PUBLICATIONS

featuring the Echo Acoustic Technology

103 Total Publications

TITLES and AUTHORS

  • Year
  • Link
  • PDF
  • + Abstract
  • Screening Pools of Compounds against Multiple Endogenously Expressed Targets in a Chemoproteomics Binding Assay
  • E Salzer, E Nixon, G Drewes, F Reinhard, G Bergamini, C Rau
  • Institution: Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline
  • Publication: Journal of Laboratory Automation (JALA) Special Issue
  • 2015
  •  

Chemoproteomics-based competition-binding assays allow the screening of compounds against endogenous proteins in cell or tissue extracts, but these assays are hampered by low throughput and high cost. Using compound pools rather than single compounds in a screening campaign holds the promise of increased efficiency and substantial cost reduction. Previous attempts to screen compounds in pools often fell short due to complex data tracking, deconvolution issues, compound interferences, and automation problems. The desire to screen compounds in a high-throughput chemoproteomics format sparked a reassessment of compound pooling. Through the integration of acoustic dispensing, we enabled a flexible pooling process, allowing mixture creation by combining randomized or specific samples to create defined pools. Automation enabled end-to-end tracking, using barcode scan check points and output files to track data and ensure integrity during the mixture creation process. The compound pooling approach proved to be highly compatible with the chemoproteomics assay technology. Pools of 10 compounds in a single well did not show compound interference effects or increased false-positive/negative rates. In the present study, four targets, TBK1, PI3Kδ, PI3Kγ, and mTOR, were screened using a chemoproteomics approach against pools of 10 compounds per well, resulting in robust hit identification.

  • Delivery of Formulated Industrial Enzymes with Acoustic Technology
  • J Hwang, M Ortiz-Maldonado, S Paramonov
  • Institution: DuPont Industrial Biosciences, Department of Chemical Biology, University of California, Berkeley
  • Publication: Journal of Laboratory Automation (JALA) Special Issue
  • 2015
  •  

Industrial enzymes are instrumental in many applications, including carbohydrate processing, fabric and household care, biofuels, food, and animal nutrition, among others. Enzymes have to be active and stable not only in harsh application conditions, but also during shipment and storage. In protein stability studies, formulated concentrated enzyme solutions are frequently diluted gravimetrically prior to enzyme activity measurements, making it challenging to move toward more high-throughput techniques using conventional robotic equipment. Current assay methods pose difficulties when measuring highly concentrated proteins. For example, plastic pipette tips can introduce error because proteins adsorb to the tip surface, despite the presence of detergents, decreasing precision and overall efficiency of protein activity assays. Acoustic liquid handling technology, frequently used for various dilute small-molecule assays, may overcome such problems. Originally shown to effectively deliver dilute solutions of small molecules, this technology is used here as an effective alternative to the aforementioned challenge with viscous concentrated protein solutions. Because the acoustic liquid handler transfers nanoliter quantities of liquids without using pipette tips and without sample loss, it rapidly and uniformly prepares assay plates for enzyme activity measurements within minutes. This increased efficiency transforms the nature of enzyme stability studies toward high precision and throughput.

  • Publication / Type:Journal of Laboratory Automation (JALA) Special Issue
  • Related Subject:industrial enzymes, formulation development, concentrated protein solution, high-throughput enzyme assay, acoustic liquid handling, acoustic droplet ejection
  • Link:http://jla.sagepub.com/content/21/1/153.full.pdf+html
  • Implementation and Challenges of Direct Acoustic Dosing into Cell-Based Assays
  • K Roberts, R Callis, T Ikeda, A Paunovic, C Simpson, E Tang, N Turton, G Walker
  • Institution: AstraZeneca PLC, Alderley Park, Cheshire, UK
  • Publication: Journal of Laboratory Automation (JALA)
  • 2015
  •  

Since the adoption of Labcyte Echo Acoustic Droplet Ejection (ADE) technology by AstraZeneca in 2005, ADE has become the preferred method for compound dosing into both biochemical and cell-based assays across AstraZeneca research and development globally. The initial implementation of Echos and the direct dosing workflow provided AstraZeneca with a unique set of challenges. In this article, we outline how direct Echo dosing has evolved over the past decade in AstraZeneca. We describe the practical challenges of applying ADE technology to 96-well, 384-well, and 1536-well assays and how AstraZeneca developed and applied software and robotic solutions to generate fully automated and effective cell-based assay workflows.

