Gregory Jefferis - Academia.edu (original) (raw)

Papers by Gregory Jefferis

Genetically encoded fluorescent proteins and immunostaining are widely used to detect cellular an... more Genetically encoded fluorescent proteins and immunostaining are widely used to detect cellular and subcellular structures in fixed biological samples. However, for thick or whole-mount tissue, each approach suffers from limitations, including limited spectral flexibility and lower signal or slow speed, poor penetration, and high background labeling, respectively. We have overcome these limitations by using transgenically expressed chemical tags for rapid, even, highsignal and low-background labeling of thick biological tissues. We first construct a platform of widely applicable transgenic Drosophila reporter lines, demonstrating that chemical labeling can accelerate staining of whole-mount fly brains by a factor of 100. Using viral vectors to deliver chemical tags into the mouse brain, we then demonstrate that this labeling strategy works well in mice. Thus this tag-based approach drastically improves the speed and specificity of labeling genetically marked cells in intact and/or thick biological samples.

Current Biology, 2015

The same sensory signal can be interpreted differently according to context. A new study in Droso... more The same sensory signal can be interpreted differently according to context. A new study in Drosophila uses cell-type-specific tools to identify neural circuits that integrate context during olfactory processing and surprisingly implicates memory-recall neurons.

Current Opinion in Neurobiology, 2015

Understanding how sensory stimuli are processed in the brain to instruct appropriate behavior is ... more Understanding how sensory stimuli are processed in the brain to instruct appropriate behavior is a fundamental question in neuroscience. Drosophila has become a powerful model system to address this problem. Recent advances in characterizing the circuits underlying pheromone processing have put the field in a position to follow the transformation of these chemical signals all the way from the sensory periphery to decision making and motor output. Here we describe the latest advances, outline emerging principles of pheromone processing and discuss future questions.

Science (New York, N.Y.), Jan 9, 2004

Current opinion in neurobiology, 2002

Recent advances in the study of the connectivity of Drosophila olfactory system include the demon... more Recent advances in the study of the connectivity of Drosophila olfactory system include the demonstration that olfactory receptor neurons project to specific glomeruli according to the receptor type they express, and that their projection neuron partners are prespecified to innervate particular glomeruli by birth order or time. This same theme of sequential generation has been observed in the generation of the three major types of mushroom body neurons.

Genes & development, 2000

Patched (Ptc), initially identified in Drosophila, defines a class of multipass membrane proteins... more Patched (Ptc), initially identified in Drosophila, defines a class of multipass membrane proteins that control cell fate and cell proliferation. Biochemical studies in vertebrates indicate that the membrane proteins Ptc and Smoothened (Smo) form a receptor complex that binds Hedgehog (Hh) morphogens. Smo transduces the Hh signal to downstream effectors. The Caenorhabditis elegans genome encodes two Ptc homologs and one related pseudogene but does not encode obvious Hh or Smo homologs. We have analyzed ptc-1 by RNAi and mutational deletion and find that it is an essential gene, although the absence of ptc-1 has no detectable effect on body patterning or proliferation. Therefore, the C. elegans ptc-1 gene is functional despite the lack of Hh and Smo homologs. We find that the activity and expression of ptc-1 is essentially confined to the germ line and its progenitors. ptc-1 null mutants are sterile with multinucleate germ cells arising from a probable cytokinesis defect. We have also...

Efforts to map neural circuits from model organisms including flies and mice are now generating m... more Efforts to map neural circuits from model organisms including flies and mice are now generating multi-terabyte datasets of 10,000s of labelled neurons. Technologies such as dense EM based reconstruction, and sparse/multicolor labeling with image registration allow neurons to be embedded within the spatial context of a circuit or a whole brain. These ever-expanding data demand new computational tools to search, organize and navigate neurons. We present a simple, but fast and sensitive, algorithm, NBLAST, for measuring pairwise neuronal similarity by position and local geometry. Inspired by the BLAST algorithm for biological sequence data, NBLAST decomposes a query and target neuron into short segments. Each matched segment pair is scored using a log-likelihood ratio scoring matrix empirically defined by the statistics of real matches and non-matches in the data.

Cold Spring Harbor Protocols, 2013

Clonal analysis with the MARCM (mosaic analysis with a repressible cell marker) system can be use... more Clonal analysis with the MARCM (mosaic analysis with a repressible cell marker) system can be used for studying cell lineage, development, and anatomy in the Drosophila olfactory system and other parts of the fly brain. To compare confocal images of labeled neurons in different brains, it may be desirable to register them to a template or standard brain. There are various image registration approaches available. Some depend on manually specifying landmarks on the brains to be registered. Others depend only on the grayscale intensity value of one of the channels in the confocal image. Another important difference between registration approaches is whether they apply linear or nonlinear (warping) transformations. Linear transformations typically include translation, rotation, and scaling along each axis. Nonlinear transformations are much more computationally intensive, but are required to register brains with different shapes. Here we describe the practical steps required for an intensity-based nonlinear registration that has been used to map the higher olfactory centers of the Drosophila brain using the staining for the presynaptic marker Bruchpilot (nc82). This registration is in fact a two-step process. The first step is a linear transformation that roughly aligns the two brains, followed by a second nonlinear step that allows different parts of the brain to move in slightly different directions.

Frontiers in Neuroinformatics, 2012

Mapping neural circuits can be accomplished by labeling a small number of neural structures per b... more Mapping neural circuits can be accomplished by labeling a small number of neural structures per brain, and then combining these structures across multiple brains. This sparse labeling method has been particularly effective in Drosophila melanogaster, where clonally related clusters of neurons derived from the same neural stem cell (neuroblast clones) are functionally related and morphologically highly stereotyped across animals. However identifying these neuroblast clones (approximately 180 per central brain hemisphere) manually remains challenging and time consuming. Here, we take advantage of the stereotyped nature of neural circuits in Drosophila to identify clones automatically, requiring manual annotation of only an initial, smaller set of images. Our procedure depends on registration of all images to a common template in conjunction with an image processing pipeline that accentuates and segments neural projections and cell bodies. We then measure how much information the presence of a cell body or projection at a particular location provides about the presence of each clone. This allows us to select a highly informative set of neuronal features as a template that can be used to detect the presence of clones in novel images. The approach is not limited to a specific labeling strategy and can be used to identify partial (e.g., individual neurons) as well as complete matches. Furthermore this approach could be generalized to studies of neural circuits in other organisms.

Journal of Neuroscience, 2011

To sense myriad environmental odors, animals have evolved multiple, large families of divergent o... more To sense myriad environmental odors, animals have evolved multiple, large families of divergent olfactory receptors. How and why distinct receptor repertoires and their associated circuits are functionally and anatomically integrated is essentially unknown. We have addressed these questions through comprehensive comparative analysis of the Drosophila olfactory subsystems that express the ionotropic receptors (IRs) and odorant receptors (ORs). We identify ligands for most IR neuron classes, revealing their specificity for select amines and acids, which complements the broader tuning of ORs for esters and alcohols. IR and OR sensory neurons exhibit glomerular convergence in segregated, although interconnected, zones of the primary olfactory center, but these circuits are extensively interdigitated in higher brain regions. Consistently, behavioral responses to odors arise from an interplay between IR-and OR-dependent pathways. We integrate knowledge on the different phylogenetic and developmental properties of these receptors and circuits to propose models for the functional contributions and evolution of these distinct olfactory subsystems.