Time resolved applications for Cryo-EM; approaches, challenges and future directions

Developments within the cryo-EM field have allowed us to generate higher-resolution "static" structures and pull out different conformational states which exist at equilibrium within the sample. Moreover, to trap non-equilibrium states and determine conformations that are present after a defined period of time (typically in the ms time frame) new approaches have been developed for the application of time-resolved cryo-EM. Here we give an overview of these different approaches and the limitations and strengths of each whilst identifying some of the current challenges to achieve higher resolutions and trap states within faster time frames. Time-resolved applications may play an important role in the ever-expanding toolkit of cryo-EM and open up new possibilities in both single particle and tomographic studies.

Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting

Despite the recent rise of RNA-seq datasets combining single-cell (sc) resolution with 4-thiouridine (4sU) labelling, analytical methods exploiting their power to dissect transcriptional bursting are lacking. Here, we present a mathematical model and Bayesian inference implementation to facilitate genome-wide joint parameter estimation and confidence quantification (R package: burstMCMC). We demonstrate that, unlike conventional scRNA-seq, 4sU scRNA-seq resolves temporal parameters and furthermore boosts inference of dimensionless parameters via a synergy between single-cell resolution and 4sU labelling. We apply our method to published 4sU scRNA-seq data and linked with ChIP-seq data, we uncover previously obscured associations between different parameters and histone modifications.

High diagnostic performance of time-resolved MR angiography in spinal arteriovenous shunts

BACKGROUND AND PURPOSE

In comparison with the limited efficacy of conventional MR imaging and the invasiveness of catheter-based digital subtraction angiography (DSA), time-resolved MR angiography (TR-MRA) has been proposed as a promising examination for early diagnosis of spinal arteriovenous shunts (SAVSs). This paper aims to investigate the diagnostic performance of TR-MRA with scan parameters optimized for SAVSs evaluation in a large number of patients.

METHODS

One hundred patients with suspected SAVSs were enrolled. Each patient underwent preoperative TR-MRA with optimized scan parameters followed by DSA. The presence or absence of SAVS, the types and the angioarchitecture of SAVSs in the TR-MRA images were diagnostically analyzed.

RESULTS

Among the final 97 patients, 80 cases (82.5 %) were diagnosed and classified by TR-MRA as spinal cord arteriovenous shunts (SCAVSs; n = 22), spinal dural arteriovenous shunts (SDAVSs; n = 48), and spinal extradural arteriovenous shunts (SEDAVSs; n = 10). The agreement for classifying SAVSs between TR-MRA and DSA was excellent (κ = 0.91). The sensitivity, specificity, PPV, NPV, and accuracy of TR-MRA for the diagnosis of SAVSs were 100 % (95 % CI, 94.3-100.0 %), 76.5 % (95 % CI, 49.8-92.2 %), 95.2 % (95 % CI, 87.6-98.5 %), 100 % (95 % CI, 71.7-100.0 %), and 95.9 % (95 % CI, 89.9-98.4 %). The accuracy rates of TR-MRA for the detection of feeding arteries were 75.9 %, 91.7 %, and 80.0 % for SCAVSs, SDAVSs, and SEDAVSs respectively.

CONCLUSION

Time-resolved MR angiography showed excellent diagnostic performance for SAVSs screening. Additionally, this method can classify SAVSs and identify feeding arteries in SDAVSs with high diagnostic accuracy.

Time-resolved X-ray scattering studies of proteins

Time-resolved small- and wide-angle X-ray scattering studies of proteins in solution based on the pump-probe approach unveil structural information from intermediates over a broad range of length and time scales. In spite of the promise of this methodology, only a fraction of the wealth of information encoded in scattering data has been extracted in studies performed thus far. Here, we discuss the methodology, summarize results from recent time-resolved X-ray scattering studies, and examine the potential to extract additional information from these scattering curves.

Defining the resilience of the human salivary microbiota by a 520-day longitudinal study in a confined environment: the Mars500 mission

BACKGROUND

The human microbiota plays several roles in health and disease but is often difficult to determine which part is in intimate relationships with the host vs. the occasional presence. During the Mars500 mission, six crewmembers lived completely isolated from the outer world for 520 days following standardized diet regimes. The mission constitutes the first spaceflight simulation to Mars and was a unique experiment to determine, in a longitudinal study design, the composition and importance of the resident vs. a more variable microbiota-the fraction of the human microbiota that changes in time and according to environmental conditions-in humans.

