LabAutomation 2006 - SLAS
LabAutomation 2006 - SLAS LabAutomation 2006 - SLAS
MP15 Josh Eckman University of Utah West Bountiful, Utah je2@utah.edu LabAutomation2006 Co-Author(s) Bruce Gale David Chang-Yen, Sriram Natarajan David Myszka, Biochemistry University of Utah A Highly-Parallel Microfluidic System for Array Fabrication and Bioassay Development A highly-parallel microfluidic system has been developed for the patterning and interrogation of surface microarrays, wherein microchannels are used to flow biomolecule solutions over discretely defined spot regions. A novel network of microfluidic channels is used to address two dimensional spot arrays, allowing hundreds of locations to be targeted in parallel. When used in conjunction with chemically activated surfaces, this process allows for increased probe surface concentration versus that of the deposition solution, limiting or removing the need for upstream purification. Surface plasmon resonance (SPR) measurement of protein flow deposition as compared to pin-spotted samples demonstrated an 86-fold increase in protein surface concentration. In addition, the process can be used to screen for biomolecules of interest from heterogeneous samples, or to conduct bioassays in a fraction of the time and with substantially less reagents. MP16 Jimmy Bruner Glaxosmithkline Durham, North Carolina jimmy.j.bruner@gsk.com Co-Author(s) Ginger Smith Jim Liacos Managing Biomek FX 3.X Software — “Tools for Consistency and Conservation” The High Throughput Biology (HTB) department at GlaxoSmithKline is developing in vitro models to better predict the efficacy of compounds in the clinic. HTB utilizes the Beckman Biomek FX as its key liquid handling robot, employing five workstations. Each system maintains a core set of liquid handling methods and assay specific methods. Additionally, for backup purposes each method exists on every Biomek FX liquid handler in the department. Approximately thirty-five HTB scientists have walk up access to the systems for dayto-day liquid handling and assay requirements. Managing multiple systems has proved to be both essential and challenging. With the advent of the Biomek 3.2 in the XP environment the HTB Automation Team took a closer look at mechanisms for managing methods both within and between the systems. In this poster we will present lessons learned and mechanisms for synchronizing cross-project contents, automating electronic backups, capturing of per-run data, and implementing accounts and permissions. 110
MP17 Alex Burgin Emerald BioSystems Bainbridge Island, Washington aburgin@decode.com Where Laboratory Technologies Emerge and Merge Co-Author(s) John Walchli Kathryn Hjerrild Mark Mixon Michael Feese Stuart Bowers Brendan Gan Lance Stewart Emerald BioSystems Gene Composer: A Tool for Optimizing Proteins and Genes for X-ray Crystallography A fundamental problem of protein crystallography is identifying a suitable protein construct since small changes in the protein can have profound effects on both expression and crystallization. We have developed a database and algorithm package, called Gene Composer, that facilitates the design of proteins and synthetic genes for X-ray crystallography. The Protein Design Module contains tools to create multiple sequence alignments, and distill protein structure information from PDB files. For example, known and predicted secondary structures, and amino acids participating in crystal, ligand, or water contacts can be highlighted within the alignments. This interface allows the user to simultaneously understand sequence conservation and known or predicted structural elements to define the best amino acid sequence for crystallization. The software also displays solvent accessible regions, highlights individual B factors, and offers suggestions for the rational mutagenesis of surface residues. In the Gene/Oligo Design Module, the user can optimize the open reading frames (codon usage, minimize mRNA secondary structures, eliminate or introduce regulatory regions, etc.) for different expression systems. Finally, Gene Composer offers tools for the design of oligonucleotides for the assembly of whole genes using standard PCR techniques. The software will be demonstrated and examples of how Gene Composer can improve both expression and crystallization will be presented. MP18 Anne E. Carpenter Whitehead Institute for Biomedical Research Massachusetts Institute of Technology Sabatini Laboratory Cambridge, Massachusetts carpenter@wi.mit.edu Co-Author(s) Thouis R. Jones Polina Golland Massachusetts Institute of Technology David M. Sabatini Whitehead Institute for Biomedical Research & MIT Free, High-Throughput Software for Automatically Measuring Cells in Images Advances in imaging hardware now allow the rapid collection of thousands of high resolution images of cells. Automatically measuring features of cells quantitatively from these images has been difficult due to the limitations and often proprietary nature of available image analysis software. We have therefore developed CellProfiler cell image analysis software to allow biologists without training in computer vision or programming to quantitatively measure cells in thousands of images automatically, without tedious user interacion. This freely available, open-source software project is modular and compatible with most image formats and movie formats, allowing adaptation to a variety of cell types and assays. We have tested the software using cells from human, mouse, yeast, and fruit fly to measure phenotypes including cell count, cell size, cell cycle distribution, and the levels and localization of proteins and phospho-proteins, including application to time-lapse and high-throughput experiments. CellProfiler will be released for free to the public in winter 2005. 111
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- Page 104 and 105: Notes LabAutomation2006 102
- Page 106 and 107: MP03 Ismail Al-Abdulmohsen Saudi Ar
- Page 108 and 109: MP07 Varouj Amirkhanian eGene, Inc.
