retina suggests that the role for c-opsin in vision was lost in the euarthropods. Our discovery of arthropsin in onychophorans and spiders dates the emergence of arthropsin to the common ancestor of Onychophora and Euarthropoda and their expression in the brain suggests a non-visual function.

Description: Background: Statin-fibrate combination therapy has been used to treat patients with acute coronary syndrome (ACS) complicated by elevated triglycerides (TG) and decreased high density lipoprotein cholesterol (HDL-C). The purpose of this study was to evaluate the influence of the combination therapy on lipids profile and apolipoprotein A5 (apoA5) level in patients with ACS. Methods: One hundred and four patients with ACS were recruited and randomly assigned into two groups: one was statin group (n = 52), given atorvastatin (20 mg QN) or other statins with equivalent dosages; the other was combination group (n = 52), given the same dose of statin plus bezafibrate (200 mg BID). Follow-up visits were scheduled at the end of 6 and 12 weeks post treatment. Serum apoA5 levels were determined using a commercial available ELISA kit. Results: (1) Compared with that of statin monotherapy, statin-bezafibrate combination treatment not only resulted in a significant reduction of TG, TC and LDL-C levels , (all p 〈 0.05), but also led to increases in HDL-C and apoA5 levels (p 〈 0.05).(2) The percentage changes of TC, TG, LDL-C and apoA5 levels in both groups were even bigger at 12 weeks after treatment than that at 6 weeks.(all p 〈 0.05). Similarly, the rates of achieving lipid-control target were higher in statin-bezafibrate combination treatment group than those in statin monotherapy group (all p 〈 0.05).(3) Spearman rank correlation analysis showed that the pre-treatment apoA5 level was positively correlated with TG (r = 0.359, p = 0.009). However, a negative correlation was observed between apoA5 and TG (r = -0.329, p = 0.017) after 12 weeks treatment. Conclusions: Statin and fibrate combination therapy is more effective than statin alone in achieving a comprehensive lipid control for ACS patients. Serum apoA5 elevation after statin and fibrate combination treatment could be due to the synergistic effect of both drugs on hypertriglyceridemia control.

Description: Not all calcite ballast is created equal: differing effects of foraminiferan and coccolith calcite on the formation and sinking of aggregates Biogeosciences Discussions, 10, 14861-14885, 2013 Author(s): K. Schmidt, C. L. De La Rocha, M. Gallinari, and G. Cortese Correlation between particulate organic carbon (POC) and calcium carbonate sinking through the deep ocean has led to the idea that ballast provided by calcium carbonate is important for the export of POC from the surface ocean. While this idea is certainly to some extent true, it is worth considering in more nuance, for example, examining the different effects on the aggregation and sinking of POC of small, non-sinking calcite particles like coccoliths and large, rapidly sinking calcite like planktonic foraminiferan tests. We have done that here in a simple experiment carried out in roller tanks that allow particles to sink continuously without being impeded by container walls. Coccoliths were efficiently incorporated into aggregates that formed during the experiment, increasing their sinking speed compared to similarly sized aggregates lacking added calcite ballast. The foraminiferan tests, which sank as fast as 700 m d −1 , became associated with only very minor amounts of POC. In addition, when they collided with other, larger, foraminferan-less aggregates, they fragmented them into two smaller, more slowly sinking aggregates. While these effects were certainly exaggerated within the confines of the roller tanks, they clearly demonstrate that calcium carbonate ballast is not just calcium carbonate ballast- different forms of calcium carbonate ballast have notably different effects on POC aggregation, sinking, and export.

Description: Background: The geographic distribution of evolutionary lineages and the patterns of gene flow upon secondary contact provide insight into the process of divergence and speciation. We explore the evolutionary history of the common lizard Zootoca vivipara (= Lacerta vivipara) in the Iberian Peninsula and test the role of the Pyrenees and the Cantabrian Mountains in restricting gene flow and driving lineage isolation and divergence. We also assess patterns of introgression among lineages upon secondary contact, and test for the role of high-elevation trans-mountain colonisations in explaining spatial patterns of genetic diversity. We use mtDNA sequence data and genome-wide AFLP loci to reconstruct phylogenetic relationships among lineages, and measure genetic structure Results: The main genetic split in mtDNA corresponds generally to the French and Spanish sides of the Pyrenees as previously reported, in contrast to genome-wide AFLP data, which show a major division between NW Spain and the rest. Both types of markers support the existence of four distinct and geographically congruent genetic groups, which are consistent with major topographic barriers. Both datasets reveal the presence of three independent contact zones between lineages in the Pyrenean region, one in the Basque lowlands, one in the low-elevation mountains of the western Pyrenees, and one in the French side of the central Pyrenees. The latter shows genetic evidence of a recent, high-altitude trans-Pyrenean incursion from Spain into France. Conclusions: The distribution and age of major lineages is consistent with a Pleistocene origin and a role for both the Pyrenees and the Cantabrian Mountains in driving isolation and differentiation of Z. vivipara lineages at large geographic scales. However, mountain ranges are not always effective barriers to dispersal, and have not prevented a recent high-elevation trans-Pyrenean incursion that has led to asymmetrical introgression among divergent lineages. Cytonuclear discordance in patterns of genetic structure and introgression at contact zones suggests selection may be involved at various scales. Suture zones are important areas for the study of lineage formation and speciation, and our results show that biogeographic barriers can yield markedly different phylogeographic patterns in different vertebrate and invertebrate taxa.

Description: Background: Loss of CpG dinucleotides in genomic DNA through methylation-induced mutation is characteristic of vertebrates and plants. However, these and other eukaryotic phyla show a range of other dinucleotide frequency biases with currently uncharacterized underlying mutational or selection mechanisms. We developed a parameterized Markov process to identify what neighbour context-dependent mutations best accounted for patterns of dinucleotide frequency biases in genomic and cytoplasmically expressed mRNA sequences of different vertebrates, other eukaryotic groups and RNA viruses that infect them. Results: Consistently, 11- to 14-fold greater frequencies of the methylation-association mutation of C to T upstream of G (depicted C[rightwards arrow]T,G) than other transitions best modelled dinucleotide frequencies in mammalian genomic DNA. However, further mutations such as G[rightwards arrow]T,T (5-fold greater than the default transversion rate) were required to account for the full spectrum of dinucleotide frequencies in mammalian sequence datasets. Consistent with modeling predictions for these two mutations, instability of both CpG and CpT dinucleotides was identified through SNP frequency analysis of human DNA sequences. Different sets of context-dependent mutations were modelled in other eukaryotes with non-methylated genomic DNA. In contrast to genomic DNA, best-fit models of dinucleotide frequencies in transcribed RNA sequences expressed in the cytoplasm from all organisms were dominated by mutations that eliminated UpA dinucleotides, observations consistent with cytoplasmically driven selection for mRNA stability. Surprisingly, mRNA sequences from organisms with methylated genomes showed evidence for additional selection against CpG through further context-dependent mutations (eg. C[rightwards arrow]A,G). Similar mutation or selection processes were identified among single-stranded mammalian RNA viruses; these potentially account for their previously described but unexplained under-representations of CpG and UpA dinucleotides. Conclusions: Methods we have developed identify mutational processes and selection pressures in organisms provide new insights into nucleotide compositional constraints and a wealth of biochemical and evolutionarily testable predictions for the future.

Description: Background: Ramie fiber extracted from stem bark is one of the most important natural fibers. Drought is a main environment stress which severely inhibits the stem growth of ramie and leads to a decrease of the fiber yield. The drought stress-regulatory mechanism of ramie is poorly understood.Result: Using Illumina sequencing, approximately 4.8 and 4.7 million (M) 21-nt cDNA tags were respectively sequenced in the cDNA libraries derived from the drought-stressed ramie (DS) and the control ramie under well water condition (CO). The tags generated from the two libraries were aligned with ramie transcriptome to annotate their function and a total of 23,912 and 22,826 ramie genes were matched by these tags of DS and CO library, respectively. Comparison of gene expression level between CO and DS ramie based on the differences of tag frequencies appearing in the two libraries revealed that there were 1516 potential drought stress-responsive genes, in which 24 genes function as transcription factor (TF). Among these 24 TFs, the unigene19721 encoding the DELLA protein which is a key negative regulator in gibberellins (GAs) signal pathway was probably markedly up-regulated under water stress for a increase of tag abundance in DS library, which is possibly responsible for the inhibition of the growth of drought-stressed ramie. In order to validate the change of expression of these potential stress-responsive TFs under water deficit condition, the unigene19721 and another eleven potential stress-responsive TFs were chosen for further expression analysis in well-watered and drought-stressed ramie by real-time quantitative PCR (qRT-PCR) and the result showed that all 12 TFs were authentically involved in the response of drought stress. Conclusion: In this study, twelve TFs involving in the response of drought stress were first found by Illumina tag-sequencing and qRT-PCR in ramie. The discovery of these drought stress-responsive TFs will be helpful for further understanding the drought stress-regulatory mechanism of ramie and improving the drought tolerance ability of ramie.