METHODS

Here, we report the characterization of the salivary microbiota from 88 samples taken during and after Mars500 mission for a total of 720 days. Amplicon sequencing of the V3-V4 regions of 16S rRNA gene was performed, and results were analyzed monitoring the diversity of the microbiota while evaluating the effect of the three main variables present in the experimental system: time, diet, and individuality of each subject.

RESULTS

Results showed statistically significant effects for either time, diet, and individuality of each subject. The main contribution came from the individuality of each subject, emphasizing salivary microbiota-personalized features, and an individual-based resilience of the microbiota.

CONCLUSIONS

The uniqueness of Mars500 mission, allowed to dampen the effect of environmental variables on salivary microbiota, highlighting its pronounced personalization even after sharing the same physical space for more than a year. Video abstract.

Luminescence lifetime imaging of ultra-long room temperature phosphorescence on a smartphone

Luminescence lifetime imaging plays an important role in distinguishing the luminescence decay rates in time-resolved luminescence imaging. However, traditional imaging instruments used for detecting lifetimes within milliseconds would be time-consuming when imaging ultra-long luminescence lifetimes over subseconds. Herein, we present an accessible and simple optical system for detecting lifetimes of persistent luminescence. A smartphone integrated with a UV LED, a dichroic mirror, and a lens was used for recording the persistent luminescence. With only a few seconds of data acquisition, a luminescence lifetime image could be processed from the video by exponential fitting of the gray level of each pixel to the delay time. Since this approach only requires single excitation, no synchronous control is needed, greatly simplifying the apparatus and saving the cost. The apparatus was successfully used for ultra-long luminescence lifetime imaging of mouse tissue dyed with a persistent luminescence molecule. This miniaturized apparatus exhibits huge potentiality in time-resolved luminescence imaging for luminescence study and biological detection.

Supersensitive and reusable perovskite nanocomposite fiber paper for time-resolved single-droplet detection

Traditional test paper cannot be reusable and needs much sample solution. In this study, a reusable perovskite nanocomposite fiber paper consisting of CsPbBr₃ quantum dots in-situ growing in the solid polymer fibers with high concentration is fabricated via microwave and electrospinning methods. RhoB is used as the sample solution because it is a hazardous matter but often occurs in printing and dyeing wastewater or appears in food as additives, and traditional detection system generally requires much sample solution (>1 ml) to concentrate for higher concentrations due to the low detection sensitivity. Just need a droplet of sample solution (<25 μl) can this perovskite fiber paper achieve 0.01 ppm of supersensitive detection, which is superior to a majority of reported detection limit. Different from traditional detection based on luminescence intensity, this detection is a new kind of time-resolved method, so that it gets rid of complex and time-consuming calibration (>1 h) usually in traditional detection, and this time-resolved detection can be achieved within ~3 min. Moreover, this perovskite fiber paper is endowed with recyclable property without losing advantages of supersensitive detection (~0.01 ppm), rapid measuring speed (<3 min), and tiny dosage (<25 μl), which is another advantage than conventional detection systems.

Self-assembly of supported lipid multi-bilayers investigated by time-resolved X-ray diffraction

Supported lipid multi-bilayers or bilayer stacks are an important model membrane system, particularly suitable for surface-sensitive characterization methods like X-ray and neutron diffraction. Spreading organic solution (sOS) is one of the most widely used protocols for the preparation of lipid multi-bilayers. Despite its great popularity, the self-assembly mechanism of the bilayers is not yet fully elucidated, limiting further improvements of this protocol. In order to solve this problem, we investigated the formation process of lipid bilayers in the sOS protocol, using in-situ time-resolved X-ray diffraction, complemented by X-ray reflectivity and molecular dynamics simulation. Results reveal a simultaneous self-assembly scheme for both cholesterol-free and cholesterol-containing bilayers, with one bilayer phase forming at the surface and the other forming in the solution. The solution phase gradually transforms into the surface phase, yielding clean single phase in the end.

Light-coupled cryo-plunger for time-resolved cryo-EM

Proteins are dynamic molecules that can undergo rapid conformational rearrangements in response to stimuli. These structural changes are often critical to protein function, and thus elucidating time-dependent conformational landscapes has been a long-standing goal of structural biology. To harness the power of single particle cryo-EM methods to enable 'time-resolved' structure determination, we have developed a light-coupled cryo-plunger that pairs flash-photolysis of caged ligands with rapid sample vitrification. The 'flash-plunger' consists of a high-power ultraviolet LED coupled with focusing optics and a motorized linear actuator, enabling the user to immobilize protein targets in vitreous ice within a programmable time window - as short as tens of milliseconds - after stimulus delivery. The flash-plunger is a simple, inexpensive and flexible tool to explore short-lived conformational states previously unobtainable by conventional sample preparation methods.

