2,719 research outputs found
Structural Characterization of OxyD, a Cytochrome P450 Involved in β−Hydroxytyrosine Formation in Vancomycin Biosynthesis
No full textThe cytochrome P450 OxyD from the balhimycin glycopeptide antibiotic biosynthetic operon of <i>Amycolatopsis mediterranei</i> is involved in the biosynthesis of the modified amino acid β−<i>R</i>−hydroxytyrosine, an essential precursor for biosynthesis of the vancomycin−type aglycone. OxyD binds the substrate tyrosine not free in solution, but rather covalently linked to the carrier protein (CP) domain of the non−ribosomal peptide synthase BpsD, exhibiting micromolar binding affinity to a tyrosine−loaded carrier protein construct. The crystal structure of OxyD was determined to 2.1−Å resolution, revealing a potential binding site for the carrier protein−bound substrate in a different orientation to that seen with the acyl carrier protein−bound P450BioI (Cryle, M. J., and Schlichting, I. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 15696−15701). A series of residues were identified across known aminoacyl−CP−oxidizing P450s that are highly conserved and cluster in the active site or potential CP binding site of OxyD. These residues appear to be characteristic for aminoacyl−CP−oxidizing P450s, allowing sequence based identification of P450 function for this subgroup of P450s that play vital roles in the biosyntheses of many important natural products in addition to the vancomycin−type antibiotics. The ability to analyze such P450 function based upon sequence data alone should prove an important tool in the analysis and identification of new medicinally relevant biomolecules
The subzero microbiome: Microbial activity in frozen and thawing soils
No full textMost of the Earth's biosphere is characterized by low temperatures (<5 °C) and cold-adapted microorganisms are widespread. These psychrophiles have evolved a complex range of adaptations of all cellular constituents to counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. Microbial life continues into the subzero temperature range, and this activity contributes to carbon and nitrogen flux in and out of ecosystems, ultimately affecting global processes. Microbial responses to climate warming and in particular, thawing of frozen soils are not yet well understood although the threat of microbial contribution to positive feedback of carbon flux is substantial. To date, several studies have examined microbial community dynamics in frozen soils and permafrost due to changing environmental conditions, and some have undertaken the complicated task of characterizing microbial functional groups and how their activity changes with changing conditions, either in situ or by isolating and characterizing macromolecules. With increasing temperature and wetter conditions microbial activity of key microbes and subsequent efflux of greenhouse gases also increase. In this review, we aim to provide an overview of microbial activity in seasonally frozen soils and permafrost. With a more detailed understanding of the microbiological activities in these vulnerable soil ecosystems, we can begin to predict and model future expectations for carbon release and climate change.Peer reviewe
Structural and Biochemical Characterization of the Cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: A Cyclo-l-leucyl-l-leucyl Dipeptide Oxidase
No full textCytochrome P450 CypX (CYP134A1), isolated from Bacillus subtilis, has previously been implicated in the three-step oxidative transformation of the diketopiperazine cyclo-l-leucyl-l-leucyl into pulcherriminic acid, a precursor of the extracellular iron chelate pulcherrimin. In this study, we present the first experimental data relating to CYP134A1, where we show that CYP134A1 binds cyclo-l-leucyl-l-leucyl with an affinity of 24.5 +/- 0.5 muM. Structurally related diketopiperazines sharing similar alkyl side chains to cyclo-l-leucyl-l-leucyl also bind to CYP134A1 with comparable affinity. CYP134A1 is capable of catalyzing the in vitro oxidation of diketopiperazine substrates when supported with several alternate electron transfer partner systems. Products containing one additional oxygen atom and which are intermediate products of the expected pulcherriminic acid were identified by GCMS. The oxidation of related diketopiperazines reveals that different oxidative pathways exist for CYP134A1-catalyzed diketopiperazine oxidation. The crystal structure of CYP134A1 has been determined to 2.7 A resolution in the absence of substrate and in the presence of bound phenylimidazole ligands to 3.1 and 3.2 A resolution. The active site is dominated by hydrophobic residues and contains an unusual proline residue in place of the normally conserved alcohol residue that typically plays an important role in oxygen activation. The B-B(2) substrate recognition loop, which forms part of the active site, shows considerable flexibility and was found in both open and closed conformations in different structures. These results represent the first insights into the structural and biochemical basis underlying the multistep oxidation catalyzed by CYP134A1.Max J. Cryle, Stephen G. Bell, and Ilme Schlichtin
Measurement of the time-dependent CP asymmetry in B0 -> J/ψ KS0 decays
No full textThis Letter reports a measurement of the CP violation observables SJ/ψK0S and CJ/ψK0S in the decay channel B0→J/ψK0S performed with 1.0 fb−1 of pp collisions at s√=7 TeV collected by the LHCb experiment. The fit to the data yields SJ/ψK0S=0.73±0.07(stat)±0.04(syst) and CJ/ψK0S=0.03±0.09(stat)±0.01(syst). Both values are consistent with the current world averages and within
expectations from the Standard Model
Carrier protein substrates in cytochrome P450−catalysed oxidation
