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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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Long non-coding RNA lnc-MX1-1 is associated with poor clinical features and promotes cellular proliferation and invasiveness in prostate cancer

Long non-coding RNAs (lncRNAs) are emerging as key molecules in human cancer genesis and progression, including prostate cancer. Large amount of lncRNAs have been found that differentially expressed between prostate cancer tissues and normal prostate tissues. Whether these lncRNAs could serve as a novel biomarker for prostate cancer diagnosis or prognosis, and their biological functions in prostate cancer need further investigation. In the present study, we identified that lncRNA lnc-MX1-1 is over-expressed in prostate cancer tissues compared with their adjacent normal prostate tissues by gene expression array profiling. The expression of lnc-MX1-1 in 60 prostate cancer cases was determined by real-time quantitative PCR and the correlations between lnc-MX1-1 expression and patients' clinical features were further analyzed. Next, we impaired lnc-MX1-1 expression using RNAi in LNCaP and 22Rv1 prostate cancer cells to explore the effects of lnc-MX1-1 on proliferation and invasiveness of the cells. Our results showed that there was a significant association between over-expression of lnc-MX1-1 and patients' clinical features such as PSA, Gleason score, metastasis, and recurrence free survival. Moreover, knockdown of lnc-MX1-1 reduced both proliferation and invasiveness of LNCaP and 22Rv1 cells. In conclusion, the results suggest that lnc-MX1-1 may serve as a potential biomarker and therapeutic target for prostate cancer. - Highlights: • LncRNA lnc-MX1-1 is up-regulated in prostate cancer. • Overexpression of lnc-MX1-1 is correlated with poor prostate cancer clinical features. • Knockdown of lnc-MX1-1 reduces proliferation and invasiveness of prostate cancer cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Temporal dynamics of CO 2 and CH 4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils

Earth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands are subjected to the immediate consequence of climate change with shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alter the nature and rate of biogeochemical transformations and significantly impact the carbon balance of the ecosystem. We tested the impacts of fluctuating hydrology and, specifically, the role of antecedent moisture conditions in determining the dominant carbon loss mechanisms in soils sampled from a tidal freshwater wetland system in the lower Columbia River, WA, USA. Our objective was to understand shifts in biogeochemical processes in response to changing soil moisture, based on soil respiration and methane production rates, and to elucidate such responses based on the observed electron acceptor and metabolite profiles under laboratory conditions. Metabolomics and biogeochemical process rates provided evidence that soil redox was the principal factor driving metabolic function. Fluctuating redox conditions altered terminal electron acceptor and donor availability and recovery strengths of their concentrations in soil such that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradation processes like sulfate and iron reduction compared to carbon loss due to methano genesis. Our results show that extended and short-term saturation created conditions conducive to increasing metabolite availability for anaerobic decomposition processes, with a significant lag in methanogenesis. In contrast,extended drying caused a cellular-level stress response and rapid recycling of alternate electron acceptors.

anaerobic respiration, tidal wetlands, methane pro↗
DOE OSTI2021

The Role of Energy Storage in the Uptake of Renewable Energy: A Model Comparison Approach

The power sector needs to ensure a rapid transition towards a low-carbon energy system to avoid the dangerous consequences of greenhouse gas emissions. Storage technologies are a promising option to provide the power system with the flexibility required when intermittent renewables are present in the electricity generation mix. This paper focuses on the role of electricity storage in energy systems with high shares of renewable sources. The study encompasses a model comparison approach where four models (GENeSYS-MOD, MUSE, NATEM, and urbs - MX) are used to analyse the storage uptake in North America. The analysis addresses the conditions affecting storage uptake in each country and its dependence on resource availability, technology costs, and public policies. Results show that storage may promote emissions reduction at lower costs when renewable mandates are in place whereas in presence of carbon taxes, renewables may compete with other low-carbon options. The study also highlights the main modelling approach shortcomings in the modelling of electricity storage in integrated assessment models.

electricity storage↗
DOE OSTI2020

Transport of coexisting Ni-Cu sulfide liquid and silicate melt in partially molten peridotite

