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2559 Janelia Publications

Showing 2341-2350 of 2559 results
05/03/11 | Robo-3--mediated repulsive interactions guide R8 axons during Drosophila visual system development.
Pappu KS, Morey M, Nern A, Spitzweck B, Dickson BJ, Zipursky SL
Proc Natl Acad Sci U S A. 2011 May 03;108(18):7571-6. doi: 10.1073/pnas.1103419108

The formation of neuronal connections requires the precise guidance of developing axons toward their targets. In the Drosophila visual system, photoreceptor neurons (R cells) project from the eye into the brain. These cells are grouped into some 750 clusters comprised of eight photoreceptors or R cells each. R cells fall into three classes: R1 to R6, R7, and R8. Posterior R8 cells are the first to project axons into the brain. How these axons select a specific pathway is not known. Here, we used a microarray-based approach to identify genes expressed in R8 neurons as they extend into the brain. We found that Roundabout-3 (Robo3), an axon-guidance receptor, is expressed specifically and transiently in R8 growth cones. In wild-type animals, posterior-most R8 axons extend along a border of glial cells demarcated by the expression of Slit, the secreted ligand of Robo3. In contrast, robo3 mutant R8 axons extend across this border and fasciculate inappropriately with other axon tracts. We demonstrate that either Robo1 or Robo2 rescues the robo3 mutant phenotype when each is knocked into the endogenous robo3 locus separately, indicating that R8 does not require a function unique to the Robo3 paralog. However, persistent expression of Robo3 in R8 disrupts the layer-specific targeting of R8 growth cones. Thus, the transient cell-specific expression of Robo3 plays a crucial role in establishing neural circuits in the Drosophila visual system by selectively regulating pathway choice for posterior-most R8 growth cones.

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05/01/11 | PALM and STORM: unlocking live-cell super-resolution.
Henriques R, Griffiths C, Hesper Rego E, Mhlanga MM
Biopolymers. 2011 May;95(5):322-31. doi: 10.1002/bip.21586

Live-cell fluorescence light microscopy has emerged as an important tool in the study of cellular biology. The development of fluorescent markers in parallel with super-resolution imaging systems has pushed light microscopy into the realm of molecular visualization at the nanometer scale. Resolutions previously only attained with electron microscopes are now within the grasp of light microscopes. However, until recently, live-cell imaging approaches have eluded super-resolution microscopy, hampering it from reaching its full potential for revealing the dynamic interactions in biology occurring at the single molecule level. Here we examine recent advances in the super-resolution imaging of living cells by reviewing recent breakthroughs in single molecule localization microscopy methods such as PALM and STORM to achieve this important goal.

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05/01/11 | Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination.
Planchon TA, Gao L, Milkie DE, Davidson MW, Galbraith JA, Galbraith CG, Betzig E
Nature Methods. 2011 May;8(5):417-23. doi: 10.1038/nmeth.1586

A key challenge when imaging living cells is how to noninvasively extract the most spatiotemporal information possible. Unlike popular wide-field and confocal methods, plane-illumination microscopy limits excitation to the information-rich vicinity of the focal plane, providing effective optical sectioning and high speed while minimizing out-of-focus background and premature photobleaching. Here we used scanned Bessel beams in conjunction with structured illumination and/or two-photon excitation to create thinner light sheets (<0.5 μm) better suited to three-dimensional (3D) subcellular imaging. As demonstrated by imaging the dynamics of mitochondria, filopodia, membrane ruffles, intracellular vesicles and mitotic chromosomes in live cells, the microscope currently offers 3D isotropic resolution down to \~{}0.3 μm, speeds up to nearly 200 image planes per second and the ability to noninvasively acquire hundreds of 3D data volumes from single living cells encompassing tens of thousands of image frames.

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05/01/11 | Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. (With commentary)
Planchon TA, Gao L, Milkie DE, Davidson MW, Galbraith JA, Galbraith CG, Betzig E
Nature Methods. 2011 May;8(5):417-23. doi: 10.1038/nmeth.1586

A key challenge when imaging living cells is how to noninvasively extract the most spatiotemporal information possible. Unlike popular wide-field and confocal methods, plane-illumination microscopy limits excitation to the information-rich vicinity of the focal plane, providing effective optical sectioning and high speed while minimizing out-of-focus background and premature photobleaching. Here we used scanned Bessel beams in conjunction with structured illumination and/or two-photon excitation to create thinner light sheets (<0.5 μm) better suited to three-dimensional (3D) subcellular imaging. As demonstrated by imaging the dynamics of mitochondria, filopodia, membrane ruffles, intracellular vesicles and mitotic chromosomes in live cells, the microscope currently offers 3D isotropic resolution down to \~{}0.3 μm, speeds up to nearly 200 image planes per second and the ability to noninvasively acquire hundreds of 3D data volumes from single living cells encompassing tens of thousands of image frames.

