@article {69825, title = {HortaCloud: An Open and Collaborative Platform for Whole Brain Neuronal Reconstructions}, journal = {bioRxiv}, year = {2025}, month = {2025 Mar 13}, abstract = {

HortaCloud is a cloud-based, open-source platform designed to facilitate the collaborative reconstruction of long-range projection neurons from whole-brain light microscopy data. By providing virtual environments directly within the cloud, it eliminates the need for costly and time-consuming data downloads, allowing researchers to work efficiently with terabyte- scale volumetric datasets. Standardization of computational resources in the cloud make deployment easier and more predictable. The pay-as-you-go cloud model reduces adoption barriers by eliminating upfront investments in expensive hardware. Finally, HortaCloud{\textquoteright}s decentralized architecture enables global collaboration between researchers and between institutions.

}, doi = {10.1101/2025.03.13.642887}, url = {https://www.biorxiv.org/content/early/2025/03/14/2025.03.13.642887}, author = {Rokicki, Konrad and Schauder, David and Olbris, Donald J. and Goina, Cristian and Clements, Jody and Edson, Patrick and Kawase, Takashi and Svirskas, Robert and Arshadi, Cameron and Feng, David and Chandrashekar, Jayaram and Ferreira, Tiago A. and MouseLight Project Team} } @article {66902, title = {Brain microvasculature has a common topology with local differences in geometry that match metabolic load.}, journal = {Neuron}, volume = {109}, year = {2021}, month = {2021 April 01}, pages = {1168}, abstract = {

The microvasculature underlies the supply networks that support neuronal activity within heterogeneous brain regions. What are common versus heterogeneous aspects of the connectivity, density, and orientation of capillary networks? To address this, we imaged, reconstructed, and analyzed the microvasculature connectome in whole adult mice brains with sub-micrometer resolution. Graph analysis revealed common network topology across the brain that leads to a shared structural robustness against the rarefaction of vessels. Geometrical analysis, based on anatomically accurate reconstructions, uncovered a scaling law that links length density, i.e., the length of vessel per volume, with tissue-to-vessel distances. We then derive a formula that connects regional differences in metabolism to differences in length density and, further, predicts a common value of maximum tissue oxygen tension across the brain. Last, the orientation of capillaries is weakly anisotropic with the exception of a few strongly anisotropic regions; this variation can impact the interpretation of fMRI data.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2021.02.006}, author = {Ji, Xiang and Ferreira, Tiago and Friedman, Beth and Liu, Rui and Liechty, Hannah and Bas, Erhan and Chandrashekar, Jayaram and Kleinfeld, David} } @article {65599, title = {Whole-brain profiling of cells and circuits in mammals by tissue clearing and light-sheet microscopy.}, journal = {Neuron}, volume = {106}, year = {2020}, month = {2020 May 06}, pages = {369-387}, abstract = {

Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.03.004}, author = {Ueda, Hiroki R and Dodt, Hans-Ulrich and Osten, Pavel and Economo, Michael N and Chandrashekar, Jayaram and Keller, Philipp J} } @article {65633, title = {Whole-brain profiling of cells and circuits in mammals by tissue clearing and light-sheet microscopy.}, journal = {Neuron}, volume = {106}, year = {2020}, month = {2020 May 06}, pages = {369-387}, abstract = {

Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.03.004}, author = {Ueda, Hiroki R and Dodt, Hans-Ulrich and Osten, Pavel and Economo, Michael N and Chandrashekar, Jayaram and Keller, Philipp J} } @article {64874, title = {Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Apr 12}, abstract = {

Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases we provide an extensive resource for further investigation of mouse neuronal cell types.

