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2689 Janelia Publications

Showing 1481-1490 of 2689 results
04/17/24 | Machine learning reveals the control mechanics of an insect wing hinge
Melis JM, Siwanowicz I, Dickinson MH
Nature. 2024 Apr 17;628(8009):795-803. doi: 10.1038/s41586-024-07293-4

Insects constitute the most species-rich radiation of metazoa, a success that is due to the evolution of active flight. Unlike pterosaurs, birds and bats, the wings of insects did not evolve from legs, but are novel structures that are attached to the body via a biomechanically complex hinge that transforms tiny, high-frequency oscillations of specialized power muscles into the sweeping back-and-forth motion of the wings. The hinge consists of a system of tiny, hardened structures called sclerites that are interconnected to one another via flexible joints and regulated by the activity of specialized control muscles. Here we imaged the activity of these muscles in a fly using a genetically encoded calcium indicator, while simultaneously tracking the three-dimensional motion of the wings with high-speed cameras. Using machine learning, we created a convolutional neural network that accurately predicts wing motion from the activity of the steering muscles, and an encoder-decoder that predicts the role of the individual sclerites on wing motion. By replaying patterns of wing motion on a dynamically scaled robotic fly, we quantified the effects of steering muscle activity on aerodynamic forces. A physics-based simulation incorporating our hinge model generates flight manoeuvres that are remarkably similar to those of free-flying flies. This integrative, multi-disciplinary approach reveals the mechanical control logic of the insect wing hinge, arguably among the most sophisticated and evolutionarily important skeletal structures in the natural world.

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01/01/17 | Machine vision methods for analyzing social interactions.
Robie AA, Seagraves KM, Egnor SE, Branson K
The Journal of Experimental Biology. 2017 Jan 01;220(Pt 1):25-34. doi: 10.1242/jeb.142281

Recent developments in machine vision methods for automatic, quantitative analysis of social behavior have immensely improved both the scale and level of resolution with which we can dissect interactions between members of the same species. In this paper, we review these methods, with a particular focus on how biologists can apply them to their own work. We discuss several components of machine vision-based analyses: methods to record high-quality video for automated analyses, video-based tracking algorithms for estimating the positions of interacting animals, and machine learning methods for recognizing patterns of interactions. These methods are extremely general in their applicability, and we review a subset of successful applications of them to biological questions in several model systems with very different types of social behaviors.

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05/27/25 | Macrophages release neuraminidase and cleaved calreticulin for programmed cell removal.
Banuelos A, Baez M, Zhang A, Yılmaz L, Kasberg W, Volk R, Georgeos N, Koren-Sedova E, Le U, Burden AT, Marjon KD, Lippincott-Schwartz J, Zaro BW, Weissman IL
Proc Natl Acad Sci U S A. 2025 May 27;122(21):e2426644122. doi: 10.1073/pnas.2426644122

Calreticulin (CALR) is primarily an endoplasmic reticulum chaperone protein that also plays a key role in facilitating programmed cell removal (PrCR) by acting as an "eat-me" signal for macrophages, directing their recognition and engulfment of dying, diseased, or unwanted cells. Recent findings have demonstrated that macrophages can transfer their own CALR onto exposed asialoglycans on target cells, marking them for PrCR. Despite the critical role CALR plays in this process, the molecular mechanisms behind its secretion by macrophages and the formation of binding sites on target cells remain unclear. Our findings show that CALR undergoes C-terminal cleavage upon secretion, producing a truncated form that functions as the active eat-me signal detectable on target cells. We identify cathepsins as potential proteases involved in this cleavage process. Furthermore, we demonstrate that macrophages release neuraminidases, which modify the surface of target cells and facilitate CALR binding. These insights reveal a coordinated mechanism through which lipopolysaccharide (LPS)-activated macrophages regulate CALR cleavage and neuraminidase activity to mark target cells for PrCR. How they recognize the cells to be targeted remains unknown.

