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Regio- and stereoselective addition of alkyl Grignard reagents to pyridine-N-oxides gave C2-alkylated N-hydroxy-1,2,5,6-tetrahydropyridines and trans-2,3-disubstituted N-hydroxy-1,2,5,6-tetrahydropyridines in good to excellent yields. These intermediates were aromatized or alternatively reduced in one-pot methodologies for efficient syntheses of alkylpyridines or piperidines, respectively. These reactions have a broad substrate scope and short reaction times.

• The phytohormone ethylene impacts secondary stem growth in plants by stimulating cambial activity, xylem development and fiber over vessel formation.
• We report the effect of ethylene on secondary cell wall formation and the molecular connection between ethylene signaling and wood formation. We applied exogenous ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) to wild-type and ethylene-insensitive hybrid aspen trees (Populus tremulaxtremuloides) and studied secondary cell wall anatomy, chemistry and ultrastructure. We furthermore analyzed the transcriptome (RNA Seq) after ACC application to wild-type and ethylene-insensitive trees.
• We demonstrate that ACC and ethylene induce gelatinous layers (G-layers) and alter the fiber cell wall cellulose microfibril angle. G-layers are tertiary wall layers rich in cellulose, typically found in tension wood of aspen trees. A vast majority of transcripts affected by ACC are downstream of ethylene perception and include a large number of transcription factors (TFs). Motif-analyses reveal potential connections between ethylene TFs (Ethylene Response Factors (ERFs), ETHYLENE INSENSITIVE 3/ETHYLENE INSENSITIVE3-LIKE1 (EIN3/EIL1)) and wood formation.
• G-layer formation upon ethylene application suggests that the increase in ethylene biosynthesis observed during tension wood formation is important for its formation. Ethylene-regulated TFs of the ERF and EIN3/EIL1 type could transmit the ethylene signal.

The transcriptional activator PrfA, a member of the Crp/Fnr family, controls the expression of some key virulence factors necessary for infection by the human bacterial pathogen Listeria monocytogenes. Phenotypic screening identified ring-fused 2-pyridone molecules that at low micromolar concentrations attenuate L. monocytogenes cellular uptake by reducing the expression of virulence genes. These inhibitors bind the transcriptional regulator PrfA and decrease its affinity for the consensus DNA-binding site. Structural characterization of this interaction revealed that one of the ring-fused 2-pyridones, compound 1, binds at two separate sites on the protein: one within a hydrophobic pocket or tunnel, located between the C- and N-terminal domains of PrfA, and the second in the vicinity of the DNA-binding helix-turn-helix motif. At both sites the compound interacts with residues important for PrfA activation and helix-turn-helix formation. Ring-fused 2-pyridones represent a new class of chemical probes for studying virulence in L. monocytogenes.

Infection by the human bacterial pathogen Listeria monocytogenes is mainly controlled by the positive regulatory factor A (PrfA), a member of the Crp/Fnr family of transcriptional activators. Published data suggest that PrfA requires the binding of a cofactor for full activity, and it was recently proposed that glutathione (GSH) could fulfill this function. Here we report the crystal structures of PrfA in complex with GSH and in complex with GSH and its cognate DNA, the hly operator PrfA box motif. These structures reveal the structural basis for a GSH-mediated allosteric mode of activation of PrfA in the cytosol of the host cell. The crystal structure of PrfAWT in complex only with DNA confirms that PrfAWT can adopt a DNA binding-compatible structure without binding the GSH activator molecule. By binding to PrfA in the cytosol of the host cell, GSH induces the correct fold of the HTH motifs, thus priming the PrfA protein for DNA interaction.

It is well known that when a short laser pulse propagates in an underdense plasma, it induces longitudinal plasma oscillations at the plasma frequency after the pulse, typically referred to as the wakefield. However, for plasma densities approaching the critical density, wakefield generation is suppressed, and instead the EM-pulse (electromagnetic pulse) undergoes nonlinear self-modulation. In this article we have studied the transition from the wakefield generation to formation of quasi-solitons as the plasma density is increased. For this purpose we have applied a one-dimensional relativistic cold fluid model, which has also been compared with particle-in-cell simulations. A key result is that the energy loss of the EM-pulse due to wakefield generation has its maximum for a plasma density of the order 10% of the critical density, but that wakefield generation is sharply suppressed when the density is increased further.

