Theoretical modeling of the terahertz spectrum of l-tyrosine leads to experimental verification of previously unobserved vibrational mode.

We have calculated the theoretical terahertz spectrum of the amino acid l-tyrosine using density functional theory (DFT). We tried two electron density functionals, Perdew-Burke-Ernzerhof (PBE) and PBE-d3. PBE-d3 includes dispersion corrections to build in van der Waals interactions, which play a role in intermolecular bonding. Both DFT models predicted a low-frequency mode that has not been previously reported. We designed an experiment to search for this mode. Using a deliberately thick sample, intense synchrotron radiation, low temperatures, and temperature variation has enabled us to observe a new resonance at 1.79 ±0.01 THz. While the PBE and PBE-d3 spectra are similar and both match the low-energy experimental data, overall the PBE-d3 appears to be slightly superior. Further refinement still of the functional may lead to even better agreement with experiment above 2.4 THz.

Determination of Vibrational Modes of l-Alanine Single Crystals by a Combination of Terahertz Spectroscopy Measurements and Density Functional Calculations.

Density-functional theory may be used to predict both the frequency and the dipole moment of the fundamental oscillations of molecular crystals. Suitably polarized photons at those frequencies excite such oscillations. Thus, in principle, terahertz spectroscopy may confirm the calculated fundamental modes of amino acids. However, reports to date have multiple shortcomings: (a) material of uncertain purity and morphology and diluted in a binder material is employed; (b) consequently, vibrations along all crystal axes are excited simultaneously; (c) data are restricted to room temperature, where resonances are broad and the background dominant; and (d) comparison with theory has been unsatisfactory (in part because the theory assumes zero temperature). Here, we overcome all four obstacles, in reporting detailed low-temperature polarized THz spectra of single-crystal l-alanine, assigning vibrational modes using density-functional theory, and comparing the calculated dipole moment vector direction to the electric field polarization of the measured spectra. Our direct and detailed comparison of theory with experiment corrects previous mode assignments for l-alanine, and reveals unreported modes, previously obscured by closely spaced spectral absorptions. The fundamental modes are thereby determined.

Terahertz tyrosine modes.

We have measured the terahertz spectrum of pure l-tyrosine at nineteen temperatures in the range 6K to 300K using a synchrotron as the source of radiation. By fitting the temperature dependence of the observed modes with a Bose-Einstein model, we determine unequivocal low-frequency modes of l-tyrosine at absolute zero temperature occur at 1.02 ± 0.01, 1.61 ± 0.01, 1.97 ± 0.01, and 2.19 ± 0.01THz. This determination is consistent with the more reliable of the earlier measurements. We conclude that many of the recently reported features in the terahertz spectrum of l-tyrosine are experimental artefacts.

High-quality, temperature-dependent terahertz spectroscopy of single crystalline L-alanine: Experiment and density-functional theory.

For the first time, the terahertz transmittance spectra of l-alanine have been measured using a single crystal. Measurements were obtained over a large temperature range (12-300 K) and revealed 18 absorptions between 20 and 250 cm-1. These modes were sharp and symmetric, a feature of single crystals and low temperatures. The spectra were directly compared to those of a powdered pellet sample. Raman spectroscopy and x-ray diffraction were used to confirm the sample's structure and purity. With increasing temperature, all modes exhibit spectral redshift, well described by a Bose-Einstein model, indicating the phonon origin of the absorptions. The exceptions are the 91 and 128 cm-1 modes. The former blueshifts. The latter initially blueshifts but transitions to redshifting. Both behaviors are anomalous. Density-functional theory modeling helped assign all the observed modes.

Temperature-dependent terahertz spectroscopy of l-phenylalanine.

Undiluted l-phenylalanine has been cooled to 6K and its transmission spectrum obtained under terahertz radiation from a synchrotron source. Three distinct absorption bands are evident: at 1.37, 2.14, and 2.32THz. Each of these tracks to lower frequency ("redshifts") as the temperature is increased from 6 to 250K. The observed shifts are in the range of 0.1-0.2THz. The form of the temperature dependence is well accounted for by a Bose-Einstein model, from which the zero-temperature frequency of each mode and the characteristic temperature of the associated phonon bath may be estimated. At 6K a fourth band is evident, at 2.65THz. However, the depth of this, touching the noise floor, coupled with the increasing opacity of the sample with temperature for frequencies beyond 2.5THz, makes it difficult to track. The frequencies of all four modes are in good accord with and thus confirm a previous calculation.

