PUBLICATIONS

featuring the Echo acoustic technology

111 Total Publications

TITLES and AUTHORS

  • Year
  • Link
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  • + Abstract
  • 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
  • Drug screen in patient cells suggests quinacrine to be repositioned for treatment of acute myeloid leukemia
  • A Eriksson, A Osterroos, S Hassan, J Gullbo, L Rickardson, M Jarvius, P Nygren, M Fryknas, R Larsson
  • Institution: Department of Medical Sciences, Uppsala University
  • Publication: Blood Cancer Journal, Nature
  • 2015
  •  

To find drugs suitable for repositioning for use against leukemia, samples from patients with chronic lymphocytic, acute myeloid and lymphocytic leukemias as well as peripheral blood mononuclear cells (PBMC) were tested in response to 1266 compounds from the LOPAC1280 library (Sigma). Twenty-five compounds were defined as hits with activity in all leukemia subgroups (o50% cell survival compared with control) at 10 μM drug concentration. Only one of these compounds, quinacrine, showed low activity in normal PBMCs and was therefore selected for further preclinical evaluation. Mining the NCI-60 and the NextBio databases demonstrated leukemia sensitivity and the ability of quinacrine to reverse myeloid leukemia gene expression. Mechanistic exploration was performed using the NextBio bioinformatic software using gene expression analysis of drug exposed acute myeloid leukemia cultures (HL-60) in the database. Analysis of gene enrichment and drug correlations revealed strong connections to ribosomal biogenesis nucleoli and translation initiation. The highest drug–drug correlation was to ellipticine, a known RNA polymerase I inhibitor. These results were validated by additional gene expression analysis performed in-house. Quinacrine induced early inhibition of protein synthesis supporting these predictions. The results suggest that quinacrine have repositioning potential for treatment of acute myeloid leukemia by targeting of ribosomal biogenesis.

  • Publication / Type:Blood Cancer Journal, Nature
  • Related Subject:screening, cancer, blood cancer, myeloid leukemia
  • Delivering an Automated and Integrated Approach to Combination Screening Using Acoustic-Droplet Technology
  • Cross K, Craggs R, Swift D, Stiaram A, Daya S, Roberts M, Hawley S, Owen P, and Isherwood V
  • Institution: AstraZeneca and Tessela plc.
  • Publication: J Lab Autom. 2015 Apr 2. DOI: 10.1177/2211068215579163
  • 2015
  •  

Drug combination testing in the pharmaceutical industry has typically been driven by late-stage opportunistic strategies rather than by early testing to identify drug combinations for clinical investigation that may deliver improved efficacy. A rationale for combinations exists across a number of diseases in which pathway redundancy or resistance to therapeutics are evident. However, early assays are complicated by the absence of both assay formats representative of disease biology and robust infrastructure to screen drug combinations in a medium-throughput capacity. When applying drug combination testing studies, it may be difficult to translate a study design into the required well contents for assay plates because of the number of compounds and concentrations involved. Dispensing these plates increases in difficulty as the number of compounds and concentration points increase and compounds are subsequently rolled onto additional labware. We describe the development of a software tool, in conjunction with the use of acoustic droplet technology, as part of a compound management platform, which allows the design of an assay incorporating combinations of compounds. These enhancements to infrastructure facilitate the design and ordering of assay-ready compound combination plates and the processing of combinations data from high-content organotypic assays.

  • Publication / Type:J Lab Autom. 2015 Apr 2. DOI: 10.1177/2211068215579163
  • Related Subject:laboratory informatics, combinations, acoustic droplet technology, apothecary, assay-ready plate, high-content screening, sample management