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At least 1,513 records · Page 84

Mechanism of tRNA-mediated +1 ribosomal frameshifting

Accurate translation of the genetic code is critical to ensure expression of proteins with correct amino acid sequences. Certain tRNAs can cause a shift out of frame (i.e., frameshifting) due to imbalances in tRNA concentrations, lack of tRNA modifications or insertions or deletions in tRNAs (called frameshift suppressors). Here, we determined the structural basis for how frameshift-suppressor tRNA SufA6 (a derivative of tRNA Pro ) reprograms the mRNA frame to translate a 4-nt codon when bound to the bacterial ribosome. After decoding at the aminoacyl (A) site, the crystal structure of the anticodon stem-loop of tRNA SufA6 bound in the peptidyl (P) site reveals ASL conformational changes that allow for recoding into the +1 mRNA frame. Furthermore, a crystal structure of full-length tRNA SufA6 programmed in the P site shows extensive conformational rearrangements of the 30S head and body domains similar to what is observed in a translocation intermediate state containing elongation factor G (EF-G). The 30S movement positions tRNA SufA6 toward the 30S exit (E) site disrupting key 16S rRNA–mRNA interactions that typically define the mRNA frame. In summary, this tRNA-induced 30S domain change in the absence of EF-G causes the ribosome to lose its grip on the mRNA and uncouples the canonical forward movement of the tRNAs during elongation.

59 BASIC BIOLOGICAL SCIENCES↗

Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar K D

Fluorogenic RNA aptamer tags with high affinity enable RNA purification and imaging. The G-quadruplex (G4) based Mango (M) series of aptamers were selected to bind a thiazole orange based (TO1-Biotin) ligand. Using a chemical biology and reselection approach, we have produced a MII.2 aptamer–ligand complex with a remarkable set of properties: Its unprecedented K D of 45 pM, formaldehyde resistance (8% v/v), temperature stability and ligand photo-recycling properties are all unusual to find simultaneously within a small RNA tag. Crystal structures demonstrate how MII.2, which differs from MII by a single A23U mutation, and modification of the TO1-Biotin ligand to TO1-6A-Biotin achieves these results. MII binds TO1-Biotin heterogeneously via a G4 surface that is surrounded by a stadium of five adenosines. Breaking this pseudo-rotational symmetry results in a highly cooperative and homogeneous ligand binding pocket: A22 of the G4 stadium stacks on the G4 binding surface while the TO1-6A-Biotin ligand completely fills the remaining three quadrants of the G4 ligand binding face. Similar optimization attempts with MIII.1, which already binds TO1-Biotin in a homogeneous manner, did not produce such marked improvements. We use the novel features of the MII.2 complex to demonstrate a powerful optically-based RNA purification system.

59 BASIC BIOLOGICAL SCIENCES↗

Pressure-induced modifications of the magnetic order in the spin-chain compound C a 3 C o 2 O 6

The structural and magnetic properties of the Ca 3 Co 2 O 6 spin-chain compound have been studied by means of neutron and x-ray powder diffraction at pressures up to 6.8 and 32 GPa, respectively. A suppression of the initial spin-density wave state (T N = 25 K) and stabilization of the collinear commensurate antiferromagnetic (AFM) state at high pressures (T NC = 26 K at P = 2.1 GPa) were observed. The pressure behavior of the competing intra- and interchain magnetic interactions was analyzed on the basis of obtained structural data and their role in the formation of the magnetic phase diagram is discussed. Here, the pressure behavior of the Néel temperature of the commensurate AFM phase was evaluated within the mean field theory approach and a good agreement with the experimental value dT NC /dP = 0.65 K/GPa was obtained.

1-dimensional spin chains↗

Modification of the Surface of Nickel by the Femtosecond Laser Pulses

Experimental results of the formation of a periodic submicron structure on the surface of polycrystalline nickel (Ni) under laser irradiation in air and in a liquid medium (distilled water) are presented. The geometry of the formed surface structures is determined by electron-microscopy methods. When irradiated in air, the structure is formed above the base surface of the sample, and when irradiated in the liquid, it is formed below the base surface. The dimensions of the pure Ni nanoparticles formed during laser ablation of the nickel sample in the liquid were determined.

