Innovative High-Throughput SAXS Methodologies Based on Photonic Lab-on-a-Chip Sensors: Application to Macromolecular Studies

A Multi-Drug Concentration Gradient Mixing Chip: A Novel Platform for High-Throughput Drug Combination Screening

Combinatorial drug therapy has emerged as a critically important strategy in medical research and patient treatment and involves the use of multiple drugs in concert to achieve a synergistic effect. This approach can enhance therapeutic efficacy while simultaneously mitigating adverse side effects. However, the process of identifying optimal drug combinations, including their compositions and dosages, is often a complex, costly, and time-intensive endeavor. To surmount these hurdles, we propose a novel microfluidic device capable of simultaneously generating multiple drug concentration gradients across an interlinked array of culture chambers. This innovative setup allows for the real-time monitoring of live cell responses. With minimal effort, researchers can now explore the concentration-dependent effects of single-agent and combination drug therapies. Taking neural stem cells (NSCs) as a case study, we examined the impacts of various growth factors-epithelial growth factor (EGF), platelet-derived growth factor (PDGF), and fibroblast growth factor (FGF)-on the differentiation of NSCs. Our findings indicate that an overdose of any single growth factor leads to an upsurge in the proportion of differentiated NSCs. Interestingly, the regulatory effects of these growth factors can be modulated by the introduction of additional growth factors, whether singly or in combination. Notably, a reduced concentration of these additional factors resulted in a decreased number of differentiated NSCs. Our results affirm that the successful application of this microfluidic device for the generation of multi-drug concentration gradients has substantial potential to revolutionize drug combination screening. This advancement promises to streamline the process and accelerate the discovery of effective therapeutic drug combinations.

On-Chip Photonic Detection Techniques for Non-Invasive In Situ Characterizations at the Microfluidic Scale

Microfluidics has emerged as a robust technology for diverse applications, ranging from bio-medical diagnostics to chemical analysis. Among the different characterization techniques that can be used to analyze samples at the microfluidic scale, the coupling of photonic detection techniques and on-chip configurations is particularly advantageous due to its non-invasive nature, which permits sensitive, real-time, high throughput, and rapid analyses, taking advantage of the microfluidic special environments and reduced sample volumes. Putting a special emphasis on integrated detection schemes, this review article explores the most relevant advances in the on-chip implementation of UV-vis, near-infrared, terahertz, and X-ray-based techniques for different characterizations, ranging from punctual spectroscopic or scattering-based measurements to different types of mapping/imaging. The principles of the techniques and their interest are discussed through their application to different systems.

In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning

Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.

Tools for computational design and high-throughput screening of therapeutic enzymes

Therapeutic enzymes are valuable biopharmaceuticals in various biomedical applications. They have been successfully applied for fibrinolysis, cancer treatment, enzyme replacement therapies, and the treatment of rare diseases. Still, there is a permanent demand to find new or better therapeutic enzymes, which would be sufficiently soluble, stable, and active to meet specific medical needs. Here, we highlight the benefits of coupling computational approaches with high-throughput experimental technologies, which significantly accelerate the identification and engineering of catalytic therapeutic agents. New enzymes can be identified in genomic and metagenomic databases, which grow thanks to next-generation sequencing technologies exponentially. Computational design and machine learning methods are being developed to improve catalytically potent enzymes and predict their properties to guide the selection of target enzymes. High-throughput experimental pipelines, increasingly relying on microfluidics, ensure functional screening and biochemical characterization of target enzymes to reach efficient therapeutic enzymes.

