Past Projects

• Toward Studying Circuit Dynamics and Stimulus Integration in Drosophila
  OCTOBER 20, 2008 - MAY 31, 2009
  VISITOR: Misha Ahrens (Ph.D. student, University College of London)
  HOST: Vivek Jayaraman and Michael Reiser (JFRC Fellows)
  
  PROJECT SUMMARY: This project brought Misha Ahrens, a Ph.D. student from the University College of London, to Janelia to collaborate with Michael Reiser and Vivek Jayaraman. Mr. Ahrens developed novel mathematical tools for analyzing the effects of certain external stimuli on neural activity and complex behavioral responses while in London. During his visit to Janelia, Mr. Ahrens performed a pilot study in Drosophila to assess the feasibility of Drosophila as a model system to test his theoretical models.
• MtDNA Nucleoid Dynamics in Models of Neurodegeneration
  JANUARY 1, 2008 - MARCH 31, 2008
  VISITOR: Dan Bogenhagen (Professor of Pharmacological Sciences, SUNY Stony Brook)
  HOST: Eric Betzig (JFRC Group Leader) and David Clayton (JFRC Lab Head)
  
  PROJECT SUMMARY: Dan Bogenhagen came to Janelia to collaborate with Eric Betzig and David Clayton. Their focus was to use super-resolution imaging techniques developed in the Betzig lab to study the mechanisms of nucleoid replication in mitochondria.
• Serial Section Electron Microscopy in the Fly Brain: Pilot study for Large-Scale Mapping
  MARCH 15, 2008 - JUNE 30, 2008
  VISITOR: Albert Cardona (Postdoctoral Fellow, University of California, Los Angeles)
  HOST: Julie Simpson (JFRC Group Leader)
  
  PROJECT SUMMARY: This project brought Albert Cardona to work with Julie Simpson and other scientists at Janelia to perform some pilot experiments toward mapping the fly brain by electron microscopy. The first objective was to install software for automatic imaging at the electron microscope. The second objective focused on sectioning, automatic imaging, and image assembly of an entire segment of the Drosophila first instar larva ventral nerve cord. The third objective was to engineer new fly lines for future functional studies. This project was very successful and helped establish new technology and protocols for a large-scale mapping project of the fly brain and nerve cord by electron microscopy.
• High-Order Control of Behavior in Drosophila
  DECEMBER 20, 2006 - DECEMBER 19, 2007
  VISITOR: Michael Dickinson (Zarem Professor of Bioengineering, California Institute of Technology)
  HOST: Michael Reiser (JFRC Fellow)
  
  PROJECT SUMMARY: Michael Dickinson came to Janelia to collaborate with Michael Reiser and others to develop behavioral assays for Drosophila. While the initial intention was to develop a system to track a walking fly (and this was done), new research objectives developed, such as the use of nano-fabricated microelectrodes, and these have evolved into a new project in collaboration with James Truman (current projects, above).
• Structure/Function Studies in the Control of Locomotion by the Drosophila Thoracic Ganglion
  MARCH 1, 2008 - FEBRUARY 28, 2009
  VISITOR: Michael Dickinson (Zarem Professor of Bioengineering, California Institute of Technology)
  HOST: : James Truman (JFRC Group Leader)
  
  PROJECT SUMMARY: Michael Dickinson returns to Janelia to collaborate primarily with James Truman. The scientific focus is to study how the small number of neurons in the Drosophila brain with descending projections into the thoracic ganglion control and integrate both major modes of locomotion in the adult: walking and flight. The four specific aims include a screen for behavioral defects using the Janelia collection of GAL4 driver lines (being generated in the Rubin and Simpson labs), the development of nanoelectrode probes for extracellular recordings, anatomical characterization of the descending neurons at the EM level, and the identification of the neural lineages involved.
• Integration of the Pfam Database and Recent HMMER Software Developments
  OCTOBERr 1, 2008 - FEBRUARY 28, 2009
  VISITOR: Robert Finn (Postdoctoral Fellow, Wellcome Trust Sanger Institute)
  HOST: Sean Eddy (JFRC Group Leader)
  
  PROJECT SUMMARY: Rob Finn is the project leader of the Pfam protein families database curated in Alex Bateman's lab at the Wellcome Trust Sanger Institute. The core of the Pfam system is built on top of a protein sequence analysis software package called HMMER. Development of the HMMER software is largely the responsibility of the team at Janelia Farm, led by Sean Eddy. The most recent development of HMMER needs to be integrated into Pfam and will require testing. The purpose of Rob Finn’s visit to the Eddy lab was to set up the basis of the collaboration that will be required.
• Plasticity Studies with Quantitative Imaging Methods
  JUNE 1, 2008 - MARCH 31, 2009
  VISITOR: Kevin Fox (Professor and Head of Research, Cardiff School of Biosciences)
  HOST: Karel Svoboda (JFRC Group Leader)
  
