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236 Publications

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    12/03/14 | Identification of loci that cause phenotypic variation in diverse species with the reciprocal hemizygosity test.
    Stern DL
    Trends in Genetics. 2014 Dec;30(12):547-554. doi: 10.1016/j.tig.2014.09.006

    The reciprocal hemizygosity test is a straightforward genetic test that can positively identify genes that have evolved to contribute to a phenotypic difference between strains or between species. The test involves a comparison between hybrids that are genetically identical throughout the genome except at the test locus, which is rendered hemizygous for alternative alleles from the two parental strains. If the two reciprocal hemizygotes display different phenotypes, then the two parental alleles must have evolved. New methods for targeted mutagenesis will allow application of the reciprocal hemizygosity test in many organisms. This review discusses the principles, advantages, and limitations of the test.

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    12/01/14 | Bone-free: soft mechanics for adaptive locomotion.
    Trimmer BA, Lin H
    Integrative and Comparative Biology. 2014 Dec;54(6):1122-35. doi: 10.1093/icb/icu076

    Muscular hydrostats (such as mollusks), and fluid-filled animals (such as annelids), can exploit their constant-volume tissues to transfer forces and displacements in predictable ways, much as articulated animals use hinges and levers. Although larval insects contain pressurized fluids, they also have internal air tubes that are compressible and, as a result, they have more uncontrolled degrees of freedom. Therefore, the mechanisms by which larval insects control their movements are expected to reveal useful strategies for designing soft biomimetic robots. Using caterpillars as a tractable model system, it is now possible to identify the biomechanical and neural strategies for controlling movements in such highly deformable animals. For example, the tobacco hornworm, Manduca sexta, can stiffen its body by increasing muscular tension (and therefore body pressure) but the internal cavity (hemocoel) is not iso-barometric, nor is pressure used to directly control the movements of its limbs. Instead, fluid and tissues flow within the hemocoel and the body is soft and flexible to conform to the substrate. Even the gut contributes to the biomechanics of locomotion; it is decoupled from the movements of the body wall and slides forward within the body cavity at the start of each step. During crawling the body is kept in tension for part of the stride and compressive forces are exerted on the substrate along the axis of the caterpillar, thereby using the environment as a skeleton. The timing of muscular activity suggests that crawling is coordinated by proleg-retractor motoneurons and that the large segmental muscles produce anterograde waves of lifting that do not require precise timing. This strategy produces a robust form of locomotion in which the kinematics changes little with orientation. In different species of caterpillar, the presence of prolegs on particular body segments is related to alternative kinematics such as "inching." This suggests a mechanism for the evolution of different gaits through changes in the usage of prolegs, rather than, through extensive alterations in the motor program controlling the body wall. Some of these findings are being used to design and test novel control-strategies for highly deformable robots. These "softworm" devices are providing new insights into the challenges faced by any soft animal navigating in a terrestrial environment.

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    12/01/14 | Quantifying histone and RNA polymerase II post-translational modification dynamics in mother and daughter cells.
    Stasevich TJ, Sato Y, Nozaki N, Kimura H
    Methods. 2014 Dec;70(2-3):77-88. doi: 10.1016/j.ymeth.2014.08.002

    Post-translational histone modifications are highly correlated with transcriptional activity, but the relative timing of these marks and their dynamic interplay during gene regulation remains controversial. To shed light on this problem and clarify the connections between histone modifications and transcription, we demonstrate how FabLEM (Fab-based Live Endogenous Modification labeling) can be used to simultaneously track histone H3 Lysine 9 acetylation (H3K9ac) together with RNA polymerase II Serine 2 and Serine 5 phosphorylation (RNAP2 Ser2ph/Ser5ph) in single living cells and their progeny. We provide a detailed description of the FabLEM methodology, including helpful tips for preparing and loading fluorescently conjugated antigen binding fragments (Fab) into cells for optimal results. We also introduce simple procedures for analyzing and visualizing FabLEM data, including color-coded scatterplots to track correlations between modifications through the cell cycle and temporal cross-correlation analysis to dissect modification dynamics. Using these methods, we find significant correlations that span cell generations, with a relatively strong correlation between H3K9ac and Ser5ph that appears to peak a few hours before mitosis and may reflect the bookmarking of genes for efficient re-initiation following mitosis. The techniques we have developed are broadly applicable and should help clarify how histone modifications dynamically contribute to gene regulation.

