Search NASA⌕ Search

SEARCH · Search NASA

Results for “Cell structure identification”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis

Malaria and cryptosporidiosis, caused by apicomplexan parasites, remain major drivers of global child mortality. New drugs for the treatment of malaria and cryptosporidiosis, in particular, are of high priority; however, there are few chemically validated targets. The natural product cladosporin is active against blood- and liver-stage Plasmodium falciparum and Cryptosporidium parvum in cell-culture studies. Target deconvolution in P. falciparum has shown that cladosporin inhibits lysyl-tRNA synthetase (PfKRS1). Here, we report the identification of a series of selective inhibitors of apicomplexan KRSs. Following a biochemical screen, a small-molecule hit was identified and then optimized by using a structure-based approach, supported by structures of both PfKRS1 and C. parvum KRS (CpKRS). In vivo proof of concept was established in an SCID mouse model of malaria, after oral administration (ED 90 = 1.5 mg/kg, once a day for 4 d). Furthermore, we successfully identified an opportunity for pathogen hopping based on the structural homology between PfKRS1 and CpKRS. This series of compounds inhibit CpKRS and C. parvum and Cryptosporidium hominis in culture, and our lead compound shows oral efficacy in two cryptosporidiosis mouse models. X-ray crystallography and molecular dynamics simulations have provided a model to rationalize the selectivity of our compounds for PfKRS1 and CpKRS vs. (human) HsKRS. Our work validates apicomplexan KRSs as promising targets for the development of drugs for malaria and cryptosporidiosis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Towards Integrating Synchrotron FTIR Microscopy with Mass Spectrometry at the Berkeley Synchrotron Infrared Structural Biology (BSISB) Program

Synchrotron-radiation-based Fourier transform infrared (SR-FTIR or sFTIR) facilities worldwide are probing both live cells and tissues non-destructively under native-like conditions. From Spectroscopic data such as those acquired through the Berkeley Synchrotron Infrared Structural Biology (BSISB) program, spatially and temporally resolved chemical information of molecular classes are obtained. However, these infrared data lack chemical specificity for precise and accurate species identification. Here, high-resolution mass spectrometry (MS) directly contrasts with these IR data attributes in its ability to provide more specific identification of the full range of molecules at the cost of sample destruction.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

Bifunctional alkaline oxygen electrodes

The authors describe the identification and testing of electrocatalysts and supports for the positive electrode of moderate-temperature, single-unit, rechargeable alkaline fuel cells. Recent work on Na(x)Pt3O4, a potential bifunctional catalyst, is described, as well as the application of novel approaches to the development of more efficient bifunctional electrode structures. The three dual-character electrodes considered here showed similar superior performance; the Pt/RhO2 and Rh/RhO2 electrodes showed slightly better performance than the Pt/IrO2 electrode. It is concluded that Na(x)Pt3O4 continues to be a promising bifunctional oxygen electrode catalyst but requires further investigation and development.

Swette, L.↗
DOE OSTI2019

Novel T9 loop conformation of filamenting temperature-sensitive mutant Z from Mycobacterium tuberculosis

As of 2017, tuberculosis had infected 1.7 billion people (23% of the population of the world) and caused ten million deaths. Mycobacterium tuberculosis (Mtb) is quickly evolving, and new strains are classified as multidrug resistant. Thus, the identification of novel druggable targets is essential to combat the proliferation of these drug-resistant strains. Filamenting temperature-sensitive mutant Z (FtsZ) is a key protein involved in cytokinesis, an important process for Mtb proliferation and viability. FtsZ is required for bacterial cell division because it polymerizes into a structure called the Z-ring, which recruits accessory division proteins to the septum. Here, the crystal structure of the MtbFtsZ protein has been determined to 3.46 Å resolution and is described as a dimer of trimers, with an inter-subunit interface between protomers AB and DE . In this work, a novel conformation of MtbFtsZ is revealed involving the T9 loop and the nucleotide-binding pocket of protomers BC and EF .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

DOE new players Carbon cycle (2016-2021)

