Conferences & Workshops

Ensembl Tutorial
May 8, 2017, from 8:30 – 4:30 pm
MET-141 at UC San Diego
Register for the event here


Weekly Events

Genetics, Bioinformatics and Systems Biology Colloquium (2016-17)

qBio Seminar Series (2016-17)

Systems Biology Career Development Seminars (Spring 2017)

Monthly Events

San Diego Bioinformatics Users Series (SDBUS)

Systems Biology Club

Microfluidics and Synthetic Biology

Investigator: Jeff Hasty

The core will provide state-of-the-art technology and expertise for the manufacture and use of high throughput, single-cell data collection devices in the life sciences. The core will assist users in designing and manufacturing custom microfluidic devices, provide users with the microscopic resources needed to gather high quality, single-cell data, and work closely with the Network Assembly and Mathematical Modeling Core to help users analyze their data.

The core is directed by Dr. Jeff Hasty and overseen by Dr. Michael Ferry. Dr. Hasty is a Professor at UCSD in the Departments of Molecular Biology and Bioengineering and the Director of the BioCircuits Institute. Dr. Hasty’s research is in the field of experimental and computational synthetic biology, particularly the analysis and creation of engineered gene circuits. Dr. Ferry is an expert in the design and construction of microchemostats, which can be used for single-cell measurements probing the effects of dynamic environments on gene expression. Dr. Ferry will provide hands-on training on how to conceive, fabricate and use microfluidic devices. He will introduce users to the tools and materials required to develop new devices as well as to the vast range of applications for the technology. Finally, a highly important task for Dr. Ferry will be to provide assistance setting up and integrating microfluidic devices with optical microscopes within each user’s lab.

The mission of the core is to increase the use of microfluidics technology in the life sciences. Too often microfluidic devices are developed as technology platforms, which due to their complexity and custom parts are difficult if not impossible to use for researchers unaffiliated with the developing lab. In contrast the core focuses on designing powerful microfluidics devices that are easy to use for those less familiar with the technology. To assist those with less experience, the core focuses on both design and training, offering our expertise to our users and helping to adapt the technology to their unique application. To further these goals, the core develops complete solutions, from the initial device design in CAD software, to its fabrication in our clean room, to the setup and execution of an experiment with our dedicated core microscopes. The members of the core have unique backgrounds with experience in both traditional engineering and molecular biology, which allows them to focus on how to design devices to answer specific biological questions. This allows our members to design microfluidic devices to address the unique requirements of many types of experiments without undue focus on the technical aspects of the technology.

Core Services

Design of microfluidic molds

A user will contact our leadership and schedule an appointment with a design specialist. The specialist will determine the user’s needs and determine if one of our off-the-shelf systems is appropriate. If a custom solution needs to be made then the specialist will work with the user to develop an appropriate design and provide the necessary CAD files upon completion.

Production of device molds

Once the mold’s design has been finalized, a user will schedule with our technician to produce the mold in our fabrication facility. The technician will produce the mold and ensure that it meets required quality control standards.

Production of microfluidic devices

Once a custom mold has been created, our technicians can make microfluidic devices from it if desired by the end user. Our technicians can also make devices from our large catalog of molds, which are in common use currently. The device is inspected for quality control purposes and delivered to the end user.

Incorporation of microfluidic devices into automated microscopy control systems

Our staff has extensive experience working with common microscopy control software such as Nikon Elements and Micro-Manager, an open source software package. If Micro-Manager is preferred, we will custom develop the necessary control scripts required to operate the hardware and to ensure compatibility with our other hardware platforms, such as the dial-a-wave system.

Computer assisted image processing

Our core has developed automated cell tracking algorithms for commonly used model organisms such as yeast and E. coli in addition to mammalian cells. These algorithms are available to core users and our staff coordinates closely with the Network Assembly and Mathematical Modeling Core to process acquired images in a manner compatible with further analysis.

Fluorescent reporter quantification

Once an experiment has been completed and images have been appropriately processed, our core can extract the fluorescence signal from each cell in a field of view. We can determine parameters such as localization and production of fluorescent proteins over the course of a multi-day experiment for each cell in the population.

Synthetic logic gate design

Users contact our technicians about the type of logic circuit they wish to design. Our technicians will assemble the relevant genetic components depending upon the organism of interest (for example variants of the TetR transcription factor for work in prokaryotes). Our technicians will then come up with a proposed circuit and arrange for its synthesis through a third-party contractor.

Synthetic circuit analysis

Users contact our technicians about the organism of interest, the type of circuit desired and the interface with other cellular systems. Our technicians then preform a feasibility analysis and come up with a proposed circuit design. Upon further consultation with our users, the circuit is sent to a third-party contractor for synthesis and then transformed into the desired organism. Our technicians can then test the circuit with our microscopy systems to ensure the desired functionality.

RNA-Seq experimental setup and template preparation

Our technicians will consult with the user to determine the appropriate experimental design and setup. Users can culture their desired organisms in their lab or in our core facility. Users can add a preservative reagent (such as RNAlater) and then transport samples to the core facility for RNA extraction. This RNA can then be transferred to Genomics and Genome Engineer Core for library preparation or other services.

Illumina MySeq next generation sequencing

Our core has recently obtained an Illumina MySeq sequencing machine. Template libraries that have been prepared by the Genomics and Genome Engineering Core can be loaded onto our core’s MySeq for analysis if desired.

Submit a request for services here