}, issn = {2050-084X}, doi = {10.7554/eLife.38619}, author = {Sugino, Ken and Clark, Erin and Schulmann, Anton and Shima, Yasuyuki and Wang, Lihua and Hunt, David L and Hooks, Bryan M and Traenkner, Dimitri and Chandrashekar, Jayaram and Picard, Serge and Lemire, Andrew L and Spruston, Nelson and Hantman, Adam W and Nelson, Sacha B} } @article {65138, title = {Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain.}, journal = {Cell}, volume = {179}, year = {2019}, month = {2019 Sep 19}, pages = {268-81}, abstract = {

Neuronal\ cell\ types\ are the nodes of neural circuits that determine the flow of information within the\ brain. Neuronal morphology, especially the shape of the axonal arbor, provides an essential descriptor of\ cell\ type and\ reveals\ how individual\ neurons\ route their output across the\ brain. Despite the importance of morphology, few\ projection\ neurons\ in the\ mouse\ brain\ have been reconstructed in their entirety. Here we present a robust and efficient platform for imaging and reconstructing complete neuronal morphologies, including axonal arbors that span substantial portions of the\ brain. We used this platform to reconstruct more than\ 1,000\ projection\ neurons\ in the motor cortex, thalamus, subiculum, and hypothalamus. Together, the reconstructed\ neurons\ constitute more than 85\ meters of axonal length and are available in a searchable online database. Axonal shapes revealed previously unknown subtypes of\ projection\ neurons\ and suggest organizational principles of\ long-range\ connectivity.

}, issn = {00928674}, doi = {10.1016/j.cell.2019.07.042}, author = {Winnubst, Johan and Bas, Erhan and Ferreira, Tiago A. and Wu, Zhuhao and Economo, Michael N. and Edson, Patrick and Arthur, Ben J. and Bruns, Christopher and Rokicki, Konrad and Schauder, David and Olbris, Donald J. and Murphy, Sean D. and Ackerman, David G. and Arshadi, Cameron and Baldwin, Perry and Blake, Regina and Elsayed, Ahmad and Hasan, Mashtura and Ramirez, Daniel and Dos Santos, Bruno and Weldon, Monet and Zafar, Amina and Dudman, Joshua T. and Gerfen, Charles R. and Hantman, Adam W. and Korff, Wyatt and Sternson, Scott M. and Spruston, Nelson and Svoboda, Karel and Chandrashekar, Jayaram} } @article {65159, title = {A repeated molecular architecture across thalamic pathways.}, journal = {Nature Neuroscience}, volume = {22}, year = {2019}, month = {2019 Sep 16}, pages = {1925-35}, abstract = {

The thalamus is the central communication hub of the forebrain and provides the cerebral cortex with inputs from sensory organs, subcortical systems and the cortex itself. Multiple thalamic regions send convergent information to each cortical region, but the organizational logic of thalamic projections has remained elusive. Through comprehensive transcriptional analyses of retrogradely labeled thalamic neurons in adult mice, we identify three major profiles of thalamic pathways. These profiles exist along a continuum that is repeated across all major projection systems, such as those for vision, motor control and cognition. The largest component of gene expression variation in the mouse thalamus is topographically organized, with features conserved in humans. Transcriptional differences between these thalamic neuronal identities are tied to cellular features that are critical for function, such as axonal morphology and membrane properties. Molecular profiling therefore reveals covariation in the properties of thalamic pathways serving all major input modalities and output targets, thus establishing a molecular framework for understanding the thalamus.

}, issn = {1546-1726}, doi = {10.1038/s41593-019-0483-3}, author = {Phillips, James W and Schulmann, Anton and Hara, Erina and Winnubst, Johan and Liu, Chenghao and Valakh, Vera and Wang, Lihua and Shields, Brenda C and Korff, Wyatt and Chandrashekar, Jayaram and Lemire, Andrew L and Mensh, Brett and Dudman, Joshua T and Nelson, Sacha B and Hantman, Adam W} } @article {64830, title = {Single-neuron axonal reconstruction: The search for a wiring diagram of the brain.}, journal = {The Journal of Comparative Neurology}, year = {2019}, month = {2019 Mar 12}, abstract = {

Reconstruction of the axonal projection patterns of single neurons has been an important tool for understanding both the diversity of cell types in the brain and the logic of information flow between brain regions. Innovative approaches now enable the complete reconstruction of axonal projection patterns of individual neurons with vastly increased throughput. Here we review how advances in genetic, imaging, and computational techniques have been exploited for axonal reconstruction. We also discuss how new innovations could enable the integration of genetic and physiological information with axonal morphology for producing a census of cell types in the mammalian brain at scale. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.24674}, author = {Economo, Michael N and Winnubst, Johan and Bas, Erhan and Ferreira, Tiago A and Chandrashekar, Jayaram} } @article {49061, title = {Cell type-specific variation of somatotopic precision across corticostriatal projections. }, journal = {bioRxiv}, year = {2018}, month = {2018 Feb 7}, abstract = {

