Leveraging Immonium Ions for Targeting Acyl-Lysine Modifications in Proteomic Datasets
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Biochemistry & Molecular Biology↗
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Potential Effects of Climate Change and Solar Radiation Modification on Renewable Energy Resources
Solar radiation modification (SRM) is a possible deliberate approach to decrease or reflect incoming solar radiation with the goal of reducing global temperatures, which have increased over the last decades due to high atmospheric greenhouse gas concentrations. Stratospheric aerosol injection, specifically, has shown potential for successfully reducing global temperatures in climate model simulations. Despite the growing literature in the areas of climate change and SRM, their combined effects on renewable energy generation, a climate change mitigation strategy, have not been addressed. In this review paper, we synthesize previous literature on the possible effects of climate change and SRM on renewable energy resources (i.e., wind energy, solar energy, biomass energy, and hydropower), review the status of climate change and SRM research, and explore potential effects of SRM on renewable energy primarily in the Continental United States (CONUS), but with global perspectives as well. We discuss the research challenges and impacts of SRM on renewable energy and conclude by discussing the potential implications of SRM for renewables for SRM governance and policy. This work is not advocating for or against SRM. It is highlighting an important potential impact for future decision makers.
Kumler, Andrew [National Renewable Energy Laborato↗
Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity
Annotation of untargeted high-resolution full-scan LC-MS metabolomics data remains challenging due to individual metabolites generating multiple LC-MS peaks arising from isotopes, adducts and fragments. Adduct annotation is a particular challenge, as the same mass difference between peaks can arise from adduct formation, fragmentation, or different biological species. To address this, here we describe a Buffer Modification Workflow (BMW), in which the same sample is run by LC-MS in both liquid chromatography solvent with 14 NH 3 -acetate buffer, and in solvent with the buffer modified with 15 NH 3 -formate. Buffer switching results in characteristic mass and signal intensity changes for adduct peaks, facilitating their annotation. This relatively simple and convenient chromatography modification annotated yeast metabolomics data with similar effectiveness to growing the yeast in isotope-labeled media. Application to mouse liver data annotated both known metabolite and known adduct peaks with 95% accuracy. Altogether, it identified 26% of ~ 27,000 liver LC-MS features as putative metabolites, of which ~ 2600 showed HMDB or KEGG database formula match. This workflow is well-suited to biological samples that cannot be readily isotope labeled, including plants, mammalian tissues, and tumors.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Prediction of histone post-translational modifications using deep learning
Abstract Motivation Histone post-translational modifications (PTMs) are involved in a variety of essential regulatory processes in the cell, including transcription control. Recent studies have shown that histone PTMs can be accurately predicted from the knowledge of transcription factor binding or DNase hypersensitivity data. Similarly, it has been shown that one can predict PTMs from the underlying DNA primary sequence. Results In this study, we introduce a deep learning architecture called DeepPTM for predicting histone PTMs from transcription factor binding data and the primary DNA sequence. Extensive experimental results show that our deep learning model outperforms the prediction accuracy of the model proposed in Benveniste et al. (PNAS 2014) and DeepHistone (BMC Genomics 2019). The competitive advantage of our framework lies in the synergistic use of deep learning combined with an effective pre-processing step. Our classification framework has also enabled the discovery that the knowledge of a small subset of transcription factors (which are histone-PTM and cell-type-specific) can provide almost the same prediction accuracy that can be obtained using all the transcription factors data. Availabilityand implementation https://github.com/dDipankar/DeepPTM. Supplementary information Supplementary data are available at Bioinformatics online.