Commentary: Plane illumination microscopy has proven to be a powerful tool for studying multicellular organisms and their development at single cell resolution. However, the light sheets employed are usually too thick to provide much benefit for imaging organelles within single cultured cells. Here we introduce the use of scanned Bessel beams to create much thinner light sheets better suited to long-term dynamic live cell imaging. Such light sheets not only minimize photobleaching and phototoxicity at the sub-cellular level, but also provide axial resolution enhancement, yielding isotropic three dimensional spatial resolution. Numerous movies are provided to demonstrate the wealth of 4D information (x,y,x,t) that can be obtained from single living cells by the method. Besides providing an attractive alternative to spinning disk, AOD-driven, or line scan confocal microscopes for high speed live cell imaging, the Bessel microscope might serve as a valuable platform for superresolution microscopy (PALM, structured Illumination, or RESOLFT), since confinement of the excitation to the focal plane makes far better use of the limited fluorescence photon budget than does the traditional epi-illumination configuration.

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Zlatic Lab
04/28/11 | A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS.
Wu Z, Sweeney LB, Ayoob JC, Chak K, Andreone BJ, Ohyama T, Kerr R, Luo L, Zlatic M, Kolodkin AL
Neuron. 2011 Apr 28;70(2):281-98. doi: 10.1016/j.neuron.2011.02.050

Longitudinal axon fascicles within the Drosophila embryonic CNS provide connections between body segments and are required for coordinated neural signaling along the anterior-posterior axis. We show here that establishment of select CNS longitudinal tracts and formation of precise mechanosensory afferent innervation to the same CNS region are coordinately regulated by the secreted semaphorins Sema-2a and Sema-2b. Both Sema-2a and Sema-2b utilize the same neuronal receptor, plexin B (PlexB), but serve distinct guidance functions. Localized Sema-2b attraction promotes the initial assembly of a subset of CNS longitudinal projections and subsequent targeting of chordotonal sensory afferent axons to these same longitudinal connectives, whereas broader Sema-2a repulsion serves to prevent aberrant innervation. In the absence of Sema-2b or PlexB, chordotonal afferent connectivity within the CNS is severely disrupted, resulting in specific larval behavioral deficits. These results reveal that distinct semaphorin-mediated guidance functions converge at PlexB and are critical for functional neural circuit assembly.

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04/22/11 | Real-time observation of transcription initiation and elongation on an endogenous yeast gene.
Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH
Science. 2011 Apr 22;332(6028):475-8. doi: 10.1126/science.1202142

Cellular messenger RNA levels are achieved by the combinatorial complexity of factors controlling transcription, yet the small number of molecules involved in these pathways fluctuates stochastically. It has not yet been experimentally possible to observe the activity of single polymerases on an endogenous gene to elucidate how these events occur in vivo. Here, we describe a method of fluctuation analysis of fluorescently labeled RNA to measure dynamics of nascent RNA–including initiation, elongation, and termination–at an active yeast locus. We find no transcriptional memory between initiation events, and elongation speed can vary by threefold throughout the cell cycle. By measuring the abundance and intranuclear mobility of an upstream transcription factor, we observe that the gene firing rate is directly determined by trans-activating factor search times.

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04/14/11 | Intracellular determinants of hippocampal CA1 place and silent cell activity in a novel environment.
Epsztein J, Brecht M, Lee AK
Neuron. 2011 Apr 14;70(1):109-20. doi: 10.1016/j.neuron.2011.03.006

For each environment a rodent has explored, its hippocampus contains a map consisting of a unique subset of neurons, called place cells, that have spatially tuned spiking there, with the remaining neurons being essentially silent. Using whole-cell recording in freely moving rats exploring a novel maze, we observed differences in intrinsic cellular properties and input-based subthreshold membrane potential levels underlying this division into place and silent cells. Compared to silent cells, place cells had lower spike thresholds and peaked versus flat subthreshold membrane potentials as a function of animal location. Both differences were evident from the beginning of exploration. Additionally, future place cells exhibited higher burst propensity before exploration. Thus, internal settings appear to predetermine which cells will represent the next novel environment encountered. Furthermore, place cells fired spatially tuned bursts with large, putatively calcium-mediated depolarizations that could trigger plasticity and stabilize the new map for long-term storage. Our results provide new insight into hippocampal memory formation.

