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At least 181 records · Page 10

Autocrine and paracrine interferon signalling as ‘ring vaccination’ and ‘contact tracing’ strategies to suppress virus infection in a host

The innate immune response, particularly the interferon response, represents a first line of defence against viral infections. The interferon molecules produced from infected cells act through autocrine and paracrine signalling to turn host cells into an antiviral state. Although the molecular mechanisms of IFN signalling have been well characterized, how the interferon response collectively contribute to the regulation of host cells to stop or suppress viral infection during early infection remain unclear. Here, we use mathematical models to delineate the roles of the autocrine and the paracrine signalling, and show that their impacts on viral spread are dependent on how infection proceeds. In particular, we found that when infection is well-mixed, the paracrine signalling is not as effective; by contrast, when infection spreads in a spatial manner, a likely scenario during initial infection in tissue, the paracrine signalling can impede the spread of infection by decreasing the number of susceptible cells close to the site of infection. Furthermore, we argue that the interferon response can be seen as a parallel to population-level epidemic prevention strategies such as ‘contact tracing’ or ‘ring vaccination’. Thus, our results here may have implications for the outbreak control at the population scale more broadly.

59 BASIC BIOLOGICAL SCIENCES↗

Difficulties in Laboratory Studies and Astronomical Observations of Organic Molecules: Hydroxyacetone and Lactic Acid

For the past 35 years, radio astronomy has revealed a rich organic chemistry in the interstellar gas, which is exceptionally complex towards active star-forming regions. New solar systems condense out of this gas and may influence the evolution of life on newly formed planets. Much of the biologically important functionality is present among the some 130 gas-phase molecules found to date, including alcohols, aldehydes, ketones, acids, amines, amides and even the simplest sugar - glycolaldehyde. Still, many unidentified interstellar radio signals remain, and their identification relies on further laboratory study. The molecules hydroxyacetone and lactic acid are relatively small organic molecules, but possess rather complex rotational spectra owing to their high asymmetry. Hydroxyacetone is particularly problematic because it possess a very low barrier to internal rotation, and exhibits strong coupling of the free-rotor states with the overall rotation of the molecule. As in the case of acetamide, a full decomposition method was employed to order the resultant eigenstates onto normal asymmetric top eigenvectors.

Apponi, A. J.↗

Synergistic Alignment of Low Aspect‐Ratio π‐Conjugated Molecules Enables Exceptional UV–vis–NIR Polarization Detection

Abstract Polarization detection enhances signal contrast and is widely utilized in diverse advanced applications. An ongoing challenge is the development of high‐performance polarization‐sensitive photodetectors based on optically anisotropic organic semiconductors, particularly in the near‐infrared (NIR) region. While uniaxially aligned π‐conjugated polymers with high aspect ratios exhibit strong linear dichroism and have shown promise, their limited NIR performance and heavy reliance on polymer material now represent critical limitations. Here, a breakthrough is reported in achieving giant linear dichroism and exceptional polarization detection with low aspect‐ratios (AR) non‐fullerene small‐molecule (NFSM) acceptors, extending polarization sensitivity from the UV–vis to the NIR range. An impressive dichroic ratio of 27.1 at 605 nm and 12.0 at 780 nm is demonstrated. The maximum polarization photocurrent ratio is 11.2 at 780 nm under parallel versus perpendicular polarized light. This unprecedented performance originates from synergistic molecular alignment, wherein NFSMs significantly enhance the uniaxial orientation of both the polymer matrix and the NFSMs themselves during self‐assembly and thermal annealing. Besides, such a linear‐polarization‐sensitive photodetectors (LPS‐PDs) are showcased in generating degree‐of‐linear‐polarization imaging. The work establishes NFSMs as a viable material system for next‐generation of organic LPS‐PDs and provides fundamental insights into structural origins of polarization sensitivity in low AR organic semiconductors.

Xue, Yingying↗

Prospects for Characterizing the Haziest Sub-Neptune Exoplanets with High-resolution Spectroscopy

