A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus

In this study, genome-wide expression profiling based on Affymetrix ATH1 arrays was used to identify discriminating responses of Arabidopsis thaliana to five herbicides, which contain active ingredients targeting two different branches of amino acid biosynthesis. One herbicide contained glyphosate, which targets 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), while the other four herbicides contain different acetolactate synthase (ALS) inhibiting compounds. In contrast to the herbicide containing glyphosate, which affected only a few transcripts, many effects of the ALS inhibiting herbicides were revealed based on transcriptional changes related to ribosome biogenesis and translation, secondary metabolism, cell wall modification and growth. The expression pattern of a set of 101 genes provided a specific, composite signature that was distinct from other major stress responses and differentiated among herbicides targeting the same enzyme (ALS) or containing the same chemical class of active ingredient (sulfonylurea). A set of homologous genes could be identified in Brassica napus that exhibited a similar expression pattern and correctly distinguished exposure to the five herbicides. Our results show the ability of a limited number of genes to classify and differentiate responses to closely related herbicides in A. thaliana and B. napus and the transferability of a complex transcriptional signature across species

Anthropogenic perturbations of the silicon cycle at the global scale: Key role of the land-ocean transition

International audienceSilicon (Si), in the form of dissolved silicate (DSi), is a key nutrient in marine and continental ecosystems. DSi is taken up by organisms to produce structural elements (e.g., shells and phytoliths) composed of amorphous biogenic silica (bSiO(2)). A global mass balance model of the biologically active part of the modern Si cycle is derived on the basis of a systematic review of existing data regarding terrestrial and oceanic production fluxes, reservoir sizes, and residence times for DSi and bSiO(2). The model demonstrates the high sensitivity of biogeochemical Si cycling in the coastal zone to anthropogenic pressures, such as river damming and global temperature rise. As a result, further significant changes in the production and recycling of bSiO(2) in the coastal zone are to be expected over the course of this century

Mechanisms driving the seasonality of air-sea CO₂ flux in the ice-free zone of the Southern Ocean and how these might evolve: A 1D vertical biogeochemical model approach

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What drives the seasonality of air-sea CO₂ fluxes in the ice-free zone of the southern ocean: A 1D coupled physical-biogeochemical model approach

International audienceThe complex biogeochemical SWAMCO-3 model has been used to assess the response of the ice-free Southern Ocean to the physical and biological mechanisms governing air-sea CO2 exchanges. For this application, the model explicitly details the dynamics of three Phytoplankton Functional Types (PFTs) of importance for C, N, P, Si, Fe cycling and air-sea CO2 exchange in this area. These are the diatoms, the pico-nanophytoplankton and the coccolithophores whose growth regulation by light, temperature and nutrients has been obtained from a literature review of phenomenological observations available for these PFTs. The performance of the SWAMCO-3 model coupled to a vertical one-dimensional physical model was first assessed at the location of the JGOFS time-series station KERFIX. The model was able to reproduce a mean seasonal cycle based on years where a maximum of chemical and biological observations are available at this location (1993–1994, 1994–1995, 1998–1999 and 2000–2001). Ocean fCO2 in equilibrium with the atmosphere are simulated both in Austral winter associated with surface layer replenishment in DIC due to deep vertical mixing and in late summer as a consequence of the warming effect on the carbonate system. A clear under-saturation is found in spring/summer. Analysis of the modelled seasonal biogeochemical and physical features shows that thermodynamical conditions are driving the air-sea exchange of CO2 in the region, while the biological activity under the control of light and iron availability, is responsible for the predicted relatively modest annual carbon sink (− 0.9 mol C m-2 y-1

A high-density random-oligonucleotide genome microarray for universal diagnostics

Microarrays offer virtually unlimited diagnostics capability, and have already been developed into diagnostic chips for many different plant pests. The full capacity of such chips, however, has lagged far behind their full potential. The main reason for this is that current chip design relies on a priori genetic information for target organisms and on a consensus on the genetic sequences to be used in particular organism groups. Such information is often unavailable and laborious to obtain. Thus, broad-application diagnostic microarrays have been limited to narrow organism groups focused on Genera of pests/pathogens or those affecting individual host crops, without applicability for simultaneous detection of diverse pests affecting many crops. This paper describes the development of a diagnostic microarray platform that has universal application based on genomic fingerprinting of any organism without a need for a priori sequence information. Taxon-specific hybridization patterns are obtained by unique hybridisation of genomic DNA to 100s–1000s of short random oligonucleotide probes. Taxon identification is then achieved by comparison of hybridisation patterns from an unknown sample against a reference-pattern database. Using bacteria as a model pathogen group, these methods deliver highly reproducible hybridisation patterns with high resolution power and enable discrimination at the species and subspecies level

