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2689 Janelia Publications

Showing 611-620 of 2689 results
Gonen Lab
12/27/17 | Common fibrillar spines of amyloid-β and human Islet Amyloid Polypeptide revealed by Micro Electron Diffraction and inhibitors developed using structure-based design.
Krotee P, Griner SL, Sawaya MR, Cascio D, Rodriguez JA, Shi D, Philipp S, Murray K, Saelices L, Lee J, Seidler P, Glabe CG, Jiang L, Gonen T, Eisenberg DS
The Journal of Biological Chemistry. 2017 Dec 27;293(8):2888-902. doi: 10.1074/jbc.M117.806109

Amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP) aggregate to form amyloid fibrils that deposit in tissues, and are associated with Alzheimer's disease (AD) and Type-II Diabetes (T2D), respectively. Individuals with T2D have an increased risk of developing AD, and conversely, AD patients have an increased risk of developing T2D. Evidence suggests that this link between AD and T2D might originate from a structural similarity between aggregates of Aβ and hIAPP. Using the cryoEM method Micro-Electron Diffraction (MicroED) we determined the atomic structures of 11-residue segments from both Aβ and hIAPP, termed Aβ 24-34 WT and hIAPP 19-29 S20G, with 64% sequence similarity. We observe a high degree of structural similarity between their backbone atoms (0.96 Å RMSD). Moreover, fibrils of these segments induce amyloid formation through self- and cross-seeding. Furthermore, inhibitors designed for one segment show cross-efficacy for full-length Aβ and hIAPP and reduce cytotoxicity of both proteins, though by apparently blocking different cytotoxic mechanisms. The similarity of the atomic structures of Aβ 24-34 WT and hIAPP 19-29 S20G offers a molecular model for cross-seeding between Aβ and hIAPP.

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09/19/18 | Communication from learned to innate olfactory processing centers is required for memory retrieval in Drosophila.
Dolan M, Belliart-Guérin G, Bates AS, Frechter S, Lampin-Saint-Amaux A, Aso Y, Roberts RJ, Schlegel P, Wong A, Hammad A, Bock D, Rubin GM, Preat T, Placais P, Jefferis GS
Neuron. 2018 Sep 19;100(3):651-68. doi: 10.1016/j.neuron.2018.08.037

The behavioral response to a sensory stimulus may depend on both learned and innate neuronal representations. How these circuits interact to produce appropriate behavior is unknown. In Drosophila, the lateral horn (LH) and mushroom body (MB) are thought to mediate innate and learned olfactory behavior, respectively, although LH function has not been tested directly. Here we identify two LH cell types (PD2a1 and PD2b1) that receive input from an MB output neuron required for recall of aversive olfactory memories. These neurons are required for aversive memory retrieval and modulated by training. Connectomics data demonstrate that PD2a1 and PD2b1 neurons also receive direct input from food odor-encoding neurons. Consistent with this, PD2a1 and PD2b1 are also necessary for unlearned attraction to some odors, indicating that these neurons have a dual behavioral role. This provides a circuit mechanism by which learned and innate olfactory information can interact in identified neurons to produce appropriate behavior.

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05/21/18 | Community-based benchmarking improves spike inference from two-photon calcium imaging data.
Berens P, Freeman J, Deneux T, Chenkov N, McColgan T, Speiser A, Macke JH, Turaga SC, Mineault P, Rupprecht P, Gerhard S, Friedrich RW, Friedrich J, Paninski L, Pachitariu M, Harris KD, Bolte B, Machado TA, Ringach D, etal
PLoS Computational Biology. 2018 May 21;14(5):e1006157. doi: 10.1371/journal.pcbi.1006157

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.

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04/21/21 | Community-based benchmarking improves spike rate inference from two-photon calcium imaging data
Berens P, Freeman J, Deneux T, Chenkov N, McColgan T, Speiser A, Macke JH, Turaga SC, Mineault P, Rupprecht P, Gerhard S, Friedrich RW, Friedrich J, Paninski L, Pachitariu M, Harris KD, Bolte B, Machado TA, Ringach D, Stone J, Rogerson LE, Sofroniew NJ, Reimer J, Froudarakis E, Euler T, Román Rosón M, Theis L, Tolias AS, Bethge M, Bush D
PLOS Computational Biology. Sep-05-2019;14(5):e1006157. doi: 10.1371/journal.pcbi.1006157

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.