Observations to characterize planets larger than Earth but smaller than Neptune have led to largely inconclusive interpretations at low spectral resolution due to hazes or clouds that obscure molecular features in their spectra. However, here we show that high-resolution spectroscopy (R ∼ 25,000–100,000) enables one to probe the regions in these atmospheres above the clouds where the cores of the strongest spectral lines are formed. We present models of transmission spectra for a suite of GJ 1214b–like planets with thick photochemical hazes covering 1–5 μm at a range of resolutions relevant to current and future ground-based spectrographs. Furthermore, we compare the utility of the cross-correlation function that is typically used with a more formal likelihood-based approach, finding that only the likelihood-based method is sensitive to the presence of haze opacity. We calculate the signal-to-noise ratio (S/N) of these spectra, including telluric contamination, Required to robustly detect a host of molecules such as CO, CO{sub 2}, H{sub 2}O, and CH{sub 4} and photochemical products like HCN as a function of wavelength range and spectral resolution. Spectra in the M band require the lowest S/N{sub res} to detect multiple molecules simultaneously. CH{sub 4} is only observable for the coolest models (T {sub eff} = 412 K) and only in the L band. We quantitatively assess how these requirements compare to what is achievable with current and future instruments, demonstrating that characterization of small cool worlds with ground-based high-resolution spectroscopy is well within reach.

79 ASTRONOMY AND ASTROPHYSICS↗

Carbon monoxide production in low energy oxygen ion bombardment of pyrolytic graphite and Kapton surfaces

The results of an investigtion of the interaction of low energy oxygen ions with pyrolytic graphite and Kapton surface are reported. CO molecules emitted from the surface as a result of the ion bombardment were detected by a mass spectrometer. Because the ion-induced signals were small compared to that arising from the CO background pressure in the vacuum system, the ion beam was modulated and the modulated component of the CO signal measured with a lock-in amplifier. The quantum yield (CO molecules emitted per incident oxygen ion) for graphite rose from 1.9 at 4.5 eV ion energy to 6.6 at 465 eV. Comparable yields were obtained for Kapton. The large size of the yields suggests contributions to the reaction process from the background O2 molecules in the vacuum system.

Horton, C. C.↗

Allosteric activation or inhibition of PI3Kγ mediated through conformational changes in the p110γ helical domain

PI3Kγ is a critical immune signaling enzyme activated downstream of diverse cell surface molecules, including Ras, PKCβ activated by the IgE receptor, and Gβγ subunits released from activated GPCRs. PI3Kγ can form two distinct complexes, with the p110γ catalytic subunit binding to either a p101 or p84 regulatory subunit, with these complexes being differentially activated by upstream stimuli. Here, using a combination of cryo electron microscopy, HDX-MS, and biochemical assays, we have identified novel roles of the helical domain of p110γ in regulating lipid kinase activity of distinct PI3Kγ complexes. We defined the molecular basis for how an allosteric inhibitory nanobody potently inhibits kinase activity through rigidifying the helical domain and regulatory motif of the kinase domain. The nanobody did not block either p110γ membrane recruitment or Ras/Gβγ binding, but instead decreased ATP turnover. We also identified that p110γ can be activated by dual PKCβ helical domain phosphorylation leading to partial unfolding of an N-terminal region of the helical domain. PKCβ phosphorylation is selective for p110γ-p84 compared to p110γ-p101, driven by differential dynamics of the helical domain of these different complexes. Nanobody binding prevented PKCβ-mediated phosphorylation. Overall, this work shows an unexpected allosteric regulatory role of the helical domain of p110γ that is distinct between p110γ-p84 and p110γ-p101 and reveals how this can be modulated by either phosphorylation or allosteric inhibitory binding partners. This opens possibilities of future allosteric inhibitor development for therapeutic intervention.

59 BASIC BIOLOGICAL SCIENCES↗

Free radical and overtone spectroscopy

In the fall of 1987 during a photoacoustic study of hydrogen peroxide's fourth vibrational overtone band, the remarkably clear and well resolved spectrum was observed. Its periodicity and K subband structure suggested that the spectrum was not of hydrogen peroxide but of a smaller near-prolate symmetric top molecule. Furthermore, the time dependent behavior of the signal indicated that chemical changes were taking place within the photoacoustic apparatus.

Reilly, James P.↗

Root gravitropism: an experimental tool to investigate basic cellular and molecular processes underlying mechanosensing and signal transmission in plants

The ability of plant organs to use gravity as a guide for growth, named gravitropism, has been recognized for over two centuries. This growth response to the environment contributes significantly to the upward growth of shoots and the downward growth of roots commonly observed throughout the plant kingdom. Root gravitropism has received a great deal of attention because there is a physical separation between the primary site for gravity sensing, located in the root cap, and the site of differential growth response, located in the elongation zones (EZs). Hence, this system allows identification and characterization of different phases of gravitropism, including gravity perception, signal transduction, signal transmission, and curvature response. Recent studies support some aspects of an old model for gravity sensing, which postulates that root-cap columellar amyloplasts constitute the susceptors for gravity perception. Such studies have also allowed the identification of several molecules that appear to function as second messengers in gravity signal transduction and of potential signal transducers. Auxin has been implicated as a probable component of the signal that carries the gravitropic information between the gravity-sensing cap and the gravity-responding EZs. This has allowed the identification and characterization of important molecular processes underlying auxin transport and response in plants. New molecular models can be elaborated to explain how the gravity signal transduction pathway might regulate the polarity of auxin transport in roots. Further studies are required to test these models, as well as to study the molecular mechanisms underlying a poorly characterized phase of gravitropism that is independent of an auxin gradient.