Multicentre study of neoadjuvant chemotherapy for stage I and II oesophageal cancer

International audienceBackground The benefit of neoadjuvant chemotherapy (NCT) for early-stage oesophageal cancer is unknown. The aim of this study was to assess whether NCT improves the outcome of patients with stage I or II disease. Methods Data were collected from 30 European centres from 2000 to 2010. Patients who received NCT for stage I or II oesophageal cancer were compared with patients who underwent primary surgery with regard to postoperative morbidity, mortality, and overall and disease-free survival. Propensity score matching was used to adjust for differences in baseline characteristics. Results Of 1173 patients recruited (181 NCT, 992 primary surgery), 651 (55·5 per cent) had clinical stage I disease and 522 (44·5 per cent) had stage II disease. Comparisons of the NCT and primary surgery groups in the matched population (181 patients in each group) revealed in-hospital mortality rates of 4·4 and 5·5 per cent respectively (P = 0·660), R0 resection rates of 91·7 and 86·7 per cent (P = 0·338), 5-year overall survival rates of 47·7 and 38·6 per cent (hazard ratio (HR) 0·68, 95 per cent c.i. 0·49 to 0·93; P = 0·016), and 5-year disease-free survival rates of 44·9 and 36·1 per cent (HR 0·68, 0·50 to 0·93; P = 0·017). Conclusion NCT was associated with better overall and disease-free survival in patients with stage I or II oesophageal cancer, without increasing postoperative morbidit

Mean hydrography on the continental shelf from 26 repeat glider deployments along Southeastern Australia

© The Author(s) 2016.Since 2008, 26 glider missions have been undertaken along the continental shelf of southeastern Australia. Typically these missions have spanned the continental shelf on the inshore edge of the East Australian Current from 29.5-33.5°S. This comprehensive dataset of over 33,600 CTD profiles from the surface to within 10 m of the bottom in water depths ranging 25-200 m provides new and unprecedented high resolution observations of the properties of the continental shelf waters adjacent to a western boundary current, straddling the region where it separates from the coast. The region is both physically and biologically significant, and is also in a hotspot of ocean warming. We present gridded mean fields for temperature, salinity and density, but also dissolved oxygen and chlorophyll-a fluorescence indicative of phytoplankton biomass. This data will be invaluable for understanding shelf stratification, circulation, biophysical and bio-geochemical interactions, as well as for the validation of high-resolution ocean models or serving as teaching material

Survival benefit of neoadjuvant treatment in clinical T3N0M0 esophageal cancer: results from a retrospective multicenter European study

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Assessing the sensitivity of the Southern Ocean’s biological carbon pump to climate change (BELCANTO II): final report