Time-Resolved Temperature-Jump Infrared Spectroscopy at a High Repetition Rate

Time-resolved temperature-jump infrared absorption spectroscopy at a 0.5 to 1 kHz repetition rate is presented. A 1 kHz neodymium-doped yttrium aluminum garnet (Nd:YAG) laser pumping an optical parametric oscillator provided >70 µJ, 3.75 µm pump pulses, which delivered a temperature jump via excitation of the O-D stretch of a D₂O solution. A 10 kHz train of mid-infrared probe pulses was used to monitor spectral changes following the temperature jump. Calibration with trifluoroacetic acid solution showed that a temperature jump of 10 K lasting for tens of microseconds was achieved, sufficient to observe fast processes in functionally relevant biomolecular mechanisms. Modeling of heating profiles across ≤10 µm path length cells and subsequent cooling dynamics are used to describe the initial <100 ns cooling at the window surface and subsequent, >10 µs cooling dynamics of the bulk solution.

How to learn from inconsistencies: Integrating molecular simulations with experimental data

Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modeling tool to interpret experimental measurements, and to use experimental data to refine our biophysical models. Thus, explicit integration and synergy between molecular simulations and experiments is fundamental for furthering our understanding of biological processes. This is especially true in the case where discrepancies between measured and simulated observables emerge. In this chapter, we provide an overview of some of the core ideas behind methods that were developed to improve the consistency between experimental information and numerical predictions. We distinguish between situations where experiments are used to refine our understanding and models of specific systems, and situations where experiments are used more generally to refine transferable models. We discuss different philosophies and attempt to unify them in a single framework. Until now, such integration between experiments and simulations have mostly been applied to equilibrium data, and we discuss more recent developments aimed to analyze time-dependent or time-resolved data.

Probing Interactions of γ-Alumina with Water via Multinuclear Solid-State NMR Spectroscopy

Interaction of γ-alumina with water are important in controlling its structure and catalytic properties. We apply solid-state multinuclear NMR spectroscopy to investigate this interaction by monitoring ¹H and ¹⁷O spectra in real-time. Surface-selective detection is made possible by adsorbing ¹⁷O-enriched water on γ-alumina nanorods. Structural evolution on the surface was selectively probed by ¹H/¹⁷O double resonance NMR and ²⁷Al NMR at ultrahigh 35.2 T magnetic field. Formation of hydroxyl species on the surface of nanorods is rapid upon the exposure of water, which involves low coordinated aluminum ions with doubly bridging and isolated hydroxyl species being generated first. Fast exchange occurs between oxygen atoms in the water molecules and bare surface sites, indicating high reactivity of these oxygen species. These results provide new insights into the structure and dynamics on the surface of γ-alumina and the methods applied here can be extended to study the interaction of other oxides with water.

Spectrally resolved luminescence lifetime detection for measuring the energy splitting of the long-lived excited states

Molecular motion plays an important role in the reverse intersystem crossing of thermally activated delayed fluorescence (TADF) materials, since the conformation varies as the molecule vibrates, leading to potential changes in the energies of excited states. Although many theoretical simulations have researched the relationship between the excited states and the molecular conformations, there are still few experimental results showing the energy level difference between different long-lived excited states. Herein, a novel method for measuring spectrally resolved luminescence lifetimes is proposed to detect the energy splitting of the long-lived excited states of a classical TADF molecule, BTZ-DMAC. A set of the time-gated luminescence spectra with different delay times were captured by a spectrograph equipped on an auto-phase-locked system, and then used for lifetime analysis at each wavelength. Unlike traditional measurement techniques, the proposed novel method does not require ultrafast laser, high-speed detector and any phase matching circuitry, thus significantly reducing the cost. This method revealed a definite energy gap between the two excited states of BTZ-DMAC with different lifetimes, indicating different conformations caused by molecular vibration. This low-cost method could be also used to detect many other luminescence materials for investigating the detail mechanisms of multiple excited states.

