The "Historical Materials BAG": A New Facilitated Access to Synchrotron X-ray Diffraction Analyses for Cultural Heritage Materials at the European Synchrotron Radiation Facility.

The European Synchrotron Radiation Facility (ESRF) has recently commissioned the new Extremely Brilliant Source (EBS). The gain in brightness as well as the continuous development of beamline instruments boosts the beamline performances, in particular in terms of accelerated data acquisition. This has motivated the development of new access modes as an alternative to standard proposals for access to beamtime, in particular via the "block allocation group" (BAG) mode. Here, we present the recently implemented "historical materials BAG": a community proposal giving to 10 European institutes the opportunity for guaranteed beamtime at two X-ray powder diffraction (XRPD) beamlines-ID13, for 2D high lateral resolution XRPD mapping, and ID22 for high angular resolution XRPD bulk analyses-with a particular focus on applications to cultural heritage. The capabilities offered by these instruments, the specific hardware and software developments to facilitate and speed-up data acquisition and data processing are detailed, and the first results from this new access are illustrated with recent applications to pigments, paintings, ceramics and wood.

Resistance training in heart failure patients: a systematic review and meta-analysis.

Aerobic training (AT) has been the primary mode of exercise training in cardiac rehabilitation. Historically, the reason for the prescription of AT was that it was speculated that although RT may be beneficial for some clinical outcomes, it may have an adverse effect on ventricular structure and function. However, RT has now made its way into current cardiac rehabilitation guidelines, including those directed towards patients with HF, albeit differences exist across institutions and guidelines. A systematic search of PubMed, EMBASE and Cochrane Trials Register on April 30, 2021, was conducted for exercise-based rehabilitation trials in HF. Randomised and controlled trials that reported on resistance training versus usual care or trials that directly compared RT to an AT intervention were included. Resistance training versus controls improves parameters of lower (SMD 0.76 (95%CI 0.26, 1.25, p = 0.003] and upper extremity muscle strength (SMD 0.85 (95%CI 0.35, 1.35), p = 0.0009], both key parameters of physical function throughout the lifespan. Importantly, RT in isolation, versus control, improves VO2peak [MD: 2.64 ml/kg/min (95%CI 1.67, 3.60), p < 0.00001] and 6MWD [MD: 49.94 m (95%CI 34.59, 65.29), p < 0.00001], without any detrimental effect on left ventricular parameters. Resistance training in HF patients is safe and improves parameters of physical function and quality of life. Where people with HF are unable to, or are not inclined to, partake in aerobic activity, RT alone is appropriate to elicit meaningful benefit.

Daiquiri: a web-based user interface framework for beamline control and data acquisition.

Daiquiri is a web-based user interface (UI) framework for control system monitoring and data acquisition designed for synchrotron beamlines. It provides simple, intuitive and responsive interfaces to control and monitor hardware, launch acquisition sequences and manage associated metadata. Daiquiri concerns itself only with the UI layer; it does not provide a scan engine or controls system but can be easily integrated with existing systems.

Structural effects of the highly protective V127 polymorphism on human prion protein.

Prion diseases, a group of incurable, lethal neurodegenerative disorders of mammals including humans, are caused by prions, assemblies of misfolded host prion protein (PrP). A single point mutation (G127V) in human PrP prevents prion disease, however the structural basis for its protective effect remains unknown. Here we show that the mutation alters and constrains the PrP backbone conformation preceding the PrP ß-sheet, stabilising PrP dimer interactions by increasing intermolecular hydrogen bonding. It also markedly changes the solution dynamics of the ß2-α2 loop, a region of PrP structure implicated in prion transmission and cross-species susceptibility. Both of these structural changes may affect access to protein conformers susceptible to prion formation and explain its profound effect on prion disease.

Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation.

Lipases (EC 3.1.1.3) are ubiquitous hydrolases for the carboxyl ester bond of water-insoluble substrates, such as triacylglycerols, phospholipids, and other insoluble substrates, acting in aqueous as well as in low-water media, thus being of considerable physiological significance with high interest also for their industrial applications. The hydrolysis reaction follows a two-step mechanism, or "interfacial activation," with adsorption of the enzyme to a heterogeneous interface and subsequent enhancement of the lipolytic activity. Among lipases, Candida antarctica lipase B (CALB) has never shown any significant interfacial activation, and a closed conformation of CALB has never been reported, leading to the conclusion that its behavior was due to the absence of a lid regulating the access to the active site. The lid open and closed conformations and their protonation states are observed in the crystal structure of CALB at 0.91 Å resolution. Having the open and closed states at atomic resolution allows relating protonation to the conformation, indicating the role of Asp145 and Lys290 in the conformation alteration. The findings explain the lack of interfacial activation of CALB and offer new elements to elucidate this mechanism, with the consequent implications for the catalytic properties and classification of lipases.

Application of in situ diffraction in high-throughput structure determination platforms.

Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given.

Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein.

Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer-monomer interface is more extensive than that at the dimer-dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the ß-sheet and the formation of an extended cross-ß structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.

Neutron structure of type-III antifreeze protein allows the reconstruction of AFP-ice interface.

Antifreeze proteins (AFPs) inhibit ice growth at sub-zero temperatures. The prototypical type-III AFPs have been extensively studied, notably by X-ray crystallography, solid-state and solution NMR, and mutagenesis, leading to the identification of a compound ice-binding surface (IBS) composed of two adjacent ice-binding sections, each which binds to particular lattice planes of ice crystals, poisoning their growth. This surface, including many hydrophobic and some hydrophilic residues, has been extensively used to model the interaction of AFP with ice. Experimentally observed water molecules facing the IBS have been used in an attempt to validate these models. However, these trials have been hindered by the limited capability of X-ray crystallography to reliably identify all water molecules of the hydration layer. Due to the strong diffraction signal from both the oxygen and deuterium atoms, neutron diffraction provides a more effective way to determine the water molecule positions (as D(2) O). Here we report the successful structure determination at 293 K of fully perdeuterated type-III AFP by joint X-ray and neutron diffraction providing a very detailed description of the protein and its solvent structure. X-ray data were collected to a resolution of 1.05 Å, and neutron Laue data to a resolution of 1.85 Å with a "radically small" crystal volume of 0.13 mm(3). The identification of a tetrahedral water cluster in nuclear scattering density maps has allowed the reconstruction of the IBS-bound ice crystal primary prismatic face. Analysis of the interactions between the IBS and the bound ice crystal primary prismatic face indicates the role of the hydrophobic residues, which are found to bind inside the holes of the ice surface, thus explaining the specificity of AFPs for ice versus water.

X-ray crystal structures of diacetates of 6-s-cis and 6-s-trans astaxanthin and of 7,8-didehydroastaxanthin and 7,8,7',8'-tetradehydroastaxanthin: comparison with free and protein-bound astaxanthins.

The crystal structures of the 6-s-cis [s-cis-(1)] and 6-s-trans [s-trans-(1)] conformers of the diacetates of astaxanthin (AXT) and those of (3S,3'S)-7,8-didehydroastaxanthin [(3S,3'S)-3,3'-dihydroxy-7,8-didehydro-beta,beta-carotene-4,4'-dione (2)] and (3S,3'S)-7,8,7',8'-tetradehydroastaxanthin [(3S,3'S)-3,3'-dihydroxy-7,8,7',8'-tetradehydro-beta,beta-carotene-4, 4'-dione (3)] are reported. The conformations of these four molecules vary in particular with the angle of twist of the end rings out of the plane of the polyene chain; for s-cis-(1), the end rings are twisted out of the plane of the polyene chain by an angle of -49.0 (5)degrees , and the conformation is therefore similar to that found for unesterified AXT as well as for the carotenoids, canthaxanthin and beta,beta-carotene. For s-trans-(1), the end rings are coplanar with the polyene chain and its conformation is much more similar to that of the protein-bound AXT in the blue protein, crustacyanin, which is found in the shell of lobsters, although s-trans-(1) shows much less bowing of the polyene chain. In (2) and (3) the end rings are also almost coplanar with the polyene chain with the end rings in (2) in the s-cis conformation, and in (3) in the s-trans conformation. Thus, an extensive ensemble of the possible beta end-ring conformations has been determined. These structures are compared with one another as well as unbound, unesterified AXT and protein-bound AXT. Also, the effect of the end-ring conformations on the colour and UV-vis spectra of the crystals was established.

The influence of drainage networks on patterns of soil respiration in a desert catchment.

Hydrologic flow and connectivity act as important determinants of ecological pattern and process in heterogeneous landscapes. Here we examine how the routing of water through the drainage network of an upper Sonoran Desert basin influences landscape patterns of soil respiration (SR) at both seasonal and event-based timescales. At seasonal timescales, SR varied up to 13-fold with downstream position in the drainage network, and annual estimates of CO2 efflux ranged from 185 g C x m(-2) x yr(-1) to 1190 g C x m(-2) x yr(-1) for sites arrayed along the same flow path. Spatial patterns of SR were unrelated to the carbon and water content of surface soils, but rather tracked changes in plant size and productivity, which in turn reflect downstream increases in groundwater availability. The relative importance of precipitation and temperature as drivers of SR also changed with landscape position, with the latter becoming more important in downstream locations. At the scale of individual precipitation events, SR increased up to 30-fold upon rewetting but typically returned to background levels within 24 h, even when soil moisture remained elevated. Unlike patterns observed at seasonal scales, event-based losses of CO2 varied across the landscape as a function of the organic-matter content in surface soils. Results from labile carbon amendments confirm that CO2 losses following precipitation pulses are initially constrained by substrate availability, not soil drying. By mediating spatial patterns of vegetation structure and soil resource availability, drainage networks represent an important physical template upon which belowground processes are organized in desert basins.