BELCANTO (BELgian research on Carbon uptake in the ANTarctic Ocean) is a longterm project aiming at applying and developing process-level studies, geochemical proxy tools and numerical tools for assessing and understanding the present-day functioning of the CO2 biological pump in the iron-limited Southern Ocean (S.O.) and for predicting its evolution in response to scenarios of increasing atmospheric CO2. Over the last four years BELCANTO implemented and developed several multi-proxy approaches for assessing nutrient consumption and carbon fluxes, including 234Thdeficit and natural silicon isotopic composition. High quality results were obtained for whole water column δ29Si-silicate and δ29Si-opal, including first ever results for the low silicate Subantarctic region. Results show that the δ29Si signature of diatoms appears to be homogeneous in the mixed layer and between diatom species. The preferential uptake of light isotope by diatoms is well reflected in the vertical distribution of silicate δ29Si, as well as in the upper ocean silicate δ29Si values which increase northwards in parallel with the decrease of silicate concentration. However, the relationship between δ29Si and silicate concentration appears complex and depends on variations in vertical and horizontal supply of silicate. Results based on other proxy tools (Baxs 234Th-deficit, f-ratio & new production) indicate relatively high particulate carbon export and absence of strong mesopelagic mineralization in the Subantarctic Zone, but relatively low export and enhanced mesopelagic mineralization further south in the Polar Front Zone and the southern ACC. Furthermore, remineralization was clearly enhanced during summer as compared to spring. Our observations of 234Th-based carbon export and new production along cross frontal transects also appear to challenge the widely accepted idea of enhanced primary and export production in the Subantarctic Zone and the Polar Frontal Zone, compared to more southern areas. Laboratory-controlled experiments on two widespread phytoplankton species (diatoms-Thalassiosira gravida and Phaeocystis Antarctica) showed an effect of Fe addition on the morphological form, enhancing the presence of the colonial form compared to the free-living cells for Phaeocystis and increasing the appearance of long chains of diatoms vs. free living cells. Under Fe enriched conditions, the maximum photosynthesis and growth rates increased. In addition the quality of the organic matter was modified, enhancing bacterial remineralization. Consequently, Fe addition may impact on the fate of the phytoplankton in the planktonic food web and the resulting efficiency of the biological pump. Accordingly, during the EIFEX large scale iron enrichment experiment, iron addition fosters a diatom bloom which appeared to broke up rather fast and to sink rapidly accordingly to 234Th measurements. This in turn triggered mesopelagic mineralization as evidenced in Baxs measurements. N-uptake experiments with Fe-limited and Fe-replete natural algal communities indicate that the effects of ammonium and iron on f-ratio and new production are not simply cumulative and that the enhancement of the f-ratio due to Fe addition depends on the ambient ammonium concentration. However the relationship between this enhancement and ammonium concentration is at present not fully understood. Our results imply that there is no simple relationship between export production and iron availability. Ammonium appears to counter the effects of iron addition on export production, particularly for HNLC areas such as the Southern Ocean. The meso-scale iron enrichment experiment performed during the EIFEX cruise, clearly showed that iron addition induced a diatom bloom but that the latter did not persist for long and collapsed soon after, thereby inducing a massive export of carbon as witnessed from significant deficits in 234Th activity. This export in turn triggered mesopelagic organic carbon mineralization as evidenced by excess Baxs contents. Measurements of pCO2, scaled using remote sensing data (sea surface temperature, chlorophyll and wind stress) and related CO2 fluxes, suggest that previous budgets of atmospheric CO2 uptake in the S.O. may be overestimated. However, our observations indicate that sea ice cover can act as an additional CO2 sink not taken into account in previous CO2 budgets. This sea-ice CO2 sink function results from physical and biogeochemical processes prevailing within the sea ice itself. Results obtained with SWAMCO-4, an idealized 1-D model of the marine planktonic system calculating C, N, P, Si, Fe cycling within the upper ocean, the export production and air-sea CO2 fluxes, suggest that the sink for atmospheric CO2 will increase in response to the raising atmospheric CO2 concentration. SWAMCO-4 simulations show that the amplitude of the predicted CO2 sink displays large regional and inter-annual variations which are related to local hydrodynamics and the dominant phytoplankton species. This is particularly acute in the Phaeocystis-dominated marginal ice zone of the Ross Sea. There the predicted annual CO2 sink appears positively related to the length of the sea ice cover period. This results from the accumulation of iron within the ice and its sudden release in the water column at the time of ice melting, favoring algal growth. The past and future evolution of the sea ice cover was conducted using the ORCA2- LIM and ECBILT-CLIO 3D ice-ocean models. The influence of the Southern Annular Mode on zonal integrated sea surface temperature and ice concentration seems to be small due to counteracting effects. Over the last 250 years, the annual mean ice coverage decreased in response to both natural and anthropogenic forcing, with the impact of the latter forcing clearly being enhanced over the last 150 years. Nowadays, the decrease of ice cover is more acute in the northern hemisphere as compared to the southern hemisphere, and this difference is due to thermal inertia of the S.O. However, model outputs predict a more abrupt decrease of S.O. sea ice extent in the future, resulting in similar decreases of annual mean sea ice extents in both hemispheres by the end of the century. In parallel, the seasonal amplitude of sea ice extent will increase. Preliminary runs with the coupled ice-ocean-biogeochemical model ORCA-LIMSWAMCO- 4, predict that the efficiency of the S.O. biological pump will be very sensitive to changes in the seasonal amplitude and the mean extent of the ice cover