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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Biochemistry of convulsions of eclampsia and experimental duplication of eclamptic intoxication
Analysis of biological hydrocarbons as life detection method for space applications - biochemistry
University of Wisconsin Theoretical Chemistry Institute research program - quantum mechanics, statistical mechanics, biochemistry, numerical analysis, and electromagnetic theory
Brain biochemistry of rats exposed to pure oxygen
Environmental biology bibliography, including citations on biochemistry, radiobiology, and bioinstrumentation
Statistical mechanics, quantum biochemistry, macromolecule theory, surface and membrane theory, transport phenomena, receptor isolation, and cancer chemotherapy in theoretical biology
Biochemistry and geochemistry of stable carbon istopes
Results are presented for a number of life sciences investigations sponsored by the Space Biomedical Research Institute at the NASA Lyndon B. Johnson Space Center and conducted as Detailed Supplementary Objectives (DSOs) on Space Shuttle flights between 1981 and 1986. An introduction and a description of the DSO program are followed by summary reports on the investigations. Reports are grouped into the following disciplines: Biochemistry and Pharmacology, Cardiovascular Effects and Fluid Shifts, Equipment Testing and Experiment Verification, Microbiology, Space Motion Sickness, and Vision. In the appendix, the status of every medical/life science DSO is presented in graphical form, which enables the flight history, the number of subjects tested, and the experiment results to be reviewed at a glance.
Biopoesis, the creation of life, implies molecular evolution from simple components, randomly distributed and in a dilute state, to form highly organized, concentrated systems capable of metabolism, replication and mutation. This chain of events must involve environmental processes that can locally lower entropy in several steps; by specific selection from an indiscriminate mixture, by concentration from dilute solution, and in the case of the mineral-induced processes, by particular effectiveness in ordering and selective reaction, directed toward formation of functional biomolecules. Numerous circumstances provide support for the notion that negatively charged molecules were functionally required and geochemically available for biopoesis. Sulfite ion may have been important in bisulfite complex formation with simple aldehydes, facilitating the initial concentration by sorption of aldehydes in positively charged surface active minerals. Borate ion may have played a similar, albeit less investigated role in forming charged sugar complexes. Among anionic species, oligophosphate ions and charged phosphate esters are likely to have been of even more wide ranging importance, reflected in the continued need for phosphate in a proposed RNA world, and extending its central role to evolved biochemistry. Phosphorylation is shown to result in selective concentration by surface sorption of compounds, otherwise too dilute to support condensation reactions. It provides protection against rapid hydrolysis of sugars and, by selective concentration, induces the oligomerization of aldehydes. As a manifestation of life arisen, phosphate already appears in an organic context in the oldest preserved sedimentary record.
The Integrated Medical Model (IMM) is a probabilistic tool, used in mission planning decision making and medical systems risk assessments. The IMM project maintains a database of over 80 medical conditions that could occur during a spaceflight, documenting an incidence rate and end case scenarios for each. In some cases, where observational data are insufficient to adequately define the inflight medical risk, the IMM utilizes external probabilistic modules to model and estimate the event likelihoods. One such medical event of interest is an unpassed renal stone. Due to a high salt diet and high concentrations of calcium in the blood (due to bone depletion caused by unloading in the microgravity environment) astronauts are at a considerable elevated risk for developing renal calculi (nephrolithiasis) while in space. Lack of observed incidences of nephrolithiasis has led HRP to initiate the development of the Renal Stone Formation Module (RSFM) to create a probabilistic simulator capable of estimating the likelihood of symptomatic renal stone presentation in astronauts on exploration missions. The model consists of two major parts. The first is the probabilistic component, which utilizes probability distributions to assess the range of urine electrolyte parameters and a multivariate regression to transform estimated crystal density and size distributions to the likelihood of the presentation of nephrolithiasis symptoms. The second is a deterministic physical and chemical model of renal stone growth in the kidney developed by Kassemi et al. The probabilistic component of the renal stone model couples the input probability distributions describing the urine chemistry, astronaut physiology, and system parameters with the physical and chemical outputs and inputs to the deterministic stone growth model. These two parts of the model are necessary to capture the uncertainty in the likelihood estimate. The model will be driven by Monte Carlo simulations, continuously randomly sampling the probability distributions of the electrolyte concentrations and system parameters that are inputs into the deterministic model. The total urine chemistry concentrations are used to determine the urine chemistry activity using the Joint Expert Speciation System (JESS), a biochemistry model. Information used from JESS is then fed into the deterministic growth model. Outputs from JESS and the deterministic model are passed back to the probabilistic model where a multivariate regression is used to assess the likelihood of a stone forming and the likelihood of a stone requiring clinical intervention. The parameters used to determine to quantify these risks include: relative supersaturation (RS) of calcium oxalate, citrate/calcium ratio, crystal number density, total urine volume, pH, magnesium excretion, maximum stone width, and ureteral location. Methods and Validation: The RSFM is designed to perform a Monte Carlo simulation to generate probability distributions of clinically significant renal stones, as well as provide an associated uncertainty in the estimate. Initially, early versions will be used to test integration of the components and assess component validation and verification (V&V), with later versions used to address questions regarding design reference mission scenarios. Once integrated with the deterministic component, the credibility assessment of the integrated model will follow NASA STD 7009 requirements.
