Dynamic Devices LM700 as an automated solution for multiple plant-breeding related applications

INTRODUCTION

Company A is a plant breeding company specialized in developing new vegetable species to actively contribute to food supply and vegetable consumption all over the world. Developing these new varieties takes a lot of time, effort and biochemical applications as DNA/RNA extraction, DNA/RNA purification and other nucleic acid  related applications. In order to keep moving forward as a company, company A is constantly looking for solutions to improve their way of working which will affect their overall goal as a company.

METHOD

A part company A’s activities is done by performing plate transfers from 96 to 384 formats, and plate transfers from 384 to 96 formats on a high throughput and magnetic bead based DNA purification. In the last years, Company A has experienced a growing demand in these tests. This project is designed to design a liquid handler that will perform below named applications in a higher throughput.

  • Stamping plates from 96 to 96 format
  • Stamping plates from 96 to 384 format
  • Stamping plates from 384 to 96 format
  • Cherry picking of samples to new plate
  • Magnetic bead based DNA purification

GOALS OF THE PROJECT

The main goal of the project is to have an automated solution, able to process flexible numbers of source and destination plates for plate transferring as well as cherry picking. Besides this, a  magnetic bead based DNA purification for up to 96 samples in a very quick and successful way was one of the goals.

The demands on the automated solution are:

  • At least equal to current situation (outsourcing) in quality and throughput
  • Flexible, increasing throughput/ additional application demands in the future
  • Robust, the solution must have low maintenance requirements
  • The system will be used dynamically, depending on workload
  • Sample results suitable for different downstream applications
  • Less manual work/interference
  • Small footprint

DESIGN OF THE SOLUTION

  • Dynamic Devices LM700 Liquid Handling system
  • Standard Technology head 96 format
  • On-deck tip washing station

RESULTS & CONCLUSION

After off- and on-site validation of all described assays the outcome showed the Dynamic Devices LM700 being sufficient for Company A’s needs, giving them more hands-off time, more flexibility and a higher throughput.

Bionex hive at customer

An Automated Solution For Novel High-Throughput Translation Modular Screening

INTRODUCTION

Anima Biotech is pioneering translation control therapeutics, a new class of drugs that specifically control protein translation as a novel strategy against hard and ‘undruggable’ targets in many diseases. Current programs are in Fibrosis, viral infections, oncology and Huntington’s disease. Anima has adapted the technology to high content screens, screening 100-200K libraries to identify translation modulators. A flexible and robust system is necessary to meet the current increasing demands in throughput. The final solution must meet the high-quality standards Anima demands of their screening assay.

METHOD

Anima has developed a new method, Protein Synthesis Monitoring (PSM), which enables monitoring of the protein synthesis process, directly from the ribosomes inside cells, using fluorescent labeled tRNAs. In PSM, tRNAs labelled as FRET donors and acceptors are introduced into the cell. A FRET signal is generated when donor- and acceptor-labeled tRNAs come in close contact, as they do in active ribosomes. The intensity of the FRET signal correlates with the number of ribosomes containing the tRNA FRET pair, providing a cell-based assay for monitoring protein synthesis. PSM can monitor overall protein synthesis, using bulk tRNA, or the synthesis of a specific protein, using one or more specifically selected pairs of tRNA enriched in the protein’s sequence.

The PSM method was adapted for high throughput screening campaigns that consist of four separate stages. All stages are labor intensive with multiple incubation steps within the process, leading up to a long process time. The four separate stages are:

  1. Cell Seeding
  2. tRNA transfection
  3. Addition of compounds
  4. Fixation and Nuclei staining

GOALS OF THE PROJECT

The main goal of the project is to have an automated solution, able to process up to 150 individual plates (384 well plates) per day. The first three stages of the total process will be included in the automation, the fourth and final stage will be performed separately from the automation.

The demands on the automated solution are:

  • At least equal to current situation (outsourcing) in quality and throughput
  • Flexible, increasing throughput demands in the future
  • Robust, the solution must have low maintenance requirements and downtime
  • Total integration of all the separate components, without manual intervention
  • The system will be used dynamically, depending on workload
  • Small footprint

The goal was to find a partner able to provide a single system containing all the equipment needed to run the assay flow through, according to the above specifications. Multiple vendors have been contacted, resulting in selection of the Bionex Hive platform.

DESIGN OF THE SOLUTION

  • BioNex Hive (including plate- and lid hotels and a HEPA filter)
  • VWorks scheduling software
  • BioNex BNX 1536
  • Liconic STX 110 incubator
  • Agilent Bravo
  • Formulatrix Tempest

RESULTS & CONCLUSION

Anima Biotech has found a partner in GC biotech, who are able to create the right relationships and provide the correct resources to arrive at the final design of the solution, meeting all specified demands. The throughput demands are superseded with the current design to accommodate future needs.

Together with GC biotech, Anima biotech created a solution that increased the throughput to 150 plates per day, with room for growth. The method is broken up in the determined three stages, allowing Anima to approach their projects from a workload point of view and use the system as needed.

