Krios I-Titan Krios I at Diamond
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Friederike
Leesch
,
Laura
Lorenzo-Orts
,
Carina
Pribitzer
,
Irina
Grishkovskaya
,
Josef
Roehsner
,
Anastasia
Chugunova
,
Manuel
Matzinger
,
Elisabeth
Roitinger
,
Katarina
Belačić
,
Susanne
Kandolf
,
Tzi-Yang
Lin
,
Karl
Mechtler
,
Anton
Meinhart
,
David
Haselbach
,
Andrea
Pauli
Diamond Proposal Number(s):
[2018127]
Abstract: Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed1,2,3,4. Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules, consisting of Habp4–eEF2 and death associated protein 1b (Dap1b) or Dap in complex with eIF5a. Both modules occupy functionally important sites and act together to stabilize ribosomes and repress translation. Dap1b (also known as Dapl1 in mammals) is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Addition of recombinant zebrafish Dap1b protein is sufficient to block translation and reconstitute the dormant egg ribosome state in a mammalian translation extract in vitro. Thus, a developmentally programmed, conserved ribosome state has a key role in ribosome storage and translational repression in the egg.
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Jan 2023
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[28087, 26608]
Abstract: Ti40Zr10Cu32Pd14Ga4 and Ti40Zr10Cu32Pd14Sn4 (in at.%) bulk metallic glasses (BMGs) with different geometries (wedges, rods, ribbons and discs) were prepared by suction casting, melt spinning and splat quenching, respectively. For comparison, the reference Ti40Zr10Cu36Pd14 BMG was cast as a rod with 2 mm diameter and in wedge-shaped form. High-energy X-ray diffraction measurements yielded a critical casting thickness of 2.4, 2.1 and at least 4 mm for the reference, Ga-containing, and Sn-containing BMGs, respectively. The extension of the supercooled liquid region of about 50 K, measured for the glassy rods and ribbons by differential scanning calorimetry, is larger than that of only 20 K found for the splat-quenched discs. As to the alloys’ mechanical properties, the Ti40Zr10Cu36Pd14 glassy rods deform plastically in compression up to a strain of 3.8% and possess a Young’s modulus of 78 GPa. The Sn- and Ga- containing BMG rods reach respectively a plastic strain of 6.1% and 4.7%, and a Young’s modulus of 72 and 63 GPa. Corrosion tests were performed by electrochemical experiments, and the highest pitting resistance was observed for Ti40Zr10Cu32Pd14Sn4 (pitting overpotential ηpit = 446 mV) compared to Ti40Zr10Cu32Pd14Ga4 (379 mV) and Ti40Zr10Cu36Pd14 (183 mV). The results of live/dead assay and cell viability revealed excellent biocompatibility for the Ga-containing BMGs.
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Jan 2023
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I22-Small angle scattering & Diffraction
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Mario
Gonzalez-Jimenez
,
Trent
Barnard
,
Ben A.
Russell
,
Nikita V.
Tukachev
,
Uroš
Javornik
,
Laure-Anne
Hayes
,
Andrew J.
Farrell
,
Sarah
Guinane
,
Hans M.
Senn
,
Andrew J.
Smith
,
Martin
Wilding
,
Gregor
Mali
,
Motohiro
Nakano
,
Yuji
Miyazaki
,
Paul
Mcmillan
,
Gabriele C.
Sosso
,
Klaas
Wynne
Diamond Proposal Number(s):
[28529]
Open Access
Abstract: A common feature of glasses is the “boson peak”, observed as an excess in the heat capacity over the crystal or as an additional peak in the terahertz vibrational spectrum. The microscopic origins of this peak are not well understood; the emergence of locally ordered structures has been put forward as a possible candidate. Here, we show that depolarised Raman scattering in liquids consisting of highly symmetric molecules can be used to isolate the boson peak, allowing its detailed observation from the liquid into the glass. The boson peak in the vibrational spectrum matches the excess heat capacity. As the boson peak intensifies on cooling, wide-angle x-ray scattering shows the simultaneous appearance of a pre-peak due to molecular clusters consisting of circa 20 molecules. Atomistic molecular dynamics simulations indicate that these are caused by over-coordinated molecules. These findings represent an essential step toward our understanding of the physics of vitrification.
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Jan 2023
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Krios III-Titan Krios III at Diamond
Krios IV-Titan Krios IV at Diamond
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Diamond Proposal Number(s):
[22238, 17057]
Abstract: The molecular mode of action of biguanides, including the drug metformin, which is widely used in the treatment of diabetes, is incompletely characterized. Here, we define the inhibitory drug-target interaction(s) of a model biguanide with mammalian respiratory complex I by combining cryo–electron microscopy and enzyme kinetics. We interpret these data to explain the selectivity of biguanide binding to different enzyme states. The primary inhibitory site is in an amphipathic region of the quinone-binding channel, and an additional binding site is in a pocket on the intermembrane-space side of the enzyme. An independent local chaotropic interaction, not previously described for any drug, displaces a portion of a key helix in the membrane domain. Our data provide a structural basis for biguanide action and enable the rational design of medicinal biguanides.
