Mechanistic Studies of the Streptomyces bingchenggensis Aldolase-Dehydratase: Implications for Substrate and Reaction Specificity in the Acetoacetate Decarboxylase-like Superfamily.

The acetoacetate decarboxylase-like superfamily (ADCSF) is a little-explored group of enzymes that may contain new biocatalysts. The low level of sequence identity (∼20%) between many ADCSF enzymes and the confirmed acetoacetate decarboxylases led us to investigate the degree of diversity in the reaction and substrate specificity of ADCSF enzymes. We have previously reported on Sbi00515, which belongs to Family V of the ADCSF and functions as an aldolase-dehydratase. Here, we more thoroughly characterize the substrate specificity of Sbi00515 and find that aromatic, unsaturated aldehydes yield lower KM and higher kcat values compared to those of other small electrophilic substrates in the condensation reaction. The roles of several active site residues were explored by site-directed mutagenesis and steady state kinetics. The lysine-glutamate catalytic dyad, conserved throughout the ADCSF, is required for catalysis. Tyrosine 252, which is unique to Sbi00515, is hypothesized to orient the incoming aldehyde in the condensation reaction. Transient state kinetics and an intermediate-bound crystal structure aid in completing a proposed mechanism for Sbi00515.

Heuristics for practitioners of policy design: Rules-of-thumb for structuring unstructured problems.

This article is an attempt to bridge the divide between academics and practitioners. Informed by both design theory and the reality of policy work, its focus is on 'problems'. From a practitioners' perspective, policy design is both an intellectual and political process, an inevitable oscillation between 'puzzling' and 'powering', in which 'messy' or unstructured problems are re-structured from problems as webs of 'undesirable situations' to problems as specific, time-and-space bound 'opportunities for improvement'. This requires a questioning habitus in practitioners of policy design. Using a socio-cognitive theory of problem processing, this paper shows how policy design is an iterative process of problem sensing, problem categorization, problem decomposition and problem definition. For each of these stages, appropriate rules-of-thumb for questioning and answering can be suggested that induce thought habits and styles for responsive and solid policy designs.

Using the Advocacy Coalition Framework and Multiple Streams policy theories to examine the role of evidence, research and other types of knowledge in drug policy.

BACKGROUND AND AIMS: The prevailing 'evidence-based policy' paradigm emphasizes a technical-rational relationship between alcohol and drug research evidence and subsequent policy action. However, policy process theories do not start with this premise, and hence provide an opportunity to consider anew the ways in which evidence, research and other types of knowledge impact upon policy. This paper presents a case study, the police deployment of drug detection dogs, to highlight how two prominent policy theories [the Advocacy Coalition Framework (ACF) and the Multiple Streams (MS) approach] explicate the relationship between evidence and policy. METHODS: The two theories were interrogated with reference to their descriptions and framings of evidence, research and other types of knowledge. The case study methodology was employed to extract data concerned with evidence and other types of knowledge from a previous detailed historical account and analysis of drug detection dogs in one Australian state (New South Wales). Different types of knowledge employed across the case study were identified and coded, and then analysed with reference to each theory. A detailed analysis of one key 'evidence event' within the case study was also undertaken. RESULTS: Five types of knowledge were apparent in the case study: quantitative program data; practitioner knowledge; legal knowledge; academic research; and lay knowledge. The ACF highlights how these various types of knowledge are only influential inasmuch as they provide the opportunity to alter the beliefs of decision-makers. The MS highlights how multiple types of knowledge may or may not form part of the strategy of policy entrepreneurs to forge the confluence of problems, solutions and politics. CONCLUSIONS: Neither the Advocacy Coalition Framework nor the Multiple Streams approach presents an uncomplicated linear relationship between evidence and policy action, nor do they preference any one type of knowledge. The implications for research and practice include the contestation of evidence through beliefs (Advocacy Coalition Framework), the importance of venues for debate (Advocacy Coalition Framework), the way in which data and indicators are transformed into problem specification (Multiple Streams) and the importance of the policy ('alternatives') stream (Multiple Streams).