Abstract Photosystem II (PSII) uses light energy to oxidize water and to reduce plastoquinone in the photosynthetic electron transport chain. O 2 is produced as a byproduct. While most members of the PSII research community agree that O 2 originates from water molecules, alternative hypotheses involving bicarbonate persist in the literature. In this perspective, we provide an overview of the important roles of bicarbonate in regulating PSII activity and assembly. Further, we emphasize that biochemistry, spectroscopy, and structural biology experiments have all failed to detect bicarbonate near the active site of O 2 evolution. While thermodynamic arguments for oxygen-centered bicarbonate oxidation are valid, the claim that bicarbonate is a substrate for photosynthetic O 2 evolution is challenged.
The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.
Biomass contains up to 14 essential elements that serve as nutrients for plant growth and development, including photosynthesis and enzyme functionalities. These elements in different chemical forms (e.g., minerals) constitute the inorganic fraction of biomass and can cause operational issues in thermal and biochemical biomass conversion technologies. In biomass gasification and pyrolysis processes, for instance, inorganics can cause fouling, tar formation, and corrosion. In catalytic and biochemical processes, inorganics can poison catalysts, alter biochemical pathways, and modify product yields and selectivity. This review provides an overview of the inorganic content in biomass feedstocks, the critical role inorganics play in plant biochemistry, the effect that inorganics have in various thermochemical and biochemical biomass conversion technologies, and different approaches to remove them from biomass. We provide recommendations for future research, focusing on developing technologies to effectively remove inorganics from biomass, using the inorganics to improve soil quality and for alternative applications, and designing biorefineries to convert demineralized biomass obtained from diverse sources.
The 23S rRNA methylating enzyme Cfr, found in pathogens including Staphylococcus aureus, Clostridium difficile, Escherichia coli, and Klebsiella pneumoniae, confers resistance to phenicols, lincosamides, oxazolidinones (including linezolid), pleuromutilins, and streptogramins A (the PhLOPS A phenotype). Cfr catalyzes methylation of the C8 position of the A2503 base in 23S rRNA, the recognition site of the above antibiotic classes. Along with the RlmN housekeeping enzyme, Cfr can also promote methylation of the C2 position of the same base. The molecular and structural basis of Cfr’s dual substrate specificity is not known, which hinders our ability to design Cfr-targeting inhibitors necessary to curb PhLOPS A resistance. Here, we present the first crystal structure of Cfr and a detailed analysis of its possible interactions with rRNA. Using structure-guided mutagenesis, mass spectrometry analysis of in cellulo 23S rRNA methylated species, and in cellulo resistance studies, we identify the key amino acids essential for Cfr methylation and multidrug resistance activity. In particular, we found that Cfr’s Q329 residue is important for C8- specific methylation. These data provide a framework for further studies of the biochemistry, structure, and inhibition of this important resistance determinant.
