v.1.0 (January, 2009) - Updated with simplified import hierarchy of upper level ontologies as part of the transition from NIFSTD 0.5 to 1.0. v1.2 (July, 2009) - New terms have been added since the January release (ID used: nlx_subcell_20090101 - 20090703) v1.1 (February, 2009) - * Duplicate classes from SAO (sao_ and nifext_ prefixed IDs) has been eliminated as identified in the NeuroLex wiki. While retiring the duplicate classes, kept the ones with most detailed annotations or merged the annotation (synonyms, definitions etc) into the ones that had more/better information regardless of their IDs with sao or nifext prefixes. * Not all sao prefixed IDs are out of date or replaced by nifext. 1.2 NIF-Subcellular: contains cell parts and subcellular structures from SAO-CORE next ID: nlx_subcell_20090212 Condensed Chromatin 0000792 Chromatin that are agglomerated into irregular masses, some attached to the nuclear envelope. Condensed Chromatin heterochromatin A compact and highly condensed form of chromatin (Gene Ontology). sao581845896 uncurated sao831502550 uncurated Regional Part Of Oligodendrocyte Regional Part Of Oligodendrocyte Portion of the nucleolus composed of densely matted filaments with scattered dark granules (Palay and Chan-Palay, 1974). C0230581 Pars Fibrosa uncurated sao1841764412 Pars Fibrosa Main Axon Main Axon uncurated sao1596975044 Used to refer to the main axonal trunk, as opposed to the collaterals. Refers to dendrites arising from another dendrite. uncurated Dendritic Branch Dendritic Branch sao884265541 Foundational Model of Anatomy Merkel's disc Merkel's disk Encapsulated nerve ending formed by the neurite of a dorsal root ganglion cell in close apposition to a Merkel cell found in the basal layer of glabrous and hairy skin, in hair follicles, and in oral and anal mucosa. The Merkel disc functions as a sensory receptor for pressure and texture information (adapted from Wikipedia) Merkel cell-neurite complex Merkels disc Merkel disk receptor February 23, 2010 Post-synaptic Density Synaptic component; electron dense cytoskeletal specialization located on the post synaptic membrane at the site of synaptic contact. The PSD is particularly prominent in glutamatergic synapses, giving the synapse an asymmetrical appearance. This type of PSD is often referred to as "asymmetrical" or Gray's Type 1 (Maryann Martone, from the CCDB Dictionary). 0014069 http://ccdb.ucsd.edu/SAO/images/psd_sw_512x512.jpg sao1196688972 BF_C000103 Post-synaptic Density Cerebellar glomerulus May 16, 2009 Dendriole uncurated Dendriole sao295057932 sao118541872 0005921 Any specialized areas of the plasma membranes of adjacent cells where the membranes are 2-4 nm apart and penetrated by a connexon (Gene Ontology). uncurated C0206117 Gap Junction http://ccdb.ucsd.edu/SAO/images/gap_junction_sw_512x512.jpg Gap Junction uncurated sao1590928667 Regional Part Of Spiny Dendrite Regional Part Of Spiny Dendrite Dense plate-like structure lying near and perpendicular to the pre-synaptic junction. Usually associated with pre-synaptic vesicles (Peters, Palay, and Webster). Pre-synaptic Ribbon sao-1488888179 http://ccdb.ucsd.edu/SAO/images/pre-syn_ribbon_sw_512x512.jpg Pre-synaptic Ribbon Maryann Martone February 23, 2010 May 19, 2009 Terminal ending of the axon of a motor neuron that forms a synapse onto a muscle cell. Motor endplate Schaffer collateral May 19, 2009 Part of axon of the CA3 pyramidal neuron that projects to hippocampal area CA1 . Maryann Martone secretory vesicle uncurated Transport Vesicle Any of the vesicles of the constitutive secretory pathway, which carry cargo from the ER to the Golgi, between Golgi cisternae, and to destinations within or outside the cell (Gene Ontolgoy). C0887882 sao885490876 Transport Vesicle 0030133 Meissner's corpuscles are encapsulated nerve endings of dorsal root ganglion cells. They are located in skin, which consist of flattened supportive cells arranged as horizontal lamellae surrounded by a connective tissue capsule, that function as mechanoreceptors for light touch. The corpuscle is between 30-140 μm in length and 40-60 μm in diameter. Meissner's corpuscle tactile corpuscle Meisner's corpuscle Meisners corpuscle Meissners corpuscle The volume enclosed by the membranes of an endosome (Gene Ontology). Endosomal Lumen Endosomal Lumen sao1547508851 endosome lumen uncurated 0031904 Regional Part Of Neuronal Cell Body uncurated sao1049717962 Regional Part Of Neuronal Cell Body Synaptic arrangement observed in thalamic glomeruli consisting of a afferent terminal synapsing on both an interneuron axon terminal and the dendrite of a relay cell. The interneuron terminal also synapses on the dendrite of a relay cell, forming a triadic arrangement. May 15, 2009 Triad Parallel fiber Regional part of a cerebellar granule cell axon referring to the bifurcation of the granule cell axon in the molecular layer into two diametrically opposed branches that are oriented parallel to the long axis of the folium. (adapted from Shepherd, G. M. The synaptic organization of the brain, 5th ed. New York: Oxford University Press, 2004. March 17, 2010 Trunk sao1078172392 Trunk uncurated Junction Complex Mitochondrial Lumen Mitochondrial Lumen Interior portion of mitochondrion bounded by the inner mitochondrial membrane and cristae membranes and containing the mitochondrial matrix. Does not include the crista or crista lumen. uncurated Inner Mitochondrial Compartment (from Peters, Palay, and Webster) sao-1899375636 true 0031980 0035061 uncurated C0230547 Interchromatin Granule Interchromatin Granule sao1049471211 A class of nuclear body measuring 20-25 nm in diameter and distributed throughout the interchromatin space, linked together by thin fibrils. They are believed to be storage centers for various snRNAs, snRNPs, serine/arginine-rich proteins and RNA polymerase II. A typical mammalian cell contains 25-50 clusters of interchromatin granules. Interchromatin granule clusters do not contain the heterogeneous nuclear RNA-binding proteins (hnRNPs) (Gene Ontology). Glia limitans The meshwork of astrocytic foot processes (glial end feet) covered by a basal lamina adjacent to the inner pial surface of the central nervous system. February 10, 2010 glial limiting membrane Meshwork of extremely fine filaments composed of polypeptides called lamins that run parallel with the inner surface of the nuclear envelope (Peters, Palay and Webster, 1991). Nuclear Lamina uncurated sao1455996588 0005652 Nuclear Lamina C1136039 The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus, composed of lamin filaments. The polypeptides of the lamina are thought to be concerned in the dissolution of the nuclear envelope and its re-formation during mitosis. The lamina is composed of lamin A and lamin C filaments cross-linked into an orthogonal lattice, which is attached via lamin B to the inner nuclear membrane through interactions with a lamin B receptor, an IFAP, in the membrane (Gene Ontology). Subplasmalemmal Coating 2007-02-23 Subplasmalemmal Coating core:definition incomplete sao1938587839 Electron dense material observed coating the cytoplasmic face of the plasma membrane in certain regions of a neuron, e.g., the axon initial segment; the nodal membrane at the Node of Ranvier February 23, 2010 Pacinian corpuscle Foundational Model of Anatomy Encapsulated nerve ending located in skin composed of nerve ending of a dorsal root ganglion neuron wrapped in 20-60 concentric lamellae composed of fibrous tissue and fibroblasts. They function as mechanoreceptors for pressure (adapted from Wikipedia) Sarah M. Maynard Paired Helical Filament Paired Helical Filament Two threads of tau protein that are wound around each other. PHF sao6603990120 Terminal pre-synaptic ending of an axon or axon collateral. Synaptic Bouton sao187426937 http://ccdb.ucsd.edu/SAO/images/syn_bouton_sw_512x512.jpg Synaptic Bouton uncurated Intercalated Disk Contact site between adjacent cells in cardiac muscle fibers. When observing tissue through a microscope, this is an identifying feature of cardiac muscle.It holds the myofibrils together and permits easy transfer of excitation (depolarization). uncurated Intercalated Disk sao1152983960 Synaptic Component sao1784069613 Synaptic Component sao1974433376 Regional Part Of Epithelial Cell uncurated Regional Part Of Epithelial Cell C0932419 Portion of the ensheathing process (either myelin or non-myelin) where the enveloping lips of the ensheathing cell come together so that their apposed plasma membranes run parallel to each other, separated by a cleft 12 nm wide (Peters, Palay and Webster, 1991). sao2127666702 Mesaxon uncurated Mesaxon uncurated Ensheathing Process sao1376748732 Ensheathing Process http://ccdb.ucsd.edu/SAO/images/ensheath_process_sw_512x512.jpg Refers to the process of the Schwann cell that surrounds an unmyelinated axon or cell soma. February 23, 2010 C bouton Synaptic bouton found in spinal cord on the soma and proximal dendrites of motor neurons 0043083 http://ccdb.ucsd.edu/SAO/images/syn_cleft_sw_512x512.jpg Synaptic Cleft The narrow gap that separates the presynaptic and postsynaptic membranes, into which a neurotransmitter is released (Gene Ontology). uncurated Synaptic Cleft http://ccdb.ucsd.edu/SAO/images/syn_cleft_2_sw_512x512.jpg C0682685 sao243541954 sao830981606 Intracellular Membrane uncurated Intracellular Membrane http://ccdb.ucsd.edu/SAO/images/mutlivesicular_body_sw_512x512.jpg Multivesicular Body Multivesicular Body A type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm (Gene Ontology). 