The striatum shows general topographic organization and regional differences in behavioral functions. How corticostriatal topography differs across cortical areas and cell types to support these distinct functions is unclear. This study contrasted corticostriatal projections from two layer 5 cell types, intratelencephalic (IT-type) and pyramidal tract (PT-type) neurons, using viral vectors expressing fluorescent reporters in Cre-driver mice. Long-range corticostriatal projections from sensory and motor cortex are somatotopic, with a decreasing somatotopic specificity as injections move from sensory to motor and frontal areas. Somatotopic organization differs between IT-type and PT-type neurons, including injections in the same site, with IT-type neurons having higher somatotopic stereotypy than PT-type neurons. Furthermore, IT-type projections from interconnected cortical areas have stronger correlations in corticostriatal targeting than PT-type projections do. Thus, as predicted by a long-standing basal ganglia model, corticostriatal projections of interconnected cortical areas form parallel circuits in basal ganglia-thalamus-cortex loops.

}, doi = {10.1101/261446}, author = {Hooks, Bryan M and Papale, Andrew E and Paletzki, Ronald and Feroze, Muhammad and Eastwood, Brian S and Couey, Jonathan J and Winnubst, Johan and Chandrashekar, Jayaram and Gerfen, Charles R} } @article {49174, title = {Dissociable structural and functional hippocampal outputs via distinct subiculum cell classes.}, journal = {Cell}, volume = {173}, year = {2018}, month = {2018 Apr 10}, pages = {1280-92}, abstract = {

The mammalian hippocampus, comprised of serially connected subfields, participates in diverse behavioral and cognitive functions. It has been postulated that parallel circuitry embedded within hippocampal subfields may underlie such functional diversity. We sought to identify, delineate, and manipulate this putatively parallel architecture in the dorsal subiculum, the primary output subfield of the dorsal hippocampus. Population and single-cell RNA-seq revealed that the subiculum can be divided into two spatially adjacent subregions associated with prominent differences in pyramidal cell gene expression. Pyramidal cells occupying these two regions differed in their long-range inputs, local wiring, projection targets, and electrophysiological properties. Leveraging gene-expression differences across these regions, we use genetically restricted neuronal silencing to show that\ these regions differentially contribute to spatial working memory. This work provides a coherent molecular-, cellular-, circuit-, and behavioral-level demonstration that the hippocampus embeds structurally and functionally dissociable streams within its serial architecture.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.03.031}, author = {Cembrowski, Mark S and Phillips, Matthew G and DiLisio, Salvatore F and Shields, Brenda C and Winnubst, Johan and Chandrashekar, Jayaram and Bas, Erhan and Spruston, Nelson} } @article {49496, title = {Distinct descending motor cortex pathways and their roles in movement.}, journal = {Nature}, volume = {563}, year = {2018}, month = {2018 Nov}, pages = {79-84}, abstract = {

Activity in the motor cortex predicts movements, seconds before they are initiated. This preparatory activity has been observed across cortical layers, including in descending pyramidal tract neurons in layer 5. A key question is how preparatory activity is maintained without causing movement, and is ultimately converted to a motor command to trigger appropriate movements. Here, using single-cell transcriptional profiling and axonal reconstructions, we identify two types of pyramidal tract neuron. Both types project to several targets in the basal ganglia and brainstem. One type projects to thalamic regions that connect back to motor cortex; populations of these neurons produced early preparatory activity that persisted until the movement was initiated. The second type projects to motor centres in the medulla and mainly\ produced late preparatory activity and motor commands. These results indicate that two types of motor cortex output neurons have specialized roles in motor control.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0642-9}, author = {Economo, Michael N and Viswanathan, Sarada and Tasic, Bosiljka and Bas, Erhan and Winnubst, Johan and Menon, Vilas and Graybuck, Lucas T and Nguyen, Thuc Nghi and Smith, Kimberly A and Yao, Zizhen and Wang, Lihua and Gerfen, Charles R and Chandrashekar, Jayaram and Zeng, Hongkui and Looger, Loren L and Svoboda, Karel} } @article {49095, title = {NeuroStorm: accelerating brain science discovery in the cloud.}, journal = {arXiv}, year = {2018}, month = {2018 Mar 09}, abstract = {

