September 13th - From Fragments to Objects: Mechanisms of Visual Integration

Pawan Sinha
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology

Learning to integrate information is a key task a child's brain has to perform during the normal developmental course. Such learning discerns relationships within and between sensory inputs. It makes explicit which entities in the sensory inputs regularly co-occur, or have systematic predictive relationships. In essence, this developmental process transforms the sensorium from an amorphous collection of primitive attributes, to one where these attributes are integrated into cliques corresponding to distinct objects. In this talk, I shall describe our work on a model of visual integration, motivated in part by experimental studies of individuals with abnormal developmental profiles.

October 11th - Three-dimensional Compositional Imaging at the Atomic Scale: Innovative Atom Probe Tomography

Thomas Kelly
Founder, Chairman, and CTO
Imago Scientific Instruments Corporation

Atom probe tomography provides three-dimensional structural and compositional analysis of materials at the atomic-scale. With recent developments in Local Electrode Atom Probe or LEAP® technology by Imago Scientific Instruments, the atom probe’s compositional imaging capabilities are now accessible to non-experts for analysis of a wide variety of materials. The advantages of Imago’s LEAP technology for speed, field of view, and ease of operation will be presented. Important examples of analyses of metals, semiconductors, thin film structures and organic materials will be shown and the role this information plays in process and materials development will be described.

December 13th - Tunneling Nanotubules; A Novel System of Cellular Communication in the Immune System

Simon Watkins
Director, Center for Biologic Imaging
University of Pittsburgh

Intercellular signals can be transmitted through neuronal synapses or through gap junctions, with the latter mediating transmission of calcium fluxes and small molecules between cells. We show here that a third form of communication between cells can be mediated by tunneling nanotubules (TNT). When myeloid-lineage dendritic cells and monocytes are triggered to flux calcium by chemical or mechanical stimulation, the signal can be propagated within seconds to other cells at distances hundreds of microns away via TNT. A complex and transient network of TNT is seen in live cells, with individual tubules exhibiting substantial variation in length and diameter. In addition to calcium fluxes, microinjected dye tracers can be transferred through these connections. Following TNT-mediated stimulation, spreading of lamellipodia occurs in dendritic cells characteristic of that seen during the phagocytic response to bacteria. These results demonstrate that nonneuronal cells can transmit signals to distant cells through a physically connected network.

February 14th - Imaging Axon Guidance in the Developing Zebrafish

Mary Halloran
Department of Zoology
University of Wisconsin-Madison

March 14th - Structure, Function and Dynamics of Viral RNA Replication Complexes

Paul Ahlquist
Howard Hughes Medical Institute
Institute for Molecular Virology
University of Wisconsin-Madison

Positive-strand RNA viruses are the largest genetic class of viruses, encompassing over one-third of all virus genera and many important pathogens. Recent studies combining light and electron microscopy with molecular genetics show that the membrane-associated RNA replication complexes of these viruses are novel mini-organelles that concentrate and sequester viral replication factors and templates, coordinate successive replication steps, and protect dsRNA replication intermediates from host defenses. We further find that the structure, assembly and function of these intracellular RNA replication complexes share multiple parallels with the replicative cores of extracellular virions from reverse-transcribing and dsRNA viruses. The results reveal unexpected links among 3 of the 6 major classes of viruses, with intriguing implications for virus evolution and control.

April 11th - Filopodia as agents of neural circuit construction and remodeling

Stephen Smith
Department of Molecular and Cellular Physiology
Stanford University

May 9th - Whole Genome Sequencing and Imaging-Based Systems Biology

Gene Myers
Janelia Farm Research Campus
Howard Hughes Medical Institute

The whole-genome shotgun sequencing method with paired end-reads has proven rapid and economical, producing high-quality reconstructions of Drosophila (2000), Human (2001) and Mouse (2001), in quick succession. We discuss the overall algorithmic strategy, and the results one can expect by comparing the whole genome assembly of Drosophila against the finished sequence.

Because the finishing phase of genome assembly is an order of magnitude more expensive then the shotgun phase, most genomes being sequenced today will never be finished. This makes the goal of building better whole genome assemblers more important than ever. We present a new string-graph approach and several other improvements, giving preliminary results. We also discuss recent advances in sequencing technology.

Much hope has been placed on comparative genomics as the easiest route to near-perfect annotation of genes and regulatory elements. We discuss the problem of gene finding and raise the issue that algorithms to date are not performing at the expected level.

This leads us to conclude with a segment on the possibility of a program of high-throughput in-situ image analysis in D. melanogaster and C. elegans embryos. We describe preliminary results on limited data sets and extrapolate on what we might be able to infer from such data. We speculate that this may be the best way to understand the developmental cis-regulatory network of the genome from a systems perspective.