0005771 sao2045955158 http://ccdb.ucsd.edu/SAO/images/multives_bodies_sw_512x512.jpg uncurated C0230825 Inclusion Body A nuclear or cytoplasmic aggregate of stainable substances, usually proteins. Cellular Inclusion Cellular Inclusion uncurated sao120573470 Nuclear Subcomponent Nuclear Subcomponent uncurated sao1499850686 sao1074198261 Post-synaptic Site Before replacing the is_Location_Of property with RO's contained_in and the site_Contained_In property with RO's contained_in, we had the two restrictions: 1) is_Location_Of some Post-synaptic Density and 2) site_Contained_In some Post-synatpic Density. Thus, now we just have one restriction: contained_in some Post-synaptic Density. Post-synaptic Site A synapse of the mossy fiber onto the dendrite of a granule cell; each mossy fiber can have up to 50 rosettes. (source: http://www.neuroanatomy.wisc.edu/cere/text/P4/mossy.htm) (http://en.wikipedia.org/wiki/Mossy_fiber_(cerebellum)) Sarah M. Maynard October 5, 2009 Mossy fiber rosette A system of insoluble protein fibrils and soluble complexes composed of carbohydrate polymers linked to protein molecules, i.e. proteoglycans, in the extracellular space. Insoluble protein fibrils are mainly of two types: collagen and elastin; the soluble polymers consist of long carbohydrate chains, linked to proteins. Maryann Martone Fmaid: 9672 May 17, 2009 Extracellular matrix S bouton Synaptic bouton found in the ventral horn of the spinal cord. S boutons range in size from 0.5 to 8 um in diameter and contain spherical synaptic vesicles, as determined by electron microscopy February 23, 2010 Mushroom Dendritic Spine sao-876577163 Mushroom Dendritic Spine uncurated http://ccdb.ucsd.edu/SAO/images/mush_dend_spine_sw_512x512.jpg uncurated 0031410 Cytoplasmic Vesicle sao180601769 A vesicle formed of membrane or protein, found in the cytoplasm of a cell (Gene Ontology). Cytoplasmic Vesicle sao2019617624 Specialized ribosome-free subdomains of synthetic endoplasmic reticulum where cargo is concentrated into vesicles tha bud from the endoplasmic reticulum for tranport to the Golgi (Horton and Ehlers, 2004). Regional Part Of RER Regional Part Of RER uncurated http://ccdb.ucsd.edu/SAO/images/syn_vesicles_2_sw_512x512.jpg uncurated http://ccdb.ucsd.edu/SAO/images/syn_vesicles_sw_512x512.jpg Secretory organelles, some 50 nm in diameter, of pre-synaptic nerve terminals; accumulate high concentrations of neurotransmitters and secrete these into the synaptic cleft by fusion with the 'active zone' of the pre-synaptic plasma membrane (Gene Ontology). sao1071221672 Synaptic Vesicle C0039065 Synaptic Vesicle 0008021 http://ccdb.ucsd.edu/SAO/images/syn_vesicles_3_sw_512x512.jpg March 18, 2009 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#sao500241072 Sarah M. Maynard sao4785563283 uncurated Amyloid Aggregate Insoluble fibrous protein aggregation sharing specific structural traits. Amyloid Aggregate Synaptic bouton found in the ventral horn of the spinal cord that range in diameter from 0.5 to 7 um and contain flattened or pleomorphic synaptic vesicles in electron microscopic preparations. F bouton February 23, 2010 Corona uncurated sao5764355747 Sarah M. Maynard The periphery of the Lewy Body. In Parkinson's Disease, it contains sperical accumulations of filaments arrange in a loose, radiating array. Corona Halo uncurated Regional Part Of Neuron Process sao-420949334 Regional Part Of Neuron Process Mixed Synapse Synaptic contact characterized by both electrical and chemical synaptic junctions. Existence of both chemical and electrotonic synapses at the same interface (Peters, Palay and Webster, 1991). Mixed Synapse sao1506103497 uncurated Calyx uncurated sao488120195 Calyx Senile Plaque Extracellular deposits of Beta-amyloid / 8-10 nm amyloid fibrils that are polymers of amyloid-Beta protein. They are located in grey matter and associated with degenerative neural structures and an abundance of microglia and astrocytes. amyloid plaques, senile druse, braindruse sao9615155060 uncurated http://ccdb.ucsd.edu/SAO/images/senile_plaque_sw_512x512.jpg Senile Plaque Sarah M. Maynard We are not sure if there is a distinction between Neuritic plaque and Senile plaque. 2006-09-28 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1196688972 Post synaptic density BF_C000103 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone 2006-07-15 Post synaptic density Mitochondrial Membrane Inner Mitochondrial Membrane Inner http://ccdb.ucsd.edu/SAO/images/mito_inner_memb_ccdb_512x512.jpg The inner membrane of the mitochondria. It is highly folded to form cristae (Gene Ontology). The inner membrane of the mitochondria. It is highly folded to form cristae (Gene Ontology). sao1371347282 C0230840 uncurated 0005743 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao3826089237 Axon projection May 17, 2009 Maryann Martone Group of myelinated or unmyelinated axons that group together. Axon bundle Puncta Adhaerentia Puncta Adhaerentia sao257629430 A small version of the zonula adharens type junction, characterized by a symmetrical adherent point between two cells. http://ccdb.ucsd.edu/SAO/images/puncta_adherens_sw_512x512.jpg uncurated Sample population 2006-10-09 2006-09-07 Bill Bug Sample population A defined subset of a population whose spatio-temporal interactions or aggregate behavior is representative of the whole population. sao1573004591 This comes from derouiche et al. J. Physol. Paris 2002 96:177 PubMedID:12445894 Peripheral Astrocyte Process Thin terminal processes of astrocytes found in sheathing, axon terminals, blood vessels, and pial surface of the brain. These processes are characterized by few glial filiments or organelles and high concentrations of the actin-binding protein ezrin. graph position temporary Peripheral Astrocyte Process It is not clear whether peripheral astrocyte process only refers to the processes surrounding synapses or also refers to the endfeet Thin terminal processes of astrocytes found in sheathing, axon terminals, blood vessels, and pial surface of the brain. Mitochondrial Site sao-1367457321 Mitochondrial Site Tail Portion Tail Portion uncurated Elongated process, devoid of cytoplasmic extensions, that courses through the hypothalamic nucleis to form small endfoot processes that terminate either on blood vessels or at the pial surface of the brain (Peters, Palay and Webster, 1991). sao1749953771 Blood brain barrier A supracellular structure formed by tight junctions between capillary endothelial cells in the brain that prevents substances from entering the brain from the vasculature, except by passage of substances through the endothelial cell. The BBB has also been defined physiologically Blood-brain barrier BBB 0043197 http://ccdb.ucsd.edu/SAO/images/dend_spine_sw_512x512.jpg sao1799103720 http://ccdb.ucsd.edu/SAO/images/dend_spine_ccdb_512x512.jpg C0872341 uncurated Dendritic Spine Protrusion from a dendrite. Spines are specialised subcellular compartments involved in the synaptic transmission. They are linked to the dendritic shaft by a restriction. Because of their bulb shape, they function as a biochemical and an electrical compartment. Spine remodeling is though to be involved in synaptic plasticity (Gene Ontology). Dendritic Spine Maryann Martone May 17, 2009 Nerve ending found in skin surrounded by layers of connective tissue. Encapsulated nerve ending Pre-synaptic Site sao2108323256 Pre-synaptic Site The dentate gyrus: fundamental neuroanatomical organization (dentate gyrus for dummies) by David G. Amaral, Helen E. Scharfman, and Pierre Lavenex PMID PMC2492885 Granule cell axons PMC2492885 June 18, 2009 The granule cells give rise to distinctive unmyelinated axons referred to as mossy fibers by Ramón y Cajal. Dentate gyrus mossy fiber Maryann Martone Refers to the bundled configuration of microtubules in the axon hillock and initial segment. Axon Microtubule Fascicle Axon Microtubule Fascicle uncurated sao707332678 Cilium sao787716553 C0008778 uncurated 0005929 Cilia arising from neurons have been described in many different regions of the nervous system. Neuronal cilia have a "9+0" pattern, that is, they are missing the central pair of microtubules that characterizes most cilia (Peters, Palay and Webster, 1991). Cilium http://ccdb.ucsd.edu/SAO/images/cilium_sw_512x512.jpg sao1950673097 Schaffer Collateral Schaffer Collateral uncurated Axon collateral of CA3 pyramidal neurons that project to CA1 and synapse in the zona radiatum. post-synaptic density cytoskeletal system UMLS Constitutional part of cell Bill Bug 2006-09-07 February 18, 2010 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1635329413 2006-07-15 cytoskeleton Maryann Martone Cytoskeletal system sao991156472 Cell Component Aggregate Object Cell Component Aggregate Object Lewy Body Lewy Body sao4933778419 Sarah M. Maynard uncurated Neuronal inclusion commonly found in damaged neurons. A spherical mass that dispaces other cells composed of abnormally phosphorylated, neurofilament proteins aggregated with ubiquitin and alpha-synuclein. They are intracytoplasmic. there are two morphological types: classical (brain stem) and cortical Lewy bodies Axon arising from cerebellar projecting cells in the cochlea, vestibular nuclei, spinal cord, reticular formation, cerebellar nuclei and basilar pontine nuclei. Mossy fibers enter through all three cerebellar peduncles and send collaterals to the deep cerebellar nuclei, then branch in the white matter and terminate in the granule cell layer. Through this branching, a given mossy fiber can innervate several folia. Mossy fibers synapse on granule cells. The synaptic contacts are made at enlargements along the length of the mossy fiber called mossy fiber rosettes. The enlargements of the rosettes give the axons as "mossy" appearance in Golgi stained preparations. (adapted from Shepherd, G. M. The synaptic organization of the brain, 5th ed. New York: Oxford University Press, 2004). Shepherd, G. M. The synaptic organization of the brain, 5th ed. New York: Oxford University Press, 2004 Cerebellar mossy fiber Cerebellar mossy fiber February 27, 2009 uncurated A configuration of ER found in Purkinje cells in the cerebellum and in axons in the lateral vestibular nucleus, consisting of a number of parallel and interconnecting tubules whose outer surfaces are covered by particles or ringlike structures (Peters, Palay and Webster, 1991). Membrane Stack Membrane Stack sao2114874506 sao2006047981 Microfilament A two-stranded helical polymer of the protein actin. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. Reference(s): ISBN:0198506732 PMID:10666339 (GO) uncurated Microfilament C0025979 sao1922892319 0005911 Intercellular Junction Site The Cell_Cell_Contact_Zone and the Intercellular_Junction are not the same. The junction only refers to the bridging complex and not the larger region where the junction resides. The intercellular_Junction is part of a larger cell-cell contact zone. The cell-cell contact zone may also contain additional junctions and cellular machinery related to the function of the junction. core:definition incomplete The site of cell-cell contact containing a morphologically identified junctional complex joining the two cells. Intercellular Junction Site Oligodendrocyte Paranodal Termination sao1354781919 Oligodendrocyte Paranodal Termination uncurated Paranodal loop Cytoplasmic pockets, or as they appear in thin sections "loops" formed by the Schwann cell in the paranodal region. These pockets are actually part of a continuous helical structure providing cytoplasmic continuity from the inntermost to the outermost layers of the myelin sheath through the cytoplasmic channel formed by the loop. Most are directly apposed to the paranodal axonal membrane Thalamic glomerulus May 16, 2009 Synaptic structure found in thalamic relay nuclei consising of a complex of afferent terminals, relay cell dendrites, interneuron dendrites and other processes. These complexes are surrounded by astrocytic processes. Shepherd, G. M. The synaptic organization of the brain, 5th ed New York: Oxford University Press, 2005 2006-09-28 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS 2006-09-28 C0021770 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao952483289 2006-07-15 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting Intermediate filament Intermediate filament Cytoskeletal element consisting of elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of higher eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: keratin filaments of mammalian epithelial cells; desmin filaments found in cells of muscles of all types; vimentin filaments found in mesenchymal cells; neurofilaments of neurons; and glial filaments found in all types of glial cells (Gene Ontology). