1
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Eckstein N, Bates AS, Champion A, Du M, Yin Y, Schlegel P, Lu AKY, Rymer T, Finley-May S, Paterson T, Parekh R, Dorkenwald S, Matsliah A, Yu SC, McKellar C, Sterling A, Eichler K, Costa M, Seung S, Murthy M, Hartenstein V, Jefferis GSXE, Funke J. Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster. Cell 2024; 187:2574-2594.e23. [PMID: 38729112 DOI: 10.1016/j.cell.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 10/04/2023] [Accepted: 03/13/2024] [Indexed: 05/12/2024]
Abstract
High-resolution electron microscopy of nervous systems has enabled the reconstruction of synaptic connectomes. However, we do not know the synaptic sign for each connection (i.e., whether a connection is excitatory or inhibitory), which is implied by the released transmitter. We demonstrate that artificial neural networks can predict transmitter types for presynapses from electron micrographs: a network trained to predict six transmitters (acetylcholine, glutamate, GABA, serotonin, dopamine, octopamine) achieves an accuracy of 87% for individual synapses, 94% for neurons, and 91% for known cell types across a D. melanogaster whole brain. We visualize the ultrastructural features used for prediction, discovering subtle but significant differences between transmitter phenotypes. We also analyze transmitter distributions across the brain and find that neurons that develop together largely express only one fast-acting transmitter (acetylcholine, glutamate, or GABA). We hope that our publicly available predictions act as an accelerant for neuroscientific hypothesis generation for the fly.
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Affiliation(s)
- Nils Eckstein
- HHMI Janelia Research Campus, Ashburn, VA, USA; Institute of Neuroinformatics UZH/ETHZ, Zurich, Switzerland
| | - Alexander Shakeel Bates
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK; Centre for Neural Circuits and Behaviour, The University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK; Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Andrew Champion
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Michelle Du
- HHMI Janelia Research Campus, Ashburn, VA, USA
| | - Yijie Yin
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Philipp Schlegel
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | - Sven Dorkenwald
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Arie Matsliah
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Szi-Chieh Yu
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Claire McKellar
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Amy Sterling
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Katharina Eichler
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Marta Costa
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Sebastian Seung
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Mala Murthy
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Volker Hartenstein
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gregory S X E Jefferis
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
| | - Jan Funke
- HHMI Janelia Research Campus, Ashburn, VA, USA.
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2
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Nern A, Lösche F, Takemura SY, Burnett LE, Dreher M, Gruntman E, Hoeller J, Huang GB, Januszewski M, Klapoetke NC, Koskela S, Longden KD, Lu Z, Preibisch S, Qiu W, Rogers EM, Seenivasan P, Zhao A, Bogovic J, Canino BS, Clements J, Cook M, Finley-May S, Flynn MA, Hameed I, Hayworth KJ, Hopkins GP, Hubbard PM, Katz WT, Kovalyak J, Lauchie SA, Leonard M, Lohff A, Maldonado CA, Mooney C, Okeoma N, Olbris DJ, Ordish C, Paterson T, Phillips EM, Pietzsch T, Salinas JR, Rivlin PK, Scott AL, Scuderi LA, Takemura S, Talebi I, Thomson A, Trautman ET, Umayam L, Walsh C, Walsh JJ, Shan Xu C, Yakal EA, Yang T, Zhao T, Funke J, George R, Hess HF, Jefferis GSXE, Knecht C, Korff W, Plaza SM, Romani S, Saalfeld S, Scheffer LK, Berg S, Rubin GM, Reiser MB. Connectome-driven neural inventory of a complete visual system. bioRxiv 2024:2024.04.16.589741. [PMID: 38659887 PMCID: PMC11042306 DOI: 10.1101/2024.04.16.589741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Vision provides animals with detailed information about their surroundings, conveying diverse features such as color, form, and movement across the visual scene. Computing these parallel spatial features requires a large and diverse network of neurons, such that in animals as distant as flies and humans, visual regions comprise half the brain's volume. These visual brain regions often reveal remarkable structure-function relationships, with neurons organized along spatial maps with shapes that directly relate to their roles in visual processing. To unravel the stunning diversity of a complex visual system, a careful mapping of the neural architecture matched to tools for targeted exploration of that circuitry is essential. Here, we report a new connectome of the right optic lobe from a male Drosophila central nervous system FIB-SEM volume and a comprehensive inventory of the fly's visual neurons. We developed a computational framework to quantify the anatomy of visual neurons, establishing a basis for interpreting how their shapes relate to spatial vision. By integrating this analysis with connectivity information, neurotransmitter identity, and expert curation, we classified the ~53,000 neurons into 727 types, about half of which are systematically described and named for the first time. Finally, we share an extensive collection of split-GAL4 lines matched to our neuron type catalog. Together, this comprehensive set of tools and data unlock new possibilities for systematic investigations of vision in Drosophila, a foundation for a deeper understanding of sensory processing.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gregory SXE Jefferis
- MRC Laboratory of Molecular Biology, Cambridge, UK and Department of Zoology, University of Cambridge, UK
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3
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Lin A, Yang R, Dorkenwald S, Matsliah A, Sterling AR, Schlegel P, Yu SC, McKellar CE, Costa M, Eichler K, Bates AS, Eckstein N, Funke J, Jefferis GSXE, Murthy M. Network Statistics of the Whole-Brain Connectome of Drosophila. bioRxiv 2024:2023.07.29.551086. [PMID: 37547019 PMCID: PMC10402125 DOI: 10.1101/2023.07.29.551086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Brains comprise complex networks of neurons and connections. Network analysis applied to the wiring diagrams of brains can offer insights into how brains support computations and regulate information flow. The completion of the first whole-brain connectome of an adult Drosophila, the largest connectome to date, containing 130,000 neurons and millions of connections, offers an unprecedented opportunity to analyze its network properties and topological features. To gain insights into local connectivity, we computed the prevalence of two- and three-node network motifs, examined their strengths and neurotransmitter compositions, and compared these topological metrics with wiring diagrams of other animals. We discovered that the network of the fly brain displays rich club organization, with a large population (30% percent of the connectome) of highly connected neurons. We identified subsets of rich club neurons that may serve as integrators or broadcasters of signals. Finally, we examined subnetworks based on 78 anatomically defined brain regions or neuropils. These data products are shared within the FlyWire Codex and will serve as a foundation for models and experiments exploring the relationship between neural activity and anatomical structure.
