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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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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

BMX: Biological modelling and interface exchange

Abstract High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1990

Application specific serial arithmetic arrays

High performance systolic arrays of serial-parallel multiplier elements may be rapidly constructed for specific applications by applying hardware description language techniques to a library of full-custom CMOS building blocks. Single clock pre-charged circuits have been implemented for these arrays at clock rates in excess of 100 Mhz using economical 2-micron (minimum feature size) CMOS processes, which may be quickly configured for a variety of applications. A number of application-specific arrays are presented, including a 2-D convolver for image processing, an integer polynomial solver, and a finite-field polynomial solver.

Winters, K.↗
NASA NTRS1938

Calculation of the chordwise load distribution over airfoil sections with plain, split, or serially hinged trailing-edge flaps

A method is presented for the rapid calculation of the incremental chordwise normal-force distribution over an airfoil section due to the deflection of a plain flap or tab, a split flap, or a serially hinged flap. This report is intended as a supplement to NACA Report no. 631, wherein a method is presented for the calculation of the chordwise normal-force distribution over an airfoil without a flap or, as it may be considered, an airfoil with flap (or flaps) neutral. The method enables the determination of the form and magnitude of the incremental normal-force distribution to be made for an airfoil-flap combination for which the section characteristics have been determined. A method is included for the calculation of the flap normal-force and hinge-moment coefficients without necessitating a determination of the normal-force distribution.

Allen, H Julian↗
DOE OSTI2012

Quantitation of Human Papillomavirus DNA in Plasma of Oropharyngeal Carcinoma Patients

Purpose: To determine whether human papillomavirus (HPV) DNA can be detected in the plasma of patients with HPV-positive oropharyngeal carcinoma (OPC) and to monitor its temporal change during radiotherapy. Methods and Materials: We used polymerase chain reaction to detect HPV DNA in the culture media of HPV-positive SCC90 and VU147T cells and the plasma of SCC90 and HeLa tumor-bearing mice, non-tumor-bearing controls, and those with HPV-negative tumors. We used real-time quantitative polymerase chain reaction to quantify the plasma HPV DNA in 40 HPV-positive OPC, 24 HPV-negative head-and-neck cancer patients and 10 non-cancer volunteers. The tumor HPV status was confirmed by p16{sup INK4a} staining and HPV16/18 polymerase chain reaction or HPV in situ hybridization. A total of 14 patients had serial plasma samples for HPV DNA quantification during radiotherapy. Results: HPV DNA was detectable in the plasma samples of SCC90- and HeLa-bearing mice but not in the controls. It was detected in 65% of the pretreatment plasma samples from HPV-positive OPC patients using E6/7 quantitative polymerase chain reaction. None of the HPV-negative head-and-neck cancer patients or non-cancer controls had detectable HPV DNA. The pretreatment plasma HPV DNA copy number correlated significantly with the nodal metabolic tumor volume (assessed using {sup 18}F-deoxyglucose positron emission tomography). The serial measurements in 14 patients showed a rapid decline in HPV DNA that had become undetectable at radiotherapy completion. In 3 patients, the HPV DNA level had increased to a discernable level at metastasis. Conclusions: Xenograft studies indicated that plasma HPV DNA is released from HPV-positive tumors. Circulating HPV DNA was detectable in most HPV-positive OPC patients. Thus, plasma HPV DNA might be a valuable tool for identifying relapse.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon–carbon (C–C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. Here, we show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme–substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C–C bond coupling chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1976

Effects of water immersion to the neck on pulmonary circulation and tissue volume in man

A rapid noninvasive breathing method is used to obtain serial measurements of the pulmonary capillary blood flow, diffusing capacity per unit of alveolar volume, combined pulmonary tissue plus capillary volume, functional residual capacity, and oxygen consumption in five normal subjects undergoing 6 h of sitting, 4 h of sitting while immersed to the neck in thermoneutral water, and 4 h of lying in thermoneutral water to the neck. The rebreathing method employed a test gas mixture containing 0.5% C2H2, 0.3% C(18)O, 10% He, 21% O2, and balance N2. It is shown that immersion to the neck in the seated posture results in significant increases in sodium excretion cardiac output, and diffusing capacity per unit of alveolar volume. The pulmonary tissue plus capillary volume did not change, demonstrating that the central vascular engorgement induced by water immersion is not accompanied by significant extravasation of fluid into the pulmonary interstitial space.