Neuroscientists are now able to acquire data at staggering rates across spatiotemporal scales. However, our ability to capitalize on existing datasets, tools, and intellectual capacities is hampered by technical challenges. The key barriers to accelerating scientific discovery correspond to the FAIR data principles: findability, global access to data, software interoperability, and reproducibility/re-usability. We conducted a hackathon dedicated to making strides in those steps. This manuscript is a technical report summarizing these achievements, and we hope serves as an example of the effectiveness of focused, deliberate hackathons towards the advancement of our quickly-evolving field.

}, url = {https://arxiv.org/abs/1803.03367}, author = {Kiar, Gregory and Anderson, Robert J and Baden, Alex and Badea, Alexandra and Bridgeford, Eric W and Champion, Andrew and Chandrashekar, Jayaram and Collman, Forrest and Duderstadt, Brandon and Evans, Alan C and Engert, Florian and Falk, Benjamin and Glatard, Tristan and Roncal, William Gray and Kennedy, David N and Maitlin-Shepard and Marren, Ryan A and Nnaemeka, Onyeka and Perlman, Eric and Seshamani, Sharmishtaas} } @article {49413, title = {Topographic precision in sensory and motor corticostriatal projections varies across cell type and cortical area.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Sep 03}, pages = {3549}, abstract = {

The striatum shows general topographic organization and regional differences in behavioral functions. How corticostriatal topography differs across cortical areas and cell types to support these distinct functions is unclear. This study contrasted corticostriatal projections from two layer 5 cell types, intratelencephalic (IT-type) and pyramidal tract (PT-type) neurons, using viral vectors expressing fluorescent reporters in Cre-driver mice. Corticostriatal projections from sensory and motor cortex are somatotopic, with a decreasing topographic specificity as injection sites move from sensory to motor and frontal areas. Topographic organization differs between IT-type and PT-type neurons, including injections in the same site, with IT-type neurons having higher topographic stereotypy than PT-type neurons. Furthermore, IT-type projections from interconnected cortical areas have stronger correlations in corticostriatal targeting than PT-type projections do. As predicted by a longstanding model, corticostriatal projections of interconnected cortical areas form parallel circuits in the basal ganglia.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05780-7}, author = {Hooks, Bryan M and Papale, Andrew E and Paletzki, Ronald F and Feroze, Muhammad W and Eastwood, Brian S and Couey, Jonathan J and Winnubst, Johan and Chandrashekar, Jayaram and Gerfen, Charles R} } @article {48044, title = {Long distance projections of cortical pyramidal neurons.}, journal = {Journal of Neuroscience Research}, year = {2016}, month = {2016 Nov 12}, abstract = {

The neuronal circuits defined by the axonal projections of pyramidal neurons in the cerebral cortex are responsible for processing sensory and other information to plan and execute behavior. Subtypes of cortical pyramidal neurons are organized across layers, with those in different layers distinguished by their patterns of axonal projections and connectivity. For example, those in layers 2 and 3 project between cortical areas to integrate sensory and other information with motor areas; while those in layers 5 and 6 also integrate information between cortical areas, but also project to subcortical structures involved in the generation of behavior. Recent advances in neuroanatomical techniques allow one to target specific subtypes of cortical pyramidal neurons and label both their inputs and projections. Combining these methods with neurophysiological recording techniques and newly introduced atlases of the mouse brain provide the opportunity to achieve a detailed view of the organization of cerebral cortical circuits.

