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2798 Janelia Publications

Showing 2391-2400 of 2798 results
02/11/25 | Symposia Report of The Annual Biological Sciences Section Meeting of the Gerontological Society of America 2023, Tampa, Florida.
Rogina B, Anderson R, Lebrasseur N, Curan S, Yousefzadeh MJ, Ghosh B, Duque G, Howlett S, Austad S, Demuth I, Gerstorf D, Korfhage J, Lombard DB, Abadir P, Christensen K, Carey JR, Alberts SC, Campos F, Palavicini JP, Palmer A, Bell J, Basisty N, de Cabo R, Gomes A, Dixit VD, Sen P, Baur JA, Imai S, Li X, Valdez G, Orr ME, Pletcher S, Andersen J, Jones L, Castillo-Azofeida D, Bonaguidi M, Suh Y, Duncan FE, Murray A, Burkewitz K, Henne M, Zhou K, Bouhrara M, Benjamini D, Kolind S, Walker KA, Reiter DA, Dean Iii D, Gorbunova V, Gladyshev VN, Palovics R, Niedernhofer LJ, Fan R, Bueckle AD, Hurley J, Esser KA, Kapahi P, Sato S, Jiang N, Ashiqueali SA, Diaz J, Mishra SP, Ralmundo N, Banarjee R, Allsopp R, Reynolds LM, Zhang B, Sebastiani P, Monti S, Schork N, Rappaport N
J Gerontol A Biol Sci Med Sci. 2025 Feb 11:. doi: 10.1093/gerona/glaf026

The aging process is universal, and it is characterized by a progressive deterioration and decrease in physiological function leading to decline on the organismal level. Nevertheless, a number of genetic and non-genetic interventions have been described, which successfully extend healthspan and lifespan in different species. Furthermore, a number of clinical trials have been evaluating the feasibility of different interventions to promote human health. The goal of the annual Biological Sciences Section of the Gerontological Society of America meeting was to share current knowledge of different topics in aging research and provide a vision of the future of aging research. The meeting gathered international experts in diverse areas of aging research including basic biology, demography, and clinical and translational studies. Specific topics included metabolism, inflammaging, epigenetic clocks, frailty, senescence, neuroscience, stem cells, reproductive aging, inter-organelle crosstalk, comparative transcriptomics of longevity, circadian clock, metabolomics, and biodemography.

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10/16/25 | Synapse Detection Efficiency in EM <I>Drosophila</I> Connectomics
Scheffer LK
bioRxiv. 2025 Oct 16:. doi: 10.1101/2025.10.16.682869

Researchers have long noted the differences in synapse count between different EM reconstructions of similar circuitry. In this paper we attempt to determine the portion of these differences that may be due to different sample preparation and imaging techniques, in particular serial-section transmission imaging (SS-TEM) compared to focused ion beam with scanning electron microscopy (FIB-SEM). To do this, we compare synapse detection in the major Drosophila EM reconstructions - FANC, MANC, FAFB (with original and new synapses), male CNS, BANC, and HemiBrain, plus several smaller reconstructions. We look at raw synapse counts to avoid any dependence on proofreading, and compensate insofar as possible for the confounds of sample sizes differences and different software detection efficiency. The result are estimates, per compartment and for the sample as a whole, of the number of synapses that would be visible to a skilled human observer. These are then compared across all samples, using regions which are reconstructed in common for each sample pair. We find that in almost all known cases where a volume has been reconstructed by both techniques, isotropic FIB-SEM reconstructions show more human-visible synapses than microtome sliced reconstructions, typically by more than 40%. This strongly suggests, but does not conclusively prove, that synapses are easier to see in isotropic FIB-SEM data.

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Spruston LabMagee Lab
11/22/12 | Synaptic amplification by dendritic spines enhances input cooperativity.
Harnett MT, Makara JK, Spruston N, Kath WL, Magee JC
Nature. 2012 Nov 22;491(7425):599-602. doi: 10.1038/nature11554

Dendritic spines are the nearly ubiquitous site of excitatory synaptic input onto neurons and as such are critically positioned to influence diverse aspects of neuronal signalling. Decades of theoretical studies have proposed that spines may function as highly effective and modifiable chemical and electrical compartments that regulate synaptic efficacy, integration and plasticity. Experimental studies have confirmed activity-dependent structural dynamics and biochemical compartmentalization by spines. However, there is a longstanding debate over the influence of spines on the electrical aspects of synaptic transmission and dendritic operation. Here we measure the amplitude ratio of spine head to parent dendrite voltage across a range of dendritic compartments and calculate the associated spine neck resistance (R(neck)) for spines at apical trunk dendrites in rat hippocampal CA1 pyramidal neurons. We find that R(neck) is large enough ( 500 MΩ) to amplify substantially the spine head depolarization associated with a unitary synaptic input by  1.5- to  45-fold, depending on parent dendritic impedance. A morphologically realistic compartmental model capable of reproducing the observed spatial profile of the amplitude ratio indicates that spines provide a consistently high-impedance input structure throughout the dendritic arborization. Finally, we demonstrate that the amplification produced by spines encourages electrical interaction among coactive inputs through an R(neck)-dependent increase in spine head voltage-gated conductance activation. We conclude that the electrical properties of spines promote nonlinear dendritic processing and associated forms of plasticity and storage, thus fundamentally enhancing the computational capabilities of neurons.