Description: Background: The great majority of afferent neurons of insect legs project into their segmental ganglion. Intersegmental projections are rare and are only formed by sense organs associated with the basal joints of the legs. Such intersegmental projections never ascend as far as the brain and they form extensive ramifications within thoracic ganglia. A few afferents of chordotonal organs of the subcoxal joints ascend as far as the suboesophageal ganglion. Results: We describe novel afferent neurons in distal segments of locust legs that project directly into the brain without forming ramifications in other ganglia. In the brain, the fibres terminate with characteristic terminals in a small neuropile previously named the superficial ventral inferior protocerebrum. The somata of these neurons are located in the tibiae and tarsi of all legs and they are located within branches of peripheral nerves, or closely associated with such branches. They are not associated with any accessory structures such as tendons or connective tissue strands as typical for insect internal mechanoreceptors such as chordotonal organs or stretch receptors. Morphologically they show great similarity to certain insect infrared receptors.We could not observe projections into the superficial ventral inferior protocerebrum after staining mandibular or labial nerves, but we confirm previous studies that showed projections into the same brain neuropile after staining maxillary and antennal nerves, indicating that most likely similar neurons are present in these appendages also. Conclusion: Because of their location deep within the lumen of appendages the function of these neurons as infrared receptors is unlikely. Their projection pattern and other morphological features indicate that the neurons convey information about an internal physiological parameter directly into a special brain neuropile. We discuss their possible function as thermoreceptors.

Description: Background: Multidrug-resistant (MDR) Salmonella isolates are associated with increased morbidity compared to antibiotic-sensitive strains and are an important health and safety concern in both humans and animals. Salmonella enterica serovar Typhimurium is a prevalent cause of foodborne disease, and a considerable number of S. Typhimurium isolates from humans and livestock are resistant to three or more antibiotics. The majority of these MDR S. Typhimurium isolates are resistant to tetracycline, a commonly used and clinically and agriculturally relevant antibiotic. Because exposure of drug-resistant bacteria to antibiotics can affect cellular processes associated with virulence, such as invasion, we investigated the effect tetracycline had on the invasiveness of tetracycline-resistant MDR S. Typhimurium isolates. Results: The isolates selected and tested were from two common definitive phage types of S. Typhimurium, DT104 and DT193, and were resistant to tetracycline and at least three other antibiotics. Although Salmonella invasiveness is temporally regulated and normally occurs during late-log growth phase, tetracycline exposure induced the full invasive phenotype in a cell culture assay during early-log growth in several DT193 isolates. No changes in invasiveness due to tetracycline exposure occurred in the DT104 isolates during early-log growth or in any of the isolates during late-log growth. Real-time PCR was used to test expression of the virulence genes hilA, prgH, and invF, and these genes were significantly up-regulated during early-log growth in most isolates due to tetracycline exposure; however, increased virulence gene expression did not always correspond with increased invasion, and therefore was not an accurate indicator of elevated invasiveness. This is the first report to assess DT193 isolates, as well as the early-log growth phase, in response to tetracycline exposure, and it was the combination of both parameters that was necessary to observe the induced invasion phenotype. Conclusions: In this report, we demonstrate that the invasiveness of MDR S. Typhimurium can be modulated in the presence of tetracycline, and this effect is dependent on growth phase, antibiotic concentration, and strain background. Identifying the conditions necessary to establish an invasive phenotype is important to elucidate the underlying factors associated with increased virulence of MDR Salmonella.

Description: Background: Mutations in the PTRF gene, coding for cavin-1, cause congenital generalized lipodystrophy type 4 (CGL4) associated with myopathy. In CGL4, symptoms are variable comprising, in addition to myopathy, smooth and skeletal muscle hypertrophy, cardiac arrhythmias, and skeletal abnormalities. Secondary features are atlantoaxial instability, acanthosis nigricans, hepatomegaly, umbilical prominence and metabolic abnormalities related to insulin resistance, such as diabetes mellitus, hyperlipidemia and hepatic steatosis.Case presentationWe describe a 3 year-old child of Moroccan origin with mild muscle phenotype, mainly characterized by mounding, muscle pain, hyperCKemia and mild caveolin 3 reduction on muscle biopsy. No CAV3 gene mutation was detected; instead we found a novel mutation, a homozygous single base pair deletion, in the PTRF gene. Only after detection of this mutation a mild generalized loss of subcutaneous fat, at first underestimated, was noticed and the diagnosis of lipodystrophy inferred. Conclusions: The PTRF gene should be investigated in patients with hyperCKemia, mild myopathy associated with spontaneous or percussion-induced muscle contractions like rippling or mounding, and no CAV3 mutation. The analysis should be performed even if cardiac or metabolic alterations are absent, particularly in young patients in whom lipodystrophy may be difficult to ascertain.

Description: Background: Magnetotactic bacteria produce membrane-enveloped magnetite crystals (magnetosomes) whose formation is controlled primarily by a gene island termed the magnetosome island (MAI). Characterization of single gene and operon function in MAI has elucidated in part the genetic basis of magnetosome formation. The mamX gene, located in the mamXY operon, is highly conserved in the MAI of all Magnetospirillum strains studied to date. Little is known regarding the function of mamX in the process of biomineralization. Results: A mamX deletion mutant ([increment]mamX) and its complemented strain (CmamX) by conjugation in M. gryphiswaldense strain MSR-1 were constructed. There were no striking differences in cell growth among [increment]mamX, CmamX, and wild-type strain (WT). [increment]mamX displayed a much weaker magnetic response than WT. Transmission electron microscopy revealed the presence of irregular, superparamagnetic magnetite particles in [increment]mamX, in contrast to regular, single-domain particles in WT and CmamX. The phenotype of [increment]mamX was similar to that of an ftsZ-like deleted mutant and mamXY operon deleted mutant reported previously. Quantitative real-time RT-PCR (qPCR) results indicated that the deletion of mamX had differential effects on the transcription levels of the other three genes in the operon. Conclusions: The MamX protein plays an important role in controlling magnetosome size, maturation, and crystal form. The four MamXY proteins appear to have redundant functions involved in magnetosome formation. Our findings provide new insights into the coordinated function of MAI genes and operons in magnetosome formation.

Description: Background: Host plant roots, mycorrhizal mycelium and microbes are important and potentially interacting factors shaping the performance of mycorrhization helper bacteria (MHB). We investigated the impact of a soil microbial community on the interaction between the extraradical mycelium of the ectomycorrhizal fungus Piloderma croceum and the MHB Streptomyces sp. AcH 505 in both the presence and the absence of pedunculate oak microcuttings. Results: Specific primers were designed to target the internal transcribed spacer of the rDNA and an intergenic region between two protein encoding genes of P. croceum and the intergenic region between the gyrA and gyrB genes of AcH 505. These primers were used to perform real-time PCR with DNA extracted from soil samples. With a sensitivity of 10 genome copies and a linear range of 6 orders of magnitude, these real-time PCR assays enabled the quantification of purified DNA from P. croceum and AcH 505, respectively. In soil microcosms, the fungal PCR signal was not affected by AcH 505 in the absence of the host plant. However, the fungal signal became weaker in the presence of the plant. This decrease was only observed in microbial filtrate amended microcosms. In contrast, the PCR signal of AcH 505 increased in the presence of P. croceum. The increase was not significant in sterile microcosms that contained plant roots. Conclusions: Real-time quantitative PCR assays provide a method for directly detecting and quantifying MHB and mycorrhizal fungi in plant microcosms. Our study indicates that the presence of microorganisms and plant roots can both affect the nature of MHB-fungus interactions, and that mycorrhizal fungi may enhance MHB growth.