The overarching scientific goals of our multidisciplinary grant was to further expand understanding about the key microorganisms (players), metabolic strategies (processes), and interspecies relationships (interactions) involved in the formation and oxidation of methane in the environment. This research applied novel environmental metagenomics, transcriptomics, and proteomic techniques, state-of-the-art analytical imaging, stable isotope geochemistry, and reaction-transport modeling to address these goals and develop an ‘ecosystems level’ understanding of the factors which regulate microbial methane cycling in anoxic sedimentary ecosystems. For decades, it was believed that the obligate step in methanogenesis catalyzed by methyl coenzyme M reductase (Mcr) was limited to a specific branch of the archaeal Domain, formerly known as the Euryarchaeota. Less than a decade ago co-I Tyson’s team published a surprising metagenomic-based discovery of divergent Mcr genes in a novel uncultured phylum (Bathyarchaeota), catalyzing a major shift in thinking about the diversity of microorganisms that encode the potential for methane (or higher alkane) metabolism in anoxic environments (Evans et al., 2015). In our work here, we further expand on the groups of archaea harboring the genomic potential for methane or hydrocarbon metabolism using environmental metagenomics and new gene targeted bioinformatics techniques. We additionally advanced understanding about the terminal electron acceptors and metabolic potential supporting the anaerobic oxidation of methane (AOM) in terrestrial ecosystems, specifically focused on new lineages of ANME archaea capable of respiring manganese oxides with methane presumably using large extracellular multi-heme cytochrome complexes. New details about specific syntrophic mechanisms underlying the exchange of electrons during sulfate-coupled methane oxidation between ANME-2 archaea and their sulfate-reducing bacterial partners were also elucidated as part of this funded project. Through a series of experimental ‘omics and single cell stable isotope probing studies with incubated environmental sediment samples and a cultured model electrogenic microorganism combined with model-based predictions. Combined, this work provides strong support for the hypothesis of direct interspecies electron transfer (DIET) is the dominant syntrophic mechanism controlling the anaerobic oxidation of methane with sulfate over other proposed mechanisms and additionally illustrates important spatial constraints and the underlying physico-chemical factors influencing AOM syntrophic consortia structure for DIET and extracellular metal respiration. This collaborative multi-institutional project successfully advanced several of our milestone goals including the identification of new microbial players containing methyl coenzyme M reductases hypothesized to be central to methane or hydrocarbon cycling in anoxic environments and enhancing fundamental knowledge about the role extracellular electron transfer plays in the ecophysiology of methanotrophic archaea respiring metal oxides and in the physical and metabolic structuring of syntrophic interactions in methane-rich sedimentary ecosystems.

03 NATURAL GAS↗
DOE OSTI2017

In situ determination of crystal structure and chemistry of minerals at Earth's deep lower mantle conditions

Recent advances in experimental techniques and data processing allow in situ determination of mineral crystal structure and chemistry up to Mbar pressures in a laser-heated diamond anvil cell (DAC), providing the fundamental information of the mineralogical constitution of our Earth's interior. This work highlights several recent breakthroughs in the field of high-pressure mineral crystallography, including the stability of bridgmanite, the single-crystal structure studies of post-perovskite and H-phase as well as the identification of hydrous minerals and iron oxides in the deep lower mantle. The future development of high-pressure crystallography is also discussed.

58 GEOSCIENCES↗
DOE OSTI2019

Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening

Tyrosyl DNA-phosphodiesterase I (TDP1) repairs type IB topoisomerase (TOP1) cleavage complexes generated by TOP1 inhibitors commonly used as anticancer agents. TDP1 also removes DNA 3' end blocking lesions generated by chain-terminating nucleosides and alkylating agents, and base oxidation both in the nuclear and mitochondrial genomes. Combination therapy with TDP1 inhibitors is proposed to synergize with topoisomerase targeting drugs to enhance selectivity against cancer cells exhibiting deficiencies in parallel DNA repair pathways. A crystallographic fragment screening campaign against the catalytic domain of TDP1 was conducted to identify new lead compounds. Crystal structures revealed two fragments that bind to the TDP1 active site and exhibit inhibitory activity against TDP1. These fragments occupy a similar position in the TDP1 active site as seen in prior crystal structures of TDP1 with bound vanadate, a transition state mimic. Using structural insights into fragment binding, several fragment derivatives have been prepared and evaluated in biochemical assays. These results demonstrate that fragment-based methods can be a highly feasible approach toward the discovery of small-molecule chemical scaffolds to target TDP1, and for the first time, we provide co-crystal structures of small molecule inhibitors bound to TDP1, which could serve for the rational development of medicinal TDP1 inhibitors.