Rapid and sensitive detection of interleukin-6 in serum via time-resolved lateral flow immunoassay

Interleukin 6 (IL-6) is an interleukin that acts as both a proinflammatory and anti-inflammatory cytokine. It can be used as a potential diagnostic biomarker for sepsis. The aim of this study was to establish an easy-to-use detection kit for rapid, quantitative and on-site detection of IL-6. To develop the new IL-6 quantitative detecting kit, a double-antibody sandwich immunofluorescent assay was employed based on europium nanoparticles (Eu-np) combined with lateral flow immunoassay (LFIA). The performance of the new developed kit was evaluated in the aspects of parallel analysis, linearity, sensitivity, precision, accuracy, specificity and clinical sample analysis. Two-hundred and fourteen serum samples were used to carry out the clinical sample analysis. The new IL-6 quantitative detecting kit exhibited a wide linear range (2-500 pg/mL) and a good sensitivity (0.37 pg/mL). The intra-assay coefficient of variation (CV) and the inter-assay CV were 5.92%-8.87% and 7.59%-9.04%, respectively. The recovery rates ranged from 102% to 106%. Furthermore, a high correlation (n = 214, r = 0.9756, p < 0.01) was obtained when compared with SIEMENS CLIA IL-6 kit. Thus, the new quantitative method for detecting IL-6 has been successfully established. The results indicated that the newly-developed strip based on Eu-np combined with LFIA was a facile, fast, highly sensitive, low-cost, reliable biosensor and suitable for rapid and point-of-care test (POCT) for IL-6 in serum.

Microfluidic sample delivery for serial crystallography using XFELs

Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) is an emerging field for structural biology. One of its major impacts lies in the ability to reveal the structure of complex proteins previously inaccessible with synchrotron-based crystallography techniques and allowing time-resolved studies from femtoseconds to seconds. The nature of this serial technique requires new approaches for crystallization, data analysis, and sample delivery. With continued advancements in microfabrication techniques, various developments have been reported in the past decade for innovative and efficient microfluidic sample delivery for crystallography experiments using XFELs. This article summarizes the recent developments in microfluidic sample delivery with liquid injection and fixed-target approaches, which allow exciting new research with XFELs. Graphical abstract.

Fluorescence spectroscopy-based study of balanced transport of charge carriers in hot-air-annealed perovskites

Using fluorescence spectroscopy, we investigate the transport of charge carriers in (p-i-n) planar perovskite (CH₃NH₃PbI_3-xCl_x) solar cells with the structure ITO/PEDOT:PSS/perovskites/PCBM/Ca/Al, in which the perovskite morphology is optimized by moisture pretreatment (MPT) and the hot-air-annealing process (HAAP). After annealing with hot air, the electron transport time of the perovskites is shortened by a factor of 3.6 (from 28.8 to 7.9 ns), eventually leading to balanced transport of electrons and holes (characterized by the fluorescence-decay time constants of 7.9 and 7.6 ns, respectively). These results are in good agreement with the observed increase in the photovoltaic conversion efficiency.

Smartphone-based apparatus for measuring upconversion luminescence lifetimes

Luminescence lifetime detection plays an important role in time-resolved detection and research. However, the traditional instruments always require expensive detectors such as time-correlated single photon counter or streak camera. Herein, a low-cost and miniaturized apparatus for measuring upconversion luminescence lifetimes was developed by using a smartphone equipped with a 980 nm CW laser and a motor. When the motor was driving the sample circling at a high linear velocity, the excited sample would emit a luminescence arc, which could be photographed by the phone camera. The rotating rate could be measured by a tuner APP and then used for transferring arc length to delay times. By analyzing the grayscale distribution of the luminescence arc, the luminescence decay curve was obtained, which was then used for exponential fit and calculating lifetimes. The images captured by different smartphones revealed similar lifetime values, suggesting a wide universality of this method. The whole system was not only remarkably cheaper but also more miniaturized than traditional instruments for measuring luminescence lifetimes, indicating the promising applications in point of care testing for time-resolved luminescence detection for bioanalysis and disease diagnosis.

Time-Resolved Cryo-electron Microscopy Using a Microfluidic Chip

With the advent of direct electron detectors, cryo-EM has become a popular choice for molecular structure determination. Among its advantages over X-ray crystallography are (1) no need for crystals, (2) much smaller sample volumes, and (3) the ability to determine multiple structures or conformations coexisting in one sample. In principle, kinetic experiments can be done using standard cryo-EM, but mixing and freezing grids require several seconds. However, many biological processes are much faster than that time scale, and the ensuing short-lived states of the molecules cannot be captured. Here, we lay out a detailed protocol for how to capture such intermediate states on the millisecond time scale with time-resolved cryo-EM.

Acquisition of Temporal HIF Transcriptional Activity Using a Secreted Luciferase Assay

Here we describe a simple method based on secreted luciferase driven by a hypoxia-inducible factor (HIF) response element (HRE) that allows the acquisition of dynamic and high-throughput data on HIF transcriptional activity during hypoxia and pharmacological activation of HIF. The sensitivity of the assay allows for the secreted luciferase to be consecutively sampled (as little as 1% of the total supernatant) over an extended time period, thus allowing the acquisition of time-resolved HIF transcriptional activity.

