Fast acoustic droplet ejection based on annular array transducer

Acoustic droplet ejection (ADE) has become the preferred method for liquid transfer in a variety of applications including synthetic biology, genotyping and drug discovery. Comparing with traditional pipetting techniques, the accuracy and data reproducibility of ADE based liquid transfer are improved, waste and cost are reduced, and cross-contamination is eliminated. The key component in the ADE system is the ultrasound transducer, which is responsible for generating focused ultrasound beam for droplet ejection. However, current ADE systems commonly utilize a single-element focused transducer with a fixed focal length that require mechanical movement to focus on the liquid surface, resulting in reduced liquid transfer efficiency. In this study, we first present a high-frequency annular array transducer for the ADE technology, which enables rapid and dynamic axial focusing to the liquid surface without mechanically moving the transducer, thereby accelerating liquid transfer. Experimental results show that the proposed 10 MHz, 5-element annular array transducer has good dynamic axial focusing ability, and can achieve accurate and stable droplet ejection of nanoliter volume at the designed focal length of 26-32 mm. Our results highlight the potential of the annular array transducer in advancing ADE system for rapid liquid transfer. This technology is expected to be useful in a variety of applications where precise and high-throughput liquid transfer is crucial.

Investigation of nanostructured lipid carriers for fast intracellular localization screening using the Echo liquid handler

In the field of precision medicine, therapy is optimized individually for each patient, enhancing efficacy while reducing side effects. This involves the identification of promising drug candidates through high-throughput screening on human derived cells in culture. However, screening of drugs which have poor solubility or permeability remains challenging, especially when targeting intracellular components. Therefore, encapsulation of drugs into advanced delivery systems such as nanostructured lipid carries (NLC) becomes necessary. Here we show that the cellular uptake of NLC with different matrix compositions can be assessed in a high-throughput screening system based on acoustic droplet ejection (ADE) technology (Echo liquid handler). Our findings indicate that surface tension and viscosity of the NLC dispersions need to be tailored to enable a reliable ADE transfer. The automated NLC uptake studies indicated that the composition of the matrix, more specifically the amount of oleic acid, significantly influenced cellular uptake. The data obtained were corroborated by imaging based and spectral flow cytometry cellular uptake studies. These findings thus not only provide the basis for a screening tool to rapidly identify the efficacy of NLC uptake but also enable a next step toward precision high-throughput drug screening under consideration of an optimized drug delivery system.

High-resolution acoustic ejection mass spectrometry for high-throughput library screening

An approach is described for high-throughput quality assessment of drug candidate libraries using high-resolution acoustic ejection mass spectrometry (AEMS). Sample introduction from 1536-well plates is demonstrated for this application using 2.5 nL acoustically dispensed sample droplets into an Open Port Interface (OPI) with pneumatically assisted electrospray ionization at a rate of one second per sample. Both positive and negative ionization are shown to be essential to extend the compound coverage of this protease inhibitor-focused library. Specialized software for efficiently interpreting this data in 1536-well format is presented. A new high-throughput method for quantifying the concentration of the components (HTQuant) is proposed that neither requires adding an internal standard to each well nor further encumbers the high-throughput workflow. This approach for quantitation requires highly reproducible peak areas, which is shown to be consistent within 4.4 % CV for a 1536-well plate analysis. An approach for troubleshooting the workflow based on the background ion current signal is also presented. The AEMS data is compared to the industry standard LC/PDA/ELSD/MS approach and shows similar coverage but at 180-fold greater throughput. Despite the same ionization process, both methods confirmed the presence of a small percentage of compounds in wells that the other did not. The data for this relatively small, focused library is compared to a larger, more chemically diverse library to indicate that this approach can be more generally applied beyond this single case study. This capability is particularly timely considering the growing implementation of artificial intelligence strategies that require the input of large amounts of high-quality data to formulate predictions relevant to the drug discovery process. The molecular structures of the 872-compound library analyzed here are included to begin the process of correlating molecular structures with ionization efficiency and other parameters as an initial step in this direction.

An Automated Cell-Free Workflow for Transcription Factor Engineering

The design and optimization of metabolic pathways, genetic systems, and engineered proteins rely on high-throughput assays to streamline design-build-test-learn cycles. However, assay development is a time-consuming and laborious process. Here, we create a generalizable approach for the tailored optimization of automated cell-free gene expression (CFE)-based workflows, which offers distinct advantages over in vivo assays in reaction flexibility, control, and time to data. Centered around designing highly accurate and precise transfers on the Echo Acoustic Liquid Handler, we introduce pilot assays and validation strategies for each stage of protocol development. We then demonstrate the efficacy of our platform by engineering transcription factor-based biosensors. As a model, we rapidly generate and assay libraries of 127 MerR and 134 CadR transcription factor variants in 3682 unique CFE reactions in less than 48 h to improve limit of detection, selectivity, and dynamic range for mercury and cadmium detection. This was achieved by assessing a panel of ligand conditions for sensitivity (to 0.1, 1, 10 μM Hg and 0, 1, 10, 100 μM Cd for MerR and CadR, respectively) and selectivity (against Ag, As, Cd, Co, Cu, Hg, Ni, Pb, and Zn). We anticipate that our Echo-based, cell-free approach can be used to accelerate multiple design workflows in synthetic biology.

