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1661 Janelia Publications

Showing 11-20 of 1661 results
10/18/19 | Superresolution architecture of cornerstone focal adhesions in human pluripotent stem cells.
Stubb A, Guzmán C, Närvä E, Aaron J, Chew T, Saari M, Miihkinen M, Jacquemet G, Ivaska J
Nature Communications. 2019 Oct 18;10(1):4756. doi: 10.1038/s41467-019-12611-w

While it is clear that key transcriptional programmes are important for maintaining pluripotency, the requirement for cell adhesion to the extracellular matrix remains poorly defined. Human pluripotent stem cells (hPSCs) form colonies encircled by an actin ring and large stable cornerstone focal adhesions (FA). Using superresolution two-colour interferometric photo-activated localisation microscopy, we examine the three-dimensional architecture of cornerstone adhesions and report vertical lamination of FA proteins with three main structural features distinct from previously studied focal adhesions: 1) integrin β5 and talin are present at high density, at the edges of cornerstone FA, adjacent to a vertical kank-rich protein wall, 2) vinculin localises higher than previously reported, displaying a head-above-tail orientation, and 3) surprisingly, actin and α-actinin are present in two discrete z-layers. Finally, we report that depletion of kanks diminishes FA patterning, and actin organisation within the colony, indicating a role for kanks in hPSC colony architecture.

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10/16/19 | Identification of cell types from single-cell transcriptomic data.
Shekhar K, Menon V
Methods in Molecular Biology. 2019 Oct 16;1935:45-77. doi: 10.1007/978-1-4939-9057-3_4

Unprecedented technological advances in single-cell RNA-sequencing (scRNA-seq) technology have now made it possible to profile genome-wide expression in single cells at low cost and high throughput. There is substantial ongoing effort to use scRNA-seq measurements to identify the "cell types" that form components of a complex tissue, akin to taxonomizing species in ecology. Cell type classification from scRNA-seq data involves the application of computational tools rooted in dimensionality reduction and clustering, and statistical analysis to identify molecular signatures that are unique to each type. As datasets continue to grow in size and complexity, computational challenges abound, requiring analytical methods to be scalable, flexible, and robust. Moreover, careful consideration needs to be paid to experimental biases and statistical challenges that are unique to these measurements to avoid artifacts. This chapter introduces these topics in the context of cell-type identification, and outlines an instructive step-by-step example bioinformatic pipeline for researchers entering this field.

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10/15/19 | Asymmetric ON-OFF processing of visual motion cancels variability induced by the structure of natural scenes.
Chen J, Mandel HB, Fitzgerald JE, Clark DA
eLife. 2019 Oct 15;8:. doi: 10.7554/eLife.47579

Animals detect motion using a variety of visual cues that reflect regularities in the natural world. Experiments in animals across phyla have shown that motion percepts incorporate both pairwise and triplet spatiotemporal correlations that could theoretically benefit motion computation. However, it remains unclear how visual systems assemble these cues to build accurate motion estimates. Here we used systematic behavioral measurements of fruit fly motion perception to show how flies combine local pairwise and triplet correlations to reduce variability in motion estimates across natural scenes. By generating synthetic images with statistics controlled by maximum entropy distributions, we show that the triplet correlations are useful only when images have light-dark asymmetries that mimic natural ones. This suggests that asymmetric ON-OFF processing is tuned to the particular statistics of natural scenes. Since all animals encounter the world's light-dark asymmetries, many visual systems are likely to use asymmetric ON-OFF processing to improve motion estimation.

