CryoEM structures of pseudouridine-free ribosome suggest impacts of chemical modifications on ribosome conformations
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99 GENERAL AND MISCELLANEOUS↗
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Alpha-Imaging Detector System Development for Large Area Monitoring
Effective management and disposal of legacy nuclear waste are essential for ensuring safe work environments and minimizing environmental impacts. Monitoring airborne actinide contamination is particularly critical due to the high internal dose potential of alpha-emitting radionuclides. Traditional continuous air monitoring systems (CAMs) used in the industry are limited in the volume of air they can sample, potentially leading to inaccurate radiation detection over large areas. For example, in 2018, elevated levels of airborne Plutonium-239 were detected beyond the controlled areas of the Hanford Plutonium Finishing Plant, highlighting the potential risks to both plant workers and nearby residents. To address these challenges, high-efficiency particulate absorbing (HEPA) air purifiers can enhance air flow by up to 1.5 orders of magnitude, thereby increasing monitoring efficiency and providing a cost-effective solution for large-area surveillance. To quantify the activities of alpha-emitting radionuclides on HEPA filters, the Savannah River National Laboratory is developing an advanced alpha-imaging detection system. This system includes scintillating materials combined with a digital scientific camera. A significant concern in operating such a large-area airborne monitoring system is the handling of HEPA filters, which may be contaminated with radioactive particles. To mitigate these hazards, it is crucial to ensure that any contamination is securely fixed onto the filters. Efforts have been made to optimize the sensitivity of scintillator-epoxy composites and apply them to HEPA filters. These materials were characterized using fluoroscence spectroscopy. These techniques confirmed the purity of the raw materials, the dispersion of scintillators in the epoxy matrix, and the stability of their optical and structural properties post-modification. The optimal scintillator-epoxy composite was selected for use on alpha-spiked HEPA filters to evaluate the efficiency of the sprayer. HEPA filters, embedded with alpha particles collected by an air purifier deployed in an airborne radiation area, have been tested to assess detection efficiency. Future work will focus on employing multiple imaging sensors simultaneously to enhance sensitivity across different regions of the HEPA filter.
Pham, Phuong [Savannah River National Laboratory (↗
Harnessing Aromatic‐Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification
Abstract Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high‐resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor‐1, which is targeted by osteoporosis drugs. These results should motivate other structure‐based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.
36 MATERIALS SCIENCE↗
Harnessing Aromatic‐Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification
Abstract Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high‐resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor‐1, which is targeted by osteoporosis drugs. These results should motivate other structure‐based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.
36 MATERIALS SCIENCE↗
Development of high throughput and in vitro assays for analyzing RNA modifications
Modifications on RNAs play major roles in their stability, translation, and enzymatic activity. Despite its importance, the current techniques are insufficient to study the structure and function of RNA modifications. Indeed, the National Academies of Science, Engineering and Medicine indicate that developing new tools and further study the function of RNA modifications is strategically a high priority for advancing science in the coming years (https://www.nationalacademies.org/our-work/toward-sequencing-and-mapping-of-rna-modifications). RNA modifications occur in all domains of life controlling processes such as RNA turnover, translation regulation, cellular defenses and bioproduction. Our preliminary data indicated that the insulin mRNA might get ADP-ribosylated by the ADP-ribosyltransferase PARP12. RNA ADP-ribosylation has been described in Escherichia coli. Combined to the fact that ADP-ribosyltransferase (PARP) genes are conserved throughout evolution we hypothesize that this modification might play essential roles in cells. Therefore, we proposed to develop sequencing techniques and in vitro enzymatic assays to identify and validate ADP-ribosylation motifs and sites. Here we report the development of RNA-seq and qPCR assays to identify ADP-ribosylated RNAs, in addition to a nicotinamide adenosine dinucleotide (NAD – ADP-ribosylation donor) consumption assay and an enzyme-linked immunosorbent assay (ELISA) to measure ADP-ribosyltransferase activity. Testing these assays with the insulin mRNA confirmed that this transcript is ADP-ribosylated. These assays will not only enable studying the function of ADP-ribosylation but can be easily adapted for studying other RNA modifications. This will open opportunities to study RNA modifications in different model systems from bacteria to viruses to plants, bringing insights into their cellular functions and the possibility of targeting them for biotechnological applications.