Evolutionary-Optimized Photonic Network Structure in White Beetle Wing Scales.

Most studies of structural color in nature concern periodic arrays, which through the interference of light create color. The "color" white however relies on the multiple scattering of light within a randomly structured medium, which randomizes the direction and phase of incident light. Opaque white materials therefore must be much thicker than periodic structures. It is known that flying insects create "white" in extremely thin layers. This raises the question, whether evolution has optimized the wing scale morphology for white reflection at a minimum material use. This hypothesis is difficult to prove, since this requires the detailed knowledge of the scattering morphology combined with a suitable theoretical model. Here, a cryoptychographic X-ray tomography method is employed to obtain a full 3D structural dataset of the network morphology within a white beetle wing scale. By digitally manipulating this 3D representation, this study demonstrates that this morphology indeed provides the highest white retroreflection at the minimum use of material, and hence weight for the organism. Changing any of the network parameters (within the parameter space accessible by biological materials) either increases the weight, increases the thickness, or reduces reflectivity, providing clear evidence for the evolutionary optimization of this morphology.

Swit_4259, an acetoacetate decarboxylase-like enzyme from Sphingomonas wittichii RW1.

The Gram-negative bacterium Sphingomonas wittichii RW1 is notable for its ability to metabolize a variety of aromatic hydrocarbons. Not surprisingly, the S. wittichii genome contains a number of putative aromatic hydrocarbon-degrading gene clusters. One of these includes an enzyme of unknown function, Swit_4259, which belongs to the acetoacetate decarboxylase-like superfamily (ADCSF). Here, it is reported that Swit_4259 is a small (28.8 kDa) tetrameric ADCSF enzyme that, unlike the prototypical members of the superfamily, does not have acetoacetate decarboxylase activity. Structural characterization shows that the tertiary structure of Swit_4259 is nearly identical to that of the true decarboxylases, but there are important differences in the fine structure of the Swit_4259 active site that lead to a divergence in function. In addition, it is shown that while it is a poor substrate, Swit_4259 can catalyze the hydration of 2-oxo-hex-3-enedioate to yield 2-oxo-4-hydroxyhexanedioate. It is also demonstrated that Swit_4259 has pyruvate aldolase-dehydratase activity, a feature that is common to all of the family V ADCSF enzymes studied to date. The enzymatic activity, together with the genomic context, suggests that Swit_4259 may be a hydratase with a role in the metabolism of an as-yet-unknown hydrocarbon. These data have implications for engineering bioremediation pathways to degrade specific pollutants, as well as structure-function relationships within the ADCSF in general.

Understanding policy persistence-The case of police drug detection dog policy in NSW, Australia.

BACKGROUND: Significant research attention has been given to understanding the processes of drug policy reform. However, there has been surprisingly little analysis of the persistence of policy in the face of opposition and evidence of ineffectiveness. In this article we analysed just such a case - police drug detection dog policy in NSW, Australia. We sought to identify factors which may account for the continuation of this policy, in spite of counter-evidence and concerted advocacy. METHODS: The analysis was conducted using the Advocacy Coalition Framework (ACF). We collated documents relating to NSW drug detection dog policy from 1995 to 2016, including parliamentary records (NSW Parliament Hansard), government and institutional reports, legislation, police procedures, books, media, and academic publications. Texts were then read, coded and classified against the core dimensions of the ACF, including subsystem actors and coalitions, their belief systems and resources and venues employed for policy debate. RESULTS: Three coalitions were identified as competing in the policy subsystem: security/law and order, civil liberties and harm reduction. Factors that aided policy stability were the continued dominance of the security/law and order coalition since they introduced the drug dog policy; a power imbalance enabling the ruling coalition to limit when and where the policy was discussed; and a highly adversarial policy subsystem. In this context even technical knowledge that dogs infringed civil liberties and increased risks of overdose were readily downplayed, leading to only incremental changes in implementation rather than policy cessation or wholesale revision. CONCLUSION: The analysis provides new insights into why the accumulation of new evidence and advocacy efforts can be insufficient to drive significant policy change. It poses a challenge for the evidence-based paradigm suggesting that in highly adversarial policy subsystems new evidence is unlikely to generate policy change without broader subsystem change, such as reducing the adversarial nature and/or providing new avenues for cross-coalition learning.