No full textEnzymes of the cytochrome P450 superfamily can catalyse many types of oxidative transformations of a diverse substrate range. This review summarises recent work on an subset of P450s that accept their substrates in carrier protein−bound form. These examples show how the oxidative power and precision that P450s bring to natural products biosynthesis can be coupled with the advantages of using a carrier protein as a scaffold for oxidatio
Selectivity in a barren landscape: the P450BioI−ACP complex
No full textThe cytochromes P450 (P450s) are a superfamily of oxidative haemoproteins that are capable of catalysing a vast range of oxidative transformations, including the oxidation of unactivated alkanes, often with high stereo− and regio−selectivity. Fatty acid hydroxylation by P450s is widespread across both bacteria and higher organisms, with the sites of oxidation and specificity of oxidation varying from system to system. Several key examples are discussed in the present article, with the focus on P450BioI (CYP107H1), a biosynthetic P450 found in the biotin operon of <i>Bacillus subtilis</i>. The biosynthetic function of P450BioI is the formation of pimelic acid, a biotin precursor, via a multiple−step oxidative cleavage of long−chain fatty acids. P450BioI is a member of an important subgroup of P450s that accept their substrates not free in solution, but rather presented by a separate carrier protein. Structural characterization of the P450BioI−ACP (acyl−carrier protein) complex has recently been performed, which has revealed the basis for the oxidation of the centre of the fatty acid chain. The P450BioI−ACP structure is the first such P450−carrier protein complex to be characterized structurally, with important implications for other biosynthetically intriguing P450−carrier protein complexes
Evidence for the decay B0→J/ψω and measurement of the relative branching fractions of meson decays to J/ψη and J/ψη′
No full textFirst evidence of the B 0 → J / ψ ω decay is found and the B s 0 → J / ψ η and B s 0 → J / ψ η ′ decays are studied using a dataset corresponding to an integrated luminosity of 1.0 fb -1 collected by the LHCb experiment in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV. The branching fractions of these decays are measured relative to that of the B 0 → J / ψ ρ 0 decay:frac(B (B 0 → J / ψ ω), B (B 0 → J / ψ ρ 0)) = 0.89 ± 0.19 (stat) - 0.13 + 0.07 (syst),frac(B (B s 0 → J / ψ η), B (B 0 → J / ψ ρ 0)) = 14.0 ± 1.2 (stat) - 1.5 + 1.1 (syst) - 1.0 + 1.1 (frac(f d, f s)),frac(B (B s 0 → J / ψ η ′), B (B 0 → J / ψ ρ 0)) = 12.7 ± 1.1 (stat) - 1.3 + 0.5 (syst) - 0.9 + 1.0 (frac(f d, f s)), where the last uncertainty is due to the knowledge of f d / f s, the ratio of b-quark hadronization factors that accounts for the different production rate of B 0 and B s 0 mesons. The ratio of the branching fractions of B s 0 → J / ψ η ′ and B s 0 → J / ψ η decays is measured to befrac(B (B s 0 → J / ψ η ′), B (B s 0 → J / ψ η)) = 0.90 ± 0.09 (stat) - 0.02 + 0.06 (syst)
Measurement of the ratio of prompt χ c to J / ψ production in pp collisions at √s = 7 TeV
No full textThe prompt production of charmonium χ c and J / ψ states is studied in proton-proton collisions at a centre-of-mass energy of √s = 7 TeV at the Large Hadron Collider. The χ c and J / ψ mesons are identified through their decays χ c → J / ψ γ and J / ψ → μ + μ - using 36 pb - 1 of data collected by the LHCb detector in 2010. The ratio of the prompt production cross-sections for χ c and J / ψ, σ (χ c → J / ψ γ) / σ (J / ψ), is determined as a function of the J / ψ transverse momentum in the range 2 < p T J / ψ < 15 GeV / c. The results are in excellent agreement with next-to-leading order non-relativistic expectations and show a significant discrepancy compared with the colour singlet model prediction at leading order, especially in the low p T J / ψ region
A Transfer Report on the Development of a Framework to Evaluate Search Interfaces for their Support of Different User Types and Search Tactics
No full textAs the understanding of search systems, user needs and seeking strategies is developing, the design of search user interfaces is evolving to support more complicated and exploratory forms of search. With the design of new search features that enable these richer modes of exploration, comes the need to better understand the support they provide. In this report a new evaluation framework is presented that analyses search features for how they a) contribute to an overall interface, b) allow users to carry out different search tactics, and c) support different types of users and their needs. The novel contributions of the framework improve on some of the limitations of typical user studies, and allow search systems to be systematically analysed in much more detail and in much less time. The presented evaluation framework is then validated in three ways. First the validity of the models used as the building blocks of the framework are investigated through related work. Second the method of integrating these building-block models is validated and strengthened by consensus of expert opinion. Third, the overall approach is validated by comparing its analyses to the results of previously carried out user studies. The validation process has shown both the value of the framework and identified areas of future work that should be addressed for the framework to be completed. This report concludes with the set of contributions that the framework makes, and why the remaining work will be challenging, but critical to the final design
Climate Justice Behind the Veil of Aggregation: IAMs, Equity, and Pareto-Optimal Abatement Pathways