ReBiA-Robotic Enabled Biological Automation: 3D Epithelial Tissue Production

The Food and Drug Administration's recent decision to eliminate mandatory animal testing for drug approval marks a significant shift to alternative methods. Similarly, the European Parliament is advocating for a faster transition, reflecting public preference for animal-free research practices. In vitro tissue models are increasingly recognized as valuable tools for regulatory assessments before clinical trials, in line with the 3R principles (Replace, Reduce, Refine). Despite their potential, barriers such as the need for standardization, availability, and cost hinder their widespread adoption. To address these challenges, the Robotic Enabled Biological Automation (ReBiA) system is developed. This system uses a dual-arm robot capable of standardizing laboratory processes within a closed automated environment, translating manual processes into automated ones. This reduces the need for process-specific developments, making in vitro tissue models more consistent and cost-effective. ReBiA's performance is demonstrated through producing human reconstructed epidermis, human airway epithelial models, and human intestinal organoids. Analyses confirm that these models match the morphology and protein expression of manually prepared and native tissues, with similar cell viability. These successes highlight ReBiA's potential to lower barriers to broader adoption of in vitro tissue models, supporting a shift toward more ethical and advanced research methods.

Acoustic droplet ejection facilitates cell-based high-throughput screenings using natural products

Natural Products (NPs) are one of the main sources for drug discovery. Many clinical drugs are NPs or NP-inspired compounds, and recently discovered New Chemical Entities (NCEs) of NPs are emerging as promising new drugs. High-Throughput Screening (HTS) of large sample sets or libraries has grown to be vital for the drug discovery field. Industrial-scale HTS of NP libraries can be limited due to the difficulties entailed in working with tiny extract volumes and the variability in viscosity of NP extracts. For these reasons, the implementation of new technologies to miniaturize different reagent volumes grows to be fundamental. Since Acoustic Droplet Ejection (ADE) emerged as a helpful tool in HTS campaigns for the transference of compound libraries. The aim of this work was to test the effectiveness of ADE for the dispensation of NP extract libraries in cell-based HTS assays.

High-Throughput Compound Quality Assessment with High-Mass-Resolution Acoustic Ejection Mass Spectrometry: An Automatic Data Processing Toolkit

Pharmacological screening heavily relies on the reliability of compound libraries. To ensure the accuracy of screening results, fast and reliable quality control (QC) of these libraries is essential. While liquid chromatography (LC) with ultraviolet (UV) or mass spectrometry (MS) detection has been employed for molecule QC on small sample sets, the analytical throughput becomes a bottleneck when dealing with large libraries. Acoustic ejection mass spectrometry (AEMS) is a high-throughput analytical platform that covers a broad range of chemical structural space. In this study, we present the utilization of an AEMS system equipped with a high-resolution MS analyzer for high-throughput compound QC. To facilitate efficient data processing, which is a key challenge for such a high-throughput application, we introduce an automatic data processing toolkit that allows for the high-throughput assessment of the sample standards' quantitative and qualitative characteristics, including purity calculation with the background processing option. Moreover, the toolkit includes a module for quantitatively comparing spectral similarity with the reference library. Integrating the described high-resolution AEMS system with the data processing toolkit effectively eliminates the analytical bottleneck, enabling a rapid and reliable compound quality assessment of large-scale compound libraries.

Merging cultures and disciplines to create a drug discovery ecosystem at Virginia commonwealth university: Medicinal chemistry, structural biology, molecular and behavioral pharmacology and computational chemistry

The Department of Medicinal Chemistry, together with the Institute for Structural Biology, Drug Discovery and Development, at Virginia Commonwealth University (VCU) has evolved, organically with quite a bit of bootstrapping, into a unique drug discovery ecosystem in response to the environment and culture of the university and the wider research enterprise. Each faculty member that joined the department and/or institute added a layer of expertise, technology and most importantly, innovation, that fertilized numerous collaborations within the University and with outside partners. Despite moderate institutional support with respect to a typical drug discovery enterprise, the VCU drug discovery ecosystem has built and maintained an impressive array of facilities and instrumentation for drug synthesis, drug characterization, biomolecular structural analysis and biophysical analysis, and pharmacological studies. Altogether, this ecosystem has had major impacts on numerous therapeutic areas, such as neurology, psychiatry, drugs of abuse, cancer, sickle cell disease, coagulopathy, inflammation, aging disorders and others. Novel tools and strategies for drug discovery, design and development have been developed at VCU in the last five decades; e.g., fundamental rational structure-activity relationship (SAR)-based drug design, structure-based drug design, orthosteric and allosteric drug design, design of multi-functional agents towards polypharmacy outcomes, principles on designing glycosaminoglycans as drugs, and computational tools and algorithms for quantitative SAR (QSAR) and understanding the roles of water and the hydrophobic effect.

Room temperature crystallography and X-ray spectroscopy of metalloenzymes

The ultrashort (10s of femtoseconds) X-ray pulses generated by X-ray free electron lasers enable the measurement of X-ray diffraction and spectroscopic data from radiation-sensitive metalloenzymes at room temperature while mostly avoiding the effects of radiation damage usually encountered when performing such experiments at synchrotron sources. Here we discuss an approach to measure both X-ray emission and X-ray crystallographic data at the same time from the same sample volume. The droplet-on-tape setup described allows for efficient sample use and the integration of different reaction triggering options in order to conduct time-resolved studies with limited sample amounts. The approach is illustrated by two examples, photosystem II that catalyzes the light-driven oxidation of water to oxygen, and isopenicillin N synthase, an enzyme that catalyzes the double ring cyclization of a tripeptide precursor into the β-lactam isopenicillin and can be activated by oxygen exposure. We describe the necessary steps to obtain microcrystals of both proteins as well as the operation procedure for the drop-on-tape setup and details of the data acquisition and processing involved in this experiment. At the end, we present how the combination of time-resolved X-ray emission spectra and diffraction data can be used to improve the knowledge about the enzyme reaction mechanism.