Begin, R.↗
DOE OSTI2014

High-Throughput Screening for Acid-Stable Oxygen Evolution Electrocatalysts in the (Mn–Co–Ta–Sb)O x Composition Space

Solar generation of fuel is a promising future energy technology, and strong acidic conditions are highly desirable for integrated solar hydrogen generators. In particular, water splitting near pH 0 is attractive due to the availability of high theoretical efficiency, high performance hydrogen evolution catalysts, and robust ion exchange membranes. The lack of a stable, earth-abundant oxygen evolution catalyst inhibits deployment of this technology, and development of such a material is hampered by the strong anti-correlation between electrochemical stability and catalytic activity of non-precious metal oxides. High-throughput screening of mixed metal oxides offers a promising route to the identification of new stable catalysts and requires careful design of experiments to combine the concepts of rapid experimentation and long-term stability. By combining serial and parallel measurement techniques, we have created a high-throughput platform to assess the catalytic activity of material libraries in the as-prepared state and after 2 h of operation. By screening the entire (Mn–Co–Ta–Sb)O x composition space, we observe that the compositions with highest initial activity comprised cobalt and manganese oxides, but combinations with antimony and tantalum offer improved stability. Finally, by combining the desired properties of catalytic activity and stability, the optimal composition regions are readily identified, demonstrating the success and fidelity of this novel high-throughput screening platform.

10 SYNTHETIC FUELS↗
DOE OSTI2021

Selective acetate recognition and sensing using SWCNTs functionalized with croconamides

Croconamides are a new class of dual-hydrogen bond donors that have attracted interest in anion recognition and sensing applications due to their strong H-bond donation capability. In this work, we report chemiresistive sensors for the detection of anions based on poly(4-vinylpyridine) (P4VP)-wrapped single-walled carbon nanotubes (SWCNTs) functionalized with croconamide-based selectors. Model structures of asymmetric N,N-substituted croconamide selectors with N,N-substitutional groups of alkyl cationic pyridinium and electron-withdrawing moieties such as aniline (6) and 3,5-bis(trifluoromethyl)phenyl (7) groups were synthesized and their binding affinities for various anions were characterized using UV–vis and 1 H NMR titrations. Switchable binding of oxoanions was observed with selector 7, wherein HSO 4 – formed hydrogen bonding interactions and acetate (AcO – ) induced deprotonation of the NH- protons of the croconamide. Large sensitivity transitions were obtained toward AcO – for both P4VP-6-SWCNT (S = 95.68 ± 2.11 %) and P4VP-7-SWCNT (S = 140.91 ± 3.68 %) at 83.33 mM, which was attributed to deprotonation of the croconamide selectors upon addition of AcO – . In conclusion, three serial sensors were assembled in a sensor array that rapid and selective screening of AcO – was demonstrated against other oxoanions such as HSO 4 – and H 2 PO 4 – in real-time.

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

Selective Photodimerization in a Cyclodextrin Metal–Organic Framework

For the most part, enzymes contain one active site wherein they catalyze in a serial manner chemical reactions between substrates both efficiently and rapidly. Imagine if a situation could be created within a chiral porous crystal containing trillions of active sites where substrates can reside in vast numbers before being converted in parallel into products. Here, we report how it is possible to incorporate 1-anthracenecarboxylate (1-AC – ) as a substrate into a γ-cyclodextrin-containing metal–organic framework (CD-MOF-1), where the metals are K + cations, prior to carrying out [4+4] photodimerizations between pairs of substrate molecules, affording selectively one of four possible regioisomers. One of the high-yielding regioisomers exhibits optical activity as a result of the presence of an 8:1 ratio of the two enantiomers following separation by high-performance liquid chromatography. The solid-state superstructure of 1-anthracenecarboxylate potassium salt (1-ACK), which is co-crystallized with γ-cyclodextrin, reveals that pairs of substrate molecules are not only packed inside tunnels between spherical cavities present in CD-MOF-1, but also stabilized—in addition to hydrogen-bonding to the C-2 and C-3 hydroxyl groups on the d-glucopyranosyl residues present in the γ-cyclodextrin tori—by combinations of hydrophobic and electrostatic interactions between the carboxyl groups in 1-AC– and four K + cations on the waistline between the two γ-cyclodextrin tori in the tunnels. Here, these non-covalent bonding interactions result in preferred co-conformations that account for the highly regio- and enantioselective [4+4] cycloaddition during photoirradiation. Theoretical calculations, in conjunction with crystallography, support the regio- and stereochemical outcome of the photodimerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Financial Innovation Among the Community Wind Sector in the United States

