Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

<p>Abstract</p> <p>Background</p> <p><it>Candida parapsilosis </it>is one of the most common causes of <it>Candida </it>infection worldwide. However, the genome sequence annotation was made without experimental validation and little is known about the transcriptional landscape. The transcriptional response of <it>C. parapsilosis </it>to hypoxic (low oxygen) conditions, such as those encountered in the host, is also relatively unexplored.</p> <p>Results</p> <p>We used next generation sequencing (RNA-seq) to determine the transcriptional profile of <it>C. parapsilosis </it>growing in several conditions including different media, temperatures and oxygen concentrations. We identified 395 novel protein-coding sequences that had not previously been annotated. We removed > 300 unsupported gene models, and corrected approximately 900. We mapped the 5' and 3' UTR for thousands of genes. We also identified 422 introns, including two introns in the 3' UTR of one gene. This is the first report of 3' UTR introns in the Saccharomycotina. Comparing the introns in coding sequences with other species shows that small numbers have been gained and lost throughout evolution. Our analysis also identified a number of novel transcriptional active regions (nTARs). We used both RNA-seq and microarray analysis to determine the transcriptional profile of cells grown in normoxic and hypoxic conditions in rich media, and we showed that there was a high correlation between the approaches. We also generated a knockout of the <it>UPC2 </it>transcriptional regulator, and we found that similar to <it>C. albicans</it>, Upc2 is required for conferring resistance to azole drugs, and for regulation of expression of the ergosterol pathway in hypoxia.</p> <p>Conclusion</p> <p>We provide the first detailed annotation of the <it>C. parapsilosis </it>genome, based on gene predictions and transcriptional analysis. We identified a number of novel ORFs and other transcribed regions, and detected transcripts from approximately 90% of the annotated protein coding genes. We found that the transcription factor Upc2 role has a conserved role as a major regulator of the hypoxic response in <it>C. parapsilosis </it>and <it>C. albicans</it>.</p

Novel inhibitors of the calcineurin/NFATc hub - alternatives to CsA and FK506?

The drugs cyclosporine A (CsA) and tacrolimus (FK506) revolutionized organ transplantation. Both compounds are still widely used in the clinic as well as for basic research, even though they have dramatic side effects and modulate other pathways than calcineurin-NFATc, too. To answer the major open question - whether the adverse side effects are secondary to the actions of the drugs on the calcineurin-NFATc pathway - alternative inhibitors were developed. Ideal inhibitors should discriminate between the inhibition of (i) calcineurin and peptidyl-prolyl cis-trans isomerases (PPIases; the matchmaker proteins of CsA and FK506), (ii) calcineurin and the other Ser/Thr protein phosphatases, and (iii) NFATc and other transcription factors. In this review we summarize the current knowledge about novel inhibitors, synthesized or identified in the last decades, and focus on their mode of action, specificity, and biological effects

Elucidation of glutamine lipid biosynthesis in marine bacteria reveals its importance under phosphorus deplete growth in Rhodobacteraceae

Marine microorganisms employ multiple strategies to cope with transient and persistent nutrient limitation, one of which, for alleviating phosphorus (P) stress, is to substitute membrane glycerophospholipids with non-P containing surrogate lipids. Such a membrane lipid remodelling strategy enables the most abundant marine phytoplankton and heterotrophic bacteria to adapt successfully to nutrient scarcity in marine surface waters. An important group of non-P lipids, the aminolipids which lack a diacylglycerol backbone, are poorly studied in marine microbes. Here, using a combination of genetic, lipidomics and metagenomics approaches, we reveal for the first time the genes (glsB, olsA) required for the formation of the glutamine-containing aminolipid. Construction of a knockout mutant in either glsB or olsA in the model marine bacterium Ruegeria pomeroyi DSS-3 completely abolished glutamine lipid production. Moreover, both mutants showed a considerable growth cost under P-deplete conditions and the olsA mutant, that is unable to produce the glutamine and ornithine aminolipids, ceased to grow under P-deplete conditions. Analysis of sequenced microbial genomes show that glsB is primarily confined to the Rhodobacteraceae family, which includes the ecologically important marine Roseobacter clade that are key players in the marine sulphur and nitrogen cycles. Analysis of the genes involved in glutamine lipid biosynthesis in the Tara ocean metagenome dataset revealed the global occurrence of glsB in marine surface waters and a positive correlation between glsB abundance and N* (a measure of the deviation from the canonical Redfield ratio), suggesting glutamine lipid plays an important role in the adaptation of marine Rhodobacteraceae to P limitation

REanalysis of the TROpospheric chemical composition over the past 40 years FIRE ENGINE View project FUELMON -remote FUEL break MONitoring for forest fire protection View project