'Chemistry at the speed of sound': automated 1536-well nanoscale synthesis of 16 scaffolds in parallel

Screening of large and diverse libraries is the 'bread and butter' in the first phase of the discovery of novel drugs. However, maintenance and periodic renewal of high-quality large compound collections pose considerable logistic, environmental and monetary problems. Here, we exercise an alternative, the 'on-the-fly' synthesis of large and diverse libraries on a nanoscale in a highly automated fashion. For the first time, we show the feasibility of the synthesis of a large library based on 16 different chemistries in parallel on several 384-well plates using the acoustic dispensing ejection (ADE) technology platform. In contrast to combinatorial chemistry, we produced 16 scaffolds at the same time and in a sparse matrix fashion, and each compound was produced by a random combination of diverse large building blocks. The synthesis, analytics, resynthesis of selected compounds, and chemoinformatic analysis of the library are described. The advantages of the herein described automated nanoscale synthesis approach include great library diversity, absence of library storage logistics, superior economics, speed of synthesis by automation, increased safety, and hence sustainable chemistry.

Exploring the Structural Variability of Dynamic Biological Complexes by Single-Particle Cryo-Electron Microscopy

Biological macromolecules and assemblies precisely rearrange their atomic 3D structures to execute cellular functions. Understanding the mechanisms by which these molecular machines operate requires insight into the ensemble of structural states they occupy during the functional cycle. Single-particle cryo-electron microscopy (cryo-EM) has become the preferred method to provide near-atomic resolution, structural information about dynamic biological macromolecules elusive to other structure determination methods. Recent advances in cryo-EM methodology have allowed structural biologists not only to probe the structural intermediates of biochemical reactions, but also to resolve different compositional and conformational states present within the same dataset. This article reviews newly developed sample preparation and single-particle analysis (SPA) techniques for high-resolution structure determination of intrinsically dynamic and heterogeneous samples, shedding light upon the intricate mechanisms employed by molecular machines and helping to guide drug discovery efforts.

Rapid prototyping of functional acoustic devices using laser manufacturing

Acoustic patterning of micro-particles has many important biomedical applications. However, fabrication of such microdevices is costly and labor-intensive. Among conventional fabrication methods, photo-lithography provides high resolution but is expensive and time consuming, and not ideal for rapid prototyping and testing for academic applications. In this work, we demonstrate a highly efficient method for rapid prototyping of acoustic patterning devices using laser manufacturing. With this method we can fabricate a newly designed functional acoustic device in 4 hours. The acoustic devices fabricated using this method can achieve sub-wavelength, complex and non-periodic patterning of microparticles and biological objects with a spatial resolution of 60 μm across a large active manipulation area of 10 × 10 mm2.

Where have all the ions gone, long time passing? Tandem quadrupole mass spectrometers with atmospheric pressure ionization sensitivity gains since the mid-1970s. A perspective

The gains in sensitivity since 1975 for quadrupole mass spectrometers equipped with atmospheric pressure ionization (API), and in particular triple quadrupole mass spectrometers (QqQs) since 1981, have been driven by the needs of the environmental, biomedical, agricultural, and other scientific research, industrial, regulatory, legal, and sporting communities to continually achieve lower limits of quantitation and identification. QqQs have realized a one-million-fold improvement in sensitivity attempting to address these needs over the past two score years. It is the purpose of this article to describe how that came about, not through an exhaustive review of the literature, but rather by describing what general approaches were used across the industry to improve sensitivity and provide some examples to illustrate its evolution. The majority of the gains came from the ion source and its interface to the vacuum system. "Sampling efficiency" is a measurement of the losses in this area so will be a focus of this review. The discovery of the phenomenon of collisional focusing was key to improving sampling efficiency because it enabled designs that increased the ion-containing gas loads from the ion source, using staged differential pumping backed by increasingly larger pumps, and prevented the scattering losses of ions in the resulting gas expansion inside vacuum. Likewise, systems with smaller pumps and lower ion-containing gas loads could be designed with size and cost reduction in mind while maintaining reasonable sampling efficiencies. As a consequence, advancements in the designs of both larger and smaller turbomolecular vacuum pumps were accelerated by pump manufacturers to accommodate the explosive growth in the use of API-QqQ and API-ion trap mass spectrometers that occurred in the 1990s and continued into the new millennium. Sampling efficiency was further improved by increasing the ion yield from electrospray by increasing the rate of droplet desolvation. An estimate of the practical limit to further sensitivity improvements beyond what has been achieved to date is provided to shed light on what to expect in the future. Lastly, the implications and unforeseen consequences of the sensitivity gains are considered with a particular focus on how they have enabled a dramatic increase in daily sample throughput on triple quadrupole and other types of mass spectrometers.

Automation and Expansion of EMMA Assembly for Fast-Tracking Mammalian System Engineering

With applications from functional genomics to the production of therapeutic biologics, libraries of mammalian expression vectors have become a cornerstone of modern biological investigation and engineering. Multiple modular vector platforms facilitate the rapid design and assembly of vectors. However, such systems approach a technical bottleneck when a library of bespoke vectors is required. Utilizing the flexibility and robustness of the Extensible Mammalian Modular Assembly (EMMA) toolkit, we present an automated workflow for the library-scale design, assembly, and verification of mammalian expression vectors. Vector design is simplified using our EMMA computer-aided design tool (EMMA-CAD), while the precision and speed of acoustic droplet ejection technology are applied in vector assembly. Our pipeline facilitates significant reductions in both reagent usage and researcher hands-on time compared with manual assembly, as shown by system Q-metrics. To demonstrate automated EMMA performance, we compiled a library of 48 distinct plasmid vectors encoding either CRISPR interference or activation modalities. Characterization of the workflow parameters shows that high assembly efficiency is maintained across vectors of various sizes and design complexities. Our system also performs strongly compared with manual assembly efficiency benchmarks. Alongside our automated pipeline, we present a straightforward strategy for integrating gRNA and Cas modules into the EMMA platform, enabling the design and manufacture of valuable genome editing resources.