Transport of coexisting sulfide and silicate melts in partially molten peridotite contributes to the redistribution of chalcophile elements within the upper mantle as well as the genesis of magmatic Ni-Cu sulfide deposits, but has not been investigated systematically. Using laboratory experiments, theoretical calculations, and X-ray synchrotron microtomography, this study documents the topology and considers controls on the extraction of two immiscible liquids during partial melting of mantle peridotite. Under hydrostatic conditions, the measured dihedral angle at silicate melt-mineral-mineral junctions is 13.7–21.3°. Silicate melt is distributed along grain edges forming incompletely interconnected melt channels that disconnected by some dead ends at melt fractions ~7–9 vol%. Application of theoretically predicted permeability (k ~10 -14 -10 -16 m 2 ) permits estimation of the extraction velocity of silicate melt of 0.7-11.1 μm/day within a single interconnected melt channel. In the absence of silicate melt, isolated sulfide droplets (3.77 vol%) show a sulfide-olivine-olivine dihedral angle of 91.5–101.3°. However, in the presence of silicate melt, sulfide droplets (average size ~2.53±2.14μm, 1σ) are partially surrounded by silicate melt and stranded in triple junctions or melt pockets due to the limitation of the smallest dimension (0.3μm) of melt channels. Thus, the extraction of sulfide liquid is highly restricted by these dead ends and the smallest dimension of melt channels during porous flow of silicate melt. In contrast, during large-strain shear deformation (strain ~1.6–2.5), initially stranded sulfide droplets were elongated and extracted with silicate melt into liquid-rich sheets with a length of several hundred microns, constantly oriented at 14.3±4.5°to the shear plane and antithetic to the shear direction. The angle is lower than that (18-30°) of those sheets containing sulfide liquid only, indicating that silicate melt dominates liquid-rich sheets. Driven by stress, silicate melt-dominated liquid-rich sheets open the appropriately oriented grain boundaries between silicate minerals, thus providing an efficient pathway for the extraction of sulfide liquid during deformation. When such sheet-like channels remain open, sulfide droplets (> millimeter-scale) can be potentially mobile through high strain domains of the upper mantle, contributing to the addition of chalcophile elements and the fertilization of the lithospheric mantle.

high P-T experiment↗
DOE OSTI2023

Dual origin of ferropericlase inclusions within super-deep diamonds

Ferropericlase [(Mg,Fe)O] is one of the major constituents of Earth's lower mantle and the most abundant mineral inclusion in sub-lithospheric diamonds. Although a lower mantle origin for ferropericlase inclusions has often been suggested, some studies have proposed that many of these inclusions may instead form at much shallower depths, in the deep upper mantle or transition zone. No straightforward method exists to discriminate ferropericlase of lower-mantle origin without characteristic mineral associations, such as co-existing former bridgmanite. To explore ferropericlase-diamond growth relationships, we have investigated the crystallographic orientation relationships (CORs), determined by single-crystal X-ray diffraction, between 57 ferropericlase inclusions and 37 diamonds from Juina (Brazil) and Kankan (Guinea). We show that ferropericlase inclusions can develop specific (16 inclusions in 12 diamonds), rotational statistical (9 inclusions in 7 diamonds) and random (32 inclusions in 25 diamond) CORs with respect to their diamond hosts. All measured inclusions showing a specific COR were found to be Fe-rich (X FeO > 0.30). Coexistence of non-randomly and randomly oriented ferropericlase inclusions within the same diamond indicates that their CORs may be variably affected by local growth conditions. However, the occurrence of specific CORs only for Fe-rich inclusions indicates that Fe-rich ferropericlases have a distinct genesis and are syngenetic with their host diamonds. In conclusion, this result provides strong support for a dual origin for ferropericlase in Earth's mantle, with Fe-rich compositions likely indicating redox growth in the upper mantle, while more Mg-rich compositions with random COR mostly representing ambient lower mantle trapped as protogenetic inclusions.

58 GEOSCIENCES↗
DOE OSTI2025

Osmotic control of the spacing of parallel shear cracks in shale growing subcritically in geologic past