Non-NASA Center↗

Fast Airborne Aerosol Size and Chemistry Measurements with the High Resolution Aerosol Mass Spectrometer during the MILAGRO Campaign

The concentration, size, and composition of non-refractory submicron aerosol (NR-PM(sub l)) was measured over Mexico City and central Mexico with a High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) onboard the NSF/NCAR C-130 aircraft as part of the MILAGRO field campaign. This was the first aircraft deployment of the HR-ToF-AMS. During the campaign the instrument performed very well, and provided 12 s data. The aerosol mass from the AMS correlates strongly with other aerosol measurements on board the aircraft. Organic aerosol (OA) species dominate the NR-PM(sub l) mass. OA correlates strongly with CO and HCN indicating that pollution (mostly secondary OA, SOA) and biomass burning (BB) are the main OA sources. The OA to CO ratio indicates a typical value for aged air of around 80 microg/cubic m (STP) ppm(exp -1). This is within the range observed in outflow from the Northeastern US, which could be due to a compensating effect between higher BB but lower biogenic VOC emissions during this study. The O/C atomic ratio for OA is calculated from the HR mass spectra and shows a clear increase with photochemical age, as SOA forms rapidly and quickly overwhelms primary urban OA, consistent with Volkamer et al. (2006) and Kleinman et al. (2008). The stability of the OA/CO while O/C increases with photochemical age implies a net loss of carbon from the OA. BB OA is marked by signals at m/z 60 and 73, and also by a signal enhancement at large m/z indicative of larger molecules or more resistance to fragmentation. The main inorganic components show different spatial patterns and size distributions. Sulfate is regional in nature with clear volcanic and petrochemical/power plant sources, while the urban area is not a major regional source for this species. Nitrate is enhanced significantly in the urban area and immediate outflow, and is strongly correlated with CO indicating a strong urban source. The importance of nitrate decreases with distance from the city likely due to evaporation. BB does not appear to be a strong source of nitrate despite its high emissions of nitrogen oxides, presumably due to low ammonia emissions. NR-chloride often correlates with HCN indicating a fire source, although other sources likely contribute as well. This is the first aircraft study of the regional evolution of aerosol chemistry from a tropical megacity.

DeCarlo, P. F.↗

In search of cellular control: signal transduction in context

The field of molecular cell biology has experienced enormous advances over the last century by reducing the complexity of living cells into simpler molecular components and binding interactions that are amenable to rigorous biochemical analysis. However, as our tools become more powerful, there is a tendency to define mechanisms by what we can measure. The field is currently dominated by efforts to identify the key molecules and sequences that mediate the function of critical receptors, signal transducers, and molecular switches. Unfortunately, these conventional experimental approaches ignore the importance of supramolecular control mechanisms that play a critical role in cellular regulation. Thus, the significance of individual molecular constituents cannot be fully understood when studied in isolation because their function may vary depending on their context within the structural complexity of the living cell. These higher-order regulatory mechanisms are based on the cell's use of a form of solid-state biochemistry in which molecular components that mediate biochemical processing and signal transduction are immobilized on insoluble cytoskeletal scaffolds in the cytoplasm and nucleus. Key to the understanding of this form of cellular regulation is the realization that chemistry is structure and hence, recognition of the the importance of architecture and mechanics for signal integration and biochemical control. Recent work that has unified chemical and mechanical signaling pathways provides a glimpse of how this form of higher-order cellular control may function and where paths may lie in the future.

Non-NASA Center↗

Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.