59 BASIC BIOLOGICAL SCIENCES↗
Template-free fabrication of fractal porous Y 2 O 3 monolithic foam and its functional modification by Ni-doping
Fractal structures which display nearly the same character at every scale exist widely in nature, however, it is still a great challenge to fabricate a fractal nanostructure. Herein, a Y 2 O 3 monolith with unique hierarchically fractal porous structure was fabricated via calcination of a fractal porous coordination polymer precursor. The monolith exhibits porous feature with the pore-size ranging from micrometers to nanometers. Interestingly, each level of the pore-wall is composed of secondary porous structures, whose pore-wall is composed of sub-level self-similar porous feature. Moreover, by Ni-doping in the coordination polymer precursor, fractal porous Ni@Y 2 O 3 was prepared, and exhibited enhanced activity in ethanol steam reforming compared with that of a common supported NiO catalyst.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Insights on the dissolution of water in an albite melt at high pressures and temperatures from a direct structural analysis
The water dissolution mechanism in silicate melts under high pressures is not well understood. Here we present the first direct structure investigation of a water-saturated albite melt to monitor the interactions between water and the network structure of silicate melt at the molecular level. In situ high-energy X-ray diffraction was carried out on the NaAlSi 3 O 8 -H 2 O system at 800 °C and 300 MPa, at the Advanced Photon Source synchrotron facility. The analysis of the X-ray diffraction data was augmented with classical Molecular Dynamics simulations of a hydrous albite melt, incorporating accurate water-based interactions. The results show that metal–oxygen bond breaking at the bridging sites occurs overwhelmingly at the Si site upon reaction with H 2 O, with subsequent Si–OH bond formation and negligible Al–OH formation. Furthermore, we see no evidence for the dissociation of the Al 3+ ion from the network structure upon breaking of the Si–O bond in the hydrous albite melt. The results also indicate that the Na + ion is an active participant in the modifications of the silicate network structure of the albite melt upon water dissolution at high P–T conditions. We do not find evidence for the Na + ion dissociating from the network structure upon depolymerization and subsequent formation of NaOH complexes. Instead, our results show that the Na + ion persists as a structure modifier with a shift away from Na–BO bonding to an increase in the extent of Na-NBO bonding, in parallel with pronounced depolymerization of the network. Our MD simulations show that the Si–O and Al–O bond lengths are expanded by about 6% in the hydrous albite melt compared to those of the dry melt at high P–T conditions. The changes in the network silicate structure of a hydrous albite melt at high pressure and temperature, as revealed in this study, must be considered in the advancement of water dissolution models of hydrous granitic (or alkali aluminosilicate) melts.
36 MATERIALS SCIENCE↗
Synthesis of Pyrimidine Modified Seleno–DNA as a Novel Approach to Antisense Candidate
Chemically modified antisense oligonucleotides (ASO) currently in pre–clinical and clinical experiments mainly focus on the 2’–position derivatizations to enhance stability and targeting affinity. Considering the possible incompatibility of 2’–modifications with RNase H stimulation and activity, we have hypothesized that the atom specific modifications on nucleobases can retain the complex structure and RNase H activity, while enhancing ASO's binding affinity, specificity, and stability against nucleases. Herein we report a novel strategy to explore our hypothesis by synthesizing the deoxynucleoside phosphoramidite building block with the seleno–modification at 5–position of thymidine, as well as its Se–oligonucleotides. Via X–ray crystal structural study, we found that the Se–modification was located in the major groove of nucleic acid duplex and didn't cause the thermal and structural perturbations. Surprisingly, our nucleobase–modified Se–DNAs were exceptionally resistant to nuclease digestion, while compatible with RNase H activity. In conclusion, this affords a novel avenue for potential anti–sense modification in the form of Se–antisense oligonucleotides (Se–ASO).
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Tuning the Coordination Environment of Rh Single Atoms on Highly Dispersed Reducible Oxides for Enhanced Reverse Water-Gas Shift Performance
Controlling the dynamic mobility of catalyst surface active sites and their interactions with the surrounding environment is critical in generating active surfaces that directly influence the catalytic activity and selectivity. Here, we report a strategy for tailoring the dispersion and electronic environment of single atom Rh catalysts by decorating the alumina support with highly dispersed (HD) cerium and molybdenum oxides. The resulting catalysts exhibit markedly different behavior in the Reverse Water Gas Shift (RWGS) reaction. In particular, Rh/MoOx(HD)/Al2O3 maintains atomically dispersed Rh even at elevated temperatures (up to 400 °C), achieving CO selectivity of up to 100% and resists sintering via the formation of a newly developed structure featuring Rh single atoms embedded in MoOx clusters. In situ spectroscopy and microscopy analyses confirm the stabilization of Rh and the dynamic evolution of Rh–Mo coordination under reaction conditions. Our findings highlight the power of support modification in steering active site structure and activity, offering a pathway toward enhanced and tunable single atom catalysts for CO2 valorization.