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Affiliation(s)
- Albert Lin
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Center for the Physics of Biological Function, Princeton University, Princeton, NJ, USA
| | - Runzhe Yang
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Computer Science Department, Princeton University, Princeton, NJ, USA
| | - Sven Dorkenwald
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Computer Science Department, Princeton University, Princeton, NJ, USA
| | - Arie Matsliah
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Amy R Sterling
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Philipp Schlegel
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Szi-Chieh Yu
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Claire E McKellar
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Marta Costa
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Katharina Eichler
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Alexander Shakeel Bates
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, UK
| | - Nils Eckstein
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, USA
| | - Jan Funke
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, USA
| | - Gregory S X E Jefferis
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mala Murthy
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
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4
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Heinrich L, Patton W, Bennett D, Ackerman D, Park G, Bogovic JA, Eckstein N, Petruncio A, Clements J, Pang S, Shan Xu C, Funke J, Korff W, Hess H, Lippincott-Schwartz J, Saalfeld S, Weigel A. Towards Generalizable Organelle Segmentation in Volume Electron Microscopy. Microsc Microanal 2023; 29:975. [PMID: 37613645 DOI: 10.1093/micmic/ozad067.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Larissa Heinrich
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Will Patton
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Davis Bennett
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - David Ackerman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Grace Park
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - John A Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | | | - Alyson Petruncio
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Jody Clements
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Song Pang
- Yale School of Medicine, New Haven, Connecticut, United States
| | - C Shan Xu
- Yale School of Medicine, New Haven, Connecticut, United States
| | - Jan Funke
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Wyatt Korff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Harald Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | | | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Aubrey Weigel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
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5
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Dorkenwald S, Matsliah A, Sterling AR, Schlegel P, Yu SC, McKellar CE, Lin A, Costa M, Eichler K, Yin Y, Silversmith W, Schneider-Mizell C, Jordan CS, Brittain D, Halageri A, Kuehner K, Ogedengbe O, Morey R, Gager J, Kruk K, Perlman E, Yang R, Deutsch D, Bland D, Sorek M, Lu R, Macrina T, Lee K, Bae JA, Mu S, Nehoran B, Mitchell E, Popovych S, Wu J, Jia Z, Castro M, Kemnitz N, Ih D, Bates AS, Eckstein N, Funke J, Collman F, Bock DD, Jefferis GS, Seung HS, Murthy M. Neuronal wiring diagram of an adult brain. bioRxiv 2023:2023.06.27.546656. [PMID: 37425937 PMCID: PMC10327113 DOI: 10.1101/2023.06.27.546656] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Connections between neurons can be mapped by acquiring and analyzing electron microscopic (EM) brain images. In recent years, this approach has been applied to chunks of brains to reconstruct local connectivity maps that are highly informative, yet inadequate for understanding brain function more globally. Here, we present the first neuronal wiring diagram of a whole adult brain, containing 5×107 chemical synapses between ~130,000 neurons reconstructed from a female Drosophila melanogaster. The resource also incorporates annotations of cell classes and types, nerves, hemilineages, and predictions of neurotransmitter identities. Data products are available by download, programmatic access, and interactive browsing and made interoperable with other fly data resources. We show how to derive a projectome, a map of projections between regions, from the connectome. We demonstrate the tracing of synaptic pathways and the analysis of information flow from inputs (sensory and ascending neurons) to outputs (motor, endocrine, and descending neurons), across both hemispheres, and between the central brain and the optic lobes. Tracing from a subset of photoreceptors all the way to descending motor pathways illustrates how structure can uncover putative circuit mechanisms underlying sensorimotor behaviors. The technologies and open ecosystem of the FlyWire Consortium set the stage for future large-scale connectome projects in other species.
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Affiliation(s)
- Sven Dorkenwald
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Computer Science Department, Princeton University, Princeton, USA
| | - Arie Matsliah
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Amy R Sterling
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Eyewire, Boston, USA
| | - Philipp Schlegel
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Szi-chieh Yu
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | | | - Albert Lin
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Center for the Physics of Biological Function, Princeton University, Princeton, USA
| | - Marta Costa
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Katharina Eichler
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Yijie Yin
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Will Silversmith
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | | | - Chris S. Jordan
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | | | - Akhilesh Halageri
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Kai Kuehner
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | | | - Ryan Morey
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Jay Gager
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | | | | | - Runzhe Yang
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Computer Science Department, Princeton University, Princeton, USA
| | - David Deutsch
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Doug Bland
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Marissa Sorek
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Eyewire, Boston, USA
| | - Ran Lu
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Thomas Macrina
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Computer Science Department, Princeton University, Princeton, USA
| | - Kisuk Lee
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Brain & Cognitive Sciences Department, Massachusetts Institute of Technology, Cambridge, USA
| | - J. Alexander Bae
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Electrical and Computer Engineering Department, Princeton University, Princeton, USA
| | - Shang Mu
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Barak Nehoran
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Computer Science Department, Princeton University, Princeton, USA
| | - Eric Mitchell
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Sergiy Popovych
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Computer Science Department, Princeton University, Princeton, USA
| | - Jingpeng Wu
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Zhen Jia
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Manuel Castro
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Nico Kemnitz
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Dodam Ih
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Alexander Shakeel Bates
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Harvard Medical School, Boston, USA
- Centre for Neural Circuits and Behaviour, The University of Oxford, Oxford, UK
| | - Nils Eckstein
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, USA
| | - Jan Funke
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, USA
| | | | - Davi D. Bock
- Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlington, USA
| | - Gregory S.X.E Jefferis
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - H. Sebastian Seung
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
- Computer Science Department, Princeton University, Princeton, USA
| | - Mala Murthy
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
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6
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Shiu PK, Sterne GR, Spiller N, Franconville R, Sandoval A, Zhou J, Simha N, Kang CH, Yu S, Kim JS, Dorkenwald S, Matsliah A, Schlegel P, Szi-chieh Y, McKellar CE, Sterling A, Costa M, Eichler K, Jefferis GS, Murthy M, Bates AS, Eckstein N, Funke J, Bidaye SS, Hampel S, Seeds AM, Scott K. A leaky integrate-and-fire computational model based on the connectome of the entire adult Drosophila brain reveals insights into sensorimotor processing. bioRxiv 2023:2023.05.02.539144. [PMID: 37205514 PMCID: PMC10187186 DOI: 10.1101/2023.05.02.539144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The forthcoming assembly of the adult Drosophila melanogaster central brain connectome, containing over 125,000 neurons and 50 million synaptic connections, provides a template for examining sensory processing throughout the brain. Here, we create a leaky integrate-and-fire computational model of the entire Drosophila brain, based on neural connectivity and neurotransmitter identity, to study circuit properties of feeding and grooming behaviors. We show that activation of sugar-sensing or water-sensing gustatory neurons in the computational model accurately predicts neurons that respond to tastes and are required for feeding initiation. Computational activation of neurons in the feeding region of the Drosophila brain predicts those that elicit motor neuron firing, a testable hypothesis that we validate by optogenetic activation and behavioral studies. Moreover, computational activation of different classes of gustatory neurons makes accurate predictions of how multiple taste modalities interact, providing circuit-level insight into aversive and appetitive taste processing. Our computational model predicts that the sugar and water pathways form a partially shared appetitive feeding initiation pathway, which our calcium imaging and behavioral experiments confirm. Additionally, we applied this model to mechanosensory circuits and found that computational activation of mechanosensory neurons predicts activation of a small set of neurons comprising the antennal grooming circuit that do not overlap with gustatory circuits, and accurately describes the circuit response upon activation of different mechanosensory subtypes. Our results demonstrate that modeling brain circuits purely from connectivity and predicted neurotransmitter identity generates experimentally testable hypotheses and can accurately describe complete sensorimotor transformations.