The 3, 5, 6, and 7 THz resonances of α-glycine.

Using an optically thin single crystal sample, mounted in a cryostat permitting cooling to 6 K, and a synchrotron as a bright light source, exceptionally well defined absorption spectra of well-characterised α-glycine have been obtained in the spectral range 2.5-7.5 THz (approximately 80-240 cm-1). Four separate resonances have been observed, respectively at 93, 152, 188, and 223 cm-1 at the lowest temperature. Each reduces in frequency (redshifts) as temperature increases. The origin of this observed behaviour is attributed to a phonon-mediated anharmonicity in the crystal potential.

Terahertz response of DL-alanine: experiment and theory.

The terahertz (THz) spectrum of dl-alanine has been measured for the first time at cryogenic temperatures and with a pure sample. Several sharp absorptions are observed, over a wide frequency range (0.8-4.8 THz), at 8 K. The sample structure and purity were confirmed with both Raman spectroscopy and X-ray diffraction. Temperature dependent spectra revealed redshifting, with increasing temperature, for all modes except one at 2.70 THz. This mode exhibits blueshifting until ≈120 K, where it starts to redshift. A Bose-Einstein distribution has been used to model the frequency shift with temperature for the four lowest energy modes. Strong correlations between the fits and data indicate that these modes are caused by phonon excitation in an anharmonic potential. Density functional theory has also been used to identify the origin of these low frequency modes. They are attributed to large scale molecular vibrations.

Anharmonicity-driven redshift and broadening of sharp terahertz features of α-glycine single crystal from 20 K to 300 K: Theory and experiment.

For the first time, large single crystals of the simplest amino acid, glycine, have been used to determine the temperature dependence of its terahertz spectrum. High-quality spectra with very sharp absorption features are observed at cryogenic temperatures. The α-glycine structure and the purity of the crystals were verified via Raman spectroscopy and X-ray diffraction. Spectral redshift with increasing temperature was observed for all absorption bands in the terahertz region (10-250 cm-1, or 1-8 THz) over the temperature range of 20-300 K. X-ray diffraction revealed expansion in all planes of the crystal lattice over the same temperature range. A Bose-Einstein distribution was used to model the frequency position shift of the two lowest-energy fundamental modes at 50 cm-1 and 69 cm-1. On this basis, we attribute the observed redshift and broadening with increasing temperature to the anharmonic potential associated with the phonon bath.

Superficial and Fundamental Correspondences in the Terahertz/IR (6-15 THz) Absorption Spectra of Aspirin and Benzoic Acid.

The terahertz absorption spectra of aspirin and benzoic acid have been measured in the range 200-500 cm-1 (6-15 THz). Density-functional theory (DFT) modeling has assigned fundamental vibrational modes to the observed absorption bands. Hydrogen bonds between the crystalline planes of aspirin resulted in better agreement between the experimental and modeled spectra than for benzoic acid. The similar structure of these two molecules suggests a similar absorption spectrum, which indeed was obtained experimentally. However, the detailed crystal structure and molecular differences result in some of the apparently common absorption bands being assigned to different vibrational modes through the DFT modeling. Thus, our study importantly reveals that even though crystalline forms of two similar molecules may have similar experimental terahertz spectra, the resemblance may be superficial rather than fundamental.

Imaging and the completion of the omics paradigm in breast cancer.

Within the field of oncology, "omics" strategies-genomics, transcriptomics, proteomics, metabolomics-have many potential applications and may significantly improve our understanding of the underlying processes of cancer development and progression. Omics strategies aim to develop meaningful imaging biomarkers for breast cancer (BC) by rapid assessment of large datasets with different biological information. In BC the paradigm of omics technologies has always favored the integration of multiple layers of omics data to achieve a complete portrait of BC. Advances in medical imaging technologies, image analysis, and the development of high-throughput methods that can extract and correlate multiple imaging parameters with "omics" data have ushered in a new direction in medical research. Radiogenomics is a novel omics strategy that aims to correlate imaging characteristics (i. e., the imaging phenotype) with underlying gene expression patterns, gene mutations, and other genome-related characteristics. Radiogenomics not only represents the evolution in the radiology-pathology correlation from the anatomical-histological level to the molecular level, but it is also a pivotal step in the omics paradigm in BC in order to fully characterize BC. Armed with modern analytical software tools, radiogenomics leads to new discoveries of quantitative and qualitative imaging biomarkers that offer hitherto unprecedented insights into the complex tumor biology and facilitate a deeper understanding of cancer development and progression. The field of radiogenomics in breast cancer is rapidly evolving, and results from previous studies are encouraging. It can be expected that radiogenomics will play an important role in the future and has the potential to revolutionize the diagnosis, treatment, and prognosis of BC patients. This article aims to give an overview of breast radiogenomics, its current role, future applications, and challenges.