Lountos, George T.↗
DOE OSTI2022

Unexpected features in the optical vibrational spectra of δ-UO 3

Uranium trioxide displays a complex chemical phase space, with at least six structurally distinct polymorphs accessible via different synthetic routes. Remarkably, despite its technological importance, full structural and electronic characterization of these polymorphs remains an open area of study. δ-UO 3 in particular has attracted significant theoretical attention due to its high point group and space group symmetries, having U (VI) in octahedral coordination with polyhedra interconnected through corner-sharing to build a 3-D cubic lattice with space group symmetry Pm-3m and Z = 1. Critical experimental information, such as its optical vibrational spectra, are not known. Here, we study the Raman and infrared (IR) spectra of δ-UO 3 together with the support of density functional theory (DFT) calculations for spectral interpretation. A symmetry analysis of the DFT-predicted phonon eigenmodes indicates that δ-UO 3 should have two IR active modes and no Raman active modes. Experimental results, however, indicate significant Raman scattering from δ-UO 3 . We therefore propose four potential explanations for this apparent contradiction: a possible tetragonal distortion to the cubic cell, the existence of a surface impurity layer, vacancy scattering, and structural activation of Raman signal. We use powder X-ray diffraction and confocal Raman spectroscopy with depth profiling to investigate these possibilities and suggest future experiments to explore this phenomenon in more detail. Understanding the lattice dynamics of δ-UO 3 is important for identification of technogenic U phases via Raman and infrared spectroscopy and our results indicate that the simple understanding of δ-UO 3 as a high-symmetry cubic structure should be reconsidered.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
NASA NTRS1976

Chemical vapor deposition growth

The chemical vapor deposition (CVD) method for the growth of Si sheet on inexpensive substrate materials is investigated. The objective is to develop CVD techniques for producing large areas of Si sheet on inexpensive substrate materials, with sheet properties suitable for fabricating solar cells meeting the technical goals of the Low Cost Silicon Solar Array Project. Specific areas covered include: (1) modification and test of existing CVD reactor system; (2) identification and/or development of suitable inexpensive substrate materials; (3) experimental investigation of CVD process parameters using various candidate substrate materials; (4) preparation of Si sheet samples for various special studies, including solar cell fabrication; (5) evaluation of the properties of the Si sheet material produced by the CVD process; and (6) fabrication and evaluation of experimental solar cell structures, using standard and near-standard processing techniques.

Ruth, R. P.↗
NASA NTRS1978

Chemical vapor deposition growth

The objective was to investigate and develop chemical vapor deposition (CVD) techniques for the growth of large areas of Si sheet on inexpensive substrate materials, with resulting sheet properties suitable for fabricating solar cells that would meet the technical goals of the Low Cost Silicon Solar Array Project. The program involved six main technical tasks: (1) modification and test of an existing vertical-chamber CVD reactor system; (2) identification and/or development of suitable inexpensive substrate materials; (3) experimental investigation of CVD process parameters using various candidate substrate materials; (4) preparation of Si sheet samples for various special studies, including solar cell fabrication; (5) evaluation of the properties of the Si sheet material produced by the CVD process; and (6) fabrication and evaluation of experimental solar cell structures, using impurity diffusion and other standard and near-standard processing techniques supplemented late in the program by the in situ CVD growth of n(+)/p/p(+) sheet structures subsequently processed into experimental cells.