CO selectivity↗
Summertime Post-Cold-Frontal Marine Stratocumulus Transition Processes over the Eastern North Atlantic
Abstract Marine boundary layer (MBL) cloud morphology associated with two summertime cold fronts over the eastern North Atlantic (ENA) is investigated using high-resolution simulations from the Weather Research and Forecasting (WRF) Model and observations from the Atmospheric Radiation Measurement (ARM) ENA Climate Research Facility. Lagrangian trajectories are used to study the evolution of post-cold-frontal MBL clouds from solid stratocumulus to broken cumulus. Clouds within specified domains in the vicinity of transitions are classified according to their degree of decoupling, and cloud-base and cloud-top breakup processes are evaluated. The Lagrangian derivative of the surface latent heat flux is found to be strongly correlated with that of the cloud fraction at cloud base in the simulations. Cloud-top entrainment instability (CTEI) is shown to operate only in the decoupled MBL. A new indicator of inversion strength at cloud top that employs the vertical gradients of equivalent potential temperature and saturation equivalent potential temperature, which can be computed directly from soundings, is proposed as an alternative to CTEI. Overall, results suggest that the deepening–warming hypothesis suggested by Bretherton and Wyant explains many of the characteristics of the summertime postfrontal MBL evolution of cloud structure over the ENA, thereby widening the phase space over which the hypothesis may be applied. A subset of the deepening–warming hypothesis involving warming initially dominating over moistening is proposed. It is postulated that changes in climate change–induced modifications in cold-frontal structure over the ENA may be accompanied by coincident changes in the location and timing of MBL cloud transitions in the post-cold-frontal environment.
54 ENVIRONMENTAL SCIENCES↗
Effect of cellulose reducing ends and primary hydroxyl groups modifications on cellulose-cellulase interactions and cellulose hydrolysis
Cellulose reducing ends are believed to play a vital role in the cellulose recalcitrance to enzymatic conversion. However, their role in insoluble cellulose accessibility and hydrolysis is not clear. Thus, in this study, reducing ends of insoluble cellulose derived from various sources were modified by applying reducing and/or oxidizing agents. Here, the effects of cellulose reducing ends modification on cellulose reducing ends, cellulose structure, and cellulose accessibility to cellulase were evaluated along with the impact on cellulose hydrolysis with complete as well purified cellulase components. Sodium borohydride (NaBH 4 ) reduction and sodium chlorite-acetic acid (SC/AA) oxidation were able to modify more than 90% and 60% of the reducing ends, respectively, while the bicinchoninic acid (BCA) reagent applied for various cycles oxidized cellulose reducing ends to various extents. X-ray diffractograms of the treated solids showed that these treatments did not change the cellulose crystalline structure and the change in crystallinity index was insignificant. Surprisingly, it was found that the cellulose reducing ends modification, either through selective NaBH 4 reduction or BCA oxidation, had a negligible impact on cellulose accessibility as well on cellulose hydrolysis rates or final conversions with complete cellulase at loadings as low as 0.5 mg protein/g cellulose. In fact, in contrast to what is traditionally believed, modifications of cellulose reducing ends by these two methods had no apparent impact on cellulose conversion with purified cellulase components and their synergy. However, SC/AA oxidation resulted in significant drop in cellulose conversion (10%–50%) with complete as well purified cellulase components. Nonetheless, further research revealed that the cause for drop in cellulose conversion for the SC/AA oxidation case was due to primary hydroxyl groups (PHGs) oxidation and not the oxidation of reducing ends. Furthermore, it was found that the PHGs modification affects cellulose accessibility and slows the cellulase uptake as well resulting in significant drop in cellulose conversions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Engineered Wood: Sustainable Technologies and Applications
Natural wood has been used for construction, fuel, and furniture for thousands of years because of its versatility, renewability, and aesthetic appeal. However, new opportunities for wood are arising as researchers have developed ways to tune the material's optical, thermal, mechanical, and ionic transport properties by chemically and physically modifying wood's naturally porous structure and chemical composition. Such modifications can be used to produce sustainable, functional materials for various emerging applications such as automobiles, construction, energy storage, and environmental remediation. In this review, we highlight recent advancements in engineered wood for sustainable technologies, including thermal and light management, environmental remediation, nanofluidics, batteries, and structural materials with high strength-to-weight ratios. Additionally, the current challenges, opportunities, and future of wood research are discussed, providing a guideline for the further development of next-generation, sustainable wood-based materials.