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Affiliation(s)
- Philip K. Shiu
- Department of Molecular and Cell Biology and Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
| | - Gabriella R. Sterne
- Department of Molecular and Cell Biology and Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
- University of Rochester Medical Center, Department of Biomedical Genetics
| | - Nico Spiller
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | | | - Andrea Sandoval
- Department of Molecular and Cell Biology and Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
| | - Joie Zhou
- Department of Molecular and Cell Biology and Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
| | - Neha Simha
- Department of Molecular and Cell Biology and Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
| | - Chan Hyuk Kang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Seongbong Yu
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jinseop S. Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Sven Dorkenwald
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Computer Science Department, Princeton University, Princeton, NJ, USA
| | - Arie Matsliah
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Philipp Schlegel
- Department of Zoology, University of Cambridge
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge
| | - Yu Szi-chieh
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Claire E. McKellar
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Amy Sterling
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Marta Costa
- Department of Zoology, University of Cambridge
| | | | - Gregory S.X.E. Jefferis
- Department of Zoology, University of Cambridge
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge
| | - Mala Murthy
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Alexander Shakeel Bates
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge
- Centre for Neural Circuits and Behaviour, The University of Oxford
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Jan Funke
- HHMI Janelia Research Campus, Ashburn, USA
| | - Salil S. Bidaye
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | - Stefanie Hampel
- Institute of Neurobiology, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico
| | - Andrew M. Seeds
- Institute of Neurobiology, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico
| | - Kristin Scott
- Department of Molecular and Cell Biology and Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
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7
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Nguyen TM, Thomas LA, Rhoades JL, Ricchi I, Yuan XC, Sheridan A, Hildebrand DGC, Funke J, Regehr WG, Lee WCA. Publisher Correction: Structured cerebellar connectivity supports resilient pattern separation. Nature 2023; 614:E18. [PMID: 36631615 DOI: 10.1038/s41586-023-05703-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Tri M Nguyen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Logan A Thomas
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Jeff L Rhoades
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Program in Neuroscience, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Ilaria Ricchi
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Neuro-X Institute, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Xintong Cindy Yuan
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Program in Neuroscience, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Arlo Sheridan
- HHMI Janelia Research Campus, Ashburn, VA, USA.,Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - David G C Hildebrand
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Laboratory of Neural Systems, The Rockefeller University, New York, NY, USA
| | - Jan Funke
- HHMI Janelia Research Campus, Ashburn, VA, USA
| | - Wade G Regehr
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Wei-Chung Allen Lee
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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8
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Yamada D, Bushey D, Li F, Hibbard KL, Sammons M, Funke J, Litwin-Kumar A, Hige T, Aso Y. Hierarchical architecture of dopaminergic circuits enables second-order conditioning in Drosophila. eLife 2023; 12:79042. [PMID: 36692262 PMCID: PMC9937650 DOI: 10.7554/elife.79042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 01/23/2023] [Indexed: 01/25/2023] Open
Abstract
Dopaminergic neurons with distinct projection patterns and physiological properties compose memory subsystems in a brain. However, it is poorly understood whether or how they interact during complex learning. Here, we identify a feedforward circuit formed between dopamine subsystems and show that it is essential for second-order conditioning, an ethologically important form of higher-order associative learning. The Drosophila mushroom body comprises a series of dopaminergic compartments, each of which exhibits distinct memory dynamics. We find that a slow and stable memory compartment can serve as an effective 'teacher' by instructing other faster and transient memory compartments via a single key interneuron, which we identify by connectome analysis and neurotransmitter prediction. This excitatory interneuron acquires enhanced response to reward-predicting odor after first-order conditioning and, upon activation, evokes dopamine release in the 'student' compartments. These hierarchical connections between dopamine subsystems explain distinct properties of first- and second-order memory long known by behavioral psychologists.
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Affiliation(s)
- Daichi Yamada
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Daniel Bushey
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Feng Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Karen L Hibbard
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Megan Sammons
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jan Funke
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Ashok Litwin-Kumar
- Department of Neuroscience, Columbia University, New York, United States
| | - Toshihide Hige
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, United States
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Yoshinori Aso
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
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9
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Sheridan A, Nguyen TM, Deb D, Lee WCA, Saalfeld S, Turaga SC, Manor U, Funke J. Local shape descriptors for neuron segmentation. Nat Methods 2023; 20:295-303. [PMID: 36585455 PMCID: PMC9911350 DOI: 10.1038/s41592-022-01711-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/01/2022] [Indexed: 12/31/2022]
Abstract
We present an auxiliary learning task for the problem of neuron segmentation in electron microscopy volumes. The auxiliary task consists of the prediction of local shape descriptors (LSDs), which we combine with conventional voxel-wise direct neighbor affinities for neuron boundary detection. The shape descriptors capture local statistics about the neuron to be segmented, such as diameter, elongation, and direction. On a study comparing several existing methods across various specimen, imaging techniques, and resolutions, auxiliary learning of LSDs consistently increases segmentation accuracy of affinity-based methods over a range of metrics. Furthermore, the addition of LSDs promotes affinity-based segmentation methods to be on par with the current state of the art for neuron segmentation (flood-filling networks), while being two orders of magnitudes more efficient-a critical requirement for the processing of future petabyte-sized datasets.
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Affiliation(s)
- Arlo Sheridan
- grid.443970.dHHMI Janelia, Ashburn, VA USA ,grid.250671.70000 0001 0662 7144Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA USA
| | - Tri M. Nguyen
- grid.38142.3c000000041936754XDepartment of Neurobiology, Harvard Medical School, Boston, MA USA
| | | | - Wei-Chung Allen Lee
- grid.38142.3c000000041936754XF.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | | | | | - Uri Manor
- grid.250671.70000 0001 0662 7144Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA USA
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10
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Malin-Mayor C, Hirsch P, Guignard L, McDole K, Wan Y, Lemon WC, Kainmueller D, Keller PJ, Preibisch S, Funke J. Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations. Nat Biotechnol 2023; 41:44-49. [PMID: 36065022 PMCID: PMC7614077 DOI: 10.1038/s41587-022-01427-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/12/2022] [Indexed: 01/19/2023]
Abstract
We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8% of cell lineages spanning 1 h, as compared to 31.8% for the competing method. Our approach improves understanding of where and when cell fate decisions are made in developing embryos, tissues, and organs.
