In the Vale lab, we are interested in developing new tools to tackle interesting problems. While these tools are often developed to address a specific problem, our hope is that they will be useful to the larger scientific community. Here are some of our past projects, and links to where you can find more information if you are interested in applying these techniques to your research.
Our lab extensively uses advanced light microscopes. To execute experiments with these technologies, our lab has often needed to push the boundaries of available software and hardware. For example, we started a project to create an open source, cross-platform software for image acquisition, called µManager. The µManager project released version 1 of the code in January 2007 and has now moved to a company, Open Imaging, set up by the development team to further develop µManager and provide µManager-related services.
Currently our lab is involved in development of dual view inverted selective plane illumination microscopy (diSPIM) and its integration with µManager. More information about this project and our ongoing collaboration with Hari Shroff and Jon Daniels can be found on iBiology and on the µManager website.
Our lab has also been involved in developing freely available open source software tools for scanning angle interference microscopy (SAIM) analysis and image acquisition, and a tool for automated angle calibration. More information about this project can be found on Github, Fiji, and the hardware page.
A postdoc in our lab, Marvin Tanenbaum, developed an in vivo signal amplification system called SunTag. In brief, a repeating peptide array (SunTag) can be appended to your protein of interest, and recruit multiple copies of an antibody fusion protein. This technology is useful for amplifying signal in vivo, as multiple GFPs can be recruited to a single molecule. For more information, see Marvin’s lab website, the original SunTag publication and this SunTag FAQ page.
ImageJ is an image processing and analysis application written in Java by Wayne Rasband. It is free and it’s source code is available, making it an extremely attractive platform for development of new image analysis tools. Here are a few of the plugins developed in the Vale lab for our image analysis applications.
In 2002 we developed, together with the labs of Pat O’Farrell and Graeme Davis a library of dsRNA molecules targeting ~ 7000 Drosophila genes that have homology to either human or C. elegans genes. In 2004 our lab discovered that many “hits” (in a screen for mitotic index changes) were caused by dsRNAs containing trinucleotide repeats (most often coding for poly-glutamate stretches). This observation made us realize that 1: these low complexity regions were accidentally represented in the RNAi library, and that 2: these regions obviously contributed to knock-down of targets other than the intended gene. We used this experience in the design of UCSF v.2 Drosophila which targets all genes of the Drosophila genome. This library was designed in January 2005 (by Nico Stuurman), and over 90% of the ~15000 dsRNAs in this library do not contain any 21bp sequence also found elsewhere in the genome. This library has been synthesized at Open Biosystems (with help by Gohta Goshima and Yi Guo), and is available both in the form of DNA and RNA. Please see the RNAi website for more information about this project.