Showing papers by "Leibniz Association published in 2012"

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Abstract: Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

A cross-platform toolkit for mass spectrometry and proteomics

Abstract: Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and quantify the proteins in biological and clinical samples1, identify pathways affected by endogenous and exogenous perturbations2, and characterize protein complexes3. Despite successes, the interpretation of vast proteomics datasets remains a challenge. There have been several calls for improvements and standardization of proteomics data analysis frameworks, as well as for an application-programming interface for proteomics data access4,5. In response, we have developed the ProteoWizard Toolkit, a robust set of open-source, software libraries and applications designed to facilitate proteomics research. The libraries implement the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats. In addition, diverse software classes enable rapid development of vendor-agnostic proteomics software. Additionally, ProteoWizard projects and applications, building upon the core libraries, are becoming standard tools for enabling significant proteomics inquiries.

Refining the theory of basic individual values.

Abstract: We propose a refined theory of basic individual values intended to provide greater heuristic and explanatory power than the original theory of 10 values (Schwartz, 1992). The refined theory more accurately expresses the central assumption of the original theory that research has largely ignored: Values form a circular motivational continuum. The theory defines and orders 19 values on the continuum based on their compatible and conflicting motivations, expression of self-protection versus growth, and personal versus social focus. We assess the theory with a new instrument in 15 samples from 10 countries (N 6,059). Confirmatory factor and multidimensional scaling analyses support discrimination of the 19 values, confirming the refined theory. Multidimensional scaling analyses largely support the predicted motivational order of the values. Analyses of predictive validity demonstrate that the refined values theory provides greater and more precise insight into the value underpinnings of beliefs. Each value correlates uniquely with external variables.

A physical, genetic and functional sequence assembly of the barley genome

Abstract: Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.

Animal personalities: consequences for ecology and evolution

Abstract: Personality differences are a widespread phenomenon throughout the animal kingdom. Past research has focused on the characterization of such differences and a quest for their proximate and ultimate causation. However, the consequences of these differences for ecology and evolution received much less attention. Here, we strive to fill this gap by providing a comprehensive inventory of the potential implications of personality differences, ranging from population growth and persistence to species interactions and community dynamics, and covering issues such as social evolution, the speed of evolution, evolvability, and speciation. The emerging picture strongly suggests that personality differences matter for ecological and evolutionary processes (and their interaction) and, thus, should be considered a key dimension of ecologically and evolutionarily relevant intraspecific variation.

CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets.

Abstract: Liquid chromatography coupled to mass spectrometry is routinely used for metabolomics experiments. In contrast to the fairly routine and automated data acquisition steps, subsequent compound annotation and identification require extensive manual analysis and thus form a major bottleneck in data interpretation. Here we present CAMERA, a Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. To evaluate the algorithms, we compared the annotation of CAMERA against a manually defined annotation for a mixture of known compounds spiked into a complex matrix at different concentrations. CAMERA successfully extracted accurate masses for 89.7% and 90.3% of the annotatable compounds in positive and negative ion modes, respectively. Furthermore, we present a novel annotation approach that combines spectral information of data acquired in opposite ion modes to further improve the annotation rate. W...

Toward Principles for Enhancing the Resilience of Ecosystem Services

Abstract: Enhancing the resilience of ecosystem services (ES) that underpin human well-being is critical for meeting current and future societal needs, and requires specific governance and management policies. Using the literature, we identify seven generic policy-relevant principles for enhancing the resilience of desired ES in the face of disturbance and ongoing change in social-ecological systems (SES). These principles are (P1) maintain diversity and redundancy, (P2) manage connectivity, (P3) manage slow variables and feedbacks, (P4) foster an understanding of SES as complex adaptive systems (CAS), (P5) encourage learning and experimentation, (P6) broaden participation, and (P7) promote polycentric governance systems. We briefly define each principle, review how and when it enhances the resilience of ES, and conclude with major research gaps. In practice, the principles often co-occur and are highly interdependent. Key future needs are to better understand these interdependencies and to operationalize and apply...