Beamstop-based low-background ptychography to image weakly scattering objects.

In recent years, X-ray ptychography has been established as a valuable tool for high-resolution imaging. Nevertheless, the spatial resolution and sensitivity in coherent diffraction imaging are limited by the signal that is detected over noise and over background scattering. Especially, coherent imaging of weakly scattering specimens suffers from incoherent background that is generated by the interaction of the central beam with matter along its propagation path in particular close to and inside of the detector. Common countermeasures entail evacuated flight tubes or detector-side beamstops, which improve the experimental setup in terms of background reduction or better coverage of high dynamic range in the diffraction patterns. Here, we discuss an alternative approach: we combine two ptychographic scans with and without beamstop and reconstruct them simultaneously taking advantage of the complementary information contained in the two scans. We experimentally demonstrate the potential of this scheme for hard X-ray ptychography by imaging a weakly scattering object composed of catalytic nanoparticles and provide the analysis of the signal-to-background ratio in the diffraction patterns.

In Situ Ptychography of Heterogeneous Catalysts using Hard X-Rays: High Resolution Imaging at Ambient Pressure and Elevated Temperature.

A new closed cell is presented for in situ X-ray ptychography which allows studies under gas flow and at elevated temperature. In order to gain complementary information by transmission and scanning electron microscopy, the cell makes use of a Protochips E-chipTM which contains a small, thin electron transparent window and allows heating. Two gold-based systems, 50 nm gold particles and nanoporous gold as a relevant catalyst sample, were used for studying the feasibility of the cell. Measurements showing a resolution around 40 nm have been achieved under a flow of synthetic air and during heating up to temperatures of 933 K. An elevated temperature exhibited little influence on image quality and resolution. With this study, the potential of in situ hard X-ray ptychography for investigating annealing processes of real catalyst samples is demonstrated. Furthermore, the possibility to use the same sample holder for ex situ electron microscopy before and after the in situ study underlines the unique possibilities available with this combination of electron microscopy and X-ray microscopy on the same sample.

Imaging Shock Waves in Diamond with Both High Temporal and Spatial Resolution at an XFEL.

The advent of hard x-ray free-electron lasers (XFELs) has opened up a variety of scientific opportunities in areas as diverse as atomic physics, plasma physics, nonlinear optics in the x-ray range, and protein crystallography. In this article, we access a new field of science by measuring quantitatively the local bulk properties and dynamics of matter under extreme conditions, in this case by using the short XFEL pulse to image an elastic compression wave in diamond. The elastic wave was initiated by an intense optical laser pulse and was imaged at different delay times after the optical pump pulse using magnified x-ray phase-contrast imaging. The temporal evolution of the shock wave can be monitored, yielding detailed information on shock dynamics, such as the shock velocity, the shock front width, and the local compression of the material. The method provides a quantitative perspective on the state of matter in extreme conditions.

Sbi00515, a Protein of Unknown Function from Streptomyces bingchenggensis, Highlights the Functional Versatility of the Acetoacetate Decarboxylase Scaffold.