Ruth, R. P.↗
DOE OSTI2020

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2020

National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions

A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts’ opinion on the development and application of multi-omic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular and functional aberrations within the lesion and within individual cells. Additionally, single-cell proteomic data will be essential for the establishment of new tools that with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included: • The best way/s to analyze single-cells from fresh and preserved tissue • Detection and analysis of secreted molecules and from single cells, especially from a tissue slice • Detection of new, previously undocumented cell type/s in the premalignant and early stage cancer tissue microenvironment • Multi-omic integration of data to support and inform proteomic measurements • Subcellular organelles – identifying abnormal structure, function, distribution and location within individual premalignant and malignant cells • How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post translational modifications (PTM) • The depth of coverage measured concurrently using single-cell techniques • Quantitation - absolute or semiquantitative? • Single methodology or multiplexed combinations? • Application of analytical methods for identification of biologically significant subsets • Data visualization of N-dimensional datasets • How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME) • Associations between intrinsic cellular processes and extrinsic stimuli • How to predict cellular responses to stress inducing stimuli • Identification of new markers for prediction of progression from precursor, benign and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells • Identification of new targets for immunoprevention or immunotherapy – identification of neoantigens and surfactome of individual cells within a lesion

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Dual Allosteric Inhibition of SHP2 Phosphatase

SHP2 is a cytoplasmic protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell proliferation, differentiation, and survival. Recently, we reported an allosteric mechanism of inhibition that stabilizes the auto-inhibited conformation of SHP2. SHP099 (1) was identified and characterized as a moderately potent, orally bioavailable, allosteric small molecule inhibitor, which binds to a tunnel-like pocket formed by the confluence of three domains of SHP2. In this report, we describe further screening strategies that enabled the identification of a second, distinct small molecule allosteric site. SHP244 (2) was identified as a weak inhibitor of SHP2 with modest thermal stabilization of the enzyme. X-ray crystallography revealed that 2 binds and stabilizes the inactive, closed conformation of SHP2, at a distinct, previously unexplored binding site—a cleft formed at the interface of the N-terminal SH2 and PTP domains. Derivatization of 2 using structure-based design resulted in an increase in SHP2 thermal stabilization, biochemical inhibition, and subsequent MAPK pathway modulation. Downregulation of DUSP6 mRNA, a downstream MAPK pathway marker, was observed in KYSE-520 cancer cells. Remarkably, simultaneous occupation of both allosteric sites by 1 and 2 was possible, as characterized by cooperative biochemical inhibition experiments and X-ray crystallography. Combining an allosteric site 1 inhibitor with an allosteric site 2 inhibitor led to enhanced pharmacological pathway inhibition in cells. This work illustrates a rare example of dual allosteric targeted protein inhibition, demonstrates screening methodology and tactics to identify allosteric inhibitors, and enables further interrogation of SHP2 in cancer and related pathologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Identification of dopant site and its effect on electrochemical activity in Mn-doped lithium titanate

Doped metal oxide materials are commonly used for applications in energy storage and conversion, such as batteries and solid oxide fuel cells. The knowledge of the electronic properties of dopants and their local environment is essential for understanding the effects of doping on the electrochemical properties. Using a combination of x-ray absorption near-edge structure spectroscopy (XANES) experiment and theoretical modeling we demonstrate that in the dilute (1 at .%) Mn-doped lithium titanate (Li 4/3 Ti 5/3 O 4 , or LTO) the dopant Mn 2+ ions reside on tetrahedral (8a) sites. First-principles Mn K-edge XANES calculations revealed the spectral signature of the tetrahedrally coordinated Mn as a sharp peak in the middle of the absorption edge rise, caused by the 1s → 4 p transition, and it is important to include the effective electron-core hole Coulomb interaction in order to calculate the intenisty of this peak accurately. Finally, this dopant location can explain the impedance of Li migration through the LTO lattice during the charge-discharge process, and, as a result, the observed remarkable 20% decrease in electrochemical capacity of the 1% Mn-doped LTO compared to pristine LTO.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Identification of a quasi-liquid phase at solid–liquid interface