Elasticity is one of the main features of cloud computing allowing customers to scale their resources based on the workload. Many autoscalers have been proposed in the past decade to decide on behalf of cloud customers when and how to provision resources to a cloud application based on the workload utilizing cloud elasticity features. However, in prior work, when a new policy is proposed, it is seldom compared to the state-of-the-art, and is often compared only to static provisioning using a predefined quality of service target. This reduces the ability of cloud customers and of cloud operators to choose and deploy an autoscaling policy, as there is seldom enough analysis on the performance of the autoscalers in different operating conditions and with different applications. In our work, we conduct an experimental performance evaluation of autoscaling policies, using as application model workflows, a popular formalism for automating resource management for applications with well-defined yet complex structures. We present a detailed comparative study of general state-of-the-art autoscaling policies, along with two new workflow-specific policies. To understand the performance differences between the seven policies, we conduct various experiments and compare their performance in both pairwise and group comparisons. We report both individual and aggregated metrics. As many workflows have deadline requirements on the tasks, we study the effect of autoscaling on workflow deadlines. Additionally, we look into the effect of autoscaling on the accounted and hourly based charged costs, and we evaluate performance variability caused by the autoscaler selection for each group of workflow sizes. Our results highlight the trade-offs between the suggested policies, how they can impact meeting the deadlines, and how they perform in different operating conditions, thus enabling a better understanding of the current state-of-the-art.

Naturally occurring modifications of the nucleosides in the anticodon region of tRNAs influence their translational decoding properties. Uridines present at the wobble position in eukaryotic cytoplasmic tRNAs often contain a 5-carbamoylmethyl (ncm(5)) or 5-methoxycarbonylmethyl (mcm(5)) side-chain and sometimes also a 2-thio or 2'-O-methyl group. The first step in the formation of the ncm5 and mcm5 side-chains requires the conserved six-subunit Elongator complex. Although Elongator has been implicated in several different cellular processes, accumulating evidence suggests that its primary, and possibly only, cellular function is to promote modification of tRNAs. In this review, we discuss the biosynthesis and function of modified wobble uridines in eukaryotic cytoplasmic tRNAs, focusing on the in vivo role of Elongator-dependent modifications in Saccharomyces cerevisiae. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.

Boreal flat bugs include a high proportion of species that are considered negatively affected by forestry. Knowledge on the biology and habitat demands of individual species is generally limited. We examined the influence on flat bugs of stand-age and clear-cutting, comparing five classes of spruce stands. The five classes were: clear-cut, unthinned, and thinned (all three products of current clear-cutting forestry), mature managed and old-growth stands (these two had never been clear-cut). We also compared unburned and recently burned mature pine forest. Fire, but not stand age, had a pronounced effect on species richness and total abundance. Aradus depressus showed a significant association with older forest stands. Aradus betulae occurred only in clear-cuts and burned forest indicating that this species is favored by disturbance in general. Aradus lugubris, Aradus crenaticollis and Aradus brevicollis were found only in the burned forest. Aradus brevicollis has not previously been shown to be associated with fire. © Springer Science+Business Media B.V. 2009.

We report on the temperature, pressure, and time (T, p, and t)-dependent features of thermal conductivity, kappa, of partially ordered, non-equilibrium state of C-60-OG, the orientational glass of Buckminsterfullerene (at T below the orientational freezing temperature T-og) made more unstable (i) by partially depressurizing its high-p formed state to elastically expand it and (ii) by further pressurizing that state to elastically contract it. The sub-T-og effects observed on heating of C-60-OG differ from those of glasses because phonon propagation depends on the ratio of two well-defined orientational states of C-60 molecules and the density of the solid. A broad peak-like feature appears at T near T-og in the kappa-T plots of C-60-OG formed at 0.7 GPa, depressurized to 0.2 GPa and heated at 0.2 GPa, which we attribute to partial overlap of the sub-T-og and T-og features. A sub-T-og local minimum appears in the kappa-T plots at T well below T-og of C-60-OG formed at 0.1 GPa, pressurized to 0.5 GPa and heated at 0.5 GPa and it corresponds to the state of maximum disorder. Although Buckminsterfullerene is regarded as an orientationally disordered crystal, variation of its properties with T and p is qualitatively different from other such crystals. We discuss the findings in terms of the nature of its disorder, sensitivity of its rotational dynamics to temperature, and the absence of the Johari-Goldstein relaxation. All seem to affect the phenomenology of its glass-like transition. 