Warmer climates boost cyanobacterial dominance in shallow lakes

Abstract: Dominance by cyanobacteria hampers human use of lakes and reservoirs worldwide. Previous studies indicate that excessive nutrient loading and warmer conditions promote dominance by cyanobacteria, but evidence from global scale field data has so far been scarce. Our analysis, based on a study of 143 lakes along a latitudinal transect ranging from subarctic Europe to southern South America, shows that although warmer climates do not result in higher overall phytoplankton biomass, the percentage of the total phytoplankton biovolume attributable to cyanobacteria increases steeply with temperature. Our results also reveal that the percent cyanobacteria is greater in lakes with high rates of light absorption. This points to a positive feedback because restriction of light availability is often a consequence of high phytoplankton biovolume, which in turn may be driven by nutrient loading. Our results indicate a synergistic effect of nutrients and climate. The implications are that in a future warmer climate, nutrient concentrations may have to be reduced substantially from present values in many lakes if cyanobacterial dominance is to be controlled.

Mobility particle size spectrometers: harmonization of technical standards and data structure to facilitate high quality long-term observations of atmospheric particle number size distributions

Abstract: Mobility particle size spectrometers often referred to as DMPS (Differential Mobility Particle Sizers) or SMPS (Scanning Mobility Particle Sizers) have found a wide range of applications in atmospheric aerosol research. However, comparability of measurements conducted world-wide is hampered by lack of generally accepted technical standards and guidelines with respect to the instrumental set-up, measurement mode, data evaluation as well as quality control. Technical standards were developed for a minimum requirement of mobility size spectrometry to perform long-term atmospheric aerosol measurements. Technical recommendations include continuous monitoring of flow rates, temperature, pressure, and relative humidity for the sheath and sample air in the differential mobility analyzer. We compared commercial and custom-made inversion routines to calculate the particle number size distributions from the measured electrical mobility distribution. All inversion routines are comparable within few per cent uncertainty for a given set of raw data. Furthermore, this work summarizes the results from several instrument intercomparison workshops conducted within the European infrastructure project EUSAAR (European Supersites for Atmospheric Aerosol Research) and ACTRIS (Aerosols, Clouds, and Trace gases Research InfraStructure Network) to determine present uncertainties especially of custom-built mobility particle size spectrometers. Under controlled laboratory conditions, the particle number size distributions from 20 to 200 nm determined by mobility particle size spectrometers of different design are within an uncertainty range of around ±10% after correcting internal particle losses, while below and above this size range the discrepancies increased. For particles larger than 200 nm, the uncertainty range increased to 30%, which could not be explained. The network reference mobility spectrometers with identical design agreed within ±4% in the peak particle number concentration when all settings were done carefully. The consistency of these reference instruments to the total particle number concentration was demonstrated to be less than 5%. Additionally, a new data structure for particle number size distributions was introduced to store and disseminate the data at EMEP (European Monitoring and Evaluation Program). This structure contains three levels: raw data, processed data, and final particle size distributions. Importantly, we recommend reporting raw measurements including all relevant instrument parameters as well as a complete documentation on all data transformation and correction steps. These technical and data structure standards aim to enhance the quality of long-term size distribution measurements, their comparability between different networks and sites, and their transparency and traceability back to raw data. © Author(s) 2012.

A robust feldspar luminescence dating method for Middle and Late Pleistocene sediments

Abstract: Luminescence dating is used extensively to provide absolute chronologies for Late Pleistocene sediments. Nowadays, most optical dates are based on quartz optically stimulated luminescence (OSL). However, the application of this signal is usually limited to the last ∼100 ka because of saturation of the quartz luminescence signal with dose. In contrast, the feldspar infrared stimulated luminescence (IRSL) dose–response curve grows to much higher doses; this has the potential to extend the datable age range by a factor of 4–5 compared with quartz OSL. However, it has been known for several decades that this IRSL signal is unstable, and this instability often gives rise to significant age underestimation. Here we test against independent age control the recently developed feldspar post-IR IRSL approach to the dating of sediments, which appears to avoid signal instability. A physical model explaining our observations is discussed, and the method is shown to be accurate back to 600 ka. The post-IR IRSL signal is reduced by exposure to daylight more slowly than that from quartz and low-temperature IRSL, preventing its general application to young (e.g. Holocene) sediments. Nevertheless, this new approach is widely applicable (feldspar of appropriate luminescence behaviour is even more ubiquitous than quartz). These characteristics make this a method of great importance for the dating of Middle and Late Pleistocene deposits.