Abstract An understanding of solid–liquid interfaces is of great importance for fundamental research as well as industrial applications. However, it has been very challenging to directly image solid–liquid interfaces with high resolution, thus their structure and properties are often unknown. Here, we report a quasi-liquid phase between metal (In, Sn) nanoparticle surfaces and an aqueous solution observed using liquid cell transmission electron microscopy. Our real-time high-resolution imaging reveals a thin layer of liquid-like materials at the interfaces with the frequent appearance of small In nanoclusters. Such a quasi-liquid phase serves as an intermediate for the mass transport from the metal nanoparticle to the liquid. Density functional theory-molecular dynamics simulations demonstrate that the positive charges of In ions greatly contribute to the stabilization of the quasi-liquid phase on the metal surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Development of High Energy Density Diaminocyclopropenium‐Phenothiazine Hybrid Catholytes for Non‐Aqueous Redox Flow Batteries

Abstract This report describes the design of diaminocyclopropenium‐phenothiazine hybrid catholytes for non‐aqueous redox flow batteries. The molecules are synthesized in a rapid and modular fashion by appending a diaminocyclopropenium (DAC) substituent to the nitrogen of the phenothiazine. Combining a versatile C‐N coupling protocol (which provides access to diverse derivatives) with computation and structure‐property analysis enabled the identification of a catholyte that displays stable two‐electron cycling at potentials of 0.64 and 1.00 V vs. Fc/Fc + as well as high solubility in all oxidation states (≥0.45 M in TBAPF 6 /MeCN). This catholyte was deployed in a high energy density two‐electron RFB, exhibiting >90 % capacity retention over 266 hours of flow cell cycling at >0.5 M electron concentration.

Yan, Yichao↗
NASA NTRS2001

Familial orthostatic tachycardia due to norepinephrine transporter deficiency

Orthostatic intolerance (OI) or postural tachycardia syndrome (POTS) is a syndrome primarily affecting young females, and is characterized by lightheadedness, palpitations, fatigue, altered mentation, and syncope primarily occurring with upright posture and being relieved by lying down. There is typically tachycardia and raised plasma norepinephrine levels on upright posture, but little or no orthostatic hypotension. The pathophysiology of OI is believed to be very heterogeneous. Most studies of the syndrome have focused on abnormalities in norepinephrine release. Here the hypothesis that abnormal norepinephrine transporter (NET) function might contribute to the pathophysiology in some patients with OI was tested. In a proband with significant orthostatic symptoms and tachycardia, disproportionately elevated plasma norepinephrine with standing, impaired systemic, and local clearance of infused tritiated norepinephrine, impaired tyramine responsiveness, and a dissociation between stimulated plasma norepinephrine and DHPG elevation were found. Studies of NET gene structure in the proband revealed a coding mutation that converts a highly conserved transmembrane domain Ala residue to Pro. Analysis of the protein produced by the mutant cDNA in transfected cells demonstrated greater than 98% reduction in activity relative to normal. NE, DHPG/NE, and heart rate correlated with the mutant allele in this family. CONCLUSION: These results represent the first identification of a specific genetic defect in OI and the first disease linked to a coding alteration in a Na+/Cl(-)-dependent neurotransmitter transporter. Identification of this mechanism may facilitate our understanding of genetic causes of OI and lead to the development of more effective therapeutic modalities.

Review, Tutorial↗
DOE OSTI2020

Identification of durable and non-durable FeN x sites in Fe–N–C materials for proton exchange membrane fuel cells

We report that while Fe–N–C materials are a promising alternative to platinum for catalysing the oxygen reduction reaction in acidic polymer fuel cells, limited understanding of their operando degradation restricts rational approaches towards improved durability. Here we show that Fe–N–C catalysts initially comprising two distinct FeN x sites (S1 and S2) degrade via the transformation of S1 into iron oxides while the structure and number of S2 were unmodified. Structure–activity correlations drawn from end-of-test 57 Fe Mössbauer spectroscopy reveal that both sites initially contribute to the oxygen reduction reaction activity but only S2 substantially contributes after 50 h of operation. From in situ 57 Fe Mössbauer spectroscopy in inert gas coupled to calculations of the Mössbauer signature of FeN x moieties in different electronic states, we identify S1 to be a high-spin FeN 4 C 12 moiety and S2 a low- or intermediate-spin FeN 4 C 10 moiety. These insights lay the groundwork for rational approaches towards Fe–N–C cathodes with improved durability in acidic fuel cells.

36 MATERIALS SCIENCE↗