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177 Janelia Publications

Showing 101-110 of 177 results
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    05/23/19 | Computational methods for stitching, alignment, and artifact correction of serial section data.
    Saalfeld S
    Methods in Cell Biology;152:261 - 276. doi: 10.1016/bs.mcb.2019.04.007

    Imaging large samples at the resolution offered by electron microscopy is typically achieved by sequentially recording overlapping tiles that are later combined to seamless mosaics. Mosaics of serial sections are aligned to reconstruct three-dimensional volumes. To achieve this, image distortions and artifacts as introduced during sample preparation or imaging need to be removed.

    In this chapter, we will discuss typical sources of artifacts and distortion, and we will learn how to use the open source software TrakEM2 to correct them.

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    05/22/19 | Busted! A dope ring with activity clocked at dawn and dusk.
    Hulse B, Jayaraman V
    Neuron. 2019 May 22;102(4):713-5. doi: 10.1016/j.neuron.2019.05.004

    Clock neurons generate circadian rhythms in behavioral activity, but the relevant pathways remain poorly understood. In this issue of Neuron, Liang et al. (2019) show that distinct clock neurons independently drive movement-promoting “ring neurons” in Drosophila through dopaminergic relays to support morning and evening locomotor activity.

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    Bock Lab
    05/21/19 | Functional and anatomical specificity in a higher olfactory centre.
    Frechter S, Bates AS, Tootoonian S, Dolan M, Manton JD, Jamasb AR, Kohl J, Bock D, Jefferis GS
    Elife. 2019 May 21;8:. doi: 10.7554/eLife.44590

    Most sensory systems are organized into parallel neuronal pathways that process distinct aspects of incoming stimuli. In the insect olfactory system, second order projection neurons target both the mushroom body, required for learning, and the lateral horn (LH), proposed to mediate innate olfactory behavior. Mushroom body neurons form a sparse olfactory population code, which is not stereotyped across animals. In contrast, odor coding in the LH remains poorly understood. We combine genetic driver lines, anatomical and functional criteria to show that the LH has ~1400 neurons and >165 cell types. Genetically labeled LHNs have stereotyped odor responses across animals and on average respond to three times more odors than single projection neurons. LHNs are better odor categorizers than projection neurons, likely due to stereotyped pooling of related inputs. Our results reveal some of the principles by which a higher processing area can extract innate behavioral significance from sensory stimuli.

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    05/21/19 | MuscleViz: Free open-source software for muscle weakness visualization.
    Wittenbach JD, Cocanougher BT, Yun P, Foley AR, Bönnemann CG
    Journal of Neuromuscular Diseases. 2019 May 21;6(2):263-266. doi: 10.3233/JND-190385

    Muscle strength testing is routine in clinical practice. Here we provide an aid to the documentation and visual conceptualization of those results - MuscleViz: a free, open-source application for visualizing the results of muscle strength testing. Its use in clinical settings streamlines the communication of physical examination findings. The tool is also useful for presenting patient data in case reports or case series. A push towards free, open-source software has benefitted other areas of science; we believe a similar effort dedicated to the development of clinical tools is worth pursuing.

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    05/21/19 | Neurogenetic dissection of the lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body.
    Dolan M, Frechter S, Bates AS, Dan C, Huoviala P, Roberts RJ, Schlegel P, Dhawan S, Tabano R, Dionne H, Christoforou C, Close K, Sutcliffe B, Giuliani B, Li F, Costa M, Ihrke G, Meissner GW, Bock DD, Aso Y, Rubin GM, Jefferis GS
    Elife. 2019 May 21;8:. doi: 10.7554/eLife.43079

    Animals exhibit innate behaviours to a variety of sensory stimuli including olfactory cues. In , one higher olfactory centre, the lateral horn (LH), is implicated in innate behaviour. However, our structural and functional understanding of the LH is scant, in large part due to a lack of sparse neurogenetic tools for this region. We generate a collection of split-GAL4 driver lines providing genetic access to 82 LH cell types. We use these to create an anatomical and neurotransmitter map of the LH and link this to EM connectomics data. We find ~30% of LH projections converge with outputs from the mushroom body, site of olfactory learning and memory. Using optogenetic activation, we identify LH cell types that drive changes in valence behavior or specific locomotor programs. In summary, we have generated a resource for manipulating and mapping LH neurons, providing new insights into the circuit basis of innate and learned olfactory behavior.

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    05/20/19 | Mechanistic characterization of RASGRP1 variants identifies an hnRNP K-regulated transcriptional enhancer contributing to SLE susceptibility.
    Molineros JE, Singh B, Terao C, Okada Y, Kaplan J, McDaniel B, Akizuki S, Sun C, Webb CF, Looger LL, Nath SK
    Frontiers in Immunology. 2019 May 20:. doi: 10.3389/fimmu.2019.01066

    Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component. We recently identified a novel SLE susceptibility locus near RASGRP1, which governs the ERK/MAPK kinase cascade and B-/T-cell differentiation and development. However, precise causal RASGRP1functional variant(s) and their mechanisms of action in SLE pathogenesis remain undefined. Our goal was to fine-map this locus, prioritize genetic variants likely to be functional, experimentally validate their biochemical mechanisms, and determine the contribution of these SNPs to SLE risk. We performed a meta-analysis across six Asian and European cohorts (9,529 cases; 22,462 controls), followed by in silico bioinformatic and epigenetic analyses to prioritize potentially functional SNPs. We experimentally validated the functional significance and mechanism of action of three SNPs in cultured T-cells. Meta-analysis identified 18 genome-wide significant (p < 5 × 10−8) SNPs, mostly concentrated in two haplotype blocks, one intronic and the other intergenic. Epigenetic fine-mapping, allelic, eQTL, and imbalance analyses predicted three transcriptional regulatory regions with four SNPs (rs7170151, rs11631591-rs7173565, and rs9920715) prioritized for functional validation. Luciferase reporter assays indicated significant allele-specific enhancer activity for intronic rs7170151 and rs11631591-rs7173565 in T-lymphoid (Jurkat) cells, but not in HEK293 cells. Following up with EMSA, mass spectrometry, and ChIP-qPCR, we detected allele-dependent interactions between heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and rs11631591. Furthermore, inhibition of hnRNP-K in Jurkat and primary T-cells downregulated RASGRP1 and ERK/MAPK signaling. Comprehensive association, bioinformatics, and epigenetic analyses yielded putative functional variants of RASGRP1, which were experimentally validated. Notably, intronic variant (rs11631591) is located in a cell type-specific enhancer sequence, where its risk allele binds to the hnRNP-K protein and modulates RASGRP1 expression in Jurkat and primary T-cells. As risk allele dosage of rs11631591 correlates with increased RASGRP1 expression and ERK activity, we suggest that this SNP may underlie SLE risk at this locus.

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    05/17/19 | De novo design of tunable, pH-driven conformational changes.
    Boyken SE, Benhaim MA, Busch F, Jia M, Back MJ, Choi H, Klima JC, Chen Z, Walkey C, Mileant A, Sahasrabuddhe A, Wei KY, Hodge EA, Byron S, Quijano-Rubio A, Sankaran B, King NP, Lippincott-Schwartz J, Wysocki VH, et al
    Science. 2019 May 17;364(6441):658-64. doi: 10.1126/science.aav7897

    The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.

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    05/03/19 | The glutamine transporter Slc38a1 regulates GABAergic neurotransmission and synaptic plasticity.
    Qureshi T, Sørensen C, Berghuis P, Jensen V, Dobszay MB, Farkas T, Dalen KT, Guo C, Hassel B, Utheim TP, Hvalby Ø, Hafting T, Harkany T, Fyhn M, Chaudhry FA
    Cerebal Cortex. 2019 May 03:. doi: 10.1093/cercor/bhz055

    GABA signaling sustains fundamental brain functions, from nervous system development to the synchronization of population activity and synaptic plasticity. Despite these pivotal features, molecular determinants underscoring the rapid and cell-autonomous replenishment of the vesicular neurotransmitter GABA and its impact on synaptic plasticity remain elusive. Here, we show that genetic disruption of the glutamine transporter Slc38a1 in mice hampers GABA synthesis, modifies synaptic vesicle morphology in GABAergic presynapses and impairs critical period plasticity. We demonstrate that Slc38a1-mediated glutamine transport regulates vesicular GABA content, induces high-frequency membrane oscillations and shapes cortical processing and plasticity. Taken together, this work shows that Slc38a1 is not merely a transporter accumulating glutamine for metabolic purposes, but a key component regulating several neuronal functions.

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    05/01/19 | Pleiotropic effects of ebony and tan on pigmentation and cuticular hydrocarbon composition in Drosophila melanogaster.
    Massey JH, Akiyama N, Bien T, Dreisewerd K, Wittkopp PJ, Yew JY, Takahashi A
    Frontiers in Physiology. 05/2019;10:518. doi: 10.3389/fphys.2019.00518

    Pleiotropic genes are genes that affect more than one trait. For example, many genes required for pigmentation in the fruit fly also affect traits such as circadian rhythms, vision, and mating behavior. Here, we present evidence that two pigmentation genes, and , which encode enzymes catalyzing reciprocal reactions in the melanin biosynthesis pathway, also affect cuticular hydrocarbon (CHC) composition in females. More specifically, we report that loss-of-function mutants have a CHC profile that is biased toward long (>25C) chain CHCs, whereas loss-of-function mutants have a CHC profile that is biased toward short (<25C) chain CHCs. Moreover, pharmacological inhibition of dopamine synthesis, a key step in the melanin synthesis pathway, reversed the changes in CHC composition seen in mutants, making the CHC profiles similar to those seen in mutants. These observations suggest that genetic variation affecting and/or activity might cause correlated changes in pigmentation and CHC composition in natural populations. We tested this possibility using the Genetic Reference Panel (DGRP) and found that CHC composition covaried with pigmentation as well as levels of and expression in newly eclosed adults in a manner consistent with the and mutant phenotypes. These data suggest that the pleiotropic effects of and might contribute to covariation of pigmentation and CHC profiles in .

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    04/29/19 | Super resolution imaging of a distinct chromatin loop in human lymphoblastoid cells.
    Jacqueline Jufen Zhu , Zofia Parteka , Byoungkoo Lee , Przemyslaw Szalaj , Ping Wang , Karolina Jodkowska , Jesse Aaron , Teng-Leong Chew , Dariusz Plewczynski , Yijun Ruan
    bioRxiv. 2019 Apr 29:. doi: 10.1101/621920

    The three-dimensional genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in genomics based on sequencing technologies inferred the very basic functional chromatin folding structures of the genome known as chromatin loops, the long-range chromatin interactions that are often mediated by protein factors. To visualize the looping structure of chromatin we applied super-resolution microscopy iPALM to image a specific chromatin loop in GM12878 cells. Totally, we have generated six images of the target chromatin region at the single molecule resolution. To infer the chromatin structures from the captured images, we modeled them as looping conformations using different computational algorithms and then evaluated the models by comparing with Hi-C data to examine the concordance. The results showed a good correlation between the imaging data and sequencing data, suggesting the visualization of higher-order chromatin structures for the very short genomic segments can be realized by microscopic imaging.

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