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08/27/18 | Macropinosome formation by tent pole ruffling in macrophages.
Condon ND, Heddleston JM, Chew T, Luo L, McPherson PS, Ioannou MS, Hodgson L, Stow JL, Wall AA
The Journal of Cell Biology. 2018 Aug 27;217(11):3873-85. doi: 10.1083/jcb.201804137

Pathogen-mediated activation of macrophages arms innate immune responses that include enhanced surface ruffling and macropinocytosis for environmental sampling and receptor internalization and signaling. Activation of macrophages with bacterial lipopolysaccharide (LPS) generates prominent dorsal ruffles, which are precursors for macropinosomes. Very rapid, high-resolution imaging of live macrophages with lattice light sheet microscopy (LLSM) reveals new features and actions of dorsal ruffles, which redefine the process of macropinosome formation and closure. We offer a new model in which ruffles are erected and supported by F-actin tent poles that cross over and twist to constrict the forming macropinosomes. This process allows for formation of large macropinosomes induced by LPS. We further describe the enrichment of active Rab13 on tent pole ruffles and show that CRISPR deletion of Rab13 results in aberrant tent pole ruffles and blocks the formation of large LPS-induced macropinosomes. Based on the exquisite temporal and spatial resolution of LLSM, we can redefine the ruffling and macropinosome processes that underpin innate immune responses.

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06/18/16 | Macular telangiectasia type 1 managed with long-term aflibercept therapy.
Kovach JL, Hess HF, Rosenfeld PJ
Ophthalmic Surgery, Lasers and Imaging Retina. 2016 Jun;47(6):593-5. doi: 10.3928/23258160-20160601-14

A 60-year-old man diagnosed with macular telangiectasia type 1 (MacTel 1) was treated for 3 years with monthly aflibercept (Eylea; Regeneron, Tarrytown, NY) and serially imaged with spectral-domain optical coherence tomography. When administered monthly, aflibercept appeared to have a beneficial effect on macular edema secondary to MacTel 1. Visual acuity preservation despite minimal chronic macular edema could be attributed to the lack of significant photoreceptor disruption.

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05/16/24 | Magnetic voluntary head-fixation in transgenic rats enables lifetime imaging of hippocampal neurons
P. D. Rich , S. Y. Thiberge , B. B. Scott , C. Guo , D. G. Tervo , C. D. Brody , A. Y. Karpova , N. D. Daw , D. W. Tank
Nat. Commun.. 2024 May 16:. doi: 10.1038/s41467-024-48505-9

The precise neural mechanisms within the brain that contribute to the remarkable lifetime persistence of memory remain unknown. Existing techniques to record neurons in animals are either unsuitable for longitudinal recording from the same cells or make it difficult for animals to express their full naturalistic behavioral repertoire. We present a magnetic voluntary head-fixation system that provides stable optical access to the brain during complex behavior. Compared to previous systems that used mechanical restraint, there are no moving parts and animals can engage and disengage entirely at will. This system is failsafe, easy for animals to use and reliable enough to allow long-term experiments to be routinely performed. Together with a novel two-photon fluorescence collection scheme that increases two-photon signal and a transgenic rat line that stably expresses the calcium sensor GCaMP6f in dorsal CA1, we are able to track and record activity from the same hippocampal neurons, during behavior, over a large fraction of animals’ lives.

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11/25/18 | Magnetocaloric materials as switchable high contrast ratio MRI labels.
Barbic M, Dodd SJ, Morris HD, Dilley N, Marcheschi B, Huston A, Harris TD, Koretsky AP
Magnetic Resonance in Medicine. 2018 Nov 25;81(4):2238-46. doi: 10.1002/mrm.27615

PURPOSE: To develop switchable and tunable labels with high contrast ratio for MRI using magnetocaloric materials that have sharp first-order magnetic phase transitions at physiological temperatures and typical MRI magnetic field strengths.

METHODS: A prototypical magnetocaloric material iron-rhodium (FeRh) was prepared by melt mixing, high-temperature annealing, and ice-water quenching. Temperature- and magnetic field-dependent magnetization measurements of wire-cut FeRh samples were performed on a vibrating sample magnetometer. Temperature-dependent MRI of FeRh samples was performed on a 4.7T MRI.

