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Bacteriophage P22 recognizes O-antigen polysaccharides of Salmonella enterica subsp. enterica (S.) with its tailspike protein (TSP). In the serovars S. Typhimurium, S. Enteritidis, and S. Paratyphi A, the tetrasaccharide repeat units of the respective O-antigens consist of an identical main chain trisaccharide but different 3,6-dideoxyhexose substituents. Here, the epimers abequose, tyvelose and paratose determine the specific serotype. P22 TSP recognizes O-antigen octasaccharides in an extended binding site with a single 3,6-dideoxyhexose binding pocket. We have isolated S. Paratyphi A octasaccharides which were not available previously and determined the crystal structure of their complex with P22 TSP. We discuss our data together with crystal structures of complexes with S. Typhimurium and S. Enteritidis octasaccharides determined earlier. Isothermal titration calorimetry showed that S. Paratyphi A octasaccharide binds P22 TSP less tightly, with a difference in binding free energy of similar to 7 kJ mol(-1) at 20 degrees C compared with S. Typhimurium and S. Enteritidis octasaccharides. Individual protein-carbohydrate contacts were probed by amino acid replacements showing that the dideoxyhexose pocket contributes to binding of all three serotypes. However, S. Paratyphi A octasaccharides bind in a conformation with an energetically unfavorable phi/epsilon glycosidic bond angle combination. In contrast, octasaccharides from the other serotypes bind as solution-like conformers. Two water molecules are conserved in all P22 TSP complexes with octasaccharides of different serotypes. They line the dideoxyhexose binding pocket and force the S. Paratyphi A octasaccharides to bind as nonsolution conformers. This emphasizes the role of solvent as part of carbohydrate binding sites.
Palaeoenvironmental implications of evaporative gaylussite crystals from Lonar Lake, central India
(2013)
We have undertaken petrographic, mineralogical, geochemical and isotopic investigations on carbonate minerals found within a 10-m-long core from Lonar Lake, central India, with the aim of evaluating their potential as palaeoenvironmental proxies. The core encompasses the entire Holocene and is the first well-dated high-resolution record from central India. While calcite and/or aragonite were found throughout the core, the mineral gaylussite was found only in two specific intervals (46303890 and 2040560 cal a BP). Hydrochemical and isotope data from inflowing streams and lake waters indicate that evaporitic processes play a dominant role in the precipitation of carbonates within this lake. Isotopic (18O and 13C) studies on the evaporative gaylussite crystals and residual bulk carbonates (calcite) from the long core show that evaporation is the major control on 18O enrichment in both the minerals. However, in case of 13C additional mechanisms, for example methanogenesis (gaylussite) and phytoplankton productivity (calcium carbonate), play an additional important role in some intervals. We also discuss the relevance of our investigation for palaeoclimate reconstruction and late Holocene monsoon variability.
We have undertaken a high resolution palaeoclimate reconstruction on radiocarbon dated palaeolake sediments from the Spiti valley, NW Himalaya. This site lies in the climatically sensitive winter westerlies and Indian Summer Monsoon (ISM) transitional regime and provides an opportunity to reconstruct the precipitation seasonality, and extreme precipitation events that are characterised by intensified erosion. The lake sediments reveal distinct lithofacies that provide evidence of changes in depositional environment and climate during early to mid Holocene (8.7-6.1 cal ka BP). We have identified three stages during the period of lake's existence: the Stage I (8.7-7.6 cal ka BP) is marked by lake establishment; Stage II (similar to 7.6-6.8 cal ka BP) by sustained cooler periods and weakened summer monsoon, and Stage III (similar to 6.8-6.1 cal ka BP) by a shift from colder to warmer climate with stronger ISM. We have identified several short term cooler periods at ca. 8.7, 8.5, 8.3 and 7.2-6.9 cal ka BP. Based on an overview of regional climate records we show that there is an abrupt switch in precipitation seasonality ca. 6.8 cal ka BP that is followed by the onset of the intensified monsoon in the NW Himalaya. (C) 2013 Elsevier Ltd and INQUA. All rights reserved.