Machine Learning-Driven, Sensor-Integrated Microfluidic Device for Monitoring and Control of Supersaturation for Automated Screening of Crystalline Materials

Integrating sensors in miniaturized devices allow for fast and sensitive detection and precise control of experimental conditions. One of the potential applications of a sensor-integrated microfluidic system is to measure the solute concentration during crystallization. In this study, a continuous-flow microfluidic mixer is paired with an electrochemical sensor to enable in situ measurement of the supersaturation. This sensor is investigated as the predictive measurement of the supersaturation during the antisolvent crystallization of l-histidine in the water-ethanol mixture. Among the various metals tested in a batch system for their sensitivity toward l-histidine, Pt showed the highest sensitivity. A Pt-printed electrode was inserted in the continuous-flow microfluidic mixer, and the cyclic voltammograms of the system were obtained for different concentrations of l-histidine and different water-to-ethanol ratios. The sensor was calibrated for different ratios of antisolvent and concentrations of l-histidine with respect to the change of the measured anodic slope. Additionally, a machine-learning algorithm using neural networks was developed to predict the supersaturation of l-histidine from the measured anodic slope. The electrochemical sensors have shown sensitivity toward l-histidine, l-glutamic acid, and o-aminobenzoic acid, which consist of functional groups present in almost 80% of small-molecule drugs on the market. The machine learning-guided electrochemical sensors can be applied to other small molecules with similar functional groups for automated screening of crystallization conditions in microfluidic devices.

An innovative data processing method for studying nanoparticle formation in droplet microfluidics using X-rays scattering

X-ray scattering techniques provide a powerful means of characterizing the formation of nanoparticles in solution. Coupling these techniques to segmented-flow microfluidic devices that offer well-defined environments gives access to in situ time-resolved analysis, excellent reproducibility, and eliminates potential radiation damage. However, analysis of the resulting datasets can be extremely time-consuming, where these comprise frames corresponding to the droplets alone, the continuous phase alone, and to both at their interface. We here describe a robust, low-cost, and versatile droplet microfluidics device and use it to study the formation of magnetite nanoparticles with simultaneous synchrotron SAXS and WAXS. Lateral outlet capillaries facilitate the X-ray analysis and reaction times of between a few seconds and minutes can be accommodated. A two-step data processing method is then described that exploits the unique WAXS signatures of the droplets, continuous phase, and interfacial region to identify the frames corresponding to the droplets. These are then sorted, and the background scattering is subtracted using an automated frame-by-frame approach, allowing the signal from the nanoparticles to be isolated from the raw data. Modeling these data gives quantitative information about the evolution of the sizes and structures of the nanoparticles, in agreement with TEM observations. This versatile platform can be readily employed to study a wide range of dynamic processes in heterogeneous systems.

Small-angle X-ray scattering for the proteomics community: current overview and future potential

Introduction: Proteins are biological nanoparticles. For structural proteomics and hybrid structural biology, complementary methods are required that allow both high throughput and accurate automated data analysis. Small-angle X-ray scattering (SAXS) is a method for observing the size and shape of particles, such as proteins and complexes, in solution. SAXS data can be used to model both the structure, oligomeric state, conformational changes, and flexibility of biomolecular samples.Areas covered: The key principles of SAXS, its sample requirements, and its current and future applications for structural proteomics are briefly reviewed. Recent technical developments in SAXS experiments are discussed, and future potential of the method in structural proteomics is evaluated.Expert opinion: SAXS is a method suitable for several aspects of integrative structural proteomics, with current technical developments allowing for higher throughput and time-resolved studies, as well as the analysis of complex samples, such as membrane proteins. Increasing automation and streamlined data analysis are expected to equip SAXS for structure-based screening workflows. Originally, structural genomics had a heavy focus on folded, crystallizable proteins and complexes - SAXS is a method allowing an expansion of this focus to flexible and disordered systems.