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11/03/15 | Synaptic circuits and their variations within different columns in the visual system of Drosophila.
Takemura S, Xu CS, Lu Z, Rivlin PK, Parag T, Olbris DJ, Plaza S, Zhao T, Katz WT, Umayam L, Weaver C, Hess HF, Horne JA, Nunez-Iglesias J, Aniceto R, Chang L, Lauchie S, Nasca A, Ogundeyi O, Sigmund C, Takemura S, Tran J, Langille C, Le Lacheur K, McLin S, Shinomiya A, Chklovskii DB, Meinertzhagen IA, Scheffer LK
Proceedings of the National Academy of Sciences of the United States of America. 2015 Nov 3;112(44):13711-6. doi: 10.1073/pnas.1509820112

We reconstructed the synaptic circuits of seven columns in the second neuropil or medulla behind the fly's compound eye. These neurons embody some of the most stereotyped circuits in one of the most miniaturized of animal brains. The reconstructions allow us, for the first time to our knowledge, to study variations between circuits in the medulla's neighboring columns. This variation in the number of synapses and the types of their synaptic partners has previously been little addressed because methods that visualize multiple circuits have not resolved detailed connections, and existing connectomic studies, which can see such connections, have not so far examined multiple reconstructions of the same circuit. Here, we address the omission by comparing the circuits common to all seven columns to assess variation in their connection strengths and the resultant rates of several different and distinct types of connection error. Error rates reveal that, overall, <1% of contacts are not part of a consensus circuit, and we classify those contacts that supplement (E+) or are missing from it (E-). Autapses, in which the same cell is both presynaptic and postsynaptic at the same synapse, are occasionally seen; two cells in particular, Dm9 and Mi1, form ≥20-fold more autapses than do other neurons. These results delimit the accuracy of developmental events that establish and normally maintain synaptic circuits with such precision, and thereby address the operation of such circuits. They also establish a precedent for error rates that will be required in the new science of connectomics.

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09/26/18 | Synaptic cleft segmentation in non-isotropic volume electron microscopy of the complete Drosophila brain.
Heinrich L, Funke J, Pape C, Nunez-Iglesias J, Saalfeld S
Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. 2018 Sep 26:317-25. doi: 10.1007/978-3-030-00934-2_36

Neural circuit reconstruction at single synapse resolution is increasingly recognized as crucially important to decipher the function of biological nervous systems. Volume electron microscopy in serial transmission or scanning mode has been demonstrated to provide the necessary resolution to segment or trace all neurites and to annotate all synaptic connections. 
Automatic annotation of synaptic connections has been done successfully in near isotropic electron microscopy of vertebrate model organisms. Results on non-isotropic data in insect models, however, are not yet on par with human annotation. 
We designed a new 3D-U-Net architecture to optimally represent isotropic fields of view in non-isotropic data. We used regression on a signed distance transform of manually annotated synaptic clefts of the CREMI challenge dataset to train this model and observed significant improvement over the state of the art. 
We developed open source software for optimized parallel prediction on very large volumetric datasets and applied our model to predict synaptic clefts in a 50 tera-voxels dataset of the complete Drosophila brain. Our model generalizes well to areas far away from where training data was available.

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Card LabFly Functional ConnectomeInvertebrate Shared Resource
01/04/23 | Synaptic gradients transform object location to action.
Dombrovski M, Peek MY, Park J, Vaccari A, Sumathipala M, Morrow C, Breads P, Zhao A, Kurmangaliyev YZ, Sanfilippo P, Rehan A, Polsky J, Alghailani S, Tenshaw E, Namiki S, Zipursky SL, Card GM
Nature. 2023 Jan 04;613(7944):534-42. doi: 10.1038/s41586-022-05562-8

To survive, animals must convert sensory information into appropriate behaviours. Vision is a common sense for locating ethologically relevant stimuli and guiding motor responses. How circuitry converts object location in retinal coordinates to movement direction in body coordinates remains largely unknown. Here we show through behaviour, physiology, anatomy and connectomics in Drosophila that visuomotor transformation occurs by conversion of topographic maps formed by the dendrites of feature-detecting visual projection neurons (VPNs) into synaptic weight gradients of VPN outputs onto central brain neurons. We demonstrate how this gradient motif transforms the anteroposterior location of a visual looming stimulus into the fly's directional escape. Specifically, we discover that two neurons postsynaptic to a looming-responsive VPN type promote opposite takeoff directions. Opposite synaptic weight gradients onto these neurons from looming VPNs in different visual field regions convert localized looming threats into correctly oriented escapes. For a second looming-responsive VPN type, we demonstrate graded responses along the dorsoventral axis. We show that this synaptic gradient motif generalizes across all 20 primary VPN cell types and most often arises without VPN axon topography. Synaptic gradients may thus be a general mechanism for conveying spatial features of sensory information into directed motor outputs.