We report the detection of a new TeV gamma-ray source, VER J0521+211, based on observations made with the VERITAS imaging atmospheric Cherenkov Telescope Array. These observations were motivated by the discovery of a cluster of >30 GeV photons in the first year of Fermi Large Area Telescope observations. VER J0521+211 is relatively bright at TeV energies, with a mean photon flux of (1.93 +/- 0.13(stat) +/- 0.78(sys)) x 10(-11) cm(-2) s(-1) above 0.2 TeV during the period of the VERITAS observations. The source is strongly variable on a daily timescale across all wavebands, from optical to TeV, with a peak flux corresponding to similar to 0.3 times the steady Crab Nebula flux at TeV energies. Follow-up observations in the optical and X-ray bands classify the newly discovered TeV source as a BL Lac-type blazar with uncertain redshift, although recent measurements suggest z = 0.108. VER J0521+211 exhibits all the defining properties of blazars in radio, optical, X-ray, and gamma-ray wavelengths.
We report results from TeV gamma-ray observations of the microquasar Cygnus X-3. The observations were made with the Very Energetic Radiation Imaging Telescope Array System (VERITAS) over a time period from 2007 June 11 to 2011 November 28. VERITAS is most sensitive to gamma rays at energies between 85 GeV and 30 TeV. The effective exposure time amounts to a total of about 44 hr, with the observations covering six distinct radio/X-ray states of the object. No significant TeV gamma-ray emission was detected in any of the states, nor with all observations combined. The lack of a positive signal, especially in the states where GeV gamma rays were detected, places constraints on TeV gamma-ray production in Cygnus X-3. We discuss the implications of the results.
We report on the detection of a very rapid TeV gamma-ray flare from BL Lacertae on 2011 June 28 with the Very Energetic Radiation Imaging Telescope Array System (VERITAS). The flaring activity was observed during a 34.6 minute exposure, when the integral flux above 200 GeV reached (3.4 +/- 0.6) x 10(-6) photons m(-2) s(-1), roughly 125% of the Crab Nebula flux measured by VERITAS. The light curve indicates that the observations missed the rising phase of the flare but covered a significant portion of the decaying phase. The exponential decay time was determined to be 13 +/- 4 minutes, making it one of the most rapid gamma-ray flares seen from a TeV blazar. The gamma-ray spectrum of BL Lacertae during the flare was soft, with a photon index of 3.6 +/- 0.4, which is in agreement with the measurement made previously by MAGIC in a lower flaring state. Contemporaneous radio observations of the source with the Very Long Baseline Array revealed the emergence of a new, superluminal component from the core around the time of the TeV gamma-ray flare, accompanied by changes in the optical polarization angle. Changes in flux also appear to have occurred at optical, UV, and GeV gamma-ray wavelengths at the time of the flare, although they are difficult to quantify precisely due to sparse coverage. A strong flare was seen at radio wavelengths roughly four months later, which might be related to the gamma-ray flaring activities. We discuss the implications of these multiwavelength results.
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
The main goal of our target article was to provide concrete recommendations for improving the replicability of research findings. Most of the comments focus on this point. In addition, a few comments were concerned with the distinction between replicability and generalizability and the role of theory in replication. We address all comments within the conceptual structure of the target article and hope to convince readers that replication in psychological science amounts to much more than hitting the lottery twice.
Replicability of findings is at the heart of any empirical science. The aim of this article is to move the current replicability debate in psychology towards concrete recommendations for improvement. We focus on research practices but also offer guidelines for reviewers, editors, journal management, teachers, granting institutions, and university promotion committees, highlighting some of the emerging and existing practical solutions that can facilitate implementation of these recommendations. The challenges for improving replicability in psychological science are systemic. Improvement can occur only if changes are made at many levels of practice, evaluation, and reward.
In a systematic approach we synthesized a new series of fluorescent probes incorporating donoracceptor (D-A) substituted 1,2,3-triazoles as conjugative -linkers between the alkali metal ion receptor N-phenylaza-[18]crown-6 and different fluorophoric groups with different electron-acceptor properties (4-naphthalimide, meso-phenyl-BODIPY and 9-anthracene) and investigated their performance in organic and aqueous environments (physiological conditions). In the charge-transfer (CT) type probes 1, 2 and 7, the fluorescence is almost completely quenched by intramolecular CT (ICT) processes involving charge-separated states. In the presence of Na+ and K+ ICT is interrupted, which resulted in a lighting-up of the fluorescence in acetonitrile. Among the investigated fluoroionophores, compound 7, which contains a 9-anthracenyl moiety as the electron-accepting fluorophore, is the only probe which retains light-up features in water and works as a highly K+/Na+-selective probe under simulated physiological conditions. Virtually decoupled BODIPY-based 6 and photoinduced electron transfer (PET) type probes 35, where the 10-substituted anthracen-9-yl fluorophores are connected to the 1,2,3-triazole through a methylene spacer, show strong ion-induced fluorescence enhancement in acetonitrile, but not under physiological conditions. Electrochemical studies and theoretical calculations were used to assess and support the underlying mechanisms for the new ICT and PET 1,2,3-triazole fluoroionophores.