}, doi = {10.1002/jnr.23978}, author = {Gerfen, Charles R and Economo, Michael N and Chandrashekar, Jayaram} } @article {47274, title = {A platform for brain-wide imaging and reconstruction of individual neurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Jan 20}, abstract = {

The structure of axonal arbors controls how signals from individual neurons are routed within the mammalian brain. However, the arbors of very few long-range projection neurons have been reconstructed in their entirety, as axons with diameters as small as 100 nm arborize in target regions dispersed over many millimeters of tissue. We introduce a platform for high-resolution, three-dimensional fluorescence imaging of complete tissue volumes that enables the visualization and reconstruction of long-range axonal arbors. This platform relies on a high-speed two-photon microscope integrated with a tissue vibratome and a suite of computational tools for large-scale image data. We demonstrate the power of this approach by reconstructing the axonal arbors of multiple neurons in the motor cortex across a single mouse brain.

}, issn = {2050-084X}, doi = {10.7554/eLife.10566}, author = {Economo, Michael N and Clack, Nathan G and Lavis, Luke D and Gerfen, Charles R and Svoboda, Karel and Myers, Eugene W and Chandrashekar, Jayaram} } @article {46189, title = {The neural representation of taste quality at the periphery.}, journal = {Nature}, volume = {517}, year = {2015}, month = {2015 Jan 15}, pages = {373-6}, abstract = {

The mammalian taste system is responsible for sensing and responding to the five basic taste qualities: sweet, sour, bitter, salty and umami. Previously, we showed that each taste is detected by dedicated taste receptor cells (TRCs) on the tongue and palate epithelium. To understand how TRCs transmit information to higher neural centres, we examined the tuning properties of large ensembles of neurons in the first neural station of the gustatory system. Here, we generated and characterized a collection of transgenic mice expressing a genetically encoded calcium indicator in central and peripheral neurons, and used a gradient refractive index microendoscope combined with high-resolution two-photon microscopy to image taste responses from ganglion neurons buried deep at the base of the brain. Our results reveal fine selectivity in the taste preference of ganglion neurons; demonstrate a strong match between TRCs in the tongue and the principal neural afferents relaying taste information to the brain; and expose the highly specific transfer of taste information between taste cells and the central nervous system.

}, keywords = {Animals, Calcium, Geniculate Ganglion, Mice, Mice, Transgenic, Neurons, Taste, Taste Buds, Taste Perception, Tongue}, issn = {1476-4687}, doi = {10.1038/nature13873}, author = {Barretto, Robert P J and Gillis-Smith, Sarah and Chandrashekar, Jayaram and Yarmolinsky, David A and Schnitzer, Mark J and Ryba, Nicholas J P and Zuker, Charles S} } @article {1767, title = {The cells and peripheral representation of sodium taste in mice.}, journal = {Nature}, volume = {464}, year = {2010}, month = {2010 Mar 11}, pages = {297-301}, abstract = {

Salt taste in mammals can trigger two divergent behavioural responses. In general, concentrated saline solutions elicit robust behavioural aversion, whereas low concentrations of NaCl are typically attractive, particularly after sodium depletion. Notably, the attractive salt pathway is selectively responsive to sodium and inhibited by amiloride, whereas the aversive one functions as a non-selective detector for a wide range of salts. Because amiloride is a potent inhibitor of the epithelial sodium channel (ENaC), ENaC has been proposed to function as a component of the salt-taste-receptor system. Previously, we showed that four of the five basic taste qualities-sweet, sour, bitter and umami-are mediated by separate taste-receptor cells (TRCs) each tuned to a single taste modality, and wired to elicit stereotypical behavioural responses. Here we show that sodium sensing is also mediated by a dedicated population of TRCs. These taste cells express the epithelial sodium channel ENaC, and mediate behavioural attraction to NaCl. We genetically engineered mice lacking ENaCalpha in TRCs, and produced animals exhibiting a complete loss of salt attraction and sodium taste responses. Together, these studies substantiate independent cellular substrates for all five basic taste qualities, and validate the essential role of ENaC for sodium taste in mice.