36 MATERIALS SCIENCE↗

pnnl/brain_ohsu

Light sheet microscopy has made possible the 3D imaging of both fixed and live biological tissue, with samples as large as the entire mouse brain. We fine-tuned an existing model, TrailMap, using expert labeled data from axonal structures in neocortex. Without changing the network architecture, we implemented nnU-Net framework modifications in data augmentation, data foreground sampling, window learning rate, and the inference overlap method. The resulting model from these combined approaches yielded an improved F1 score

Oostrom, Marjolein↗

A Synchronized Sensor Array for Remote Monitoring of Avian and Bat Interactions with Offshore Renewable Energy Facilities

Wind energy production in the U.S. is projected to increase to 35% of our nation’s energy by 2050. This substantial increase in the U.S. is only a portion of the global wind industry growth, as many countries strive to reduce greenhouse gas emissions. A major environmental concern and potential market barrier for expansion of wind energy is bird and bat mortality from impacts with turbine blades, towers, and nacelles. Carcass surveys are the standard protocol for quantifying mortality at onshore sites. This method is imperfect, however, due to survey frequency at remote sites, removal of carcasses by scavengers between surveys, searcher efficiency, and other biases as well as delays of days to weeks or more in obtaining information on collision events. Furthermore, carcass surveys are not feasible at offshore wind energy sites. Near-real-time detection and quantification of interaction rates is possible at both onshore and offshore wind facilities using an onboard, integrated sensor package with data transmitted to central processing centers. We developed and experimentally tested an array of sensors that continuously monitors for interactions (including impacts) of birds and bats with wind turbines. The synchronized array includes three sensor nodes: (1) vibration (accelerometers and contact microphones), (2) optical (visual and infrared spectrum cameras), and (3) bioacoustics (acoustic and ultrasonic microphones). Accelerometers and contact acoustic microphones are placed at the root of each blade to detect impact vibrations and sound waves propagating through the structure. On-board data processing algorithms using wavelet analysis detect impact signals exceeding background vibration. Stereo-visual and infrared cameras were placed on the nacelle to allow target tracking, distance, and size calculations. On-board image processing and target detection algorithms identify moving targets within the camera field of view. Bioacoustic recorders monitor vocalizations and echolocations to aid in identifying organisms involved in interactions. Data from all sensors are temporarily stored in ring (i.e., circular) buffers with a duration varying by sensor type. Detection of target presence or impact by any of the sensors can trigger the archiving of data from all buffers for transmission to a central data processing center for evaluation and post-processing. This mitigates the risk of “data mortgages” posed by continual recording and minimizes personnel time required to manually review event data. We first conducted individual component tests at laboratories and field sites in Corvallis and Newport, Oregon, and Seattle and Sequim, Washington. We conducted additional component tests on research wind turbines at the North American Wind Research and Training Center, Mesalands Community College (MCC; General Electric 1.5 MW turbine), New Mexico, and the National Wind Technology Center, National Renewable Energy Laboratory (NREL; Controls Advanced Research Turbines 3 [CART 3] 600 kW Westinghouse turbine), Colorado. We conducted fully integrated system tests at NREL in October 2014 and April 2015. We used only research wind turbines so that we could conduct controlled, experimentally generated impacts using empty and water-filled tennis balls shot from a compressed air cannon on the ground. The approx. 57-140 g tennis balls (depending on water content) were at the upper mass range for bats, but lower mass range for marine birds. Therefore, the ability to detect collisions of most seabirds is likely greater than our experiments demonstrate, but possibly lower for some bats depending on the background signal of a given turbine. Vibration data demonstrated that background signals of operating turbines varied markedly among the CART 3 under normal operation (greatest), GE (moderate), and CART 3 during idle rotation (generator not engaged; least). In total, we measured 63 experimental blade impacts on the two research turbines. Impaction detection was dependent on background signals, position of impact on the blade (a tip strike resulted in the strongest impact signal), and impact kinetics (velocity of ball and whether the ball struck the surface of the blade or the leading edge of the blade struck the ball). Overall detection percentage ranged from 100% for the “quietest” conditions (CART 3 idle rotation), down to 35% for the noisiest (CART 3 normal operation). Impact signals were detected from sensors on more than one blade (i.e., blades other than the blade struck) 50% - 75% of the time. Stereo imaging provided valuable metrics, but increased data processing and equipment cost. Given the cost of cameras with sufficient resolution for target identification, we suggest mounting cameras directly on the blades to continuously view the entire rotor swept area with the fewest number of cameras. Bioacoustic microphones provide taxonomic identification, as well as information on ambient noise levels. They also assist in identifying environmental conditions such as hail storms, high winds, thunder, lightning, etc., that may contribute to a collision or a false positive detection. We demonstrated a proof of concept for an integrated sensor array to detect and identify bird and bat collisions with wind turbines. The next phase of research and development for this system will miniaturize and integrate sensors from all three nodes into a single wireless package that can be attached directly to the blade. This next generation system would use all “smart” sensors capable of onboard data processing to drastically reduce data streams and processing time on a central computer. A provisional patent for the blade mounted system was submitted by Oregon State University and recorded by the U.S. Patent and Trademark Office (application no. 62313028). Eventually, technology and industry advances will allow this low cost monitoring system to be designed into materials during manufacturing so that all turbines could be monitored with either a subset or full suite of sensors. As standard equipment on all commercial turbines, the sensor suite would allow the industry to effectively monitor whether individual turbines were causing mortalities or not and under what circumstances. It would also provide real-time evaluation of mechanical and structural integrity of a turbine via vibration, image, and acoustic data streams, thereby permitting modifications in operation to limit environmental or mechanical damage.