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Jan 2023
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I15-Extreme Conditions
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Diamond Proposal Number(s):
[24144]
Open Access
Abstract: BiFeO3-BaTiO3 (BF-BT) solid solutions exhibit great promise as the basis for high temperature piezoelectric transducers and energy storage dielectrics, but the fundamental mechanisms governing their functional properties require further clarification. In the present study, both pure and niobium-doped 0.7BF-0.3BT ceramics are synthesized by solid state reaction and their structure-property relationships are systematically investigated. It is shown that substituting a low concentration of Ti with Nb at a level of 0.5 at% increases the resistivity of BF-BT ceramics and facilitates ferroelectric switching at high electric field levels. Stable planar piezoelectric coupling factor values are achieved with a variation from 0.35 to 0.45 over the temperature range from 100 to 430 °C. In addition to the ferroelectric-paraelectric phase transformation at the Curie point (~ 430 °C), a frequency-dependent relaxation of the dielectric permittivity and associated loss peak are observed over the temperature range from -50 to +150 °C. These effects are correlated with anomalous enhancement of the remanent polarization and structural (rhombohedral) distortion with increasing temperature, indicating the occurrence of a re-entrant relaxor ferroelectric transformation on cooling. The results of the study provide new insight into the thermal evolution of structure and the corresponding functional properties in BF-BT and related solid solutions.
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Jan 2023
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I03-Macromolecular Crystallography
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Xiao
Liu
,
Raphael
Reinbold
,
Shuang
Liu
,
Ryan A.
Herold
,
Patrick
Rabe
,
Stéphanie
Duclos
,
Rahul B.
Yadav
,
Martine I.
Abboud
,
Sandrine
Thieffine
,
Fraser A.
Armstrong
,
Lennart
Brewitz
,
Christopher J.
Schofield
Diamond Proposal Number(s):
[23459]
Open Access
Abstract: Variants of isocitrate dehydrogenase (IDH) 1 and 2 (IDH1/2) alter metabolism in cancer cells by catalyzing the NADPH-dependent reduction of 2-oxoglutate (2OG) to (2R)-hydroxyglutarate (2HG). However, it is unclear how derivatives of 2OG can affect cancer cell metabolism. Here, we used synthetic C3 and C4 alkylated 2OG derivatives to investigate the substrate selectivities of the most common cancer-associated IDH1 variant (R132H IDH1), of two cancer-associated IDH2 variants (R172K IDH2, R140Q IDH2), and of wildtype IDH1/2. Absorbance-based, NMR and electrochemical assays were employed to monitor wildtype IDH1/2 and IDH1/2 variant-catalyzed 2OG derivative turnover in the presence and absence of 2OG. Our results reveal that 2OG derivatives can serve as substrates of the investigated IDH1/2 variants, but not of wildtype IDH1/2, and have the potential to act as 2OG-competitive inhibitors. Kinetic parameters reveal that some 2OG derivatives, including the natural product 3-methyl-2OG, are equally or even more efficient IDH1/2 variant substrates compared to 2OG. Furthermore, NMR and mass spectrometry studies confirmed IDH1/2 variant-catalyzed production of alcohols in the cases of the 3-methyl-, 3-butyl-, and 3-benzyl-substituted 2OG derivatives; a crystal structure of 3-butyl-2OG with an IDH1 variant (R132C/S280F IDH1) reveals active site binding. The combined results highlight the potential for (i) IDH1/2 variant-catalyzed reduction of 2-oxoacids other than 2OG in cells, (ii) modulation of IDH1/2 variant activity by 2-oxoacid natural products, including some present in common foods, (iii) inhibition of IDH1/2 variants via active site binding rather than the established allosteric mode of inhibition, and (iv) possible use of IDH1/2 variants as biocatalysts.
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Jan 2023
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[29806]
Open Access
Abstract: Small-angle X-ray scattering (SAXS) can be used for structural determination of biological macromolecules and polymers in their native states (e.g. liquid phase). This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. In an attempt to improve the reliability of such experiments, the reduction of radiation damage occurring from exposure to X-rays is required. One such method, is to use scavenger molecules to protect macromolecules against radicals produced during radiation exposure, such as reactive oxygen species (ROS). In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). In this case, we monitor the radiation induced changes of G5P during bio-SAXS measurments and the resulting microscopic energy-damage relation was determined from microdosimetric calculations by Monte-Carlo based particle scattering simulations with TOPAS/Geant4 and a custom target-model. This resulted in a median-lethal energy deposit of pure G5P at 4 mg mL−1 of E1/2 = 7 ± 5 eV, whereas a threefold increase of energy-deposit was needed under the presence of Ectoine to reach the same level of damage. This indicates that Ectoine increases the possible exposure time before radiation-damage to G5P is observed. Furthermore, the dominant type of damage shifted from aggregation in pure solutions towards a fragmentation for solutions containing Ectoine as a cosolute. These results are interpreted in terms of indirect radiation damage by reactive secondary species, as well as post-irradiation effects, related to preferential-exclusion of the cosolute from the protein surface. Hence, Ectoine is shown to provide a non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies.