}, keywords = {Animals, Behavior, Epithelial Sodium Channel, Mice, Sodium, Taste, Taste Buds, Transgenic}, issn = {1476-4687}, doi = {10.1038/nature08783}, author = {Chandrashekar, Jayaram and Kuhn, Christina and Oka, Yuki and Yarmolinsky, David A and Hummler, Edith and Ryba, Nicholas J P and Zuker, Charles S} } @article {1768, title = {The taste of carbonation.}, journal = {Science}, volume = {326}, year = {2009}, month = {2009 Oct 16}, pages = {443-5}, abstract = {

Carbonated beverages are commonly available and immensely popular, but little is known about the cellular and molecular mechanisms underlying the perception of carbonation in the mouth. In mammals, carbonation elicits both somatosensory and chemosensory responses, including activation of taste neurons. We have identified the cellular and molecular substrates for the taste of carbonation. By targeted genetic ablation and the silencing of synapses in defined populations of taste receptor cells, we demonstrated that the sour-sensing cells act as the taste sensors for carbonation, and showed that carbonic anhydrase 4, a glycosylphosphatidylinositol-anchored enzyme, functions as the principal CO2 taste sensor. Together, these studies reveal the basis of the taste of carbonation as well as the contribution of taste cells in the orosensory response to CO2.

}, keywords = {Action Potentials, Animals, Benzolamide, Bicarbonates, Calcium Channels, Carbon Dioxide, Carbonated Beverages, Carbonic Anhydrase Inhibitors, Carbonic Anhydrase IV, Carbonic Anhydrases, Cell Surface, Chorda Tympani Nerve, Gene Expression Profiling, Mice, Protons, Receptors, Taste, Taste Buds, Taste Perception, Transgenic}, issn = {1095-9203}, doi = {10.1126/science.1174601}, author = {Chandrashekar, Jayaram and Yarmolinsky, David and von Buchholtz, Lars and Oka, Yuki and Sly, William and Ryba, Nicholas J P and Zuker, Charles S} } @article {1773, title = {The cells and logic for mammalian sour taste detection.}, journal = {Nature}, volume = {442}, year = {2006}, month = {2006 Aug 24}, pages = {934-8}, abstract = {

Mammals taste many compounds yet use a sensory palette consisting of only five basic taste modalities: sweet, bitter, sour, salty and umami (the taste of monosodium glutamate). Although this repertoire may seem modest, it provides animals with critical information about the nature and quality of food. Sour taste detection functions as an important sensory input to warn against the ingestion of acidic (for example, spoiled or unripe) food sources. We have used a combination of bioinformatics, genetic and functional studies to identify PKD2L1, a polycystic-kidney-disease-like ion channel, as a candidate mammalian sour taste sensor. In the tongue, PKD2L1 is expressed in a subset of taste receptor cells distinct from those responsible for sweet, bitter and umami taste. To examine the role of PKD2L1-expressing taste cells in vivo, we engineered mice with targeted genetic ablations of selected populations of taste receptor cells. Animals lacking PKD2L1-expressing cells are completely devoid of taste responses to sour stimuli. Notably, responses to all other tastants remained unaffected, proving that the segregation of taste qualities even extends to ionic stimuli. Our results now establish independent cellular substrates for four of the five basic taste modalities, and support a comprehensive labelled-line mode of taste coding at the periphery. Notably, PKD2L1 is also expressed in specific neurons surrounding the central canal of the spinal cord. Here we demonstrate that these PKD2L1-expressing neurons send projections to the central canal, and selectively trigger action potentials in response to decreases in extracellular pH. We propose that these cells correspond to the long-sought components of the cerebrospinal fluid chemosensory system. Taken together, our results suggest a common basis for acid sensing in disparate physiological settings.

}, keywords = {Action Potentials, Animals, Calcium Channels, Cell Surface, Computational Biology, Gene Expression Profiling, Hydrogen-Ion Concentration, Membrane Glycoproteins, Mice, Neurons, Phosphoproteins, Receptors, Spinal Cord, Taste, Tongue, Transgenic}, issn = {1476-4687}, doi = {10.1038/nature05084}, author = {Huang, Angela L and Chen, Xiaoke and Hoon, Mark A and Chandrashekar, Jayaram and Guo, Wei and Tr{\"a}nkner, Dimitri and Ryba, Nicholas J P and Zuker, Charles S} } @article {1771, title = {The receptors and cells for mammalian taste.}, journal = {Nature}, volume = {444}, year = {2006}, month = {2006 Nov 16}, pages = {288-94}, abstract = {

The emerging picture of taste coding at the periphery is one of elegant simplicity. Contrary to what was generally believed, it is now clear that distinct cell types expressing unique receptors are tuned to detect each of the five basic tastes: sweet, sour, bitter, salty and umami. Importantly, receptor cells for each taste quality function as dedicated sensors wired to elicit stereotypic responses.