  PROJECT SUMMARY: Kevin Fox is a leading expert on plasticity mechanisms in the visual and somatosensory cortex. This project brought Professor Fox and postdoc Sandra Kuhlman to Janelia to collaborate with Karel Svoboda. The scientific focus was to study plasticity of circuits in the mouse barrel cortex and somatosensory whisker cortex using new imaging and circuit mapping techniques developed in the Svoboda lab.
• Mapping Neuropile Compartments and Neuropile Foci in the Drosophila Brain
  OCTOBER 1, 2007 - DECEMBER 31, 2007
  VISITOR: Volker Hartenstein (Professor of Molecular, Cell & Developmental Biology, University of California, Los Angeles)
  HOSTS: Julie Simpson and Gene Myers (JFRC Group Leaders)
  
  PROJECT SUMMARY: This project brought Professor Volker Hartenstein, an expert in Drosophila neuroanatomy, to Janelia to work with Julie Simpson, Gene Myers, and other scientists. The project laid the groundwork for a mapping project by defining and unifying existing models of brain regions. The first objective was to define and name neuropile compartments and fiber tracts by light analysis using a neuronal marker, nc82. The second objective was to further define small subdivisions (“foci”) within the neuropile compartments using a lineage-based approach. This project was very successful and brought Professor Hartenstein back to Janelia to share his expertise in a large-scale mapping project of the fly brain (current projects, above).
• Development of an In Vivo Approach to Study Network Function in the Locust Central Complex
  MAY 15, 2008 - JUNE 7, 2008
  VISITOR: Stanley Heinze (Professor of Biology and Animal Physiology, University of Marburg)
  HOST: Vivek Jayaraman (JFRC Fellow)
  
  PROJECT SUMMARY:This project brought Stanley Heinze to Janelia to collaborate with Vivek Jayaraman. The overall aim of the collaboration was the development of a reliable method for paired recordings from polarization-sensitive neurons of the central-complex of the fly brain, while simultaneously loading the neurons with Ca⁺⁺-sensitive dyes for in vivo identification of the neuron type and imaging of dendrites.
• Studies on the Drosophila Brain
  OCTOBER 1, 2008 - DECEMBER 31, 2008
  VISITOR: Martin Heisenberg (Professor and Head of Department for Genetics and Neurobiology, Universität Würzburg)
  HOST: Gerry Rubin (JFRC Director)
  
  PROJECT SUMMARY: Professor Martin Heisenberg is a very senior and prominent scientist with pioneering expertise and knowledge in Drosophila neurogenetics. While at Janelia, Professor Heisenberg made progress toward two objectives: to work on a book on the epistemology of neuroscience from the perspective of behavior and to give a lecture series on topics related to studies on the fly brain. Professor Heisenberg's expert knowledge was so greatly appreciated that he will return to Janelia to consult with scientists at Janelia and to collaborate with the Rubin lab to analyze reagents, which are uniquely available in the Rubin lab (new GAL4 expression driver lines). The scientific focus will be to study circuits involved in controlling behavior.
• Unraveling the Neural Code in the Mammalian Olfactory Bulb
  JUNE 1, 2008 - MAY 31, 2009
  VISITOR: Alexei Koulakov (Associate Professor, Cold Spring Harbor Laboratory)
  HOST: Dima Rinberg (JFRC Fellow)
  
  PROJECT SUMMARY: This project brought Alexei Koulakov to collaborate with Dmitry Rinberg for three months plus additional short visits throughout the project year. Dr. Koulakov has expertise in theoretical neurobiology and modeling and this proposal focused on combining bioinformatics with genetic and electrophysiological techniques towards the construction of a verifiable model for olfactory coding in the mouse brain.
• Social Behavior in Rodents
  FEBRUARY 1, 2008 - JANUARY 31, 2009
  VISITOR: Zachary Mainen (group leader, Instituto Gulbenkian de Ciência, Portugal)
  HOST: Alla Karpova (JFRC group leader)
  
  PROJECT SUMMARY: Zachary Mainen came to Janelia to collaborate primarily with Alla Karpova and post-doc Dougal Gowanlock Tervo. Dr. Mainen is a leader in the study of rodent behavior The scientific focus was to develop an animal model of reciprocity in rats with the aim of eventually studying the neural circuits that underlie this task.
• Construction and Characterization of Transgenic RNAi Lines to Inactivate 1,000 Drosophila Genes with Nervous System Functions
  JANUARY 1, 2007 - DECEMBER 31, 2008
  