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF Microfilament Microfilament http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao2006047981 2006-07-15 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated sao-82111036 Cell Protrusion uncurated Cell Protrusion Eosinophilic cytoplasmic lesion, 5 to 15 micrometers in diameter, with a dense eosinphilic core surrounded by a halo of 10 to 20 nm wide radially oriented alpha-synuclein fibrils. sao4749542545 Classical Lewy Body Classical Lewy Body Sarah M. Maynard uncurated uncurated Cellular Subcomponent sao628508602 Cellular Subcomponent Zonula Adhaerens Adherent, symmetrical junction characterized by widened extracellular space and filamentous material (Peters, Palay and Webster, 1991). sao1400623473 fascia adhaerens http://ccdb.ucsd.edu/SAO/images/zonula_adherens_sw_512x512.jpg uncurated Zonula Adhaerens sao-1828894864 uncurated Cell Process Cell Process Regional Part Of Nucleolus Regional Part Of Nucleolus uncurated sao113580911 uncurated Schwann Cell Compact Myelin The portion of the myelin sheath in which layers of cell membrane are tightly juxtaposed, completely excluding cytoplasm. The juxtaposed cytoplasmic surfaces form the major dense line, while the juxtaposed extracellular surfaces form the interperiod line visible in electron micrographs (Gene Ontology). Schwann Cell Compact Myelin sao-1123256993 Membrane Bound Ribosome A ribosome that is attached to a intracellular membrane. Does not itself have a membrane surrounding it. sao1291545653 uncurated Membrane Bound Ribosome February 24, 2009 The space occupied by the endoneurium. Endoneurial Space Sessile Dendritic Spine uncurated Sessile Dendritic Spine sao1536532595 0005840 Ribosome http://ccdb.ucsd.edu/SAO/images/ribosomes_sw_512x512.jpg sao1429207766 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins (Gene Ontology). Ribosome uncurated C0035553 uncurated Structure that exists outside the cell. Sarah M. Maynard Extracellular Structure Extracellular Structure sao9117790637 http://ccdb.ucsd.edu/SAO/images/stubby_dend_spine_sw_512x512.jpg Stubby Dendritic Spine uncurated Stubby Dendritic Spine sao317384566 uncurated Schwann Cell Myelin Sheath sao-593830697 An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system (Gene Ontology). Schwann Cell Myelin Sheath http://ccdb.ucsd.edu/SAO/images/myelin_sheath_sw_512x512.jpg RER Membrane sao3089754107 RER Membrane C0206364 sao1048004962 Tyrosine Kinase Receptor uncurated A class of cellular receptors that have an intrinsic protein-tyrosine kinase activity (MSH). Tyrosine Kinase Receptor Grumose foamy spheroid body is a spheroidal supracellular structure with a foamy appearance in haematoxylin and eosin stains that vary from 10 to 50 microns in diameter and contain amorphous debris-like material found in the brains in certain neurodegenerative conditions. PMID: 7477732 Grumose foamy spheroid body February 12, 2010 Olfactory glomerulus Glomerulus located in the olfactory bulb formed by the incoming axons of olfactory receptor cells synapsing onto the dendritic branches of one or more mitral cells. The olfactory glomerulus is roughly spherical and is partially or wholly encapsulated by glial processes. Maryann Martone May 16, 2009 sao1579007712 Cell Interior uncurated Cell Interior Golgi Subcomponent Golgi Subcomponent uncurated sao624292949 Endosomal Membrane Endosomal Membrane uncurated sao978443756 sao700839054 Need to determine what is the proper relationships between an electrotonic synapse and a gap junction An intercellular junction recognized in electron micrographs as a 7 layered structure with 4 dense lines, two from each of the plasma membranes, alternating with 3 lighter lines. The plaque is composed of multiple intercellular gap junction channels. Gap Junction Plaque Gap Junction Plaque Contact Site Contact Site sao447856407 Sites of close apposition of the inner and outer mitochondrial membrane (Perkins and Frey, 2000). uncurated http://ccdb.ucsd.edu/SAO/images/mito_outer_memb_ccdb_512x512.jpg Mitochondrial Membrane Outer The membrane on the outer surface of the mitochondrion, interfacing with the cell cytoplasm (Gene Ontology). Mitochondrial Membrane Outer C0230839 sao1289741256 uncurated 0005741 0005575 Cell part which has a definable shape, bounded predominantly by bonafide boundaries and is countable (FMA). Cellular Component Equivalent to "constitutional part" in the FMA--a primary partition of an anatomical structure into its compositionally distinct anatomical elements. In the context of the whole, an element is any relatively simple component of which a larger, more complex anatomical structure is compounded; i.e., teh partition is compositional rather than spatial (Mejino JLV et al., 2003). sao976831666 Lumen Cargo Lumen Cargo Refers to cargo carried in the lumen of the vesicle; may be crystalized or otherwise bound, e.g., insulin. Terminal Loop Terminal Loop uncurated Portion of myelin-forming Schwann cell consisting of terminal cytoplasmic extensions adhered to the axon at the beginning and end of the myelin sheath. sao924713546 sao2048701763 uncurated We are unclear why this is causing an inconsistency error. Perivascular Endfoot Perivascular Endfoot From Reactime: Regions within compact myelin in which the cytoplasmic faces of the enveloping myelin sheath are not tightly juxtaposed, and include cytoplasm from the cell responsible for making the myelin. Schmidt-Lanterman clefts occur in the compact myelin internode, while lateral loops are analogous structures found in the paranodal region adjacent to the nodes of Ranvier. Schmidtt-Lanterman Cleft sao254777664 Schmidtt-Lanterman Cleft http://ccdb.ucsd.edu/SAO/images/Schmidtt-Lanterman_cleft_sw_512x512.jpg uncurated Regional Part Of Spine Apparatus Regional Part Of Spine Apparatus sao1682692988 uncurated Amorphous Vesicle uncurated Category of non-SER vesicle described by Clooney et al. (2002) in dendrites, categorized by smooth membranes, electron-lucent interiors and irregular shapes. Sometimes occurrs in clumps. These vesicles contained gold taken up from the extracellular space, suggesting that they may be part of the endosomal pathway. Amorphous Vesicle sao1531915298 sao110773650 uncurated Dendritic Microtubule Dendritic Microtubule sao1153182838 The lipid bilayer surrounding any membrane-bounded vesicle in the cell (Gene Ontology). Vesicle Membrane Vesicle Membrane uncurated C1167317 0012506 0005643 Nuclear Pore C0028587 Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined (Gene Ontology). http://ccdb.ucsd.edu/SAO/images/nucl_pore_2_sw_512x512.jpg uncurated Nuclear Pore sao220861693 http://ccdb.ucsd.edu/SAO/images/nucl_pore_sw_512x512.jpg sao895885284 uncurated Regional Part Of Glial Cell Regional Part Of Glial Cell sao587592318 Neurotransmitter Receptor Role Cell surface receptors that bind signalling molecules released by neurons and convert these signals into intracellular changes influencing the behavior of cells. Neurotransmitter is used here in its most general sense, including not only messengers that act to regulate ion channels, but also those which act on second messenger systems and those which may act at a distance from their release sites. Included are receptors for neuromodulators, neuroregulators, neuromediators, and neurohumors, whether or not located at synapses (MSH). Neurotransmitter receptor role uncurated C0034828 Juxtaparanode Juxtaparanode sao758620702 Region of nodal complex adjacent to the paranode uncurated sao203987954 Axonal Growth Cone Axonal Growth Cone May 17, 2009 Schaffer collaterals Maryann Martone Group of axons arising from hippocampal CA3 pyramidal neurons projecting to area CA1. Regional Part Of SER Regional Part Of SER sao-699412220 uncurated sao18239917 uncurated Axonal Spine Axonal Spine Refers to spine that originates from the axon, usually the initial segment (Peters, Palay and Webster, 1991). May 16, 2009 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#birnlex_1152_2 Node Of Ranvier This class has been retired. uncurated sao571652273 C0034667 Node Of Ranvier Site located at the gaps in the myelin sheaths of myelinated axons. Axon diameter is generally decreased in the nodal region, compared to the internode. Ranvier's nodes allow saltatory conduction, that is, jumping of impulses from node to node, which is faster and more energetically favorable than continuous conduction (MSH). Microtubule Fascicle uncurated Refers to a bundle of closely apposed microtubules running parallel to each other. sao1872343973 Microtubule Fascicle sao601362597 Lewy Neurite Elongated neuronal process, described in brains of patients with Parkinson's disease, many of which exhibit side branches and have more than one branching point. Stains positively for ubiquitin in brainstem and forebrain regions affected in Parkinson's disease. uncurated Lewy Neurite Thin Dendritic Spine http://ccdb.ucsd.edu/SAO/images/thin_dend_spine_sw_512x512.jpg Thin Dendritic Spine uncurated sao1232858786 Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines (Gene Ontology). 0043198 Dendritic Shaft http://ccdb.ucsd.edu/SAO/images/dend_shaft_ccdb_512x512.jpg Dendritic Shaft uncurated sao2034472720 BF_C000106 sao-946766835 Synaptic Site Synaptic Site Paranode Axon sao936144858 May 28, 2009 Paranode Axon http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 uncurated sao181458425 uncurated Glial Limiting Endfoot Process of astrocyte that extends to the surface of the central nervous system. Together, they form the glial limiting membrane or glial limitans. Glial Limiting Endfoot uncurated Pre-synaptic Grid A hexagonal array of electron dense particles attched to the cyotplasmic face of the presynaptic membrane, revealed by staining with ethanolic phosphotungstic acid (Peters, Palay and Webster, 1991). sao1730664005 Pre-synaptic Grid Dense plexus formed by the descending collaterals of cerebellar basket cells tha wrap around the Purkinje cell axonal initial segment. uncurated Pinceau Fiber Pinceau Fiber sao109906988 Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins (Gene Ontology). 