Filter
Associated Lab
- Ahrens Lab (4) Apply Ahrens Lab filter
- Aso Lab (1) Apply Aso Lab filter
- Betzig Lab (3) Apply Betzig Lab filter
- Beyene Lab (1) Apply Beyene Lab filter
- Card Lab (3) Apply Card Lab filter
- Clapham Lab (1) Apply Clapham Lab filter
- Darshan Lab (2) Apply Darshan Lab filter
- Dickson Lab (2) Apply Dickson Lab filter
- Dudman Lab (3) Apply Dudman Lab filter
- Espinosa Medina Lab (3) Apply Espinosa Medina Lab filter
- Feliciano Lab (1) Apply Feliciano Lab filter
- Fitzgerald Lab (3) Apply Fitzgerald Lab filter
- Funke Lab (5) Apply Funke Lab filter
- Harris Lab (1) Apply Harris Lab filter
- Hermundstad Lab (6) Apply Hermundstad Lab filter
- Hess Lab (7) Apply Hess Lab filter
- Jayaraman Lab (3) Apply Jayaraman Lab filter
- Keleman Lab (1) Apply Keleman Lab filter
- Keller Lab (1) Apply Keller Lab filter
- Lavis Lab (13) Apply Lavis Lab filter
- Lee (Albert) Lab (1) Apply Lee (Albert) Lab filter
- Leonardo Lab (1) Apply Leonardo Lab filter
- Lippincott-Schwartz Lab (7) Apply Lippincott-Schwartz Lab filter
- Liu (Zhe) Lab (5) Apply Liu (Zhe) Lab filter
- Looger Lab (7) Apply Looger Lab filter
- O'Shea Lab (1) Apply O'Shea Lab filter
- Pachitariu Lab (4) Apply Pachitariu Lab filter
- Pedram Lab (1) Apply Pedram Lab filter
- Podgorski Lab (1) Apply Podgorski Lab filter
- Reiser Lab (3) Apply Reiser Lab filter
- Romani Lab (3) Apply Romani Lab filter
- Rubin Lab (1) Apply Rubin Lab filter
- Saalfeld Lab (6) Apply Saalfeld Lab filter
- Scheffer Lab (1) Apply Scheffer Lab filter
- Singer Lab (1) Apply Singer Lab filter
- Spruston Lab (2) Apply Spruston Lab filter
- Stern Lab (8) Apply Stern Lab filter
- Sternson Lab (3) Apply Sternson Lab filter
- Stringer Lab (5) Apply Stringer Lab filter
- Svoboda Lab (6) Apply Svoboda Lab filter
- Tebo Lab (1) Apply Tebo Lab filter
- Tillberg Lab (3) Apply Tillberg Lab filter
- Turaga Lab (2) Apply Turaga Lab filter
- Turner Lab (2) Apply Turner Lab filter
- Vale Lab (2) Apply Vale Lab filter
Associated Project Team
- COSEM (1) Apply COSEM filter
- Fly Descending Interneuron (1) Apply Fly Descending Interneuron filter
- Fly Functional Connectome (2) Apply Fly Functional Connectome filter
- FlyLight (4) Apply FlyLight filter
- GENIE (1) Apply GENIE filter
- Tool Translation Team (T3) (2) Apply Tool Translation Team (T3) filter
Associated Support Team
- Anatomy and Histology (3) Apply Anatomy and Histology filter
- Cryo-Electron Microscopy (4) Apply Cryo-Electron Microscopy filter
- Fly Facility (6) Apply Fly Facility filter
- Integrative Imaging (3) Apply Integrative Imaging filter
- Janelia Experimental Technology (3) Apply Janelia Experimental Technology filter
- Molecular Genomics (5) Apply Molecular Genomics filter
- Primary & iPS Cell Culture (2) Apply Primary & iPS Cell Culture filter
- Project Technical Resources (5) Apply Project Technical Resources filter
- Quantitative Genomics (2) Apply Quantitative Genomics filter
- Scientific Computing Systems (1) Apply Scientific Computing Systems filter
- Viral Tools (6) Apply Viral Tools filter
- Vivarium (1) Apply Vivarium filter
Publication Date
- December 2022 (12) Apply December 2022 filter
- November 2022 (17) Apply November 2022 filter
- October 2022 (12) Apply October 2022 filter
- September 2022 (14) Apply September 2022 filter
- August 2022 (13) Apply August 2022 filter
- July 2022 (17) Apply July 2022 filter
- June 2022 (10) Apply June 2022 filter
- May 2022 (21) Apply May 2022 filter
- April 2022 (8) Apply April 2022 filter
- March 2022 (14) Apply March 2022 filter
- February 2022 (16) Apply February 2022 filter
- January 2022 (12) Apply January 2022 filter
- Remove 2022 filter 2022
166 Janelia Publications
Showing 131-140 of 166 resultsRNA-guided systems, such as CRISPR-Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies. Structural studies of these systems have illuminated how the RNA and protein jointly recognize and cleave their substrates, guiding rational engineering for further technology development. Recent work identified a new class of RNA-guided systems, termed OMEGA, which include IscB, the likely ancestor of Cas9, and the nickase IsrB, a homologue of IscB lacking the HNH nuclease domain. IsrB consists of only around 350 amino acids, but its small size is counterbalanced by a relatively large RNA guide (roughly 300-nt ωRNA). Here, we report the cryogenic-electron microscopy structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with its cognate ωRNA and a target DNA. We find the overall structure of the IsrB protein shares a common scaffold with Cas9. In contrast to Cas9, however, which uses a recognition (REC) lobe to facilitate target selection, IsrB relies on its ωRNA, part of which forms an intricate ternary structure positioned analogously to REC. Structural analyses of IsrB and its ωRNA as well as comparisons to other RNA-guided systems highlight the functional interplay between protein and RNA, advancing our understanding of the biology and evolution of these diverse systems.
