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At least 433 records · Page 24

Monte-Carlo Simulation of Radiation Track Structure and Calculation of Dose Deposition in Nanovolumes

INTRODUCTION: The radiation track structure is of crucial importance to understand radiation damage to molecules and subsequent biological effects. Of a particular importance in radiobiology is the induction of double-strand breaks (DSBs) by ionizing radiation, which are caused by clusters of lesions in DNA, and oxidative damage to cellular constituents leading to aberrant signaling cascades. DSB can be visualized within cell nuclei with gamma-H2AX experiments. MATERIAL AND METHODS: In DSB induction models, the DSB probability is usually calculated by the local dose obtained from a radial dose profile of HZE tracks. In this work, the local dose imparted by HZE ions is calculated directly from the 3D Monte-Carlo simulation code RITRACKS. A cubic volume of 5 micron edge (Figure 1) is irradiated by a (Fe26+)-56 ion of 1 GeV/amu (LET approx.150 keV/micron) and by a fluence of 450 H+ ions, 300 MeV/amu (LET approx. 0.3 keV/micron). In both cases, the dose deposited in the volume is approx.1 Gy. The dose is then calculated into each 3D pixels (voxels) of 20 nm edge and visualized in 3D. RESULTS AND DISCUSSION: The dose is deposited uniformly in the volume by the H+ ions. The voxels which receive a high dose (orange) corresponds to electron track ends. The dose is deposited differently by the 56Fe26+ ion. Very high dose (red) is deposited in voxels with direct ion traversal. Voxels with electron track ends (orange) are also found distributed around the path of the track. In both cases, the appearance of the dose distribution looks very similar to DSBs seen in gammaH2AX experiments, particularly when the visualization threshold is applied. CONCLUSION: The refinement of the dose calculation to the nanometer scale has revealed important differences in the energy deposition between high- and low-LET ions. Voxels of very high dose are only found in the path of high-LET ions. Interestingly, experiments have shown that DSB induced by high-LET radiation are more difficult to repair. Therefore, this new approach may be useful to understand the nature of DSB and oxidative damage induced by ionizing radiation.

Plante, I.↗

Conical Intersection Passages of Molecules Probed by X-ray Diffraction and Stimulated Raman Spectroscopy

Conical intersections (CoIns) play an important role in ultrafast relaxation channels. Their monitoring remains a formidable experimental challenge. We theoretically compare the probing of the S 2 → S 1 CoIn passage in 4-thiouracil by monitoring its vibronic coherences, using off-resonant X-ray-stimulated Raman spectroscopy (TRUECARS) and time resolved X-ray diffraction (TRXD). The quantum nuclear wavepacket (WP) dynamics provides an accurate picture of the photoinduced dynamics. Upon photoexcitation, the WP oscillates among the Franck–Condon point, the S2 minimum, and the CoIn with a 70 fs period. A vibronic coherence first emerges at 20 fs and can be observed until the S 2 state is fully depopulated. The distribution of the vibronic frequencies involved in the coherence is recorded by the TRUECARS spectrogram. Here, the TRXD signal provides spatial images of electron densities associated with the CoIn. In combination, the two signals provide a complementary picture of the nonadiabatic passage, which helps in the study of the underlying photophysics in thiobases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantitative evaluation of perfluorinated alkanethiol molecular order on gold surfaces