An integrated logic system for time-resolved fluorescent "turn-on" detection of cysteine and histidine base on terbium (III) coordination polymer-copper (II) ensemble

Cysteine (Cys) and histidine (His) both play indispensable roles in many important biological activities. An enhanced Cys level can result in Alzheimer's and cardiovascular diseases. Likewise, His plays a significant role in the growth and repair of tissues as well as in controlling the transmission of metal elements in biological bases. Therefore, it is meaningful to detect Cys and His simultaneously. In this work, a novel terbium (III) coordination polymer-Cu (II) ensemble (Tb(3+)/GMP-Cu(2+)) was proposed. Guanosine monophosphate (GMP) can self-assemble with Tb(3+) to form a supramolecular Tb(3+) coordination polymer (Tb(3+)/GMP), which can be suited as a time-resolved probe. The fluorescence of Tb(3+)/GMP would be quenched upon the addition of Cu(2+), and then the fluorescence of the as-prepared Tb(3+)/GMP-Cu(2+) ensemble would be restored again in the presence of Cys or His. By incorporating N-Ethylmaleimide and Ni(2+) as masking agents, Tb(3+)/GMP-Cu(2+) was further exploited as an integrated logic system and a specific time-resolved fluorescent "turn-on" assay for simultaneously sensing His and Cys was designed. Meanwhile it can also be used in plasma samples, showing great potential to meet the need of practical application.

Time-resolved visible and infrared absorption spectroscopy data obtained using photosystem I particles with non-native quinones incorporated into the A1 binding site

Time-resolved visible and infrared absorption difference spectroscopy data at both 298 and 77 K were obtained using cyanobacterial menB⁻ mutant photosystem I particles with several non-native quinones incorporated into the A₁ binding site. Data was obtained for photosystem I particles with phylloquinone (2-methyl-3-phytyl-1,4-naphthoquinone), 2-bromo-1,4-naphthoquinone, 2-chloro-1,4-naphthoquinone, 2-methyl-1,4-naphthoquinone, 2,3-dibromo-1,4-naphthoquinone, 2,3-dichloro-1,4-naphthoquinone, and 9,10-anthraquinone incorporated. Transient absorption data were obtained at 487 and 703 nm in the visible spectral range, and 1950–1100 cm⁻¹ in the infrared region. Time constants obtained from fitting the time-resolved infrared and visible data are in good agreement. The measured time constants are crucial for the development of appropriate kinetic models that can describe electron transfer processes in photosystem I, “Modeling Electron Transfer in Photosystem I” Makita and Hastings (2016) [1].

Fast Atomic-Scale Chemical Imaging of Crystalline Materials and Dynamic Phase Transformations

Atomic-scale phenomena fundamentally influence materials form and function that makes the ability to locally probe and study these processes critical to advancing our understanding and development of materials. Atomic-scale chemical imaging by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) is a powerful approach to investigate solid crystal structures. Inefficient X-ray emission and collection, however, require long acquisition times (typically hundreds of seconds), making the technique incompatible with electron-beam sensitive materials and study of dynamic material phenomena. Here we describe an atomic-scale STEM-EDS chemical imaging technique that decreases the acquisition time to as little as one second, a reduction of more than 100 times. We demonstrate this new approach using LaAlO3 single crystal and study dynamic phase transformation in beam-sensitive Li[Li0.2Ni0.2Mn0.6]O2 (LNMO) lithium ion battery cathode material. By capturing a series of time-lapsed chemical maps, we show for the first time clear atomic-scale evidence of preferred Ni-mobility in LNMO transformation, revealing new kinetic mechanisms. These examples highlight the potential of this approach toward temporal, atomic-scale mapping of crystal structure and chemistry for investigating dynamic material phenomena.

A 100 kHz Time-Resolved Multiple-Probe Femtosecond to Second Infrared Absorption Spectrometer

We present a dual-amplifier laser system for time-resolved multiple-probe infrared (IR) spectroscopy based on the ytterbium potassium gadolinium tungstate (Yb:KGW) laser medium. Comparisons are made between the ytterbium-based technology and titanium sapphire laser systems for time-resolved IR spectroscopy measurements. The 100 kHz probing system provides new capability in time-resolved multiple-probe experiments, as more information is obtained from samples in a single experiment through multiple-probing. This method uses the high repetition-rate probe pulses to repeatedly measure spectra at 10 µs intervals following excitation allowing extended timescales to be measured routinely along with ultrafast data. Results are presented showing the measurement of molecular dynamics over >10 orders of magnitude in timescale, out to 20 ms, with an experimental time response of <200 fs. The power of multiple-probing is explored through principal component analysis of repeating probe measurements as a novel method for removing noise and measurement artifacts.

