Direct evaluation of self-quenching behavior of fluorophores at high concentrations using an evanescent field

The quantum yield of a fluorophore is reduced when two or more identical fluorophores are in close proximity to each other. The study of protein folding or particle aggregation is can be done based on this above-mentioned phenomenon—called self-quenching. However, it is challenging to characterize the self-quenching of a fluorophore at high concentrations because of the inner filter effect, which involves depletion of excitation light and re-absorption of emission light. Herein, a novel method to directly evaluate the self-quenching behavior of fluorophores was developed. The evanescent field from an objective-type total internal reflection fluorescence (TIRF) microscope was used to reduce the path length of the excitation and emission light to ~100 nm, thereby supressing the inner filter effect. Fluorescence intensities of sulforhodamine B, fluorescein isothiocyanate (FITC), and calcein solutions with concentrations ranging from 1 μM to 50 mM were directly measured to evaluate the concentration required for 1000-fold degree of self-quenching and to examine the different mechanisms through which the fluorophores undergo self-quenching.

Open-top axially swept light sheet microscopy

Open-top light sheet microscopy (OT-LSM) is a specialized microscopy for the high throughput cellular imaging of large tissues including optically cleared tissues by having all the optical setup below the sample stage. Current OT-LSM systems had relatively low axial resolutions by using weakly focused light sheets to cover the imaging field of view (FOV). In this report, open-top axially swept LSM (OTAS-LSM) was developed for high-throughput cellular imaging with the improved axial resolution. OTAS-LSM swept the tightly focused excitation light sheet across the imaging FOV by using an electro tunable lens (ETL) and collected emission light at the focus of light sheet with a camera in the rolling shutter mode. OTAS-LSM was developed by using air objective lenses and a water prism for simplicity and it had on-axis optical aberration associated with the mismatch of refractive indices between air and immersion medium. The effects of optical aberration were analyzed by both simulation and experiment. The image resolutions were 1.5-1.6μm, and approximately 140% of the aberration-free theoretical values. The newly developed OTAS-LSM was applied to the imaging of optically cleared mouse brain and small intestine and it could visualize neuronal networks in the single cell level. OTAS-LSM might be useful for the high-throughput cellular examination of optically cleared large tissues.

The structure of hydrodynamic γ-ray burst jets

ABSTRACT After being launched, gamma-ray burst (GRB) jets propagate through dense media prior to their breakout. The jet-medium interaction results in the formation of a complex structured outflow, often referred to as a ‘structured jet’. The underlying physics of the jet-medium interaction that sets the post-breakout jet morphology has never been explored systematically. Here, we use a suite of 3D simulations to follow the evolution of hydrodynamic long and short gamma-ray bursts (lGRBs and sGRBs) jets after breakout to study the post-breakout structure induced by the interaction. Our simulations feature Rayleigh–Taylor fingers that grow from the cocoon into the jet, mix cocoon with jet material and destabilize the jet. The mixing gives rise to a previously unidentified region sheathing the jet from the cocoon, which we denote the jet–cocoon interface (JCI). lGRBs undergo strong mixing, resulting in most of the jet energy to drift into the JCI, while in sGRBs weaker mixing is possible, leading to a comparable amount of energy in the two components. Remarkably, the jet structure (jet-core plus JCI) can be characterized by simple universal angular power-law distributions, with power-law indices that depend solely on the mixing level. This result supports the commonly used power-law angular distribution, and disfavours Gaussian jets. At larger angles, where the cocoon dominates, the structure is more complex. The mixing shapes the prompt emission light curve and implies that typical lGRB afterglows are different from those of sGRBs. Our predictions can be used to infer jet characteristics from prompt and afterglow observations.

Precise imaging of mitochondria in cancer cells by real-time monitoring of nitroreductase activity with a targetable and activatable fluorescent probe

A probe with a targetable feature and ratiometric fluorescence as well as NIR emission light-up response to nitroreductase is presented for the precise imaging of mitochondria in cancer cells by real-time monitoring of nitroreductase activity.

Time-dependent behaviour of quasar proximity zones at z ∼ 6

ABSTRACT Since the discovery of z ∼ 6 quasars two decades ago, studies of their Ly α-transparent proximity zones have largely focused on their utility as a probe of cosmic reionization. But even when in a highly ionized intergalactic medium, these zones provide a rich laboratory for determining the time-scales that govern quasar activity and the concomitant growth of their supermassive black holes. In this work, we use a suite of 1D radiative transfer simulations of quasar proximity zones to explore their time-dependent behaviour for activity time-scales from ∼103 to 108 yr. The sizes of the simulated proximity zones, as quantified by the distance at which the smoothed Ly α transmission drops below 10 per cent (denoted Rp), are in excellent agreement with observations, with the exception of a handful of particularly small zones that have been attributed to extremely short ≲104 lifetimes. We develop a physically motivated semi-analytic model of proximity zones which captures the bulk of their equilibrium and non-equilibrium behaviour, and use this model to investigate how quasar variability on ≲105 yr time-scales is imprinted on the distribution of observed proximity zone sizes. We show that large variations in the ionizing luminosity of quasars on time-scales of ≲104 yr are disfavoured based on the good agreement between the observed distribution of Rp and our model prediction based on ‘lightbulb’ (i.e. steady constant emission) light curves.