Self-assembled monolayers (SAMs) of perfluoroalkanethiols [CF3(CF2)xCH2CH2SH (x = 3, 5, 7, and 9)] on gold were characterized by x-ray photoelectron spectroscopy (XPS), near edge x-ray absorption fine structure (NEXAFS), and static time-of-flight secondary ion mass spectrometry (ToF-SIMS). Perfluoroalkanethiols of several chain lengths were synthesized using a known hydride reduction method for transforming commercially available perfluoroalkyliodides to corresponding perfluoroalkanethiols. This strategy provides improved product yields compared to other known routes based on hydrolysis from the common thioacetyl perfluoroalkyl intermediate. Angle-dependent XPS analysis revealed that CF3(CF2)xCH2CH2SH (x = 5, 7, and 9; F6, F8, and F10, respectively) SAMs on gold exhibited significant enrichment of the terminal CF3 group at the outer monolayer surface with the sulfur present as a metal-bound thiolate located at the monolayer-gold interface. XPS of the CF3(CF2)3CH2CH2SH (F4) monolayer revealed a thin film with a significant (>50%) amount of hydrocarbon contamination consistent with poorly organized monolayers, while the longest thiol (F10) showed XPS signals attributed to substantial ordering and anisotropy. ToF-SIMS spectra from all four SAMs contained molecular ions representative of the particular perfluorinated thiol used to prepare the monolayer. NEXAFS methods were used to determine degrees of ordering and average tilt for molecules comprising monolayers. The SAMs prepared from the longest (F10) thiols exhibited the highest degree of ordering with the molecular axis nearly perpendicular to the gold surface. The degree of ordering decreased significantly with decreasing length of the perfluorocarbon tail.

Biophysics↗

The use of the transmission windows of the Fabry-Perot interferometer in the detection of Raman scattered radiation from atmospheric gases.

Demonstration that the use of the Fabry-Perot interferometer as a filter with transmission windows occurring at regular intervals in wave numbers provides a highly sensitive method for detection of atmospheric gases using their rotational Raman spectra excited by a suitable laser. Some of the operating advantages include signal gains of several orders of magnitude, a simple direct interpretation of the results in terms of the density and types of the gaseous constituents, size and weight reductions from conventional apparatus, ease of operation, and relative freedom from interference from other molecules in the scattering volume. This method is compared with the techniques that have been discussed in the literature by other workers in the field.

Smith, W. H.↗

FOXM1-activated SIRT4 inhibits NF-κB signaling and NLRP3 inflammasome to alleviate kidney injury and podocyte pyroptosis in diabetic nephropathy

Highlights: • FOXM1 is downregulated in kidney tissues of patients with DN. • Overexpression of FOXM1 alleviates kidney injury in DN modeled mice. • Overexpression of FOXM1 reduces pyroptosis of HG-treated podocytes. • FOXM1 activates SIRT4 to inhibit the NFκB pathway and the NLRP3 inflammasome. • Downregulation of SIRT4 blocks the protective roles of FOXM1 in podocytes and mice. Forkhead box M1 (FOXM1) has been reported to play a protective role against acute kidney injury by driving tubular regeneration. This study aims to probe the function of FOXM1 in diabetic nephropathy (DN) and the molecules involved. FOXM1 was poorly expressed in DN-diseased kidney tissues. A murine model of DN was established, and podocytes cells (MPC5) were treated with high-glucose (HG) for in vitro studies. FOXM1 overexpression improved kidney function and reduced pathological changes in mice, and it increased the expression of the podocyte marker Nephrin in kidney tissues. In vitro, FOXM1 increased viability and reduced pyroptosis of the HG-treated MPC5 cells, and it elevated the expression of the podocyte marker Nephrin whereas reduced the expression of pyroptosis-related NLRP3 inflammasome and cleaved caspase 1. FOXM1 bound to the promoter of sirtuin 4 (SIRT4) to induce transcriptional activation. Downregulation of SIRT4 blocked the protective roles of FOXM1 both in vivo and in vitro. Phosphorylation of nuclear factor-kappa B (NF-κB) in HG-treated cells was suppressed by FOXM1 but restored after SIRT4 inhibition. In conclusion, this study suggested that FOXM1 transcriptionally activates SIRT4 and inhibits NF-κB signaling and the NLRP3 inflammasome to alleviate kidney injury and podocyte pyroptosis in DN.