• Metacaspases are a subgroup of caspase homologues represented in bacteria, algae and plants. Although type I and type II metacaspases are present in plants, recently discovered and uncharacterized type III metacaspases can only be found in algae which have undergone secondary endosymbiosis.
• We analysed the expression levels of all 13 caspase homologues in the cryptophyte Guillardia theta invivo and biochemically characterized its only type III metacaspase, GtMC2, invitro.
• Type III metacaspase GtMC2 was shown to be an endopeptidase with a preference for basic amino acids in the P1 position, which exhibited specific N-terminal proteolytic cleavage for full catalytic efficiency. Autolytic processing, as well as the activity of the mature enzyme, required the presence of calcium ions in low millimolar concentrations. In GtMC2, two calcium-binding sites were identified, one with a dissociation constant at low and the other at high micromolar concentrations.
• We show high functional relatedness of type III metacaspases to type I metacaspases. Moreover, our data suggest that the low-affinity calcium-binding site is located in the p10 domain, which contains a well-conserved N-terminal region. This region can only be found in type I/II/III metacaspases, but is absent in calcium-independent caspase homologues.

Root phenology is important in controlling carbon and nutrient fluxes in terrestrial ecosystems, yet, remains largely unexplored, especially in the Arctic. We compared below- and aboveground phenology and ending of the growing season in two contrasting vegetation types of subarctic tundra: heath and meadow, and their response to experimental warming in autumn. 

Root phenology was measured in-situ with minirhizotrons and compared with aboveground phenology assessed with repeat digital photography. 

The end of the growing season, both below- and aboveground, was similar in meadow and heath and the belowground growing season ended later than aboveground in the two vegetation types. Root growth was higher and less equally distributed over time in meadow compared to heath. The warming treatment increased air and soil temperature by 0.5 A degrees C and slightly increased aboveground greenness, but did not affect root growth or prolong the below- and aboveground growing season in either of the vegetation types. 

These results imply that vegetation types differ in root dynamics and suggest that other factors than temperature control autumnal root growth in these ecosystems. Further investigations of root phenology will help to identify those drivers, in which including responses of functionally contrasting vegetation types will help to estimate how climate change affects belowground processes and their roles in ecosystem function.

UNLABELLED: Bacteria utilize complex type IV secretion systems (T4SSs) to translocate diverse effector proteins or DNA into target cells. Despite the importance of T4SSs in bacterial pathogenesis, the mechanism by which these translocation machineries deliver cargo across the bacterial envelope remains poorly understood, and very few studies have investigated the use of synthetic molecules to disrupt T4SS-mediated transport. Here, we describe two synthetic small molecules (C10 and KSK85) that disrupt T4SS-dependent processes in multiple bacterial pathogens. Helicobacter pylori exploits a pilus appendage associated with the cag T4SS to inject an oncogenic effector protein (CagA) and peptidoglycan into gastric epithelial cells. In H. pylori, KSK85 impedes biogenesis of the pilus appendage associated with the cag T4SS, while C10 disrupts cag T4SS activity without perturbing pilus assembly. In addition to the effects in H. pylori, we demonstrate that these compounds disrupt interbacterial DNA transfer by conjugative T4SSs in Escherichia coli and impede vir T4SS-mediated DNA delivery by Agrobacterium tumefaciens in a plant model of infection. Of note, C10 effectively disarmed dissemination of a derepressed IncF plasmid into a recipient bacterial population, thus demonstrating the potential of these compounds in mitigating the spread of antibiotic resistance determinants driven by conjugation. To our knowledge, this study is the first report of synthetic small molecules that impair delivery of both effector protein and DNA cargos by diverse T4SSs.

IMPORTANCE: Many human and plant pathogens utilize complex nanomachines called type IV secretion systems (T4SSs) to transport proteins and DNA to target cells. In addition to delivery of harmful effector proteins into target cells, T4SSs can disseminate genetic determinants that confer antibiotic resistance among bacterial populations. In this study, we sought to identify compounds that disrupt T4SS-mediated processes. Using the human gastric pathogen H. pylori as a model system, we identified and characterized two small molecules that prevent transfer of an oncogenic effector protein to host cells. We discovered that these small molecules also prevented the spread of antibiotic resistance plasmids in E. coli populations and diminished the transfer of tumor-inducing DNA from the plant pathogen A. tumefaciens to target cells. Thus, these compounds are versatile molecular tools that can be used to study and disarm these important bacterial machines.

There is no strife, no prejudice, no national conflict in outer space as yet. Its hazards are hostile to us all. Its conquest deserves the best of all mankind, and its opportunity for peaceful cooperation many never come again. But why, some say, the moon? Why choose this as our goal? And they may well ask why climb the highest mountain?

We choose to go to the moon. We choose to go to the moon in this decade and do the other things, not because they are easy, but because they are hard, because that goal will serve to organize and measure the best of our energies and skills, because that challenge is one that we are willing to accept, one we are unwilling to postpone, and one which we intend to win, and the others, too.