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Keleman LabFetter Lab
06/30/15 | Synaptic Orb2A bridges memory acquisition and late memory consolidation in Drosophila.
Krüttner S, Traunmüller L, Dag U, Jandrasits K, Stepien B, Iyer N, Fradkin LG, Noordermeer JN, Mensh BD, Keleman K
Cell Reports. 2015 Jun 30;11(12):1953-65. doi: 10.1016/j.celrep.2015.05.037

To adapt to an ever-changing environment, animals consolidate some, but not all, learning experiences to long-term memory. In mammals, long-term memory consolidation often involves neural pathway reactivation hours after memory acquisition. It is not known whether this delayed-reactivation schema is common across the animal kingdom or how information is stored during the delay period. Here, we show that, during courtship suppression learning, Drosophila exhibits delayed long-term memory consolidation. We also show that the same class of dopaminergic neurons engaged earlier in memory acquisition is also both necessary and sufficient for delayed long-term memory consolidation. Furthermore, we present evidence that, during learning, the translational regulator Orb2A tags specific synapses of mushroom body neurons for later consolidation. Consolidation involves the subsequent recruitment of Orb2B and the activity-dependent synthesis of CaMKII. Thus, our results provide evidence for the role of a neuromodulated, synapse-restricted molecule bridging memory acquisition and long-term memory consolidation in a learning animal.

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09/26/18 | Synaptic partner prediction from point annotations in insect brains.
Buhmann J, Krause R, Lentini RC, Eckstein N, Cook M, Turaga SC, Funke J
MICCAI 2018: Medical Image Computing and Computer Assisted Intervention. 2018 Sep 26:. doi: 10.1007/978-3-030-00934-2_35

High-throughput electron microscopy allows recording of lar- ge stacks of neural tissue with sufficient resolution to extract the wiring diagram of the underlying neural network. Current efforts to automate this process focus mainly on the segmentation of neurons. However, in order to recover a wiring diagram, synaptic partners need to be identi- fied as well. This is especially challenging in insect brains like Drosophila melanogaster, where one presynaptic site is associated with multiple post- synaptic elements. Here we propose a 3D U-Net architecture to directly identify pairs of voxels that are pre- and postsynaptic to each other. To that end, we formulate the problem of synaptic partner identification as a classification problem on long-range edges between voxels to encode both the presence of a synaptic pair and its direction. This formulation allows us to directly learn from synaptic point annotations instead of more ex- pensive voxel-based synaptic cleft or vesicle annotations. We evaluate our method on the MICCAI 2016 CREMI challenge and improve over the current state of the art, producing 3% fewer errors than the next best method.

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09/16/24 | Synaptic Specializations at Dopamine Release Sites Orchestrate Efficient and Precise Neuromodulatory Signaling
Bulumulla C, Walpita D, Iyer N, Eddison M, Patel R, Alcor D, Ackerman D, Beyene AG
bioRxiv. 2024 Sep 16:. doi: 10.1101/2024.09.16.613338

Dopamine is a key chemical neuromodulator that plays vital roles in various brain functions. Traditionally, neuromodulators like dopamine are believed to be released in a diffuse manner and are not commonly associated with synaptic structures where pre- and postsynaptic processes are closely aligned. Our findings challenge this conventional view. Using single-bouton optical measurements of dopamine release, we discovered that dopamine is predominantly released from varicosities that are juxtaposed against the processes of their target neurons. Dopamine axons specifically target neurons expressing dopamine receptors, forming synapses to release dopamine. Interestingly, varicosities that were not directly apposed to dopamine receptor-expressing processes or associated with neurons lacking dopamine receptors did not release dopamine, regardless of their vesicle content. The ultrastructure of dopamine release sites share common features of classical synapses. We further show that the dopamine released at these contact sites induces a precise, dopamine-gated biochemical response in the target processes. Our results indicate that dopamine release sites share key characteristics of conventional synapses that enable relatively precise and efficient neuromodulation of their targets.

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09/05/25 | Synaptic targets of circadian clock neurons influence core clock parameters.
Scholz-Carlson E, Iyer AR, Nern A, Ewer J, Fernandez MP
Sci Adv. 2025 Sep 05;11(36):eadw4666. doi: 10.1126/sciadv.adw4666

Neuronal connectivity in the circadian clock network is essential for robust endogenous timekeeping. In the circadian clock network, the small ventral lateral neurons (sLNs) serve as critical pacemakers. Peptidergic communication mediated by the neuropeptide (PDF), released by sLNs, has been well characterized. In contrast, little is known about the role of the synaptic connections that sLNs form with downstream neurons. Connectomic analyses revealed that the sLNs form strong synaptic connections with previously uncharacterized neurons called superior lateral protocerebrum 316 (SLP316). Here, we show that silencing the synaptic output from the SLP316 neurons via tetanus toxin expression shortened the free-running period, whereas hyperexciting them by expressing the bacterial voltage-gated sodium channel resulted in period lengthening. Under light-dark cycles, silencing SLP316 neurons caused lower daytime activity and higher daytime sleep. Our results reveal that the main postsynaptic partners of key pacemaker neurons are a nonclock neuronal cell type that regulates the timing of sleep and activity.

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