Leveraging Immonium Ions for Targeting Acyl-Lysine Modifications in Proteomic Datasets
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Biochemistry & Molecular Biology↗
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An Investigation of the Aerodynamic Characteristics of an 0.08-Scale Model of the Chance Vought XF7U-1 Airplane in the Langley High-Speed 7- by 10-Foot Tunnel. Part V - Wing-Alone Tests and Effect of Modifications to the Vertical Fins, Speed Brakes, and Fuselage TED No. NACA DE308: Wing-Alone Tests and Effect of Modifications to the Vertical Fins, Speed Brakes, and Fuselage, TED No. NACA DE308 - Part V
Tests have been conducted in the Langley high-speed 7- by 10-foot tunnel over a Mach number range from 0.40 to 0.91 to determine the stability and control characteristics of an 0.08-scale model of the Chance Vought XF7U-1 airplane. The wing-alone tests and the effect of the various vertical-fin modifications, speed-brake modifications, and fuselage modifications on the aerodynamic characteristics in pitch and yaw are presented in the present paper with a limited analysis of the results. Also included are tuft studies of the flow for some of the modifications tested.
Kuhri, Richard E.↗
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↗
Description, validation, and modification of the Guyton model for space-flight applications. Part A. Guyton model of circulatory, fluid and electrolyte control. Part B. Modification of the Guyton model for circulatory, fluid and electrolyte control
The mathematical model that has been a cornerstone for the systems analysis of space-flight physiological studies is the Guyton model describing circulatory, fluid and electrolyte regulation. The model and the modifications that are made to permit simulation and analysis of the stress of weightlessness are described.
Leonard, J. I.↗
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 the streamtube curvature program. Volume 1: Program modifications and user's manual
The improvements which have been incorporated in the Streamtube Curvature Program to enhance both its computational and diagnostic capabilities are described. Detailed descriptions are given of the revisions incorporated to more reliably handle the jet stream-external flow interaction at trailing edges. Also presented are the augmented boundary layer procedures and a variety of other program changes relating to program diagnostics and extended solution capabilities. An updated User's Manual, that includes information on the computer program operation, usage, and logical structure, is presented. User documentation includes an outline of the general logical flow of the program and detailed instructions for program usage and operation. From the standpoint of the programmer, the overlay structure is described. The input data, output formats, and diagnostic printouts are covered in detail and illustrated with three typical test cases.
Ferguson, D. R.↗
Influence of linear profile modification and loading conditions on the dynamic tooth load and stress of high contact ratio gears
A computer simulation for the dynamic response of high-contact-ratio spur gear transmissions is presented. High contact ratio gears have the potential to produce lower dynamic tooth loads and minimum root stress but they can be sensitive to tooth profile errors. The analysis presented examines various profile modifications under realistic loading conditions. The effect of these modifications on the dynamic load (force) between mating gear teeth and the dynamic root stress is presented. Since the contact stress is dependent on the dynamic load, minimizing dynamic loads will also minimize contact stresses. It is shown that the combination of profile modification and the applied load (torque) carried by a gear system has a significant influence on gear dynamics. The ideal modification at one value of applied load will not be the best solution for a different load. High-contact-ratio gears were found to require less modification than standard low-contact-ratio gears. High-contact-ratio gears are more adversely affected by excess modification than by under modification. In addition, the optimal profile modification required to minimize the dynamic load (hence the contact stress) on a gear tooth differs from the optimal modification required to minimize the dynamic root (bending) stress. Computer simulation can help find the design tradeoffs to determine the best profile modification to satisfy the conflicting constraints of minimizing both the load and root stress in gears which must operate over a range of applied loads.
Lee, Chinwai↗