No full textHumanity faces the unprecedented global challenge of climate change. The sheer complexity and uncertainty of this problem renders mere intuitive reasoning insufficient. To aid global climate negotiations, Integrated Assessment Models (IAMs) are used to analyze the interplay between climate and the economy. More specifically, IAMs account for how greenhouse gas emissions affect climate change, how climate change affects economic production, and how economic production affects GHG emissions. We can use IAMs to project trends in emissions and gross domestic product, assess the costs and benefits of climate policies, and estimate the social carbon cost required to achieve stated emissions reduction targets. Although IAMs are central to informing decision-making to avoid catastrophic consequences, policy recommendations resulting from IAMs commonly prompt a very heterogeneous distribution of risks and benefits across the globe. During the recent 2021 United Nations Climate Change Conference (COP26), it became clear that equity is a central issue in the climate action debate. Emerging economies consider currently suggested abatement policies unjust in light of the historical CO2 generation of high-income countries and the strongly increasing need for energy in low-income countries. The term double inequality has been coined to describe the inverse relationship between the distributions of risks and responsibilities. In fact, the regions that are the least responsible for historical and mostly current CO2 emissions around the world, exhibit the highest degree of vulnerability to climate damages. In order to enable international cooperation and have a shot at meeting the Paris Agreement target, we require policies that promote more equitable mitigation pathways. Equity is therefore an eminently pressing topic, yet most IAM studies largely neglect it due to the implicit use of a utilitarian social welfare function that aggregates risks and benefits over space and time, thus losing sight of distributional consequences. In order to account for distributional justice, we transform the RICE model into a simulation model and embed it in a many-objective simulation-optimization setup such that we can find Pareto-optimal climate mitigation pathways for different problem formulations. Next to using four ethical premises (rooted in utilitarianism, sufficientarianism, egalitarianism, and prioritarianism), we also direct particular attention to the disaggregation of utility and disutility within each of these ethical premises. The reason for this disaggregation is based on the incommensurability of these two. Usually, IAMs maximize aggregate variables such as welfare. If we also consider the minimization of welfare loss, which is based on economic damages as one of the objectives, we can enable a potentially fairer distribution of not only consumption but economic damages. We argue that we can find climate justice behind the veil of aggregation. What we mean by this is that more equitable policy recommendations are obscured and lie hidden behind a bulwark of highly aggregated variables. If we look beyond this obstruction by the means of disaggregation, we are better equipped to find climate justice. In order to get to the bottom of this, we ask the following question: How are Pareto-optimal climate abatement pathways affected by the disaggregation of utility and disutility in alternative ethical problem formulations when using an integrated assessment model under deep uncertainty?To answer this question, we use a framework that is called multi-scenario multi-objective robust decision-making. For each of the eight problem formulations (4 ethical premises x 2 levels of aggregation), we use a multi-objective evolutionary algorithm to find Pareto-optimal policies. We reevaluate their performances under uncertainty by comparing their climate abatement pathways across the problem formulations. On a high-level, we can summarize our key findings as: - dominance of aggregation levels over ethical premises - correlation between low welfare and high welfare loss - general dominance of egalitarian aggregated Pareto-optimal policies - shared misery via egalitarian disaggregated Pareto-optimal policiesThe effect of disaggregating utility and disutility is stronger than originally expected. Using disaggregated problem formulations yields substantially different pathways even within the same ethical premise. These results are promising as we could transfer these insights to other more complex IAMs such as IMAGE and MESSAGE. Overall, this could be also good news for the equity debate. Using alternative ethical premises and disaggregating incommensurate objectives such as utility and disutility can offer alternative policy recommendations and resulting climate abatement pathways which could in turn enable more equity. What we likely need now, is a stronger dialogue between the modelers and policy analysts on the one side and the stakeholders and decision-makers on the other side. The latter ones should not just blindly trust in the magical outputs of a model but they need to be involved to decide what problem formulations we need to use as there is no correct way to frame a complex real-world problem. As unmitigated climate damages exhibit an independent impact on a region's well-being, we could render IAMs more useful for climate policy if we a) acknowledge that the classical notion of welfare is obsolete, b) use a multi-objective approach, and c) let the decision-makers decide how they want to trade-off the various objectives in post. In this manner, we could use IAMs to advance into the direction of enabling a transition of more climate justice.https://github.com/max-reddel/PyRICE_2022 Associated GitHub repositoryEngineering and Policy Analysi
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