60 APPLIED LIFE SCIENCES↗

Interleukin-35 inhibits lipopolysaccharide-induced endothelial cell activation by downregulating inflammation and apoptosis

Inflammation is an essential factor contributing to sepsis-induced endothelial cell (EC) activation. Interleukin-35 (IL-35) is an anti-inflammatory/immunosuppressive cytokine that exerts protective effects on many inflammatory diseases. In this study, we investigated the effects of IL-35 on lipopolysaccharide (LPS)-induced EC activation and the potential underlying mechanism. Human umbilical vein endothelial cells (HUVECs) were incubated with LPS (1 μg/ml) for 24 h and then cocultured with different concentrations (0, 1, 10, or 100 ng/ml) of recombinant human IL-35 (rhIL-35) for 12 h. Flow cytometry analysis revealed that IL-35 inhibited LPS-induced HUVEC apoptosis in a dose-dependent manner. RT-qPCR and Western blot analyses showed significantly higher mRNA and protein levels of the adhesion molecules intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1) and the inflammatory factors IL-6 and IL-8 in the LPS group than in the control group. These changes were alleviated by IL-35 treatment, suggesting that IL-35 protects ECs by downregulating inflammation. Furthermore, IL-35 induced signal transducer and activator of transcription 1 (STAT1) and STAT4 activation and promoted their interaction. Blocking STAT1 or STAT4 expression by fludarabine (STAT1 inhibitor) treatment or siRNA-STAT4-interfering fragment transfection inhibited the protective effect of IL-35 on ECs. Moreover, we observed a similar protective effect of IL-35 treatment on ECs in a mouse sepsis model induced by intraperitoneal LPS injection. This study indicated that IL-35 exerts anti-inflammatory and antiapoptotic effects on LPS-induced EC activation by activating the STAT1 and STAT4 signaling pathways.

60 APPLIED LIFE SCIENCES↗

Resonant Stimulated X-ray Raman Spectroscopy of Mixed-Valence Manganese Complexes

Resonant stimulated X-ray Raman spectroscopy of the bimetallic [Mn III Mn IV (μ-O) 2 (μ-OAC)(tacn) 2 ] 2+ manganese complex is investigated in a simulation study. A pump–probe sequence of resonant X-ray Raman excitations is employed to generate and monitor valence-electron wave packets at selected regions in the molecule, by exploiting element specific core-excited states. A two-color protocol is presented, with pump and probe pulses tuned to the Mn and N K-edges. A natural orbital decomposition allows the visualization of the electron dynamics underlying the signal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A red-emitting carborhodamine for monitoring and measuring membrane potential

Biological membrane potentials, or voltages, are a central facet of cellular life. Optical methods to visualize cellular membrane voltages with fluorescent indicators are an attractive complement to traditional electrode-based approaches, since imaging methods can be high throughput, less invasive, and provide more spatial resolution than electrodes. Recently developed fluorescent indicators for voltage largely report changes in membrane voltage by monitoring voltage-dependent fluctuations in fluorescence intensity. However, it would be useful to be able to not only monitor changes but also measure values of membrane potentials. This study discloses a fluorescent indicator which can address both. We describe the synthesis of a sulfonated tetramethyl carborhodamine fluorophore. When this carborhodamine is conjugated with an electron-rich, methoxy (-OMe) containing phenylenevinylene molecular wire, the resulting molecule, CRhOMe, is a voltage-sensitive fluorophore with red/far-red fluorescence. Using CRhOMe, changes in cellular membrane potential can be read out using fluorescence intensity or lifetime. In fluorescence intensity mode, CRhOMe tracks fast-spiking neuronal action potentials (APs) with greater signal-to-noise than state-of-the-art BeRST 1 (another voltage-sensitive fluorophore). CRhOMe can also measure values of membrane potential. The fluorescence lifetime of CRhOMe follows a single exponential decay, substantially improving the quantification of membrane potential values using fluorescence lifetime imaging microscopy (FLIM). The combination of red-shifted excitation and emission, mono-exponential decay, and high voltage sensitivity enable fast FLIM recording of APs in cardiomyocytes. The ability to both monitor and measure membrane potentials with red light using CRhOMe makes it an important approach for studying biological voltages.

59 BASIC BIOLOGICAL SCIENCES↗

Development of a modulator to measure water vapor selectively in a gaseous mixture

Selective thermal modulation (STM) is a technique which produces a concentration-dependent pulse by selectively modulating a sample in a gas stream. Several types of modulation techniques, both chemical and physical, using adsorption, decomposition, and catalytic and mechanical methods have been developed for use with multiplex gas chromatography. Two of these applications involve selective modulation of the components present in the sample gas stream. The selective modulation of the concentration of specific sample molecules or classes of molecules provides additional analytical selectivity which can lead to selective detection. For some specific applications, the column may even be eliminated. Chemical modulation by absorption of a substance from the sample stream by a stationary phase will also produce a change in the signal intensity. Removal of a substance from the sample stream results in a signal containing a vacancy peak. In the work reported here, a selective thermal modulation technique has been developed as a method for determination of water vapor for possible use in Mars' atmosphere.