Microbial consortia have high relevance in natural environments. Here we present the production of polyhydroxyalkanoates (PHA) from agro-industrial residues by a synthetic interkingdom consortium formed by the saprotrophic fungus Ophiostoma piceae CECT 20146, which encodes a wide range of lignocellulolytic enzymes, and a natural PHA producer, Pseudomonas putida KT2440. Two agro-industrial residues were utilized: Brewer's Spent Grain (BSG) as a carbon/nitrogen source and biofilm scaffold and waste cooking oil (WCO) as a carbon source for PHA synthesis. Through biochemistry, microscopy, and omics analyses, it is shown that P. putida accumulates up to 40.2% of intracellular PHA when the quorum sensing molecule, farnesol (naturally produced by O. piceae) is added, thanks to the increased proliferation of P. putida cells. An interactive Shiny application has also been developed for an easy visualization and comprehension of all the transcriptomics and metabolomics data: https://jgf-bioinformatics.shinyapps.io/Visualization_app/. These results support the increased PHA production of the consortium by an induction of gene phaG, which redirects intermediaries of the fatty acid biosynthesis to PHA precursors, and the repression of the PHA depolymerase phaZ in P. putida. The trophic interaction between microorganisms seems to rely on the citric acid produced by O. piceae and the glycerol liberated from WCO, which can both be consumed by P. putida. Bioreactor scale-up experiments allowed a 3.3-fold increase in the PHA concentration in the consortium (6.7 g·L-1) without pretreatment or sterilization of the substrates, laying the groundwork for the implementation of an industrial consolidated bioprocess (CBP).
Stacking interactions are a recurring motif in supramolecular chemistry and biochemistry, where a persistent theme is a preference for parallel-displaced aromatic rings rather than face-to-face π-stacking. This is usually explained in terms of quadrupole–quadrupole interactions between the arene moieties but that interpretation is inconsistent with accurate calculations, which reveal that the quadrupolar picture is qualitatively wrong. At typical π-stacking distances, quadrupolar electrostatics may differ in sign from an exact calculation based on charge densities of the interacting arenes. We apply symmetry-adapted perturbation theory to dimers composed of substituted benzene and various aromatic heterocycles, which display a wide range of electrostatic interactions, and we investigate the interplay of Pauli repulsion, dispersion, and electrostatics as it pertains to parallel-displaced π-stacking. Profiles of energy components along cofacial slip-stacking coordinates support a prominent role for the “van der Waals model” (dispersion in competition with Pauli repulsion), even for polar monomers where electrostatic interactions are significant. While electrostatic interactions are necessary to explain the optimal face-to-face π-stacking distance and to account for the relative orientation of one polar arene with respect to another, we find no evidence to support continued invocation of quadrupolar electrostatics as a basis for π-stacking. Our results suggest that a driving force for offset-stacking exists even in the absence of electrostatic interactions. Consequently, tuning electrostatics via functionalization does not guarantee that slip-stacking can be avoided. This has implications for rational design of soft materials and other supramolecular architectures.
Abstract Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the termini of substrates. However, our knowledge of structural features distinguishing closely related C-degron substrate-E3 pairings is limited. Here, by systematically comparing ubiquitylation activities towards a suite of common model substrates, and defining interactions by biochemistry, crystallography, and cryo-EM, we reveal principles of C-degron recognition across the KLHDCX family of Cullin-RING ligases (CRLs). First, a motif common across these E3 ligases anchors a substrate’s C-terminus. However, distinct locations of this C-terminus anchor motif in different blades of the KLHDC2, KLHDC3, and KLHDC10 β-propellers establishes distinct relative positioning and molecular environments for substrate C-termini. Second, our structural data show KLHDC3 has a pre-formed pocket establishing preference for an Arg or Gln preceding a C-terminal Gly, whereas conformational malleability contributes to KLHDC10’s recognition of varying features adjacent to substrate C-termini. Finally, additional non-consensus interactions, mediated by C-degron binding grooves and/or by distal propeller surfaces and substrate globular domains, can substantially impact substrate binding and ubiquitylatability. Overall, the data reveal combinatorial mechanisms determining specificity and plasticity of substrate recognition by KLDCX-family C-degron E3 ligases.
Abstract Weak transitions between quantum states are of fundamental importance for a broad range of phenomena from analytical biochemistry to precision physics, but generally challenge experimental detection. Due to their small cross sections scaling with the absolute square of their transition matrix elements, spectroscopic measurements often fail in particular in the presence of competing background processes. Here we introduce a general concept to break this scaling law and enhance the transition probability by exploiting a stronger laser-coupled pathway to the same excited state. We demonstrate the concept experimentally by attosecond transient absorption spectroscopy in helium atoms. The quasi-forbidden transitions from the ground state 1s 2 to the weakly coupled doubly excited 2p3dandsp 2,4− states are boosted by an order of magnitude. Enhancing single-photon-suppressed transitions can find widespread applicability, from spectral diagnostics of complex molecules in life and chemical sciences to precision spectroscopy of weak transitions in metastable atomic nuclei in the search for new physics.