The Influence of Acquisition Delay for Calibration-Free Laser-Induced Breakdown Spectroscopy

Time-resolved spectra of neutral and ionized atomic emissions from slag sample are measured by laser-induced breakdown spectroscopy (LIBS). Various factors affecting the calibration-free CF-LIBS method are carefully analyzed, and subsequently these factors are either avoided or corrected. Plasma temperature and electron density are calculated by Saha-Boltzmann plot and Stark broadening of Ca, respectively. At the same time, self-absorption and local thermodynamic equilibrium have been carefully studied. An automatic spectral lines elimination algorithm is applied to calculate plasma temperature and element concentration. The calculated element concentrations show marked changes with acquisition time increasing. Due to the influence of continuous spectrum at early times and self-absorption at late times, the large absolute errors sum is obtained in these two periods. The smallest absolute errors sum corresponds to the gate delay time 1.5 μs < td < 2 μs for our experimental setup.

GHz laser-free time-resolved transmission electron microscopy: A stroboscopic high-duty-cycle method

A device and a method for producing ultrashort electron pulses with GHz repetition rates via pulsing an input direct current (dc) electron beam are provided. The device and the method are based on an electromagnetic-mechanical pulser (EMMP) that consists of a series of transverse deflecting cavities and magnetic quadrupoles. The EMMP modulates and chops the incoming dc electron beam and converts it into pico- and sub-pico-second electron pulse sequences (pulse trains) at >1GHz repetition rates, as well as controllably manipulates the resulting pulses. Ultimately, it leads to negligible electron pulse phase-space degradation compared to the incoming dc beam parameters. The temporal pulse length and repetition rate for the EMMP can be continuously tunable over wide ranges. Applying the EMMP to a transmission electron microscope (TEM) with any dc electron source (e.g. thermionic, Schottky, or field-emission source), a GHz stroboscopic high-duty-cycle TEM can be realized. Unlike in many recent developments in time-resolved TEM that rely on a sample pumping laser paired with a laser launching electrons from a photocathode to probe the sample, there is no laser in the presented experimental set-up. This is expected to be a significant relief for electron microscopists who are not familiar with laser systems. The EMMP and the sample are externally driven by a radiofrequency (RF) source synchronized through a delay line. With no laser pumping the sample, the problem of the pump laser induced residual heating/damaging the sample is eliminated. As many RF-driven processes can be cycled indefinitely, sampling rates of 1-50GHz become accessible. Such a GHz stroboscopic TEM would open up a new paradigm for in situ and in operando experiments to study samples externally driven electromagnetically. Complementary to the lower (MHz) repetition rates experiments enabled by laser photocathode TEM, new experiments in the multi-GHz regime will be enabled by the proposed RF design. Because TEM is also a platform for various analytical methods, there are infinite application opportunities in energy and electronics to resolve charge (electronic and ionic) transport, and magnetic, plasmonic and excitonic dynamics in advanced functional materials. In addition, because the beam duty-cycle can be as high as ~10(-1) (or 10%), detection can be accomplished by commercially available detectors. In this article, we report an optimal design of the EMMP. The optimal design was found using an analytical generalized matrix approach in the thin lens approximation along with detailed beam dynamics taking actual realistic dc beam parameters in a TEM operating at 200keV.

Europium nanoparticle-based simple to perform dry-reagent immunoassay for the detection of hepatitis B surface antigen

Hepatitis B infection, caused by hepatitis B virus (HBV), presents a huge global health burden. Serological diagnosis of HBV mainly relies on the detection of hepatitis B surface antigen (HBsAg). Although there are high sensitivity commercial HBsAg enzyme immunoassays (EIAs) available, many low-resource laboratories lacking trained technicians continue to use rapid point-of-care assays with low sensitivities for HBsAg detection, due to their simplicity to operate. We developed a time-resolved fluorometric dry-reagent HBsAg immunoassay which meets the detection limit of high sensitivity EIAs but is simple to operate. To develop the assay, anti-HBsAg monoclonal antibody coated on europium nanoparticles was dried atop of biotinylated anti-HBsAg polyclonal antibody immobilized on streptavidin-coated microtiter wells. To test a sample in dry-reagent assay, serum sample and assay buffer were added to the wells, incubated, washed and europium signals were measured. The assay showed a detection limit of 0.25 ng/ml using HBsAg spiked in serum sample. When evaluated with 24 HBV positive and 37 negative serum samples, assay showed 100% sensitivity and specificity. Assay wells are stable for at least 26 weeks when stored at 4°C, and can tolerate elevated temperatures of up to 35°C for two weeks. The developed assay has high potential to be used in low-resource laboratories.