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10/15/19 | Developmental organization of central neurons in the adult Drosophila ventral nervous system.
Shepherd D, Sahota V, Court R, Williams DW, Truman JW
Journal of Comparative Neurology. 2019 Oct 15;527(15):2573-2598. doi: 10.1002/cne.24690

We have used MARCM to reveal the adult morphology of the post embryonically produced neurons in the thoracic neuromeres of the Drosophila VNS. The work builds on previous studies of the origins of the adult VNS neurons to describe the clonal organization of the adult VNS. We present data for 58 of 66 postembryonic thoracic lineages, excluding the motor neuron producing lineages (15 and 24) which have been described elsewhere. MARCM labels entire lineages but where both A and B hemilineages survive (e.g., lineages 19, 12, 13, 6, 1, 3, 8, and 11), the two hemilineages can be discriminated and we have described each hemilineage separately. Hemilineage morphology is described in relation to the known functional domains of the VNS neuropil and based on the anatomy we are able to assign broad functional roles for each hemilineage. The data show that in a thoracic hemineuromere, 16 hemilineages are primarily involved in controlling leg movements and walking, 9 are involved in the control of wing movements, and 10 interface between both leg and wing control. The data provide a baseline of understanding of the functional organization of the adult Drosophila VNS. By understanding the morphological organization of these neurons, we can begin to define and test the rules by which neuronal circuits are assembled during development and understand the functional logic and evolution of neuronal networks.

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10/15/19 | Developmental organization of central neurons in the adult Drosophila ventral nervous system.
Shepherd D, Sahota V, Court R, Williams DW, Truman JW
Journal of Comparative Neurology. 2019 Oct 15;527(15):2573-2598. doi: 10.1002/cne.24690

We have used MARCM to reveal the adult morphology of the post embryonically produced neurons in the thoracic neuromeres of the Drosophila VNS. The work builds on previous studies of the origins of the adult VNS neurons to describe the clonal organization of the adult VNS. We present data for 58 of 66 postembryonic thoracic lineages, excluding the motor neuron producing lineages (15 and 24) which have been described elsewhere. MARCM labels entire lineages but where both A and B hemilineages survive (e.g., lineages 19, 12, 13, 6, 1, 3, 8, and 11), the two hemilineages can be discriminated and we have described each hemilineage separately. Hemilineage morphology is described in relation to the known functional domains of the VNS neuropil and based on the anatomy we are able to assign broad functional roles for each hemilineage. The data show that in a thoracic hemineuromere, 16 hemilineages are primarily involved in controlling leg movements and walking, 9 are involved in the control of wing movements, and 10 interface between both leg and wing control. The data provide a baseline of understanding of the functional organization of the adult Drosophila VNS. By understanding the morphological organization of these neurons, we can begin to define and test the rules by which neuronal circuits are assembled during development and understand the functional logic and evolution of neuronal networks.

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10/15/19 | The gene influences male mating success through sex comb melanization.
Massey JH, Chung D, Siwanowicz I, Stern DL, Wittkopp PJ
eLife. 2019 10 15;8:. doi: 10.7554/eLife.49388

males perform a series of courtship behaviors that, when successful, result in copulation with a female. For over a century, mutations in the gene, named for its effects on pigmentation, have been known to reduce male mating success. Prior work has suggested that influences mating behavior through effects on wing extension, song, and/or courtship vigor. Here, we rule out these explanations, as well as effects on the nervous system more generally, and find instead that the effects of on male mating success are mediated by its effects on pigmentation of male-specific leg structures called sex combs. Loss of expression in these modified bristles reduces their melanization, which changes their structure and causes difficulty grasping females prior to copulation. These data illustrate why the mechanical properties of anatomy, not just neural circuitry, must be considered to fully understand the development and evolution of behavior.

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10/11/19 | The organization of the second optic chiasm of the optic lobe.
Shinomiya K, Horne JA, McLin S, Wiederman M, Nern A, Plaza SM, Meinertzhagen IA
Frontiers in Neural Circuits. 2019 Oct 11;13:65. doi: 10.3389/fncir.2019.00065