NASA Center ARC↗

Characterization of Titan Entry Radiative Heating in the Low Density Electric Arc Shock Tube

Prediction of aftbody radiative heating for Dragonfly’s entry at Titan requires accurate models to inform the design of its thermal protection systems. Previously reported investigations of shock layer aftbody radiation in the Electric Arc Shock Tube (EAST) at NASA Ames Research Center focused on the lower altitude/higher density part of the trajectory. This paper presents the first optical emission spectroscopy measurements of an ongoing test series in the new aluminum Low Density Shock Tube (LDST), recently installed at EAST, focusing on the radiative heating characterization through the higher altitude portion of Dragonfly’s entry path. Experimental data collected at a fill pressure of 0.1 Torr and shock velocities between 5.2 and 6.2 km/s show favorable agreement to similar conditions previously tested in the 4" High-Velocity Shock Tube, as well as improvements in the signal to noise ratio and available test time. Simulations employing DPLR and NEQAIR underpredict the experimental radiance, with increasing discrepancy from the NIR towards the UV wavelength range, thus motivating further efforts in improving the current non-Boltzmann model for the CN molecule.

A Fagnani↗

Experimental upper bounds for resonance-enhanced entangled two-photon absorption cross section of indocyanine green

Resonant intermediate states have been proposed to increase the efficiency of entangled two-photon absorption (ETPA). Although resonance-enhanced ETPA (r-ETPA) has been demonstrated in atomic systems using bright squeezed vacuum, it has not been studied in organic molecules. We investigate for the first time r-ETPA in an organic molecular dye, indocyanine green (ICG), when excited by broadband entangled photons in near-IR. Similar to many reported virtual state mediated ETPA (v-ETPA) measurements, no r-ETPA signals are measured, with an experimental upper bound for the cross section placed at 6(±2) × 10 −23 cm 2 . In addition, the classical resonance-enhanced two-photon absorption (r-TPA) cross section of ICG at 800 nm is measured for the first time to be 20(±13) GM, where 1 GM equals 10 −50 cm 4 s, suggesting that having a resonant intermediate state does not significantly enhance two-photon processes in ICG. Furthermore, the spectrotemporally resolved emission signatures of ICG excited by entangled photons are also presented to support this conclusion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultrafast optical modulation of vibrational strong coupling in ReCl(CO) 3 (2,2-bipyridine)

Polaritons – hybrid light-matter states formed from the strong coupling of a bright molecular transition with a confined photonic mode – may offer new opportunities for optical control of molecular behavior. Vibrational strong coupling (VSC) has been reported to impact ground-state chemical reactivity, but its influence on electronic excited-state dynamics remains unexplored. Here, we take a first step towards excited-state VSC by demonstrating optical modulation of the ReCl(CO) 3 (bpy), (bpy = 2,2-bipyridine) complex under VSC using femtosecond ultraviolet (UV)-pump/infrared (IR)-probe spectroscopy. We establish ground-state VSC of ReCl(CO) 3 (bpy) in a microfluidic Fabry-Pérot cavity equipped with indium tin oxide (ITO)-coated mirrors. ITO is effectively dichroic as it is reflective in the IR and transmissive in the UV-visible and therefore minimizes optical interference. Excitation with UV pump light drives ReCl(CO) 3 (bpy) into a manifold of electronic excited states that subsequently undergo non-radiative relaxation dynamics. We probe the transient response of the strongly-coupled system in the mid-IR, observing both Rabi contraction and cavity-filtered excited-state absorption signatures. We reconstruct the intrinsic response of intracavity molecules from the transient cavity transmission spectra to enable quantitative comparison with extracavity control experiments. We report no changes in the excited-state dynamics of ReCl(CO) 3 (bpy) under ground-state VSC. However, we do observe significant amplification of transient vibrational signals due to classical cavity-enhanced optical effects. This effort lays the groundwork to pursue direct excited-state VSC aimed at modulating photochemical reactivity.