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    12/01/14 | Quantum dot-based multiphoton fluorescent pipettes for targeted neuronal electrophysiology.
    Andrasfalvy BK, Galiñanes GL, Huber D, Barbic M, Macklin JJ, Susumu K, Delehanty JB, Huston AL, Makara JK, Medintz IL
    Nature Methods. 2014 Dec;11(12):1237-41. doi: 10.1038/nmeth.3146

    Targeting visually identified neurons for electrophysiological recording is a fundamental neuroscience technique; however, its potential is hampered by poor visualization of pipette tips in deep brain tissue. We describe quantum dot-coated glass pipettes that provide strong two-photon contrast at deeper penetration depths than those achievable with current methods. We demonstrated the pipettes' utility in targeted patch-clamp recording experiments and single-cell electroporation of identified rat and mouse neurons in vitro and in vivo.

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    Baker Lab
    12/01/14 | The neuronal basis of how sexual experience modulates male aggression.
    Liang XH, Rao Y, Zhou C
    National Science Review. 2014 Dec ;1(4):473-4. doi: 10.1093/nsr/nwu059
    11/25/14 | Post-acquisition image based compensation for thickness variation in microscopy section series.
    Hanslovsky P, Bogovic JA, Saalfeld S
    IEEE International Symposium on Biomedical Imaging. 2014 Nov 25:507-11

    Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as that of Drosophila melanogaster. The process of removing ultrathin layers from a solid block containing the specimen, however, is a fragile procedure and has limited precision with respect to section thickness. We have developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series. First experiments show promising results on both serial section Transmission Electron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) series. We made our solution available as Open Source plugins for the TrakEM2 software and the ImageJ distribution Fiji.

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    11/14/14 | Variance predicts salience in central sensory processing.
    Hermundstad AM, Briguglio JJ, Conte MM, Victor JD, Balasubramanian V, Tkačik G
    eLife. 2014;3:. doi: 10.7554/eLife.03722

    Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime--when sampling limitations constrain performance--efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability.

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    11/08/14 | Photohighlighting approaches to access membrane dynamics of the Golgi apparatus.
    Sengupta P, Lippincott-Schwartz J
    Methods in cell biology. 2013;118:217-34. doi: 10.1016/B978-0-12-417164-0.00013-6

    By providing quantitative, visual data of live cells, fluorescent protein-based microscopy techniques are furnishing novel insights into the complexities of membrane trafficking pathways and organelle dynamics. In this chapter, we describe experimental protocols employing fluorescent protein-based photohighlighting techniques to quantify protein movement into and out of the Golgi apparatus, an organelle that serves as the central sorting and processing station of the secretory pathway. The methods allow kinetic characteristics of Golgi-associated protein trafficking to be deciphered, which can help clarify how the Golgi maintains itself as a steady-state structure despite a continuous flux of secretory cargo passing into and out of this organelle. The guidelines presented in this chapter can also be applied to examine the dynamics of other intracellular organelle systems, elucidating mechanisms for how proteins are maintained in specific organelles and/or circulated to other destinations within the cell.

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    11/07/14 | Making biology transparent.
    Höckendorf B, Lavis LD, Keller PJ
    Nature Biotechnology. 2014 Nov 7;32(11):1104-5. doi: 10.1038/nbt.3061

    The molecular and cellular architecture of the organs in a whole mouse is revealed through optical clearing.

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    11/07/14 | The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes.
    DeSalvo MK, Hindle SJ, Rusan ZM, Orng S, Eddison M, Halliwill K, Bainton RJ
    Frontiers in Neuroscience. 2014 Nov 7;8:346. doi: 10.3389/fnins.2014.00346

    Central nervous system (CNS) function is dependent on the stringent regulation of metabolites, drugs, cells, and pathogens exposed to the CNS space. Cellular blood-brain barrier (BBB) structures are highly specific checkpoints governing entry and exit of all small molecules to and from the brain interstitial space, but the precise mechanisms that regulate the BBB are not well understood. In addition, the BBB has long been a challenging obstacle to the pharmacologic treatment of CNS diseases; thus model systems that can parse the functions of the BBB are highly desirable. In this study, we sought to define the transcriptome of the adult Drosophila melanogaster BBB by isolating the BBB surface glia with fluorescence activated cell sorting (FACS) and profiling their gene expression with microarrays. By comparing the transcriptome of these surface glia to that of all brain glia, brain neurons, and whole brains, we present a catalog of transcripts that are selectively enriched at the Drosophila BBB. We found that the fly surface glia show high expression of many ATP-binding cassette (ABC) and solute carrier (SLC) transporters, cell adhesion molecules, metabolic enzymes, signaling molecules, and components of xenobiotic metabolism pathways. Using gene sequence-based alignments, we compare the Drosophila and Murine BBB transcriptomes and discover many shared chemoprotective and small molecule control pathways, thus affirming the relevance of invertebrate models for studying evolutionary conserved BBB properties. The Drosophila BBB transcriptome is valuable to vertebrate and insect biologists alike as a resource for studying proteins underlying diffusion barrier development and maintenance, glial biology, and regulation of drug transport at tissue barriers.

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