Beyond the Plankton Ecology Group (PEG) Model : Mechanisms Driving Plankton Succession

Abstract: The seasonal succession of plankton is an annually repeated process of community assembly during which all major external factors and internal interactions shaping communities can be studied. A quarter of a century ago, the state of this understanding was described by the verbal plankton ecology group (PEG) model. It emphasized the role of physical factors, grazing and nutrient limitation for phytoplankton, and the role of food limitation and fish predation for zooplankton. Although originally targeted at lake ecosystems, it was also adopted by marine plankton ecologists. Since then, a suite of ecological interactions previously underestimated in importance have become research foci: overwintering of key organisms, the microbial food web, parasitism, and food quality as a limiting factor and an extended role of higher order predators. A review of the impact of these novel interactions on plankton seasonal succession reveals limited effects on gross seasonal biomass patterns, but strong effects on species replacements.

Results of the ontology alignment evaluation initiative 2012

Abstract: Ontology matching consists of finding correspondences between semantically related entities of two ontologies. OAEI campaigns aim at comparing ontology matching systems on precisely defined test cases. These test cases can use ontologies of different nature (from simple thesauri to expressive OWL ontologies) and use different modalities, e.g., blind evaluation, open evaluation, consensus. OAEI 2012 offered 7 tracks with 9 test cases followed by 21 participants. Since 2010, the campaign has been using a new evaluation modality which provides more automation to the evaluation. This paper is an overall presentation of the OAEI 2012 campaign.

B cell depletion therapy ameliorates autoimmune disease through ablation of IL-6–producing B cells

Abstract: B cells have paradoxical roles in autoimmunity, exerting both pathogenic and protective effects. Pathogenesis may be antibody independent, as B cell depletion therapy (BCDT) leads to amelioration of disease irrespective of autoantibody ablation. However, the mechanisms of pathogenesis are poorly understood. We demonstrate that BCDT alleviates central nervous system autoimmunity through ablation of IL-6–secreting pathogenic B cells. B cells from mice with experimental autoimmune encephalomyelitis (EAE) secreted elevated levels of IL-6 compared with B cells from naive controls, and mice with a B cell–specific IL-6 deficiency showed less severe disease than mice with wild-type B cells. Moreover, BCDT ameliorated EAE only in mice with IL-6–sufficient B cells. This mechanism of pathogenesis may also operate in multiple sclerosis (MS) because B cells from MS patients produced more IL-6 than B cells from healthy controls, and this abnormality was normalized with B cell reconstitution after Rituximab treatment. This suggests that BCDT improved disease progression, at least partly, by eliminating IL-6–producing B cells in MS patients. Taking these data together, we conclude that IL-6 secretion is a major mechanism of B cell–driven pathogenesis in T cell–mediated autoimmune disease such as EAE and MS.

A combinatorial TIR1/AFB–Aux/IAA co-receptor system for differential sensing of auxin

Abstract: The plant hormone auxin regulates virtually every aspect of plant growth and development. Auxin acts by binding the F-box protein transport inhibitor response 1 (TIR1) and promotes the degradation of the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) transcriptional repressors. Here we show that efficient auxin binding requires assembly of an auxin co-receptor complex consisting of TIR1 and an Aux/IAA protein. Heterologous experiments in yeast and quantitative IAA binding assays using purified proteins showed that different combinations of TIR1 and Aux/IAA proteins form co-receptor complexes with a wide range of auxin-binding affinities. Auxin affinity seems to be largely determined by the Aux/IAA. As there are 6 TIR1/AUXIN SIGNALING F-BOX proteins (AFBs) and 29 Aux/IAA proteins in Arabidopsis thaliana, combinatorial interactions may result in many co-receptors with distinct auxin-sensing properties. We also demonstrate that the AFB5–Aux/IAA co-receptor selectively binds the auxinic herbicide picloram. This co-receptor system broadens the effective concentration range of the hormone and may contribute to the complexity of auxin response.

Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley

Abstract: Robbie Waugh and colleagues report that the EARLINESS PER SE (EPS2) locus is associated with spring growth habit and environmental adaptation in barley. Resequencing the barley homolog of CENTRORADIALIS, located within the EPS2 locus, in 216 spring and 207 winter barley accessions identified haplotypes at HvCEN that correspond with winter or spring growth habit. As early farming spread from the Fertile Crescent in the Near East around 10,000 years before the present1, domesticated crops encountered considerable ecological and environmental change. Spring-sown crops that flowered without the need for an extended period of cold to promote flowering and day length–insensitive crops able to exploit the longer, cooler days of higher latitudes emerged and became established. To investigate the genetic consequences of adaptation to these new environments, we identified signatures of divergent selection in the highly differentiated modern-day spring and winter barleys. In one genetically divergent region, we identify a natural variant of the barley homolog of Antirrhinum CENTRORADIALIS2 (HvCEN) as a contributor to successful environmental adaptation. The distribution of HvCEN alleles in a large collection of wild and landrace accessions indicates that this involved selection and enrichment of preexisting genetic variants rather than the acquisition of mutations after domestication.