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Card Lab
10/03/16 | Comparative approaches to escape.
Peek MY, Card GM
Current Opinion in Neurobiology. 2016 Oct 3;41:167-173. doi: 10.1016/j.conb.2016.09.012

Neural circuits mediating visually evoked escape behaviors are promising systems in which to dissect the neural basis of behavior. Behavioral responses to predator-like looming stimuli, and their underlying neural computations, are remarkably similar across species. Recently, genetic tools have been applied in this classical paradigm, revealing novel non-cortical pathways that connect loom processing to defensive behaviors in mammals and demonstrating that loom encoding models from locusts also fit vertebrate neural responses. In both invertebrates and vertebrates, relative spike-timing in descending pathways is a mechanism for escape behavior choice. Current findings suggest that experimentally tractable systems, such as Drosophila, may be applicable models for sensorimotor processing and persistent states in higher organisms.

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05/31/23 | Comparative connectomics and escape behavior in larvae of closely related Drosophila species.
Zhu J, Boivin J, Pang S, Xu CS, Lu Z, Saalfeld S, Hess HF, Ohyama T
Current Biology. 2023 May 31:. doi: 10.1016/j.cub.2023.05.043

Evolution has generated an enormous variety of morphological, physiological, and behavioral traits in animals. How do behaviors evolve in different directions in species equipped with similar neurons and molecular components? Here we adopted a comparative approach to investigate the similarities and differences of escape behaviors in response to noxious stimuli and their underlying neural circuits between closely related drosophilid species. Drosophilids show a wide range of escape behaviors in response to noxious cues, including escape crawling, stopping, head casting, and rolling. Here we find that D. santomea, compared with its close relative D. melanogaster, shows a higher probability of rolling in response to noxious stimulation. To assess whether this behavioral difference could be attributed to differences in neural circuitry, we generated focused ion beam-scanning electron microscope volumes of the ventral nerve cord of D. santomea to reconstruct the downstream partners of mdIV, a nociceptive sensory neuron in D. melanogaster. Along with partner interneurons of mdVI (including Basin-2, a multisensory integration neuron necessary for rolling) previously identified in D. melanogaster, we identified two additional partners of mdVI in D. santomea. Finally, we showed that joint activation of one of the partners (Basin-1) and a common partner (Basin-2) in D. melanogaster increased rolling probability, suggesting that the high rolling probability in D. santomea is mediated by the additional activation of Basin-1 by mdIV. These results provide a plausible mechanistic explanation for how closely related species exhibit quantitative differences in the likelihood of expressing the same behavior.

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Card Lab
04/30/25 | Comparative connectomics of Drosophila descending and ascending neurons.
Stürner T, Brooks P, Serratosa Capdevila L, Morris BJ, Javier A, Fang S, Gkantia M, Cachero S, Beckett IR, Marin EC, Schlegel P, Champion AS, Moitra I, Richards A, Klemm F, Kugel L, Namiki S, Cheong HS, Kovalyak J, Tenshaw E, Parekh R, Phelps JS, Mark B, Dorkenwald S, Bates AS, Matsliah A, Yu S, McKellar CE, Sterling A, Seung HS, Murthy M, Tuthill JC, Lee WA, Card GM, Costa M, Jefferis GS, Eichler K
Nature. 2025 Apr 30:. doi: 10.1038/s41586-025-08925-z

In most complex nervous systems there is a clear anatomical separation between the nerve cord, which contains most of the final motor outputs necessary for behaviour, and the brain. In insects, the neck connective is both a physical and an information bottleneck connecting the brain and the ventral nerve cord (an analogue of the spinal cord) and comprises diverse populations of descending neurons (DNs), ascending neurons (ANs) and sensory ascending neurons, which are crucial for sensorimotor signalling and control. Here, by integrating three separate electron microscopy (EM) datasets, we provide a complete connectomic description of the ANs and DNs of the Drosophila female nervous system and compare them with neurons of the male nerve cord. Proofread neuronal reconstructions are matched across hemispheres, datasets and sexes. Crucially, we also match 51% of DN cell types to light-level data defining specific driver lines, as well as classifying all ascending populations. We use these results to reveal the anatomical and circuit logic of neck connective neurons. We observe connected chains of DNs and ANs spanning the neck, which may subserve motor sequences. We provide a complete description of sexually dimorphic DN and AN populations, with detailed analyses of selected circuits for reproductive behaviours, including male courtship (DNa12; also known as aSP22) and song production (AN neurons from hemilineage 08B) and female ovipositor extrusion (DNp13). Our work provides EM-level circuit analyses that span the entire central nervous system of an adult animal.