Targeting PP2A and proteasome activity ameliorates features of allergic airway disease in mice.

BACKGROUND: Asthma is an allergic airway disease (AAD) caused by aberrant immune responses to allergens. Protein phosphatase-2A (PP2A) is an abundant serine/threonine phosphatase with anti-inflammatory activity. The ubiquitin proteasome system (UPS) controls many cellular processes, including the initiation of inflammatory responses by protein degradation. We assessed whether enhancing PP2A activity with fingolimod (FTY720) or 2-amino-4-(4-(heptyloxy) phenyl)-2-methylbutan-1-ol (AAL(S) ), or inhibiting proteasome activity with bortezomib (BORT), could suppress experimental AAD. METHODS: Acute AAD was induced in C57BL/6 mice by intraperitoneal sensitization with ovalbumin (OVA) in combination with intranasal (i.n) exposure to OVA. Chronic AAD was induced in mice with prolonged i.n exposure to crude house dust mite (HDM) extract. Mice were treated with vehicle, FTY720, AAL(S) , BORT or AAL(S) +BORT and hallmark features of AAD assessed. RESULTS: AAL(S) reduced the severity of acute AAD by suppressing tissue eosinophils and inflammation, mucus-secreting cell (MSC) numbers, type 2-associated cytokines (interleukin (IL)-33, thymic stromal lymphopoietin, IL-5 and IL-13), serum immunoglobulin (Ig)E and airway hyper-responsiveness (AHR). FTY720 only suppressed tissue inflammation and IgE. BORT reduced bronchoalveolar lavage fluid (BALF) and tissue eosinophils and inflammation, IL-5, IL-13 and AHR. Combined treatment with AAL(S) +BORT had complementary effects and suppressed BALF and tissue eosinophils and inflammation, MSC numbers, reduced the production of type 2 cytokines and AHR. AAL(S) , BORT and AAL(S) +BORT also reduced airway remodelling in chronic AAD. CONCLUSION: These findings highlight the potential of combination therapies that enhance PP2A and inhibit proteasome activity as novel therapeutic strategies for asthma.

Surface effects of vapour-liquid-solid driven Bi surface droplets formed during molecular-beam-epitaxy of GaAsBi.

Herein we investigate a (001)-oriented GaAs1-xBix/GaAs structure possessing Bi surface droplets capable of catalysing the formation of nanostructures during Bi-rich growth, through the vapour-liquid-solid mechanism. Specifically, self-aligned "nanotracks" are found to exist trailing the Bi droplets on the sample surface. Through cross-sectional high-resolution transmission electron microscopy the nanotracks are revealed to in fact be elevated above surface by the formation of a subsurface planar nanowire, a structure initiated mid-way through the molecular-beam-epitaxy growth and embedded into the epilayer, via epitaxial overgrowth. Electron microscopy studies also yield the morphological, structural, and chemical properties of the nanostructures. Through a combination of Bi determination methods the compositional profile of the film is shown to be graded and inhomogeneous. Furthermore, the coherent and pure zincblende phase property of the film is detailed. Optical characterisation of features on the sample surface is carried out using polarised micro-Raman and micro-photoluminescence spectroscopies. The important light producing properties of the surface nanostructures are investigated through pump intensity-dependent micro-PL measurements, whereby relatively large local inhomogeneities are revealed to exist on the epitaxial surface for important optical parameters. We conclude that such surface effects must be considered when designing and fabricating optical devices based on GaAsBi alloys.

A pathogenic role for tumor necrosis factor-related apoptosis-inducing ligand in chronic obstructive pulmonary disease.