Brains must represent the outside world so that animals survive and thrive. In early sensory systems, neural populations have diverse receptive fields structured to detect important features in inputs, yet significant variability has been ignored in classical models of sensory neurons. We model neuronal receptive fields as random, variable samples from parametrized distributions in two sensory modalities, using data from insect mechanosensors and neurons of mammalian primary visual cortex. We show that these random feature neurons perform a randomized wavelet transform on inputs which removes high frequency noise and boosts the signal. Our result makes a significant theoretical connection between the foundational concepts of receptive fields in neuroscience and random features in artificial neural networks. Further, these random feature neurons enable learning from fewer training samples and with smaller networks in artificial tasks. This structured random model of receptive fields provides a unifying, mathematically tractable framework to understand sensory encodings across both spatial and temporal domains.
Brains must represent the outside world so that animals survive and thrive. In early sensory systems, neural populations have diverse receptive fields structured to detect important features in inputs, yet significant variability has been ignored in classical models of sensory neurons. We model neuronal receptive fields as random, variable samples from parameterized distributions and demonstrate this model in two sensory modalities using data from insect mechanosensors and mammalian primary visual cortex. Our approach leads to a significant theoretical connection between the foundational concepts of receptive fields and random features, a leading theory for understanding artificial neural networks. The modeled neurons perform a randomized wavelet transform on inputs, which removes high frequency noise and boosts the signal. Further, these random feature neurons enable learning from fewer training samples and with smaller networks in artificial tasks. This structured random model of receptive fields provides a unifying, mathematically tractable framework to understand sensory encodings across both spatial and temporal domains.
Associative memory formation and recall in the fruit fly Drosophila melanogaster is subserved by the mushroom body (MB). Upon arrival in the MB, sensory information undergoes a profound transformation from broadly tuned and stereotyped odorant responses in the olfactory projection neuron (PN) layer to narrowly tuned and nonstereotyped responses in the Kenyon cells (KCs). Theory and experiment suggest that this transformation is implemented by random connectivity between KCs and PNs. However, this hypothesis has been challenging to test, given the difficulty of mapping synaptic connections between large numbers of brain-spanning neurons. Here, we used a recent whole-brain electron microscopy volume of the adult fruit fly to map PN-to-KC connectivity at synaptic resolution. The PN-KC connectome revealed unexpected structure, with preponderantly food-responsive PN types converging at above-chance levels on downstream KCs. Axons of the overconvergent PN types tended to arborize near one another in the MB main calyx, making local KC dendrites more likely to receive input from those types. Overconvergent PN types preferentially co-arborize and connect with dendrites of αβ and α'β' KC subtypes. Computational simulation of the observed network showed degraded discrimination performance compared with a random network, except when all signal flowed through the overconvergent, primarily food-responsive PN types. Additional theory and experiment will be needed to fully characterize the impact of the observed non-random network structure on associative memory formation and recall.
Signaling through the TNF-family receptor Fas/CD95 can trigger apoptosis or non-apoptotic cellular responses and is essential for protection from autoimmunity. Receptor clustering has been observed following interaction with Fas ligand (FasL), but the stoichiometry of Fas, particularly when triggered by membrane-bound FasL, the only form of FasL competent at inducing programmed cell death, is not known. Here we used super-resolution microscopy to study the behavior of single molecules of Fas/CD95 on the plasma membrane after interaction of Fas with FasL on planar lipid bilayers. We observed rapid formation of Fas protein superclusters containing more than 20 receptors after interactions with membrane-bound FasL. Fluorescence correlation imaging demonstrated recruitment of FADD dependent on an intact Fas death domain, with lipid raft association playing a secondary role. Flow-cytometric FRET analysis confirmed these results, and also showed that some Fas clustering can occur in the absence of FADD and caspase-8. Point mutations in the Fas death domain associated with autoimmune lymphoproliferative syndrome (ALPS) completely disrupted Fas reorganization and FADD recruitment, confirming structure-based predictions of the critical role that these residues play in Fas-Fas and Fas-FADD interactions. Finally, we showed that induction of apoptosis correlated with the ability to form superclusters and recruit FADD.