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Affiliation(s)
| | - Peter Hirsch
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Faculty of Mathematics and Natural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leo Guignard
- HHMI Janelia, Ashburn, VA, USA
- CNRS, UTLN, LIS 7020, Turing Centre for Living Systems, Aix Marseille University, Marseille, France
| | - Katie McDole
- HHMI Janelia, Ashburn, VA, USA
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Yinan Wan
- HHMI Janelia, Ashburn, VA, USA
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Dagmar Kainmueller
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Faculty of Mathematics and Natural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
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11
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Zhu PP, Hung HF, Batchenkova N, Nixon-Abell J, Henderson J, Zheng P, Renvoisé B, Pang S, Xu CS, Saalfeld S, Funke J, Xie Y, Svara F, Hess HF, Blackstone C. Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons. Hum Mol Genet 2022; 31:2779-2795. [PMID: 35348668 PMCID: PMC9402237 DOI: 10.1093/hmg/ddac072] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/15/2022] [Accepted: 03/20/2022] [Indexed: 08/12/2023] Open
Abstract
Hereditary spastic paraplegias (HSPs) comprise a large group of inherited neurologic disorders affecting the longest corticospinal axons (SPG1-86 plus others), with shared manifestations of lower extremity spasticity and gait impairment. Common autosomal dominant HSPs are caused by mutations in genes encoding the microtubule-severing ATPase spastin (SPAST; SPG4), the membrane-bound GTPase atlastin-1 (ATL1; SPG3A) and the reticulon-like, microtubule-binding protein REEP1 (REEP1; SPG31). These proteins bind one another and function in shaping the tubular endoplasmic reticulum (ER) network. Typically, mouse models of HSPs have mild, later onset phenotypes, possibly reflecting far shorter lengths of their corticospinal axons relative to humans. Here, we have generated a robust, double mutant mouse model of HSP in which atlastin-1 is genetically modified with a K80A knock-in (KI) missense change that abolishes its GTPase activity, whereas its binding partner Reep1 is knocked out. Atl1KI/KI/Reep1-/- mice exhibit early onset and rapidly progressive declines in several motor function tests. Also, ER in mutant corticospinal axons dramatically expands transversely and periodically in a mutation dosage-dependent manner to create a ladder-like appearance, on the basis of reconstructions of focused ion beam-scanning electron microscopy datasets using machine learning-based auto-segmentation. In lockstep with changes in ER morphology, axonal mitochondria are fragmented and proportions of hypophosphorylated neurofilament H and M subunits are dramatically increased in Atl1KI/KI/Reep1-/- spinal cord. Co-occurrence of these findings links ER morphology changes to alterations in mitochondrial morphology and cytoskeletal organization. Atl1KI/KI/Reep1-/- mice represent an early onset rodent HSP model with robust behavioral and cellular readouts for testing novel therapies.
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Affiliation(s)
- Peng-Peng Zhu
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hui-Fang Hung
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Natalia Batchenkova
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathon Nixon-Abell
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
- Cambridge Institute for Medical Research, Cambridge CB2 0XY, UK
| | - James Henderson
- Cambridge Institute for Medical Research, Cambridge CB2 0XY, UK
| | - Pengli Zheng
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Benoit Renvoisé
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Song Pang
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - C Shan Xu
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Stephan Saalfeld
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Jan Funke
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Yuxiang Xie
- Synaptic Function Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fabian Svara
- ariadne.ai ag, CH-6033 Buchrain, Switzerland
- Research Center Caesar, D-53175 Bonn, Germany
| | - Harald F Hess
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Craig Blackstone
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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12
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Baker CA, McKellar C, Pang R, Nern A, Dorkenwald S, Pacheco DA, Eckstein N, Funke J, Dickson BJ, Murthy M. Neural network organization for courtship-song feature detection in Drosophila. Curr Biol 2022; 32:3317-3333.e7. [PMID: 35793679 PMCID: PMC9378594 DOI: 10.1016/j.cub.2022.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/18/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Animals communicate using sounds in a wide range of contexts, and auditory systems must encode behaviorally relevant acoustic features to drive appropriate reactions. How feature detection emerges along auditory pathways has been difficult to solve due to challenges in mapping the underlying circuits and characterizing responses to behaviorally relevant features. Here, we study auditory activity in the Drosophila melanogaster brain and investigate feature selectivity for the two main modes of fly courtship song, sinusoids and pulse trains. We identify 24 new cell types of the intermediate layers of the auditory pathway, and using a new connectomic resource, FlyWire, we map all synaptic connections between these cell types, in addition to connections to known early and higher-order auditory neurons-this represents the first circuit-level map of the auditory pathway. We additionally determine the sign (excitatory or inhibitory) of most synapses in this auditory connectome. We find that auditory neurons display a continuum of preferences for courtship song modes and that neurons with different song-mode preferences and response timescales are highly interconnected in a network that lacks hierarchical structure. Nonetheless, we find that the response properties of individual cell types within the connectome are predictable from their inputs. Our study thus provides new insights into the organization of auditory coding within the Drosophila brain.
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Affiliation(s)
- Christa A Baker
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Claire McKellar
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA; Janelia Research Campus, HHMI, Ashburn, VA, USA
| | - Rich Pang
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | | | - Sven Dorkenwald
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA; Computer Science, Princeton University, Princeton, NJ, USA
| | - Diego A Pacheco
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Nils Eckstein
- Janelia Research Campus, HHMI, Ashburn, VA, USA; Institute of Neuroinformatics UZH/ETHZ, Zurich, Switzerland
| | - Jan Funke
- Janelia Research Campus, HHMI, Ashburn, VA, USA
| | | | - Mala Murthy
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA.
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13
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Buhmann J, Sheridan A, Malin-Mayor C, Schlegel P, Gerhard S, Kazimiers T, Krause R, Nguyen TM, Heinrich L, Lee WCA, Wilson R, Saalfeld S, Jefferis GSXE, Bock DD, Turaga SC, Cook M, Funke J. Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set. Nat Methods 2021; 18:771-774. [PMID: 34168373 PMCID: PMC7611460 DOI: 10.1038/s41592-021-01183-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 05/10/2021] [Indexed: 02/03/2023]
Abstract
We develop an automatic method for synaptic partner identification in insect brains and use it to predict synaptic partners in a whole-brain electron microscopy dataset of the fruit fly. The predictions can be used to infer a connectivity graph with high accuracy, thus allowing fast identification of neural pathways. To facilitate circuit reconstruction using our results, we develop CIRCUITMAP, a user interface add-on for the circuit annotation tool CATMAID.
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Affiliation(s)
- Julia Buhmann
- HHMI Janelia Research Campus, Ashburn, VA, USA
- Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, Switzerland
| | | | | | | | - Stephan Gerhard
- Harvard Medical School, Boston, MA, USA
- UniDesign Solutions GmbH, Zürich, Switzerland
| | | | - Renate Krause
- HHMI Janelia Research Campus, Ashburn, VA, USA
- Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, Switzerland
| | | | | | | | | | | | | | | | | | - Matthew Cook
- Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jan Funke
- HHMI Janelia Research Campus, Ashburn, VA, USA.
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14
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Lundberg E, Funke J, Uhlmann V, Gerlich D, Walter T, Carpenter A, Coehlo LP. Which image-based phenotypes are most promising for using AI to understand cellular functions and why? Cell Syst 2021; 12:384-387. [PMID: 34015259 DOI: 10.1016/j.cels.2021.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Funke J, Prasse C, Dietrich C, Ternes TA. Ozonation products of zidovudine and thymidine in oxidative water treatment. Water Res X 2021; 11:100090. [PMID: 33604534 PMCID: PMC7873472 DOI: 10.1016/j.wroa.2021.100090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 05/08/2023]
Abstract
Ozonation is an advanced treatment technology that is increasingly used for the removal of organic micropollutants from wastewater and drinking water. However, reaction of organic compounds with ozone can also result in the formation of toxic transformation products. In the present study, the degradation of the antiviral drug zidovudine during ozonation was investigated. To obtain further insights into the reaction mechanisms and pathways, results of zidovudine were compared with the transformation of the naturally occurring derivative thymidine. Kinetic experiments were accompanied by elucidation of formed transformation products using lab-scale batch experiments and subsequent liquid chromatography - high resolution mass spectrometry (LC-HRMS) analysis. Degradation rate constants for zidovudine with ozone in the presence of t-BuOH as radical scavenger varied between 2.8 ∙ 104 M-1 s-1 (pH 7) and 3.2 ∙ 104 M-1 s-1 (pH 3). The structural difference of zidovudine to thymidine is the exchange of the OH-moiety by the azide function at position 3'. In contrast to inorganic azide, no reaction with ozone was observed for the organic bound azide. In total, nine transformation products (TPs) were identified for both zidovudine and thymidine. Their formation can be attributed to the attack of ozone at the C-C-double bond of the pyrimidine-base. As a result of rearrangements, the primary ozonide decomposed in three pathways forming two different TPs, including hydroperoxide TPs. Rearrangement reactions followed by hydrolysis and subsequent release of H2O2 further revealed a cascade of TPs containing amide moieties. In addition, a formyl amide riboside and a urea riboside were identified as TPs indicating that oxidations of amide groups occur during ozonation processes.