REanalysis of the TROpospheric chemical composition over thepast 40 years (RETRO)Objectives:• exploit (often under-utilised) existing data sets from ground based stations,aircraft, and satellite instruments, integrating these into common datasets,• develop tools for the analysis, interpretation and exploitation of the data,• formulate recommendations for future measurement strategies,• assess changes in trace compound emissions and their effect on troposphericchemical composition and aerosols, and the associated radiative forcing, overthe past 40 years,• provide an assessment of uncertainties caused by climate variability,• evaluate emission control strategies in Europe,• predict changes over the next 20 years in tropospheric composition, andradiative forcing through model studies using the emission scenarios definedfor the IPCC 2001 climate assessment,• analyze the magnitude of intercontinental pollutant transport.Scientific achievements:• first detailed, comprehensive and consistent data sets on global emissionsfrom fossil and biofuel combustion and from open vegetation burningcovering the time period 1960-2000; available as gridded data sets with0.5°×0.5° and monthly mean resolution,• first global long-term atmospheric chemistry integrations with several stateof-the-art models using the ERA-40 meteorological data, the RETROemissions and other constrains in a consistent and well-documented manner,• analysis of key parameters controlling the interannual and seasonalvariability and the longer-term trends in the tropospheric composition relatedto ozone and its precursors,• development of new software tools for the analysis of observational data andmodel results; standardisation of model output and data formats anddefinition of model evaluation metrics and skill scores,• development of a comprehensive data base for tropospheric compositionobservations with complete metadata definition and a user-friendly interfacefor data access,• multi-model analysis of specific scenarios related to power generation andthe traffic sector in OECD countries,• contributions to the IPCC 4th assessment report through participation in amulti-model assessment study coordinated by the ACCENT network ofexcellenceMain deliverables:• gridded data sets of global emissions from 1960 to 2000 (D1-4)• gridded data sets of simulated concentrations of ozone and ozone precursorsfrom 1960 to 2000 (D4-3)• data base of atmospheric observationsreport on the RETRO emission inventories (D1-6)o report on trend analysis based on observational data (D2-3)o reports on sensitivity studies (D3-2, D3-3 and D3-4)o report on the long-term reanalysis simulations (D4-4)o reports on changes in UV and radiative forcing (D5-1 and D5-2)o analysis of past policy measures including scenario studies (D5-5)All RETRO deliverables are available on the RETRO ftp serverftp://ftp.retro.enes.org/pub or via the RETRO web pages http://retro.enes.org.Socio-economic relevance and policy implications:Understanding past trends in large-scale air pollution is a key requirement toformulate future strategies to enhance air quality in Europe and elsewhere. Due tothe scarcity of observational data (particularly for years before 1990), numericalmodels are the only way to obtain comprehensive and consistent information onpast trends in tropospheric ozone and related substances. The model simulationsin RETRO also allow for evaluating the impact of important parameters on theinterannual variability of air pollution in Europe. From specific sensitivity studiesthe roles of meteorological variability, variability in anthropogenic emissions andvariability in wildland fire emissions could be determined. Scenario calculationson the impact of certain policy measures to reduce emissions from powergeneration or from the traffic sector provide a direct answer to the potentialconsequences of the introduction of more stringent air pollution abatementmeasures. Due to the effects of intercontinental transport of air pollution, localmeasures may not always achieve the expected results. These issues can only beaddressed with comprehensive, well-constrained global model simulations as theywere pioneered in the RETRO project. Several of the tools and methodologiesdeveloped in RETRO are now applied in ongoing projects with a more immediatepolicy link (especially the FP6 integrated project GEMS and the multi-modelassessment activity under the auspices of the task force on hemispheric transportof air pollution).Conclusions:• RETRO contributed significant developments to advance the state-of-the-artin global atmospheric chemistry modelling in terms of new long-termemissions data and the first comprehensive long-term multi-modelintegrations of atmospheric chemistry and transport,• The RETRO models generally show very good consistency in terms ofinterannual variability and trend patterns, but they occasionally differsignificantly in the absolute values of the simulated concentrations of ozoneand its precursors,• Comparison with observations shows that the RETRO models often capturethe atmospheric variability patterns rather well and that the mean modelgenerally provides a reasonable description of the chemical state of theatmosphere. Some exceptions are noted, in particular the absence of anincreasing ozone trend over central Europe in the 1990s which is clearly seenfrom measurements at several mountain stations,• According to the RETRO simulations, summertime boundary layerconcentrations of ozone over Europe increased between 5 and 15 ppb (10-20%) between 1960 and the year 2000. Further abatement measures in thetraffic sector (introduction of the EURO 5 standard in all OECD countries)could lead to a reduction of summertime ozone by 8-10%.• A renewed effort following on the RETRO activities would be highlydesirable in order to further expand the available emission data sets(inclusion of SO2, aerosol precursors and greenhouse gases and review ofnatural emissions), to further investigate the underlying causes fortropospheric composition change and to include the analysis of feedbacksbetween tropospheric ozone, climate change and aerosols.Dissemination of results:• more than 30 articles appeared in peer reviewed scientific journals with director indirect contributions from the RETRO project,• RETRO project results were presented in more than 100 conferencecontributions and presentations at international meetings,• a specific session on “tropospheric trends and variability” was inaugurated atthe EGU General Symposium 2004 and was repeated in 2006 and 2007,• RETRO emission data sets are being used in several ongoing researchprojects (e.g. GEMS and TFHTAP, GREENCYCLES, etc.),• All RETRO data sets and reports are available on the RETRO ftp serverftp://ftp.retro.enes.org/pub or via the RETRO web pages athttp://retro.enes.org

Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity

International audienc