59 BASIC BIOLOGICAL SCIENCES↗

Supramolecular Metal Halide Complexes for High-Temperature Nonlinear Optical Switches

Nonlinear optical (NLO) switching materials, which exhibit reversible intensity modulation in response to thermal stimuli, have found extensive applications across diverse fields, including sensing, photoelectronics, and photonic applications. While significant progress has been made in solid-state NLO switching materials, these materials typically showcase their highest NLO performance near room temperature. However, this performance drastically deteriorates upon heating, primarily due to the phase transition undergone by the materials from non-centrosymmetric to centrosymmetric phase. Here, we introduce a new class of NLO switching materials, solid-state supramolecular compounds 18-Crown-6 ether@Cu 2 Cl 4 ·4H 2 O (1·4H 2 O), exhibiting reversible and stable NLO switching when subjected to near-infrared (NIR) photoexcitation and/or thermal stimuli. The reversible crystal structure in response to external stimuli is attributed to the presence of a weakly coordinated bridging water molecule, facilitated by hydrogen bonding/chelation interactions between the metal halide and crown-ether supramolecules. We observed an exceptionally high second-harmonic generation (SHG) signal under continuous photoexcitation, even at temperatures exceeding 110°C. In addition, the bridging water molecules within the complex can be released and recaptured in a fully reversible manner, all without requiring excessive energy input. This feature allows for precise control of SHG signal activation and deactivation through structural transformations, resulting in a high-contrast off/on ratio, reaching values in the million-fold range.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Correlating transcription and protein expression profiles of immune biomarkers following lipopolysaccharide exposure in lung epithelial cells

Universal and early recognition of pathogens occurs through recognition of evolutionarily conserved pathogen associated molecular patterns (PAMPs) by innate immune receptors and the consequent secretion of cytokines and chemokines. The intrinsic complexity of innate immune signaling and associated signal transduction challenges our ability to obtain physiologically relevant, reproducible and accurate data from experimental systems. One of the reasons for the discrepancy in observed data is the choice of measurement strategy. Immune signaling is regulated by the interplay between pathogen-derived molecules with host cells resulting in cellular expression changes. However, these cellular processes are often studied by the independent assessment of either the transcriptome or the proteome. Correlation between transcription and protein analysis is lacking in a variety of studies. In order to methodically evaluate the correlation between transcription and protein expression profiles associated with innate immune signaling, we measured cytokine and chemokine levels following exposure of human cells to the PAMP lipopolysaccharide (LPS) from the Gram-negative pathogen Pseudomonas aeruginosa . Expression of 84 messenger RNA (mRNA) transcripts and 69 proteins, including 35 overlapping targets, were measured in human lung epithelial cells. We evaluated 50 biological replicates to determine reproducibility of outcomes. Following pairwise normalization, 16 mRNA transcripts and 6 proteins were significantly upregulated following LPS exposure, while only five (CCL2, CSF3, CXCL5, CXCL8/IL8, and IL6) were upregulated in both transcriptomic and proteomic analysis. This lack of correlation between transcription and protein expression data may contribute to the discrepancy in the immune profiles reported in various studies. The use of multiomic assessments to achieve a systems-level understanding of immune signaling processes can result in the identification of host biomarker profiles for a variety of infectious diseases and facilitate countermeasure design and development.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluation of upwelling infrared radiance from earth's atmosphere

Basic equations for calculating the upwelling atmospheric radiation are presented which account for various sources of radiation coming out at the top of the atmosphere. The theoretical formulation of the transmittance models (line-by-line and quasi-random band model) and the computational procedures used for the evaluation of the transmittance and radiance are discussed in detail. By employing the Lorentz line-by-line and quasi-random computer programs, model calculations were made to determine the upwelling radiance and signal change in the wave number interval of CO fundamental band. These results are useful in determining the effects of different interfering molecules, water vapor profiles, ground temperatures, and ground emittances on the upwelling radiance and signal change. This information is of vital importance in establishing the feasibility of measuring the concentrations of pollutants in the atmosphere from a gas filter correlation instrument flown on an aircraft or mounted on a satellite.

Gupta, S. K.↗

Dynamics of molecular associates in methanol/water mixtures

The dynamics of molecular associates in a methanol/water mixture was investigated using quasielastic neutron scattering. By measuring the signal from four methanol/water samples differing only by their isotopic composition, the relative motion of the water to methanol molecules, i.e. their mutual dynamics, was determined at the nanoscale. The thus obtained nanoscopic mutual diffusion coefficient signals a significantly slower process than the single particle diffusion of either methanol or water in the system as well as their macroscopic mutual diffusion. The data do not provide any indication of microsegregation in this preeminent alcohol/water mixture; however, they do indicate the existence of long lived but dynamic molecular associates of water and methanol molecules. Our analysis of the structural relaxation shows that the lifetime of molecular association through hydrogen bonding determines the fact that viscosity of the mixtures at intermediate concentrations is higher than that of both pure components.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Submillimetric Spectroscopic Observations of Volatiles in Comet C-2004 Q2 (Machholz)