The acetoacetate decarboxylase-like superfamily (ADCSF) is a group of ~4000 enzymes that, until recently, was thought to be homogeneous in terms of the reaction catalyzed. Bioinformatic analysis shows that the ADCSF consists of up to seven families that differ primarily in their active site architectures. The soil-dwelling bacterium Streptomyces bingchenggensis BCW-1 produces an ADCSF enzyme of unknown function that shares a low level of sequence identity (~20%) with known acetoacetate decarboxylases (ADCs). This enzyme, Sbi00515, belongs to the MppR-like family of the ADCSF because of its similarity to the mannopeptimycin biosynthetic protein MppR from Streptomyces hygroscopicus. Herein, we present steady state kinetic data that show Sbi00515 does not catalyze the decarboxylation of any α- or ß-keto acid tested. Rather, we show that Sbi00515 catalyzes the condensation of pyruvate with a number of aldehydes, followed by dehydration of the presumed aldol intermediate. Thus, Sbi00515 is a pyruvate aldolase-dehydratase and not an acetoacetate decarboxylase. We have also determined the X-ray crystal structures of Sbi00515 in complexes with formate and pyruvate. The structures show that the overall fold of Sbi00515 is nearly identical to those of both ADC and MppR. The pyruvate complex is trapped as the Schiff base, providing evidence that the Schiff base chemistry that drives the acetoacetate decarboxylases has been co-opted to perform a new function, and that this core chemistry may be conserved across the superfamily. The structures also suggest possible catalytic roles for several active site residues.

Structural and functional characterization of MppR, an enduracididine biosynthetic enzyme from streptomyces hygroscopicus: functional diversity in the acetoacetate decarboxylase-like superfamily.

The nonproteinogenic amino acid enduracididine is a critical component of the mannopeptimycins, cyclic glycopeptide antibiotics with activity against drug-resistant pathogens, including methicillin-resistant Staphylococcus aureus. Enduracididine is produced in Streptomyces hygroscopicus by three enzymes, MppP, MppQ, and MppR. On the basis of primary sequence analysis, MppP and MppQ are pyridoxal 5'-phosphate-dependent aminotransferases; MppR shares a low, but significant, level of sequence identity with acetoacetate decarboxylase. The exact reactions catalyzed by each enzyme and the intermediates involved in the route to enduracididine are currently unknown. Herein, we present biochemical and structural characterization of MppR that demonstrates a catalytic activity for this enzyme and provides clues about its role in enduracididine biosynthesis. Bioinformatic analysis shows that MppR belongs to a previously uncharacterized family within the acetoacetate decarboxylase-like superfamily (ADCSF) and suggests that MppR-like enzymes may catalyze reactions diverging from the well-characterized, prototypical ADCSF decarboxylase activity. MppR shares a high degree of structural similarity with acetoacetate decarboxylase, though the respective quaternary structures differ markedly and structural differences in the active site explain the observed loss of decarboxylase activity. The crystal structure of MppR in the presence of a mixture of pyruvate and 4-imidazolecarboxaldehyde shows that MppR catalyzes the aldol condensation of these compounds and subsequent dehydration. Surprisingly, the structure of MppR in the presence of "4-hydroxy-2-ketoarginine" shows the correct 4R enantiomer of "2-ketoenduracididine" bound to the enzyme. These data, together with bioinformatic analysis of MppR homologues, identify a novel family within the acetoacetate decarboxylase-like superfamily with divergent active site structure and, consequently, biochemical function.

Damage investigation on tungsten and diamond diffractive optics at a hard x-ray free-electron laser.

Focusing hard x-ray free-electron laser radiation with extremely high fluence sets stringent demands on the x-ray optics. Any material placed in an intense x-ray beam is at risk of being damaged. Therefore, it is crucial to find the damage thresholds for focusing optics. In this paper we report experimental results of exposing tungsten and diamond diffractive optics to a prefocused 8.2 keV free-electron laser beam in order to find damage threshold fluence levels. Tungsten nanostructures were damaged at fluence levels above 500 mJ/cm(2). The damage was of mechanical character, caused by thermal stress variations. Diamond nanostructures were affected at a fluence of 59 000 mJ/cm(2). For fluence levels above this, a significant graphitization process was initiated. Scanning Electron Microscopy (SEM) and µ-Raman analysis were used to analyze exposed nanostructures.

Full spatial characterization of a nanofocused x-ray free-electron laser beam by ptychographic imaging.