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Jan 2023
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I08-Scanning X-ray Microscopy beamline (SXM)
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Christina L.
Davis
,
Ryan A.
Venturelli
,
Alexander B.
Michaud
,
Jon R.
Hawkings
,
Amanda M.
Achberger
,
Trista J.
Vick-Majors
,
Brad E.
Rosenheim
,
John E.
Dore
,
August
Steigmeyer
,
Joel D.
Barker
,
Liane G.
Benning
,
Matthew R.
Siegfried
,
John C.
Priscu
,
Brent C.
Christner
,
Carlo
Barbante
,
Mark
Bowling
,
Justin
Burnett
,
Timothy
Campbell
,
Billy
Collins
,
Cindy
Dean
,
Dennis
Duling
,
Helen A.
Fricker
,
Alan
Gagnon
,
Christopher
Gardner
,
Dar
Gibson
,
Chloe
Gustafson
,
David
Harwood
,
Jonas
Kalin
,
Kathy
Kasic
,
Ok-Sun
Kim
,
Edwin
Krula
,
Amy
Leventer
,
Wei
Li
,
W. Berry
Lyons
,
Patrick
Mcgill
,
James
Mcmanis
,
David
Mcpike
,
Anatoly
Mironov
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Molly
Patterson
,
Graham
Roberts
,
James
Rot
,
Cathy
Trainor
,
Martyn
Tranter
,
John
Winans
,
Bob
Zook
,
Mark L.
Skidmore
Diamond Proposal Number(s):
[25828]
Open Access
Abstract: Ice streams that flow into Ross Ice Shelf are underlain by water-saturated sediments, a dynamic hydrological system, and subglacial lakes that intermittently discharge water downstream across grounding zones of West Antarctic Ice Sheet (WAIS). A 2.06 m composite sediment profile was recently recovered from Mercer Subglacial Lake, a 15 m deep water cavity beneath a 1087 m thick portion of the Mercer Ice Stream. We examined microbial abundances, used 16S rRNA gene amplicon sequencing to assess community structures, and characterized extracellular polymeric substances (EPS) associated with distinct lithologic units in the sediments. Bacterial and archaeal communities in the surficial sediments are more abundant and diverse, with significantly different compositions from those found deeper in the sediment column. The most abundant taxa are related to chemolithoautotrophs capable of oxidizing reduced nitrogen, sulfur, and iron compounds with oxygen, nitrate, or iron. Concentrations of dissolved methane and total organic carbon together with water content in the sediments are the strongest predictors of taxon and community composition. δ¹³C values for EPS (−25 to −30‰) are consistent with the primary source of carbon for biosynthesis originating from legacy marine organic matter. Comparison of communities to those in lake sediments under an adjacent ice stream (Whillans Subglacial Lake) and near its grounding zone provide seminal evidence for a subglacial metacommunity that is biogeochemically and evolutionarily linked through ice sheet dynamics and the transport of microbes, water, and sediments beneath WAIS.
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Jan 2023
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[28534]
Open Access
Abstract: N-Acyl indolines 4 are potent, non-covalent Notum inhibitors developed from a covalent virtual screening hit 2a. The lead compounds were simple to synthesise, achieved excellent potency in a biochemical Notum-OPTS assay and restored Wnt signalling in a cell-based TCF/LEF reporter assay. Multiple high resolution X-ray structures established a common binding mode of these inhibitors with the indoline bound centred in the palmiteolate pocket with key interactions being aromatic stacking and a water mediated hydrogen bond to the oxyanion hole. These N-acyl indolines 4 will be useful tools for use in vitro studies to investigate the role of Notum in disease models, especially when paired with a structurally related covalent inhibitor (e.g. 4w and 2a). Overall, this study highlights the designed switch from covalent to non-covalent Notum inhibitors and so illustrates a complementary approach for hit generation and target inhibition.
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Jan 2023
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I15-Extreme Conditions
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Open Access
Abstract: Geothermal heat from the Earth`s crust is a source of natural and renewable energy. This energy can be extracted and used for generating electricity and heating of houses in the winter months. However, in order to extract energy from a well, we need to use material that can sustain contact with geothermal steam and is resistant to corrosion of the geothermal fluid and non-condensing gases such as hydrogen sulfide (H2S) and carbon dioxide (CO2), chloride ions (Cl−), and hydrogen fluoride (HF). An interesting alternative to today's materials are bimetals, composed of two different materials where the layer in contact with the aggressive environment is made of a noble material, while the outer layer (typically low-carbon steel) strengthens the composite and additionally provides good weldability.
This paper presents the microstructure, phase composition, and distribution of residual stresses of the bimetallic system nickel-chromium-molybdenum alloy (Alloy 625) cladded on the ferritic pressure vessel steel P355NH base material.
The bimetal has been prepared by explosion welding and is its use is geared for transport of highly corrosive media and as a material for heat exchangers, condensers, etc.
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Jan 2023
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