Time-resolved single-crystal X-ray crystallography

In this chapter the development of time-resolved crystallography is traced from its beginnings more than 30 years ago. The importance of being able to “watch” chemical processes as they occur rather than just being limited to three-dimensional pictures of the reactant and final product is emphasised, and time-resolved crystallography provides the opportunity to bring the dimension of time into the crystallographic experiment. The technique has evolved in time with developments in technology: synchrotron radiation, cryoscopic techniques, tuneable lasers, increased computing power and vastly improved X-ray detectors. The shorter the lifetime of the species being studied, the more complex is the experiment. The chapter focusses on the results of solid-state reactions that are activated by light, since this process does not require the addition of a reagent to the crystalline material and the single-crystalline nature of the solid may be preserved. Because of this photoactivation, time-resolved crystallography is often described as “photocrystallography”. The initial photocrystallographic studies were carried out on molecular complexes that either underwent irreversible photoactivated processes where the conversion took hours or days. Structural snapshots were taken during the process. Materials that achieved a metastable state under photoactivation and the excited (metastable) state had a long enough lifetime for the data from the crystal to be collected and the structure solved. For systems with shorter lifetimes, the first time-resolved results were obtained for macromolecular structures, where pulsed lasers were used to pump up the short lifetime excited state species and their structures were probed by using synchronised X-ray pulses from a high-intensity source. Developments in molecular crystallography soon followed, initially with monochromatic X-ray radiation, and pump-probe techniques were used to establish the structures of photoactivated molecules with lifetimes in the micro- to millisecond range. For molecules with even shorter lifetimes in the sub-microsecond range, Laue diffraction methods (rather than using monochromatic radiation) were employed to speed up the data collections and reduce crystal damage. Future developments in time-resolved crystallography are likely to involve the use of XFELs to complete “single-shot” time-resolved diffraction studies that are already proving successful in the macromolecular crystallographic field.</p

Influence of heterogeneous refractivity on optical wave propagation in coastal environments

Spatial variations of refractivity significantly dictate the characteristics of optical wave propagation through the atmosphere. Consequently, the ability to simulate such propagation is highly dependent upon the accurate characterization of refractivity along the propagation path. Unfortunately, the scarcity of high spatiotemporal resolution observational data has forced many past studies of optical wave propagation to assume horizontally homogeneous (HH) atmospheric conditions. However, the (adverse) impact of such an assumption has not been quantified in the literature. In this paper, we attempt to fill this void by utilizing a mesoscale modeling-based approach to explicitly simulate atmospheric refraction. We then compare the differences of the HH refractivity fields to the mesoscale model-derived refractivity fields by means of a realistic atmospheric event and through ray tracing simulations. In this study, we model a coastal low-level jet, a common coastal atmospheric phenomenon which is associated with heterogeneous thermal and refractivity fields. Observational data from a radiosonde and a radar wind profiler near the northeastern region of the United States are used for model validation. The observed characteristics of low-level jet (e.g., evolution, intensity, location) and associated temperature inversion are found to be reasonably well captured by the mesoscale model. The simulated nighttime refractivity gradient field manifests significant spatial heterogeneity; over land, the refractivity gradient is much stronger and amplified near the ground, whereas it becomes much weaker over the ocean. We quantify the effect of this heterogeneity on optical ray trajectories by simulating a suite of rays and documenting the variability of their altitudes at certain propagation ranges. It is found that the altitude of optical rays may vary tens of meters during a diurnal cycle, and at nighttime the rays may bend downward by more than 150 m at a range of 100 km. We run additional ray tracing simulations using refractivity profiles from a single location and assuming HH refractivity along the propagation path. It is observed that the HH approach yields instantaneous ray bending magnitudes up to 30 % less than the ray bending based on the refractivity simulated by the mesoscale model. At the same time, it is found that the mesoscale model-based refractivity fields may have uncertainty introduced by different factors associated with the model configuration. Of these factors, turbulence parameterization is explored in-depth and found to be responsible for more uncertainty than spatial grid resolution. To be more specific, different turbulence parameterizations are found to produce significantly varying temperature inversion parameters (e.g., height, magnitude), which are critical factors influencing ray trajectories. Collectively, these results highlight the potential advantages and disadvantages of utilizing a mesoscale model to simulate refractivity in coastal areas as opposed to assuming HH refractivity

The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region

We studied functional effect of rs12722489 single nucleotide polymorphism located in the first intron of human IL2RA gene on transcriptional regulation. This polymorphism is associated with multiple autoimmune conditions (rheumatoid arthritis, multiple sclerosis, Crohn's disease, and ulcerative colitis). Analysis in silico suggested significant difference in the affinity of estrogen receptor (ER) binding site between alternative allelic variants, with stronger predicted affinity for the risk (G) allele. Electrophoretic mobility shift assay showed that purified human ERα bound only G variant of a 32-bp genomic sequence containing rs12722489. Chromatin immunoprecipitation demonstrated that endogenous human ERα interacted with rs12722489 genomic region in vivo and DNA pull-down assay confirmed differential allelic binding of amplified 189-bp genomic fragments containing rs12722489 with endogenous human ERα. In a luciferase reporter assay, a kilobase-long genomic segment containing G but not A allele of rs12722489 demonstrated enhancer properties in MT-2 cell line, an HTLV-1 transformed human cell line with a regulatory T cell phenotype