17 WIND ENERGY↗

Late-time growth weakly affects the significance of high-redshift massive galaxies

Recent observations by the James Webb Space Telescope have revealed massive galaxies at very high redshift ( z ≃ 7 − 15 ). The question of whether the existence of such galaxies is expected in the corresponding JWST surveys has received a lot of attention, though the answer straddles areas of cosmology and complex astrophysical details of high-redshift galaxy formation. The growth rate of density fluctuations determines the amplitude of overdensities that collapse to form galaxies. Late-time modifications of growth, combined with measurements at both z ∼ 1 from large-scale structure and z ∼ 1000 from the cosmic microwave background, affect the predictions for the abundance of first galaxies in the universe. In this paper, we point out that the late-time growth rate of structure affects the statistical significance of high-redshift, high-mass objects very weakly. Consequently, if the existence and abundance of these objects are confirmed to be unexpected, the variations in the late-time growth history are unlikely to explain these anomalies.

Xia, Qianran↗

High conductivity magnesium alloy

A castable, moldable, or extrudable magnesium-based alloy that includes one or more insoluble additives. The insoluble additives can be used to enhance the mechanical properties of the structure, such as ductility and/or tensile strength. The final structure can be enhanced by heat treatment, as well as deformation processing such as extrusion, forging, or rolling, to further improve the strength of the final structure as compared to the non-enhanced structure. The magnesium-based composite has improved thermal and mechanical properties by the modification of grain boundary properties through the addition of insoluble nanoparticles to the magnesium alloys. The magnesium-based composite can have a thermal conductivity that is greater than 180 W/m-K, and/or ductility exceeding 15-20% elongation to failure.

Sherman, Andrew J.↗

High conductivity magnesium alloy

A castable, moldable, or extrudable magnesium-based alloy that includes one or more insoluble additives. The insoluble additives can be used to enhance the mechanical properties of the structure, such as ductility and/or tensile strength. The final structure can be enhanced by heat treatment, as well as deformation processing such as extrusion, forging, or rolling, to further improve the strength of the final structure as compared to the non-enhanced structure. The magnesium-based composite has improved thermal and mechanical properties by the modification of grain boundary properties through the addition of insoluble nanoparticles to the magnesium alloys. The magnesium-based composite can have a thermal conductivity that is greater than 180 W/m-K, and/or ductility exceeding 15-20% elongation to failure.

Sherman, Andrew J.↗

Structure-Guided Identification of Resistance Breaking Antimalarial N -Myristoyltransferase Inhibitors

The attachment of myristate to the N-terminal glycine of certain proteins is largely a co-translational modification catalyzed by N-myristoyltransferase (NMT), and involved in protein membrane-localization. Pathogen NMT is a validated therapeutic target in numerous infectious diseases including malaria. In Plasmodium falciparum , NMT substrates are important in essential processes including parasite gliding motility and host cell invasion. Here, we generated parasites resistant to a particular NMT inhibitor series and show that resistance in an in vitro parasite growth assay is mediated by a single amino acid substitution in the NMT substrate-binding pocket. The basis of resistance was validated and analyzed with a structure-guided approach using crystallography, in combination with enzyme activity, stability, and surface plasmon resonance assays, allowing identification of another inhibitor series unaffected by this substitution. We suggest that resistance studies incorporated early in the drug development process help selection of drug combinations to impede rapid evolution of parasite resistance.