0016604 uncurated Nuclear Body C0230595 Nuclear Body sao505137457 sao797538226 Vesicle Lumen uncurated The volume enclosed by the membrane or protein that forms a vesicle (Gene Ontology). 0031983 Vesicle Lumen Maryann Martone Axons arising from multipolar neurons in the entorhinal cortex projecting to the hippocampal formation. The fibers penetrate the hippocampal sulcus to terminate in the dentate gyrus and also project to area CA1 and the subiculum. Perforant path May 17, 2009 Peg And Socket Contact uncurated Peg And Socket Contact sao1943947957 Contact between endothelial cell and pericyte consisting of membrane invaginations extending from either cell type, which contain tight-, gap-, and adherence junctions (Armulik et al., Circ Res 97: 512, 2005). Mitochondrial Adhaerens Complex MAC Mitochondrial Adhaerens Complex sao1933817066 mitochondrial-associated adherens complex uncurated An adherens plaque attached by filamentous strands to mitochondrion found in large synaptic terminals in the calyc of Held. The peripheral membrane facing the plaque is flattened and faces the synaptic presynaptic membrane (Perkins and Ellisman, 2005). Core sao6587439252 Sarah M. Maynard Core uncurated The center portion of the Lewy Body. In Parkinson's Disease, it contains a matted meshwork of filaments. uncurated Portion of the tanycyte that lies within the ependyma and contains the nucleus (Peters, Palay and Webster, 1991). Somatic Portion Somatic Portion sao401910342 Regional Part Of Schwann Cell uncurated Regional Part Of Schwann Cell sao195217619 Axon Axon uncurated May 5, 2010 Cell appendage of a neuron that consists of an axon hillock, an axon proper, axon collaterals and an axon terminal (FMA) 0030424 http://ccdb.ucsd.edu/SAO/images/axon_sw_512x512.jpg Fiber The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals which are the site of storage and release of neurotransmitter (Gene Ontology). C0004461 sao1770195789 Vascular Endfoot sao2064469343 http://ccdb.ucsd.edu/SAO/images/vasc_endfoot_sw_512x512.jpg uncurated Vascular Endfoot May 1, 2009 Glutamate Receptor http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao587592318 C0061465 Glutamate Receptor sao1164727693 uncurated Maryann Martone Ipsilateral associatioinal commissural projection May 17, 2009 Group of axons that arises from cells in the dentate gyrus polymorphic layer that terminate on the spines of granule cell dendrites on both the ipsilateral and contralateral sides. Ipsilateral associational-commissural projection Shepherd, G. M. The synaptic organization of the brain, 5th ed New York: Oxford University Press, 2005 sao1588493326 A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane (Gene Ontology). C0025979 Actin Filament http://ccdb.ucsd.edu/SAO/images/act_filament_sw_512x512.jpg 0005884 Actin Filament uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 Internode Axon uncurated Internode Axon sao830092290 May 28, 2009 Spinule sao553737851 http://ccdb.ucsd.edu/SAO/images/spinule_sw_512x512.jpg Spinule uncurated Ribbon Synapse uncurated Type of synapse characterized by an electron-dense ribbon, lamella (bar) or spherical body in the presynaptic process cytoplasm (Sjostrand, 1953; Ladman, 1958; Gray and Pease, 1971). It usually sits in or just above an evaginated ridge of the terminal membrane..." - Dowling (1987) Ribbon Synapse sao1884931180 C0026046 Microtubule http://ccdb.ucsd.edu/SAO/images/microtubules_2_sw_512x512.jpg sao1846835077 uncurated http://ccdb.ucsd.edu/SAO/images/microtubules_sw_512x512.jpg 0005874 Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle (Gene Ontology). Microtubule Maryann Martone sao2128156969 Spine Mat 2007-02-09 Spine Mat A configuration of somatic spines found on ciliary ganglion neurons in the embryonic and adult brain consisting of patches of closely spaced spines lying flat against the soma. (Shoop et al., 2000). uncurated Anatomical space occurring within a cell, usually formed by intracellular membranes. sao1289190043 Cellular Space Cellular Space Vesicle Cargo Vesicle Cargo sao1490223249 Need to determine whether this should be a part of a vesicle; I think it shouldn't be Refers to the contents contained in the vesicle. sao1395777368 Intercellular Junction Intercellular Junction Early Endosome Small irregularly shaped intracellular vesicles to which endocytosed molecules are initially delivered (GO: 0005769). July 14, 2009 Intracristal Space true uncurated sao508958414 Intracristal Space The space bounded by the cristae membrane sao1956231674 uncurated Golgi Lumen Golgi Lumen Terminal process of astrocyte abutting non-neuronal surfaces in the brain. Endfoot Endfoot graph position temporary uncurated sao388182739 uncurated Active Zone Dense Projection sao494258938 Active Zone Dense Projection Electron dense projection extending from the cytomatrix into the cytoplasm on which synaptic vesicles are tethered (Zhai and Bellen, 2004). Glial Subcompartment uncurated Glial Subcompartment sao1253297813 uncurated Mitochondrial Subcomponent Mitochondrial Subcomponent sao666410040 Masa H. Sato, Ryosuke L Ohniwa, and Tomohiro Uemura, SNAREs in Plant Endocytosis and the Post-Golgi Traffic, Plant Cell Monogr, September 2005, DOI: 10.1007/7089 012 Late endosomes are vesicular structures that accumulate internalized components after their passage through early endosomes (GO: 0005700). July 14, 2009 Late Endosome sao-965204139 Branched Dendritic Spine uncurated http://ccdb.ucsd.edu/SAO/images/branched_dend_spine_sw_512x512.jpg Branched Dendritic Spine sao1825845900 uncurated Crista Junction Crista Junction Tubular structures of relatively uniform size that connect mitochondrial cristae to the inner mitchondrial membrane (Perkins and Ellisman, 2003). Square arrays of closely spaced intramembrane particles, 4-6 nm in size seen in astrocyte processes, now known to contain aquaporins. square array uncurated Orthogonal Array Orthogonal Array sao1747012216 Equivalent to "regional part" in the FMA--a primary partition that spatially subdivides an anatomical structure into sets of diverse constiutional parts that share a given location within the whole; i.d., the partition is spatial instead of compositional (Mejino JLV et al., 2003). Regional Part Of Cell Regional Part Of Cell uncurated sao340271629 hemichannel, connexon complex 0005922 Connexon sao445019788 uncurated Connexon Assembly of 6 connexins into a hemichannel that forms one half of a gap junction. In some cells, the hemichannel is active as a conduit between the cytoplasm and the extracellular space. Wikipedia C0230609 Trans Face Trans Face 0005802 uncurated sao1039242387 The concave side of the Golgi apparatus, from which secretory vesicles emerge (Gene Ontology). Intercellular Gap Janction Channel Junctional complex consisting of two connexons that come together to form a communicating pore between two cells Dendritic Growth Cone sao1594955670 Dendritic Growth Cone http://ccdb.ucsd.edu/SAO/images/dend_growth_cone_sw_512x512.jpg uncurated Extended Chromatin 0000791 euchromatin Extended Chromatin uncurated A dispersed and relatively uncompacted form of chromatin (Gene Ontology). sao445485807 Apical Pole Of Neuron Portion of a cell soma closest to the point where the apical dendrite emerges. sao1877927224 Apical Pole Of Neuron uncurated sao1455064842 Vesicle Subcomponent Vesicle Subcomponent 0048238 sao927884761 uncurated SER Lumen SER Lumen smooth endoplasmic reticulum lumen The volume enclosed by the membranes of the smooth endoplasmic reticulum (Gene Ontology). sao1956738165 Look into the relationship of Macular and zonula adhaerentia and determine whether they are all subclasses of adhaerent junction Macular Adhaerentia uncurated Macular Adhaerentia uncurated Laminated Body sao506721981 Laminated Body July 14, 2009 Glial Cytoplasmic Inclusion Glial Cytoplasmic Inclusion http://ccdb.ucsd.edu/SAO/images/node_ccdb_512x512.jpg Nodal Complex sao873654461 Nodal Complex Autolysosome uncurated Autophagolysosome, degrading autophagic vacuole (AVd) Autolysosome sao8444068431 A type of secondary lysosome in which a primary lysosome has fused with the outer membrane of an autophagosome. It is involved in the second step of autophagy in which it degrades contents with acidic lysosomal hydrolases. Sarah M. Maynard A specialized presynaptic plasma membrane region where synaptic vesicles dock and fuse (Gene Ontology). Pre-synaptic Active Zone Pre-synaptic Active Zone sao792027222 0048786 http://ccdb.ucsd.edu/SAO/images/active_zone_sw_512x512.jpg uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1846835077 Microtubule http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated C0026046 2006-09-28 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone 2006-07-15 Microtubule Axon Terminal Axon Terminal The distal terminations of axons which are specialized for the release of neurotransmitters. Also included are varicosities along the course of axons which have similar specializations and also release transmitters. Presynaptic terminals in both the central and peripheral nervous systems are included (MSH). sao2007137787 http://ccdb.ucsd.edu/SAO/images/axon_term_sw_512x512.jpg uncurated Non Membrane Bound Organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes (Gene Ontology). 0043228 uncurated Non Membrane Bound Organelle sao1456184038 Axon Hillock C0228079 uncurated Cone shaped elevation from which the axon originates; in Nissl stained preparations, the axon hillock usually can be identified as a region of the perikaryon that is distinguished by a deficiency of Nissl substance (Peters, Palay and Webster, 1991). 