Baisya, Dipankar Ranjan (ORCID:0000000267847359)↗
Radiation-induced modifications in copper oxide growth
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Bishop, Jessica L.↗
Modification of cell wall polysaccharide guides cell division in Streptococcus mutans
In ovoid-shaped, Gram-positive bacteria, MapZ guides FtsZ-ring positioning at cell equators. The cell wall of the ovococcus Streptococcus mutans contains peptidoglycan decorated with serotype c carbohydrates (SCCs). In the present study, we identify the major cell separation autolysin AtlA as an SCC-binding protein. AtlA binding to SCC is attenuated by the glycerol phosphate (GroP) modification. Using fluorescently labeled AtlA constructs, we mapped SCC distribution on the streptococcal surface, revealing enrichment of GroP-deficient immature SCCs at the cell poles and equators. The immature SCCs co-localize with MapZ at the equatorial rings throughout the cell cycle. In GroP-deficient mutants, AtlA is mislocalized, resulting in dysregulated cellular autolysis. These mutants display morphological abnormalities associated with MapZ mislocalization, leading to FtsZ-ring misplacement. Altogether, our data support a model in which maturation of a cell wall polysaccharide provides the molecular cues for the recruitment of cell division machinery, ensuring proper daughter cell separation and FtsZ-ring positioning.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Oxidation and Associated Pore Structure Modification During Experimental Alteration of Granite
Weathering plays a crucial role in a number of environmental processes, and the microstructure and evolution of multi-scale pore space is a critically important factor in the weathering of geological formations. In igneous rocks the infiltration of meteoric water into initially relatively dry material can cause the rock to begin to disaggregate, increasing porosity and surface area, and allowing further disaggregation and weathering to occur. These processes, in turn, allow biota to colonize the rock, further enhancing the weathering rate. In some igneous rocks this may be driven by oxidation of primary minerals. One such mineral, biotite, has been repeatedly mentioned as a cause of cracking during oxidation. However, the scale-dependence of the processes by which this occurs are poorly understood. We cannot, therefore, accurately extrapolate laboratory reaction rates to the field in predictive numerical models. In order to better understand the effects of oxidation and test the hypothesis that fracture and disaggregation are initiated by swelling of oxidizing biotites, we reacted granite cores in a selenic acid-rich aqueous solution at 200°C for up to 438 days. Elevated temperatures and selenic acid were used to provide relatively fast reaction rates and highly oxidizing conditions in sealed reaction vessels. These experiments were analyzed using a combination of imaging, X-ray diffraction, Mössbauer spectroscopy, and small- and ultra-small angle neutron scattering to interrogate porosity and microfracture formation. The experimental results show little observable biotite swelling, but significant transport and growth of iron oxides and/or clays along grain boundaries throughout the sample. Significant increases in porosity were also observed at the sample rim, likely associated with feldspar alteration. Fractures and transport were observed throughout the core, suggesting that stresses due to crystallization pressures caused by the growing iron phases may be the initiating factors in granite weathering, possibly followed by biotite swelling after sufficient permeability is achieved.
Anovitz, Lawrence M.↗
Tuning the Number of Active Sites and Turnover Frequencies by Surface Modification of Supported ReO4/(SiO2-Al2O3) Catalysts for Olefin Metathesis
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99 GENERAL AND MISCELLANEOUS↗
Modification of Catalytic Properties of Hollandite Manganese Oxide by Ag Intercalation for Oxidative Acetalization of Ethanol to Diethoxyethane
The effect of addition of Ag to the catalytic properties of hollandite manganese oxide (HMO) was investigated for the oxidative acetalization of ethanol to diethoxyethane. Based on analysis with HRTEM, XRD, and EXAFS, Ag introduced onto HMO by deposition/precipitation was found to be present in different forms in the final catalyst depending on the calcination temperature. It could exist as nanoparticles on the outside surface of HMO nanorods for samples calcined at 60 °C, and as Ag atoms intercalated into the tunnels of the HMO structure for samples calcined at 500 °C. NH 3 desorption results showed that intercalation of Ag resulted in stronger Lewis acidic sites on HMO, which DFT computational results suggested to be due to Ag-induced electron redistribution in the HMO framework. Here, the intercalation of Ag atoms also made the HMO more easily reducible by lowering the H 2 reduction temperature from 500 to 200 °C. Consequently, the sample with intercalated Ag was more active for ethanol oxidation to acetaldehyde, achieving nearly 100% conversion of ethanol and acetaldehyde by 360 °C, and acetalization of acetaldehyde with ethanol to produce diethoxyethane selectively, resulting in 93.5% diethoxyethane yield, which was 10% higher than with samples containing Ag nanoparticles on HMO. This study demonstrated a little-studied phenomenon in which a metal alters the catalytic properties of an oxide electronically but not structurally and without direct participation in the reaction.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural basis for selective modification of Rho and Ras GTPases by Clostridioides difficile toxin B
Toxin B (TcdB) is a primary cause of Clostridioides difficile infection (CDI). This toxin acts by glucosylating small GTPases in the Rho/Ras families, but the structural basis for TcdB recognition and selectivity of specific GTPase substrates remain unsolved. Here, we report the cocrystal structures of the glucosyltransferase domain (GTD) of two distinct TcdB variants in complex with human Cdc42 and R-Ras, respectively. These structures reveal a common structural mechanism by which TcdB recognizes Rho and R-Ras. Furthermore, we find selective clustering of adaptive residue changes in GTDs that determine their substrate preferences, which helps partition all known TcdB variants into two groups that display distinct specificities toward Rho or R-Ras. Mutations that selectively disrupt GTPases binding reduce the glucosyltransferase activity of the GTD and the toxicity of TcdB holotoxin. These findings establish the structural basis for TcdB recognition of small GTPases and reveal strategies for therapeutic interventions for CDI.
