PUBLICATIONS

featuring the Echo acoustic technology

108 Total Publications

TITLES and AUTHORS

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  • 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
  • Axitinib Effectively Inhibits BCR-ABL1(T315I) with a Distinct Binding Confirmation
  • Pemovska T., Johnson E., Kontro M., Repasky G., Chen J., Wells P, Ciaran N., Cronin C., McTigue M.,
  • Institution: Institute for Molecular Medicine Finland; University of Helsinki; La Jolla Laboratories, Pfizer
  • Publication: Nature 519, 102-105 (March 5, 2015), doi:10.1038/nature14119
  • 2015
  •  

The BCR-ABL1 fusion gene is a driver oncogene in chronic myeloid leukaemia and 30–50% of cases of adult acute lymphoblastic leukaemia1. Introduction of ABL1 kinase inhibitors (for example, imatinib) has markedly improved patient survival2, but acquired drug resistance remains a challenge3, 4, 5. Point mutations in the ABL1 kinase domain weaken inhibitor binding6 and represent the most common clinical resistance mechanism...

  • Delivering an Automated and Integrated Approach to Combination Screening Using Acoustic-Droplet Technology
  • K Cross, R Craggs, D Swift, A Sitaram, S Daya, M Roberts, S Hawley, P Owen, B Isherwood
  • Institution: Discovery Sciences, AstraZeneca R&D, Macclesfield, UK
  • Publication: Journal of Laboratory Automation (JALA)
  • 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:Journal of Laboratory Automation (JALA)
  • Related Subject:laboratory informatics, combinations, acoustic droplet technology, apothecary, assay-ready plate, high-content screening, sample management
  • Link:http://jla.sagepub.com/content/21/1/143.full.pdf+html
  • Identification of b-hematin inhibitors in the MMV Malaria Box
  • Fong K., Sandlin R. and Wright D.
  • Institution: Vanderbilt University
  • Publication: International Journal for Parasitology: Drugs and Drug Resistance, Volume 5, Issue 3, December 2015
  • 2015
  •  

The Malaria Box, assembled by the Medicines for Malaria Venture, is a set of 400 structurally diverse, commercially available compounds with demonstrated activity against blood-stage Plasmodium falciparum. The compounds are a representative subset of the 20,000 in vitro antimalarials identified from the high-throughput screening efforts of St. Jude Children's Research Hospital (TN, USA), Novartis and GlaxoSmithKline. In addition, a small set of active compounds from commercially available libraries was added to this group, but it has not previously been published. Elucidation of the biochemical pathways on which these compounds act is a major challenge; therefore, access to these compounds has been made available free of charge to the investigator community. Here, the Malaria Box compounds were tested for activity against the formation of b-hematin, a synthetic form of the heme detoxification biomineral, hemozoin. Further, the mechanism of action of these compounds within the malaria parasite was explored. Ten of the Malaria Box compounds demonstrated significant inhibition of b-hematin formation. In this assay, doseeresponse data revealed IC50 values ranging from 8.7 to 22.7 mM for these hits, each of which is more potent than chloroquine (a known inhibitor of hemozoin formation). The in vitro antimalarial activity of these ten hits was confirmed in cultures of the chloroquine sensitive D6 strain of the parasite resulting in IC50 values of 135e2165 nM, followed by testing in the multidrug resistant strain, C235. Cultures of P. falciparum (D6) were then examined for their heme distribution following treatment with nine of the commercially available confirmed compounds, seven of which disrupted the hemozoin pathway.