Fundamentals to function: Quantitative and scalable approaches for measuring protein stability

Folding a linear chain of amino acids into a three-dimensional protein is a complex physical process that ultimately confers an impressive range of diverse functions. Although recent advances have driven significant progress in predicting three-dimensional protein structures from sequence, proteins are not static molecules. Rather, they exist as complex conformational ensembles defined by energy landscapes spanning the space of sequence and conditions. Quantitatively mapping the physical parameters that dictate these landscapes and protein stability is therefore critical to develop models that are capable of predicting how mutations alter function of proteins in disease and informing the design of proteins with desired functions. Here, we review the approaches that are used to quantify protein stability at a variety of scales, from returning multiple thermodynamic and kinetic measurements for a single protein sequence to yielding indirect insights into folding across a vast sequence space. The physical parameters derived from these approaches will provide a foundation for models that extend beyond the structural prediction to capture the complexity of conformational ensembles and, ultimately, their function.

OSTE+ for in situ SAXS analysis with droplet microfluidic devices

In recent years, microfluidic-based sample preparation techniques have emerged as a powerful tool for measurements at large scale X-ray facilities. Most often the microfluidic device was a form of hybrid system, i.e. an assembly of different materials, because a simple, versatile and inexpensive microfabrication method, on the one hand, and X-ray compatibility, on the other hand, cannot generally be achieved by the same material. The arrival of a new polymer family based on off-stoichiometric thiol-ene-epoxy (OSTE+) has recently redistributed the cards. In this context, we studied the relevance and the compatibility of OSTE+ for small-angle X-ray scattering (SAXS) studies. The material was characterized regarding its X-ray properties (transmission coefficient, attenuation coefficient, scattering pattern and polymer aging under X-ray light) and their comparison with those of the usual polymers used in microfluidics and/or for synchrotron radiation experiments. We show that OSTE+ has a better SAXS signal than polyimide, the polymer of reference in the SAXS community. Then a detailed protocol to manufacture a suitably thin full OSTE+ chip (total thickness <500 μm) is described and the potency of full OSTE+ devices for in situ SAXS studies is highlighted in two case-studies: the characterization of gold nanoparticles and the precipitation of cerium oxalate particles, both in moving droplets. Additionally, a method to analyze the scattering signals from droplet and carrier phase in a segmented flow is proposed.

SAS-cam: a program for automatic processing and analysis of small-angle scattering data

Small-angle X-ray scattering (SAXS) is a widely used method for investigating biological macromolecules in structural biology, providing information on macromolecular structures and dynamics in solution. Modern synchrotron SAXS beamlines are characterized as high-throughput, capable of collecting large volumes of data and thus demanding fast data processing for efficient beamline operations. This article presents a fully automated and high-throughput SAXS data analysis pipeline, SAS-cam, primarily based on the SASTBX package. Five modules are included in SAS-cam, encompassing the data analysis process from data reduction to model interpretation. The model parameters are extracted from SAXS profiles and stored in an HTML summary file, ready for online visualization using a web browser. SAS-cam can provide the user with the possibility of optimizing experimental parameters based on real-time feedback and it therefore significantly improves the efficiency of beam time. SAS-cam is installed on the BioSAXS beamline at the Shanghai Synchrotron Radiation Facility. The source code is available upon request.

Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology

Small-angle X-ray scattering (SAXS) has emerged as an enabling integrative technique for comprehensive analyses of macromolecular structures and interactions in solution. Over the past two decades, SAXS has become a mainstay of the structural biologist's toolbox, supplying multiplexed measurements of molecular shape and dynamics that unveil biological function. Here, we discuss evolving SAXS theory, methods, and applications that extend the field of small-angle scattering beyond simple shape characterization. SAXS, coupled with size-exclusion chromatography (SEC-SAXS) and time-resolved (TR-SAXS) methods, is now providing high-resolution insight into macromolecular flexibility and ensembles, delineating biophysical landscapes, and facilitating high-throughput library screening to assess macromolecular properties and to create opportunities for drug discovery. Looking forward, we consider SAXS in the integrative era of hybrid structural biology methods, its potential for illuminating cellular supramolecular and mesoscale structures, and its capacity to complement high-throughput bioinformatics sequencing data. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.

