Mixing and jetting analysis using continuous flow microfluidic sample delivery devices

Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography

Time-resolved crystallography enables the visualization of protein molecular motion during a reaction. Although light is often used to initiate reactions in time-resolved crystallography, only a small number of proteins can be activated by light. However, many biological reactions can be triggered by the interaction between proteins and ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D-printed microchannels in conjunction with a micronozzle. The diffusive mixing enables the study of the dynamics of samples in viscous media. The device design allows mixing of the ligands and protein crystals in 2 to 20 s. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within lipidic cubic phase, can be mixed efficiently. The potential of this approach for time-resolved membrane protein crystallography to support the development of new drugs is discussed.

Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme

Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.

Engraving of stainless-steel wires to improve optical quality of closed-loop wire-guided flow jet systems for optical and X-ray spectroscopy

This paper describes performance enhancement developments to a closed-loop pump-driven wire-guided flow jet (WGJ) for ultrafast X-ray spectroscopy of liquid samples. Achievements include dramatically improved sample surface quality and reduced equipment footprint from 7 × 20 cm² to 6 × 6 cm², cost, and manufacturing time. Qualitative and quantitative measurements show that micro-scale wire surface modification yields significant improvements to the topography of the sample liquid surface. By manipulating their wettability, it is possible to better control the liquid sheet thickness and to obtain a smooth liquid sample surface, as demonstrated in this work.

Asymmetric Spray Characteristics According to Y-Jet Nozzle Orifice Shape and Spray Conditions

The Y-jet nozzle is a twin-fluid nozzle that has a larger operating range and simpler structure than other twin-fluid nozzles. Furthermore, it offers outstanding atomization quality even at low flow rates, mak ing it simple to atomize viscous liquids. However, because of the structure of the Y-jet nozzle, having an asymmetrical spray pattern is limited. Most existing experimental studies focused on the orifice diameter and mixing tube length. In this study, two types of elliptical nozzles and one type of circular nozzle were tested. We found that the elliptical nozzle's asymmetric spray characteristics are different from those of the circular type. Furthermore, it was demonstrated that the spray characteristics were different even in ellipsoids, with only the major and minor axes differing.

Numerical simulation and parameter optimization of micromixer device using fuzzy logic technique

The objective of this study is the design, simulation, and performance optimization of a micromixer device using the three input parameters of device structure, flow rate and diffusion coefficient of gold nanoparticles while the output parameters are concentration, velocity, pressure and time domain analysis. Each input parameter in the microfluidic chip influences the system output. The data were gathered through extensive study in order to optimize the diffusion control. The fuzzy logic approach is used to optimize the performance of the device with respect to the input parameters. In this study, we have chosen three different flow rates of 1, 5, and 10 μL min^-1, three different diffusion coefficient values of low, average and high diffusivity gold nanofluids (15.3 e^-12, 15.3 e^-11, 15.3 e^-10 m² s^-1) which are used in three different shapes of micromixer device, Y-shaped straight channel micromixer, herringbone-shaped micromixer, and herringbone shape with obstacles micromixer, and we measured the output performance, such as mixing efficiency, pressure drop, concentration across the microchannel and time domain. The data were obtained by fuzzy logic analysis and it was found that the herringbone shape with obstacles micromixer shows 100% mixing efficiency within a short duration of 5000 μm, and complete mixing was achieved within 10 seconds with a low pressure drop of 128 Pa.

Perspective: Structure determination of protein-ligand complexes at room temperature using X-ray diffraction approaches

The interaction between macromolecular proteins and small molecule ligands is an essential component of cellular function. Such ligands may include enzyme substrates, molecules involved in cellular signalling or pharmaceutical drugs. Together with biophysical techniques used to assess the thermodynamic and kinetic properties of ligand binding to proteins, methodology to determine high-resolution structures that enable atomic level interactions between protein and ligand(s) to be directly visualised is required. Whilst such structural approaches are well established with high throughput X-ray crystallography routinely used in the pharmaceutical sector, they provide only a static view of the complex. Recent advances in X-ray structural biology methods offer several new possibilities that can examine protein-ligand complexes at ambient temperature rather than under cryogenic conditions, enable transient binding sites and interactions to be characterised using time-resolved approaches and combine spectroscopic measurements from the same crystal that the structures themselves are determined. This Perspective reviews several recent developments in these areas and discusses new possibilities for applications of these advanced methodologies to transform our understanding of protein-ligand interactions.