Results generated are equal in quality compared to the current situation.  Detailed results of the experiments cannot be shown because of classified information.

app wizz custom made software printscreen

AppWizz custom software

The main restraint of many users to comfortably use automated solutions in the lab is the complexity of operation. The software associated with automated solutions and the complexity of the hardware can be overwhelming in the beginning. However, when accustomed to the use of the system, most users are extremely happy with the decreased amount of repetitive assays performed on a daily base.

When implementing a liquid handling solution for daily use, the variation per assay is often limited to a select number of variables such as amount of reactions per run. To accommodate for these repetitive assays and to maintain the necessary flexibility in the daily operations of the lab, GC biotech offers a Graphical User Interface (GUI) called AppWizz which can be configured by the process administrator. The AppWizz GUI combined with the experienced programming skills of the applications specialists will result in an easy to use automated setting for your liquid handling needs.

The AppWizz software is created around your specific assays and variables and guides the user through the setup of the assay. It will communicate with the operator and will indicate the exact amount of reagents, samples and plate setup to perform the assay without errors and unnecessary delays.

The software can be data file controlled making communications with a Laboratory Information System (LIMS) easy and an advantage. There is no need for file transfer via third party devices such as USB carriers. Due to the custom design of the software, the parameters needed for this specific communication are completely adaptable for any LIMS system.

By adapting the design of the GUI for each customer and assay, the software feels comfortable and looks familiar for every user independent of the situation.

Many applications have been incorporated in the AppWizz software in the past such as:

  • DNA isolation
  • DNA purification (magnetic bead based)
  • NGS library preparation
  • DNA Normalization
  • ELISA setup

For your specific assay needs, please contact us for more information.

Automated DNA extraction, Normalization and PCR setup

Automated DNA extraction, Normalization and PCR setup

A major Dutch blood bank approached us to play a role in the automation of their DNA extraction, normalization and PCR setup. The project was designed to form a centralized molecular platform within the organization. The platform is operated by several technicians from different departments. Therefor ease-of-use and flexibility plays a big role in daily operation. The organizations frontrunner role in quality standards required the project to have a validated sample tracking and tracing throughout the process. The process contains four major parts described below.

1. DNA extraction

DNA extraction is performed on a Chemagic MSM I. DNA extraction is based upon magnetic bead techniques. The Chemagic MSM I is one of the few systems allowing samples to be used ranging from 200 μl up to 10 ml.

The samples in this project origin from different sample materials such as, blood, tissue, cell culture and buccal swabs. The input volume from blood varies from 200 μl up to 3 ml. The system is adapted in a way that all these assays can be performed on the same system with minimum effort to change in between different sample types. If possible, different sample types can be combined to achieve a higher throughput on the platform.

All sample preparations are done on an Xperimate liquid handler with an extended arm. The extended arm picks and places all reaction plates onto the Chemagic MSM I.

2. Normalization

For all downstream assays, Normalization is required. The Normalization starts with a concentration measurement by a Trinean DropSense 96. The required sample volume is transferred by either the Xperimate or the Xiril liquid handler onto the DropPlate consumable. All data is transferred to the DropSense and quantification is performed. A worklist including the dilution volumes is created automatically and normalization is performed. The normalization factor is based upon the demands of the downstream application.

3. PCR setup

PCR setup is split into two major assays. The first assay is PCR mix preparation. The mix can either be prepared in exact amounts used during an assay, where volumes are calculated based upon the amount of samples, or it can be prepared in bulk for storage.

Any PCR mix can be prepared. To maintain flexibility, the specifications of the PCR mix are stored in the middleware software. When a new mix is added or the preparation of any mix changes, this is in full user control. Simply uploading the new settings will allow changes in mix preparation to be implemented easily.

PCR setup is a similar process. After starting the protocol, based on the worklist(s), the system will track and trace all samples, plates and reagents and performs the PCR setup. If different PCR conditions are included in the same run, the system will split them over several reaction plates.

All PCR mix and PCR setup reactions are performed on a Xiril Neon 150 liquid handler. The system is equipped with 8 channels and enough cooled decktrays to store all components. The integrated barcode reader scans all plates before starting the transfer. All data is collected throughout the run and stored in the workfiles for the LIMS system.

4. ProtoBase Middleware Database and Software

Quality plays a central role within the project. To achieve maximum quality and sample tracking and tracing, a custom made middleware software package is designed, including Graphical User Interface, called ProtoBase.

The ProtoBase Database contains all sample, reagents and consumables information. It also contains all assay information. Based upon the demands of the assay, ProtoBase stores all this information and allows the user to perform any assay and combine where possible. The data is communicated with the central LIMS software for long term storage.

The Graphical User Interface shows the user all options and sample lists ready for any assay in the process. Whether it is DNA extraction, normalization, PCR mix preparation or PCR setup, all settings and variables are shown. This allows the user to enter the process at any step ensuring maximum flexibility.

The user controlled access ensures that settings are not changed without the proper access level.

 

GC Biotech

Fully automated genomic