Grant Abstracts 2012   Broad Institute Inc. Feng Zhang Cambridge, MA $1,000,000 June 2012 Neuropsychiatric diseases arise from a combination of genetic and environmental factors that influence the molecular, morphological and physiological properties of neurons and glia in the brain.  Elucidation and treatment of these diseases will benefit from understanding how specific brain cell types connect and signal in neural circuits, and how genetic factors affect their cellular function.  Transgenic techniques have been widely used to target specific cell populations with fluorescent reporter (e.g. GFP) and modulator (e.g. channelrhodopsin-2) genes to probe their role in disease mechanisms.  However these conventional gene targeting strategies depend on the identification of unique molecular markers and promoters and are largely limited to the mouse, whereas other animal models that are commonly used for neuroscience and disease studies (e.g. rats and primates) are still mostly inaccessible.  Additionally, since many non-rodent animal models have long reproductive cycles, fundamentally new approaches for cell-type specific gene targeting are highly desirable.  The researchers propose to develop and apply a generalizable genetic circuit for detecting endogenous transcription states to enable conditional genetic manipulation of specific cell types.  The proposed technology could have broad applications for both disease research as well future therapeutic interventions.   J. David Gladstone Institutes Sheng Ding, Steve Finkbeiner, Shinya Yamanaka San Francisco, CA $1,000,000 June 2012 The human brain can carry out more operations per second than the most powerful computer.  It also has capacities no computer is likely to ever have, such as consciousness and self- awareness.  Thanks to human induced pluripotent stem cells and other induced neural precursor cells, scientists can now make, in theory, any type of brain cell from adult skin cells.  Still, only a few types of human brain cells have been made, and the process for making them remains inefficient.  The investigators propose to establish an interdisciplinary program to understand how cells that are reprogrammed to pluripotency can be instructed to generate each type of cell in the brain.  They have assembled a team that can create, in the laboratory, a number of cell types that compose the brain.  In this project they propose to make certain brain cells (e.g., von Economo neurons that are thought to confer unique abilities, such as emotional and social salience, to the human brain) that do not exist in standard laboratory animals.  This work could lay the foundation for both the development of cellular therapies to treat neurological diseases and for a greater understanding of what makes us unique as humans.   Oregon Health & Science University Joe Gray Portland, OR $1,000,000 June 2012 This project will initiate development of image-based approaches that will allow architectural analysis of the nanoscale molecular assemblies that regulate information flow in cells.  The team will coordinately develop multi-scale imaging, labeling chemistry and computer science to visualize specific molecular assemblies in cells and to localize these relative to cellular ultrastructural features using a new integrated light and electron microscope (iLEM) to analyze the signaling architecture.  The iLEM consists of a custom-designed fluorescent microscope mounted on the side port of a transmission electron microscope.  The project team will develop the technologies to enable the detection of the molecular structures that regulate information flow within cells and learn how these structures assemble, integrate signals from multiple sources, and shuttle the information to action centers in cells that control activities such as growth, death and movement.  The research team expects that their iLEM analysis approaches eventually will be broadly applicable to studies of regulatory signal networks in normal and diseased tissues.   University of California, San Diego Steven Dowdy, Yitzhak Tor San Diego, CA $1,000,000 June 2012 The discovery of RNA interference (RNAi), a natural gene silencing mechanism with exquisite selectivity for all 23,000 human mRNAs, opened the door to a global therapeutic approach that can be tailored to keep evolutionary pace with pandemic viral outbreaks or for personalized medicine.  However, use of RNAi as a therapeutic is severely hindered by the negatively charged phosphate backbone: it simply cannot enter cells on its own.  Current RNAi delivery approaches utilize nanoparticles that are 5,000-fold larger than the actual RNAi cargo, which due to this size, have inherently poor pharmacological properties.  Using an interdisciplinary chemistry and molecular approach, we seek funds to build a paradigm shifting RNAi technology that radically shrinks the delivery size to the smallest possible, self delivering monomeric RNAi-inducing molecule via synthesis of neutral, bioreversible phosphotriester RiboNucleic Neutrals.  Once inside cells, cytoplasmic enzymes unmask the phosphate groups and convert them into negatively charged, active RNAi molecules.  Although the technology has broad applicability, the team will establish efficacy of this delivery system in mouse models of cancer.   University of Wisconsin, Madison Aseem Ansari, Parameswaran Ramanathan, Jennifer Reed, David C. Schwartz Madison, WI $1,000,000 June 2012 The ability to compose or “program” genomes to perform desired functions will yield insights into how gene networks govern life and will stimulate innovation in many disciplines that interface with biology.  The current approach to synthetic genomes involves copying an existing small genome via time-intensive and cost-prohibitive methods.  The UW team of engineers, chemists and biologists seeks to create a multifaceted system – a genome foundry – that permits rapid, inexpensive fabrication of de novo designed genomes.  The interdisciplinary team, will develop an integrated system to enable design-to-fabricated genome production.  The proposed “genome foundries” will comprise an inter-locking suite of computational tools, nanofluidic instrumentation, hardware fabrication languages, and custom-designed synthetic gene switches. The new technology envisioned could enable widespread invention of genome-aided solutions to fundamental and applied problems and the ability to compose and automate the synthesis of large DNA molecules could spur innovations in DNA-based nano-device fabrication and DNA computing.