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236 Publications

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    01/22/14 | Cell-type-specific labeling of synapses in vivo through synaptic tagging with recombination.
    Chen Y, Akin O, Nern A, Tsui CY, Pecot MY, Zipursky SL
    Neuron. 2014 Jan 22;81(2):280-93. doi: 10.1016/j.neuron.2013.12.021

    The study of synaptic specificity and plasticity in the CNS is limited by the inability to efficiently visualize synapses in identified neurons using light microscopy. Here, we describe synaptic tagging with recombination (STaR), a method for labeling endogenous presynaptic and postsynaptic proteins in a cell-type-specific fashion. We modified genomic loci encoding synaptic proteins within bacterial artificial chromosomes such that these proteins, expressed at endogenous levels and with normal spatiotemporal patterns, were labeled in an inducible fashion in specific neurons through targeted expression of site-specific recombinases. Within the Drosophila visual system, the number and distribution of synapses correlate with electron microscopy studies. Using two different recombination systems, presynaptic and postsynaptic specializations of synaptic pairs can be colabeled. STaR also allows synapses within the CNS to be studied in live animals noninvasively. In principle, STaR can be adapted to the mammalian nervous system.

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    01/21/14 | Structure-based neuron retrieval across Drosophila brains.
    Ganglberger F, Schulze F, Tirian L, Novikov A, Dickson B, Bühler K, Langs G
    Neuroinformatics. 2014 Jan 21;12(3):423-34. doi: 10.1007/s12021-014-9219-4

    Comparing local neural structures across large sets of examples is crucial when studying gene functions, and their effect in the Drosophila brain. The current practice of aligning brain volume data to a joint reference frame is based on the neuropil. However, even after alignment neurons exhibit residual location and shape variability that, together with image noise, hamper direct quantitative comparison and retrieval of similar structures on an intensity basis. In this paper, we propose and evaluate an image-based retrieval method for neurons, relying on local appearance, which can cope with spatial variability across the population. For an object of interest marked in a query case, the method ranks cases drawn from a large data set based on local neuron appearance in confocal microscopy data. The approach is based on capturing the orientation of neurons based on structure tensors and expanding this field via Gradient Vector Flow. During retrieval, the algorithm compares fields across cases, and calculates a corresponding ranking of most similar cases with regard to the local structure of interest. Experimental results demonstrate that the similarity measure and ranking mechanisms yield high precision and recall in realistic search scenarios.

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    01/20/14 | Lessons from the neurons themselves.
    Scheffer L
    Design Automation Conference (ASP-DAC), 2014 19th Asia and South Pacific. 2014 Jan 20-23:197-200. doi: 10.1109/ASPDAC.2014.6742889

    Natural neural circuits, optimized by millions of years of evolution, are fast, low power, robust, and adapt in response to experience, all characteristics we would love to have in systems we ourselves design. Recently there have been enormous advances in understanding how neurons implement computations within the brain of living creatures. Can we use this new-found knowledge to create better artificial system? What lessons can we learn from the neurons themselves, that can help us create better neuromorphic circuits?

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    01/17/14 | Proteome analysis and conditional deletion of the EAAT2 glutamate transporter provide evidence against a role of EAAT2 in pancreatic insulin secretion in mice.
    Zhou Y, Waanders LF, Holmseth S, Guo C, Berger UV, Li Y, Lehre A, Lehre KP, Danbolt NC
    The Journal of Biological Chemistry. 2014 Jan 17;289(3):1329-44. doi: 10.1074/jbc.M113.529065

    Islet function is incompletely understood in part because key steps in glutamate handling remain undetermined. The glutamate (excitatory amino acid) transporter 2 (EAAT2; Slc1a2) has been hypothesized to (a) provide islet cells with glutamate, (b) protect islet cells against high extracellular glutamate concentrations, (c) mediate glutamate release, or (d) control the pH inside insulin secretory granules. Here we floxed the EAAT2 gene to produce the first conditional EAAT2 knock-out mice. Crossing with Nestin-cyclization recombinase (Cre) eliminated EAAT2 from the brain, resulting in epilepsy and premature death, confirming the importance of EAAT2 for brain function and validating the genetic construction. Crossing with insulin-Cre lines (RIP-Cre and IPF1-Cre) to obtain pancreas-selective deletion did not appear to affect survival, growth, glucose tolerance, or β-cell number. We found (using TaqMan RT-PCR, immunoblotting, immunocytochemistry, and proteome analysis) that the EAAT2 levels were too low to support any of the four hypothesized functions. The proteome analysis detected more than 7,000 islet proteins of which more than 100 were transporters. Although mitochondrial glutamate transporters and transporters for neutral amino acids were present at high levels, all other transporters with known ability to transport glutamate were strikingly absent. Glutamate-metabolizing enzymes were abundant. The level of glutamine synthetase was 2 orders of magnitude higher than that of glutaminase. Taken together this suggests that the uptake of glutamate by islets from the extracellular fluid is insignificant and that glutamate is intracellularly produced. Glutamine synthetase may be more important for islets than assumed previously.