Description: Background: Little is known about the Phasmatodea gut microbial community, including whether phasmids have symbiotic bacteria aiding in their digestion. While symbionts are near ubiquitous in herbivorous insects, the Phasmatodea's distinctively thin body shape precludes the gut enlargements needed for microbial fermentation. High-throughput sequencing was used to characterize the entire microbiota of the fat bodies, salivary glands, and anterior and posterior midguts of two species of walking stick. Results: Most bacterial sequences belonged to a strain of Spiroplasma (Tenericutes) found primarily in the posterior midgut of the parthenogenetic species Ramulus artemis (Phasmatidae). Beyond this, no significant differences were found between the R. artemis midgut sections or between that species and Peruphasma schultei (Pseudophasmatidae). Histological analysis further indicated a lack of bacteriocytes. Conclusions: Phasmids are unlikely to depend on bacteria for digestion, suggesting they produce enzymes endogenously that most other herbivorous insects obtain from symbionts. This conclusion matches predictions based on phasmid anatomy. The role of Spiroplasma in insects warrants further study.

Description: Background: High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag or barcode that is attached to the sequencing or amplification primer and hence appears at the beginning of the sequence in every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence.Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and Levenshtein codes.ResultLevenshtein codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this paper we demonstrate the decreased error correction capability of Levenshtein codes in a DNA context and suggest an adaptation of Levenshtein codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaption we take the DNA context into account and redefine the word length whenever an insertion or deletion is revealed. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors. Conclusion: We present an adaptation of Levenshtein codes to DNA contexts capable of correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of recovering the new length of the corrupted codeword and of correcting on average more random mutations than traditional Levenshtein or Hamming codes.As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance.

Description: Background: Angiogenesis is the main therapeutic mechanism of cell therapy for cardiovascular diseases, but diabetes is reported to reduce the function and number of progenitor cells. Therefore, we studied the effect of streptozotocin-induced diabetes on the bone marrow-mesenchymal stem cell (MSC) function, and examined whether diabetes-impaired MSC could be rescued by pretreatment with oxytocin. Results: MSCs were isolated and cultured from diabetic (DM) or non-diabetic (non-DM) rat, and proliferation rate was compared. DM-MSC was pretreated with oxytocin and compared with non-DM-MSC. Angiogenic capacity was estimated by tube formation and Matrigel plug assay, and therapeutic efficacy was studied in rat myocardial infarction (MI) model.The proliferation and angiogenic activity of DM-MSC were severely impaired but significantly improved by pretreatment with oxytocin. Kruppel-like factor 2 (KLF2), a critical angiogenic factor, was dramatically reduced in DM-MSC and significantly restored by oxytocin. In the Matrigel plug assay, vessel formation of DM-BMSCs was attenuated but was recovered by oxytocin. In rat MI model, DM-MSC injection did not ameliorate cardiac injury, whereas oxytocin-pretreated DM-MSC improved cardiac function and reduced fibrosis. Conclusions: Our results show that diabetes influenced MSC by reducing angiogenic capacity and therapeutic potential. We demonstrate the striking effect of oxytocin on stem cell dysfunction and suggest the use of oxytocin as a priming reagent in autologous stem cell therapy.

Description: Background: Temperature is one of key environmental parameters that affect the whole life of fishes and an increasing number of studies have been directed towards understanding the mechanisms of cold acclimation in fish. However, the adaptation of larvae to cold stress and the cold-specific transcriptional alterations in fish larvae remain largely unknown. In this study, we characterized the development of cold-tolerance in zebrafish larvae and investigated the transcriptional profiles under cold stress using RNA-seq. Results: Pre-exposure of 96hpf zebrafish larvae to cold stress (16[degree sign]C) for 24 h significantly increased their survival rates under severe cold stress (12[degree sign]C). RNA-seq generated 272 million raw reads from six sequencing libraries and about 92% of the processed reads were mapped to the reference genome of zebrafish. Differential expression analysis identified 1,431 up- and 399 down-regulated genes. Gene ontology enrichment analysis of cold-induced genes revealed that RNA splicing, ribosome biogenesis and protein catabolic process were the most highly overrepresented biological processes. Spliceosome, proteasome, eukaryotic ribosome biogenesis and RNA transport were the most highly enriched pathways for genes up-regulated by cold stress. Moreover, alternative splicing of 197 genes and promoter switching of 64 genes were found to be regulated by cold stress. A shorter isoform of stk16 that lacks 67 amino acids at the N-terminus was specifically generated by skipping the second exon in cold-treated larvae. Alternative promoter usage was detected for per3 gene under cold stress, which leading to a highly up-regulated transcript encoding a truncated protein lacking the C-terminal domains. Conclusions: These findings indicate that zebrafish larvae possess the ability to build cold-tolerance under mild low temperature and transcriptional and post-transcriptional regulations are extensively involved in this acclimation process.

Description: Background: Apoptosis is a highly controlled process of cell death that can be induced by periodontopathogens. The present study aimed to investigate the expression of Fas and Bcl-2 proteins by CD3+ T cells in vitro under stimulation by total Porphyromonas gingivalis antigens and purified recombinant P. gingivalis HmuY protein. Results: CD3+ T cells derived from CP patients and stimulated with HmuY expressed higher levels of Bcl-2 compared to identical cells stimulated with P. gingivalis crude extract or cells derived from NP control subjects (p = 0.043). Conclusion: The authors hypothesize that P. gingivalis HmuY plays a role in the pathogenesis of chronic periodontitis, possibly by reducing or delaying apoptosis in T cells through a pathway involving the Bcl-2 protein.

Description: Background: It is increasingly recognized that the bacteria that live in and on the human body (the microbiome) can play an important role in health and disease. The composition of the microbiome is potentially influenced by both internal factors (such as phylogeny and host physiology) and external factors (such as diet and local environment), and interspecific comparisons can aid in understanding the importance of these factors. Results: To gain insights into the relative importance of these factors on saliva microbiome diversity, we here analyze the saliva microbiomes of chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) from two sanctuaries in Africa, and from human workers at each sanctuary. The saliva microbiomes of the two Pan species are more similar to one another, and the saliva microbiomes of the two human groups are more similar to one another, than are the saliva microbiomes of human workers and apes from the same sanctuary. We also looked for the existence of a core microbiome and find no evidence for a taxon-based core saliva microbiome for Homo or Pan. In addition, we studied the saliva microbiome from apes from the Leipzig Zoo, and found an extraordinary diversity in the zoo ape saliva microbiomes that is not found in the saliva microbiomes of the sanctuary animals. Conclusions: The greater similarity of the saliva microbiomes of the two Pan species to one another, and of the two human groups to one another, are in accordance with both the phylogenetic relationships of the hosts as well as with host physiology. Moreover, the results from the zoo animals suggest that novel environments can have a large impact on the microbiome, and that microbiome analyses based on captive animals should be viewed with caution as they may not reflect the microbiome of animals in the wild.

Description: Background: The choice of variable selection methods to identify important variables for binary classification modeling is critical to produce stable models that are interpretable, that generate accurate predictions and have minimum bias. This work is motivated by data on clinical and laboratory features of severe dengue infections (dengue hemorrhagic fever, DHF) obtained from 51 individuals enrolled in a prospective observational study of acute human dengue infections. Results: We carry out a comprehensive performance comparison using several classification models for DHF over the dengue data set. We compared variable selection results by Multivariate Adaptive Regression Splines, Learning Ensemble, Random Forest, Bayesian Moving Averaging, Stochastic Search Variable Selection, and Generalized Regularized Logistics Regression. Model averaging methods (bagging, boosting and ensemble learners) have higher accuracy, but the generalized regularized regression model has the highest predictive power because the linearity assumptions of candidate predictors are strongly satisfied via deviance chi-square testing procedures. Bootstrapping applications for evaluating predictive regression coefficients in regularized regression model are performed. Conclusions: Feature reduction methods introduce inherent biases and therefore are data-type dependent. We propose that these limitations can be overcome using an exhaustive approach for searching feature space. Using this approach, we results suggest that IL-10, platelet and lymphocyte counts are the major features for predicting dengue DHF on the basis of blood chemistries and cytokine measurements.