The emergence of hard X-ray free electron lasers (XFELs) enables new insights into many fields of science. These new sources provide short, highly intense, and coherent X-ray pulses. In a variety of scientific applications these pulses need to be strongly focused. In this article, we demonstrate focusing of hard X-ray FEL pulses to 125 nm using refractive x-ray optics. For a quantitative analysis of most experiments, the wave field or at least the intensity distribution illuminating the sample is needed. We report on the full characterization of a nanofocused XFEL beam by ptychographic imaging, giving access to the complex wave field in the nanofocus. From these data, we obtain the full caustic of the beam, identify the aberrations of the optic, and determine the wave field for individual pulses. This information is for example crucial for high-resolution imaging, creating matter in extreme conditions, and nonlinear x-ray optics.

Ronchi test for characterization of nanofocusing optics at a hard x-ray free-electron laser.

We demonstrate the use of the classical Ronchi test to characterize aberrations in focusing optics at a hard x-ray free-electron laser. A grating is placed close to the focus and the interference between the different orders after the grating is observed in the far field. Any aberrations in the beam or the optics will distort the interference fringes. The method is simple to implement and can provide single-shot information about the focusing quality. We used the Ronchi test to measure the aberrations in a nanofocusing Fresnel zone plate at the Linac Coherent Light Source at 8.194 keV.

Scanning X-ray nanodiffraction: from the experimental approach towards spatially resolved scattering simulations.

: An enhancement on the method of X-ray diffraction simulations for applications using nanofocused hard X-ray beams is presented. We combine finite element method, kinematical scattering calculations, and a spot profile of the X-ray beam to simulate the diffraction of definite parts of semiconductor nanostructures. The spot profile could be acquired experimentally by X-ray ptychography. Simulation results are discussed and compared with corresponding X-ray nanodiffraction experiments on single SiGe dots and dot molecules.

Full optical characterization of coherent x-ray nanobeams by ptychographic imaging.

Scanning coherent diffraction microscopy (ptychography) is an emerging hard x-ray microscopy technique that yields spatial resolutions well below the lateral size of the probing nanobeam. Besides a high resolution image of the object, the complex wave field of the probe can be reconstructed at the position of the object. By verifying the consistency of several independent wave field measurements along the optical axis, we address the question of how well the reconstruction represents the nanobeam. With a single ptychogram the wave field can be properly determined over a large range along the optical axis, also at positions inaccessible otherwise.

Scientific advice and public policy: expert advisers' and policymakers' discourses on boundary work.

This article reports on considerable variety and diversity among discourses on their own jobs of boundary workers of several major Dutch institutes for science-based policy advice. Except for enlightenment, all types of boundary arrangements/work in the Wittrock-typology (Social knowledge and public policy: eight models of interaction. In: Wagner P (ed) Social sciences and modern states: national experiences and theoretical crossroads. Cambridge University Press, Cambridge, 1991) do occur. 'Divergers' experience a gap between science and politics/policymaking; and it is their self-evident task to act as a bridge. They spread over four discourses: 'rational facilitators', 'knowledge brokers', 'megapolicy strategists', and 'policy analysts'. Others aspire to 'convergence'; they believe science and politics ought to be natural allies in preparing collective decisions. But 'policy advisors' excepted, 'postnormalists' and 'deliberative proceduralists' find this very hard to achieve.

A concise synthesis of (+/-)-cacalol.

A simple synthesis of the natural product cacalol has been developed that proceeds in seven steps and 21-25% overall yield. Ortho-lithiation of 4-methylanisole and alkylation with 5-iodo-1-pentene, followed by intramolecular Friedel-Crafts alkylation, gave 5-methoxy-1,8-dimethyltetralin. This compound was then formylated in the 6-position. Baeyer-Villiger oxidation and hydrolysis of the resulting formate gave 6-hydroxy-5-methoxy-1,8-dimethyltetralin. Alkylation of the phenolic hydroxyl group with chloroacetone followed by cyclodehydration gave cacalol methyl ether. Deprotection of this aryl methyl ether yielded cacalol.