Chronic obstructive pulmonary disease (COPD) is a life-threatening inflammatory respiratory disorder, often induced by cigarette smoke (CS) exposure. The development of effective therapies is impaired by a lack of understanding of the underlining mechanisms. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a cytokine with inflammatory and apoptotic properties. We interrogated a mouse model of CS-induced experimental COPD and human tissues to identify a novel role for TRAIL in COPD pathogenesis. CS exposure of wild-type mice increased TRAIL and its receptor messenger RNA (mRNA) expression and protein levels, as well as the number of TRAIL(+)CD11b(+) monocytes in the lung. TRAIL and its receptor mRNA were also increased in human COPD. CS-exposed TRAIL-deficient mice had decreased pulmonary inflammation, pro-inflammatory mediators, emphysema-like alveolar enlargement, and improved lung function. TRAIL-deficient mice also developed spontaneous small airway changes with increased epithelial cell thickness and collagen deposition, independent of CS exposure. Importantly, therapeutic neutralization of TRAIL, after the establishment of early-stage experimental COPD, reduced pulmonary inflammation, emphysema-like alveolar enlargement, and small airway changes. These data provide further evidence for TRAIL being a pivotal inflammatory factor in respiratory diseases, and the first preclinical evidence to suggest that therapeutic agents that target TRAIL may be effective in COPD therapy.

Mucosal production of uric acid by airway epithelial cells contributes to particulate matter-induced allergic sensitization.

Exposure to particulate matter (PM), a major component of air pollution, contributes to increased morbidity and mortality worldwide. PM induces innate immune responses and contributes to allergic sensitization, although the mechanisms governing this process remain unclear. Lung mucosal uric acid has also been linked to allergic sensitization. The links among PM exposure, uric acid, and allergic sensitization remain unexplored. We therefore investigated the mechanisms behind PM-induced allergic sensitization in the context of lung mucosal uric acid. PM10 and house dust mite exposure selectively induced lung mucosal uric acid production and secretion in vivo, which did not occur with other challenges (lipopolysaccharide, virus, bacteria, or inflammatory/fibrotic stimuli). PM10-induced uric acid mediates allergic sensitization and augments antigen-specific T-cell proliferation, which is inhibited by uricase. We then demonstrate that human airway epithelial cells secrete uric acid basally and after stimulation through a previously unidentified mucosal secretion system. Our work discovers a previously unknown mechanism of air pollution-induced, uric acid-mediated, allergic sensitization that may be important in the pathogenesis of asthma.

Mechanism of periodic height variations along self-aligned VLS-grown planar nanostructures.

In this study we report in-plane nanotracks produced by molecular-beam-epitaxy (MBE) exhibiting lateral self-assembly and unusual periodic and out-of-phase height variations across their growth axes. The nanotracks are synthesized using bismuth segregation on the GaAsBi epitaxial surface, which results in metallic liquid droplets capable of catalyzing GaAsBi nanotrack growth via the vapor-liquid-solid (VLS) mechanism. A detailed examination of the nanotrack morphologies is carried out employing a combination of scanning electron and atomic force microscopy and, based on the findings, a geometric model of nanotrack growth during MBE is developed. Our results indicate diffusion and shadowing effects play significant roles in defining the interesting nanotrack shape. The unique periodicity of our lateral nanotracks originates from a rotating nucleation "hot spot" at the edge of the liquid-solid interface, a feature caused by the relative periodic circling of the non-normal ion beam flux incident on the sample surface, inside the MBE chamber. We point out that such a concept is divergent from current models of crawling mode growth kinetics and conclude that these effects may be utilized in the design and assembly of planar nanostructures with controlled non-monotonous structure.

Tumor necrosis factor-related apoptosis-inducing ligand translates neonatal respiratory infection into chronic lung disease.

Respiratory infections in early life can lead to chronic respiratory disease. Chlamydia infections are common causes of respiratory disease, particularly pneumonia in neonates, and are linked to permanent reductions in pulmonary function and the induction of asthma. However, the immune responses that protect against early-life infection and the mechanisms that lead to chronic lung disease are incompletely understood. Here we identify novel roles for tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) in promoting Chlamydia respiratory infection-induced pathology in early life, and subsequent chronic lung disease. By infecting TRAIL-deficient neonatal mice and using neutralizing antibodies against this factor and its receptors in wild-type mice, we demonstrate that TRAIL is critical in promoting infection-induced histopathology, inflammation, and mucus hypersecretion, as well as subsequent alveolar enlargement and impaired lung function. This suggests that therapeutic agents that target TRAIL or its receptors may be effective treatments for early-life respiratory infections and associated chronic lung disease.

Collective librations of water molecules in the crystal lattice of rubidium bromide: experiment and simulation.