0043203 Axon Hillock sao627227260 Large dense cored vesicles, up to 150-200 nm in diameter found in neurosecretory cells in the hypothalamus. The electron dense appearance is dependent upon fixation (Peters, Palay and Webster, 1991). Neurosecretory Vesicle uncurated sao2031592629 Neurosecretory Vesicle sao118944228 graph position temporary I'm having difficulty deciding whether this is a regional part of a mitochondrion or whether it is a site; today it is a regional part. 0005758 Mitochondrial Intermembrane Space C1166886 Mitochondrial Intermembrane Space The region between the inner and outer lipid bilayers of the mitochondrial envelope. (Gene Ontology). true Coiled body Jane Bugea http://genetics.cwru.edu/matera3.html Cajal body February 17, 2010 August 31, 2009 GO_0015030 uncurated sao1470121605 Active Zone Cytomatrix Active Zone Cytomatrix Filamentous matrix immediately internal to the plasma membrane docking zone (Zhai and Bellen, 2004). uncurated Axolemma The plasma membrane of an axon; it is a specialized trilaminar random mosaic of protein molecules floating within a fluid matrix of highly mobile phospholipid molecules, 7-8 nm in thickness (Gene Ontology). sao250772229 0030673 Axolemma Inter-Golgi Transport Vesicle A vesicle that mediates transport of cargo within the Golgi complex (for example, between cisternae of the Golgi stack) (Gene Ontology). uncurated 0030143 Inter-Golgi Transport Vesicle sao1382918459 Recurrent Collateral Recurrent Collateral uncurated Axon collateral that ramifies in the area of the soma of the cell of origin. sao1642494436 Basal Body 0005932 A short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium or flagellum that is similar in structure to a centriole. The basal body serves as a nucleation site for axoneme growth (Gene Ontology). sao11978067 C0230744 uncurated http://ccdb.ucsd.edu/SAO/images/basal_bodies_sw_512x512.jpg Basal Body Initial Segment Initial Segment uncurated sao256000789 Portion of the axon proximal to the neuronal cell body, at the level of the axon hillock. The action potentials that propagate along the axon are generated at the level of this initial segment (Gene Ontology). 0043194 http://ccdb.ucsd.edu/SAO/images/init_seg_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/init_seg_sw_512x512.jpg Pyramidal Neuronal Cell Body sao-820130069 uncurated Pyramidal Neuronal Cell Body sao1037637579 Refers to integral membrane proteins carried via the vesicle membrane. Membrane Cargo Membrane Cargo Free Ribosome Free Ribosome uncurated sao1139385046 sao451912436 golgi cisternae C0018042 0005794 uncurated Golgi Apparatus Golgi Apparatus http://ccdb.ucsd.edu/SAO/images/golgi_app_sw_512x512.jpg A stack of flattened vesicles that functions in posttranslational processing and sorting of proteins, receiving them from the RER and directing them to secretory vesicles, lysosomes, or the cell membrane. The movement of proteins takes place by transfer vesicles that bud off from the rough endoplasmic reticulum or Golgi apparatus and fuse with the Golgi, lysosomes or cell membrane. (From Glick, Glossary of Biochemistry and Molecular Biology, 1990) (MSH) Region of nodal complex adjacent to the nodal region Paranode Paranode sao-234066064 Dense Material sao1004601938 uncurated Dense Material Regional Part Of Granule Cell Axon March 17, 2010 C0230810 uncurated http://ccdb.ucsd.edu/SAO/images/spine_app_2_sw_512x512.jpg Spine Apparatus A specialization of the endomembrane system found in some classes of spines consisting of two or more closely apposed lamellae with interspersed dense material. http://ccdb.ucsd.edu/SAO/images/spine_app_3_sw_512x512.jpg sao725931194 Spine Apparatus uncurated Nucleolar compartment consisting of large numbers of small, extremely dense granules 150-300 A in diameter, suspended in a matting of fine filaments (Palay and Chan-Palay, 1974). Pars Granulosa sao1217793903 Pars Granulosa C0230580 Excrescence Excrescence sao-961694769 uncurated Supra Cellular Structure uncurated Supra Cellular Structure A morphological or functional domain formed by parts of two or more cells, e.g., neuropil, dendritic bundles. sao508165343 Supracellular Structure Spine Head sao952643730 Spine Head uncurated Functional role of nerve cell 2007-08-25 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug 2007-08-25 Functional role of nerve cell sao289211478 uncurated Chemical Synapse Chemical Synapse Pre-synaptic Dense Body sao1111202255 Pre-synaptic Dense Body Electron dense structure anchored to the presynaptic membrane closely associated with large numbers of synaptic vesicles, which appear to be tethered to the dense body by several short filaments (from Parsons and Sterling, 2003). ribbon Part of axon located at the gaps between adjacent myelin sheaths characterized by a slightly larger diameter than paranodal axon and the presence of a dense coating on the axolemma. Node Of Ranvier Axon uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 sao-188049490 Node Of Ranvier Axon May 28, 2009 uncurated C1166687 0000262 sao1186327184 Mitochondrial Chromosome Mitochondrial Chromosome A chromosome found in the mitochondrion of a eukaryotic cell (Gene Ontology). sao1329750433 Membrane Surface uncurated Membrane Surface sao1571698684 uncurated Barr Body Barr Body uncurated sao1038025871 Polyribosome http://ccdb.ucsd.edu/SAO/images/polyribosome_sw_512x512.jpg C0032592 http://ccdb.ucsd.edu/SAO/images/polyribosome2_sw_512x512.jpg A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed) (MSH). Polyribosome http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao183270081 Regional Part Of Myelinated Axon sao1791490892 Regional Part Of Myelinated Axon This class has been retired. uncurated May 28, 2009 Insoluble fibrils that form in pathological conditions characterized by Lewy bodies, such as Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. Alpha-synuclein is the primary structural component. Sarah M. Maynard uncurated Alpha-Synuclein Fibril sao7474011676 Alpha-Synuclein Fibril sao-206157942 Internode Part of nodal complex located underneath the compact myelin in between nodes of Ranvier Internode Specialization of the hypolemmal cisterna consisting of either single profiles or closely apposed stacks of ER in which the lumen is obliterated, lying 10-20 nm beneath the plasma membrane (Peters, Palay and Webster, 1991). http://ccdb.ucsd.edu/SAO/images/cisternae_sw_512x512.jpg sao128470897 Sub-surface Cisternae uncurated Sub-surface Cisternae Hypolemmal Cisternae uncurated sao1634374950 Specialized part of the smooth endoplasmic reticulum that closely underlies the plasma membrane, usually within 60 nm or closer (Peters, Palay and Webster, 1991). Hypolemmal Cisternae Part of mitochondrial inner membrane that runs parallel to the outer mitochondrial membrane Inner Bounding Mitochondrial Membrane sao18461326 Inner Bounding Mitochondrial Membrane uncurated uncurated sao1612527463 Nuclear Inner Membrane 0005637 The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope (Gene Ontology). Nuclear Inner Membrane uncurated Regional Part Of Tanycyte Regional Part Of Tanycyte sao877341397 Intermediate Filament 0005882 sao952483289 Intermediate Filament A distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of higher eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: keratin filaments of mammalian epithelial cells; desmin filaments found in cells of muscles of all types; vimentin filaments found in mesenchymal cells; neurofilaments of neurons; and glial filaments found in all types of glial cells (Gene Ontology). uncurated C0021770 Subregional Part Of Neuron Process Subcompartment of a compartment. sao183270081 Subregional Part Of Neuron Process uncurated Sarah M. Maynard PMID: 18026741 January 9, 2009 Bunina Body Bunina Body Bunina bodies are small eosinphilic granular inclusions that are 1-3 microns in diameter in the anterior horn cells, appearing either singly or in a group. Sometimes they are arranded in small beaded chains. They stain bright red with hematoxylin and eosin (H&E) staining, deep blue with phospotungstic acid hematoxylin and blue with Luxol fast blue. They express cystatin C and consist of electron-dense amorphous material that contains tubules or vesicular structures. The amorphous material frequently includes a cytoplasmis island containing neurofilaments and other micro-organelles. uncurated Abnormal structures located in distal dendrites. Filamentous bundles made up of straight and paried helical filaments which contain ubiquitin and tau. sao9537723288 Neuropil Thread Sarah M. Maynard Neuropil Thread http://ccdb.ucsd.edu/SAO/images/cristae_ccdb_512x512.jpg Cristae 0030061 C0230844 sao333328131 Cristae Any of the inward folds of the mitochondrial inner membrane. (Gene Ontology) uncurated Granular Vesicle uncurated Vesicle of varying size, but usually larger than 45 nm, that has an electron dense "granular" core, associated with noradrenergic and peptidergic cells. sao478230652 Granular Vesicle sao1186862860 Basal Pole Of Neuron Portion of a cell soma closest to the point where the basilar dendrite emerges. Basal Pole Of Neuron uncurated uncurated sao1362520468 0030139 C0887883 Endocytic Vesicle Endocytic Vesicle A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 2006-07-15 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1316272517 Neurofilament Neurofilament 2006-09-28 Pick Body Pick Bodies are composed of numerous tau fibrils arranged in a disorderly array. Tau protein is a major component. Pick bodies also stain for ubiquitin, alpha-synuclein, and apolipoprotein E. January 9, 2009 Sarah M. Maynard Pick Body 0005798 uncurated C0230767 Any vesicles associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell (Gene Ontology). Golgi-associated Vesicle sao819927218 Golgi-associated Vesicle http://ccdb.ucsd.edu/SAO/images/glycogen_granule_sw_512x512.jpg 0042587 Glycogen Granule Glycogen Granule sao1081228141 uncurated C0017911 Cytoplasmic bead-like structures of animal cells, visible by electron microscope. Each granule is a functional unit with the biosynthesis and catabolism of glycogen being catalyzed by enzymes bound to the granule surface (Gene Ontology). Appears as small, electron dense particles 20-40 nm in diameter. Glycogen is difficult to fix in vivo so amounts may be underestimated (Peters, Palay and Webster). sao1514682949 uncurated Cytoplasmic Surface Cytoplasmic Surface Endocytic Zone sao517367952 Region of the spine within several hundred nanometers of the post synaptic specialization characterized by the presence of coated pits. It is believed that this zone may be specialized for endocytosis. These coated pits are never observed in membrane associated with the post synaptic specialization (Blanpied and Ehlers, 2004). Endocytic Zone Supracellular structure formed by the descending axon collaterals of several cerebellar basket cells that wrap around the Purkinje cell initial segment. Although the axons contain many vesicles and form terminal endings, most do not synapse directly on the Purkinje cell initial segment but rather end blindly. Pinceau uncurated Pinceau sao732341560 uncurated Plasma membrane juxtaposed to the PSD where synaptic vesicle fusion occurs (Zhai and Bellen, 2004). Active Zone Plasma Membrane Active Zone Plasma Membrane sao2038461087 Pial Endfoot sao1447478620 Pial Endfoot uncurated uncurated Dendritic Tree Dendritic Tree sao172297168 BF_C000102 The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches. uncurated Coated Tip sao694815499 Coated tips of tubular endosomes that appear to be vesicles in the process of budding off (Clooney et al., 2002). Coated Tip sao561419532 uncurated Golgi Lamellae Golgi Lamellae uncurated 0045334 A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology). Clathrin Coated Endocytic Vesicle sao1243595998 Clathrin Coated Endocytic Vesicle http://ccdb.ucsd.edu/SAO/images/clath_coated_endocy_vesicle_sw_512x512.jpg The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a post-synaptic potential responsible of the muscle contraction (Gene Ontology). 