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06/06/24 | Comparative connectomics of the descending and ascending neurons of the Drosophila nervous system: stereotypy and sexual dimorphism
Stürner T, Brooks P, Serratosa Capdevila L, Morris BJ, Javier A, Fang S, Gkantia M, Cachero S, Beckett IR, Champion AS, Moitra I, Richards A, Klemm F, Kugel L, Namiki S, Cheong HS, Kovalyak J, Tenshaw E, Parekh R, Schlegel P, Phelps JS, Mark B, Dorkenwald S, Bates AS, Matsliah A, Yu S, McKellar CE, Sterling A, Seung S, Murthy M, Tuthill J, Lee WA, Card GM, Costa M, Jefferis GS, Eichler K
bioRxiv. 2024 Jun 06:. doi: 10.1101/2024.06.04.596633

In most complex nervous systems there is a clear anatomical separation between the nerve cord, which contains most of the final motor outputs necessary for behaviour, and the brain. In insects, the neck connective is both a physical and information bottleneck connecting the brain and the ventral nerve cord (VNC, spinal cord analogue) and comprises diverse populations of descending (DN), ascending (AN) and sensory ascending neurons, which are crucial for sensorimotor signalling and control.Integrating three separate EM datasets, we now provide a complete connectomic description of the ascending and descending neurons of the female nervous system of Drosophila and compare them with neurons of the male nerve cord. Proofread neuronal reconstructions have been matched across hemispheres, datasets and sexes. Crucially, we have also matched 51% of DN cell types to light level data defining specific driver lines as well as classifying all ascending populations.We use these results to reveal the general architecture, tracts, neuropil innervation and connectivity of neck connective neurons. We observe connected chains of descending and ascending neurons spanning the neck, which may subserve motor sequences. We provide a complete description of sexually dimorphic DN and AN populations, with detailed analysis of circuits implicated in sex-related behaviours, including female ovipositor extrusion (DNp13), male courtship (DNa12/aSP22) and song production (AN hemilineage 08B). Our work represents the first EM-level circuit analyses spanning the entire central nervous system of an adult animal.

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Cardona LabZlatic Lab
01/06/21 | Comparative Connectomics Reveals How Partner Identity, Location, and Activity Specify Synaptic Connectivity in Drosophila.
Valdes-Aleman J, Fetter RD, Sales EC, Heckman EL, Venkatasubramanian L, Doe CQ, Landgraf M, Cardona A, Zlatic M
Neuron. 2021 Jan 06;109(1):105-22. doi: 10.1016/j.neuron.2020.10.004

The mechanisms by which synaptic partners recognize each other and establish appropriate numbers of connections during embryonic development to form functional neural circuits are poorly understood. We combined electron microscopy reconstruction, functional imaging of neural activity, and behavioral experiments to elucidate the roles of (1) partner identity, (2) location, and (3) activity in circuit assembly in the embryonic nerve cord of Drosophila. We found that postsynaptic partners are able to find and connect to their presynaptic partners even when these have been shifted to ectopic locations or silenced. However, orderly positioning of axon terminals by positional cues and synaptic activity is required for appropriate numbers of connections between specific partners, for appropriate balance between excitatory and inhibitory connections, and for appropriate functional connectivity and behavior. Our study reveals with unprecedented resolution the fine connectivity effects of multiple factors that work together to control the assembly of neural circuits.

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Riddiford Lab
10/01/09 | Comparative endocrinology in the 21st century.
Denver RJ, Hopkins PM, McCormick SD, Propper CR, Riddiford L, Sower SA, Wingfield JC
Integrative and Comparative Biology. 2009 Oct;49(4):339-48. doi: 10.1093/icb/icp082

Hormones coordinate developmental, physiological, and behavioral processes within and between all living organisms. They orchestrate and shape organogenesis from early in development, regulate the acquisition, assimilation, and utilization of nutrients to support growth and metabolism, control gamete production and sexual behavior, mediate organismal responses to environmental change, and allow for communication of information between organisms. Genes that code for hormones; the enzymes that synthesize, metabolize, and transport hormones; and hormone receptors are important targets for natural selection, and variation in their expression and function is a major driving force for the evolution of morphology and life history. Hormones coordinate physiology and behavior of populations of organisms, and thus play key roles in determining the structure of populations, communities, and ecosystems. The field of endocrinology is concerned with the study of hormones and their actions. This field is rooted in the comparative study of hormones in diverse species, which has provided the foundation for the modern fields of evolutionary, environmental, and biomedical endocrinology. Comparative endocrinologists work at the cutting edge of the life sciences. They identify new hormones, hormone receptors and mechanisms of hormone action applicable to diverse species, including humans; study the impact of habitat destruction, pollution, and climatic change on populations of organisms; establish novel model systems for studying hormones and their functions; and develop new genetic strains and husbandry practices for efficient production of animal protein. While the model system approach has dominated biomedical research in recent years, and has provided extraordinary insight into many basic cellular and molecular processes, this approach is limited to investigating a small minority of organisms. Animals exhibit tremendous diversity in form and function, life-history strategies, and responses to the environment. A major challenge for life scientists in the 21st century is to understand how a changing environment impacts all life on earth. A full understanding of the capabilities of organisms to respond to environmental variation, and the resilience of organisms challenged by environmental changes and extremes, is necessary for understanding the impact of pollution and climatic change on the viability of populations. Comparative endocrinologists have a key role to play in these efforts.

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