In the relatively brief history of utility-scale wind generation, the 'community wind' sector - defined here as consisting of relatively small utility-scale wind power projects that are at least partly owned by one or more members of the local community - has played a vitally important role as a 'test bed' or 'proving ground' for wind turbine manufacturers. In the 1980s and 1990s, for example, Vestas and other now-established European wind turbine manufacturers relied heavily on community wind projects in Scandinavia and Germany to install - and essentially field-test - new turbine designs. The fact that orders from community wind projects seldom exceeded more than a few turbines at a time enabled the manufacturers to correct any design flaws or manufacturing defects fairly rapidly, and without the risk of extensive (and expensive) serial defects that can accompany larger orders. Community wind has been slower to take root in the United States - the first such projects were installed in the state of Minnesota around the year 2000. Just as in Europe, however, the community wind sector in the U.S. has similarly served as a proving ground - but in this case for up-and-coming wind turbine manufacturers that are trying to break into the broader U.S. wind power market. For example, community wind projects have deployed the first U.S. installations of wind turbines from Suzlon (in 2003), DeWind (2008), Americas Wind Energy (2008) and later Emergya Wind Technologies (2010),1 Goldwind (2009), AAER/Pioneer (2009), Nordic Windpower (2010), Unison (2010), and Alstom (2011). Just as it has provided a proving ground for new turbines, so too has the community wind sector in the United States served as a laboratory for experimentation with innovative new financing structures. For example, a variation of one of the most common financing arrangements in the U.S. wind market today - the 'partnership flip structure' - was first developed by community wind projects in Minnesota more than a decade ago (and is therefore sometimes referred to as the 'Minnesota flip' model) before being adapted by the broader wind market. More recently, a handful of community wind projects built in the United States over the past year have been financed via new and creative structures that push the envelope of wind project finance in the U.S. - in many cases, moving beyond the now-standard partnership flip structures. These projects include: (1) a 4.5 MW project in Maine that combines low-cost government debt with local tax equity, (2) a 25.3 MW project in Minnesota using a sale/leaseback structure, (3) a 10.5 MW project in South Dakota financed by an intrastate offering of both debt and equity, (4) a 6 MW project in Washington state that taps into 'New Markets Tax Credits' using an 'inverted' or 'pass-through' lease structure, and (5) a 9 MW project in Oregon that combines a variety of state and federal incentives and loans with unconventional equity from high-net-worth individuals. In most cases, these are first-of-their-kind financing structures that could serve as useful examples for other projects - both community and commercial wind alike. This new wave of financial innovation occurring in the community wind sector has been facilitated by policy changes, most of them recent. Most notably, the American Recovery and Reinvestment Act of 2009 ('the Recovery Act') enables, for a limited time, wind power (and other types of) projects to elect either a 30% investment tax credit ('ITC') or a 30% cash grant (the 'Section 1603 grant') in lieu of the federal incentive that has historically been available to wind projects in the U.S. - a 10-year production tax credit ('PTC'). This flexibility, in turn, enables wind power projects to pursue lease financing for the first time - leasing is not possible under the PTC. Because they are based on a project's cost rather than energy generation, the 30% ITC and Section 1603 grant also reduce performance risk relative to the PTC - this, too, is an important enabler of lease financing. Finally, by providing a cash rather than tax incentive, the Section 1603 grant alone reduces (but does not eliminate) the need for tax appetite among project owners. All of these policy changes can be particularly useful to community wind projects, and have helped to support the different financial structures mentioned above. This special report - which is distilled from a longer Berkeley Lab report - briefly describes just two of these innovative new financing structures: the sale/leaseback structure used in Minnesota and the intrastate offering conducted in South Dakota. Readers interested in more detail on these two structures, as well as the other three projects not covered here, are encouraged to reference the full Berkeley Lab report.