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Menon Lab
04/01/11 | Hallmarks of molecular action of microtubule stabilizing agents: effects of epothilone B, ixabepilone, peloruside A, and laulimalide on microtubule conformation.
Khrapunovich-Baine M, Menon V, Yang CH, Northcote PT, Miller JH, Angeletti RH, Fiser A, Horwitz SB, Xiao H
The Journal of biological chemistry. 2011 Apr 1;286(13):11765-78. doi: 10.1074/jbc.M110.162214

Microtubule stabilizing agents (MSAs) comprise a class of drugs that bind to microtubule (MT) polymers and stabilize them against disassembly. Several of these agents are currently in clinical use as anticancer drugs, whereas others are in various stages of development. Nonetheless, there is insufficient knowledge about the molecular modes of their action. Recent studies from our laboratory utilizing hydrogen-deuterium exchange in combination with mass spectrometry (MS) provide new information on the conformational effects of Taxol and discodermolide on microtubules isolated from chicken erythrocytes (CET). We report here a comprehensive analysis of the effects of epothilone B, ixabepilone (IXEMPRA(TM)), laulimalide, and peloruside A on CET conformation. The results of our comparative hydrogen-deuterium exchange MS studies indicate that all MSAs have significant conformational effects on the C-terminal H12 helix of α-tubulin, which is a likely molecular mechanism for the previously observed modulations of MT interactions with microtubule-associated and motor proteins. More importantly, the major mode of MT stabilization by MSAs is the tightening of the longitudinal interactions between two adjacent αβ-tubulin heterodimers at the interdimer interface. In contrast to previous observations reported with bovine brain tubulin, the lateral interactions between the adjacent protofilaments in CET are particularly strongly stabilized by peloruside A and laulimalide, drugs that bind outside the taxane site. This not only highlights the significance of tubulin isotype composition in modulating drug effects on MT conformation and stability but also provides a potential explanation for the synergy observed when combinations of taxane and alternative site binding drugs are used.

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04/01/11 | Wireless neural/EMG telemetry systems for small freely moving animals.
Harrison RR, Fotowat H, Chan R, Kier RJ, Olberg R, Leonardo A, Gabbiani F
IEEE Transactions on Biomedical Circuits and Systems. 2011 Apr;5(2):103-11. doi: 10.1109/TBCAS.2011.2131140

We have developed miniature telemetry systems that capture neural, EMG, and acceleration signals from a freely moving insect or other small animal and transmit the data wirelessly to a remote digital receiver. The systems are based on custom low-power integrated circuits (ICs) that amplify, filter, and digitize four biopotential signals using low-noise circuits. One of the chips also digitizes three acceleration signals from an off-chip microelectromechanical-system accelerometer. All information is transmitted over a wireless ~ 900-MHz telemetry link. The first unit, using a custom chip fabricated in a 0.6- μm BiCMOS process, weighs 0.79 g and runs for two hours on two small batteries. We have used this system to monitor neural and EMG signals in jumping and flying locusts as well as transdermal potentials in weakly swimming electric fish. The second unit, using a custom chip fabricated in a 0.35-μ m complementary metal-oxide semiconductor CMOS process, weighs 0.17 g and runs for five hours on a single 1.5-V battery. This system has been used to monitor neural potentials in untethered perching dragonflies.

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03/30/11 | Automated high speed stitching of large 3D microscopic images.
Yu Y, Peng H
2011 8TH IEEE International Symposium on Biomedical Imaging: From Nano to Macro. 2011 Mar 30:238-41. doi: 10.1109/isbi.2011.5872396

High-resolution microscopic imaging of biological samples often produces multiple 3D image tiles to cover a large field of view of specimen. Usually each tile has a large size, in the range of hundreds of megabytes to several gigabytes. For many of our image data sets, existing software tools are often unable to stitch those 3D tiles into a panoramic view, thus impede further data analysis. We propose a simple, but accurate, robust, and automatic method to stitch a group of image tiles without a priori adjacency information of them. We first use a multiscale strategy to register a pair of 3D image tiles rapidly, achieving about 8~10 times faster speed and 10 times less memory requirement compared to previous methods. Then we design a minimum-spanning-tree based method to determine the optimal adjacency of tiles. We have successfully stitched large image stacks of model animals including C. elegans, fruit fly, dragonfly, and mouse, which could not be stitched by several existing methods.

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