Herein, we report the synthesis of two phenylaza-[18]crown-6 lariat ethers with a coumarin fluorophore (1 and 2) and we reveal that compound 1 is an excellent probe for K+ ions under simulated physiological conditions. The presence of a 2-methoxyethoxy lariat group at the ortho position of the anilino moiety is crucial to the substantially increased stability of compounds 1 and 2 over their lariat-free phenylaza-[18] crown-6 ether analogues. Probe 1 shows a high K+/Na+ selectivity and a 2.5-fold fluorescence enhancement was observed in the presence of 100 mm K+ ions. A fluorescent membrane sensor, which was prepared by incorporating probe 1 into a hydrogel, showed a fully reversible response, a response time of 150 s, and a signal change of 7.8% per 1 mm K+ within the range 1-10 mm K+. The membrane was easily fabricated (only a single sensing layer on a solid polyester support), yet no leaching was observed. Moreover, compound 1 rapidly permeated into cells, was cytocompatible, and was suitable for the fluorescent imaging of K+ ions on both the extracellular and intracellular levels.
In aquatic systems, terrestrial dissolved organic matter (t-DOM) is known to stimulate bacterial activities in the water column, but simultaneous effects of autumnal leaf input on water column and sediment microbial dynamics in littoral zones of lakes remain largely unknown. The study's objective was to determine the effects of leaf litter on bacterial metabolism in the littoral water and sediment, and subsequently, the consequences for carbon cycling and food web dynamics. Therefore, in late fall, we simultaneously measured water and sediment bacterial metabolism in the littoral zone of a temperate shallow lake after adding terrestrial particulate organic matter (t-POM), namely, maize leaves. To better evaluate bacterial production (BP) and community respiration (CR) in sediments, we incubated sediment cores with maize leaves of different quality (nonleached and leached) under controlled laboratory conditions. Additionally, to quantify the incorporated leaf carbon into microbial biomass, we determined carbon isotopic ratios of fatty acids from sediment and leaf-associated microbes from a laboratory experiment using C-13-enriched beech leaves. The concentrations of dissolved organic carbon (DOC) increased significantly in the lake after the addition of maize leaves, accompanied by a significant increase in water BP. In contrast, sediment BP declined after an initial peak, showing no positive response to t-POM addition. Sediment BP and CR were also not stimulated by t-POM in the laboratory experiment, either in short-term or in long-term incubations, except for a short increase in CR after 18 hours. However, this increase might have reflected the metabolism of leaf-associated microorganisms. We conclude that the leached t-DOM is actively incorporated into microbial biomass in the water column but that the settling leached t-POM (t-POML) does not enter the food web via sediment bacteria. Consequently, t-POML is either buried in the sediment or introduced into the aquatic food web via microorganisms (bacteria and fungi) directly associated with t-POML and via benthic macroinvertebrates by shredding of t-POML. The latter pathway represents a benthic shortcut which efficiently transfers t-POML to higher trophic levels.