Controllable Droplet Ejection of Multiple Reagents through Focused Acoustic Beams

Acoustic droplet ejection (ADE) technology has revolutionized fluid handling with its contactless and fast fluid transfer. For precise droplet ejection and stable droplet coalescence at the target substrates for further detection, the input power of the ADE system needs to be adjusted. Currently, the existing power control method depends on scanning the source fluid wells one by one, which cannot afford precise and highly efficient droplet velocity adjustment, and the complicated operation caused by the repeated power evaluation processes for thousands of fluid transfers will waste much time. We propose a new method, which realizes the controllable ejection of multiple reagents by analyzing the effect of the product of kinematic viscosity and surface tension of the reagents on the droplet initial velocity. The experimental results obtained by ejecting dimethyl sulfoxide coincide well with the predicted results, and the relative error in the droplet initial velocity is mostly less than 8%. On the basis of the input power prediction method proposed in this paper, the ADE system is successfully constructed for continuous dispensing of polystyrene microspheres as cell surrogates, which provided an advanced liquid handling solution for research in biochemistry and other fields.

High-Throughput Analysis from Complex Matrices: Acoustic Ejection Mass Spectrometry from Phase-Separated Fluid Samples

Acoustic ejection mass spectrometry is a novel high-throughput analytical technology that delivers high reproducibility without carryover observed. It eliminates the chromatography step used to separate analytes from matrix components. Fully-automated liquid–liquid extraction is widely used for sample cleanup, especially in high-throughput applications. We introduce a workflow for direct AEMS analysis from phase-separated liquid samples and explore high-throughput analysis from complex matrices. We demonstrate the quantitative determination of fentanyl from urine using this two-phase AEMS approach, with a LOD lower than 1 ng/mL, quantitation precision of 15%, and accuracy better than ±10% over the range of evaluation (1–100 ng/mL). This workflow offers simplified sample preparation and higher analytical throughput for some bioanalytical applications, in comparison to an LC-MS based approach.

Picomole-Scale Synthesis and Screening of Macrocyclic Compound Libraries by Acoustic Liquid Transfer

Macrocyclic compounds are an attractive class of therapeutic ligands against challenging targets, such as protein-protein interactions. However, the development of macrocycles as drugs is hindered by the lack of large combinatorial macrocyclic libraries, which are cumbersome, expensive, and time consuming to make, screen, and deconvolute. Here, we established a strategy for synthesizing and screening combinatorial libraries on a picomolar scale by using acoustic droplet ejection to combine building blocks at nanoliter volumes, which reduced the reaction volumes, reagent consumption, and synthesis time. As a proof-of-concept, we assembled a 2700-member target-focused macrocyclic library that we could subsequently assay in the same microtiter synthesis plates, saving the need for additional transfers and deconvolution schemes. We screened the library against the MDM2-p53 protein-protein interaction and generated micromolar and sub-micromolar inhibitors. Our approach based on acoustic liquid transfer provides a general strategy for the development of macrocycle ligands.

Macrodrop-Impact-Mediated Fluid Microdispensing

High-resolution fluid dispensing techniques play a critical role in modern digital microfluidics, micro-biosensing, and advanced fabrication. Though most of existing dispensers can achieve precise and high-throughput fluid dispensing, they suffer from some inherent problems, such as specially fabricated dispensing micronozzles/microtips, large operating systems, low volume tunability, and poor performance for low surface tension liquids and liquids containing solid/liquid additives. Herein, the authors propose a facile, low-frequency micro dispensing technique based on the Rayleigh-Plateau instability of singular liquid jets, which are stimulated by the air cavity collapse arising in the impact of microliter drops on non-wetting surfaces. This novel dispensing strategy is capable to produce single microdrops of low-viscosity liquids with a tunable volume from picoliters to nanoliters, and the operational surface tension range covers most laboratory solvents. The dispensing function is implemented without using small-dimension nozzles/tips and enables handling diverse complex liquids. Moreover, the rather simple operating platform allows the integration of the whole dispensing function into a handy portable device with a low cost. Employing this microdispensing technique, the authors have controlled microchemical reactions, handled liquid samples in biological analysis, and fabricated smart materials and devices. The authors envision that this rational microdrop generator would find applications in various research areas.

Building protein networks in synthetic systems from the bottom-up

The recent development of synthetic biology has expanded the capability to design and construct protein networks outside of living cells from the bottom-up. The new capability has enabled us to assemble protein networks for the basic study of cellular pathways, expression of proteins outside cells, and building tissue materials. Furthermore, the integration of natural and synthetic protein networks has enabled new functions of synthetic or artificial cells. Here, we review the underlying technologies for assembling protein networks in liposomes, water-in-oil droplets, and biomaterials from the bottom-up. We cover the recent applications of protein networks in biological transduction pathways, energy self-supplying systems, cellular environmental sensors, and cell-free protein scaffolds. We also review new technologies for assembling protein networks, including multiprotein purification methods, high-throughput assay screen platforms, and controllable fusion of liposomes. Finally, we present existing challenges towards building protein networks that rival the complexity and dynamic response akin to natural systems. This review addresses the gap in our understanding of synthetic and natural protein networks. It presents a vision towards developing smart and resilient protein networks for various biomedical applications.