Description: Background: Sjogren's syndrome is characterized by lymphocytic infiltration of the exocrine glands, together with polyclonal B-cell activation, and lung diseases are well-known complications of the disease. Therefore, in most cases associated with Sjogren's syndrome, infiltrating lymphocytes in the lung specimen exhibit the features of B-cells. We herein report an atypical case of lymphoproliferative pulmonary involvement in a patient with Sjogren's syndrome.Case presentationA 46-year-old female was admitted to our hospital because of an abnormal chest roentgenogram finding on a medical checkup. Chest computed tomography showed randomly-distributed micronodules and patchy ground-glass opacities. A surgical biopsied specimen showed an atypical pattern of interstitial pneumonia with numerous lymphoid follicles. Among the infiltrating lymphocytes in the lung, only the monoclonality of the T-cells was proven by a gene rearrangement analysis, but there was no cytological atypicality or genetic disorder revealed by testing the bone marrow aspirate. A diagnosis of Sjogren's syndrome was made based on the patient's other symptoms and these negative findings. The patient's pulmonary lesions have been successfully treated and remission has been maintained for over three years with corticosteroid treatment alone. Conclusion: The present patient was an atypical case of lymphoproliferative pulmonary involvement in a patient with Sjogren's syndrome. Although monoclonality of the infiltrating T-cells was proven, the clinical course and the findings of the imaging and laboratory examinations were inconsistent with the previously-reported cases of primary pulmonary T-cell lymphoma. This suggests that the monoclonality of lymphocytes does not always define malignancy. The diagnosis of malignant lymphoma or lymphoproliferative diseases should be made clinically, pathologically and cytogenetically to rule out other similar diseases.

Description: Background: In cross breeding, it is important to choose a good parental combination that has high probability of generating offspring with desired characteristics. This study examines a method for predicting the segregation of target traits in a progeny population based on genome-wide markers and phenotype data of parental cultivars. Results: The proposed method combines segregation simulation and Bayesian modeling for genomic selection. Marker segregation in a progeny population was simulated based on parental genotypes. Posterior marker effects sampled via Markov Chain Monte Carlo were used to predict the segregation pattern of target traits. The posterior distribution of the proportion of progenies that fulfill selection criteria was calculated and used for determining a promising cross and the necessary size of the progeny population. We applied the proposed method to Japanese pear (Pyrus pyrifolia Nakai) data to demonstrate the method and to show how it works in the selection of a promising cross. Verification using an actual breeding population suggests that the segregation of target traits can be predicted with reasonable accuracy, especially in a highly heritable trait. The uncertainty in predictions was reflected on the posterior distribution of the proportion of progenies that fulfill selection criteria. A simulation study based on the real marker data of Japanese pear cultivars also suggests the potential of the method. Conclusions: The proposed method is useful to provide objective and quantitative criteria for choosing a parental combination and the breeding population size.

Description: Background: Gene reshuffling, point mutations and horizontal gene transfer contribute to bacterial genome variation, but require the genome to rewire its transcriptional circuitry to ensure that inserted, mutated or reshuffled genes are transcribed at appropriate levels. The genomes of Epsilonproteobacteria display very low synteny, due to high levels of reshuffling and reorganisation of gene order, but still share a significant number of gene orthologs allowing comparison. Here we present the primary transcriptome of the pathogenic Epsilonproteobacterium Campylobacter jejuni, and have used this for comparative and predictive transcriptomics in the Epsilonproteobacteria. Results: Differential RNA-sequencing using 454 sequencing technology was used to determine the primary transcriptome of C. jejuni NCTC 11168, which consists of 992 transcription start sites (TSS), which included 29 putative non-coding and stable RNAs, 266 intragenic (internal) TSS, and 206 antisense TSS. Several previously unknown features were identified in the C. jejuni transcriptional landscape, like leaderless mRNAs and potential leader peptides upstream of amino acid biosynthesis genes. A cross-species comparison of the primary transcriptomes of C. jejuni and the related Epsilonproteobacterium Helicobacter pylori highlighted a lack of conservation of operon organisation, position of intragenic and antisense promoters or leaderless mRNAs. Predictive comparisons using 40 other Epsilonproteobacterial genomes suggests that this lack of conservation of transcriptional features is common to all Epsilonproteobacterial genomes, and is associated with the absence of genome synteny in this subdivision of the Proteobacteria. Conclusions: Both the genomes and transcriptomes of Epsilonproteobacteria are highly variable, both at the genome level by combining and division of multicistronic operons, but also on the gene level by generation or deletion of promoter sequences and 5[prime] untranslated regions. Regulatory features may have evolved after these species split from a common ancestor, with transcriptome rewiring compensating for changes introduced by genomic reshuffling and horizontal gene transfer.

Description: Phenology as a strategy for carbon optimality: a global model Biogeosciences Discussions, 10, 15107-15152, 2013 Author(s): S. Caldararu, D. W. Purves, and P. I. Palmer Phenology is essential to our understanding of biogeochemical cycles and the climate system. We develop a global mechanistic model of leaf phenology based on the hypothesis that phenology is a strategy for optimal carbon gain at the canopy level so that trees adjust leaf gains and losses in response to environmental factors such as light, temperature and soil moisture, to achieve maximum carbon assimilation. We fit this model to five years of satellite observations of leaf area index (LAI) using a Bayesian fitting algorithm. We show that our model is able to reproduce phenological patterns for all vegetation types and use it to explore variations in growing season length and the climate factors that limit leaf growth for different biomes. Phenology in wet tropical areas is limited by leaf age physiological constraints while at higher latitude leaf seasonality is limited by low temperature and light availability. Leaf growth in grassland regions is limited by water availability but often in combination with other factors. This model will advance the current understanding of phenology for ecosystem carbon models and our ability to predict future phenological behaviour.

Description: Background: Hypersensitivity pneumonitis is defined as an allergic lung disease that occurs in response to inhalation of fungal antigens, bacterial antigens, chemicals, dusts, or animal proteins. The incidence of summer-type hypersensitivity pneumonitis is higher in the summer season, especially in Japan, due to the influence of the hot and humid environment and the common style of wood house or old concrete condominiums.Case presentationThe present report describes a case of a middle-aged married couple who lived in the same house and who simultaneously suffered from summer-type hypersensitivity pneumonitis. This report analyzes these two cases in terms of environmental research and its microbiological, radiological, and pathological aspects. This case report is followed by a review of family occurrences of summer-type hypersensitivity pneumonitis from 22 studies with a total of 49 patients (including the two present cases) in Japan. Conclusion: Summer-type hypersensitivity pneumonitis may be unrecognized and misdiagnosed as pneumonia or other respiratory diseases. A greater understanding of the clinical, pathologic, and environmental features of summer-type hypersensitivity pneumonitis might help improve diagnosis and delivery of appropriate management for this condition.

Description: Background: Cell migration is a fundamental biological process and has an important role in the developing brain by regulating a highly specific pattern of connections between nerve cells. Cell migration is required for axonal guidance and neurite outgrowth and involves a series of highly co-ordinated and overlapping signalling pathways. The non-receptor tyrosine kinase, Focal Adhesion Kinase (FAK) has an essential role in development and is the most highly expressed kinase in the developing CNS. FAK activity is essential for neuronal cell adhesion and migration. Results: The objective of this study was to optimise a protocol for the differentiation of the neuroblastoma cell line, SH-SY5Y. We determined the optimal extracellular matrix proteins and growth factor combinations required for the optimal differentiation of SH-SY5Y cells into neuronal-like cells and determined those conditions that induce the expression of FAK. It was confirmed that the cells were morphologically and biochemically differentiated when compared to undifferentiated cells. This is in direct contrast to commonly used differentiation methods that induce morphological differentiation but not biochemical differentiation. Conclusions: We conclude that we have optimised a protocol for the differentiation of SH-SY5Y cells that results in a cell population that is both morphologically and biochemically distinct from undifferentiated SH-SY5Y cells and has a distinct adhesion and spreading pattern and display extensive neurite outgrowth. This protocol will provide a neuronal model system for studying FAK activity during cell adhesion and migration events.

Description: Background: Life history tradeoffs may result from temporal and physiological constraints intrinsic to an organism. When faced with limited time and energy, compromises occur and these resources are allocated among essential activities, such as body growth, maintenance, foraging, mating, and offspring care. We investigated potential tradeoffs that may occur between reproductive activities and feeding performance in female Arizona Bark Scorpions (Centruroides sculpturatus) by comparing the time taken to capture prey between non-reproductive and reproductive females (gravid females and females exhibiting maternal care, i.e. carrying offspring on their backs). Results: Gravid females were as efficient at catching prey as non-gravid females. To control for variation in the duration of the maternal care period, we removed all offspring from all post-parturient females after 5 days. Brooding females and females 24 hours following offspring removal (FOR) did not successfully capture prey within the 900-second trial period. Twenty-eight days FOR, females caught prey faster than females displaying maternal care and females 24 hours FOR, but were not as efficient at catching prey as non-gravid and gravid females. When pursuing prey, C. sculpturatus exhibiting maternal care used an active foraging strategy more frequently than non-gravid, gravid, and females 28 days FOR. In contrast, non-gravid, gravid, and females 28 days FOR used active and ambush foraging with similar frequency. Conclusions: Our data suggest that reproduction does not significantly reduce the predatory efficiency of gravid C. sculpturatus, and that these females can cope with increasing body mass and the physiological costs of gestation. However, the observation that brooding females and females 24 hours FOR did not catch prey within the trial period indicates that maternal care significantly reduces predatory efficiency in these scorpions. Females 28 days FOR were still not as efficient at catching prey as non-gravid and gravid females, suggesting that reproductive costs extend for at least 4 weeks after the end of the maternal care period. Preferential use of an active foraging strategy by brooding females may increase prey encounter rates, allowing the scorpions to more rapidly replenish energy reserves depleted during reproduction. However, active foraging may be energetically costly and increase predation risk for brooding females. Our findings regarding antagonistic interactions between reproduction and feeding in female C. sculpturatus demonstrate the pervasive nature of reproductive costs for viviparous females, and may provide insight on factors that influence the diversity of reproductive strategies observed in nature.