59 BASIC BIOLOGICAL SCIENCES↗

Finite scale theory: Predicting nature’s shocks

In this paper, we describe a continuum model that accurately reproduces the experimentally measured structure of physical shocks in a perfect gas. In this work, we begin by presenting a history of shock structure research, theoretical, experimental and numerical, to quantify the significant discrepancies between Navier–Stokes predictions and laboratory measurements. In our first main result, we discuss modifications that generalize the Chapman–Enskog approximation and lead to a new continuum model termed the Finite Scale Equations. In our second main result, we use this continuum model to calculate shock structure with results comparable in accuracy to numerical simulations based on the Boltzmann equation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Advances in the Understanding of ELM Suppression by Resonant Magnetic Perturbations (RMPs) in DIII-D and Implications for ITER

Experiments on DIII-D have expanding the operating window for RMP ELM suppression to higher q95 with dominant electron heating and fully non-inductive current drive relevant to advanced modes of ITER operation. Robust ELM suppression has also been obtained with a reduced coil set, mitigating the risk of coil failure in maintaining ELM suppression in ITER. These results significantly expand the operating space and reduce risk for obtaining RMP ELM suppression in ITER. Efforts have also been made to search for 3D cause of ELM suppression. No internal non-axisymmetric structure is detected at the top of the pedestal, indicating that the dominant effect of the RMP is to produce an n=0 transport modification of the profiles. Linear two fluid MHD simulations using M3D-C1 indicate resonant field penetration and significant magnetic stochasticity at the top of the pedestal, consistent with the absence of detectable 3D structure in that region. A profile database was developed to compare the scaling of the pedestal and global confinement with the applied 3D field strength in ELM suppressed and ELM mitigated plasmas. The EPED pedestal model accurately predicts the measured pedestal pressure at the threshold of ELM suppression, increasing confidence in theoretical projections to ITER pedestal conditions. Both the H-factor (H(sub)98y2) and thermal energy confinement time do not degrade substantially with applied RMP fields near the threshold of ELM suppression, enhancing confidence in the compatibility of ITER high performance operation with RMP ELM suppression.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Shape coexistence at N=20 and N=28: Study of 0{sub 2}{sup +} states in {sup 34}Si and {sup 44}S

It is well known that the nuclear shell structure changes for the most exotic nuclei. One of the consequences of this phenomenon is the modification of the 'classical' magic numbers, as experimentally observed at N = 20 and N = 28. Nevertheless, the mechanisms responsible for such changes are still under discussion and more experimental information is needed to better constrain the theoretical models. In these proceedings, we report on the discovery and the experimental study by precise spectroscopy experiments of the 0{sub 2}{sup +} state in {sup 34}Si and {sup 44}S. The {sup 34}Si is located between the magic spherical {sup 36}S and the deformed {sup 32}Mg, member of the so-called island of inversion, whereas {sup 44}S is located between the magic spherical {sup 48}Ca and the deformed {sup 42}Si. Therefore, the structure of these nuclei, and in particular the phenomenon of shape coexistence, is of crucial importance to understand how the intruder configurations progressively dominate the ground state structure of the most exotic nuclei at both N = 20 and N = 28.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Cellulolytic enzyme-aided extraction of hemicellulose from switchgrass and its characteristics

The isolation of biomass components with their intact structure is integral for understanding the characteristics of biomass. Compared to other major biomass components such as cellulose and lignin, hemicellulose remains a challenging component to be isolated from the plant cell wall without significant depolymerization and modification. Here, a novel cellulolytic enzyme-aided hemicellulose (CEH) isolation method was developed to isolate hemicellulose with a near-native branched structure from switchgrass. The structural characteristics of CEH were investigated and compared with hemicelluloses isolated by conventional alkaline extracted hemicellulose (AEH) and DMSO extracted hemicellulose (DMSOH) methods. Gel permeation chromatography (GPC) analysis indicated that CEH had a weight-average molecular weight of 44 kDa, which was comparable to that of AEH (43 kDa) but higher than that of DMSOH (37 kDa). The chemical composition analysis revealed that CEH retained a higher proportion of glucuronic acid compared to AEH and DMSOH. The 2D 13 C– 1 H heteronuclear single quantum coherence (HSQC) NMR spectra containing the β-(1,4)-linked-D-xylan backbone, non-reducing-end peaks and both α- and β-reducing-end peaks in CEH were comparable to the spectra of the commercial beechwood xylan. CEH showed a highly branched hemicellulose structure, which retained methoxyl groups, O -acetyl groups, and 4- O -methyl-glucuronic acid attached to the xylan backbone.