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    01/16/14 | Distribution of ESCRT machinery at HIV assembly sites reveals virus scaffolding of ESCRT subunits.
    Van Engelenburg SB, Shtengel G, Sengupta P, Waki K, Jarnik M, Ablan SD, Freed EO, Hess HF, Lippincott-Schwartz J
    Science. 2014 Jan 16;343(6171):653-6. doi: 10.1126/science.1247786

    The human immunodeficiency virus (HIV) hijacks the endosomal sorting complexes required for transport (ESCRT) to mediate virus release from infected cells. The nanoscale organization of ESCRT machinery necessary for mediating viral abscission is unclear. Here, we applied three-dimensional superresolution microscopy and correlative electron microscopy to delineate the organization of ESCRT components at HIV assembly sites. We observed ESCRT subunits localized within the head of budding virions and released particles, with head-localized levels of CHMP2A decreasing relative to Tsg101 and CHMP4B upon virus abscission. Thus, the driving force for HIV release may derive from initial scaffolding of ESCRT subunits within the viral bud interior followed by plasma membrane association and selective remodeling of ESCRT subunits.

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    Baker Lab
    01/16/14 | Genetic identification and separation of innate and experience-dependent courtship behaviors in Drosophila.
    Pan Y, Baker BS
    Cell. 2014 Jan 16;156(1-2):236-48. doi: 10.1016/j.cell.2013.11.041

    Wild-type D. melanogaster males innately possess the ability to perform a multistep courtship ritual to conspecific females. The potential for this behavior is specified by the male-specific products of the fruitless (fru(M)) gene; males without fru(M) do not court females when held in isolation. We show that such fru(M) null males acquire the potential for courtship when grouped with other flies; they apparently learn to court flies with which they were grouped, irrespective of sex or species and retain this behavior for at least a week. The male-specific product of the doublesex gene (dsx(M)) is necessary and sufficient for the acquisition of the potential for such experience-dependent courtship. These results reveal a process that builds, via dsx(M) and social experience, the potential for a more flexible sexual behavior, which could be evolutionarily conserved as dsx-related genes that function in sexual development are found throughout the animal kingdom.

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    01/15/14 | Comparing thoracic and intra-nasal pressure transients to monitor active odor sampling during odor-guided decision making in the mouse.
    Reisert J, Golden GJ, Matsumura K, Smear M, Rinberg D, Gelperin A
    Journal of Neuroscience Methods. 2014 Jan 15;221:8-14. doi: 10.1016/j.jneumeth.2013.09.006

    BACKGROUND: Recording of physiological parameters in behaving mice has seen an immense increase over recent years driven by, for example, increased miniaturization of recording devices. One parameter particularly important for odorant-driven behaviors is the breathing frequency, since the latter dictates the rate of odorant delivery to the nasal cavity and the olfactory receptor neurons located therein. NEW METHOD: Typically, breathing patterns are monitored by either measuring the breathing-induced temperature or pressure changes in the nasal cavity. Both require the implantation of a nasal cannula and tethering of the mouse to either a cable or tubing. To avoid these limitations we used an implanted pressure sensor which reads the thoracic pressure and transmits the data telemetrically, thus making it suitable for experiments which require a freely moving animal. RESULTS: Mice performed a Go/NoGo odorant-driven behavioral task with the implanted pressure sensor, which proved to work reliably to allow recording of breathing signals over several weeks from a given animal. COMPARISON TO EXISTING METHOD(S): We simultaneously recorded the thoracic and nasal pressure changes and found that measuring the thoracic pressure change yielded similar results compared to measurements of nasal pressure changes. CONCLUSION: Telemetrically recorded breathing signals are a feasible method to monitor odorant-guided behavioral changes in breathing rates. Its advantages are most significant when recording from a freely moving animal over several weeks. The advantages and disadvantages of different methods to record breathing patterns are discussed.

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    01/13/14 | Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.
    Wheeler TJ, Clements J, Finn RD
    BMC Bioinformatics. 2014 Jan 13;15:7. doi: 10.1186/1471-2105-15-7

    BACKGROUND: Logos are commonly used in molecular biology to provide a compact graphical representation of the conservation pattern of a set of sequences. They render the information contained in sequence alignments or profile hidden Markov models by drawing a stack of letters for each position, where the height of the stack corresponds to the conservation at that position, and the height of each letter within a stack depends on the frequency of that letter at that position. RESULTS: We present a new tool and web server, called Skylign, which provides a unified framework for creating logos for both sequence alignments and profile hidden Markov models. In addition to static image files, Skylign creates a novel interactive logo plot for inclusion in web pages. These interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. CONCLUSION: Skylign is available as a website, a scriptable web service with a RESTful interface, and as a software package for download. Skylign’s interactive logos are easily incorporated into a web page with just a few lines of HTML markup. Skylign may be found at

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    01/13/14 | Superresolution imaging of biological systems using photoactivated localization microscopy.
    Sengupta P, Van Engelenburg SB, Lippincott-Schwartz J
    Chemical reviews. 2014 Mar 26;114(6):3189-202. doi: 10.1021/cr400614m
    01/10/14 | A fully genetically encoded protein architecture for optical control of peptide ligand concentration.
    Daniel Schmidt , Paul Tillberg , Fei Chen , Edward Boyden

    Ion channels are among the most important proteins in biology, regulating the activity of excitable cells and changing in diseases. Ideally it would be possible to actuate endogenous ion channels, in a temporally precise and reversible manner, and without requiring chemical cofactors. Here we present a modular protein architecture for fully genetically encoded, light-modulated control of ligands that modulate ion channels of a targeted cell. Our reagent, which we call a lumitoxin, combines a photoswitch and an ion channel-blocking peptide toxin. Illumination causes the photoswitch to unfold, lowering the toxin’s local concentration near the cell surface, and enabling the ion channel to function. We explore lumitoxin modularity by showing operation with peptide toxins that target different voltage-dependent K+ channels. The lumitoxin architecture may represent a new kind of modular protein-engineering strategy for designing light-activated proteins, and thus may enable development of novel tools for modulating cellular physiology.

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