In this study, we presented a new approach for quantification of bicarbonate (HCO3-) molecules bound to PSII. Our method, which is based on a combination of membrane-inlet mass spectrometry (MIMS) and O-18-labelling, excludes the possibility of "non-accounted" HCO3- by avoiding (1) the employment of formate for removal of HCO3- from PSII, and (2) the extremely low concentrations of HCO3-/CO2 during online MIMS measurements. By equilibration of PSII sample to ambient CO2 concentration of dissolved CO2/HCO3-, the method ensures that all physiological binding sites are saturated before analysis. With this approach, we determined that in spinach PSII membrane fragments 1.1 +/- 0.1 HCO3- are bound per PSII reaction center, while none was bound to isolated PsbO protein. Our present results confirmed that PSII binds one HCO3- molecule as ligand to the non-heme iron of PSII, while unbound HCO3- optimizes the water-splitting reactions by acting as a mobile proton shuttle.

We consider the problem of periodic motion planning and of designing stabilising feedback control laws for such motions in underactuated mechanical systems. A novel periodic motion planning method is proposed. Each state is parametrised by a truncated Fourier series. Then we use numerical optimisation to search for the parameters of the trigonometric polynomial exploiting the measure of discrepancy in satisfying the passive dynamics equations as a performance index. Thus an almost feasible periodic motion is found. Then a linear controller is designed and stability analysis is given to verify that solutions of the closed-loop system stay inside a tube around the planned approximately feasible periodic trajectory. Experimental results for a double rotary pendulum are shown, while numerical simulations are given for models of a spacecraft with liquid sloshing and of a chain of mass spring system.

Water relations in plant communities are influenced both by contrasting functional groups (grasses and shrubs) and by climate change via complex effects on interception, uptake, and transpiration. We modeled the effects of functional group replacement and biomass increase, both of which can be outcomes of invasion and vegetation management, and climate change on ecological drought (soil water potential below which photosynthesis stops) in 340 semiarid grassland sites over 30year periods. Relative to control vegetation (climate and site-determined mixes of functional groups), the frequency and duration of drought were increased by shrubs and decreased by annual grasses. The rankings of shrubs, control vegetation, and annual grasses in terms of drought effects were generally consistent in current and future climates, suggesting that current differences among functional groups on drought effects predict future differences. Climate change accompanied by experimentally increased biomass (i.e., the effects of invasions that increase community biomass or management that increases productivity through fertilization or respite from grazing) increased drought frequency and duration and advanced drought onset. Our results suggest that the replacement of perennial temperate semiarid grasslands by shrubs, or increased biomass, can increase ecological drought in both current and future climates.

This study investigated interfacial reactions between aqueous Ce(III) and two synthetic nanosized Mn (hydr-) oxides (manganite: gamma-MnOOH, and vernadite: delta-MnO2) in the absence and presence of Nordic Lake fulvic acid (NLFA) at circumneutral pH by batch experiments and cryogenic X-ray photoelectron spectroscopy (XPS). The surfaces of manganite and vernadite were negatively charged (XPS-derived loadings of (Na+ K)/Cl > 1) and loaded with 0.42-4.33 Ce ions nm(-2). Manganite stabilized Ce-oxidation states almost identical to those for vernadite (approximately 75% Ce(IV) and 25% Ce(III)), providing the first experimental evidence that also a Mn (III) phase (manganite) can act as an important scavenger for Ce(IV) and thus, contribute to the decoupling of Ce from its neighboring rare earth elements and the development of Ce anomaly. In contrast, when exposed to Ce (III)-NLFA complexes, the oxidation of Ce by these two Mn (hydr-) oxides was strongly suppressed, suggesting that the formation of Ce(III) complexes with fulvic acid can stabilize Ce(III) even in the presence of oxidative Mn-oxide surfaces. The experiments also showed that Ce(III) complexed with excess NLFA was nearly completely removed, pointing to a strong preferential sorption of Ce(III)-complexed NLFA over free NLFA. This finding suggests that the Ce(III)-NLFA complexes were most likely sorbed by their cation side, i.e. Ce(III) bridging between oxide groups on the Mn (hydr-) oxides and negatively-charged functional groups in NLFA. Hence, Ce(III) was in direct contact with the oxidative manganite and vernadite but despite that not oxidized. An implication is that in organic-rich environments there may be an absence of Ce(IV) and Ce anomaly despite otherwise favorable conditions for Ce(III) oxidation.