A new atmospherically relevant oxidant of sulphur dioxide

Abstract: Atmospheric oxidation is a key phenomenon that connects atmospheric chemistry with globally challenging environmental issues, such as climate change, stratospheric ozone loss, acidification of soils and water, and health effects of air quality. Ozone, the hydroxyl radical and the nitrate radical are generally considered to be the dominant oxidants that initiate the removal of trace gases, including pollutants, from the atmosphere. Here we present atmospheric observations from a boreal forest region in Finland, supported by laboratory experiments and theoretical considerations, that allow us to identify another compound, probably a stabilized Criegee intermediate (a carbonyl oxide with two free-radical sites) or its derivative, which has a significant capacity to oxidize sulphur dioxide and potentially other trace gases. This compound probably enhances the reactivity of the atmosphere, particularly with regard to the production of sulphuric acid, and consequently atmospheric aerosol formation. Our findings suggest that this new atmospherically relevant oxidation route is important relative to oxidation by the hydroxyl radical, at least at moderate concentrations of that radical. We also find that the oxidation chemistry of this compound seems to be tightly linked to the presence of alkenes of biogenic origin.

Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops.

Abstract: Drought is one of the most serious production constraint for world agriculture and is projected to worsen with anticipated climate change. Inter-disciplinary scientists have been trying to understand and dissect the mechanisms of plant tolerance to drought stress using a variety of approaches; however, success has been limited. Modern genomics and genetic approaches coupled with advances in precise phenotyping and breeding methodologies are expected to more effectively unravel the genes and metabolic pathways that confer drought tolerance in crops. This article discusses the most recent advances in plant physiology for precision phenotyping of drought response, a vital step before implementing the genetic and molecular-physiological strategies to unravel the complex multilayered drought tolerance mechanism and further exploration using molecular breeding approaches for crop improvement. Emphasis has been given to molecular dissection of drought tolerance by QTL or gene discovery through linkage and association mapping, QTL cloning, candidate gene identification, transcriptomics and functional genomics. Molecular breeding approaches such as marker-assisted backcrossing, marker-assisted recurrent selection and genome-wide selection have been suggested to be integrated in crop improvement strategies to develop drought-tolerant cultivars that will enhance food security in the context of a changing and more variable climate.

Toward interoperable bioscience data

Abstract: To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.

A Tutorial on Hierarchically Structured Constructs

Abstract: Many psychological constructs are conceived to be hierarchically structured and thus to operate at various levels of generality. Alternative confirmatory factor analytic (CFA) models can be used to study various aspects of this proposition: (a) The one-factor model focuses on the top of the hierarchy and contains only a general construct, (b) the first-order factor model focuses on the intermediate level of the hierarchy and contains only specific constructs, and both (c) the higher order factor model and (d) the nested-factor model consider the hierarchy in its entirety and contain both general and specific constructs (e.g., bifactor model). This tutorial considers these CFA models in depth, addressing their psychometric properties, interpretation of general and specific constructs, and implications for model-based score reliabilities. The authors illustrate their arguments with normative data obtained for the Wechsler Adult Intelligence Scale and conclude with recommendations on which CFA model is most appropriate for which research and diagnostic purposes.

The Alarmin Interleukin-33 Drives Protective Antiviral CD8+ T Cell Responses

Abstract: Pathogen-associated molecular patterns decisively influence antiviral immune responses, whereas the contribution of endogenous signals of tissue damage, also known as damage-associated molecular patterns or alarmins, remains ill defined. We show that interleukin-33 (IL-33), an alarmin released from necrotic cells, is necessary for potent CD8(+) T cell (CTL) responses to replicating, prototypic RNA and DNA viruses in mice. IL-33 signaled through its receptor on activated CTLs, enhanced clonal expansion in a CTL-intrinsic fashion, determined plurifunctional effector cell differentiation, and was necessary for virus control. Moreover, recombinant IL-33 augmented vaccine-induced CTL responses. Radio-resistant cells of the splenic T cell zone produced IL-33, and efficient CTL responses required IL-33 from radio-resistant cells but not from hematopoietic cells. Thus, alarmin release by radio-resistant cells orchestrates protective antiviral CTL responses.