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Affiliation(s)
- Jan Funke
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068, Koblenz, Germany
| | - Carsten Prasse
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068, Koblenz, Germany
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Christian Dietrich
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068, Koblenz, Germany
| | - Thomas A. Ternes
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068, Koblenz, Germany
- Corresponding author.
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16
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Phelps JS, Hildebrand DGC, Graham BJ, Kuan AT, Thomas LA, Nguyen TM, Buhmann J, Azevedo AW, Sustar A, Agrawal S, Liu M, Shanny BL, Funke J, Tuthill JC, Lee WCA. Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy. Cell 2021; 184:759-774.e18. [PMID: 33400916 PMCID: PMC8312698 DOI: 10.1016/j.cell.2020.12.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 02/08/2023]
Abstract
To investigate circuit mechanisms underlying locomotor behavior, we used serial-section electron microscopy (EM) to acquire a synapse-resolution dataset containing the ventral nerve cord (VNC) of an adult female Drosophila melanogaster. To generate this dataset, we developed GridTape, a technology that combines automated serial-section collection with automated high-throughput transmission EM. Using this dataset, we studied neuronal networks that control leg and wing movements by reconstructing all 507 motor neurons that control the limbs. We show that a specific class of leg sensory neurons synapses directly onto motor neurons with the largest-caliber axons on both sides of the body, representing a unique pathway for fast limb control. We provide open access to the dataset and reconstructions registered to a standard atlas to permit matching of cells between EM and light microscopy data. We also provide GridTape instrumentation designs and software to make large-scale EM more accessible and affordable to the scientific community.
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Affiliation(s)
- Jasper S Phelps
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA; Program in Neuroscience, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - David Grant Colburn Hildebrand
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA; Program in Neuroscience, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Brett J Graham
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron T Kuan
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Logan A Thomas
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Tri M Nguyen
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Julia Buhmann
- HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Anthony W Azevedo
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Anne Sustar
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Sweta Agrawal
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Mingguan Liu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan L Shanny
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jan Funke
- HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - John C Tuthill
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Wei-Chung Allen Lee
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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17
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Kuan AT, Phelps JS, Thomas LA, Nguyen TM, Han J, Chen CL, Azevedo AW, Tuthill JC, Funke J, Cloetens P, Pacureanu A, Lee WCA. Dense neuronal reconstruction through X-ray holographic nano-tomography. Nat Neurosci 2020; 23:1637-1643. [PMID: 32929244 PMCID: PMC8354006 DOI: 10.1038/s41593-020-0704-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/05/2020] [Indexed: 12/21/2022]
Abstract
Imaging neuronal networks provides a foundation for understanding the nervous system, but resolving dense nanometer-scale structures over large volumes remains challenging for light microscopy (LM) and electron microscopy (EM). Here we show that X-ray holographic nano-tomography (XNH) can image millimeter-scale volumes with sub-100-nm resolution, enabling reconstruction of dense wiring in Drosophila melanogaster and mouse nervous tissue. We performed correlative XNH and EM to reconstruct hundreds of cortical pyramidal cells and show that more superficial cells receive stronger synaptic inhibition on their apical dendrites. By combining multiple XNH scans, we imaged an adult Drosophila leg with sufficient resolution to comprehensively catalog mechanosensory neurons and trace individual motor axons from muscles to the central nervous system. To accelerate neuronal reconstructions, we trained a convolutional neural network to automatically segment neurons from XNH volumes. Thus, XNH bridges a key gap between LM and EM, providing a new avenue for neural circuit discovery.
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Affiliation(s)
- Aaron T Kuan
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Jasper S Phelps
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Program in Neuroscience, Harvard University, Boston, MA, USA
| | - Logan A Thomas
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Tri M Nguyen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Julie Han
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Chiao-Lin Chen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Anthony W Azevedo
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - John C Tuthill
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Jan Funke
- HHMI Janelia Research Campus, Ashburn, VA, USA
| | | | - Alexandra Pacureanu
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
- ESRF, The European Synchrotron, Grenoble, France.
| | - Wei-Chung Allen Lee
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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18
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Menschner A, Bloch H, Hensel S, Funke J. Lösungsansatz für das modulare, zustandsgesteuerte Labor und Technikum. CHEM-ING-TECH 2020. [DOI: 10.1002/cite.202055349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anna Menschner
- Semodia GmbH c/o TU Dresden Helmholtzstr. 10 01069 Dresden Deutschland
| | - Henry Bloch
- Semodia GmbH c/o TU Dresden Helmholtzstr. 10 01069 Dresden Deutschland
| | - Stephan Hensel
- Semodia GmbH c/o TU Dresden Helmholtzstr. 10 01069 Dresden Deutschland
| | - Jan Funke
- Semodia GmbH c/o TU Dresden Helmholtzstr. 10 01069 Dresden Deutschland
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19
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Funke J, Tschopp F, Grisaitis W, Sheridan A, Singh C, Saalfeld S, Turaga SC. Large Scale Image Segmentation with Structured Loss Based Deep Learning for Connectome Reconstruction. IEEE Trans Pattern Anal Mach Intell 2019; 41:1669-1680. [PMID: 29993708 DOI: 10.1109/tpami.2018.2835450] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present a method combining affinity prediction with region agglomeration, which improves significantly upon the state of the art of neuron segmentation from electron microscopy (EM) in accuracy and scalability. Our method consists of a 3D U-Net, trained to predict affinities between voxels, followed by iterative region agglomeration. We train using a structured loss based on Malis, encouraging topologically correct segmentations obtained from affinity thresholding. Our extension consists of two parts: First, we present a quasi-linear method to compute the loss gradient, improving over the original quadratic algorithm. Second, we compute the gradient in two separate passes to avoid spurious gradient contributions in early training stages. Our predictions are accurate enough that simple learning-free percentile-based agglomeration outperforms more involved methods used earlier on inferior predictions. We present results on three diverse EM datasets, achieving relative improvements over previous results of 27, 15, and 250 percent. Our findings suggest that a single method can be applied to both nearly isotropic block-face EM data and anisotropic serial sectioned EM data. The runtime of our method scales linearly with the size of the volume and achieves a throughput of $\sim$∼ 2.6 seconds per megavoxel, qualifying our method for the processing of very large datasets.
