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179 Janelia Publications

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    Lavis LabLooger Lab
    12/23/20 | Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning.
    Unger EK, Keller JP, Altermatt M, Liang R, Matsui A, Dong C, Hon OJ, Yao Z, Sun J, Banala S, Flanigan ME, Jaffe DA, Hartanto S, Carlen J, Mizuno GO, Borden PM, Shivange AV, Cameron LP, Sinning S, Underhill SM, Olson DE, Amara SG, Temple Lang D, Rudnick G, Marvin JS, Lavis LD, Lester HA, Alvarez VA, Fisher AJ, Prescher JA, Kash TL, Yarov-Yarovoy V, Gradinaru V, Looger LL, Tian L
    Cell. 2020 Dec 23;183(7):1986-2002.e26. doi: 10.1016/j.cell.2020.11.040

    Serotonin plays a central role in cognition and is the target of most pharmaceuticals for psychiatric disorders. Existing drugs have limited efficacy; creation of improved versions will require better understanding of serotonergic circuitry, which has been hampered by our inability to monitor serotonin release and transport with high spatial and temporal resolution. We developed and applied a binding-pocket redesign strategy, guided by machine learning, to create a high-performance, soluble, fluorescent serotonin sensor (iSeroSnFR), enabling optical detection of millisecond-scale serotonin transients. We demonstrate that iSeroSnFR can be used to detect serotonin release in freely behaving mice during fear conditioning, social interaction, and sleep/wake transitions. We also developed a robust assay of serotonin transporter function and modulation by drugs. We expect that both machine-learning-guided binding-pocket redesign and iSeroSnFR will have broad utility for the development of other sensors and in vitro and in vivo serotonin detection, respectively.

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    12/21/21 | Structure and RNA template requirements of RNA-DEPENDENT RNA POLYMERASE 2.
    Fukudome A, Singh J, Mishra V, Reddem E, Martinez-Marquez F, Wenzel S, Yan R, Shiozaki M, Yu Z, Wang JC, Takagi Y, Pikaard CS
    Proceedings of the National Academy of Sciences of the U.S.A.. 2021 Dec 21;118(51):. doi: 10.1073/pnas.2115899118

    RNA-dependent RNA polymerases play essential roles in RNA-mediated gene silencing in eukaryotes. In , RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) physically interacts with DNA-dependent NUCLEAR RNA POLYMERASE IV (Pol IV) and their activities are tightly coupled, with Pol IV transcriptional arrest, induced by the nontemplate DNA strand, somehow enabling RDR2 to engage Pol IV transcripts and generate double-stranded RNAs. The double-stranded RNAs are then released from the Pol IV-RDR2 complex and diced into short-interfering RNAs that guide RNA-directed DNA methylation and silencing. Here we report the structure of full-length RDR2, at an overall resolution of 3.1 Å, determined by cryoelectron microscopy. The N-terminal region contains an RNA-recognition motif adjacent to a positively charged channel that leads to a catalytic center with striking structural homology to the catalytic centers of multisubunit DNA-dependent RNA polymerases. We show that RDR2 initiates 1 to 2 nt internal to the 3' ends of its templates and can transcribe the RNA of an RNA/DNA hybrid, provided that 9 or more nucleotides are unpaired at the RNA's 3' end. Using a nucleic acid configuration that mimics the arrangement of RNA and DNA strands upon Pol IV transcriptional arrest, we show that displacement of the RNA 3' end occurs as the DNA template and nontemplate strands reanneal, enabling RDR2 transcription. These results suggest a model in which Pol IV arrest and backtracking displaces the RNA 3' end as the DNA strands reanneal, allowing RDR2 to engage the RNA and synthesize the complementary strand.

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    12/16/21 | Synaptic targets of photoreceptors specialized to detect color and skylight polarization in .
    Kind E, Longden KD, Nern A, Zhao A, Sancer G, Flynn MA, Laughland CW, Gezahegn B, Ludwig HD, Thomson AG, Obrusnik T, Alarcón PG, Dionne H, Bock DD, Rubin GM, Reiser MB, Wernet MF
    eLife. 2021 Dec 16;10:. doi: 10.7554/eLife.71858