The geological genesis of natural cracks in sedimentary rocks such as shale is a problem that needs to be understood to improve the technology of hydraulic fracturing as well as deep sequestration of harmful fluids. Why are the vertical natural cracks roughly parallel and equidistant, and why is the spacing roughly 10 cm rather than 1 cm or 100 cm? Fracture mechanics of critical cracks cannot answer this question. Neither can the material heterogeneity. The growth of critical parallel cracks is impossible because the relative crack face displacements would immediately localize into one crack, leading to an earthquake. The cracks must have formed, on the tectonic time scale, by a slow growth of subcritical shear cracks governed by the Charles-Evans law. The idea advanced here is that what controls the crack spacing is the balance between the reduction, due to shear dilatancy, of the concentration of ions such as Na + and Cl - in each fracture process zone (PFZ), which decelerates the cracks, and the restoration of ion concentration by diffusion of ions from the space between the cracks into the FPZ. This diffusion of water is driven mainly by the osmotic pressure gradient, which offsets the deceleration and depends strongly on the crack spacing. A simple analytical solution of the steady state is rendered possible by approximating the ion concentration profiles between adjacent cracks by parabolic arcs. Applying this theory to Woodford shale yields the approximate crack spacing of 10 cm, which is realistic. Furthermore, the stability of unlimited parallel mode II frictional crack growth is proven by examining the second variation of the free energy. Water concentration drop in the FPZ due to shear dilatancy and its restoration by water diffusion from the inter-crack space have similar effect, although probably much weaker.

42 ENGINEERING↗
DOE OSTI2013

Two-dimensional titanium carbonitrides and their hydroxylated derivatives: Structural, electronic properties and stability of MXenes Ti{sub 3}C{sub 2−x}N{sub x}(OH){sub 2} from DFTB calculations

The structural, electronic properties and stability of the new MXene compounds—two-dimensional pristine carbonitrides Ti{sub 3}C{sub 2−x}N{sub x} and their hydroxylated derivatives Ti{sub 3}C{sub 2−x}N{sub x}(OH){sub 2} are studied by means of DFTB calculations. The genesis of the properties is discussed in the sequence: binary MXenes Ti{sub 3}C{sub 2} (Ti{sub 3}N{sub 2})→hydroxylated forms Ti{sub 3}C{sub 2}(OH){sub 2} (Ti{sub 3}N{sub 2}(OH){sub 2})→pristine MXene Ti{sub 3}C{sub 2−x}N{sub x}→hydroxylated Ti{sub 3}C{sub 2−x}N{sub x}(OH){sub 2}. All examined materials are metallic-like. The most favorable type of OH-covering is presented by the occupation of the hollow sites between three neighboring carbon (nitrogen) atoms. Two-dimensional MXene carbonitrides with random distribution of C and N atoms are found to be thermodynamically more favorable. - Graphical abstract: The side views of the optimized atomic structures of some examined hydroxylated derivatives of MXene Ti{sub 3}CN and their electronic band structures. Display Omitted - Highlights: • Very recently 2D titanium carbonitrides have been synthesized. • Structural, electronic properties and stability for these materials were evaluated. • The hydroxylated derivatives of 2D titanium carbonitrides are examined.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Diffusion behavior of copper atoms under Cu(II) reduction in Cucurbit[8]uril cavity at elevated temperatures

In this paper we describe copper clusters and nanoparticles formation by the reduction of copper (II) ions inside cavities of macrocycle molecules using supramolecular compound [Cu(Cyclen)(H{sub 2}O)@CB[8]](NO{sub 3}){sub 2}·12H{sub 2}O followed by Cu atoms diffusion between macrocycle CB[8] molecules. To understand the copper cluster genesis and nanoparticles formation x-ray powder diffraction (XRD), electron paramagnetic resonance (EPR), FTIR-spectroscopies, HRTEM and thermal analysis were used. It was found that atomic Cu(0) was not fixed in the cavity under heating, and Cu clusters and nanoparticles were formed by heating of supramolecular compound powder at 200–340 °C in He, but more preferably in H{sub 2}. The process was partially reversible after heating the powder up to 300 °C for 15 min and air exposure for a few months. The process was irreversible after heating of the sample at temperatures higher than 340 °C due to CB[8] cavitand decomposition. In general, exposure of the samples to air leads to oxidation and hydration clusters of Cu. Nanoparticles up to 600 nm in size formed on the surface of agglomerated polycrystalline powder at temperatures lower than 200 °C. The clusters less than 7 nm and 40 nm in size were formed at 300 °C inside and outside agglomerating polycrystalline powder, respectively. The diffusion coefficient of copper atoms inside polycrystalline CB[8] agglomerates equal to 10{sup −10} cm{sup 2}/s by heating the samples at 300 °C was found. - Graphical abstract: Copper nanoparticles and clusters are formed by the reduction of copper (II) ions inside cavities of macrocycle molecules at 200–340 °C in He, but more preferably in H{sub 2} using supramolecular compound [Cu(Cyclen)(H{sub 2}O)@CB[8]](NO{sub 3}){sub 2}·12H{sub 2}O followed by Cu atoms diffusion between macrocycle CB[8] molecules. Nanoparticles up to 600 nm in size formed on the surface of agglomerated polycrystalline powder at temperatures lower than 200 °C. The clusters less than 7 nm and 40 nm in size were formed at 300 °C inside and outside agglomerating polycrystalline powder, respectively. - Highlights: • We considered Cu NP's formation at CuCyclen thermolysis in H{sub 2} and He. • Initial complex CuCyclen was located inside cavitand CB[8]. • Cu(0) reduced in cavities diffuse between CB[8] molecules and Cu nuclei appear. • NPs less than 7 and 50 nm were formed inside and outside the CB[8] powder. • Coefficient of Cu(O) diffusion is 10{sup −10} cm{sup 2}/s for temperature at 300 °C.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Combination of imaging mass spectrometry and electron microscopy for quasi nondestructive surface analysis