}, keywords = {Animals, G-Protein-Coupled, Humans, Receptors, Signal Transduction, Taste, Taste Buds}, issn = {1476-4687}, doi = {10.1038/nature05401}, author = {Chandrashekar, Jayaram and Hoon, Mark A and Ryba, Nicholas J P and Zuker, Charles S} } @article {1774, title = {The receptors and coding logic for bitter taste.}, journal = {Nature}, volume = {434}, year = {2005}, month = {2005 Mar 10}, pages = {225-9}, abstract = {

The sense of taste provides animals with valuable information about the nature and quality of food. Bitter taste detection functions as an important sensory input to warn against the ingestion of toxic and noxious substances. T2Rs are a family of approximately 30 highly divergent G-protein-coupled receptors (GPCRs) that are selectively expressed in the tongue and palate epithelium and are implicated in bitter taste sensing. Here we demonstrate, using a combination of genetic, behavioural and physiological studies, that T2R receptors are necessary and sufficient for the detection and perception of bitter compounds, and show that differences in T2Rs between species (human and mouse) can determine the selectivity of bitter taste responses. In addition, we show that mice engineered to express a bitter taste receptor in {\textquoteright}sweet cells{\textquoteright} become strongly attracted to its cognate bitter tastants, whereas expression of the same receptor (or even a novel GPCR) in T2R-expressing cells resulted in mice that are averse to the respective compounds. Together these results illustrate the fundamental principle of bitter taste coding at the periphery: dedicated cells act as broadly tuned bitter sensors that are wired to mediate behavioural aversion.

}, keywords = {Animals, Food Preferences, G-Protein-Coupled, Humans, Inbred BALB C, Inbred C57BL, Knockout, Mice, Palate, Physical Stimulation, Receptors, Species Specificity, Substrate Specificity, Taste, Tongue}, issn = {1476-4687}, doi = {10.1038/nature03352}, author = {Mueller, Ken L and Hoon, Mark A and Erlenbach, Isolde and Chandrashekar, Jayaram and Zuker, Charles S and Ryba, Nicholas J P} } @article {1777, title = {Coding of sweet, bitter, and umami tastes: different receptor cells sharing similar signaling pathways.}, journal = {Cell}, volume = {112}, year = {2003}, month = {2003 Feb 7}, pages = {293-301}, abstract = {

Mammals can taste a wide repertoire of chemosensory stimuli. Two unrelated families of receptors (T1Rs and T2Rs) mediate responses to sweet, amino acids, and bitter compounds. Here, we demonstrate that knockouts of TRPM5, a taste TRP ion channel, or PLCbeta2, a phospholipase C selectively expressed in taste tissue, abolish sweet, amino acid, and bitter taste reception, but do not impact sour or salty tastes. Therefore, despite relying on different receptors, sweet, amino acid, and bitter transduction converge on common signaling molecules. Using PLCbeta2 taste-blind animals, we then examined a fundamental question in taste perception: how taste modalities are encoded at the cellular level. Mice engineered to rescue PLCbeta2 function exclusively in bitter-receptor expressing cells respond normally to bitter tastants but do not taste sweet or amino acid stimuli. Thus, bitter is encoded independently of sweet and amino acids, and taste receptor cells are not broadly tuned across these modalities.