Description: Background: External development and optical transparency of embryos make zebrafish exceptionally suitable for in vivo insertional mutagenesis using fluorescent proteins to visualize expression patterns of mutated genes. Recently developed Gene Breaking Transposon (GBT) vectors greatly improve the fidelity and mutagenicity of transposon-based gene trap vectors. Results: We constructed and tested a bipartite GBT vector with Gal4-VP16 as the primary gene trap reporter. Our vector also contains a UAS:eGFP cassette for direct detection of gene trap events by fluorescence. To confirm gene trap events, we generated a UAS:mRFP tester line. We screened 270 potential founders and established 41 gene trap lines. Three of our gene trap alleles display homozygous lethal phenotypes ranging from embryonic to late larval: nsftpl6, atp1a3atpl10 and flrtpl19. Our gene trap cassette is flanked by direct loxP sites, which enabled us to successfully revert nsftpl6, atp1a3atpl10 and flrtpl19 gene trap alleles by injection of Cre mRNA. The UAS:eGFP cassette is flanked by direct FRT sites. It can be readily removed by injection of Flp mRNA for use of our gene trap alleles with other tissue-specific GFP-marked lines. The Gal4-VP16 component of our vector provides two important advantages over other GBT vectors. The first is increased sensitivity, which enabled us to detect previously unnoticed expression of nsf in the pancreas. The second advantage is that all our gene trap lines, including integrations into non-essential genes, can be used as highly specific Gal4 drivers for expression of other transgenes under the control of Gal4 UAS. Conclusions: The Gal4-containing bipartite Gene Breaking Transposon vector presented here retains high specificity for integrations into genes, high mutagenicity and revertibility by Cre. These features, together with utility as highly specific Gal4 drivers, make gene trap mutants presented here especially useful to the research community.

Description: Background: Little is known about the Phasmatodea gut microbial community, including whether phasmids have symbiotic bacteria aiding in their digestion. While symbionts are near ubiquitous in herbivorous insects, the Phasmatodea’s distinctively thin body shape precludes the gut enlargements needed for microbial fermentation. High-throughput sequencing was used to characterize the entire microbiota of the fat bodies, salivary glands, and anterior and posterior midguts of two species of walking stick. Results: Most bacterial sequences belonged to a strain of Spiroplasma (Tenericutes) found primarily in the posterior midgut of the parthenogenetic species Ramulus artemis (Phasmatidae). Beyond this, no significant differences were found between the R. artemis midgut sections or between that species and Peruphasma schultei (Pseudophasmatidae). Histological analysis further indicated a lack of bacteriocytes. Conclusions: Phasmids are unlikely to depend on bacteria for digestion, suggesting they produce enzymes endogenously that most other herbivorous insects obtain from symbionts. This conclusion matches predictions based on phasmid anatomy. The role of Spiroplasma in insects warrants further study.

Description: Background: Very little is known about manganese (Mn)-toxicity-responsive genes in citrus plants. Seedlings of 'Xuegan' (Citrus sinensis) and 'Sour pummelo' (Citrus grandis) were irrigated for 17 weeks with nutrient solution containing 2 muM (control) or 600 muM (Mn-toxicity) MnSO4. The objectives of this study were to understand the mechanisms of citrus Mn-tolerance and to identify differentially expressed genes, which might be involved in Mn-tolerance. Results: Under Mn-toxicity, the majority of Mn in seedlings was retained in the roots; C. sinensis seedlings accumulated more Mn in roots and less Mn in shoots (leaves) than C. grandis ones and Mn concentration was lower in Mn-toxicity C. sinensis leaves compared to Mn-toxicity C. grandis ones. Mn-toxicity affected C. grandis seedling growth, leaf CO2 assimilation, total soluble concentration, phosphorus (P) and magenisum (Mg) more than C. sinensis. Using cDNA-AFLP, we isolated 42 up-regulated and 80 down-regulated genes in Mn-toxicity C. grandis leaves. They were grouped into the following functional categories: biological regulation and signal transduction, carbohydrate and energy metabolism, nucleic acid metabolism, protein metabolism, lipid metabolism, cell wall metabolism, stress responses and cell transport. However, only 7 up-regulated and 8 down-regulated genes were identified in Mn-toxicity C. sinensis ones. The responses of C. grandis leaves to Mn-toxicity might include following several aspects: (1) accelerating leaf senescence; (2) activating the metabolic pathway related to ATPase synthesis and reducing power production; (3) decreasing cell transport; (4) inhibiting protein and nucleic acid metabolisms; (5) impairing the formation of cell wall; and (6) triggering multiple signal transduction pathways. We also identified many new Mn-toxicity-responsive genes involved in biological and signal transduction, carbohydrate and protein metabolisms, stress responses and cell transport. Conclusions: Our results demonstrated that C. sinensis was more tolerant to Mn-toxicity than C. grandis, and that Mn-toxicity affected gene expression far less in C. sinensis leaves. This might be associated with more Mn accumulation in roots and less Mn accumulation in leaves of Mn-toxicity C. sinensis seedlings than those of C. grandis seedlings. Our findings increase our understanding of the molecular mechanisms involved in the responses of plants to Mn-toxicity.

Description: Background: Two-partner secretion systems in Gram-negative bacteria consist of an outer membrane protein TpsB that mediates the secretion of a cognate TpsA protein into the extracellular milieu. TpsA proteins have diverse, often virulence-related functions, and some of them inhibit the growth of related bacteria. In Neisseria meningitidis, several functions have been attributed to the TpsA proteins. Downstream of the tpsB and tpsA genes, several shorter tpsA-related gene cassettes, called tpsC, are located interspersed with intervening open-reading frames (IORFs). It has been suggested that the tpsC cassettes may recombine with the tpsA gene as a mechanism of antigenic variation. Here, we investigated (i) whether TpsA of N. meningitidis also has growth-inhibitory properties, (ii) whether tpsC cassettes recombine with the tpsA gene, and (iii) what the consequences of such recombination events might be. Results: We demonstrate that meningococcal TpsA has growth-inhibitory properties and that the IORF located immediately downstream of tpsA confers immunity to the producing strain. Although bioinformatics analysis suggests that recombination between tpsC cassettes and tpsA occurs, detailed analysis of the tpsA gene in a large collection of disease isolates of three clonal complexes revealed that the frequency is very low and cannot be a mechanism of antigenic variation. However, recombination affected growth inhibition. In vitro experiments revealed that recombination can be mediated through acquirement of tpsC cassettes from the environment and it identified the regions involved in the recombination. Conclusions: Meningococcal TpsA has growth-inhibitory properties. Recombination between tpsA and tpsC cassettes occurs in vivo but is rare and has consequences for growth inhibition. A recombination model is proposed and we propose that the main goal of recombination is the collection of new IORFs for protection against a variety of TpsA proteins.

Description: Background: Sequencing of the genome of Propionibacterium acnes produced a catalogue of genes many of which enable this organism to colonise skin and survive exposure to the elements. Despite this platform, there was little understanding of the gene regulation that gives rise to an organism that has a major impact on human health and wellbeing and causes infections beyond the skin. To address this situation, we have undertaken a genome--wide study of gene regulation using a combination of improved differential and global RNA-sequencing and an analytical approach that takes into account the inherent noise within the data. Results: We have produced nucleotide-resolution transcriptome maps that identify and differentiate sites of transcription initiation from sites of stable RNA processing and mRNA cleavage. Moreover, analysis of these maps provides strong evidence for 'pervasive' transcription and shows that contrary to initial indications it is not biased towards the production of antisense RNAs. In addition, the maps reveal an extensive array of riboswitches, leaderless mRNAs and small non-protein-coding RNAs alongside vegetative promoters and post-transcriptional events, which includes unusual tRNA processing. The identification of such features will inform models of complex gene regulation, as illustrated here for ribonucleotide reductases and a potential quorum-sensing, two-component system. Conclusions: The approach described here, which is transferable to any bacterial species, has produced a step increase in whole-cell knowledge of gene regulation in P. acnes. Continued expansion of our maps to include transcription associated with different growth conditions and genetic backgrounds will provide a new platform from which to computationally model the gene expression that determines the physiology of P. acnes and its role in human disease.