cavity-enhanced spectroscopy↗

Copernicus observational searches for OH and H2O in diffuse clouds

An intensive search for OH and H2O in the directions of sigma Sco, alpha Cam, and micron Per was undertaken with the Copernicus satellite. Multiple scans were carried out over the wavelength region for the expected absorption features due to the OH D-X and H2O C-X transitions. The feature due to OH was detected marginally towards sigma Sco, and only an upper limit can be given towards alpha Cam. H2O was not detected in any of the stars at the signal level accumulated. The OH abundance towards sigma Sco and the respective lower limits for the OH/H2O ratios are discussed with regard to the extant models for the steady state abundances of OH and H2O, and shown not to be inconsistent with ion-molecule schemes.

Smith, W. H.↗

Microwave, Millimeter, Submillimeter, and Far Infrared Spectral Databases

The spectrum of most known astrophysical molecules is derived from transitions between a few hundred to a few hundred thousand energy levels populated at room temperature. In the microwave and millimeter wave regions. spectroscopy is almost always performed with traditional microwave techniques. In the submillimeter and far infrared microwave technique becomes progressively more technologically challenging and infrared techniques become more widely employed as the wavelength gets shorter. Infrared techniques are typically one to two orders of magnitude less precise but they do generate all the strong features in the spectrum. With microwave technique, it is generally impossible and rarely necessary to measure every single transition of a molecular species, so careful fitting of quantum mechanical Hamiltonians to the transitions measured are required to produce the complete spectral picture of the molecule required by astronomers. The fitting process produces the most precise data possible and is required in the interpret heterodyne observations. The drawback of traditional microwave technique is that precise knowledge of the band origins of low lying excited states is rarely gained. The fitting of data interpolates well for the range of quantum numbers where there is laboratory data, but extrapolation is almost never precise. The majority of high resolution spectroscopic data is millimeter or longer in wavelength and a very limited number of molecules have ever been studied with microwave techniques at wavelengths shorter than 0.3 millimeters. The situation with infrared technique is similarly dire in the submillimeter and far infrared because the black body sources used are competing with a very significant thermal background making the signal to noise poor. Regardless of the technique used the data must be archived in a way useful for the interpretation of observations.

Pearson, J. C.↗

Enzymatic Activity Detection via Electrochemistry for Enceladus

Electrochemical detection of biological molecules is a pertinent topic and application in many fields such as medicine, environmental spills, and life detection in space. Proteases, a class of molecules of interest in the search for life, catalyze the hydrolysis of peptides. Trypsin, a specific protease, was chosen to investigate an optimized enzyme detection system using electrochemistry. This study aims at providing the ideal functionalization of an electrode that can reliably detect a signal indicative of an enzymatic reaction from an Enceladus sample.

astrobiolog↗

Exploring Local Vibrational Structure in Protein-Bound Chlorophyll a: Isotope-Enrichment Experiments and Electrostatic Analysis

Local chlorophyll (Chl) vibrations play an essential role in biological photosynthesis by facilitating rapid energy transfer between pigments. In research studies, they also provide a useful spectroscopic probe of the local protein environment that surrounds each pigment. However, measuring the complete vibrational absorption spectrum of a protein-bound Chl molecule is much more difficult than, for example, Chl in neat solvent due to overlap with protein vibrations that typically drown out Chl vibrational features. Resonance Raman and fluorescence spectroscopies provide a way around this problem for Franck–Condon active vibrations, but these often rely on cryogenic measurement conditions and fail to capture vibrational signatures from, e.g., ester-group vibrations that lack coupling to a convenient electronic transition. In the present contribution, we use 13 C-enrichment of the protein backbone to shift protein background signals to lower frequency, providing a largely clean spectral window in which to study local Chl a C═O stretch modes. A room-temperature absorption spectrum for Chl a in the water-soluble chlorophyll protein (WSCP) of Lepidium virginicum is thus extracted as a difference between protein-plus-pigment and protein-only vibrational spectra. Excellent agreement in the molecular fingerprint region with the vibrational spectrum of Chl a in organic solvents confirms that the resulting spectrum represents the response of the protein-bound Chl a molecule. Furthermore, the ester group resonance is observed to shift in response to the S53P mutation that eliminates a 17 3 ester group hydrogen bond from the protein environment. Finally, we analyze these experimental results using MD-based electrostatic analysis, finding that electric-field mapping at the C atom of the ester group provides a satisfactory explanation for the observed frequency shifts between organic solvent and protein environment. MD analysis further suggests that a red-shifted ester peak observed experimentally for the S53P mutant results from solvation of the 17 3 Chl ester group due increase water penetration into the Chl-binding pocket relative to wild-type WSCP. Here, we anticipate that these results will prove useful both for benchmarking future simulation work and as a reference for interpreting Chl vibrational spectra as a probe of pigment–protein interactions.