Flexible Pico-Liter Acoustic Droplet Ejection Based on High-Frequency Ultrasound Transducer

Acoustic droplet ejection (ADE) uses the acoustic energy produced by a focused ultrasound beam to provide a noncontact, highly precise, automatic, and cost-effective liquid transfer method for life science applications. The reported minimum precision of the current acoustic liquid transfer technology is 1 nL. Since precision improvement always brings valuable results in biological research, it is highly necessary to develop pico-liter precision liquid transfer technology. In this work, we developed a 40-MHz ultrahigh -frequency focused ultrasound transducer with a large aperture of 7×7 mm² and a wide bandwidth of 76.4%. The designed transducer can successfully eject pico-liter droplets, and the droplet ejection accuracy ranges from 28 to 439 pL. The effects of the acoustic parameters, including excitation amplitude, pulsewidth, and frequency, on the size of the ejected droplet were studied. A wide range of ejected droplet sizes could be obtained by adjusting the acoustic parameters, thereby making liquid transfer flexible. The flexible pico-liter liquid transfer based on the wide-bandwidth, high-frequency ultrasound transducer is easier to achieve automatically, and thus it has broad prospects in biological research and industrial applications.

Multiscale 3D Bioprinting by Nozzle-Free Acoustic Droplet Ejection

Bioprinting allows the manufacture of complex cell-laden hydrogel constructs that can mature into tissue replacements in subsequent cell culture processes. The nozzles used in currently available bioprinters limit the print resolution and at dimensions below 100 µm clogging is expected. Most critically, the reduction of nozzle diameter also increases shear stress during printing. At critical shear stress, mechanical damage to printed cells triggers cell death. To overcome these limitations, a novel 3D bioprinting method based on the principle of acoustic droplet ejection (ADE) is introduced here. The absence of a nozzle in this method minimizes critical shear stress. A numerical simulation reveals that maximum shear stress during the ADE process is 2.7 times lower than with a Ø150 µm microvalve nozzle. Printing of cell clusters contained in droplets at the millimeter length scale, as well as in droplets the size of a single cell, is feasible. The precise 3D build-up of cell-laden structures is demonstrated and evidence is provided that there are no negative effects on stem cell morphology, proliferation, or differentiation capacities. This multiscale acoustic bioprinting technique thus holds promise for cell-preserving creation of complex and individualized cell-laden 3D hydrogel structures.

Breast tumours maintain a reservoir of subclonal diversity during expansion

Our knowledge of copy number evolution during the expansion of primary breast tumours is limited^1,2. Here, to investigate this process, we developed a single-cell, single-molecule DNA-sequencing method and performed copy number analysis of 16,178 single cells from 8 human triple-negative breast cancers and 4 cell lines. The results show that breast tumours and cell lines comprise a large milieu of subclones (7-22) that are organized into a few (3-5) major superclones. Evolutionary analysis suggests that after clonal TP53 mutations, multiple loss-of-heterozygosity events and genome doubling, there was a period of transient genomic instability followed by ongoing copy number evolution during the primary tumour expansion. By subcloning single daughter cells in culture, we show that tumour cells rediversify their genomes and do not retain isogenic properties. These data show that triple-negative breast cancers continue to evolve chromosome aberrations and maintain a reservoir of subclonal diversity during primary tumour growth.

A review on acoustic droplet ejection technology and system

The pace of change in chemical and biological research enabled by improved detection systems demands fundamental liquid handling and sample preparation changes. The acoustic droplet ejection (ADE)-based liquid handling method has the advantages of improving precision and data reproducibility, reducing costs, hands-on time, and eliminating waste. ADE gradually replaced traditional aspiration-and-dispense liquid-handling robots in applications such as synthetic biology, genotyping, personalized medicine, and next-generation sequencing. This review emphatically introduces the setup of the ADE system and the critical technologies of each part, including acoustic droplet generation, optimized design of the source fluid wells, droplet coalescence, and power control. The advantages and disadvantages of these technologies are discussed, and the future development of acoustic droplet ejection technology is also predicted.

High-Throughput Mass Spectrometry for Hit Identification: Current Landscape and Future Perspectives

For nearly two decades mass spectrometry has been used as a label-free, direct-detection method for both functional and affinity-based screening of a wide range of therapeutically relevant target classes. Here, we present an overview of several established and emerging mass spectrometry platforms and summarize the unique strengths and performance characteristics of each as they apply to high-throughput screening. Multiple examples from the recent literature are highlighted in order to illustrate the power of each individual technique, with special emphasis given to cases where the use of mass spectrometry was found to be differentiating when compared with other detection formats. Indeed, as many of these examples will demonstrate, the inherent strengths of mass spectrometry-sensitivity, specificity, wide dynamic range, and amenability to complex matrices-can be leveraged to enhance the discriminating power and physiological relevance of assays included in screening cascades. It is our hope that this review will serve as a useful guide to readers of all backgrounds and experience levels on the applicability and benefits of mass spectrometry in the search for hits, leads, and, ultimately, drugs.

Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources

Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.

High-throughput in situ experimental phasing

In this article, a new approach to experimental phasing for macromolecular crystallography (MX) at synchrotrons is introduced and described for the first time. It makes use of automated robotics applied to a multi-crystal framework in which human intervention is reduced to a minimum. Hundreds of samples are automatically soaked in heavy-atom solutions, using a Labcyte Inc. Echo 550 Liquid Handler, in a highly controlled and optimized fashion in order to generate derivatized and isomorphous crystals. Partial data sets obtained on MX beamlines using an in situ setup for data collection are processed with the aim of producing good-quality anomalous signal leading to successful experimental phasing.

Creating and screening natural product libraries

Covering: up to 2020The National Cancer Institute of the United States (NCI) has initiated a Cancer Moonshot program entitled the NCI Program for Natural Product Discovery. As part of this effort, the NCI is producing a library of 1 000 000 partially purified natural product fractions which are being plated into 384-well plates and provided to the research community free of charge. As the first 326 000 of these fractions have now been made available, this review seeks to describe the general methods used to collect organisms, extract those organisms, and create a prefractionated library. Importantly, this review also details both cell-based and cell-free bioassay methods and the adaptations necessary to those methods to productively screen natural product libraries. Finally, this review briefly describes post-screen dereplication and compound purification and scale up procedures which can efficiently identify active compounds and produce sufficient quantities of natural products for further pre-clinical development.