We report on a combination of imaging mass spectrometry (MS) and scanning electron microscopy (SEM) developed in a custom designed time-of-flight (TOF) MS instrument with laser post-ionization of sputtered atoms. Elemental (by MS) and topographical (by SEM) mapping of surfaces of heavily contaminated Si collectors from the NASA Genesis sample return mission enabled obtaining much more accurate and detailed depth distribution of the Solar Wind Mg and Ca implanted in these collectors. This is because the cleanest areas were identified by the SEM/MS mapping, and high resolution sputter depth profiling at these locations revealed near-surface (0-15 nm) depth distribution of Mg and Ca, that were used for more accurate fluence calculations of these Solar Wind species. MS imaging was virtually nondestructive at primary ion fluence 10(12) cm(-2), causing no effect on accuracy and precision of quantitative depth profiling that followed the imaging. We also demonstrate importance of such an approach by directly comparing high resolution depth profiles measured on clean areas versus arbitrarily selected areas.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2017

SIMS microanalysis of the Strelley Pool Formation cherts and the implications for the secular-temporal oxygen-isotope trend of cherts

The significance of oxygen isotope ratios in Archean chert has long been debated. Cherts from the c. 3.4 Ga Strelley Pool Formation (SPF) (Pilbara Craton, Western Australia) host some of the oldest stromatolite and microfossil evidence for life, but the genesis and timing of silica cements has been unclear. Field relations, petrography and a combination of laser fluorination and in-situ SIMS measurements of δ 18 O in quartz show that bedded cherts of the SPF were originally precipitated as carbonates and were later widely replaced by quartz. Three localities were studied and analyzed for δ 18 O(Qz) in chert: 1) Camel Creek: foliated, metamorphosed, bedded cherts and meter-scale black chert veins; 2) Unconformity Ridge and ABDP8 drill core: stromatolitic and bedded chert overlying basal detrital quartz sandstone; and 3) the Trendall locality: “bedded” stromatolitic chert replacing original dolomite, low temperature hydrothermal quartz, and mm- to decimeter-scale chert-quartz veins. Laser fluorination (mm-scale) values of δ18O(Qz) range from: 14.2 to 18.2‰ VSMOW at Camel Creek; 9.3 to 18.9‰ at Unconformity Ridge; and 13.7 to 25.7‰ at Trendall. Values of δ 18 O(Qz) in cm to decimeter-scale hydrothermal chert veins cutting bedded carbonates at Trendall range from ca. 15 to 16‰, whereas “bedded cherts” are 17 to 26‰. These laser data include the highest δ 18 O values reported for cherts in Paleoarchean sediments and are up to 4‰ higher than the upper limit of ~22‰ reported in other studies, in apparent contrast to the long-standing secular-temporal trend which shows such high δ 18 O only in younger chert. However, analysis by laser fluorination at the 1-mm scale cannot resolve microtextures seen petrographically. In contrast, in-situ SIMS analyses can resolve petrographic microtextures and show δ 18 O(Qz) at 10-μm scale have an even greater range of 7–31‰ in “bedded” cherts at the Trendall locality, up to 9‰ above the secular-temporal trend. Textures observed optically at the Trendall locality were classified as: microquartz, mesoquartz, chalcedony, megaquartz veins, and cavity megaquartz. SEM-CL imaging shows two generations of meso- and megaquartz; bright CL with well-developed growth zoning, and dark CL with massive or mottled texture. Microquartz is the earliest textural generation of quartz and has a maximum δ 18 O(Qz) of ~22‰ by SIMS. Dark-CL mesoquartz has similar δ 18 O to microquartz and is interpreted to also be early. Bright-zoned-CL mesoquartz, which formed post-Archean, has even higher δ 18 O, up to 29‰. Vein megaquartz crosscuts most quartz generations and has a restricted range of δ 18 O, mostly from 16 to 19‰. Chalcedony pseudomorphs rhombic cavities and fractures, lines the edges of veins, and has similar δ 18 O to veins (16–19‰). Late cavity megaquartz is bright and zoned by CL, grows into late open cavities, and has the highest δ 18 O(Qz) values reported from the Pilbara, up to 31.3‰. Thus, the highest-δ 18 O quartz cements at the Trendall locality are the youngest and may be related to weathering. Early silicification and the formation of microquartz, chalcedony and low δ 18 O mesoquartz occurred during low temperature hydrothermal activity in the Archean. None of the SPF quartz examined is interpreted to have formed as a direct precipitate from Paleoarchean seawater. Thus, values of δ 18 O(Qz) do not record either water chemistry or temperature of Archean oceans. In-situ SIMS analysis shows that high-δ 18 O(Qz) values above 22‰ are only found in late-forming cavity megaquartz and bright-zoned-CL mesoquartz at the Trendall locality. The SPF results from our sample suite demonstrate the ability to resolve complex history using detailed petrography and SIMS analysis. Similar studies may show equal complexity of δ 18 O(Qz) data for other localities that are interpreted to show secular-temporal trends for chert. The apparent increase of δ 18 O(Qz) through time may reflect differences in diagenesis, and/or an inherent and previously unrecognized sampling bias that compares fundamentally different populations of quartz, such as Archean hydrothermal chert from volcanic greenstone belts, with unrelated Phanerozoic biogenic quartz.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Formation and energetics of amorphous rare earth (RE) carbonates in the RE 2 O 3 –CO 2 –H 2 O system