Electrically stimulated droplet injector for reduced sample consumption in serial crystallography

With advances in X-ray free-electron lasers (XFELs), serial femtosecond crystallography (SFX) has enabled the static and dynamic structure determination for challenging proteins such as membrane protein complexes. In SFX with XFELs, the crystals are typically destroyed after interacting with a single XFEL pulse. Therefore, thousands of new crystals must be sequentially introduced into the X-ray beam to collect full data sets. Because of the serial nature of any SFX experiment, up to 99% of the sample delivered to the X-ray beam during its "off-time" between X-ray pulses is wasted due to the intrinsic pulsed nature of all current XFELs. To solve this major problem of large and often limiting sample consumption, we report on improvements of a revolutionary sample-saving method that is compatible with all current XFELs. We previously reported 3D-printed injection devices coupled with gas dynamic virtual nozzles (GDVNs) capable of generating samples containing droplets segmented by an immiscible oil phase for jetting crystal-laden droplets into the path of an XFEL. Here, we have further improved the device design by including metal electrodes inducing electrowetting effects for improved control over droplet generation frequency to stimulate the droplet release to matching the XFEL repetition rate by employing an electrical feedback mechanism. We report the improvements in this electrically triggered segmented flow approach for sample conservation in comparison with a continuous GDVN injection using the microcrystals of lysozyme and 3-deoxy-D-manno-octulosonate 8-phosphate synthase and report the segmented flow approach for sample injection applied at the Macromolecular Femtosecond Crystallography instrument at the Linear Coherent Light Source for the first time.

Sieve-Like CNT Film Coupled with TiO2 Nanowire for High-Performance Continuous-Flow Photodegradation of Rhodamine B under Visible Light Irradiation

Continuous-flow photoreactors hold great promise for the highly efficient photodegradation of pollutants due to their continuity and sustainability. However, how to enable a continuous-flow photoreactor with the combined features of high photodegradation efficiency and durability as well as broad-wavelength light absorption and large-scale processing remains a significant challenge. Herein, we demonstrate a facile and effective strategy to construct a sieve-like carbon nanotube (CNT)/TiO2 nanowire film (SCTF) with superior flexibility (180° bending), high tensile strength (75-82 MPa), good surface wettability, essential light penetration and convenient visible light absorption. Significantly, the unique architecture, featuring abundant, well-ordered and uniform mesopores with ca. 70 µm in diameter, as well as a homogenous distribution of TiO2 nanowires with an average diameter of ca. 500 nm, could act as a "waterway" for efficient solution infiltration through the SCTF, thereby, enabling the photocatalytic degradation of polluted water in a continuous-flow mode. The optimized SCTF-2.5 displayed favorable photocatalytic behavior with 96% degradation of rhodamine B (RhB) within 80 min and a rate constant of 0.0394 min-1. The continuous-flow photodegradation device made using SCTF-2.5 featured exceptional photocatalytic behavior for the continuous degradation of RhB under simulated solar irradiation with a high degradation ratio (99.6%) and long-term stability (99.2% retention after working continuously for 72 h). This work sheds light on new strategies for designing and fabricating high-performance continuous-flow photoreactors toward future uses.

MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography

MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.

Recent Advances and Future Perspectives on Microfluidic Mix-and-Jet Sample Delivery Devices

The integration of the Gas Dynamic Virtual Nozzle (GDVN) and microfluidic technologies has proven to be a promising sample delivery solution for biomolecular imaging studies and has the potential to be transformative for a range of applications in physics, biology, and chemistry. Here, we review the recent advances in the emerging field of microfluidic mix-and-jet sample delivery devices for the study of biomolecular reaction dynamics. First, we introduce the key parameters and dimensionless numbers involved in their design and characterisation. Then we critically review the techniques used to fabricate these integrated devices and discuss their advantages and disadvantages. We then summarise the most common experimental methods used for the characterisation of both the mixing and jetting components. Finally, we discuss future perspectives on the emerging field of microfluidic mix-and-jet sample delivery devices. In summary, this review aims to introduce this exciting new topic to the wider microfluidics community and to help guide future research in the field.