14 SOLAR ENERGY↗

Hydration and Restructuring of Polar Polymer Interfaces: Implications in Antifouling and Responsive Materials

Manipulating polymer interfaces is crucial for understanding how structure influences function in applications spanning biofouling prevention to energy storage. Moreover, observing how polymers adapt their microscopic structure to changes in their local environment can reveal essential properties that govern their performance in such applications, providing key insights into how to design more effective interfaces. Here, in this study, a series of “grafting-from” polymer brushes with side chains varying in charge, are probed by sum frequency generation (SFG) and modeled using all-atom molecular dynamics (MD) simulations to elucidate how chemical makeup and charge mediate interfacial restructuring in dry versus hydrated states. Results show that charge, in progressing from nonpolar to cationic to zwitterionic, results in dramatic changes in interfacial structure and overall hydration. While net neutral systems, regardless of bulk phase polarity, show minimal interfacial water structuring, the cationic species exhibits strong bulk water signals from the surface potential. Meanwhile, the polymer brushes themselves restructure in water differently independent of charge, impacting the functional groups that are presented to the aqueous phase. Nonpolar and cationic species for instance undergo a change in alkyl group orientations to accommodate hydrating water molecules, whereas the zwitterionic polymer becomes completely disordered in water. Overall, the structure-based behavior trends presented herein have implications in antifouling applications and responsive material interfaces.

biointerface↗

Applying Crystallography and 19 F NMR to investigate dynamics and partner protein interactions in a long chain Flavodoxin

Flavodoxin (Fld) is a small FMN containing protein that is involved in single electron transfer. The long‐chain flavodoxin in Rhodopseudomonas palustris bacteria replaces ferredoxin as a low‐potential electron carrier when iron is scarce. Thus it is proposed to interact with the bifurcating electron transfer flavoprotein (ETF) that yields low‐potential electrons. A surface loop on Fld interacts with another of Fld's partner proteins, so we hypothesize that it also mediates Fld's interaction with ETF. To monitor interactions with ETF directly and investigate dynamics in this loop, we are using 19 F NMR in solution. 19 F is hyperresponsive to changes in its chemical environment with a chemical shift range of >300 ppm. To provide a static reference point and assess structural heterogeneity, we are also exploiting X‐ray crystallography. In this study we selectively fluorinated the five tyrosine residues in Fld. We obtained resonance assignments from 19 F spectra of Fld variants in which individual tyrosine residues have been replaced. We obtain well resolved signals for each residue, but the resonances' linewidths indicate dynamics that affects some resonances more than others. Y90 residue displays two resonances demonstrating two different conformations that interconvert slowly on an NMR time scale. Meanwhile the crystal structure solved at 2.1Å resolution reveals two molecules per asymmetric unit providing two perspectives on the details of the structure. The crystal symmetry is monoclinic in contrast to most of the other Flds, which are orthorhombic. Interestingly, the long loop bearing Y121 and Y123 is not well resolved in chain B of the crystal structure, and the NMR line of Y123 is exceptionally broad, both indicating that the loop is dynamic and capable of altering its conformation to accomodate binding to a partner protein. Future directions include monitoring the changes in the 19 F NMR of the Fld when titrated with the partner protein, temperature dependence of the NMR spectrum and relaxation studies to evaluate time scales of motions.

Khan, Sharique↗