14 Search Results

This review article describes the co-evolution of structural biology as a discipline and the Protein Data Bank (PDB), established in 1971 as the first open-access data resource in biology by like-minded structural scientists. As the PDB archive grew in size and scope to encompass macromolecular crystallography, NMR spectroscopy, and cryo-electron microscopy, new technologies were developed to ingest, validate, curate, store, and distribute the information. Community engagement ensured that the needs of structural biologists (data depositors) and data consumers were met. Today, the archive houses more than 230,000 experimentally determined structures of proteins, nucleic acids, and macromolecular machines and their complexesmore » with one another and small-molecule ligands. Aggregate costs of PDB data preservation are ~1% of the cost of structure determination. The enormous impact of PDB data on basic and applied research and education across the natural and medical sciences is presented and highlighted with illustrative examples. Enablement of de novo protein structure prediction (AlphaFold2, RoseTTAfold, OpenFold, etc.) is the most widely appreciated benefit of having a corpus of rigorously validated, expertly curated 3D biostructure data.« less

Lysine carbamylation is a non-enzymatic protein post-translational modification (PTM) that plays important roles in regulating enzymatic activity and the pathogenesis of diseases such as atherosclerosis, rheumatoid arthritis, and uremia. The progress of understanding the roles of carbamylation in biological systems has been delayed due to lack of systematic assays to study its functions. To aggravate this scenario, carbamylation is a major artifact in proteomics analysis given that urea, which is used during sample preparation, induces carbamylation. In addition, anti-acetyllysine antibodies co-purify carbamylated and acetylated peptides. In a recent paper, we leveraged co-purification with anti-acetyllysine antibodies to develop a method formore » analyzing carbamylated proteomes. In this perspective article, we discuss how this method may be applied to characterize the physiological functions of carbamylation in humans and other biological models, as well as the utility of establishing novel disease biomarkers.« less

Quality control (QC) is an essential part of fuel cell technology industrialization, providing means to reduce cost of components, enhancing the reliability of the final product, and offering specification guidance for new entrants in the supply chain. The membrane electrode assembly (MEA), including membrane, catalyst layer (CL), and gas diffusion layer (GDL), as well as bipolar plate (BP), are key components of a proton exchange membrane (PEM) fuel cell, and the attributes of each component strongly correlate with the cell performance and longevity. To ensure the quality of the fuel cell, it is of great importance to characterize the propertiesmore » with respect to the standardization of component/sub-component specifications. In collaboration with the fuel cell industry, this work aims at establishing compendiums of attributes, or so-called books of attributes, of key fuel cell components for the QC of PEM fuel cells through reviewing, identifying, categorizing, and prioritizing the main attributes/properties that determine their functionalities. The books of attributes for the major PEM fuel cell components include catalyst coated membrane (CCM) as a sub-assembly, GDL, and BP. To address the full spectrum of fuel cell components, gaskets and sub-gaskets are also included.« less

Whistler mode chorus waves have recently been established as the most likely candidate for scattering relativistic electrons to produce the electron microbursts observed by low altitude satellites and balloons. These waves would have to propagate from the equatorial source region to significantly higher magnetic latitude in order to scatter electrons of these relativistic energies. This theoretically proposed propagation has never been directly observed. We present the first direct observations of the same discrete rising tone chorus elements propagating from a near equatorial (Van Allen Probes) to an off-equatorial (Arase) satellite. The chorus is observed first on the more equatorial satellitemore » and is found to be more oblique and significantly attenuated at the off-equatorial satellite. Further, this is consistent with the prevailing theory of chorus propagation and with the idea that chorus must propagate from the equatorial source region to higher latitudes. Ray tracing of chorus at the observed frequencies confirms that these elements could be generated parallel to the field at the equator, and propagate through the medium unducted to Van Allen Probes A and then to Arase with the observed time delay, and have the observed obliquity and intensity at each satellite.« less

Even as the field of microbiome research has made huge strides in mapping microbial community composition in a variety of environments and organisms, explaining the phenotypic influences on the host by microbial taxa – both known and unknown – and their specific functions still remain major challenges. A pressing need is the ability to assign specific functions in terms of enzymes and small molecules to specific taxa or groups of taxa in the community. This knowledge will be crucial for advancing personalized therapies based on the targeted modulation of microbes or metabolites that have predictable outcomes to benefit the humanmore » host. This perspective article advocates for the combined use of standards-free metabolomics and activity-based protein profiling strategies to address this gap in functional knowledge in microbiome research via the identification of novel biomolecules and the attribution of their production to specific microbial taxa.« less

HALO (HAgis LOcust) solves the initial value Vlasov-Maxwell problem perturbatively for application to certain nonlinear wave-particle problems in tokamak plasmas. It uses the same basic approach as the HAGIS code for wave evolution but is built on the LOCUST-GPU full-orbit code for the solution of the Hamiltonian fast particle motion in cylindrical coordinates. The wave amplitude and particle evolution include all finite Larmour radius effects. We describe and benchmark the currently implemented Alfvén eigenmode workflow, demonstrating correct particle motion, linear and nonlinear power transfer. Here, the formulation and numerical scheme are sufficiently general as to allow easy future implementation ofmore » different kinds of eigenmodes, such as modes close to the ion-cyclotron frequency. The code can model multiple eigenmodes and multiple fast ion species simultaneously, and supports the general form of the equilibrium distribution in constants of motion.« less

DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of in situ assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. There are several different methods for analyzing DNA-SIP data and despite the power of SIP experiments, it remains difficult to comprehensively evaluate method accuracy across a wide range of experimental parameters. We have developed a toolset (SIPSim) thatmore » simulates DNA-SIP data, and we use this toolset to systematically evaluate different methods for analyzing DNA-SIP data. Specifically, we employ SIPSim to evaluate the effects that key experimental parameters (e.g., level of isotopic enrichment, number of labeled taxa, relative abundance of labeled taxa, community richness, community evenness, and beta-diversity) have on the specificity, sensitivity, and balanced accuracy (defined as the product of specificity and sensitivity) of DNA-SIP analyses. Furthermore, SIPSim can predict analytical accuracy and power as a function of experimental design and community characteristics, and thus should be of great use in the design and interpretation of DNA-SIP experiments.« less

Here, we present a numerical method for modeling the mechanical effects of nonlinearly-compliant joints in elasto-plastic media. The method uses a series of strain-rate and stress update algorithms to determine joint closure, slip, and solid stress within computational cells containing multiple “embedded” joints. This work facilitates efficient modeling of nonlinear wave propagation in large spatial domains containing a large number of joints that affect bulk mechanical properties. We implement the method within the massively parallel Lagrangian code GEODYN-L and provide verification and examples. We highlight the ability of our algorithms to capture joint interactions and multiple weakness planes within individualmore » computational cells, as well as its computational efficiency. We also discuss the motivation for developing the proposed technique: to simulate large-scale wave propagation during the Source Physics Experiments (SPE), a series of underground explosions conducted at the Nevada National Security Site (NNSS).« less