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20
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Abbas A, Schneider I, Bollmann A, Funke J, Oehlmann J, Prasse C, Schulte-Oehlmann U, Seitz W, Ternes T, Weber M, Wesely H, Wagner M. What you extract is what you see: Optimising the preparation of water and wastewater samples for in vitro bioassays. Water Res 2019; 152:47-60. [PMID: 30660097 DOI: 10.1016/j.watres.2018.12.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 05/25/2023]
Abstract
The assessment of water quality is crucial for safeguarding drinking water resources and ecosystem integrity. To this end, sample preparation and extraction is critically important, especially when investigating emerging contaminants and the toxicity of water samples. As extraction methods are rarely optimised for bioassays but rather adopted from chemical analysis, this may result in a misrepresentation of the actual toxicity. In this study, surface water, groundwater, hospital and municipal wastewater were used to characterise the impacts of common sample preparation techniques (acidification, filtration and solid phase extraction (SPE)) on the outcomes of eleven in vitro bioassays. The latter covered endocrine activity (reporter gene assays for estrogen, androgen, aryl-hydrocarbon, retinoic acid, retinoid X, vitamin D, thyroid receptor), mutagenicity (Ames fluctuation test), genotoxicity (umu test) and cytotoxicity. Water samples extracted using different SPE sorbents (Oasis HLB, Supelco ENVI-Carb+, Telos C18/ENV) at acidic and neutral pH were compared for their performance in recovering biological effects. Acidification, commonly used for stabilisation, significantly altered the endocrine activity and toxicity of most (waste)water samples. Sample filtration did not affect the majority of endpoints but in certain cases affected the (anti-)estrogenic and dioxin-like activities. SPE extracts (10.4 × final concentration), including WWTP effluents, induced significant endocrine effects that were not detected in aqueous samples (0.63 × final concentration), such as estrogenic, (anti-)androgenic and dioxin-like activities. When ranking the SPE methods using multivariate Pareto optimisation an extraction with Telos C18/ENV at pH 7 was most effective in recovering toxicity. At the same time, these extracts were highly cytotoxic masking the endpoint under investigation. Compared to that, extraction at pH 2.5 enriched less cytotoxicity. In summary, our study demonstrates that sample preparation and extraction critically affect the outcome of bioassays when assessing the toxicity of water samples. Depending on the water matrix and the bioassay, these methods need to be optimised to accurately assess water quality.
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Affiliation(s)
- Aennes Abbas
- Department Aquatic Ecotoxicology, Goethe University Frankfurt am Main, Max-von-Laue-Str. 13, D-60438, Frankfurt, Germany.
| | - Ilona Schneider
- Department Aquatic Ecotoxicology, Goethe University Frankfurt am Main, Max-von-Laue-Str. 13, D-60438, Frankfurt, Germany.
| | - Anna Bollmann
- Zweckverband Landeswasserversorgung, Am Spitzigen Berg 1, D-89129, Langenau, Germany
| | - Jan Funke
- IWW Rheinisch-Westfälisches Institut für Wasser Beratungs- und Entwicklungsgesellschaft mbH, Moritzstraße 26, D-45476, Muelheim an der Ruhr, Germany
| | - Jörg Oehlmann
- Department Aquatic Ecotoxicology, Goethe University Frankfurt am Main, Max-von-Laue-Str. 13, D-60438, Frankfurt, Germany
| | - Carsten Prasse
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ulrike Schulte-Oehlmann
- Department Aquatic Ecotoxicology, Goethe University Frankfurt am Main, Max-von-Laue-Str. 13, D-60438, Frankfurt, Germany
| | - Wolfram Seitz
- Zweckverband Landeswasserversorgung, Am Spitzigen Berg 1, D-89129, Langenau, Germany
| | - Thomas Ternes
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, D-56068, Koblenz, Germany
| | - Marcus Weber
- Department of Numerical Analysis and Modelling, Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB), Takustraße 7, D-14195, Berlin, Germany
| | - Henning Wesely
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, D-56068, Koblenz, Germany
| | - Martin Wagner
- Department Aquatic Ecotoxicology, Goethe University Frankfurt am Main, Max-von-Laue-Str. 13, D-60438, Frankfurt, Germany; Department of Biology, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
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21
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Abstract
Automatic image segmentation is critical to scale up electron microscope (EM) connectome reconstruction. To this end, segmentation competitions, such as CREMI and SNEMI, exist to help researchers evaluate segmentation algorithms with the goal of improving them. Because generating ground truth is time-consuming, these competitions often fail to capture the challenges in segmenting larger datasets required in connectomics. More generally, the common metrics for EM image segmentation do not emphasize impact on downstream analysis and are often not very useful for isolating problem areas in the segmentation. For example, they do not capture connectivity information and often over-rate the quality of a segmentation as we demonstrate later. To address these issues, we introduce a novel strategy to enable evaluation of segmentation at large scales both in a supervised setting, where ground truth is available, or an unsupervised setting. To achieve this, we first introduce new metrics more closely aligned with the use of segmentation in downstream analysis and reconstruction. In particular, these include synapse connectivity and completeness metrics that provide both meaningful and intuitive interpretations of segmentation quality as it relates to the preservation of neuron connectivity. Also, we propose measures of segmentation correctness and completeness with respect to the percentage of "orphan" fragments and the concentrations of self-loops formed by segmentation failures, which are helpful in analysis and can be computed without ground truth. The introduction of new metrics intended to be used for practical applications involving large datasets necessitates a scalable software ecosystem, which is a critical contribution of this paper. To this end, we introduce a scalable, flexible software framework that enables integration of several different metrics and provides mechanisms to evaluate and debug differences between segmentations. We also introduce visualization software to help users to consume the various metrics collected. We evaluate our framework on two relatively large public groundtruth datasets providing novel insights on example segmentations.
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Heinrich L, Funke J, Pape C, Nunez-Iglesias J, Saalfeld S. Synaptic Cleft Segmentation in Non-isotropic Volume Electron Microscopy of the Complete Drosophila Brain. Medical Image Computing and Computer Assisted Intervention – MICCAI 2018 2018. [DOI: 10.1007/978-3-030-00934-2_36] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Funke J, Klein J, Moreno-Noguer F, Cardona A, Cook M. TED: A Tolerant Edit Distance for segmentation evaluation. Methods 2017; 115:119-127. [PMID: 28108198 DOI: 10.1016/j.ymeth.2016.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/29/2016] [Accepted: 12/30/2016] [Indexed: 11/15/2022] Open
Abstract
In this paper, we present a novel error measure to compare a computer-generated segmentation of images or volumes against ground truth. This measure, which we call Tolerant Edit Distance (TED), is motivated by two observations that we usually encounter in biomedical image processing: (1) Some errors, like small boundary shifts, are tolerable in practice. Which errors are tolerable is application dependent and should be explicitly expressible in the measure. (2) Non-tolerable errors have to be corrected manually. The effort needed to do so should be reflected by the error measure. Our measure is the minimal weighted sum of split and merge operations to apply to one segmentation such that it resembles another segmentation within specified tolerance bounds. This is in contrast to other commonly used measures like Rand index or variation of information, which integrate small, but tolerable, differences. Additionally, the TED provides intuitive numbers and allows the localization and classification of errors in images or volumes. We demonstrate the applicability of the TED on 3D segmentations of neurons in electron microscopy images where topological correctness is arguable more important than exact boundary locations. Furthermore, we show that the TED is not just limited to evaluation tasks. We use it as the loss function in a max-margin learning framework to find parameters of an automatic neuron segmentation algorithm. We show that training to minimize the TED, i.e., to minimize crucial errors, leads to higher segmentation accuracy compared to other learning methods.