Characterization of a new highly sensitive immunometric assay for thyroglobulin with reduced interference from autoantibodies

Measurements of serum thyroglobulin (Tg) with sensitive immunoassays are of great importance for the management of patients with differentiated thyroid carcinomas. However, interference of circulating autoantibodies to Tg (hTgAb) hampers the usefulness of most assays. We have produced a panel of monoclonal antibodies (mAbs) selected to bind Tg in the presence of Tg autoantibodies and developed a sensitive immunoassay for Tg with minor interference by hTgAbs. The antibodies were characterized by cross-inhibition and immunoassay combination studies, as well as affinity estimation. The within-run and total imprecision of the assay were determined with 2664 samples in 60 separate runs. The most sensitive assay combination with superior protection against autoantibodies consisted of two solid phase mAbs and two tracer mAbs with distinct binding sites. The assay was linear and displayed a wide dynamic range up to 1342 μg/l with a functional sensitivity of 0.1 μg/l and a total imprecision of less than 10 %. There was good agreement between the new high sensitive immunofluorometric assay (IFMA) and two well-established Tg assays from Brahms Kryptor and Roche Diagnostics. Mean difference between the new IFMA and the Kryptor assay was 0.059 μg/l with a 95 % confidence interval of −0.032 to 0.151 μg/l, whereas the mean difference between the new IFMA and the Roche assay was −0.80 μg/l with a 95 % confidence interval of −1.24 to −0.35 μg/l.

Resolution and Characterization of Chemical Steps in Enzyme Catalytic Sequences by Using Low-Temperature and Time-Resolved, Full-Spectrum EPR Spectroscopy in Fluid Cryosolvent and Frozen Solution Systems

Approaches to the resolution and characterization of individual chemical steps in enzyme catalytic sequences, by using temperatures in the cryogenic range of 190-250 K, and kinetics measured by time-resolved, full-spectrum electron paramagnetic resonance spectroscopy in fluid cryosolvent and frozen solution systems, are described. The preparation and performance of the adenosylcobalamin-dependent ethanolamine ammonia-lyase enzyme from Salmonella typhimurium in the two systems exemplifies the biochemical and spectroscopic methods. General advantages of low-temperature studies are (1) slowing of reaction steps, so that measurements can be made by using straightforward T-step kinetic methods and commercial instrumentation, (2) resolution of individual reaction steps, so that first-order kinetic analysis can be applied, and (3) accumulation of intermediates that are not detectable at room temperatures. The broad temperature range from room temperature to 190 K encompasses three regimes: (1) temperature-independent mean free energy surface (corresponding to native behavior); (2) the narrow temperature region of a glass-like transition in the protein, over which the free energy surface changes, revealing dependence of the native reaction on collective protein/solvent motions; and (3) the temperature range below the glass transition region, for which persistent reaction corresponds to nonnative, alternative reaction pathways, in the vicinity of the native configurational envelope. Representative outcomes of low-temperature kinetics studies are portrayed on Eyring and free energy surface (landscape) plots, and guidelines for interpretations are presented.

Silver nanoparticles-enhanced time-resolved fluorescence sensor for VEGF(165) based on Mn-doped ZnS quantum dots

A silver nanoparticles (AgNPs)-enhanced time-resolved fluorescence (TR-FL) sensor based on long-lived fluorescent Mn-doped ZnS quantum dots (QDs) is developed for the sensitive detection of vascular endothelial growth factor-165 (VEGF165), a predominant cancer biomarker in cancer angiogenesis. The aptamers bond with the Mn-doped ZnS QDs and the BHQ-2 quencher-labelling strands hybridized in duplex are coupled with streptavidin (SA)-functionalized AgNPs to form the AgNPs-enhanced TR-FL sensor, showing lower fluorescence intensity in the duplex state due to the fluorescence resonance energy transfer (FRET) between the Mn-doped ZnS QDs and quenchers. Upon the addition of VEGF165, the BHQ-2 quencher-labelling strands of the duplex are displaced, leading to the disruption of the FRET. As a result, the fluorescence of the Mn-doped QDs within the proximity of the AgNPs is recovered. The FL signal can be measured free of the interference of short-lived background by setting appropriate delay time and gate time, which offers a signal with high signal-to-noise ratio in photoluminescent biodetection. Compared with the bare TR-FL sensor, the AgNPs-based TR-FL sensor showed a huge improvement in fluorescence based on metal-enhanced fluorescence (MEF) effect, and the sensitivity increased 11-fold with the detection limit of 0.08 nM. In addition, the sensor provided a wide range of linear detection from 0.1 nM to 16 nM.