Integration of Acoustic Liquid Handling into Quantitative Analysis of Biological Matrix Samples

Acoustic liquid handlers deliver small volumes (nL-µL) of multiple fluid types with accuracy and dynamic viscosity profiling. They are widely used in the pharmaceutical industry with applications extending from high-throughput screening in compound management to gene expression sequencing, genomic and epigenetic assays, and cell-based assays. The capability of the Echo to transfer small volumes of multiple types of fluids could benefit bioanalysis assays by minimization of sample volume and by simplifying dilution procedures by direct dilution. In this study, we evaluated the Labcyte Echo 525 liquid handler for its ability to deliver small volumes of sample preparations in biological matrix (plasma and serum) and to assess the feasibility of integration of the Echo with three types of bioanalytical assay platforms: microplate enzyme-linked immunosorbent assay, Gyrolab immunoassay, and liquid chromatography with tandem mass spectrometry. The results demonstrated acceptable consistency of dispensed plasma samples from multiple lots and species by the Echo. Equivalent assay performance demonstrated between the Echo and manual liquid procedures indicated great potential for the integration of the Echo with the bioanalytical assay, which allows the successful implementation of microsampling strategies in drug discovery and development.

NanoGBS: A Miniaturized Procedure for GBS Library Preparation

High-throughput reduced-representation sequencing (RRS)-based genotyping methods, such as genotyping-by-sequencing (GBS), have provided attractive genotyping solutions in numerous species. Here, we present NanoGBS, a miniaturized and eco-friendly method for GBS library construction. Using acoustic droplet ejection (ADE) technology, NanoGBS libraries were constructed in tenfold smaller volumes compared to standard methods (StdGBS) and leading to a reduced use of plastics of up to 90%. A high-quality DNA library and SNP catalogue were obtained with extensive overlap (96%) in SNP loci and 100% agreement in genotype calls compared to the StdGBS dataset with a high level of accuracy (98.5%). A highly multiplexed pool of GBS libraries (768-plex) was sequenced on a single Ion Proton PI chip and yielded enough SNPs (~4K SNPs; 1.5 SNP per cM, on average) for many high-volume applications. Combining NanoGBS library preparation and increased multiplexing can dramatically reduce (72%) genotyping cost per sample. We believe that this approach will greatly facilitate the adoption of marker applications where extremely high throughputs are required and cost is still currently limiting.

Droplet Incubation and Splitting in Open Microfluidic Channels

Droplet-based microfluidics enables compartmentalization and controlled manipulation of small volumes. Open microfluidics provides increased accessibility, adaptability, and ease of manufacturing compared to closed microfluidic platforms. Here, we begin to build a toolbox for the emerging field of open channel droplet-based microfluidics, combining the ease of use associated with open microfluidic platforms with the benefits of compartmentalization afforded by droplet-based microfluidics. We develop fundamental microfluidic features to control droplets flowing in an immiscible carrier fluid within open microfluidic systems. Our systems use capillary flow to move droplets and carrier fluid through open channels and are easily fabricated through 3D printing, micromilling, or injection molding; further, droplet generation can be accomplished by simply pipetting an aqueous droplet into an empty open channel. We demonstrate on-chip incubation of multiple droplets within an open channel and subsequent transport (using an immiscible carrier phase) for downstream experimentation. We also present a method for tunable droplet splitting in open channels driven by capillary flow. Additional future applications of our toolbox for droplet manipulation in open channels include cell culture and analysis, on-chip microscale reactions, and reagent delivery.

High-Throughput, Off-Chip Microdroplet Generator Enabled by a Spinning Conical Frustum

Although droplet-based microfluidics has been broadly used as a versatile tool in biology, chemistry, and nanotechnology, its rather complicated microfabrication process and the requirement of specialized hardware and operating skills hinder researchers fully unleashing the potential of this powerful platform. Here, we develop an integrated microdroplet generator enabled by a spinning conical frustum for the versatile production of near-monodisperse microdroplets in a high-throughput and off-chip manner. The construction and operation of this generator are simple and straightforward without the need of microfabrication, and we demonstrate that the generator is able to passively and actively control the size of the produced microdroplets. In addition to water microdroplets, this generator can produce microdroplets of liquid metal that would be difficult to produce in conventional microfluidic platforms as liquid metal has high surface tension. Moreover, we demonstrate that this generator can produce solid hydrogel microparticles and fibers using integrated ultraviolet (UV) light. In the end, we further explore the ability of this generator for forming double emulsions by coflowing two immiscible liquids. Given the remarkable abilities demonstrated by this platform and the tremendous potential of microdroplets, this user-friendly method may revolutionize the future of droplet-based chemical synthesis and biological analysis.

Next-Generation Compound Delivery Platforms to Support Miniaturized Biology

Recent advancements in science and engineering are revolutionizing our understanding of an individual's disease, and with this knowledge we are gaining an increasingly sophisticated understanding of how discovery can be transformed to deliver personalized medicines. To reach this future state, we must reengineer our approach to enable the use of more relevant human cellular models earlier in the drug discovery process. Stem cells and primary human cells represent more disease-relevant models than immortalized cell lines; however, due to both availability and cost, their use is limited in lead generation activities. Miniaturization of cellular assays below microtiter plate volumes will enable the use of more relevant cells in screening, but this would require a change in how test molecules are introduced to the biology. With these shifting paradigms, Discovery Supply teams at GlaxoSmithKline (GSK) are modernizing our sample handling approaches. Various emerging technologies such as microarrays, nanowells, and microfluidic devices could bring fundamental changes in conventional sample handling support as we transition from microtiter plates to well-less platforms. The discussion here is exploratory in nature and reviews ongoing proof-of-concept experiments. Our ultimate goal is to industrialize the sample management platforms to support future miniaturized biological assay systems.