    Color and polarization provide complementary information about the world and are detected by specialized photoreceptors. However, the downstream neural circuits that process these distinct modalities are incompletely understood in any animal. Using electron microscopy, we have systematically reconstructed the synaptic targets of the photoreceptors specialized to detect color and skylight polarization in Drosophila, and we have used light microscopy to confirm many of our findings. We identified known and novel downstream targets that are selective for different wavelengths or polarized light, and followed their projections to other areas in the optic lobes and the central brain. Our results revealed many synapses along the photoreceptor axons between brain regions, new pathways in the optic lobes, and spatially segregated projections to central brain regions. Strikingly, photoreceptors in the polarization-sensitive dorsal rim area target fewer cell types, and lack strong connections to the lobula, a neuropil involved in color processing. Our reconstruction identifies shared wiring and modality-specific specializations for color and polarization vision, and provides a comprehensive view of the first steps of the pathways processing color and polarized light inputs.

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    12/14/20 | Cis-regulatory variation in the shavenbaby gene underlies intraspecific phenotypic variation, mirroring interspecific divergence in the same trait.
    Soverna AF, Rodriguez NC, Korgaonkar A, Hasson E, Stern DL, Frankel N
    Evolution. 2020 Dec 14:. doi: 10.1111/evo.14142

    Despite considerable progress in recent decades in dissecting the genetic causes of natural morphological variation, there is limited understanding of how variation within species ultimately contributes to species differences. We have studied patterning of the non-sensory hairs, commonly known as "trichomes," on the dorsal cuticle of first-instar larvae of Drosophila. Most Drosophila species produce a dense lawn of dorsal trichomes, but a subset of these trichomes were lost in D. sechellia and D. ezoana due entirely to regulatory evolution of the shavenbaby (svb) gene. Here, we describe intraspecific variation in dorsal trichome patterns of first-instar larvae of D. virilis that is similar to the trichome pattern variation identified previously between species. We found that a single large effect QTL, which includes svb, explains most of the trichome number difference between two D. virilis strains and that svb expression correlates with the trichome difference between strains. This QTL does not explain the entire difference between strains, implying that additional loci contribute to variation in trichome numbers. Thus, the genetic architecture of intraspecific variation exhibits similarities and differences with interspecific variation that may reflect differences in long-term and short-term evolutionary processes.

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    12/14/20 | The connectome of the adult mushroom body provides insights into function.
    Li F, Lindsey JW, Marin EC, Otto N, Dreher M, Dempsey G, Stark I, Bates AS, Pleijzier MW, Schlegel P, Nern A, Takemura S, Eckstein N, Yang T, Francis A, Braun A, Parekh R, Costa M, Scheffer LK, Aso Y, Jefferis GS, Abbott LF, Litwin-Kumar A, Waddell S, Rubin GM
    eLife. 2020 Dec 14;9:. doi: 10.7554/eLife.62576

    Making inferences about the computations performed by neuronal circuits from synapse-level connectivity maps is an emerging opportunity in neuroscience. The mushroom body (MB) is well positioned for developing and testing such an approach due to its conserved neuronal architecture, recently completed dense connectome, and extensive prior experimental studies of its roles in learning, memory and activity regulation. Here we identify new components of the MB circuit in , including extensive visual input and MB output neurons (MBONs) with direct connections to descending neurons. We find unexpected structure in sensory inputs, in the transfer of information about different sensory modalities to MBONs, and in the modulation of that transfer by dopaminergic neurons (DANs). We provide insights into the circuitry used to integrate MB outputs, connectivity between the MB and the central complex and inputs to DANs, including feedback from MBONs. Our results provide a foundation for further theoretical and experimental work.

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    12/11/21 | Unraveling Single-Particle Trajectories Confined in Tubular Networks
    Yunhao Sun , Zexi Yu , Christopher Obara , Keshav Mittal , Jennifer Lippincott-Schwarz , Elena F Koslover
    arXiv. 2021 Dec 11:

    The analysis of single particle trajectories plays an important role in elucidating dynamics within complex environments such as those found in living cells. However, the characterization of intracellular particle motion is often confounded by confinement of the particles within non-trivial subcellular geometries. Here, we focus specifically on the case of particles undergoing Brownian motion within a tubular network, as found in some cellular organelles. An unraveling algorithm is developed to uncouple particle motion from the confining network structure, allowing for an accurate extraction of the diffusion coefficient, as well as differentiating between Brownian and fractional Brownian dynamics. We validate the algorithm with simulated trajectories and then highlight its application to an example system: analyzing the motion of membrane proteins confined in the tubules of the peripheral endoplasmic reticulum in mammalian cells. We show that these proteins undergo diffusive motion with a well-characterized diffusivity. Our algorithm provides a generally applicable approach for disentangling geometric morphology and particle dynamics in networked architectures.