Amorphous materials are of interest in the genesis of crystalline solids. They are often the first to precipitate from supersaturated solutions and are in the nanometer size range, transforming into a nanocrystalline metastable phase, and then to thermodynamically stable phases. One must seek knowledge of the composition, structure, thermodynamics, kinetics, and reaction pathways that relate the amorphous and crystalline phases. The subject of this study is the amorphous phases in the system RE 2 O 3 -CO 2 –H 2 O (RE- La, Nd, Dy,Yb). They were synthesized via direct precipitation and urea hydrolysis, and characterized by powder XRD, DTA with mass spectrometric analysis of the evolved gases. Phases have the non-stoichiometric composition RE 2 O 3 ·xCO 2 ·yH 2 O (1 < x < 3, 3 < y <7), which is different from that of crystalline simple carbonates and hydroxycarbonates. Thus we consider them to be amorphous precursors, rather than amorphous carbonates. High temperature oxide melt solution calorimetry in molten sodium molybdate solvent was used to derive their enthalpies of formation from oxides and elements. Increase of energetic stability per mole of RE 2 O 3 compounds occurs in the order: RE 2 O 3 → 2RE(OH)3→ 2REO(OH) → RE 2 O 2 CO 3 → Amorphous precursor → 2(REOHCO 3 ) → RE 2 (CO 3 ) 3 ·yH 2 O. We calculated the enthalpies of possible transformations of amorphous precursors to crystalline phases and conclude that thermodynamics determines the dependence of the crystallizing products on the temperature and partial pressure of CO 2 and H 2 O. Amorphous precursors are clearly intermediate in the synthesis, and ternary phases containing both H 2 O and CO 2 compete with each other in terms of thermodynamic stability. The energy landscape obtained here will allow one to directly synthesize specific products and control their functionality.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