17 WIND ENERGY↗
DOE OSTI2019

Imaging the event-prone coronary artery plaque

Acute coronary events, the dreaded manifestation of coronary atherosclerosis, remain one of the main contributors to mortality and disability in the developed world. The majority of those events are associated with atherosclerotic plaques-related thrombus formation following an acute disruption, that being rupture or erosion, of an event-prone lesion. These historically termed vulnerable plaques have been the target of numerous benchtop and clinical research endeavors, yet to date without solid results that would allow for early identification and potential treatment. Technological leaps in cardiovascular imaging have provided novel insights into the formation and role of the event-prone plaques. From intracoronary optical coherence tomography that has enhanced our understanding of the pathophysiological mechanisms of plaque disruption, over coronary computed tomography angiography that enables non-invasive serial plaque imaging, and positron emission tomography poised to be rapidly implemented into clinical practice to the budding field of plaque imaging with cardiac magnetic resonance, we summarize the invasive and non-invasive imaging modalities currently available in our armamentarium. Finally, the current status and potential future imaging directions are critically appraised.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2026

High-entropy 1D halide perovskite piezoelectrics found by megalibrary synthesis and rapid nonlinear optical screening

Piezoelectric molecular crystals offer excellent compositional and structural tunability and sustainable processability. However, their discovery is slow, primarily due to the serial synthesis and screening processes used. Here, we report an approach that combines massively parallel megalibrary synthesis with scanning second harmonic generation (SHG) microscopy for rapid screening of piezoelectric molecular crystals. Megalibraries consisting of more than 1,000,000 compositionally distinct but positionally encoded TMCM x TMA (1–x) Cd y Pb (1–y) ClzBr (3–z) (TMCM: trimethylchloromethylammonium, TMA: tetramethylammonium; 0 ≤ x ≤ 1, 0 ≤ y ≤ 1, 0 ≤ z ≤ 3) nanocrystals were synthesized. The megalibraries were rapidly screened by SHG microscopy to identify notable noncentrosymmetric structures, which were then tested for piezoelectricity, facilitating discovery of a high-entropy noncentrosymmetric material with a large d 33 (TMCM 0.75 TMA 0.25 Cd 0.75 Pb 0.25 Cl 1.5 Br 1.5 , 42.8 picocoulombs per newton). Furthermore, this approach enabled systematic investigation of the Curie temperature (T C )–composition relationship in the TMCMCdCl z Br (3–z) system, facilitating reverse design of materials with targeted T C . Our work establishes a powerful approach to accelerate the discovery and design of unusual piezoelectrics for next-generation electronics and optics.

Li, Jun [Northwestern University, Evanston, IL (Un↗
DOE OSTI2014

Cheetah : software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data

The emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A 2A adenosine receptor (A 2A AR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A 2A AR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A 2A AR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. Furthermore, these developments will enable structure determination from smaller and/or weakly diffracting microcrystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

NSLS-II biomedical beamlines for micro-crystallography, FMX, and for highly automated crystallography, AMX: New opportunities for advanced data collection

We present the final design of the x-ray optics and experimental stations of two macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source-II. The microfocusing FMX beamline will deliver a flux of ∼5×10{sup 12} ph/s at 1 Å into a 1 – 20 µm spot, its flux density surpassing current MX beamlines by up to two orders of magnitude. It covers an energy range from 5 – 30 keV. The highly automated AMX beamline is optimized for high throughput, with beam sizes from 4 – 100 µm, an energy range of 5 – 18 keV and a flux at 1 Å of ∼10{sup 13} ph/s. A focus in designing the beamlines lay on achieving high beam stability, for example by implementing a horizontal bounce double crystal monochromator at FMX. A combination of compound refractive lenses and bimorph mirror optics at FMX supports rapid beam size changes. Central components of the in-house developed experimental stations are horizontal axis goniometers with a target sphere of confusion of 100 nm, piezo-slits for dynamic beam size changes during diffraction experiments, dedicated secondary goniometers for data collection from specimen in crystallization plates, and next generation pixel array detectors. FMX and AMX will support a broad range of biomedical structure determination methods from serial crystallography on micron-sized crystals, to structure determination of complexes in large unit cells, to rapid sample screening and room temperature data collection of crystals in trays.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Application of High Performance Computing for Simulating the Unstable Dynamics of Dilute Spark-Ignited Combustion

In collaboration with a major automotive manufacturer, we are using computational simulations of in-cylinder combustion to understand the multi-scale nonlinear physics of the dilute stability limit. Because some key features of dilute combustion can take thousands of successive cycles to develop, the computation time involved in using complex models to simulate these effects has limited industrys ability to exploit simulations in optimizing advanced engines. We describe a novel approach for utilizing parallel computations to reveal long-timescale features of dilute combustion without the need to simulate many successive engine cycles in series. Our approach relies on carefully guided, concurrent, single-cycle simulations to create metamodels that preserve the long-timescale features of interest. We use a simplified combustion model to develop and demonstrate our strategy for adaptively guiding the concurrent simulations to generate metamodels. We next will implement this strategy with higher-fidelity, multi-scale combustion models on large computing facilities to generate more refined metamodels. The refined metamodels can then be used to accelerate engine development because of their efficiency. Similar approaches might also be used for rapidly exploring the dynamics of other complex multi-scale systems that evolve with serial dependency on time.