Description: Background: Nutritional guidance and diet control play important roles in the treatment of obesity and non-alcoholic fatty liver. However, in Japan, nutritional guidance is difficult to provide in practice. Therefore, we evaluated the effects of providing the 'once-a-day' intervention of a healthy lunch on various metabolic parameters. Methods: For a 1-month preparatory period, 10 subjects generally consumed the lunches that were provided by the worksite cafeteria. This was followed by a 1-week washout period, after which, the subjects consumed healthy, low-calorie, well-balanced lunches for a 1-month test period. After the preparatory and test periods, blood samples were obtained from all subjects. The serum levels of indices relevant to metabolic syndrome and fatty liver were measured. Results: Serum alanine aminotransferase activity significantly decreased by 20.3% after the healthy intervention. However, the indices of metabolic syndrome did not significantly change. Analysis of the relationship between serum alanine aminotransferase activity and nutrient content indicated that the improvement of serum alanine aminotransferase status was due to the higher vegetable content and lower animal-source protein of the meals provided. Conclusions: In summary, the 'once-a-day' intervention of providing a healthy lunch improved serum alanine aminotransferase status. A diet high in vegetables and low in animal-based protein is important in maintaining a healthy condition.

Description: Background: Pancreatic cancer is a deadly disease with a five-year survival of less than 5%. A better understanding of the underlying biology may suggest novel therapeutic targets. Recent surveys of the pancreatic cancer genome have uncovered numerous new alterations; yet systematic functional characterization of candidate cancer genes has lagged behind. To address this challenge, here we have devised a highly-parallel RNA interference-based functional screen to evaluate many genomically-nominated candidate pancreatic cancer genes simultaneously. Results: For 185 candidate pancreatic cancer genes, selected from recurrently altered genomic loci, we performed a pooled shRNA library screen of cell growth/viability across 10 different cell lines. Knockdown-associated effects on cell growth were assessed by enrichment or depletion of shRNA hairpins, by hybridization to barcode microarrays. A novel analytical approach (COrrelated Phenotypes for On-Target Effects; COPOTE) was used to discern probable on-target knockdown, based on identifying different shRNAs targeting the same gene and displaying concordant phenotypes across cell lines. Knockdown data were integrated with genomic architecture and gene-expression profiles, and selected findings validated using individual shRNAs and/or independent siRNAs. The pooled shRNA library design delivered reproducible data. In all, COPOTE analysis identified 52 probable on-target gene-knockdowns. Knockdown of known oncogenes (KRAS, MYC, SMURF1 and CCNE1) and a tumor suppressor (CDKN2A) showed the expected contrasting effects on cell growth. In addition, the screen corroborated purported roles of PLEKHG2 and MED29 as 19q13 amplicon drivers. Most notably, the analysis also revealed novel possible oncogenic functions of nucleoporin NUP153 (ostensibly by modulating TGFbeta signaling) and Kruppel-like transcription factor KLF5 in pancreatic cancer. Conclusions: By integrating physical and functional genomic data, we were able to simultaneously evaluate many candidate pancreatic cancer genes. Our findings uncover new facets of pancreatic cancer biology, with possible therapeutic implications. More broadly, our study provides a general strategy for the efficient characterization of candidate genes emerging from cancer genome studies.

Description: Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks.Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs.Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes.Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further.

Description: Background: Acute adrenal insufficiency is a potentially lethal condition rarely caused by bilateral adrenal haemorrhage due to heparin use. Most of the times, it is difficult to establish the diagnosis, as symptoms are not specific. Few cases have been reported in the literature.Case presentationA 52-year-old Caucasian woman presented with abdominal pain, vomiting and weakness nine days after arthroplasty and heparin use. Hyperkalemia, low cortisol and high adrenocorticotropic hormone levels were found, indicating adrenal insufficiency. Magnetic resonance imaging of the upper abdomen was compatible with preceding adrenal haemorrhage. Hydrocortisone and fludrocortisone were administered. Review of the literature revealed 36 cases of postoperative adrenal haemorrhage which are presented briefly. Conclusion: Postoperative acute adrenal insufficiency due to haemorrhage is a rare condition. If patients are treated based on clinical suspicion, they have good chances to survive. Hydrocortisone is given permanently in the majority of the patients.

Description: Timing of sea ice retreat can alter phytoplankton community structure in the western Arctic Ocean Biogeosciences Discussions, 10, 15153-15180, 2013 Author(s): given_name prefix surname suffix, A. Fujiwara, T. Hirawake, K. Suzuki, I. Imai, and S.-I. Saitoh This study assesses the response of phytoplankton assemblages to recent climate change, especially with regard to the shrinking of sea ice in the northern Chukchi Sea of the western Arctic Ocean. Distribution patterns of phytoplankton groups in the late summers of 2008–2010 were analyzed based on HPLC pigment signatures and, the following four major algal groups were inferred via multiple regression and cluster analyses: prasinophytes, diatoms, haptophytes and dinoflagellates. A remarkable interannual difference in the distribution pattern of the groups was found in the northern basin area. Haptophytes dominated and dispersed widely in warm surface waters in 2008, whereas prasinophytes dominated in cold water in 2009 and 2010. A difference in the onset date of sea ice retreat was evident among years – the sea ice retreat in 2008 was 1–2 months earlier than in 2009 and 2010. The spatial distribution of early sea ice retreat matched the areas in which a shift in algal community composition was observed. Steel-Dwass's multiple comparison tests were used to assess the physical, chemical and biological parameters of the four clusters. We found a statistically significant difference in temperature between the haptophyte-dominated cluster and the other clusters, suggesting that the change in the phytoplankton communities was related to the earlier sea ice retreat in 2008 and the corollary increase in sea surface temperatures. Longer periods of open water during the summer, which are expected in the future, may affect food webs and biogeochemical cycles in the western Arctic due to shifts in phytoplankton community structure.

Description: Background: The apolipoprotein M (APOM) T-778C gene polymorphism has been associated with serum lipid levels and the risk of coronary artery disease (CAD), but the results are inconclusive. The purpose of this meta-analysis was to detect the association between the APOM T-778C polymorphism and serum lipid levels and the risk of CAD in the Chinese population. Methods: Databases of MEDLINE, EMBASE, the Cochrane Library and CNKI were systematically searched. Data were extracted using standardized methods. The association was assessed by mean difference (MD) with 95% confidence intervals (CI) or odds ratio (OR) with 95% CI. Results: Ten studies with 4,413 patients were included in this meta-analysis. Pooled effects indicated that CT+CC group had higher levels of total cholesterol (TC) (MD:-0.36, 95% CI: -0.53 -- -0.19, P 〈 0.0001) and low-density lipoprotein cholesterol (LDL-C) (MD: -0.08, 95% CI: -0.16 -- -0.01, P = 0.03) than TT group. There was no difference in the levels of triglyceride (MD: 0.06, 95% CI: -0.04 -- 0.15, P = 0.22) and high-density lipoprotein cholesterol (MD: 0.00, 95% CI: -0.03--0.03, P = 0.93) between TT and CT+CC groups. Pooled effects showed that CAD group had higher CT+CC genotype frequency than control group (OR: 1.97, 95% CI: 1.62--2.39, P 〈 0.00001; heterogeneity test x2 = 2.96, P = 0.71, I2 = 0%). Conclusions: The results of the current meta-analysis show that the CT+CC group has higher levels of TC and LDL-C than the TT group. Moreover, there is also a prominent association between APOM T-778C polymorphism and the risk of CAD in the Chinese population, the CT+CC genotype is associated with increased risk of CAD.