TBX3, a downstream target of TGF-β1, inhibits mesangial cell apoptosis

Chronic kidney disease (CKD) is an increasingly common condition characterized by progressive loss of functional nephrons leading to renal failure. TGF-β1-induced mesangial cell (MC) phenotype alterations have been linked to the genesis of CKD. Here we show that TGF-β1 regulates TBX3 gene expression in MC. This gene encodes for two main isoforms, TBX3.1 and TBX3+2α. TBX3.1 has been implicated in cell immortalization, proliferation and apoptosis by inhibiting p14{sup ARF}-Mdm2-p53 pathway, while TBX3+2α role has not been defined. We demonstrated that TBX3 overexpression abrogated MC apoptosis induced by serum deprivation. Moreover, we observed an enhancement in TBX3 protein expression both in glomerular and tubular regions in the model of 5/6 nephrectomy, temporally related to increased expression of TGF-β1, type IV collagen and fibronectin. Our results indicate that TBX3 acts as an anti-apoptotic factor in MC in vitro and may be involved in the mechanism by which TGF-β1 induces glomerulosclerosis and tubular fibrosis during the progression of nephropathies. - Highlights: • TBX3 isoforms are upregulated by TGF-b1 in mesangial cells. • TBX3 isoforms have different subcellular distribution profile in mesangial cells. • TBX3 isoforms exhibit antiapoptotic action in mesangial cells. • TBX3 protein is overexpressed in a model of nephropathy (5/6 nephrectomy)

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

The β-catenin signaling pathway induces aggressive potential in breast cancer by up-regulating the chemokine CCL5

β-Catenin signaling plays a pivotal role in the genesis of a variety of malignant tumors, but its role in breast cancer has not been fully elucidated. Here, we examined whether deregulation of β-catenin signaling is related to the aggressive characteristics of certain types of breast cancers. Analysis of cytokine levels in MDA-MB-231 cells overexpressing a constitutively active form of β-catenin (CAβ-catenin) revealed a higher level of CCL5 expression. Cells transfected with CAβ-catenin or stimulated with recombinant CCL5 exhibited increased cell invasion activity and spheroid formation in vitro. Furthermore, CAβ-catenin-transfected MDA-MB-231 cells formed larger tumor masses that contained more Ki-67-positive cells and infiltrating lymphocytes than did the control cells. An inhibitor of CCR5 and a pan-CXCR neutralizing antibody dramatically reduced CAβ-catenin-promoted activities. In addition to CCL5, 6-BIO, a chemical activator of β-catenin, induced cell invasion and spheroid formation in MDA-MB-231 cells. Furthermore, high levels of nuclear β-catenin accumulation were detected in breast cancer in patients with metastasis but not in those without metastasis. Nuclear β-catenin localization is related to increased CCL5 production in breast cancer. These findings suggest that β-catenin expression enhances tumor progression via chemokine production in breast cancers and that β-catenin signaling is a critical regulator of the aggressive traits of breast cancers. - Highlights: •The expression of chemokines, especially CCL5, is positively regulated by β-catenin signaling •The inhibition of CCR5 signaling suppressed β-catenin-induced tumor spreading in vitro and in vivo. • β-catenin was detected in cell nuclei in specimens from carcinoma regions of metastasized breast cancer • β-catenin nuclear translocation and cytokines have implications in leading to metastasis events.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

MicroRNA-133b inhibits hepatocellular carcinoma cell progression by targeting Sirt1

MicroRNAs (miRNAs) are a class of small non-coding RNAs that function as critical gene regulators by targeting mRNAs for translational repression or degradation. In this study, we showed that the expression level of miR-133b was decreased, while Sirt1 mRNA expression levels were increased in hepatocellular carcinoma (HCC) and cell lines, and we identified Sirt1 as a novel direct target of miR-133b. The over-expression of miR-133b suppressed Sirt1 expression. In addition, miR-133b over-expression resulted in attenuating HCC cell proliferation and invasion together with apoptosis increase in vitro. HepG2 cell transplantation revealed that up-regulation of miR-133b could inhibit HCC tumor genesis in vivo. Forced expression of Sirt1 partly rescued the effect of miR-133b in vitro. Furthermore, our study showed that miR-133b over-expression or Sirt1 down-regulation elevated E-cadherin expression, and repressed glypican-3 (GPC3) and the anti-apoptotic proteins (Bcl-2, Bcl-xL, and Mcl-1) expression. The inhibition of GPC3 expression repressed Bcl-2, Bcl-xL, and Mcl-1 expression, and elevated E-cadherin expression. Moreover, the Sirt1 up-regulation resulted in increases in HCC cell proliferation and invasion together with decreases apoptosis, and increases in the cytosolic accumulation and nuclear translocation of the transcription factor β-catenin in vitro. But the effect of Sirt1 up-regulation was partly reversed by GPC3 down-regulation in vitro. Taken together, these findings provide insight into the role and mechanism of miR-133b in regulating HCC cell proliferation, invasion and apoptosis via the miR-133b/Sirt1/GPC3/Wnt β-catenin axis, and miR-133b may serve as a potential therapeutic target in HCC in the future. - Highlights: • Sirt1 is a direct target of miR-133b in HCC. • miR-133b over-expression suppresses HCC progression in vitro and in vivo. • Sirt1 restoration reverses the effect of miR-133b over-expression on HCC cells. • GPC3 down-regulation reverses the effect of Sirt1 up-regulation on HCC cells. • Sirt1 activates Wnt β-catenin signaling by GPC3 in vitro.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations

Alchemical free energy simulations have long been utilized to predict free energy changes for binding affinity and solubility of small molecules. However, while the theoretical foundation of these methods is well established, seamlessly handling many of the practical aspects regarding the preparation of the different thermodynamic end states of complex molecular systems and the numerous processing scripts often remains a burden for successful applications. Here, we present CHARMM-GUI Free Energy Calculator (http://www.charmm-gui.org/input/fec) that provides various alchemical free energy perturbation molecular dynamics (FEP/MD) systems with input and post-processing scripts for NAMD and GENESIS. Four submodules are available: Absolute Ligand Binder (for absolute ligand binding FEP/MD), Relative Ligand Binder (for relative ligand binding FEP/MD), Absolute Ligand Solvator (for absolute ligand solvation FEP/MD), and Relative Ligand Solvator (for relative ligand solvation FEP/MD). Each module is designed to build multiple systems of a set of selected ligands at once for high-throughput FEP/MD simulations. The capability of Free Energy Calculator is illustrated by absolute and relative solvation FEP/MD of a set of ligands and absolute and relative binding FEP/MD of a set of ligands for T4-lysozyme in solution and the adenosine A 2A receptor in a membrane. The calculated free energy values are overall consistent with the experimental and published free energy results (within ~1 kcal/mol). We hope that Free Energy Calculator is useful to carry out high-throughput FEP/MD simulations in the field of biomolecular sciences and drug discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Birth of the Hydrated Electron via Charge-Transfer-to-Solvent Excitation of Aqueous Iodide

A primary means to generate hydrated electrons in laboratory experiments is excitation to the charge-transfer-to-solvent (CTTS) state of a solute such as I – (aq), but this initial step in the genesis of e – (aq) has never been simulated directly using ab initio molecular dynamics. Here, we report the first such simulations, combining ground- and excited-state simulations of I – (aq) with a detailed analysis of fluctuations in the Coulomb potential experienced by the nascent solvated electron. What emerges is a two-step picture of the evolution of e – (aq) starting from the CTTS state: I – (aq) + hν → I –* (aq) → I • (aq) + e – (aq). Notably, the equilibrated ground state of e – (aq) evolves from I –* (aq) without any nonadiabatic transitions, simply as a result of solvent reorganization. The methodology used here should be applicable to other photochemical electron transfer processes in solution, an important class of problems directly relevant to photocatalysis and energy transfer.

Carter-Fenk, Kevin↗
DOE OSTI2022

Understanding Hydrogenation Chemistry at MgB 2 Reactive Edges from Ab Initio Molecular Dynamics

Solid-state hydrogen storage materials often operate via transient, multistep chemical reactions at complex interfaces that are difficult to capture. Here, we use direct ab initio molecular dynamics simulations at accelerated temperatures and hydrogen pressures to probe the hydrogenation chemistry of the candidate material MgB 2 without a priori assumption of reaction pathways. Focusing on highly reactive ($10\overline{1}0$) edge planes where initial hydrogen attack is likely to occur, we track mechanistic steps toward the formation of hydrogen-saturated BH 4 – units and key chemical intermediates, involving H 2 dissociation, generation of functionalities and molecular complexes containing BH 2 and BH 3 motifs, and B–B bond breaking. Further, the genesis of higher-order boron clustering is also observed. Different charge states and chemical environments at the B-rich and Mg-rich edge planes are found to produce different chemical pathways and preferred speciation, with implications for overall hydrogenation kinetics. The reaction processes rely on B–H bond polarization and fluctuations between ionic and covalent character, which are critically enabled by the presence of Mg 2+ cations in the nearby interphase region. Our results provide guidance for devising kinetic improvement strategies for MgB 2 -based hydrogen storage materials, while also providing a template for exploring chemical pathways in other solid-state energy storage reactions.

08 HYDROGEN↗