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Affiliation(s)
- Jan Funke
- Institut de Robòtica i Informàtica Industrial, UPC/CSIC, Barcelona, Spain; Janelia Research Campus, VA, Ashburn, United States; Institute of Neuroinformatics, UZH/ETH, Zurich, Switzerland.
| | - Jonas Klein
- Institute of Neuroinformatics, UZH/ETH, Zurich, Switzerland.
| | | | | | - Matthew Cook
- Institute of Neuroinformatics, UZH/ETH, Zurich, Switzerland.
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24
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Funke J, Prasse C, Ternes TA. Identification of transformation products of antiviral drugs formed during biological wastewater treatment and their occurrence in the urban water cycle. Water Res 2016; 98:75-83. [PMID: 27082694 DOI: 10.1016/j.watres.2016.03.045] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 05/21/2023]
Abstract
The fate of five antiviral drugs (abacavir, emtricitabine, ganciclovir, lamivudine and zidovudine) was investigated in biological wastewater treatment. Investigations of degradation kinetics were accompanied by the elucidation of formed transformation products (TPs) using activated sludge lab experiments and subsequent LC-HRMS analysis. Degradation rate constants ranged between 0.46 L d(-1) gSS(-1) (zidovudine) and 55.8 L d(-1) gSS(-1) (abacavir). Despite these differences of the degradation kinetics, the same main biotransformation reaction was observed for all five compounds: oxidation of the terminal hydroxyl-moiety to the corresponding carboxylic acid (formation of carboxy-TPs). In addition, the oxidation of thioether moieties to sulfoxides was observed for emtricitabine and lamivudine. Antiviral drugs were detected in influents of municipal wastewater treatment plants (WWTPs) with concentrations up to 980 ng L(-1) (emtricitabine), while in WWTP effluents mainly the TPs were found with concentration levels up to 1320 ng L(-1) (carboxy-abacavir). Except of zidovudine none of the original antiviral drugs were detected in German rivers and streams, whereas the concentrations of the TPs ranged from 16 ng L(-1) for carboxy-lamivudine up to 750 ng L(-1) for carboxy-acyclovir. These concentrations indicate an appreciable portion from WWTP effluents present in rivers and streams, as well as the high environmental persistence of the carboxy-TPs. As a result three of the carboxylic TPs were detected in finished drinking water.
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Affiliation(s)
- Jan Funke
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Carsten Prasse
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany; Department of Civil & Environmental Engineering of California at Berkeley, Berkeley, CA 94720, United States
| | - Thomas A Ternes
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany.
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25
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Jung E, Funke J. Kosmetik im Wandel der Jahrtausende. Akt Dermatol 2015. [DOI: 10.1055/s-0034-1391962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - J. Funke
- Psychologisches Institut der Universität Heidelberg
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26
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Funke J, Prasse C, Lütke Eversloh C, Ternes TA. Oxypurinol - A novel marker for wastewater contamination of the aquatic environment. Water Res 2015; 74:257-265. [PMID: 25753675 DOI: 10.1016/j.watres.2015.02.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 06/04/2023]
Abstract
The anti-gout agent allopurinol is one of the most prescribed pharmaceuticals in Germany and is widely metabolized into oxypurinol (80%) as well as the corresponding riboside conjugates (10%) within the human body. To investigate the occurrence of allopurinol and oxypurinol in the urban water cycle an analytical method was developed based on solid phase extraction (SPE) and subsequent liquid chromatography electrospray-ionization tandem mass spectrometry (LC-MS/MS). In raw wastewater concentration levels of oxypurinol ranged up to 26.6 μg L(-1), whereas allopurinol was not detected at all. In wastewater treatment plant (WWTP) effluents, concentrations of allopurinol were <LOQ, whereas oxypurinol concentrations ranged from 2.3 μg L(-1) to 21.7 μg L(-1). Elevated concentrations of oxypurinol in biologically treated wastewater originate from the transformation of allopurinol as well as the cleavage of allopurinol-9-riboside, which was confirmed by laboratory experiments with activated sludge taken from a municipal WWTP. Further tracking of oxypurinol in the urban water cycle revealed its presence in rivers and streams (up to 22.6 μg L(-1)), groundwater (up to 0.38 μg L(-1)) as well as in finished drinking water (up to 0.30 μg L(-1)). Due to the high biological stability and the almost ubiquitous presence in the urban water cycle at elevated concentrations, oxypurinol might be used as marker for domestic wastewater in the environment. This was confirmed by correlation analysis to other wastewater markers with strong correlations of the concentrations of oxypurinol and carbamazepine (r(2) = 0.89) as well as of oxypurinol and primidone (r(2) = 0.82).
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Affiliation(s)
- Jan Funke
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Carsten Prasse
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | | | - Thomas A Ternes
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany.
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27
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Vilz TO, Funke J, Pantelis D, Lingohr P, Wolff M, Kalff JC, Schäfer N. [Surgical Therapy and Prognostic Factors for Carcinoma of Vater's Papilla]. Zentralbl Chir 2015; 141:263-9. [PMID: 25906020 DOI: 10.1055/s-0034-1383412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Carcinoma of ampulla of Vater are rare tumours of the GI-tract with an improved prognosis compared to other periampullary tumours. Analysis of survival and prognostic factors are limited due to the low incidence of the carcinoma. The intention of this study in patients with papillary carcinoma was to evaluate short- and long-term survival and to identify prognostic factors for pancreatectomy and reconstruction using pancreatogastrostomy as treatment of carcinoma of Vater's ampulla. PATIENTS AND METHODS Between 1989 and 2008 76 patients with a carcinoma of the ampulla of Vater were treated by oncological resection followed by pancreatogastrostomy. Various factors such as demographics, perioperative factors, histopathological findings as well as short- and long-term survival were evaluated retrospectively. Data were analysed statistically using Kaplan-Meier estimates of survival with log-rank test and uni- and multivariate analysis with Cox regression. RESULTS The overall 5-year survival was 46 %, the 10-year survival 26 % for resected patients. By univariate analysis we could demonstrate that lymph node metastasis is the only predictor for outcome. In the multivariate analysis, age, sex, grading and especially lymph node status were a significant predictor for the survival of patients. CONCLUSION In the current patient cohort lymph node status was the most important independent predictor of outcome after resection of carcinoma of Vater's papilla.