Arrays of actin filaments (F-actin) near the apical surface of epithelial cells (medioapical arrays) contribute to apical constriction and morphogenesis throughout phylogeny. Here, super-resolution approaches (grazing incidence structured illumination, GI-SIM and lattice light sheet, LLSM) microscopy resolve individual, fluorescently labeled F-actin and bipolar myosin filaments that drive amnioserosa cell shape changes during dorsal closure in . In expanded cells, F-actin and myosin form loose, apically domed meshworks at the plasma membrane. The arrays condense as cells contract, drawing the domes into the plane of the junctional belts. As condensation continues, individual filaments are no longer uniformly apparent. As cells expand, arrays of actomyosin are again resolved - some F-actin turnover likely occurs, but a large fraction of existing filaments rearrange. In morphologically isotropic cells, actin filaments are randomly oriented and during contraction, are drawn together but remain essentially randomly oriented. In anisotropic cells, largely parallel actin filaments are drawn closer to one another. Our images offer unparalleled resolution of F-actin in embryonic tissue show that medioapical arrays are tightly apposed to the plasma membrane, are continuous with meshworks of lamellar F-actin and thereby constitute modified cell cortex. In concert with other tagged array components, super-resolution imaging of live specimens will offer new understanding of cortical architecture and function. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].
The three-dimensional (3D) genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in 3D genomics inferred the very basic functional chromatin folding structures known as chromatin loops, the long-range chromatin interactions that are mediated by protein factors and dynamically extruded by cohesin. We combined the use of FISH staining of a very short (33 kb) chromatin fragment, interferometric photoactivated localization microscopy (iPALM), and traveling salesman problem-based heuristic loop reconstruction algorithm from an image of the one of the strongest CTCF-mediated chromatin loops in human lymphoblastoid cells. In total, we have generated thirteen good quality images of the target chromatin region with 2-22 nm oligo probe localization precision. We visualized the shape of the single chromatin loops with unprecedented genomic resolution which allowed us to study the structural heterogeneity of chromatin looping. We were able to compare the physical distance maps from all reconstructed image-driven computational models with contact frequencies observed by ChIA-PET and Hi-C genomic-driven methods to examine the concordance between single cell imaging and population based genomic data.
Arrays of actin filaments (F-actin) near the apical surface of epithelial cells (medioapical arrays) contribute to apical constriction and morphogenesis throughout phylogeny. Here, superresolution approaches (grazing incidence structured illumination, GI-SIM, and lattice light sheet, LLSM) microscopy resolve individual, fluorescently labeled F-actin and bipolar myosin filaments that drive amnioserosa cell shape changes during dorsal closure in . In expanded cells, F-actin and myosin form loose, apically domed meshworks at the plasma membrane. The arrays condense as cells contract, drawing the domes into the plane of the junctional belts. As condensation continues, individual filaments are no longer uniformly apparent. As cells expand, arrays of actomyosin are again resolved-some F-actin turnover likely occurs, but a large fraction of existing filaments rearrange. In morphologically isotropic cells, actin filaments are randomly oriented and during contraction are drawn together but remain essentially randomly oriented. In anisotropic cells, largely parallel actin filaments are drawn closer to one another. Our images offer unparalleled resolution of F-actin in embryonic tissue, show that medioapical arrays are tightly apposed to the plasma membrane and are continuous with meshworks of lamellar F-actin. Medioapical arrays thereby constitute modified cell cortex. In concert with other tagged array components, superresolution imaging of live specimens will offer new understanding of cortical architecture and function.
Animal wings deform during flight in ways that can enhance lift, facilitate flight control, and mitigate damage. Monitoring the structural and aerodynamic state of the wing is challenging because deformations are passive, and the flow fields are unsteady; it requires distributed mechanosensors that respond to local airflow and strain on the wing. Without a complete map of the sensor arrays, it is impossible to model control strategies underpinned by them. Here, we present the first systematic characterization of mechanosensors on the dragonfly's wings: morphology, distribution, and wiring. By combining a cross-species survey of sensor distribution with quantitative neuroanatomy and a high-fidelity finite element analysis, we show that the mechanosensors are well placed to perceive features of the wing dynamics relevant to flight. This work describes the wing sensory apparatus in its entirety and advances our understanding of the sensorimotor loop that facilitates exquisite flight control in animals with highly deformable wings.
Triple-negative breast cancer (TNBC) has a poor clinical outcome, due to a lack of actionable therapeutic targets. Herein we define lysosomal acid lipase A (LIPA) as a viable molecular target in TNBC and identify a stereospecific small molecule (ERX-41) that binds LIPA. ERX-41 induces endoplasmic reticulum (ER) stress resulting in cell death, and this effect is on target as evidenced by specific LIPA mutations providing resistance. Importantly, we demonstrate that ERX-41 activity is independent of LIPA lipase function but dependent on its ER localization. Mechanistically, ERX-41 binding of LIPA decreases expression of multiple ER-resident proteins involved in protein folding. This targeted vulnerability has a large therapeutic window, with no adverse effects either on normal mammary epithelial cells or in mice. Our study implicates a targeted strategy for solid tumors, including breast, brain, pancreatic and ovarian, whereby small, orally bioavailable molecules targeting LIPA block protein folding, induce ER stress and result in tumor cell death.