59 BASIC BIOLOGICAL SCIENCES↗
Southern Company Services: Project 2: Tall Tower Wind Technical Potential for the Southeast (Modifications 4, 5), Project 4: Offshore Wind Potential for Southern Company Services (Modifications 7, 8)
Project 2: The National Laboratory of the Rockies (NLR) and Southern Company Services (SCS) seek to establish an agreement to assess the technical potential for wind energy in the Southeastern U.S. SCS has requested that NLR conduct a detailed assessment of system performance, available capacity, transmission distance, and levelized cost of electricity (LCOE) at turbine hub heights of 100m to 160m within the SCS service territory. NLR will also provide an assessment of utility photovoltaic (PV) technical potential within the SCS service territory. NLR has unique modeling capabilities to assist SCS with high spatial and temporal resolution assessment of wind and PV technical potential, considering geospatial constraints. Project 4: NLR and SCS seek to develop a spatially explicit techno-economic assessment for offshore wind energy in the Southeastern U.S. The analysis aims to characterize the regional sensitivities of offshore wind plant costs and performance, underwater cabling, potential siting constraints, and landfall spur transmission costs.
17 WIND ENERGY↗
Modifications to Solar Titan-130 Combustion Systems for Efficient, High Turndown Operation
The project team of Southwest Research Institute® (SwRI®), Solar Turbines Incorporated (Solar), the Electric Power Research Institute (EPRI), the University of California, Irvine (UCI), and the Georgia Institute of Technology (Georgia Tech) investigated methods to allow higher efficiency part-load operation of a Solar Titan 130 gas turbine. The objective was to develop a low-emission combustion system capable of sustaining combustion and avoiding lean blowout during high turndown operation, which would allow the gas turbine to operate as efficiently as possible at part load. Currently, electric utility markets are beginning to experience substantial increases in renewable energy generation. Some of these renewable energy sources have highly variable output in an uncontrolled manner. In order to maintain grid stability, there is a need for power plants to ramp up power to the grid rapidly to make up for drops in renewable generation. This is often termed spinning reserve, but the size of this reserve may need to increase as renewable penetration into the electric utility market increases. Small combined heat and power (CHP) power plants provide a promising option for meeting this spinning reserve requirement. In order to operate in spinning reserve while still meeting the heat requirements for the CHP, the gas turbine needs to operate efficiently at very low loads. Efficient, high turndown operations in this engine are limited by the lean flammability limit of the premixed combustion system. This project sought enhance the lean operability range of the Titan 130 combustor. First, the project team participated in a brainstorming activity and ultimately selected two concepts to explore: fuel augmentation with hydrogen (H2) to improve the stability at lean operating conditions and modifications to the fuel nozzle to improve the emissions performance at lean operating conditions. Analytical and laboratory investigations were accomplished by UCI to investigate the efficacy of H2 addition at improving lean blow out (LBO) limits and the resulting emissions. These investigations used a variety of chemical reactor network (CRN) and CFD models, validated against laboratory data, to model the impact of H 2 and inform the experimental efforts accomplished by SwRI and Solar. Ultimately, both the CRN and CFD models yielded generally good agreement with the experimental data below a particular temperature threshold. Atmospheric tests of a full-scale T130 annular combustor were performed at SwRI facilities in San Antonio, Texas, to investigate the use of H 2 addition. For these tests, the T130 combustion system remained largely unchanged; minor modifications were performed to the fuel ducting to allow for the safe use of H 2 . The test ultimately demonstrated that the addition of H 2 to the fuel mixture significantly increased the AFR ratio at which the combustor could operate. This improvement to the LBO limit should allow for less use of compressor bleed and less throttling needed by the inlet guide vanes (IGV). This in turn could result in more efficient operation of the gas turbine at lower load points. The second modification explored in this work was a direct modification to the T130 injector. The project team hypothesized that modifications to the pilot of the T130 injector could provide lower emissions at high turn-down operations. These modifications were manufactured and explored by the team at Solar. High pressure rig tests, originally slated to occur at SwRI, were ultimately accomplished by Solar to maintain overall project budget and mitigate cost growth attributable to supply chain issues and inflation. The pressurized rig tests ultimately showed that the SwRI Project No. 18.24153 - DE-EE0008415 Page 2 Final Technical Report January 24, 2024 modifications did not significantly alter the performance of the combustion system at the high turn-down conditions; both the modified injectors and the baseline configuration exhibited elevated emissions comparted to the full-load operating condition. A final set of studies performed by EPRI investigated the benefit-cost of flexible CHP as well as a grid interconnection study for the California Independent System Operator (CAISO) grid. These studies considered: traditional CHP with no spinning reserve available for on-demand grid support, 50% flexible CHP where 50% of the machine’s capacity is consumed by on-site baseload operations while providing an additional 50% capacity for on-demand grid support, and 70% flexible CHP where 70% of capacity is consumed on-site by baseload operations and 30% is available for on-demand grid support. In all cases, the analyses showed a benefit-to-cost ratio greater than unity implying a positive net present value for all configurations. However, the traditional CHP showed the most economic benefit. These results are sensitive to several factors, many of which are not fully known and may vary over time. Thus site owners must be convinced that taking up the increased costs and risks from flexible CHP would be worth implementing. As the grid in California and across the country transition to incorporate larger renewable energy generation, flexible CHP can provide much needed operating reserves and dispatchability. Alternative fuel options, such as hydrogen blending and biofuels, may also lower carbon intensities of CHP. Flexible CHP should be examined in the evolving market to understand innovative business models, changes market rules and services, and new technologies.