Standard quantum chemical methods are used for accurate calculation of thermochemical properties such as enthalpies of formation, entropies and Gibbs energies of formation. Equilibrium reactions are widely investigated and experimental measurements often lead to a range of reaction Gibbs energies and equilibrium constants. It is useful to calculate these equilibrium properties from quantum chemical methods in order to address the experimental differences. Furthermore, most standard calculation methods differ in accuracy and feasibility of the system size. Hence, asystematic comparison of equilibrium properties calculated with different numerical algorithms would provide a useful reference. We select two well-known gas phase equilibrium reactions with small molecules: covalent dimer formation of NO2 (2NO(2) reversible arrow N2O4) and the synthesis of NH3 (N-2 + 3 H-2 reversible arrow 2NH(3)). We test four quantum chemical methods denoted by G3B3, CBS-APNO, W1 and CCSD(T) with aug-cc-pVXZ basis sets (X = 2, 3, and 4), to obtain thermochemical data for NO2, N2O4, and NH3. The calculated standard formation Gibbs energies Delta(f)G degrees are used to calculate standard reaction Gibbs energies Delta(r)G degrees and standard equilibrium constants K-eq for the two reactions. Standard formation enthalpies Delta H-f degrees are calculated in a more reliable way using high-level methods such as W1 and CCSD(T). Standard entropies S degrees for the molecules are calculated well within the range of experiments for all methods, however, the values of standard formation Gibbs energies Delta(f)G degrees show some dependence on the choice of the method. High-level methods perform better for the calculation of molecular energies, however, simpler methods such as G3B3 and CBS-APNO perform quite well in the calculation of total reaction energies and equilibrium constants, provided that the chemical species involved do not exhibit molecular geometries that are difficult to handle by the applied method. The temperature dependence of standard reaction Gibbs energy Delta(r)G degrees for the NH3 reaction is discussed by using the calculated standard formation Gibbs energies Delta(f)G degrees of the reaction species at 298.15 K. The corresponding equilibrium constant K-eq as a function of temperature is found to be close to experimental values.
Several mechanisms are proposed to be part of the earthquake triggering process, including static stress interactions and dynamic stress transfer. Significant differences of these mechanisms are particularly expected in the spatial distribution of aftershocks. However, testing the different hypotheses is challenging because it requires the consideration of the large uncertainties involved in stress calculations as well as the appropriate consideration of secondary aftershock triggering which is related to stress changes induced by smaller pre- and aftershocks. In order to evaluate the forecast capability of different mechanisms, I take the effect of smaller--magnitude earthquakes into account by using the epidemic type aftershock sequence (ETAS) model where the spatial probability distribution of direct aftershocks, if available, is correlated to alternative source information and mechanisms. Surface shaking, rupture geometry, and slip distributions are tested. As an approximation of the shaking level, ShakeMaps are used which are available in near real-time after a mainshock and thus could be used for first-order forecasts of the spatial aftershock distribution. Alternatively, the use of empirical decay laws related to minimum fault distance is tested and Coulomb stress change calculations based on published and random slip models. For comparison, the likelihood values of the different model combinations are analyzed in the case of several well-known aftershock sequences (1992 Landers, 1999 Hector Mine, 2004 Parkfield). The tests show that the fault geometry is the most valuable information for improving aftershock forecasts. Furthermore, they reveal that static stress maps can additionally improve the forecasts of off--fault aftershock locations, while the integration of ground shaking data could not upgrade the results significantly. In the second part of this work, I focused on a procedure to test the information content of inverted slip models. This allows to quantify the information gain if this kind of data is included in aftershock forecasts. For this purpose, the ETAS model based on static stress changes, which is introduced in part one, is applied. The forecast ability of the models is systematically tested for several earthquake sequences and compared to models using random slip distributions. The influence of subfault resolution and segment strike and dip is tested. Some of the tested slip models perform very good, in that cases almost no random slip models are found to perform better. Contrastingly, for some of the published slip models, almost all random slip models perform better than the published slip model. Choosing a different subfault resolution hardly influences the result, as long the general slip pattern is still reproducible. Whereas different strike and dip values strongly influence the results depending on the standard deviation chosen, which is applied in the process of randomly selecting the strike and dip values.
A Biosensor for aromatic aldehydes comprising the mediator dependent PaoABC-Aldehyde oxidoreductase
(2013)
A novel aldehyde oxidoreductase (PaoABC) from Escherichia coli was utilized for the development of an oxygen insensitive biosensor for benzaldehyde. The enzyme was immobilized in polyvinyl alcohol and currents were measured for aldehyde oxidation with different one and two electron mediators with the highest sensitivity for benzaldehyde in the presence of hexacyanoferrate(III). The benzaldehyde biosensor was optimized with respect to mediator concentration, enzyme loading and pH using potassium hexacyanoferrate(III). The linear measuring range is between 0.5200 mu M benzaldehyde. In correspondence with the substrate selectivity of the enzyme in solution the biosensor revealed a preference for aromatic aldehydes and less effective conversion of aliphatic aldehydes. The biosensor is oxygen independent, which is a particularly attractive feature for application. The biosensor can be applied to detect contaminations with benzaldehyde in solvents such as benzyl alcohol, where traces of benzaldehyde in benzyl alcohol down to 0.0042?% can be detected.