Fluorescence lifetime excitation cytometry by kinetic dithering

Flow cytometers are powerful high-throughput devices that capture spectroscopic information from individual particles or cells. These instruments provide a means of multi-parametric analyses for various cellular biomarkers or labeled organelles and cellular proteins. However, the spectral overlap of fluorophores limits the number of fluorophores that can be used simultaneously during experimentation. Time-resolved parameters enable the quantification of fluorescence decay kinetics, thus circumventing common issues associated with intensity-based measurements. This contribution introduces fluorescence lifetime excitation cytometry by kinetic dithering (FLECKD) as a method to capture multiple fluorescence lifetimes using a hybrid time-domain approach. The FLECKD approach excites fluorophores by delivering short pulses of light to cells or particles by rapid dithering and facilitates measurement of complex fluorescence decay kinetics by flow cytometry. Our simulations demonstrated a resolvable fluorescence lifetime value as low as 1.8 ns (±0.3 ns) with less than 20% absolute error. Using the FLECKD instrument, we measured the shortest average fluorescence lifetime value of 2.4 ns and found the system measurement error to be ±0.3 ns (SEM), from hundreds of monodisperse and chemically stable fluorescent microspheres. Additionally, we demonstrate the ability to detect two distinct excited state lifetimes from fluorophores in single cells using FLECKD. This approach presents a new ability to resolve multiple fluorescence lifetimes while retaining the fluidic throughput of a cytometry system. The ability to discriminate more than one average fluorescence lifetime expands the current capabilities of high-throughput and intensity-based cytometry assays as the need to tag one single cell with multiple fluorophores is now widespread.

Highly accelerated aortic 4D flow MR imaging with variable-density random undersampling

PURPOSE

To investigate an effective time-resolved variable-density random undersampling scheme combined with an efficient parallel image reconstruction method for highly accelerated aortic 4D flow MR imaging with high reconstruction accuracy.

MATERIALS AND METHODS

Variable-density Poisson-disk sampling (vPDS) was applied in both the phase-slice encoding plane and the temporal domain to accelerate the time-resolved 3D Cartesian acquisition of flow imaging. In order to generate an improved initial solution for the iterative self-consistent parallel imaging method (SPIRiT), a sample-selective view sharing reconstruction for time-resolved random undersampling (STIRRUP) was introduced. The performance of different undersampling and image reconstruction schemes were evaluated by retrospectively applying those to fully sampled data sets obtained from three healthy subjects and a flow phantom.

RESULTS

Undersampling pattern based on the combination of time-resolved vPDS, the temporal sharing scheme STIRRUP, and parallel imaging SPIRiT, were able to achieve 6-fold accelerated 4D flow MRI with high accuracy using a small number of coils (N=5). The normalized root mean square error between aorta flow waveforms obtained with the acceleration method and the fully sampled data in three healthy subjects was 0.04±0.02, and the difference in peak-systolic mean velocity was -0.29±2.56cm/s.

CONCLUSION

Qualitative and quantitative evaluation of our preliminary results demonstrate that time-resolved variable-density random sampling is efficient for highly accelerating 4D flow imaging while maintaining image reconstruction accuracy.

Investigation of energy transfer mechanisms between Bi(2+) and Tm(3+) by time-resolved spectrum

Here, we report for the first time the optical properties of Bi(2+) and Tm(3+) co-doped germanate glasses and elucidate the potential of this material as substrates to improve the performance of CdTe solar cell. A strong emission peak at 800nm is observed under the excitation of 450-700nm in this material. The energy transfer processes from the transitions of Bi(2+) [(2)P3/2(1)→(2)P1/2]: Tm(3+) [(3)H6→(3)H4] are investigated by time-resolved luminescence spectroscopy. A cover glass exhibiting an ultra-broadband response spectrum covering the entire solar visible wavelength region is suggested to enhance the conversion efficiency of CdTe solar cells significantly.

SAXS in inorganic and bioinspired research

In situ and time-resolved structural information about emergent microstructures that progressively develop during the formation of inorganic or biologically mediated solid phases from solution is fundamental for understanding of the mechanisms driving complex precipitation reactions, for example, during biomineralization. In this brief chapter, we present the use of small- and wide-angle X-ray scattering (SAXS and WAXS) techniques and show how SAXS can be used to gather structural information on the nanoscale properties of the de novo-forming entities. We base the discussion on several worked examples of inorganic materials such as calcium carbonate, silica, and perovskite-type titanates.