  • Smart DNA Fabrication Using Sound Waves: Applying Acoustic Dispensing Technologies to Synthetic Biology
  • P Kanigowska, Y Shen, Y Zheng, S Rosser, Y Cai
  • Institution: School of Biological Sciences, University of Edinburgh, BGI-Shenzhen
  • Publication: Journal of Laboratory Automation (JALA) Special Issue
  • 2015

Acoustic droplet ejection (ADE) technology uses focused acoustic energy to transfer nanoliter-scale liquid droplets with high precision and accuracy. This noncontact, tipless, low-volume dispensing technology minimizes the possibility of cross-contamination and potentially reduces the costs of reagents and consumables. To date, acoustic dispensers have mainly been used in screening libraries of compounds. In this paper, we describe the first application of this powerful technology to the rapidly developing field of synthetic biology, for DNA synthesis and assembly at the nanoliter scale using a Labcyte Echo 550 acoustic dispenser. We were able to successfully downscale PCRs and the popular one-pot DNA assembly methods, Golden Gate and Gibson assemblies, from the microliter to the nanoliter scale with high assembly efficiency, which effectively cut the reagent cost by 20- to 100-fold. We envision that acoustic dispensing will become an instrumental technology in synthetic biology, in particular in the era of DNA foundries.

  • Unlocking the Potential of High-Throughput Drug Combination Assays Using Acoustic Dispensing
  • G Chan, S Wilson, S Schmidt, J Moffat
  • Institution: Department of Biochemical and Cellular Pharmacology, Department of Immunology, Genentech
  • Publication: Journal of Laboratory Automation (JALA) Special Issue
  • 2015
  •  

Assessment of synergistic effects of drug combinations in vitro is a critical part of anticancer drug research. However, the complexities of dosing and analyzing two drugs over the appropriate range of doses have generally led to compromises in experimental design that restrict the quality and robustness of the data. In particular, the use of a single dose response of combined drugs, rather than a full two-way matrix of varying doses, has predominated in higher-throughput studies. Acoustic dispensing unlocks the potential of high-throughput dose matrix analysis. We have developed acoustic dispensing protocols that enable compound synergy assays in a 384-well format. This experimental design is considerably more efficient and flexible with respect to time, reagent usage, and labware than is achievable using traditional serial-dilution approaches. Data analysis tools integrated in Genedata Screener were used to efficiently deconvolute the combination compound mapping scheme and calculate compound potency and synergy metrics. We have applied this workflow to evaluate interactions among drugs targeting different nodes of the mitogen-activated protein kinase pathway in a panel of cancer cell lines.

  • Publication / Type:Journal of Laboratory Automation (JALA) Special Issue
  • Related Subject:acoustic droplet ejection, screening data analysis, informatics and software, HTS, high-throughput screening, automated biology
  • Link:http://jla.sagepub.com/content/21/1/125.full.pdf+html
  • Compound Transfer by Acoustic Droplet Ejection Promotes Quality and Efficiency in Ultra-High-Throughput Screening Campaigns
  • Dawes T., Turincio R., Jones S., Rodriguez R., Gadiagellan D., Thana P., Clark K., Gustafson A., Orr
  • Institution: Genentech
  • Publication: Journal of Laboratory Automation (JALA) Special Issue
  • 2015
  •  

Acoustic droplet ejection (ADE) as a means of transferring library compounds has had a dramatic impact on the way in which high-throughput screening campaigns are conducted in many laboratories. Two Labcyte Echo ADE liquid handlers form the core of the compound transfer operation in our 1536-well based ultra-high-throughput screening (uHTS) system. Use of these instruments has promoted flexibility in compound formatting in addition to minimizing waste and eliminating compound carryover. We describe the use of ADE for the generation of assay-ready plates for primary screening as well as for follow-up dose-response evaluations. Custom software has enabled us to harness the information generated by the ADE instrumentation. Compound transfer via ADE also contributes to the screening process outside of the uHTS system. A second fully automated ADE-based system has been used to augment the capacity of the uHTS system as well as to permit efficient use of previously picked compound aliquots for secondary assay evaluations. Essential to the utility of ADE in the high-throughput screening process is the high quality of the resulting data. Examples of data generated at various stages of high-throughput screening campaigns are provided. Advantages and disadvantages of the use of ADE in high-throughput screening are discussed.

  • Compound Transfer by Acoustic Droplet Ejection Promotes Quality and Efficiency in Ultra-High-Throughput Screening Campaigns
  • T Dawes, R Turincio, S Jones, R Rodriguez, D Gadiagellan, P Thana, K Clark, A Gustafson, Linda Orren
  • Institution: Genentech, Gadgitech, Labcyte
  • Publication: Journal of Laboratory Automation (JALA)
  • 2015
  •  

Acoustic droplet ejection (ADE) as a means of transferring library compounds has had a dramatic impact on the way in which high-throughput screening campaigns are conducted in many laboratories. Two Labcyte Echo ADE liquid handlers form the core of the compound transfer operation in our 1536-well based ultra-high-throughput screening (uHTS) system. Use of these instruments has promoted flexibility in compound formatting in addition to minimizing waste and eliminating compound carryover. We describe the use of ADE for the generation of assay-ready plates for primary screening as well as for follow-up dose-response evaluations. Custom software has enabled us to harness the information generated by the ADE instrumentation. Compound transfer via ADE also contributes to the screening process outside of the uHTS system. A second fully automated ADE-based system has been used to augment the capacity of the uHTS system as well as to permit efficient use of previously picked compound aliquots for secondary assay evaluations. Essential to the utility of ADE in the high-throughput screening process is the high quality of the resulting data. Examples of data generated at various stages of high-throughput screening campaigns are provided. Advantages and disadvantages of the use of ADE in high-throughput screening are discussed.

  • qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping
  • Mitchell L, Phillips N, Lafont A, Martin J, Cutting R, and Boeke J
  • Institution: Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, New York Univ
  • Publication: J. Vis. Exp. (99), e52941, doi:10.3791/52941 (2015)
  • 2015
  •  

The Synthetic Yeast Genome Project (Sc2.0) aims to build 16 designer yeast chromosomes and combine them into a single yeast cell. To date one synthetic chromosome, synIII1, and one synthetic chromosome arm, synIXR2, have been constructed and their in vivo function validated in the absence of the corresponding wild type chromosomes. An important design feature of Sc2.0 chromosomes is the introduction of PCRTags, which are short, re-coded sequences within open reading frames (ORFs) that enable differentiation of synthetic chromosomes from their wild type counterparts. PCRTag primers anneal selectively to either synthetic or wild type chromosomes and the presence/absence of each type of DNA can be tested using a simple PCR assay. The standard readout of the PCRTag assay is to assess presence/absence of amplicons by agarose gel electrophoresis However, with an average PCRTag amplicon density of one per 1.5 kb and a genome size of ~12 Mb, the completed Sc2.0 genome will encode roughly 8,000 PCRTags. To improve throughput, we have developed a real time PCR-based detection assay for PCRTag genotyping that we call qPCRTag analysis. The workflow specifies 500 nl reactions in a 1,536 multiwell plate, allowing us to test up to 768 PCRTags with both synthetic and wild type primer pairs in a single experiment.

  • Acoustic Dispensing Preserves the Potency of Therapeutic Peptides throughout the Entire Drug Discovery Workflow
  • J Naylor, A Rossi, D Hornigold
  • Institution: Cardiovascular and Metabolic Disease, MedImmune, Cambridge, UK
  • Publication: Journal of Laboratory Automation (JALA)
  • 2015

Routine peptide structure-activity relationship screening requires the serial dilution of peptides to produce full concentration-response curves. Established tip-based protocols involve multiple tip changes and high exposure to plasticware. In the case of peptides, this becomes a challenge, since peptides can adsorb to plastic, resulting in an observed loss of potency. Various methods can be employed to prevent peptide loss during compound handling, such as the inclusion of bovine serum albumin or solvents in assay buffer and the siliconization of plasticware, yet protein binding remains unpredictable. The degree of variation by which peptides will adhere to plasticware can confuse results and cause inaccuracies in potency predictions. We evaluated acoustic noncontact methods for peptide serial dilution and compared it with traditional tip-based methods, on the effect on potency curves for glucagon-like peptide-1 and glucagon peptide analogues. The current study demonstrates the benefits of noncontact dispensing for high-density microplate assay preparation of peptides using nanoliter droplets across our entire drug discovery workflow, from in vitro high-throughput screening to drug exposure determinations from in vivo samples.

  • Low-Cost, High-Throughput Sequencing of DNA Assemblies Using a Highly Multiplexed Nextera Process
  • E Shapland, et. al.
  • Institution: Amyris, Inc. and TOTAL New Energies USA, Inc.
  • Publication: ACS Synth. Biol., Article ASAP DOI: 10.1021/sb500362n
  • 2015
  •  

In recent years, next-generation sequencing (NGS) technology has greatly reduced the cost of sequencing whole genomes, whereas the cost of sequence verification of plasmids via Sanger sequencing has remained high. Consequently, industrial-scale strain engineers either limit the number of designs or take short cuts in quality control. Here, we show that over 4000 plasmids can be completely sequenced in one Illumina MiSeq run for less than $3 each (15× coverage), which is a 20-fold reduction over using Sanger sequencing (2× coverage). We reduced the volume of the Nextera tagmentation reaction by 100-fold and developed an automated workflow to prepare thousands of samples for sequencing. We also developed software to track the samples and associated sequence data and to rapidly identify correctly assembled constructs having the fewest defects. As DNA synthesis and assembly become a centralized commodity, this NGS quality control (QC) process will be essential to groups operating high-throughput pipelines for DNA construction.

  • Publication / Type:ACS Synth. Biol., Article ASAP DOI: 10.1021/sb500362n
  • Related Subject:synthetic biology; next-generation sequencing; NGS; high throughput, DNA Assembly, Sequencing, Echo® Liquid Handler for Screening and OMICS
  • Link:http://pubs.acs.org/doi/full/10.1021/sb500362n