Visual pathways from the compound eye of an insect relay to four neuropils, successively the lamina, medulla, lobula, and lobula plate in the underlying optic lobe. Among these neuropils, the medulla, lobula, and lobula plate are interconnected by the complex second optic chiasm, through which the anteroposterior axis undergoes an inversion between the medulla and lobula. Given their complex structure, the projection patterns through the second optic chiasm have so far lacked critical analysis. By densely reconstructing axon trajectories using a volumetric scanning electron microscopy (SEM) technique, we reveal the three-dimensional structure of the second optic chiasm of , which comprises interleaving bundles and sheets of axons insulated from each other by glial sheaths. These axon bundles invert their horizontal sequence in passing between the medulla and lobula. Axons connecting the medulla and lobula plate are also bundled together with them but do not decussate the sequence of their horizontal positions. They interleave with sheets of projection neuron axons between the lobula and lobula plate, which also lack decussations. We estimate that approximately 19,500 cells per hemisphere, about two thirds of the optic lobe neurons, contribute to the second chiasm, most being Tm cells, with an estimated additional 2,780 T4 and T5 cells each. The chiasm mostly comprises axons and cell body fibers, but also a few synaptic elements. Based on our anatomical findings, we propose that a chiasmal structure between the neuropils is potentially advantageous for processing complex visual information in parallel. The EM reconstruction shows not only the structure of the chiasm in the adult brain, the previously unreported main topic of our study, but also suggest that the projection patterns of the neurons comprising the chiasm may be determined by the proliferation centers from which the neurons develop. Such a complex wiring pattern could, we suggest, only have arisen in several evolutionary steps.

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10/09/19 | Computational neuroethology: A call to action.
Datta SR, Anderson DJ, Branson K, Perona P, Leifer A
Neuron. 2019 Oct 09;104(1):11-24. doi: 10.1016/j.neuron.2019.09.038

The brain is worthy of study because it is in charge of behavior. A flurry of recent technical advances in measuring and quantifying naturalistic behaviors provide an important opportunity for advancing brain science. However, the problem of understanding unrestrained behavior in the context of neural recordings and manipulations remains unsolved, and developing approaches to addressing this challenge is critical. Here we discuss considerations in computational neuroethology-the science of quantifying naturalistic behaviors for understanding the brain-and propose strategies to evaluate progress. We point to open questions that require resolution and call upon the broader systems neuroscience community to further develop and leverage measures of naturalistic, unrestrained behavior, which will enable us to more effectively probe the richness and complexity of the brain.

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10/09/19 | Learning from action: reconsidering movement signaling in midbrain dopamine neuron activity.
Coddington LT, Dudman JT
Neuron. 2019 Oct 09;104(1):63-77. doi: 10.1016/j.neuron.2019.08.036

Animals infer when and where a reward is available from experience with informative sensory stimuli and their own actions. In vertebrates, this is thought to depend upon the release of dopamine from midbrain dopaminergic neurons. Studies of the role of dopamine have focused almost exclusively on their encoding of informative sensory stimuli; however, many dopaminergic neurons are active just prior to movement initiation, even in the absence of sensory stimuli. How should current frameworks for understanding the role of dopamine incorporate these observations? To address this question, we review recent anatomical and functional evidence for action-related dopamine signaling. We conclude by proposing a framework in which dopaminergic neurons encode subjective signals of action initiation to solve an internal credit assignment problem.

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10/06/19 | Expansion microscopy: scalable and convenient super-resolution microscopy.
Tillberg PW, Chen F
Annual Review of Cell and Developmental Biology. 2019 Oct 6;35:683-701. doi: 10.1146/annurev-cellbio-100818-125320

Expansion microscopy (ExM) is a physical form of magnification that increases the effective resolving power of any microscope. Here, we describe the fundamental principles of ExM, as well as how recently developed ExM variants build upon and apply those principles. We examine applications of ExM in cell and developmental biology for the study of nanoscale structures as well as ExM's potential for scalable mapping of nanoscale structures across large sample volumes. Finally, we explore how the unique anchoring and hydrogel embedding properties enable postexpansion molecular interrogation in a purified chemical environment. ExM promises to play an important role complementary to emerging live-cell imaging techniques, because of its relative ease of adoption and modification and its compatibility with tissue specimens up to at least 200 μm thick. Expected final online publication date for the , Volume 35 is October 7, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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