Dispersion of carbon nanotubes and its influence on the mechanical properties of the cement matrix

Abstract: An appropriate dispersion of carbon nanotubes (CNTs) is a prerequisite for their use in improving the mechanical properties of cement-based composites In this study two types of carbon nanotubes (CNTs) having different morphologies were investigated To obtain a uniform distribution of CNTs in the cement matrix, the effect of sonication on the deagglomeration of CNTs in combination with anionic and nonionic surfactants in varying concentrations was quantitatively investigated when preparing aqueous dispersions of CNTs for the subsequent use in cement paste The relationships between the quality of CNT-dispersion on the one hand and the sonication time and surfactant concentration on the other were determined using UV–vis spectroscopy After dispersion, nitrogen-doped CNTs were found mostly as individual, broken CNTs In contrast, after the treatment of the mixture of single-, double-, and multi-walled CNTs, a net-like distribution was observed where destruction of the CNTs due to sonication could not be distinguished Modification of the cement pastes with dispersions of CNTs led to a pronounced increase, up to 40%, in compressive strength and, in some cases, to a moderate increase in tensile strength under high strain-rate loading However, no significant improvement in strength was observed for quasi-static loading Microscopic examination revealed that the bridging of the C–S–H phases differed depending on the type of CNT This explained, at least partly, the observed effects of CNT-addition on the mechanical properties of hardened cement pastes

DNA damage checkpoints in stem cells, ageing and cancer

Abstract: DNA damage induces cell-intrinsic checkpoints, including p53 and retinoblastoma (RB), as well as upstream regulators (exonuclease 1 (EXO1), ataxia telangiectasia mutated (ATM), ATR, p16(INK4a) and p19(ARF)) and downstream targets (p21, PUMA (p53 upregulated modulator of apoptosis) and sestrins). Clearance of damaged cells by cell-intrinsic checkpoints suppresses carcinogenesis but as a downside may impair stem cell and tissue maintenance during ageing. Modulating the activity of DNA damage checkpoints can either accelerate or decelerate tissue ageing and age-related carcinogenesis. The outcome depends on cell-intrinsic and cell-extrinsic mechanisms that regulate the clearance of damaged cells and on the molecular context in ageing tissues, including the level of DNA damage accumulation itself.

Genome-wide association studies for agronomical traits in a world wide spring barley collection.

Abstract: Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits. In this study we explored the genetic basis of variation for the traits heading date, plant height, thousand grain weight, starch content and crude protein content in a diverse collection of 224 spring barleys of worldwide origin. The whole panel was genotyped with a customized oligonucleotide pool assay containing 1536 SNPs using Illumina's GoldenGate technology resulting in 957 successful SNPs covering all chromosomes. The morphological trait "row type" (two-rowed spike vs. six-rowed spike) was used to confirm the high level of selectivity and sensitivity of the approach. This study describes the detection of QTL for the above mentioned agronomic traits by GWAS. Population structure in the panel was investigated by various methods and six subgroups that are mainly based on their spike morphology and region of origin. We explored the patterns of linkage disequilibrium (LD) among the whole panel for all seven barley chromosomes. Average LD was observed to decay below a critical level (r2-value 0.2) within a map distance of 5-10 cM. Phenotypic variation within the panel was reasonably large for all the traits. The heritabilities calculated for each trait over multi-environment experiments ranged between 0.90-0.95. Different statistical models were tested to control spurious LD caused by population structure and to calculate the P-value of marker-trait associations. Using a mixed linear model with kinship for controlling spurious LD effects, we found a total of 171 significant marker trait associations, which delineate into 107 QTL regions. Across all traits these can be grouped into 57 novel QTL and 50 QTL that are congruent with previously mapped QTL positions. Our results demonstrate that the described diverse barley panel can be efficiently used for GWAS of various quantitative traits, provided that population structure is appropriately taken into account. The observed significant marker trait associations provide a refined insight into the genetic architecture of important agronomic traits in barley. However, individual QTL account only for a small portion of phenotypic variation, which may be due to insufficient marker coverage and/or the elimination of rare alleles prior to analysis. The fact that the combined SNP effects fall short of explaining the complete phenotypic variance may support the hypothesis that the expression of a quantitative trait is caused by a large number of very small effects that escape detection. Notwithstanding these limitations, the integration of GWAS with biparental linkage mapping and an ever increasing body of genomic sequence information will facilitate the systematic isolation of agronomically important genes and subsequent analysis of their allelic diversity.