13-cis-Beta,beta-carotene and 15-cis-beta,beta-carotene.

13-cis-Beta,beta-carotene, C(40)H(56), crystallizes with a complete molecule in the asymmetric unit, whereas 15-cis-beta,beta-carotene, also C(40)H(56), has twofold symmetry about an axis through the central bond of the polyene chain. The polyene methyl groups are arranged on one side of the polyene chains for each molecule and the 6-s-cis beta end groups, with the cyclohexene rings in half-chair conformations, are twisted out of the planes of the polyene chains by angles ranging from 41.37 (17) to 52.2 (4) degrees. The molecules in each structure pack so that the arms of one occupy the cleft of the next, and there is significant pi-pi stacking of the almost-parallel polyene chains of the 15-cis isomer, which approach at distances of 3.319 (1)-3.591 (1) A.

Unravelling the chemical basis of the bathochromic shift in the lobster carapace; new crystal structures of unbound astaxanthin, canthaxanthin and zeaxanthin.

The crystal structures of the unbound carotenoids, synthetic astaxanthin (3S,3'S:3R,3'S:3R,3'R in a 1:2:1 ratio), canthaxanthin and (3R,3'S, meso)-zeaxanthin are compared with each other and the protein bound astaxanthin molecule in the carotenoprotein, beta-crustacyanin. Three new crystal forms of astaxanthin have been obtained, using different crystallization conditions, comprising a chloroform solvate, a pyridine solvate and an unsolvated form. In each structure, the astaxanthin molecules, which are similar to one another, are centrosymmetric and adopt the 6-s-cis conformation; the end rings are bent out of the plane of the polyene chain by angles of -42.6 (5), -48.9 (5) and -50.4 (3) degrees , respectively, and are disordered, showing the presence of both R and S configurations (in a 1:1 ratio). In the crystal packing of the chloroform and pyridine solvates, the astaxanthin molecules show pair-wise end-to-end intermolecular hydrogen bonding of the adjacent 3-hydroxyl and 4-keto oxygens, whereas in the unsolvated crystal form, the hydrogen-bonding interaction is intermolecular. In addition, there are intermolecular C-H hydrogen bonds in all three structures. The canthaxanthin structure, measured at 100 and 293 K, also adopts the 6-s-cis conformation, but with disorder of one end ring only. The rotation of the end rings out of the plane of the polyene chains (ca -50 degrees for each structure) is similar to that of astaxanthin. A number of possible C-H hydrogen bonds to the keto O atoms are also observed. (3R,3'S, meso)-zeaxanthin is centrosymmetric with a C5-C6-C7-C8 torsion angle of -74.9 (3) degrees ; the molecules show pair-wise hydrogen bonding between the hydroxyl O atoms. In addition, for all the crystal structures the polyene chains were arranged one above the other, with intermolecular distances of 3.61-3.79 A, indicating the presence of pi-stacking interactions. Overall, these six crystal structures provide an ensemble of experimentally derived results that allow several key parameters, thought to influence colour tuning of the bathochromic shift of astaxanthin in crustacyanin, to be varied. The fact that the colour of each of the six crystals remains red, rather than turning blue, is therefore especially significant.

Mechanisms of benthic algal recovery following spates: comparison of simulated and natural events.

We conducted a manipulative field experiment to examine individual and interactive effects of scour and short-term nutrient enrichment (4 h exposure) on postspate recovery of benthic algae in a desert stream. We then compared recovery from these simulated-spate conditions to algal recovery patterns following a natural spate that increased water-column nutrient levels for 2 weeks. That event differentially scoured communities on artificial substrata in place for a long-term experiment, significantly reducing biomass in 49-day-old communities but causing no significant reduction of biomass in older, 133-day-old communities. Thus, we were able to examine recovery of scoured and non-scoured benthic algal communities under natural post-spate conditions. Both natural and simulated spates reduced actual and relative abundances of diatoms within communities. In the manipulative experiment, scoured communities accrued biomass more rapidly than those not subjected to scour, but short-term enrichment had not effect. Accrual of diatoms and green algae was stimulated by the scour manipulations, while cyanobacteria maintained equal rates of growth in all treatments. Following the natural spate, diatom and green-algal densities increased in scoured communities, but recovery of algal biomass was slow on both scoured and non-scoured substrata, primarily because cyanobacteria, the dominant algal group on all tiles, did not increase under exposure to highly nitrate-enriched waters. Rates of algal cell accrual were inversely correlated with the amount of algal biomass present at the start of a recovery sequence. Algal immigration rates measured immediately after the natural spate and during an interflood period in the same season did not differ, indicating that the algal drift pool was not augmented by disturbance. Benthic algal recovery following spates is strongly influenced by the degree of scour generated by the event, but recovery patterns are also affected by the length of post-spate enrichment and the taxonomic composition of the affected community.