High-Throughput DNA Plasmid Transfection Using Acoustic Droplet Ejection Technology

The Labcyte Echo acoustic liquid handler allows accurate droplet ejection at high speed from a source well plate to a destination plate. It has already been used in various miniaturized biological assays, such as quantitative PCR (q-PCR), quantitative real-time PCR (q-RT-PCR), protein crystallization, drug screening, cell dispensing, and siRNA transfection. However, no plasmid DNA transfection assay has been published so far using this dispensing technology. In this study, we evaluated the ability of the Echo 550 device to perform plasmid DNA transfection in 384-well plates. Due to the high throughput of this device, we simultaneously optimized the three main parameters of a transfection process: dilution of the transfection reagent, DNA amount, and starting DNA concentration. We defined a four-step protocol whose optimal settings allowed us to transfect HeLa cells with up to 90% efficiency and reach a co-expression of nearly 100% within transfected cells in co-transfection experiments. This fast, reliable, and automated protocol opens new ways to easily and rapidly identify optimal transfection settings for a given cell type. Furthermore, it permits easy software-based transfection control and multiplexing of plasmids distributed on wells of a source plate. This new development could lead to new array applications, such as human ORFeome protein expression or CRISPR-Cas9-based gene function validation in nonpooled screening strategies.

An on-demand femtoliter droplet dispensing system based on a gigahertz acoustic resonator

On-demand droplet dispensing systems are indispensable tools in bioanalytical fields, such as microarray fabrication. Biomaterial solutions can be very limited and expensive, so minimizing the use of solution per spot produced is highly desirable. Here, we proposed a novel droplet dispensing method which utilizes a gigahertz (GHz) acoustic resonator to deposit well-defined droplets on-demand. This ultra-high frequency acoustic resonator induces a highly localized and strong body force at the solid-liquid interface, which pushes the liquid to generate a stable and sharp "liquid needle" and further delivers droplets to the target substrate surface by transient contact. This approach is between contact and non-contact methods, thus avoiding some issues of traditional methods (such as nozzle clogging or satellite spots). We demonstrated the feasibility of this approach by fabricating high quality DNA and protein microarrays on glass and flexible substrates. Notably, the spot size can be delicately controlled down to a few microns (femtoliter in volume). Because of the CMOS compatibility, we expect this technique to be readily applied to advanced biofabrication processes.

Characterization and Use of TurboLuc Luciferase as a Reporter for High-Throughput Assays

Luciferase-based reporter assays are powerful tools for monitoring gene expression in cells because of their ultrasensitive detection capacity and wide dynamic range. Here we describe the characterization and use of a luciferase reporter enzyme derived from the marine copepod Metridia luciferase family, referred to as TurboLuc luciferase (TurboLuc). To develop TurboLuc, the wild-type luciferase was modified to decrease its size, increase brightness, slow luminescent signal decay, and provide for efficient intracellular expression. To determine the enzyme susceptibility to compound inhibition and judge the suitability of using of TurboLuc as a reporter in screening assays, purified TurboLuc enzyme was screened for inhibitors using two different compound libraries. No inhibitors of this enzyme were identified in a library representative of typical diverse low molecular weight (LMW) compounds using a purified TurboLuc enzyme assay supporting that such libraries will show very low interference with this enzyme. We were able to identify a few inhibitors from a purified natural product library which can serve as useful tools to validate assays using TurboLuc. In addition to the inhibitor profile for TurboLuc we describe the use of this reporter in cells employing miniaturized assay volumes within 1536-well plates. TurboLuc luciferase is the smallest luciferase reporter enzyme described to date (16 kDa), shows bright luminescence and low interference by LMW compounds, and therefore should provide an ideal reporter in assays applied to high-throughput screening.

Automating drug discovery

Small-molecule drug discovery can be viewed as a challenging multidimensional problem in which various characteristics of compounds - including efficacy, pharmacokinetics and safety - need to be optimized in parallel to provide drug candidates. Recent advances in areas such as microfluidics-assisted chemical synthesis and biological testing, as well as artificial intelligence systems that improve a design hypothesis through feedback analysis, are now providing a basis for the introduction of greater automation into aspects of this process. This could potentially accelerate time frames for compound discovery and optimization and enable more effective searches of chemical space. However, such approaches also raise considerable conceptual, technical and organizational challenges, as well as scepticism about the current hype around them. This article aims to identify the approaches and technologies that could be implemented robustly by medicinal chemists in the near future and to critically analyse the opportunities and challenges for their more widespread application.

Interlaboratory Reproducibility of Droplet Digital Polymerase Chain Reaction Using a New DNA Reference Material Format

Use of droplet digital PCR technology (ddPCR) is expanding rapidly in the diversity of applications and number of users around the world. Access to relatively simple and affordable commercial ddPCR technology has attracted wide interest in use of this technology as a molecular diagnostic tool. For ddPCR to effectively transition to a molecular diagnostic setting requires processes for method validation and verification and demonstration of reproducible instrument performance. In this study, we describe the development and characterization of a DNA reference material (NMI NA008 High GC reference material) comprising a challenging methylated GC-rich DNA template under a novel 96-well microplate format. A scalable process using high precision acoustic dispensing technology was validated to produce the DNA reference material with a certified reference value expressed in amount of DNA molecules per well. An interlaboratory study, conducted using blinded NA008 High GC reference material to assess reproducibility among seven independent laboratories demonstrated less than 4.5% reproducibility relative standard deviation. With the exclusion of one laboratory, laboratories had appropriate technical competency, fully functional instrumentation, and suitable reagents to perform accurate ddPCR based DNA quantification measurements at the time of the study. The study results confirmed that NA008 High GC reference material is fit for the purpose of being used for quality control of ddPCR systems, consumables, instrumentation, and workflow.