0031594 Neuromuscular Junction Neuromuscular Junction uncurated NMJ sao1124888485 http://ccdb.ucsd.edu/SAO/images/sym_synapse_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/electrotonic_syn_sw_512x512.jpg Electrotonic Synapse uncurated Electrotonic Synapse sao1311109124 Electrotonic synapses are gap junctions that allow the passage of ions directly from cell to cell. Ultrastructurally, it can be recognized as a 7 layered structure with 4 dense lines, two from each of the plasma membranes, alternating with 3 lighter lines. Electrotonic synapses are generally symmetric and display little or no dense material associated with the cytoplasmic face of the plasma membrane (Peters, Palay and Webster, 1991). Electrical Synapse Dense Core Vesicle sao772007592 Dense Core Vesicle 40-60 nm vesicle containing an electron dense granule, 15-20 nm in diameter (Peters, Palay and Webster, 1991). uncurated C0887944 http://ccdb.ucsd.edu/SAO/images/dense_core_vesicle_sw_512x412.jpg C1166749 0030120 Vesicle Coat sao1177708494 Refers to any specialized coating present on a vesicle membrane, e.g., clathrin. Vesicle Coat Protein Filament uncurated Filament sao7561423738 This is a placeholder. This refers to a protein configuration, but we think it belongs elsewhere. A fibril is actually a minute fiber or filament. Filament could refer to protein filament. A long chain of proteins, such as those found in hair, muscle, or in flagella Sarah M. Maynard Filament A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle (Gene Ontology). uncurated C0007708 Centriole 0005814 sao95019936 http://ccdb.ucsd.edu/SAO/images/centriole_sw_512x512.jpg Centriole Chromatin C0008546 0000785 Chromatin The ordered and organized complex of DNA and protein that forms the chromosome (Gene Ontology). uncurated sao1615953555 Site of contact between the inner and outer mitochondrial membrane found in neuronal mitochondria; may play a role in maintaining the structural integrity of the inner and outer boundary membranes (Perkins and Ellisman, 2005). Bridge Contact Site sao1858501007 uncurated Bridge Contact Site We still don't know if the synapse, in the sense that it is typically used, belongs here or whether large, multicontact synapses like the neuromuscular junction and the calycl synapse of Held, belong here and not simple synapses sao1299635018 Maryann Martone Cell Cell Contact Zone Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions, e.g., the intercalated disk of muscle uncurated Cell Cell Contact Zone Cellular inclusions found in cytoplasm that resemble nuclioli and stain with basophilic stains. They are ball-like structures about .9 microns in diameter and lack a limiting membrane. Structurally, they are composed of tightly packed fine filaments attached to them by means of fine filaments that radiate from their periphery. They were first discribed by Grillo in 1970. (from Peters, Palay, Webster) sao138430598 Nematosome uncurated Nematosome sao1570660411 Endosomal component consisting of cylindrical shaped tubues, ~50 nm in diameter, with smooth outer membranes an dark, grainy interiors (Clooney et al., 2002). Clathrin-like protein coats occur at the ends of some tubular compartments. Tubular Endosome Tubular Endosome uncurated sao413722576 Peri Cellular Basket uncurated Peri Cellular Basket Ramification of basket cell axon surrounding cell bodies, forming the characteristic peri-cellular baskets from which the cell class derives its name. sao273773228 BF_C000112 Apical Dendrite Apical Dendrite uncurated sao2254405550 Bill Bug A collection of independent organismal entities engaged in some form of spatio-temporal interaction or aggregate behavior 2006-09-07 Population Population uncurated Endosome C0034850 0005768 sao1720343330 A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation (GO). Endosome uncurated Neck Portion sao901230115 Elongated portion of the tanycyte that sticks into the periventricular layer of neuropil where it appears to contact a blood vessel; characterized by numerous cytoplasmic extensions (Peters, Palay and Webster, 1991). Neck Portion Mitochondrial Space Spaces defined by the inner and outer mitochondrial membranes sao-343550527 Mitochondrial Space true uncurated Pre-synaptic Active Zone Component Pre-synaptic Active Zone Component sao1911631652 The space between the inner and outer nuclear membranes Intranuclear Membrane Space sao1908934319 uncurated Intranuclear Membrane Space sao248349196 Refers to a microtubule found in a nerve cell. The term "neurotubule" may now be obselete; however, it was used in earlier findings. uncurated Neurotubule Neurotubule C0752063 sao499555322 Resembles lysosomes in appearance (Peters, Palay and Webster, 1991). According to the latter, peroxisome is synonymous with microbodies. Peroxisome uncurated Peroxisome A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2) (Gene Ontology). 0005777 Schwann Cell Microvillus Small finger-like extension of the Schwann cell that contact the nodal membrane but are not closely apposed to each other like the paranodal lops (Sosinsky et al., 2005) sao1890444066 Schwann Cell Microvillus uncurated Pinocytic Vesicle sao1925368674 uncurated Pinocytic Vesicle Sarah M. Maynard sao1342297498 Amyloid Fibril A fibril composed of amyloid protein. http://ccdb.ucsd.edu/SAO/images/amyloid_filament_sw_512x512.jpg Amyloid Fibril Extracellular Space That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid (Gene Ontology). Extracellular Space uncurated sao1425028079 0005616 http://ccdb.ucsd.edu/SAO/images/extracell_space_sw_512x512.jpg 0005730 Nucleolus sao1820400233 uncurated A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome (Gene Ontology). http://ccdb.ucsd.edu/SAO/images/nucleolus_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/nucleoli_sw_512x512.jpg Nucleolus C0007609 Do spines only have a post synaptic density? (Maryann Martone) Spine sao1145756102 uncurated With the restrictions we are trying to say that if you are a spine, you may have one or more of the following parts, a head, a neck or a spinule. If you have one of these parts then you are likely a spine. May 28, 2009 Spine sao1819509473 0048237 RER Lumen The volume enclosed by the membranes of the rough endoplasmic reticulum (Gene Ontology). RER Lumen rough endoplasmic reticulum lumen uncurated sao1140587416 Primary Lysosome A lysosome before it has fused with a vesicle or vacuole (Gene Ontology). Primary Lysosome 0005766 C0230814 uncurated C-fiber February 27, 2009 C-fiber The axon of dorsal root ganglion cells that are responsive to pain and temperature. C-fibers are small in diameter (0.2-1.5 um) and unmyelinated. 2006-07-15 Site located at the gaps in the myelin sheaths of myelinated axons. Axon diameter is generally decreased in the nodal region, compared to the internode. Ranvier's nodes allow saltatory conduction, that is, jumping of impulses from node to node, which is faster and more energetically favorable than continuous conduction (MSH). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting Node of Ranvier 2006-09-28 Specialized supracellular structures found in myelinated axons at the gaps between the myelin sheaths. The Node of Ranvier consists of the axonal membrane at the gap, the surrounding myelin processes and additional components such as astrocytic processes or basal lamina, depending upon whether the Node occurs in axons in the peripheral or central nervous system. C0034667 Node of Ranvier http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Spiny Bracelet Of Nageotte Paranodal terminations of Schwann cells that do not directly contact the paranodal axon membane. Usually found in thicker myelin. (Sosinsky et al., 2005) sao937871668 uncurated Spiny Bracelet Of Nageotte Sarah M. Maynard Protein Aggregate An insoluble mass of misfolded proteins. uncurated Protein Aggregate sao7016027781 sao9515821206 We need to check if any plaques do not amyloid and if amyloid is beta. We are not sure if there is a distinction between Neuritic plaque and Senile plaque. A characteristic form of amyloid plaque. Has an extracellular core of amyloid fibrils surrounded by dystrophic dendrites and axons, some of which contain protein filaments, activated microglia and reactive astrocytes. Neuritic Plaque Neuritic plaque Sarah M. Maynard uncurated Pre-synaptic Component sao386529203 Pre-synaptic Component A formation or growth of cells. uncurated Plaque Plaque sao9137852997 Sarah M. Maynard uncurated sao7547390221 Sarah M. Maynard Collagen Fibril Delicate fibrils of collagen in connective tissue. It is composed of molecules of tropocollagen aggregated in linear array. Collagen Fibril http://ccdb.ucsd.edu/SAO/images/neuropil_sw_512x512.jpg sao205380252 C0228081 A dense intricate feltwork of interwoven fine glial processes, fibrils, synaptic terminals, axons, and dendrites interspersed among the nerve cells in the gray matter of the central nervous system (MSH). uncurated Neuropil Neuropil A type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter (Gene Ontology). C0027834 Neurofilament 0005883 sao1316272517 http://ccdb.ucsd.edu/SAO/images/neurofilament_sw_512x512.jpg Neurofilament uncurated Nucleolus-associated Heterochromatin Nucleolus-associated Heterochromatin uncurated Dense particles of heterochromatin, consisting of a loosely twisted strang ~600 A thick, found associated with the nucleolus (Palay and Chan-Palay, 1974). sao1210952635 uncurated Nuclear Membrane Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space (Gene Ontology). sao1687101204 Nuclear Membrane C0028584 0031965 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 May 28, 2009 uncurated Juxta Paranode Axon sao1191319089 Juxta Paranode Axon Region of axon immediately adjacent to the paranode. Regional Part Of Basket cell axon Regional Part Of Basket Cell Axon uncurated Terminal pre-synaptic ending of an axon or axon collateral. sao1586851177 uncurated 0043226 C0029219 Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane (Gene Ontology). Organelle sao1539965131 Organelle sao1186642361 Oligodendrocyte Compact Myelin uncurated The portion of the myelin sheath in which layers of cell membrane are tightly juxtaposed, completely excluding cytoplasm. The juxtaposed cytoplasmic surfaces form the major dense line, while the juxtaposed extracellular surfaces form the interperiod line visible in electron micrographs (Gene Ontology). 