RESULTS: Temperature-dependent MRI clearly demonstrated image contrast changes due to the sharp magnetic state transition of the FeRh samples in the MRI magnetic field (4.7T) and at a physiologically relevant temperature (~37°C).

CONCLUSION: A magnetocaloric material, FeRh, was demonstrated to act as a high contrast ratio switchable MRI contrast agent due to its sharp first-order magnetic phase transition in the DC magnetic field of MRI and at physiologically relevant temperatures. A wide range of magnetocaloric materials are available that can be tuned by materials science techniques to optimize their response under MRI-appropriate conditions and be controllably switched in situ with temperature, magnetic field, or a combination of both.

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05/18/22 | Maintaining a stable head direction representation in naturalistic visual environments
Hannah Haberkern , Shivam S Chitnis , Philip M Hubbard , Tobias Goulet , Ann M Hermundstad , Vivek Jayaraman
bioRxiv. 2022 May 18:. doi: 10.1101/2022.05.17.492284

Many animals rely on a representation of head direction for flexible, goal-directed navigation. In insects, a compass-like head direction representation is maintained in a conserved brain region called the central complex. This head direction representation is updated by self-motion information and by tethering to sensory cues in the surroundings through a plasticity mechanism. However, under natural settings, some of these sensory cues may temporarily disappear—for example, when clouds hide the sun—and prominent landmarks at different distances from the insect may move across the animal's field of view during translation, creating potential conflicts for a neural compass. We used two-photon calcium imaging in head-fixed Drosophila behaving in virtual reality to monitor the fly's compass during navigation in immersive naturalistic environments with approachable local landmarks. We found that the fly's compass remains stable even in these settings by tethering to available global cues, likely preserving the animal's ability to perform compass-driven behaviors such as maintaining a constant heading.

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10/03/24 | Maintaining and updating accurate internal representations of continuous variables with a handful of neurons.
Noorman M, Hulse BK, Jayaraman V, Romani S, Hermundstad AM
Nat Neurosci. 2024 Oct 03:. doi: 10.1038/s41593-024-01766-5

Many animals rely on persistent internal representations of continuous variables for working memory, navigation, and motor control. Existing theories typically assume that large networks of neurons are required to maintain such representations accurately; networks with few neurons are thought to generate discrete representations. However, analysis of two-photon calcium imaging data from tethered flies walking in darkness suggests that their small head-direction system can maintain a surprisingly continuous and accurate representation. We thus ask whether it is possible for a small network to generate a continuous, rather than discrete, representation of such a variable. We show analytically that even very small networks can be tuned to maintain continuous internal representations, but this comes at the cost of sensitivity to noise and variations in tuning. This work expands the computational repertoire of small networks, and raises the possibility that larger networks could represent more and higher-dimensional variables than previously thought.

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Druckmann LabSvoboda Lab
05/03/17 | Maintenance of persistent activity in a frontal thalamocortical loop.
Guo ZV, Inagaki HK, Daie K, Druckmann S, Gerfen CR, Svoboda K
Nature. 2017 May 03;545(7653):181-6. doi: 10.1038/nature22324

Persistent neural activity maintains information that connects past and future events. Models of persistent activity often invoke reverberations within local cortical circuits, but long-range circuits could also contribute. Neurons in the mouse anterior lateral motor cortex (ALM) have been shown to have selective persistent activity that instructs future actions. The ALM is connected bidirectionally with parts of the thalamus, including the ventral medial and ventral anterior-lateral nuclei. We recorded spikes from the ALM and thalamus during tactile discrimination with a delayed directional response. Here we show that, similar to ALM neurons, thalamic neurons exhibited selective persistent delay activity that predicted movement direction. Unilateral photoinhibition of delay activity in the ALM or thalamus produced contralesional neglect. Photoinhibition of the thalamus caused a short-latency and near-complete collapse of ALM activity. Similarly, photoinhibition of the ALM diminished thalamic activity. Our results show that the thalamus is a circuit hub in motor preparation and suggest that persistent activity requires reciprocal excitation across multiple brain areas.

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