Description: Background: The adhesion of lactobacilli to the vaginal surface is of paramount importance to develop their probiotic functions. For this reason, the role of HeLa cell surface proteoglycans in the attachment of Lactobacillus salivarius Lv72, a mutualistic strain of vaginal origin, was investigated. Results: Incubation of cultures with a variety of glycosaminoglycans (chondroitin sulfate A and C, heparin and heparan sulfate) resulted in marked binding interference. However, no single glycosaminoglycan was able to completely abolish cell binding, the sum of all having an additive effect that suggests cooperation between them and recognition of specific adhesins on the bacterial surface. In contrast, chondroitin sulfate B enhanced cell to cell attachment, showing the relevance of the stereochemistry of the uronic acid and the sulfation pattern on binding. Elimination of the HeLa surface glycosaminoglycans with lyases also resulted in severe adherence impairment. Advantage was taken of the Lactobacillus-glycosaminoglycans interaction to identify an adhesin from the bacterial surface. This protein, identify as a soluble binding protein of an ABC transporter system (OppA) by MALDI-TOF/(MS), was overproduced in Escherichia coli, purified and shown to interfere with L. salivarius Lv72 adhesion to HeLa cells. Conclusions: These data suggest that glycosaminoglycans play a fundamental role in attachment of mutualistic bacteria to the epithelium that lines the cavities where the normal microbiota thrives, OppA being a bacterial adhesin involved in the process.

Description: Background: Many scientific disciplines rely on correct taxon delineations and identifications. So does a great part of the general public as well as decision makers. Researchers, students and enthusiastic amateurs often feel frustrated because information about species remains scattered, difficult to access, or difficult to decipher. Together, this affects almost anyone who wishes to identify species or verify identifications. Many remedies have been proposed, but we argue that the role of natural history collections remains insufficiently appreciated. We suggest using state-of-the-art mass imaging technology and to join forces to create a global natural history metacollection on the internet, providing access to the morphology of tens of millions of specimens and making them available for automated digital image analysis.DiscussionRobotic high-resolution imaging technology and fast (high performance) computer-based image stitching make it now feasible to digitize entire collection drawers typically used for arthropod collections, or trays or containers used for other objects. Resolutions of 500 megapixels and much higher are already utilized to capture the contents of 40x50 cm collection drawers, providing amazing detail of specimens. Flanked by metadata entry, this helps to create access to tens of thousands of specimens in days. By setting priorities and combining the holdings of the most comprehensive collections for certain taxa, drawer digitizing offers the unique opportunity to create a global, virtual metacollection.The taxonomic and geographic coverage of such a collection could never be achieved by a single institution or individual. We argue that by joining forces, many new impulses will emerge for systematic biology, related fields and understanding of biodiversity in general.Digitizing drawers containing unidentified, little-curated specimens is a contribution towards the beginning of a new era of online curation. It also will help taxonomists and curators to discover and process the millions of "gems" of undescribed species hidden in museum accessions.SummaryOur proposal suggests creating virtual, high-resolution image resources that will, for the first time in history, provide access for expert scientists as well as students and the general public to the enormous wealth of the world's natural history collections. We foresee that this will contribute to a better understanding, appreciation and increased use of biodiversity resources and the natural history collections serving this cause.

Description: Background: A number of studies have implicated the direct involvement of the liver in dengue virus (DENV) infection, and it has been widely shown that liver cells subsequently undergo apoptosis. The mechanism by which liver cells undergo apoptosis in response to DENV infection remains unclear. To provide further information on the mechanism of apoptosis in DENV infected liver cells, HepG2 cells were infected with DENV 2 and analyzed for the induction of ER stress, apoptosis and autophagy. Results: In response to DENV infection, HepG2 cells showed the induction of both the ER resident unfolded protein response as well as the Noxa/PUMA stress response pathways. Proteolytic activation of caspases 4, 7, 8 and 9 was observed as well as changes in mitochondrial transmembrane potential. Increased monodansylcadaverine staining was observed in DENV infected cells, consistent with the previously reported induction of autophagy. Conclusions: These results are consistent with a model in which the induction of multiple ER stress pathways is coupled with the induction of multiple cell death pathways as a mechanism to ensure the removal of infected liver cells from the system.

Description: Background: Mediating DNA damage-induced apoptosis is an important genome-maintenance function of the mismatch repair (MMR) system. Defects in MMR not only cause carcinogenesis, but also render cancer cells highly resistant to chemotherapeutics, including alkylating agents. To understand the mechanisms of MMR-mediated apoptosis and MMR-deficiency-caused drug resistance, we analyze a model alkylating agent (N-methyl-N'-nitro-N-nitrosoguanidine, MNNG)-induced changes in protein phosphorylation and abundance in two cell lines, the MMR-proficient TK6 and its derivative MMR-deficient MT1. Results: Under an experimental condition that MNNG-induced apoptosis was only observed in MutSalpha-proficient (TK6), but not in MutSalpha-deficient (MT1) cells, quantitative analysis of the proteomic data revealed differential expression and phosphorylation of numerous individual proteins and clusters of protein kinase substrates, as well differential activation of response pathways/networks in MNNG-treated TK6 and MT1 cells. Many alterations in TK6 cells are in favor of turning on the apoptotic machinery, while many of those in MT1 cells are to promote cell proliferation and anti-apoptosis. Conclusions: Our work provides novel molecular insights into the mechanism of MMR-mediated DNA damage-induced apoptosis.

Description: Background: The specialisation of mammalian cells in time and space requires genes associated with specific pathways and functions to be co-ordinately expressed. Here we have combined a large number of publically available microarray datasets derived from human primary cells and analysed large correlation graphs of these data. Results: Using the network analysis tool BioLayout Express3D we identify robust co-associations of genes expressed in a wide variety of cell lineages. We discuss the biological significance of a number of these associations, in particular the coexpression of key transcription factors with the genes that they are likely to control. Conclusions: We consider the regulation of genes in human primary cells and specifically in the human mononuclear phagocyte system. Of particular note is the fact that these data do not support the identity of putative markers of antigen-presenting dendritic cells, nor classification of M1 and M2 activation states, a current subject of debate within immunological field. We have provided this data resource on the BioGPS web site (www.biogps.org) and on macrophages.com (www.macrophages.com).

Description: Background: Performing multiple tests in primary research is a frequent subject of discussion. This discussion originates from the fact that when multiple tests are performed, it becomes more likely to reject one of the null hypotheses, conditional on that these hypotheses are true and thus commit a type one error. Several correction methods for multiple testing are available. The primary aim of this study was to assess the quantity of articles published in two highly esteemed orthopedic journals in which multiple testing was performed. The secondary aims were to determine in which percentage of these studies a correction was performed and to assess the risk of committing a type one error if no correction was applied. Methods: The 2010 annals of two orthopedic journals (A and B) were systematically hand searched by two independent investigators. All articles on original research in which statistics were applied were considered. Eligible publications were reviewed for the use of multiple testing with respect to predetermined criteria. Results: A total of 763 titles were screened and 127 articles were identified and included in the analysis. A median of 15 statistical inference results were reported per publication in both journal A and B. Correction for multiple testing was performed in 15% of the articles published in journal A and in 6% from journal B. The estimated median risk of obtaining at least one significant result for uncorrected studies was calculated to be 54% for both journals. Conclusion: This study shows that the risk of false significant findings is considerable and that correcting for multiple testing is only performed in a small percentage of all articles published in the orthopedic literature reviewed.

Description: Background: Ischemic preconditioning has been proposed to involve changes in mitochondrial H+ and K+ fluxes, in particular through activation of uncoupling proteins and ATP-sensitive K+ channels (MitoKATP). The objectives of the present study were to explore how increased H+ and K+ fluxes influence heart mitochondrial physiology with regard to production and scavenging of reactive oxygen species (ROS), volume changes and resistance to calcium-induced mitochondrial permeability transition (mPT). Results: Isolated rat heart mitochondria were exposed to a wide concentration range of the protonophore CCCP or the potassium ionophore valinomycin to induce increased H+ and K+ conductance, respectively. Simultaneous monitoring of mitochondrial respiration and calcium retention capacity (CRC) demonstrated that the relative increase in respiration caused by valinomycin or CCCP correlated with a decrease in CRC, and that no level of respiratory uncoupling was associated with enhanced resistance to mPT. Mitochondria suspended in hyperosmolar buffer demonstrated a dose-dependent reduction in CRC with increasing osmolarity. However, mitochondria in hypoosmolar buffer to increase matrix volume did not display increased CRC. ROS generation was reduced by both K+- and H+-mediated respiratory uncoupling. The ability of heart mitochondria to detoxify H2O2 was substantially greater than the production rate. The H2O2 detoxification was dependent on respiratory substrates and was dramatically decreased following calcium-induced mPT, but was unaffected by uncoupling via increased K+ and H+ conductance. Conclusion: It is concluded that respiratory uncoupling is not directly beneficial to rat heart mitochondrial resistance to calcium overload irrespective of whether H+ or K+ conductance is increased. The negative effects of respiratory uncoupling thus probably outweigh the reduction in ROS generation and a potential positive effect by increased matrix volume, resulting in a net sensitization of heart mitochondria to mPT activation.