0043218 Oligodendrocyte Compact Myelin Calnexin (CNX) is a 90kDa integral protein of the endoplasmic reticulum (ER). It consists of a large (50 kDa) N-terminal calcium-binding lumenal domain, a single transmembrane helix and a short (90 residues), acidic cytoplasmic tail. February 27, 2009 Calnexin Calnexin uncurated Branch Point Of Dendrite sao-1348591767 Branch Point Of Dendrite uncurated Secondary Lysosome Vacuole formed by the fusion of a lysosome with an organelle (autosome) or with a primary phagosome (Gene Ontology). 0005767 C0230815 Secondary Lysosome sao1549842807 dendritic tuft April 28, 2010 sao1340260079 Tuft The terminal specialization found in some types of dendrites consisting of numerous small terminal branches, giving the dendrite a tufted appearance. Tuft uncurated uncurated Zonula Occludens Zonula Occludens sao1939999134 0005923 tight junction A belt-like region of very close contact between the plasma membranes of adjacent cells so that the intercellular space is completely occluded. They occur in epithelia and brain endothelia (Gene Ontology). Schwann Cell Paranodal Termination Schwann Cell Paranodal Termination Cytoplasmic pockets, or as they appear in thin sections "loops" formed by the Schwann cell in the paranodal region. These pockets are actually part of a continuous helical structure providing cytoplasmic continuity from the inntermost to the outermost layers of the myelin sheath through the cytoplasmic channel formed by the loop. Most are directly apposed to the paranodal axonal membrane uncurated sao-1067215520 sao1036339110 uncurated http://ccdb.ucsd.edu/SAO/images/er2_sw_512x512.jpg The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached) (Gene Ontology). Endoplasmic Reticulum Endoplasmic Reticulum 0005783 http://ccdb.ucsd.edu/SAO/images/er_sw_512x512.jpg C0014239 Cortical Lewy Body has Regional Part some Regional_Part_of_Lewy_Body restriction violated because Cortical Lewy Body lacks halo. Cortical Lewy Body uncurated Lesion that is less well defined than a Classical Lewy Body and lacks a halo. sao4040591221 Sarah M. Maynard Spine Related Site sao553711217 Spine Related Site uncurated Coated Pit sao1969557946 Coated Pit Specialized sites on the plasma membrane exhibiting a clathrin coat; likely vesicles in the process of pinching off (Conner and Schmid, 2003). C0009143 Lumenal Surface uncurated sao120818728 Lumenal Surface Hippocampal mossy fiber Axon of dentate gyrus granule cell projecting to hippocampal area CA3, characterized by expansions (mossy fiber expansions) giving the fibers a mossy appearance. These unmyelinated axons were first described by Ramon y Cajal. April 28, 2010 Dentate gyrus mossy fiber March 18, 2010 Calyx Of Held sao1684283879 uncurated Calyx Of Held Proteasomes are large protein complexes inside all eukaryotes and archaea, as well as in some bacteria. In eukaryotes, they are located in the nucleus and the cytoplasm. Proteasome February 23, 2009 Proteasome Nucleus 0005634 C0007610 uncurated sao1702920020 http://ccdb.ucsd.edu/SAO/images/nucleus_sw_512x512.jpg Nucleus A membrane-bounded organelle of eukaryotic cells that contains the chromosomes. It is the primary site of DNA replication and RNA synthesis in the cell (Gene Ontology). Neuronal Cytoplasmic Inclusion Neuronal Cytoplasmic Inclusion August 11, 2009 Jane Bugea NCI I'm not sure whether this should be a type of neuropil or a type of synaptic complex. (Maryann Martone) Glomerulus sao587858733 Large synaptic bouton found in areas like olfactory bulb, cerebellar cortex and thalamus, that contacts many post-synaptic targets. http://ccdb.ucsd.edu/SAO/images/glomerulus_sw_512x512.jpg Glomerulus uncurated Type of neuropil characterized by a large synaptic bouton that contacts many post-synaptic targets found in areas like olfactory bulb, cerebellar cortex and thalamus. June 22, 2009 Cellular Membrane sao6433132645 Cellular Membrane SER Subcomponent uncurated SER Subcomponent sao1842028314 Endosomal Subcomponent sao1683772610 uncurated Endosomal Subcomponent Basal Lamina 0005605 A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix (Gene Ontology). uncurated sao1397492660 C0242195 Basal Lamina Fibrillary Inclusion Cellular inclusion found in cytoplasm of giant cells of Dieters in lateral vestibular nucleus of the rat consisting of circular areas filled with fine slender filaments about 10 nanometers in diameter, delimited by a wall of varying complexity either a single continuous membrane or a tubular network consisting of a fine filamentous material giving the wall a honeycomb appearance. Similar structures have been discribed in the ventral cochlear nucleus, spinal cord, substantia nigra. First described by Sitelo and Palay, 1968. (from Peters, Palay, and Webster) Fibrillary Inclusion uncurated sao967812059 uncurated sao1279474730 An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system (Gene Ontology). C0026973 0043209 Oligodendrocyte Myelin Sheath Oligodendrocyte Myelin Sheath Synaptophysin February 24, 2009 Synaptophysin (syp I) is a synaptic vesicle membrane protein Synaptophysin autophagic vacuole, initial autophagic vacuole (AVi) Sarah M. Maynard Autophagosome uncurated A vesicle with a double membrance derived from the Endoplasmic Reticulum that encloses cytoplasmic material and organelles to be degraded. Its formation is the first step of the process of autophagy. sao8663416959 Autophagosome Vesicle C0042219 0031982 Any small, fluid-filled, spherical organelle enclosed by membrane or protein (Gene Ontology). sao221389602 uncurated Vesicle Cell role August 20, 2009 uncurated 0005759 sao1804523077 C0230843 The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes concerned with fatty-acid oxidation and enzymes of the tricarboxylic acid cycle (Gene Ontology). Mitochondrial Matrix Mitochondrial Matrix Vesicular Component sao138219748 Vesicular Component uncurated Membrane Bound Organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane (Gene Ontology). Membrane Bound Organelle 0043227 uncurated sao414196390 umls_ID: C0230664 Membrane Receptor Membrane Receptor http://ccdb.ucsd.edu/SAO/images/filopodium_sw_512x512.jpg uncurated Filopodium sao-1046371754 0030175 Thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone; usually approximately 0.1 um wide, 5-10 um long, can be up to 50 um long in axon growth cones; contains a loose bundle of about 20 actin filaments oriented with their plus ends pointing outward (Gene Ontology) Filopodium Age Associated Age Associated uncurated sao2017162875 Need to look this one up and see what this really meant. Dense Body An electron dense body, some of which contain granules (Peters, Palay and Webster (1991) sao730872736 Dense Body Not clear if this should be described as an organelle or an inclusion. graph position temporary sao914572699 uncurated 0045202 Synapse The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell; the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane (Gene Ontology). Synapse uncurated Regional Part Of Axon Regional Part Of Axon sao280355188 Neuronal Cell Body Cell body which consists of the plasma membrane and the cytoplasm surrounding the nucleus of the neuron (FMA). C0599444 soma Neuronal Cell Body uncurated sao1044911821 uncurated neck Spine Neck pedicle Spine Neck sao1642908940 sao879919129 A membrane coat found on coated pits and some coated vesicles; consists of polymerized clathrin triskelions, each comprising three clathrin heavy chains and three clathrin light chains, linked to the membrane via one of the AP adaptor complexes (Gene Ontology). Clathrin Coat C1166728 uncurated 0030118 Clathrin Coat uncurated Sarah Maynard Aggregate Object sao3826089237 Aggregate Object February 12, 2009 Astrocyte Sheath Astrocyte Sheath Trans Golgi Network Trans Golgi Network uncurated sao9456487 0005802 C0887838 A network of membrane compartments, located at the cytoplasmic side of the golgi apparatus, where proteins and lipids are sorted for transport to various locations in the cell or cell membrane (MSH). C0024369 sao585356902 uncurated 0005764 Any of a group of related cytoplasmic, membrane bound organelles that are found in most animal cells and that contain a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions (Gene Ontology). Lysosome Lysosome sao1241866791 Large Vesicle Vesicles of same size and content of coated vesicles; posited by Clooney et al. (2002) to represent coated vesicles after uncoating. Large Vesicle uncurated Glial Filament Glial Filament uncurated sao-1863852493 The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes (Gene Ontology). uncurated sao1617136075 0005640 Nuclear Outer Membrane Nuclear Outer Membrane sao671419673 Microvilli uncurated Microvilli http://ccdb.ucsd.edu/SAO/images/microvilli_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/microvilli_sw_512x512.jpg Node Related Site sao-596411490 Node Related Site Site defined with respect to the Node of Ranvier, e.g., node, paranode, juxtaparanode C0010854 Cytosol sao101633890 uncurated 0005829 The part of the cytoplasm that does not contain membranous or particulate subcellular components (UMLS). Cytosol uncurated Terminal Specialization sao28175134 Terminal Specialization Neurite Neuron Process Neuron Process sao-867568886 Fibril A minute fibril or filament. This is a placeholder. Fibril uncurated sao5051906853 Sarah M. Maynard sao1379604862 Lamellar Body Membranous inclusions composed of stacks of unperforated cisternae derived from the granular endoplasmic reticulum. Cisternae are spaced at intervals of about 30-40 nm (Peters, Palay and Webster, 1991). 0042599 Lamellar Body uncurated Cytochrome c Cytochrome c February 23, 2009 A small heme protein found loosely associated with the inner membrane of the mitochondrion. Sarah M. Maynard Regional Part Of Lewy Body sao1894609662 Regional Part Of Lewy Body uncurated Subcellular entity subcellular_structure Maryann Marotone Entity derived from a cell or cells. The anatomical scale of these objects roughly corresponds to that which would be visible in high resolution light microscopy or conventional electron microscopy, e.g., nanometers to microns. Example: mitochondrion, dendrite, extracellular matrix. March 15, 2010 Septate Junction An intercellular junction found in invertebrate epithelia that is characterised by a ladder like appearance in electron micrographs. Thought to provide structural strength and to provide a barrier to diffusion of solutes through the intercellular space. Occur widely in transporting epithelia and are controversially considered analogous to tight junctions (zonula occludens) Biology-online.org graph position temporary 0005918 sao427941916 Septate Junction Projection neuron Projection neuron role 2007-08-26 A principal projection neuron in a neuronal circuit whose axon extends beyond the region where its soma is located to synapse on the dendrites of cells in other regions of the nervous system (BB). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Principal neuron role CA3 Pyramidal neurons are principal neurons projecting out of the CA3 cytoarchitectural part of the hippocampus of vertebrates. Principal neuron March 31, 2009 Cerebellar Purkinje neurons are principal neurons projecting out from the cerebellar cortex of vertebrates. Principal neuron role http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug 0030868 The lipid bilayer surrounding the smooth endoplasmic reticulum (Gene Ontology). sao1596955044 uncurated SER Membrane SER Membrane cell membrane uncurated http://ccdb.ucsd.edu/SAO/images/plas_memb2_sw_512x512.jpg Plasma Membrane Plasma Membrane 0005886 C0007603 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins (Gene Ontology). http://ccdb.ucsd.edu/SAO/images/plas_memb_3_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/plas_memb_sw_512x512.jpg sao1663586795 Flame-shaped Neurofibrillary Tangle February 12, 2009 Flame-shaped Neurofibrillary Tangle Astrocyte Process http://ccdb.ucsd.edu/SAO/images/astrocyte_process_sw_512x512.jpg Astrocyte Process Refers to processes of astrocytes extending from the cell soma that wrap around neurons and conform to cellular components in the neuropil. uncurated sao1630537580 Mitochondrial Membrane Mitochondrial Membrane sao1045389829 uncurated Extracellular Surface Extracellular Surface sao2135015805 uncurated A branching protoplasmic process of a neuron that receive and integrate signals coming from axons of other neurons, and convey the resulting signal to the body of the cell (Gene Ontology). http://ccdb.ucsd.edu/SAO/images/dend_ccdb_512x512.jpg uncurated One of several similar processes that issue from the perikaryon of a neuron, generally specialized for receiving synaptic input from other neurons or transduction of signals from the environment. sao1211023249 C0011305 Dendrite Dendrite 0030425 Docked Vesicle sao403156667 Synaptic vesicle docked at the pre-synaptic active zone. uncurated Docked Vesicle mossy fiber expansion dentate gyrus mossy fiber expansion dentate gyrus granule cell axonal bouton Synaptic expansion of hippocampal mossy fiber axon that makes contact with the thorny excrescences of hippocampal CA3 pyramidal cell dendrites Hippocampal mossy fiber expansion May 11, 2010 Multivesicular bodies surrounded by and connected with multiple tubular compartments with associated vesicles. MVB-tubule complexes are posited by Clooney et al. (2002) to correspond to sorting endosomes. uncurated Sorting Endosome sao1028571114 Sorting Endosome sao1970895398 Cell Regional Part Aggregate Object Cell Regional Part Aggregate Object http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Supracellular structure consisting of a dense intricate feltwork of interwoven fine glial processes, fibrils, synaptic terminals, axons, and dendrites interspersed among the nerve cells in the gray matter of the central nervous system. http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#MeSH_defSource Neuropil http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBO-UBO.owl#birnlex_3 2006-07-15 Neuropil May 15, 2009 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao205380252 This class has been retired. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting C0228081 Mitochondrion 0005739 sao1860313010 http://ccdb.ucsd.edu/SAO/images/mito_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/mito_ccdb_512x512.jpg A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration (Gene Ontology). C0026237 uncurated Mitochondrion mitochondria Regional Part Of Spine uncurated sao866168499 Regional Part Of Spine Skein-like inclusions are intracytoplasmic filamentous structures that are frequently encountered in preparations immunostained for ubiquitin. In H&E preparations (staining with hematoxylin and eosin) they are hardly visible or sometimes detected as faintly eosinophilic structures. January 9, 2009 Skein-like Inclusion Sarah M. Maynard Skein-like Inclusion PMID: 18026741 sao2048514053 Somatic Spine Somatic Spine uncurated Spine emanating from the cell soma. http://ccdb.ucsd.edu/SAO/images/somatic_spine_sw_512x512.jpg sao1635329413 Cytoskeletal Element uncurated Cytoskeletal Element Shepherd, G. M. The Synaptic organization of the brain, 5th ed., New York: Oxford University Press, 2004. Climbing fiber February 12, 2009 Climbing fiber Axon of inferior olive neuron that projects to the cerebellar cortex, largely via the inferior cerebellar peduncle. They range in diameter from 1-3 um and are myelinated util they enter the granule cell layer. They give off collaterals to the deep cerebellar nuclei. They synapse extensively with the dendrites of Purkinje cells in the molecular layer, where each fiber branches repeatedly to "climb" along the Purkinje cell dendritic tree. Each Purkinje cell is innervated by only a single climbing fiber. Post-synaptic Component Post-synaptic Component sao1507566336 uncurated sao-1686050947 Regional Part Of Mitochondrial Membrane Regional Part Of Mitochondrial Membrane sao-1819020575 Regional Part Of Cell Component uncurated Regional Part Of Cell Component 0005790 uncurated C0230789 Smooth Endoplasmic Reticulum sao710427438 Smooth Endoplasmic Reticulum The smooth ER has no ribosomes attached to it. The smooth is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER (Gene Ontology). http://ccdb.ucsd.edu/SAO/images/ser_sw_512x512.jpg intrinsic neuron http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Intrinsic neuron role Intrinsic neuron role http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug We are leaving off "interneuron" for now, as it has different connotations in vertebrates and invertebrates March 31, 2009 2007-08-26 local circuit neuron An interneuron participating in aneuronal circuit where all the neurons are bounded within a defined and limited region of the nervous system.(BB). local circuit neuron role Cis Face uncurated sao632188024 Cis Face CA3 pyramidal cell dendrite Dendrite of a hippocampal CA3 pyramidal cell May 11, 2010 Neuron Protrusion sao-250931889 Neuron Protrusion uncurated Hyaline Inclusion Sarah M. Maynard Hyaline Inclusion Pale eosinophilic inclusions with halos in H&E (hematoxylin and eosin) preparations. January 9, 2009 graph position temporary uncurated Vellous Process sao1189060993 is this the same as what is now termed the peripheral astrocyte process? Refers to the fine, veil-like terminal processes of protoplasmic astrocytes. Vellous Process uncurated Nissl Body Stacks of rough endoplasmic reticulum that stain intensely with basophilic dyes. Nissl Body sao793088923 Basilar Dendrite Basal Dendrite sao1079900774 uncurated Basilar Dendrite Sarah M. Maynard Neurofibrillary Tangle sao2409833926 Intracellular mass of paired, hellically wound protein filaments (PHF) lying in the cytoplasm of neuronal cell bodies and neuritic cell processes. They contain an abnormally phosporylated form of a microtuble associated with protein, tau. uncurated Neurofibrillary Tangle uncurated neuron compartment sao864921383 Regional Part Of Neuron Regional Part Of Neuron The Hippocampus book by Andersen et al. Thorny excrescence Large complex spine. Each excrescence is formed by a cluster of spine heads (Amaral, 1978) May 11, 2010 0005791 Nissl substance C0230779 Rough Endoplasmic Reticulum sao1881364067 Rough Endoplasmic Reticulum uncurated The rough (or granular) ER has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae (Gene Ontology). uncurated sao577473346 Category for vesicles observed in electron micrographs with unknown function. Vesicle Other Vesicle Other sao1546288504 uncurated Regional Part Of Golgi Regional Part Of Golgi Kato S. 2008 Amyotrophic lateral sclerosis models and human neuropathology: similarities and differences. Acta Neuropathol 115:97-114. page 101 Lewy Body-like Hyaline Inclusion Lewy Body-like Hyaline Inclusion Sarah M. Maynard In H&E preparations, neuronal LBHIs show an eosinphilic core with a paler peripheral halo, and their name is derived from their H&E staining features, which resemble those of Lewy bodies in patients with Parkinson's disease. Neuronal Lewy Body-like Hyaline Inclusions consist of filaments and granular materials, exhibit dense cores with rough preipheral halos and lack a limiting membrane. The filaments of these inclusions are composed of approximately 15-25 nm granule-coated fibrils in association with normal 10-nm neurofilaments. January 9, 2009 Axon Collateral uncurated Axon Collateral sao1470140754 Smaller branches of an axon that emanate from the main axon cylinder. That part of the nuclear content other than the chromosomes or the nucleolus (Gene Ontology). C0682537 uncurated Nucleoplasm Nucleoplasm sao661522542 0005654 sao685712019 Regional Part Of Astrocyte uncurated Regional Part Of Astrocyte Glial scar Fibrous scar consisting predominately of reactive astrocytes, microglia and extracellular matrix molecules formed after injury to the central nervous system (adapted from Rolls et al., Nature Reviews Neuroscience 10: 235, 2009) Star-shaped Neurofibrillary Tangle February 12, 2009 Star-shaped Neurofibrillary Tangle 2007-08-25 http://www.ifomis.org/bfo/1.1/snap#Role Functional role of cell http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated August 20, 2009 Functional role of cell http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug uncurated sao1122901839 Irregularly shaped clumps of denatured or misfolded proteins observed in some neurons after a period of ischemia that stain heavily with osmium in electon microscopic preparations. Sarah M. Maynard Dark Material Dark Material January 9, 2009 Transferrin Transferrin is a blood plasma protein for iron ion delivery which in humans is encoded by the TF gene. Transferrin Sarah M. Maynard Endoplasmic Reticulum Exit Site Specialized ribosome-free subdomains of synthetic endoplasmic reticulum where cargo is concentrated into vesicles tha bud from the endoplasmic reticulum for tranport to the Golgi (Horton and Ehlers, 2004). Endoplasmic Reticulum Exit Site uncurated sao124393998 spine-like process found on some neurons, e.g., periglomerular cells of olfactory cortex May 11, 2010 Gemmule sao1524397168 Junctional Site Junctional Site uncurated Regional Part Of Dendrite Regional Part Of Dendrite sao420754792 Regional Part Of Pyramidal cell axon May 19, 2009 Maryann Martone Glial Inclusion August 11, 2009 Glial Inclusion Jane Bugea Argyrophilic Glial Inclusion SNpc