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Affiliation(s)
- T O Vilz
- Klinik und Poliklinik für Allgemein-, Viszeral-, Thorax- und Gefäßchirurgie, Universitätsklinikum Bonn, Deutschland
| | - J Funke
- Klinik und Poliklinik für Allgemein-, Viszeral-, Thorax- und Gefäßchirurgie, Universitätsklinikum Bonn, Deutschland
| | - D Pantelis
- Klinik und Poliklinik für Allgemein-, Viszeral-, Thorax- und Gefäßchirurgie, Universitätsklinikum Bonn, Deutschland
| | - P Lingohr
- Klinik und Poliklinik für Allgemein-, Viszeral-, Thorax- und Gefäßchirurgie, Universitätsklinikum Bonn, Deutschland
| | - M Wolff
- Abteilung für Allgemein- und Viszeralchirurgie, St. Elisabeth-Krankenhaus Mayen, Deutschland
| | - J C Kalff
- Klinik und Poliklinik für Allgemein-, Viszeral-, Thorax- und Gefäßchirurgie, Universitätsklinikum Bonn, Deutschland
| | - N Schäfer
- Klinik und Poliklinik für Allgemein-, Viszeral-, Thorax- und Gefäßchirurgie, Universitätsklinikum Bonn, Deutschland
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28
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Degen C, Kettner SE, Fischer H, Lohse J, Funke J, Schwieren C, Goeschl T, Schröder J. Comprehension of climate change and environmental attitudes across the lifespan. Z Gerontol Geriatr 2014; 47:490-4. [PMID: 25119704 DOI: 10.1007/s00391-014-0675-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Given the coincidence of the demographic change and climate change in the upcoming decades the aging voter gains increasing importance in climate change mitigation and adaptation processes. It is generally assumed that information status and comprehension of complex processes underlying climate change are prerequisites for adopting pro-environmental attitudes and taking pro-environmental actions. In a cross-sectional study, we investigated in how far (1) environmental knowledge and comprehension of feedback processes underlying climate change and (2) pro-environmental attitudes change as a function of age. Our sample consisted of 92 participants aged 25-75 years (mean age 49.4 years, SD 17.0). Age was negatively related to comprehension of system structures inherent to climate change, but positively associated with level of fear of consequences and anxiousness towards climate change. No significant relations were found between environmental knowledge and pro-environmental attitude. These results indicate that, albeit understanding of relevant structures of the climate system is less present in older age, age is not a limiting factor for being engaged in the complex dilemma of climate change. Results bear implications for the communication of climate change and pro-environmental actions in aging societies.
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Affiliation(s)
- C Degen
- Universitätsklinikum Heidelberg, Voßstr. 4, 69115, Heidelberg, Germany,
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Funke J, Böttjer J, Stadler R. Schleimhautmelanome des weiblichen äußeren Genitaltrakts. Akt Dermatol 2004. [DOI: 10.1055/s-2004-835556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Funke J, Böttjer J, Stadler R. Der unbekannte Primarius bei metastasiertem malignen Melanom ist nicht selten „bekannt“. Akt Dermatol 2004. [DOI: 10.1055/s-2004-832548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Ebel H, Semmelmann G, Schomäcker K, Balogh A, Volz M, Funke J, Schicha H, Klug N. Effects of high cervical spinal cord stimulation (CSCS) on regional cerebral blood flow after induced subarachnoid haemorrhage in rats. Acta Neurochir Suppl 2002; 77:225-7. [PMID: 11563293 DOI: 10.1007/978-3-7091-6232-3_48] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- H Ebel
- Department of Neurosurgery, University of Cologne, Germany
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Ebel H, Schomäcker K, Balogh A, Volz M, Funke J, Schicha H, Klug N. High cervical spinal cord stimulation (CSCS) increases regional cerebral blood flow after induced subarachnoid haemorrhage in rats. Minim Invasive Neurosurg 2001; 44:167-71. [PMID: 11696887 DOI: 10.1055/s-2001-18149] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The effects of high cervical spinal cord stimulation (cSCS) on regional cerebral blood flow (rCBF) were investigated after experimentally induced subarachnoid haemorrhage (SAH) in rats by the means of (99m)Tc-HMPAO. The experiments were carried out on a total of 24 Wistar rats, divided in three groups [group I: control without SAH, group II: SAH, group III: SAH and cSCS]. (99m)Tc-HMPAO was administered intravenously (group II/group III) 48 hours after induction of SAH. In group III, (99m)Tc-HMPAO was given after 3 hours of cSCS. All animals were sacrificed 30 minutes after application on (99m)Tc-HMPAO. Radioactivities were determined in blood, cerebrum and cerebellum. The ratio cerebrum/blood and cerebellum/blood was calculated to ascertain "extraction rate" in the sample differentially. The following mean values were calculated for the cerebellum/blood ratio: Group I: 1.06, SD: 0.21; Group II: 0.66, SD: 0.21; Group III: 1.00, SD: 0.37. Comparing the mean values a highly significant difference could be found between group II and III (p = 0.007) and between group I and II (p = 0.0019), respectively. Calculations of the cerebrum/blood ratio revealed similar results. After SAH cSCS enhances cerebral and cerebellar blood flow in rats. Possibly, cSCD constitutes a new therapeutic approach in the treatment of disturbed regional cerebral blood flow after SAH.
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Affiliation(s)
- H Ebel
- Department of Neurosurgery, University of Cologne, Germany.
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Buchner A, Funke J, Berry DC. Negative correlations between control performance and verbalizable knowledge: indicators for implicit learning in process control tasks? Q J Exp Psychol A 1995; 48:166-87. [PMID: 7754081 DOI: 10.1080/14640749508401383] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Negative correlations between task performance in dynamic control tasks and verbalizable knowledge, as assessed by a post-task questionnaire, have been interpreted as dissociations that indicate two antagonistic modes of learning, one being "explicit", the other "implicit". This paper views the control tasks as finite-state automata and offers an alternative interpretation of these negative correlations. It is argued that "good controllers" observe fewer different state transitions and, consequently, can answer fewer post-task questions about system transitions than can "bad controllers". Two experiments demonstrate the validity of the argument by showing the predicted negative relationship between control performance and the number of explored state transitions, and the predicted positive relationship between the number of explored state transitions and questionnaire scores. However, the experiments also elucidate important boundary conditions for the critical effects. We discuss the implications of these findings, and of other problems arising from the process control paradigm, for conclusions about implicit versus explicit learning processes.
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Affiliation(s)
- A Buchner
- University of Trier, Federal Republic of Germany
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Stangl MJ, Lee KK, Funke J, Schraut WH. Labelling of class II positive dendritic cells by ex vivo perfusion of murine small bowel grafts prior to transplantation. Transplant Proc 1990; 22:2062-3. [PMID: 2143874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- M J Stangl
- Department of Surgery, University Health Center of Pittsburgh, Pennsylvania
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Abstract
Early assessment, detection, and therapeutic intervention in maladaptive maternal behavior can be facilitated by a simple nursing appraisal instrument employed initially on the third postpartum day. The Funke-Irby Interactional Assessment not only discriminates between early adaptive and maladaptive maternal behaviors, but it also illustrates a mother's progress or lack of progress toward adaptive mothering, making the instrument useful to the community health nurse during the early postdelivery weeks. This instrument has been effectively used as a screening device for nurses making decisions about the need for further referral for family therapy.
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Funke J, Niskala H, Field PA. [A slide-tape presentation]. Infirm Can 1975; 17:17. [PMID: 54341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Funke J, Niskala H, Field PA. Slide-tape helps recruitment. Can Nurse 1975; 71:27. [PMID: 53096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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