Terahertz spectroscopy of RbBr reveals four prominent absorption lines at room temperature and a further 15 lines at 10 K. Via density-functional-theory (DFT) numerical modelling using the PBE0 hybrid GGA functional, all the absorptions are identified as correlated librations of water molecules in the RbBr lattice. Each libration mode is a combination of rocking, wagging and twisting motions of the water molecules. The number of libration lines and numerical modelling show that the C2v symmetry of water in RbBr is broken. Our modelling shows that the distribution of libration amplitudes and phases for different water molecules in the RbBr unit cell varies greatly between the different modes. All librational lines red-shift with increasing temperature. The rate of change for most lines is in the range 60-90 MHz K(-1) (or (2-3) × 10(-3) cm(-1) K(-1)). Two lines shift more rapidly with temperature, at rates of 240 and 300 MHz K(-1) (or (8 and 10) × 10(-3) cm(-1) K(-1)), respectively. Furthermore, the temperature dependence of the linewidth distinguishes two groups of lines. For one group, with weak linear temperature dependence of linewidth, cubic anharmonic terms in the RbBr crystal field are significant. This group is mainly associated with fully symmetric correlated librations. For the second group, with strong non-linear temperature dependence of the linewidth, quartic anharmonic terms in the RbBr crystal field are significant. However, the distribution of libration amplitudes, as well as the type of libration modes, influence the temperature dependence of the red shift, the linewidth, and the intensity, as well. Our combined experimental and theoretical investigation confirms the necessity of obtaining low-temperature data to observe all the calculated modes; moreover, the richness of detail in the temperature dependence of the data invites further modelling spanning a range of temperatures.

Constitutive production of IL-13 promotes early-life Chlamydia respiratory infection and allergic airway disease.

Deleterious responses to pathogens during infancy may contribute to infection and associated asthma. Chlamydia respiratory infections in early life are common causes of pneumonia and lead to reduced lung function and asthma. We investigated the role of interleukin-13 (IL-13) in promoting early-life Chlamydia respiratory infection, infection-induced airway hyperresponsiveness (AHR), and severe allergic airway disease (AAD). Infected infant Il13(-/-) mice had reduced infection, inflammation, and mucus-secreting cell hyperplasia. Surprisingly, infection of wild-type (WT) mice did not increase IL-13 production but reduced IL-13Rα2 decoy receptor levels compared with sham-inoculated controls. Infection of WT but not Il13(-/-) mice induced persistent AHR. Infection and associated pathology were restored in infected Il13(-/-) mice by reconstitution with IL-13. Stat6(-/-) mice were also largely protected. Neutralization of IL-13 during infection prevented subsequent infection-induced severe AAD. Thus, early-life Chlamydia respiratory infection reduces IL-13Rα2 production, which may enhance the effects of constitutive IL-13 and promote more severe infection, persistent AHR, and AAD.

Effect of neonatal respiratory infection on adult BALB/c hippocampal glucocorticoid and mineralocorticoid receptors.

The current study investigated the effects of neonatal infection with Chlamydia muridarum bacteria on glucocorticoid (GR) and mineralocorticoid (MR) receptors in the adult mouse hippocampus. In male adults infected at birth, circulating corticosterone was significantly increased when compared to same sex controls; while neonatal infection resulted in female adults with significantly increased GR mRNA compared to same sex controls. When comparing males and females after neonatal infection, males had significantly less GR protein than females. Interestingly, after control treatment, males had significantly more GR mRNA, MR mRNA, and GR protein with significantly lower corticosterone than females. Neonatal respiratory infection significantly impacts adult hippocampal GR and MR, and circulating corticosterone in a sex-specific manner potentially altering stress responsivity.

Programming of the lung by early-life infection.

Many important human diseases, such as asthma, have their developmental origins in early life. Respiratory infections in particular may alter the course of asthma and may either protect against or promote the development of this disease. It is likely that the nature of the effects depends on the type and age of infection and is determined by the impact of infection on the immune and respiratory systems. Immunity in early life is plastic and can be moulded by antigen encounter, which may enhance or reinforce the asthmatic phenotype of early life, or induce protective responses. Chlamydial respiratory infections have specific effects and may increase asthma severity in early life by promoting systemic interleukin 13 responses and causing permanent changes in lung structure. Respiratory viral infections, such as those of respiratory syncytial virus and rhinovirus, promote pro-asthmatic responses in early life that contribute to the induction of asthma. By contrast, probiotics or infection or exposure to certain bacteria, such as Streptococcus pneumoniae, may have protective effects in asthma by increasing the numbers and activity of regulatory T cells. Here, we review the impact of infections on the developmental origins of asthma. Understanding these effects may lead to new therapeutic approaches for asthma that either target deleterious infections or utilize beneficial ones.