Applications of chemogenomic library screening in drug discovery

The allure of phenotypic screening, combined with the industry preference for target-based approaches, has prompted the development of innovative chemical biology technologies that facilitate the identification of new therapeutic targets for accelerated drug discovery. A chemogenomic library is a collection of selective small-molecule pharmacological agents, and a hit from such a set in a phenotypic screen suggests that the annotated target or targets of that pharmacological agent may be involved in perturbing the observable phenotype. In this Review, we describe opportunities for chemogenomic screening to considerably expedite the conversion of phenotypic screening projects into target-based drug discovery approaches. Other applications are explored, including drug repositioning, predictive toxicology and the discovery of novel pharmacological modalities.

Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis

High-quality immunoreagents enhance the performance and reproducibility of immunoassays and, in turn, the quality of both biological and clinical measurements. High quality recombinant immunoreagents are generated using antibody-phage display. One metric of antibody quality – the binding affinity – is quantified through the dissociation constant (K_D) of each recombinant antibody and the target antigen. To characterize the K_D of recombinant antibodies and target antigen, we introduce affinity electrophoretic mobility shift assays (EMSAs) in a high-throughput format suitable for small volume samples. A microfluidic card comprised of free-standing polyacrylamide gel (fsPAG) separation lanes supports 384 concurrent EMSAs in 30 s using a single power source. Sample is dispensed onto the microfluidic EMSA card by acoustic droplet ejection (ADE), which reduces EMSA variability compared to sample dispensing using manual or pin tools. The K_D for each of a six-member fragment antigen-binding fragment library is reported using ~25-fold less sample mass and ~5-fold less time than conventional heterogeneous assays. Given the form factor and performance of this micro- and mesofluidic workflow, we have developed a sample-sparing, high-throughput, solution-phase alternative for biomolecular affinity characterization.

Better, Faster, Cheaper: Getting the Most Out of High-Throughput Screening with Zebrafish

The field of toxicology is undergoing a vast change with high-throughput (HT) approaches that rapidly query huge swaths of chemico-structural space for bioactivity and hazard potential. Its practicality is due in large part to switching from high-cost, low-throughput mammalian models to faster and cheaper alternatives. We believe this is an improved approach because the immense breadth of the resulting data sets a foundation for predictive structure-activity-based toxicology. Moreover, rapidly uncovering structure-related bioactivity drives better decisions about where to commit resources to drill down to a mechanism, or pursue commercial leads. While hundreds of different in vitro toxicology assays can collectively serve as an alternative to mammalian animal model testing, far greater efficiency and ultimately more relevant data are obtained from the whole animal. The developmental zebrafish, with its well-documented advantages over many animal models, is now emerging as a true biosensor of chemical activity. Herein, we draw on nearly a decade of experience developing high-throughput toxicology screens in the developmental zebrafish to summarize the best practices in fulfilling the better, faster, cheaper goals. We include optimization and harmonization of dosing volume, exposure paradigms, chemical solubility, chorion status, experimental duration, endpoint definitions, and statistical analysis.

Acoustic Droplet Ejection Technology and Its Application in High-Throughput RNA Interference Screening

The development of acoustic droplet ejection (ADE) technology has resulted in many positive changes associated with the operations in a high-throughput screening (HTS) laboratory. Originally, this liquid transfer technology was used to simply transfer DMSO solutions of primarily compounds. With the introduction of Labcyte's Echo 555, which has aqueous dispense capability, the application of this technology has been expanded beyond its original use. This includes the transfer of many biological reagents solubilized in aqueous buffers, including siRNAs. The Echo 555 is ideal for siRNA dispensing because it is accurate at low volumes and a step-down dilution is not necessary. The potential for liquid carryover and cross-contamination is eliminated, as no tips are needed. Herein, we describe the siRNA screening platform at Southern Research's HTS Center using the ADE technology. With this technology, an siRNA library can be dispensed weeks or even months in advance of the assay itself. The protocol has been optimized to achieve assay parameters comparable to small-molecule screening parameters, and exceeding the norm reported for genomewide siRNA screens.

Technologies That Enable Accurate and Precise Nano- to Milliliter-Scale Liquid Dispensing of Aqueous Reagents Using Acoustic Droplet Ejection

Acoustic liquid handling uses high-frequency acoustic signals that are focused on the surface of a fluid to eject droplets with high accuracy and precision for various life science applications. Here we present a multiwell source plate, the Echo Qualified Reservoir (ER), which can acoustically transfer over 2.5 mL of fluid per well in 25-nL increments using an Echo 525 liquid handler. We demonstrate two Labcyte technologies-Dynamic Fluid Analysis (DFA) methods and a high-voltage (HV) grid-that are required to maintain accurate and precise fluid transfers from the ER at this volume scale. DFA methods were employed to dynamically assess the energy requirements of the fluid and adjust the acoustic ejection parameters to maintain a constant velocity droplet. Furthermore, we demonstrate that the HV grid enhances droplet velocity and coalescence at the destination plate. These technologies enabled 5-µL per destination well transfers to a 384-well plate, with accuracy and precision values better than 4%. Last, we used the ER and Echo 525 liquid handler to perform a quantitative polymerase chain reaction (qPCR) assay to demonstrate an application that benefits from the flexibility and larger volume capabilities of the ER.