  VISITORS: Norbert Perrimon (HHMI investigator and Professor of Genetics, Harvard Medical School) and Charles Zuker (HHMI Investigator and Professor of Biology and Neuroscience, UC San Diego)
  HOST: Gerry Rubin (JFRC Director)
  
  PROJECT SUMMARY: This was the second (and final) year for a project that brought two HHMI investigators to Janelia to collaborate with Gerry Rubin. This was an infrastructural project with very specific and concrete goals: to develop gene inhibition reagents to target about 1,000 genes that have relevance to CNS function. These included genes involved in neurotransmission, connectivity and path finding, behavior, ion channels, and transcription factors preferentially expressed in the nervous system. In the first year, technology was developed to support the project and the production of the reagents themselves had begun. The second year saw the near completion of the collection and some phenotypic characterization. The project was the basis for a large grant that will be funded by the NIH to construct similar reagents for the rest of the fly genome.
• Image Processing for Registering Fly Brains and Tracing Neurons in Sparsely Sained 3-D Stacks
  AUGUST 20, 2007 - DECEMBER 20, 2007
  VISITOR: Sven Rahmann (Group Leader in the AG Genominformatik, Technische Fakultät, at the Universität Bielefeld)
  HOST: Gene Myers (JFRC Group Leader)
  
  PROJECT SUMMARY: Sven Rahmann came to work with Gene Myers' group at Janelia to develop software for the analysis of neural structure in the fly.
• Novel Approaches to Controlled Gene Expression in the Mouse Nervous System
  JUNE 1, 2007 - MAY 31, 2008
  
  VISITOR: Thomas Südhof (HHMI Investigator and Professor of Molecular Genetics, University of Texas Southwestern Medical Center at Dallas)
  HOST: Alla Karpova and Sean Eddy (JFRC Group Leaders)
  
  PROJECT SUMMARY: This project brought Professor Tom Südhof in 2007 to Janelia to develop new methods to express transgenes in specific locations in the mouse brain. This technology is well advanced in Drosophila and other invertebrate models, but has lagged in the mouse. The ability to specifically express activity reporters, cell tracers and reagents to manipulate neural activity is crucial to the full exploitation of the mouse as a genetic model to study the brain. This collaboration led to the development of four (4) new transgenic mouse lines that will be used by multiple labs at Janelia to drive cell-type specific expression in the mouse brain.
• Novel ncRNA-Encoding Genes in Salmonella typhimurium
  APRIL 1, 2008 - MAY 31, 2008
  VISITOR: Coral del Val Muñoz (Department of Computer Science and Artificial Intelligence, University of Granada, Spain)
  HOST: Elena Rivas (JFRC Fellow)
  
  PROJECT SUMMARY: This project brought Dr. Coral del Val Muñoz to Janelia to work with Elena Rivas. This work focused on the identification of possible riboswitch candidates for Salmonella typhi, in particular focusing on genes that are involved in the pathogenic behavior of Salmonella using a computational strategy developed by Elena Rivas and Sean Eddy.
• The Role of Sniffing for the Processing of Olfactory Information in Rat Mitral Cells
  JUNE 1, 2006 - NOVEMBER 30, 2007
  VISITOR: Matt Wachowiak (Assistant Professor of Biology, Boston University)
  HOST: Dmitry Rinberg (JFRC Fellow)
  
  PROJECT SUMMARY: This project brought Matt Wachowiak and his student Dan Wesson to Janelia. They worked intensively with Dmitry Rinberg to develop a head fixed assay for sniffing behavior in the rat.
• A Pilot Study to Explore Multistable Perception by Drosophila
  JANUARY 1, 2008 - MARCH 31, 2008
  VISITOR: Daw-An Wu (Postdoctoral Fellow, Vision Science Lab, Harvard)
  HOST: Michael Reiser (JFRC Fellow)
  
  PROJECT SUMMARY: This project brought Daw-An Wu to Janelia to collaborate with Michael Reiser to undertake exploratory experiments in order to attempt to detect multistable perception in Drosophila. In this case they focused on the unification of the images generated by the two eyes, using flight-orientation behavior as an assay.
• Assigning Internal Energies to Unfolded, Single-Stranded RNA and DNA
  SEPTEMBER 1, 2006 - JUNE 30, 2007
  VISITOR: Michael Zuker (Professor, Rensselaer Polytechnic Institute)
  HOST: Sean Eddy (JFRC Group Leader)
  
  PROJECT SUMMARY: This project brought Michael Zuker to do a one-year sabbatical with Sean Eddy. They collaborated on software to analyze and predict RNA structure from primary sequence.