20 FOSSIL-FUELED POWER PLANTS↗
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↗
Raman Laser-Induced Structural Modification in CVD-Grown Monolayer MoS 2 for Multi-Purposed Nanofabrication
Molybdenum disulfide (MoS 2 ) has been extensively explored to be utilized as an electronic material in a variety of device applications. In particular, the tunability of MoS 2 enhances its electrical properties making it an intriguing candidate for field-effect transistors (FETs), while also extending beyond electrical properties to structural phase engineering. Laser-induced modifications, particularly with Raman lasers, offer a straightforward method to modulate materials via thermal processes with precise patterning control and energy-level flexibility. However, most studies on the modification of MoS 2 have focused on multilayered structures or have been conducted under low-power laser conditions, leaving the feasibility of structural modifications in monolayer MoS 2 elusive. In this study, we fundamentally elucidated the effects of high-power Raman laser irradiation on the surface of chemical vapor deposition (CVD)-grown monolayer MoS 2 under ambient conditions and uncovered the underlying mechanisms of laser-induced modifications by applying intense photon energy with highly interactive reactions. Our results revealed both etching and deposition phenomena in two discernible regions, and it can be demonstrated by intensity regimes based on the spatial distribution of laser irradiance within the laser-irradiated spot. Furthermore, phase transition was found to be inhibited due to the promoted oxidation and the deposition of hydrogenated amorphous carbon (a-C:H), and p-type doping was observed, likely occurring in the region beneath the a-C:H deposition as substitutional doping on the 2H phase of MoS 2 . To compare the thermal effects, MoS 2 modifications were further analyzed using simplified heat transfer estimations. In conclusion, these findings deepen our understanding of how Raman laser irradiation modifies MoS 2 under ambient conditions, providing guidelines for optimizing its modification processes.
36 MATERIALS SCIENCE↗
30S subunit recognition and G1405 modification by the aminoglycoside-resistance 16S ribosomal RNA methyltransferase RmtC
Acquired ribosomal RNA (rRNA) methylation has emerged as a significant mechanism of aminoglycoside resistance in pathogenic bacterial infections. Modification of a single nucleotide in the ribosome decoding center by the aminoglycoside-resistance 16S rRNA (m 7 G1405) methyltransferases effectively blocks the action of all 4,6-deoxystreptamine ring-containing aminoglycosides, including the latest generation of drugs. To define the molecular basis of 30S subunit recognition and G1405 modification by these enzymes, we used a S-adenosyl-L-methionine analog to trap the complex in a postcatalytic state to enable determination of a global 3.0 Å cryo-electron microscopy structure of the m 7 G1405 methyltransferase RmtC bound to the mature Escherichia coli 30S ribosomal subunit. This structure, together with functional analyses of RmtC variants, identifies the RmtC N-terminal domain as critical for recognition and docking of the enzyme on a conserved 16S rRNA tertiary surface adjacent to G1405 in 16S rRNA helix 44 (h44). To access the G1405 N7 position for modification, a collection of residues across one surface of RmtC, including a loop that undergoes a disorder-to order transition upon 30S subunit binding, induces significant distortion of h44. This distortion flips G1405 into the enzyme active site where it is positioned for modification by two almost universally conserved RmtC residues. Further, these studies expand our understanding of ribosome recognition by rRNA modification enzymes and present a more complete structural basis for future development of strategies to inhibit m 7 G1405 modification to resensitize bacterial pathogens to aminoglycosides.
59 BASIC BIOLOGICAL SCIENCES↗