36 MATERIALS SCIENCE↗
Structure of the human SAGA coactivator complex
The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are noteworthy functional and compositional differences for this complex in metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure of human SAGA (hSAGA) and show how the arrangement of distinct structural elements results in a globally divergent organization from that of yeast, with a different interface tethering the core module to the TRRAP subunit, resulting in a dramatically altered geometry of functional elements and with the integration of a metazoan-specific splicing module. Our hSAGA structure reveals the presence of an inositol hexakisphosphate (InsP 6 ) binding site in TRRAP and an unusual property of its pseudo-(Ψ)PIKK. Finally, we map human disease mutations, thus providing the needed framework for structure-guided drug design of this important therapeutic target for human developmental diseases and cancer.
59 BASIC BIOLOGICAL SCIENCES↗
Understanding the local structure of disordered carbons from cellulose and lignin
An electron microscopy investigation was performed to understand the relationship between the microstructure and properties of carbonized cellulose and lignin (softwood kraft lignin) relative to the structure of the original biomass components. Structure details at micro- and molecular levels were investigated by scanning transmission electron microscopy. Atomic-resolution images revealed the presence of random disordered carbon in carbonized cellulose (C-CNC) and of large domains of well-ordered carbon with graphite sheet structure in carbonized lignin (C-Lignin). These structural differences explain why C-CNC exhibits higher surface area and porosity than C-Lignin. The presence of certain well-ordered carbon in carbonized lignin indicates some of the carbon in lignin are graphitized with heat treatment temperature up to 950 °C. This result is encouraging for future endeavors of attaining acceptable modulus of carbon fiber from lignin given suitable modifications to the chemistry and structure of lignin. The results of this research contribute to an improved understanding of the carbonization mechanism of the key cellulose and lignin components of biomass materials.
54 ENVIRONMENTAL SCIENCES↗
Chemical structure–property relationships in nanocelluloses
Abstract Nanocelluloses, nanoscale cellulosic particles or fibrils, are an appealing class of nanomaterials with enormous potential for sustainable development. They have great promise to target some of the 17 Sustainable Development Goals outlined by the United Nations. Nanocelluloses are derived from the most abundant biopolymer in the world, cellulose, which have multiple hydroxyl groups on their surface, enabling a vast range of chemical modifications. The interplay between the chemical structure and physicochemical properties of nanocelluloses is crucial to engineering the next generation of green, functional nanomaterials. In this review paper, we provide a comprehensive account of the structure–property relationships in nanocelluloses, which may establish the basis for the design of precision bio‐based materials. Chemical modifications of nanocelluloses, including hydrolysis, oxidation, esterification, amidation, and polymer grafting, provide an array of chemical and physical properties that open opportunities in a diverse spectrum of applications. We review how chemical modifications affect the physicochemical properties of nanocelluloses, such as thermal stability, hydrophobicity, and dispersibility in nonpolar media. Understanding nanocellulose chemical structure–property relationships is integral to the development of sustainable material platforms based on the most renewable biopolymer on earth.
59 BASIC BIOLOGICAL SCIENCES↗
Microstructural modification of a high-pressure die-cast A380 alloy through friction stir processing and its effect on mechanical properties
Aluminum alloy A380 is one of the major high-pressure die-cast (HPDC) alloys fabricated in the die casting sector. However, microstructural features such as shrinkage and gas porosity, entrapped oxide inclusions, change in the morphology of eutectic Si particles as a function of casting location, and the presence of multiple second phase particulates, especially Fe-bearing phases in HPDC A380 alloy results in limited ductility, thus, affecting its structural application. However, through proper modification of the as-cast microstructure, it is possible to improve the mechanical performance of alloy A380. In this study, we report the effect of friction stir processing (FSP), a well-known severe plastic deformation (SPD) and thermomechanical processing tool for selective microstructural modification, on A380. FSP effectively refines the as-cast microstructure and breaks down the coarse Si particles, creating a homogenized distribution of equiaxed Si particles in the aluminum matrix. Additionally, FSP eliminates porosity that acts as crack initiation sites, leading to improved mechanical strength and ductility.
Friction stir processing, Aluminum alloys, Mechani↗