Finney, Charles↗
DOE OSTI2019

The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity

Deoxynucleotide triphosphohydrolases (dNTPases) play a critical role in cellular survival and DNA replication through the proper maintenance of cellular dNTP pools. While the vast majority of these enzymes display broad activity toward canonical dNTPs, such as the dNTPase SAMHD1 that blocks reverse transcription of retroviruses in macrophages by maintaining dNTP pools at low levels, Escherichia coli ( Ec )-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. However, the mechanism behind dGTP selectivity is unclear. Here we present the free-, ligand (dGTP)- and inhibitor (GTP)-bound structures of hexameric Ec- dGTPase, including an X-ray free-electron laser structure of the free Ec- -dGTPase enzyme to 3.2 Å. To obtain this structure, we developed a method that applied UV-fluorescence microscopy, video analysis, and highly automated goniometer-based instrumentation to map and rapidly position individual crystals randomly located on fixed target holders, resulting in the highest indexing rates observed for a serial femtosecond crystallography experiment. Our structures show a highly dynamic active site where conformational changes are coupled to substrate (dGTP), but not inhibitor binding, since GTP locks dGTPase in its apo- form. Moreover, despite no sequence homology, Ec- dGTPase and SAMHD1 share similar active-site and HD motif architectures; however, Ec- dGTPase residues at the end of the substrate-binding pocket mimic Watson–Crick interactions providing guanine base specificity, while a 7-Å cleft separates SAMHD1 residues from dNTP bases, abolishing nucleotide-type discrimination. Furthermore, the structures shed light on the mechanism by which long distance binding (25 Å) of single-stranded DNA in an allosteric site primes the active site by conformationally “opening” a tyrosine gate allowing enhanced substrate binding.

Barnes, Christopher O.↗
DOE OSTI2014

The role of growth factors in maintenance of stemness in bone marrow-derived mesenchymal stem cells

Highlights: • Expression of FGF-2, FGF-4, EGF, and HGF decreased during long-term culture of BMSCs. • Loss of growth factors induced autophagy, senescence and decrease of stemness. • FGF-2 increased proliferation potential via AKT and ERK activation in BMSCs. • FGF-2 suppressed LC3-II expression and down-regulated senescence of BMSCs. • HGF was important in maintenance of the differentiation potential of BMSCs. - Abstract: Mesenchymal stem cells (MSCs) are an active topic of research in regenerative medicine due to their ability to secrete a variety of growth factors and cytokines that promote healing of damaged tissues and organs. In addition, these secreted growth factors and cytokines have been shown to exert an autocrine effect by regulating MSC proliferation and differentiation. We found that expression of EGF, FGF-4 and HGF were down-regulated during serial passage of bone marrow-derived mesenchymal stem cells (BMSCs). Proliferation and differentiation potentials of BMSCs treated with these growth factors for 2 months were evaluated and compared to BMSCs treated with FGF-2, which increased proliferation of BMSCs. FGF-2 and -4 increased proliferation potentials at high levels, about 76- and 26-fold, respectively, for 2 months, while EGF and HGF increased proliferation of BMSCs by less than 2.8-fold. Interestingly, differentiation potential, especially adipogenesis, was maintained only by HGF treatment. Treatment with FGF-2 rapidly induced activation of AKT and later induced ERK activation. The basal level of phosphorylated ERK increased during serial passage of BMSCs treated with FGF-2. The expression of LC3-II, an autophagy marker, was gradually increased and the population of senescent cells was increased dramatically at passage 7 in non-treated controls. But FGF-2 and FGF-4 suppressed LC3-II expression and down-regulated senescent cells during long-term (i.e. 2 month) cultures. Taken together, depletion of growth factors during serial passage could induce autophagy, senescence and down-regulation of stemness (proliferation via FGF-2/-4 and differentiation via HGF) through suppression of AKT and ERK signaling.

60 APPLIED LIFE SCIENCES↗