59 BASIC BIOLOGICAL SCIENCES↗

Designing Glass and Crystalline Phases of Metal–Bis(acetamide) Networks to Promote High Optical Contrast

Owing to their high tunability and predictable structures, metal–organic materials offer a powerful platform to study glass formation and crystallization processes and to design glasses with unique properties. In this work, we report a novel series of glass-forming metal–ethylenebis(acetamide) networks that undergo reversible glass and crystallization transitions below 200 °C. The glass-transition temperatures, crystallization kinetics, and glass stability of these materials are readily tunable, either by synthetic modification or by liquid-phase blending, to form binary glasses. Pair distribution function (PDF) analysis reveals extended structural correlations in both single and binary metal–bis(acetamide) glasses and highlights the important role of metal–metal correlations during structural evolution across glass–crystal transitions. Notably, the glass and crystalline phases of a Co–ethylenebis(acetamide) binary network feature a large reflectivity contrast ratio of 4.8 that results from changes in the local coordination environment around Co centers. These results provide new insights into glass–crystal transitions in metal–organic materials and have exciting implications for optical switching, rewritable data storage, and functional glass ceramics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Intrinsic disorder in the regulatory N-terminal domain of diacylglycerol acyltransferase 1 from Brassica napus

Proteins with multifunctional regulatory domains often demonstrate structural plasticity or protein disorder, allowing the binding of multiple regulatory factors and post-translational modifications. While the importance of protein disorder is clear, it also poses a challenge for in vitro characterization. Here, we report protein intrinsic disorder in a plant molecular system, which despite its prevalence is less studied. We present a detailed biophysical characterization of the entire cytoplasmic N-terminal domain of Brassica napus diacylglycerol acyltransferase, (DGAT1), which includes an inhibitory module and allosteric binding sites. Our results demonstrate that the monomeric N-terminal domain can be stabilized for biophysical characterization and is largely intrinsically disordered in solution. This domain interacts with allosteric modulators of DGAT1, CoA and oleoyl-CoA, at micromolar concentrations. Furthermore, while solution scattering studies indicate conformational heterogeneity in the N-terminal domain of DGAT1, there is a small gain of secondary structure induced by ligand binding.

59 BASIC BIOLOGICAL SCIENCES↗

Spectroscopic characterization of Mn 2+ and Cd 2+ coordination to phosphorothioates in the conserved A9 metal site of the hammerhead ribozyme

Phosphorothioate modifications have widespread use in the field of nucleic acids. As substitution of sulfur for oxygen can alter metal coordination preferences, the phosphorothioate metal-rescue experiment is a powerful method for identifying metal coordination sites that influence specific properties in a large RNAs. The A9/G10.1 metal binding site of the hammerhead ribozyme (HHRz) has previously been shown to be functionally important through phosphorothioate rescue experiments. While an A9-S Rp substitution is inhibitory in Mg 2+ , thiophilic Cd 2+ rescues HHRz activity. Mn 2+ is also often used in phosphorothioate metal-rescue studies but does not support activity for the A9-S Rp HHRz. Here, we use EPR, electron spin-echo envelope modulation (ESEEM), and X-ray absorption spectroscopic methods to directly probe the structural consequences of Mn 2+ and Cd 2+ coordination to R p and S p phosphorothioate modifications at the A9/G10.1 site in the truncated hammerhead ribozyme (tHHRz). The results demonstrate that while Cd 2+ does indeed bind to S in the thio-substituted ligand, Mn 2+ coordinates to the non–sulfur oxo group of this phosphorothioate, regardless of isomer. Computational models demonstrate the energetic preference of Mn—O over Mn—S coordination in metal-dimethylthiophosphate models. In the case of the tHHRz, the resulting Mn 2+ coordination preference of oxygen in either R p or S p A9 phosphorothioates differentially tunes catalytic activity, with Mn—O coordination in the A9-S Rp phosphorothioate enzyme being inhibitory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