Submillimeter spectroscopic observations of comets provide an important tool for understanding their chemical composition and enable a taxonomic classification. Aims. We aim to determine the production rates of several parent- and product volatiles and the C-12/C-13 isotopic carbon ratio in the long-period comet C/2004 Q2 (Machholz), which is likely to originate from the Oort Cloud. Methods. The line emission from several molecules in the coma was measured with high signal-to-noise ratio in January 2005 at heliocentric distance of 1.2 AU by means of high-resolution spectroscopic observations using the Submillimeter Telescope (SMT) at the Arizona Radio Observatory (ARO). Results. We have obtained production rates of several volatiles (CH3OH, HCN, H(sup 13)CN, HNC, H2CO, CO, and CS) by comparing the observed and simulated line-integrated intensities. We calculated the synthetic profiles using a radiative transfer code that includes collisions between neutrals and electrons, and the effects of radiative pumping of the fundamental vibrational levels by solar infrared radiation. Furthermore, multiline observations of the CH3OH J = 7-6 series allow us to estimate the rotational temperature using the rotation diagram technique. We find that the CH3OH population distribution of the levels sampled by these lines can be described by a rotational temperature of 40 +/- 3 K. Derived mixing ratios relative to hydrogen cyanide are CO/CH3OH/H2CO/CS/HNC/HC-13N/HCN= 30.9/24.6/4.8/0.57/0.031/0.013/1 assuming a pointing offset of 8" due to the uncertain ephemeris at the time of the observations and the telescope pointing error. Conclusions. The measured relative molecular abundances in C/2004 Q2 (Machholz) are between low- to typical values of those obtained in Oort Cloud comets, suggesting that it has visited the inner solar system previously and undergone thermal processing. The HNC/HCN abundance ratio of approx 3.1% is comparable to that found in other comets, accounting for the dependence on the heliocentric distance, and could possibly be explained by ion-molecule chemical processes in the low-temperature atmosphere. From a tentative HC-13N detection, the measured value of 97 +/- 30 for the HC-12N/HC-13N isotopologue pair is consistent with a telluric value. The outgassing variability observed in the HCN production rates over a period of two hours is consistent with the rotation of the nucleus derived using different observational techniques.

chemical composition↗

The contribution of Compton ionization to ultrafast x-ray scattering

We investigate the role of Compton ionization in ultrafast non-resonant x-ray scattering using a molecular model system, which includes the ionization continuum via an orthonormalized plane wave ansatz. Elastic and inelastic components of the scattering signal, as well as coherent-mixed scattering that arises from electron dynamics, are calculated. By virtue of a near-quantitative distinction between scattering related to electronic transitions into bound and continuum states, we demonstrate how Compton ionization contributes to the coherent-mixed component. Analogous to inelastic scattering, the contribution to the coherent-mixed signal is significant and particularly manifests at intermediate and high-momentum transfers. Strikingly, for molecules with inversion symmetry, the exclusion of bound or continuum transitions may lead to the prediction of spurious coherent-mixed signals. We conclude that qualitative and quantitative accuracies of predicted scattering signals on detectors without energy resolution require that elements of the two-electron density operator are used. This approach inherently accounts for all accessible electronic transitions, including ionization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Intramolecular carbon isotope signals reflect metabolite allocation in plants

Abstract Stable isotopes at natural abundance are key tools to study physiological processes occurring outside the temporal scope of manipulation and monitoring experiments. Whole-molecule carbon isotope ratios (13C/12C) enable assessments of plant carbon uptake yet conceal information about carbon allocation. Here, we identify an intramolecular 13C/12C signal at tree-ring glucose C-5 and C-6 and develop experimentally testable theories on its origin. More specifically, we assess the potential of processes within C3 metabolism for signal introduction based (inter alia) on constraints on signal propagation posed by metabolic networks. We propose that the intramolecular signal reports carbon allocation into major metabolic pathways in actively photosynthesizing leaf cells including the anaplerotic, shikimate, and non-mevalonate pathway. We support our theoretical framework by linking it to previously reported whole-molecule 13C/12C increases in cellulose of ozone-treated Betula pendula and a highly significant relationship between the intramolecular signal and tropospheric ozone concentration. Our theory postulates a pronounced preference for leaf cytosolic triose-phosphate isomerase to catalyse the forward reaction in vivo (dihydroxyacetone phosphate to glyceraldehyde 3-phosphate). In conclusion, intramolecular 13C/12C analysis resolves information about carbon uptake and allocation enabling more comprehensive assessments of carbon metabolism than whole-molecule 13C/12C analysis.

54 ENVIRONMENTAL SCIENCES↗