Description: Background: Most turtles from the Middle and Late Jurassic of Asia are referred to the newly defined clade Xinjiangchelyidae, a group of mostly shell-based, generalized, small to mid-sized aquatic froms that are widely considered to represent the stem lineage of Cryptodira. Xinjiangchelyids provide us with great insights into the plesiomorphic anatomy of crown-cryptodires, the most diverse group of living turtles, and they are particularly relevant for understanding the origin and early divergence of the primary clades of extant turtles. Results: Exceptionally complete new xinjiangchelyid material from the ?Qigu Formation of the Turpan Basin (Xinjiang Autonomous Province, China) provides new insights into the anatomy of this group and is assigned to Xinjiangchelys wusu n. sp. A phylogenetic analysis places Xinjiangchelys wusu n. sp. in a monophyletic polytomy with other xinjiangchelyids, including Xinjiangchelys junggarensis, X. radiplicatoides, X. levensis and X. latiens. However, the analysis supports the unorthodox, though tentative placement of xinjiangchelyids and sinemydids outside of crown-group Testudines. A particularly interesting new observation is that the skull of this xinjiangchelyid retains such primitive features as a reduced interpterygoid vacuity and basipterygoid processes. Conclusions: The homology of basipterygoid processes is confidently demonstrated based on a comprehensive review of the basicranial anatomy of Mesozoic turtles and a new nomenclatural system is introduced for the carotid canal system of turtles. The loss of the basipterygoid process and the bony enclosure of the carotid circulation system occurred a number of times independently during turtle evolution suggesting that the reinforcement of the basicranial region was essential for developing a rigid skull, thus paralleling the evolution of other amniote groups with massive skulls.

Description: Background: The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions. Results: By analysing 67 completely sequenced plant genomes 775 myosins were identified and manually assembled. Phylogenetic trees of the myosin motor domains revealed orthologous and paralogous relationships and were consistent with recent species trees. Based on the myosin inventories and the phylogenetic trees, we have identified duplications of the entire myosin motor protein family at timings consistent with 23 WGDs, that had been reported before. We also predict 6 WGDs based on further protein family duplications. Notably, the myosin data support the two recently reported WGDs in the common ancestor of all extant angiosperms. We predict single WGDs in the Manihot esculenta and Nicotiana benthamiana lineages, two WGDs for Linum usitatissimum and Phoenix dactylifera, and a triplication or two WGDs for Gossypium raimondii. Our data show another myosin duplication in the ancestor of the angiosperms that could be either the result of a single gene duplication or a remnant of a WGD. Conclusions: We have shown that the myosin inventories in angiosperms retain evidence of numerous WGDs that happened throughout plant evolution. In contrast to other protein families, many myosins are still present in extant species. They are closely related and have similar domain architectures, and their phylogenetic grouping follows the genome duplications. Because of its broad taxonomic sampling the dataset provides the basis for reliable future identification of further whole genome duplications.

Description: Background: The coexistence of macromolecular replicators and thus the stability of presumed prebiotic replicator communities have been shown to critically depend on spatially constrained catalytic cooperation among RNA-like modular replicators. The necessary spatial constraints might have been supplied by mineral surfaces initially, preceding the more effective compartmentalization in membrane vesicles which must have been a later development of chemical evolution. Results: Using our surface-bound RNA world model -- the Metabolic Replicator Model (MRM) platform -- we show that the mobilities on the mineral substrate surface of both the macromolecular replicators and the small molecules of metabolites they produce catalytically are the key factors determining the stable persistence of an evolvable metabolic replicator community. Conclusion: The effects of replicator mobility and metabolite diffusion on different aspects of replicator coexistence in MRM are determined, including the maximum attainable size of the metabolic replicator system and its resistance to the invasion of parasitic replicators. We suggest a chemically plausible hypothetical scenario for the evolution of the first protocell starting from the surface-bound MRM system.

Description: Background: Edwardsiella tarda is an enterobacterium which causes edwardsiellosis, a fatal disease of cultured fishes such as red sea bream, eel, and flounder. Preventing the occurrence of E. tarda infection has thus been an important issue in aquaculture. E. tarda has been isolated from other animals and from many environments; however, the relationship between the genotype and evolutionary process of this pathogen is not fully understood. To clarify this relationship, we sequenced and compared the genomes of pathogenic and non-pathogenic E. tarda strains isolated from fish, human, and eel pond using next-generation sequencing technology. Results: Eight strains of E. tarda were sequenced with high accuracy (〉99.9%) with coverages from 50- to 400-fold. The obtained reads were mapped to a public reference genome. By comparing single nucleotide and insertion/deletion polymorphisms, we found that an attenuated strain of E. tarda had a loss-of-function mutation in a gene related to the type III secretion system (T3SS), suggesting that this gene is involved in the virulence of E. tarda. A comprehensive gene comparison indicated that fish pathogenic strains possessed a type VI secretion system (T6SS) and pilus assembly genes in addition to the T3SS. Moreover, we found that an E. tarda strain isolated from red sea bream harbored two pathogenicity islands of T3SS and T6SS, which were absent in other strains. In particular, this T3SS was homologous to the locus of enterocyte effacement (LEE) in enteropathogenic and enterohemorrhagic Escherichia coli. Evolutionary analysis suggested that this locus, here named Et-LEE (E. tarda LEE), was introgressed into the E. tarda genome through horizontal transfer. Conclusions: We found significant differences in the presence/absence of virulence-related genes among E. tarda strains, reflecting their evolutionary relationship. In particular, a single genotype previously proposed for fish-pathogenic strains may be further divided into two subgroups. Furthermore, the current study demonstrated, for the first time, that a fish pathogenic bacterium carried a LEE-like pathogenicity island which was previously reported only in zoonotic pathogenic enterobacteria. These findings will contribute to the exploration of strain-specific drug targets against E. tarda in aquafarms, while also shedding light on the evolution of pathogenesis in enterobacteria.

Description: Uptake of phytodetritus by benthic foraminifera under oxygen depletion at the Indian Margin (Arabian Sea) Biogeosciences Discussions, 10, 15305-15335, 2013 Author(s): A. J. Enge, U. Witte, M. Kucera, and P. Heinz Benthic foraminifera in sediments on the Indian margin of the Arabian Sea where the oxygen minimum zone (OMZ) impinges on the continental slope are exposed to particularly severe levels of oxygen depletion. Food supply for the benthic community is high but delivered in distinct pulses during upwelling and water mixing events associated with summer and winter monsoon periods. In order to investigate the response by benthic foraminifera to such pulsed food delivery under oxygen concentrations of less than 0.1 mL L −1 (4.5 μmol L −1 ), an in situ isotope labeling experiment ( 13 C, 15 N) was performed at the western continental slope of India at 540 m water depth (OMZ core region). The assemblage of living foraminifera (〉125 μm) in the uppermost centimeter at this depth is characterized by an unexpectedly high population density of 3982 ind. 10 cm −2 and a strong dominance by few calcareous species. For the experiment, we concentrated on the nine most abundant taxa, which constitute 93% of the entire foraminifera population at 0–1 cm sediment depth. Increased concentrations of 13 C and 15 N in the cytoplasm indicate that all investigated taxa took up the labeled phytodetritus during the 4 day experimental phase. In total, these nine species had assimilated 113.8 mg C m −2 (17.5% of the total added carbon). The uptake of nitrogen by the three most abundant taxa ( Bolivina aff. B. dilatata , Cassidulina sp., Bulimina gibba ) was 2.7 mg N m −2 (2% of the total added nitrogen) and showed the successful application of 15 N as tracer in foraminiferal studies. The short-term response to the offered phytodetritus varied largely among foraminiferal species with Uvigerina schwageri being by far the most important species in short-term processing whereas the most abundant taxa Bolivina aff. B. dilatata and Cassidulina sp. showed comparably low uptake of the offered food. We suggest that the observed species-specific differences are related to individual biomass of species and to specific feeding preferences. The high numbers of living foraminifera and their rapid response to deposited fresh phytodetritus demonstrate the importance of foraminifera in short-term carbon cycling under oxygen-depleted conditions. We propose that foraminifera at the studied site benefit from unique adaptations in their metabolisms to nearly anoxic conditions as well as from the exclusion of macrofauna and the resulting relaxation of competition for food and low predation pressure.

Description: Background: Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data.The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first "Archetypal Analysis" of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas aeruginosa isolated from the airways of cystic fibrosis patients. Results: Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. Conclusions: Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data.