- Page 110 and 111: MP11 Sibani Biswal University of Be
- Page 114 and 115: MP19 Ismet Celebi National Institut
- Page 116 and 117: MP23 Robin Clark deCODE Biostructur
- Page 118 and 119: MP27 J. Colin Cox Duke University M
- Page 120 and 121: MP31 Frank Doffing IMM - Institut f
- Page 122 and 123: MP35 Aoife Gallagher Deerac Fluidic
- Page 124 and 125: MP39 Yunseok Heo University of Mich
- Page 126 and 127: MP43 David Humphries Lawrence Berke
- Page 128 and 129: MP47 Joohoon Kim University of Texa
- Page 130 and 131: MP51 Michelle Li Saint Louis Univer
- Page 132 and 133: MP55 Philip Manning Procter & Gambl
- Page 134 and 135: MP59 Irena Nikcevic University of C
- Page 136 and 137: MP63 Qiaosheng Pu Virginia Commonwe
- Page 138 and 139: MP67 Alexander Roth National Instit
- Page 140 and 141: MP71 Sang Jun Son University of Mar
- Page 142 and 143: MP75 Lois Tack PerkinElmer Life & A
- Page 144 and 145: MP79 Angelo Trivelli J Craig Venter
- Page 146 and 147: MP83 Tracy Worzella Promega Corpora
- Page 148 and 149: MP87 Peter Greenhalgh Astech Projec
- Page 150 and 151: MP91 David Ferrick Seahorse Bioscie
- Page 152 and 153: MP95 Christine Brideau Merck Frosst
- Page 154 and 155: TP01 Marc Pfeifer Roche Molecular S
- Page 156 and 157: TP05 Marcy Engelstein Millipore Cor
- Page 158 and 159: TP09 Aoife Gallagher Deerac Fluidic
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MP15<br />
Josh Eckman<br />
University of Utah<br />
West Bountiful, Utah<br />
je2@utah.edu<br />
<strong>LabAutomation</strong><strong>2006</strong><br />
Co-Author(s)<br />
Bruce Gale<br />
David Chang-Yen,<br />
Sriram Natarajan<br />
David Myszka, Biochemistry<br />
University of Utah<br />
A Highly-Parallel Microfluidic System for Array Fabrication and Bioassay Development<br />
A highly-parallel microfluidic system has been developed for the patterning and interrogation of surface microarrays, wherein microchannels<br />
are used to flow biomolecule solutions over discretely defined spot regions. A novel network of microfluidic channels is used to address<br />
two dimensional spot arrays, allowing hundreds of locations to be targeted in parallel. When used in conjunction with chemically activated<br />
surfaces, this process allows for increased probe surface concentration versus that of the deposition solution, limiting or removing the need<br />
for upstream purification. Surface plasmon resonance (SPR) measurement of protein flow deposition as compared to pin-spotted samples<br />
demonstrated an 86-fold increase in protein surface concentration. In addition, the process can be used to screen for biomolecules of<br />
interest from heterogeneous samples, or to conduct bioassays in a fraction of the time and with substantially less reagents.<br />
MP16<br />
Jimmy Bruner<br />
Glaxosmithkline<br />
Durham, North Carolina<br />
jimmy.j.bruner@gsk.com<br />
Co-Author(s)<br />
Ginger Smith<br />
Jim Liacos<br />
Managing Biomek FX 3.X Software — “Tools for Consistency and Conservation”<br />
The High Throughput Biology (HTB) department at GlaxoSmithKline is developing in vitro models to better predict the efficacy of<br />
compounds in the clinic. HTB utilizes the Beckman Biomek FX as its key liquid handling robot, employing five workstations. Each system<br />
maintains a core set of liquid handling methods and assay specific methods. Additionally, for backup purposes each method exists on<br />
every Biomek FX liquid handler in the department. Approximately thirty-five HTB scientists have walk up access to the systems for dayto-day<br />
liquid handling and assay requirements. Managing multiple systems has proved to be both essential and challenging. With the<br />
advent of the Biomek 3.2 in the XP environment the HTB Automation Team took a closer look at mechanisms for managing methods both<br />
within and between the systems. In this poster we will present lessons learned and mechanisms for synchronizing cross-project contents,<br />
automating electronic backups, capturing of per-run data, and implementing accounts and permissions.<br />
110