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    12/09/21 | Bidirectional synaptic plasticity rapidly modifies hippocampal representations.
    Milstein AD, Li Y, Bittner KC, Grienberger C, Soltesz I, Magee JC, Romani S
    eLife. 2021 Dec 09;10:. doi: 10.7554/eLife.73046

    Learning requires neural adaptations thought to be mediated by activity-dependent synaptic plasticity. A relatively non-standard form of synaptic plasticity driven by dendritic calcium spikes, or plateau potentials, has been reported to underlie place field formation in rodent hippocampal CA1 neurons. Here we found that this behavioral timescale synaptic plasticity (BTSP) can also reshape existing place fields via bidirectional synaptic weight changes that depend on the temporal proximity of plateau potentials to pre-existing place fields. When evoked near an existing place field, plateau potentials induced less synaptic potentiation and more depression, suggesting BTSP might depend inversely on postsynaptic activation. However, manipulations of place cell membrane potential and computational modeling indicated that this anti-correlation actually results from a dependence on current synaptic weight such that weak inputs potentiate and strong inputs depress. A network model implementing this bidirectional synaptic learning rule suggested that BTSP enables population activity, rather than pairwise neuronal correlations, to drive neural adaptations to experience.

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    12/07/21 | A genetically defined insula-brainstem circuit selectively controls motivational vigor.
    Deng H, Xiao X, Yang T, Ritola K, Hantman A, Li Y, Huang ZJ, Li B
    Cell. 2021 Dec 07:. doi: 10.1016/j.cell.2021.11.019

    The anterior insular cortex (aIC) plays a critical role in cognitive and motivational control of behavior, but the underlying neural mechanism remains elusive. Here, we show that aIC neurons expressing Fezf2 (aIC), which are the pyramidal tract neurons, signal motivational vigor and invigorate need-seeking behavior through projections to the brainstem nucleus tractus solitarii (NTS). aIC neurons and their postsynaptic NTS neurons acquire anticipatory activity through learning, which encodes the perceived value and the vigor of actions to pursue homeostatic needs. Correspondingly, aIC → NTS circuit activity controls vigor, effort, and striatal dopamine release but only if the action is learned and the outcome is needed. Notably, aIC neurons do not represent taste or valence. Moreover, aIC → NTS activity neither drives reinforcement nor influences total consumption. These results pinpoint specific functions of aIC → NTS circuit for selectively controlling motivational vigor and suggest that motivation is subserved, in part, by aIC's top-down regulation of dopamine signaling.

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    12/07/21 | Image-based representation of massive spatial transcriptomics datasets.
    Stephan Preibisch , Nikos Karaiskos , Nikolaus Rajewsky
    bioRxiv. 2021 Dec 07:. doi: 10.1101/2021.12.07.471629

    We present STIM, an imaging-based computational framework for exploring, visualizing, and processing high-throughput spatial sequencing datasets. STIM is built on the powerful ImgLib2, N5 and BigDataViewer (BDV) frameworks enabling transfer of computer vision techniques to datasets with irregular measurement-spacing and arbitrary spatial resolution, such as spatial transcriptomics data generated by multiplexed targeted hybridization or spatial sequencing technologies. We illustrate STIM’s capabilities by representing, visualizing, and automatically registering publicly available spatial sequencing data from 14 serial sections of mouse brain tissue.

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    12/06/21 | A genetically encoded fluorescent biosensor for extracellular L-lactate.
    Nasu Y, Murphy-Royal C, Wen Y, Haidey JN, Molina RS, Aggarwal A, Zhang S, Kamijo Y, Paquet M, Podgorski K, Drobizhev M, Bains JS, Lemieux MJ, Gordon GR, Campbell RE
    Nature Communications. 2021 Dec 06;12(1):7058. doi: 10.1038/s41467-021-27332-2

    L-Lactate, traditionally considered a metabolic waste product, is increasingly recognized as an important intercellular energy currency in mammals. To enable investigations of the emerging roles of intercellular shuttling of L-lactate, we now report an intensiometric green fluorescent genetically encoded biosensor for extracellular L-lactate. This biosensor, designated eLACCO1.1, enables cellular resolution imaging of extracellular L-lactate in cultured mammalian cells and brain tissue.

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