An Interdigital Capacitor for Microwave Heating at 25 GHz and Wideband Dielectric Sensing of nL Volumes in Continuous Microfluidics

This paper proposes a miniature microwave-microfluidic chip based on continuous microfluidics and a miniature interdigital capacitor (IDC). The novel chip consists of three individually accessible heaters, three platinum temperature sensors and two liquid cooling and mixing zones. The IDC is designed to achieve localized, fast and uniform heating of nanoliter volumes flowing through the microfluidic channel. The heating performance of the IDC located on the novel chip was evaluated using a fluorescent dye (Rhodamine B) diluted in demineralized water on a novel microwave-optical-fluidic (MOF) measurement setup. The MOF setup allows simultaneous microwave excitation of the IDC by means of a custom-made printed circuit board (connected to microwave equipment) placed in a top stage of a microscope, manipulation of liquid flowing through the channel located over the IDC with a pump and optical inspection of the same liquid flowing over the IDC using a fast camera, a light source and the microscope. The designed IDC brings a liquid volume of around 1.2 nL from room temperature to 100 °C in 21 ms with 1.58 W at 25 GHz. Next to the heating capability, the designed IDC can dielectrically sense the flowing liquid. Liquid sensing was evaluated on different concentration of water-isopropanol mixtures, and a reflection coefficient magnitude change of 6 dB was recorded around 8.1 GHz, while the minimum of the reflection coefficient magnitude shifted in the same frequency range for 60 MHz.

The role of small-angle scattering in structure-based screening applications

In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging. Such information is important when for example investigating conformational changes involved in inhibitory and regulatory mechanisms where binding events do not necessarily cause functional changes. Thus, we summarise here the current and prospective capabilities of SAXS-based screening in the context of other methods that yield structural information. Broad guidelines are also provided to assist readers in preparing screening protocols that are tailored to available X-ray sources.

Microfluidic devices for small-angle neutron scattering

A comparative examination is presented of materials and approaches for the fabrication of microfluidic devices for small-angle neutron scattering (SANS). Representative inorganic glasses, metals, and polymer materials and devices are evaluated under typical SANS configurations. Performance criteria include neutron absorption, scattering background and activation, as well as spatial resolution, chemical compatibility and pressure resistance, and also cost, durability and manufacturability. Closed-face polymer photolithography between boron-free glass (or quartz) plates emerges as an attractive approach for rapidly prototyped microfluidic SANS devices, with transmissions up to ∼98% and background similar to a standard liquid cell (I ≃ 10-3 cm-1). For applications requiring higher durability and/or chemical, thermal and pressure resistance, sintered or etched boron-free glass and silicon devices offer superior performance, at the expense of various fabrication requirements, and are increasingly available commercially.

High-Throughput Optofluidic Acquisition of Microdroplets in Microfluidic Systems

Droplet optofluidics technology aims at manipulating the tiny volume of fluids confined in micro-droplets with light, while exploiting their interaction to create "digital" micro-systems with highly significant scientific and technological interests. Manipulating droplets with light is particularly attractive since the latter provides wavelength and intensity tunability, as well as high temporal and spatial resolution. In this review study, we focus mainly on recent methods developed in order to monitor real-time analysis of droplet size and size distribution, active merging of microdroplets using light, or to use microdroplets as optical probes.

Protein separation under a microfluidic regime

Lab-on-a-Chip (LoC), or micro-Total Analysis Systems (μTAS), is recognized as a powerful analytical technology with high capabilities, though end-user products for protein purification are still far from being available on the market. Remarkable progress has been achieved in the separation of nucleic acids and proteins using electrophoretic microfluidic devices, while pintsize devices have been developed for protein isolation according to miniaturized chromatography principles (size, charge, affinity, etc.). In this work, we review the latest advances in the fabrication of components, detection methods and commercial implementation for the separation of biological macromolecules based on microfluidic systems, with some critical remarks on the perspectives of their future development towards standardized microfluidic systems and protocols. An outlook on the current needs and future applications is also presented.