Origin and evolution of antibiotic resistance: the common mechanisms of emergence and spread in water bodies

Abstract: The environment, and especially fresh water, constitutes a reactor where the evolution and the rise of new resistances occur. In rivers or streams, bacteria from different sources such as urban, industrial and agricultural waste, probably selected by intensive antibiotic usage, are collected and mixed with environmental species. This may cause two effects on the development of antibiotic resistances: First, the contamination of water by antibiotics or other pollutants lead to the rise of resistance due to selection processes. For instance, of strains over-expressing broad range defensive mechanisms, such as efflux pumps. Second, since environmental species are provided with intrinsic antibiotic resistance mechanisms, the mixture with allochthonous species is likely to cause genetic exchange. In this context, the role of phages and integrons for the spread of resistance mechanisms appears significant. Allochthonous species could acquire new resistances from environmental donors and introduce the newly acquired resistance mechanisms into the clinics. This is illustrated by clinically relevant resistance mechanisms, such as the fluoroquinolones resistance genes qnr. Freshwater appears to play an important role in the emergence and in the spread of antibiotic resistances, highlighting the necessity for strategies of water quality improvement. Moreover, further knowledge is needed to better understand the role of the environment as reservoir of antibiotic resistances and to assess the risk of spread of antibiotic resistances via water bodies.

Fast and selective sugar conversion to alkyl lactate and lactic acid with bifunctional carbon-silica catalysts.

Abstract: A novel catalyst design for the conversion of mono- and disaccharides to lactic acid and its alkyl esters was developed. The design uses a mesoporous silica, here represented by MCM-41, which is filled with a polyaromatic to graphite-like carbon network. The particular structure of the carbon-silica composite allows the accommodation of a broad variety of catalytically active functions, useful to attain cascade reactions, in a readily tunable pore texture. The significance of a joint action of Lewis and weak Bronsted acid sites was studied here to realize fast and selective sugar conversion. Lewis acidity is provided by grafting the silica component with Sn(IV), while weak Bronsted acidity originates from oxygen-containing functional groups in the carbon part. The weak Bronsted acid content was varied by changing the amount of carbon loading, the pyrolysis temperature, and the post-treatment procedure. As both catalytic functions can be tuned independently, their individual role and optimal balance can be...

Database of diazotrophs in global ocean: abundance, biomass and nitrogen fixation rates

Abstract: . Marine N2 fixing microorganisms, termed diazotrophs, are a key functional group in marine pelagic ecosystems. The biological fixation of dinitrogen (N2) to bioavailable nitrogen provides an important new source of nitrogen for pelagic marine ecosystems and influences primary productivity and organic matter export to the deep ocean. As one of a series of efforts to collect biomass and rates specific to different phytoplankton functional groups, we have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling about 12 000 direct field measurements of cyanobacterial diazotroph abundances (based on microscopic cell counts or qPCR assays targeting the nifH genes) and N2 fixation rates. Biomass conversion factors are estimated based on cell sizes to convert abundance data to diazotrophic biomass. The database is limited spatially, lacking large regions of the ocean especially in the Indian Ocean. The data are approximately log-normal distributed, and large variances exist in most sub-databases with non-zero values differing 5 to 8 orders of magnitude. Reporting the geometric mean and the range of one geometric standard error below and above the geometric mean, the pelagic N2 fixation rate in the global ocean is estimated to be 62 (52–73) Tg N yr−1 and the pelagic diazotrophic biomass in the global ocean is estimated to be 2.1 (1.4–3.1) Tg C from cell counts and to 89 (43–150) Tg C from nifH-based abundances. Reporting the arithmetic mean and one standard error instead, these three global estimates are 140 p 9.2 Tg N yr−1, 18 p 1.8 Tg C and 590 p 70 Tg C, respectively. Uncertainties related to biomass conversion factors can change the estimate of geometric mean pelagic diazotrophic biomass in the global ocean by about p70%. It was recently established that the most commonly applied method used to measure N2 fixation has underestimated the true rates. As a result, one can expect that future rate measurements will shift the mean N2 fixation rate upward and may result in significantly higher estimates for the global N2 fixation. The evolving database can nevertheless be used to study spatial and temporal distributions and variations of marine N2 fixation, to validate geochemical estimates and to parameterize and validate biogeochemical models, keeping in mind that future rate measurements may rise in the future. The database is stored in PANGAEA ( doi:10.1594/PANGAEA.774851 ).