}, keywords = {Action Potentials, Afferent, Animals, Cell Membrane, Cell Surface, Cells, Citric Acid, Cultured, Female, Glutamic Acid, GTP-Binding Proteins, Isoenzymes, Knockout, Male, Membrane Proteins, Mice, Neurons, Phospholipase C beta, Quinine, Receptors, Sensory Receptor Cells, Signal Transduction, Sucrose, Taste, Taste Buds, TRPM Cation Channels, Type C Phospholipases}, issn = {0092-8674}, author = {Zhang, Yifeng and Hoon, Mark A and Chandrashekar, Jayaram and Mueller, Ken L and Cook, Boaz and Wu, Dianqing and Zuker, Charles S and Ryba, Nicholas J P} } @article {1776, title = {The receptors for mammalian sweet and umami taste.}, journal = {Cell}, volume = {115}, year = {2003}, month = {2003 Oct 31}, pages = {255-66}, abstract = {

Sweet and umami (the taste of monosodium glutamate) are the main attractive taste modalities in humans. T1Rs are candidate mammalian taste receptors that combine to assemble two heteromeric G-protein-coupled receptor complexes: T1R1+3, an umami sensor, and T1R2+3, a sweet receptor. We now report the behavioral and physiological characterization of T1R1, T1R2, and T1R3 knockout mice. We demonstrate that sweet and umami taste are strictly dependent on T1R-receptors, and show that selective elimination of T1R-subunits differentially abolishes detection and perception of these two taste modalities. To examine the basis of sweet tastant recognition and coding, we engineered animals expressing either the human T1R2-receptor (hT1R2), or a modified opioid-receptor (RASSL) in sweet cells. Expression of hT1R2 in mice generates animals with humanized sweet taste preferences, while expression of RASSL drives strong attraction to a synthetic opiate, demonstrating that sweet cells trigger dedicated behavioral outputs, but their tastant selectivity is determined by the nature of the receptors.

}, keywords = {Animals, Flavoring Agents, G-Protein-Coupled, Gene Deletion, Humans, In Situ Hybridization, kappa, Knockout, Mice, Opioid, Protein Isoforms, Protein Subunits, Receptors, Sodium Glutamate, Sucrose, Taste, Taste Buds}, issn = {0092-8674}, author = {Zhao, Grace Q and Zhang, Yifeng and Hoon, Mark A and Chandrashekar, Jayaram and Erlenbach, Isolde and Ryba, Nicholas J P and Zuker, Charles S} } @article {1778, title = {An amino-acid taste receptor.}, journal = {Nature}, volume = {416}, year = {2002}, month = {2002 Mar 14}, pages = {199-202}, abstract = {

The sense of taste provides animals with valuable information about the nature and quality of food. Mammals can recognize and respond to a diverse repertoire of chemical entities, including sugars, salts, acids and a wide range of toxic substances. Several amino acids taste sweet or delicious (umami) to humans, and are attractive to rodents and other animals. This is noteworthy because L-amino acids function as the building blocks of proteins, as biosynthetic precursors of many biologically relevant small molecules, and as metabolic fuel. Thus, having a taste pathway dedicated to their detection probably had significant evolutionary implications. Here we identify and characterize a mammalian amino-acid taste receptor. This receptor, T1R1+3, is a heteromer of the taste-specific T1R1 and T1R3 G-protein-coupled receptors. We demonstrate that T1R1 and T1R3 combine to function as a broadly tuned L-amino-acid sensor responding to most of the 20 standard amino acids, but not to their D-enantiomers or other compounds. We also show that sequence differences in T1R receptors within and between species (human and mouse) can significantly influence the selectivity and specificity of taste responses.

}, keywords = {Alleles, Amino Acids, Animals, Calcium Signaling, Cell Line, Cell Surface, Chorda Tympani Nerve, Dose-Response Relationship, Drug, G-Protein-Coupled, Genetic, Heterotrimeric GTP-Binding Proteins, Humans, Inosine Monophosphate, Mice, Mutation, Polymorphism, Protein Subunits, Receptors, Stereoisomerism, Structure-Activity Relationship, Substrate Specificity, Taste, Taste Buds, Transfection}, issn = {0028-0836}, doi = {10.1038/nature726}, author = {Nelson, Greg and Chandrashekar, Jayaram and Hoon, Mark A and Feng, Luxin and Zhao, Grace and Ryba, Nicholas J P and Zuker, Charles S} }