NIF-Subcellular: contains cell parts and subcellular structures from SAO-CORE and Gene Ontology Cellular Component (GO-CC) next ID: nlx_subcell_20090212 1.3 (May 2012) 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 * Not all sao prefixed IDs are out of date or replaced by nifext. 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) BIRNLex-OBO-UBO:birnlex_8 true birn_annot:_birnlex_retired_class NIF-Cell:nifext_142 NIF-GrossAnatomy:birnlex_878 This class classifies fine under 'Constitutional part of cell', while loaded with NIF-GrossAnatomy.owl module. Cytoskeletal system NIF-Molecule:sao1231384859 NIF-Molecule:sao1246280606 This class classifies fine under 'Enzyme', while loaded with NIF-Molecule.owl module. Synthetic Enzyme NIF-Molecule:sao26622963 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#sao500241072 March 18, 2009 This class classifies fine under 'Macromolecule' while loaded with NIF-Molecule.owl module. Protein FMA_83604 February 23, 2010 Foundational Model of Anatomy Pacinian corpuscle 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) FMA_83605 Meisner's corpuscle Meisners corpuscle Meissner's corpuscle tactile corpuscle Meissners corpuscle 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. FMA_83606 February 23, 2010 Foundational Model of Anatomy Merkel cell-neurite complex Merkel disk receptor Merkel's disc Merkel's disk Merkels disc 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) birnlex_10 2006-09-07 UMLS Bill Bug Constitutional part of cell true cytoskeletal system post-synaptic density birnlex_1142 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBO-UBO.owl#birnlex_3 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao205380252 C0228081 2006-07-15 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 http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS May 15, 2009 This class has been retired. Neuropil true Neuropil birnlex_1152_2 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. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting C0034667 2006-07-15 http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS 2006-09-28 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). Node of Ranvier birnlex_13 2006-09-07 Bill Bug 2006-10-09 A defined subset of a population whose spatio-temporal interactions or aggregate behavior is representative of the whole population. Sample population Sample population birnlex_2534 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 2007-08-26 March 31, 2009 intrinsic neuron local circuit neuron local circuit neuron role An interneuron participating in aneuronal circuit where all the neurons are bounded within a defined and limited region of the nervous system.(BB). We are leaving off "interneuron" for now, as it has different connotations in vertebrates and invertebrates Intrinsic neuron role Intrinsic neuron role birnlex_2536 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://www.ifomis.org/bfo/1.1/snap#Role 2007-08-25 August 20, 2009 Functional role of cell Functional role of cell birnlex_2537 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 2007-08-25 2007-08-25 Functional role of nerve cell Functional role of nerve cell birnlex_788 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1846835077 C0026046 2006-07-15 http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS 2006-09-28 Microtubule true Microtubule birnlex_846 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1316272517 2006-07-15 2006-09-28 Neurofilament true Neurofilament birnlex_878 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1635329413 2006-07-15 February 18, 2010 cytoskeleton Maryann Martone Cytoskeletal system true birnlex_879 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#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao952483289 C0021770 2006-07-15 http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS 2006-09-28 Intermediate filament true Intermediate filament birnlex_886 BF_C000103 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1196688972 2006-07-15 2006-09-28 Post synaptic density true Post synaptic density birnlex_888 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao2006047981 2006-07-15 2006-09-28 Microfilament true Microfilament nlx_330 March 17, 2010 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. nlx_467 May 11, 2010 The Hippocampus book by Andersen et al. Thorny excrescence Large complex spine. Each excrescence is formed by a cluster of spine heads (Amaral, 1978) nlx_sub_1008001 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 2007-08-26 March 31, 2009 Principal neuron Projection neuron Projection neuron role 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). Principal neuron role CA3 Pyramidal neurons are principal neurons projecting out of the CA3 cytoarchitectural part of the hippocampus of vertebrates. Cerebellar Purkinje neurons are principal neurons projecting out from the cerebellar cortex of vertebrates. Principal neuron role nlx_subcell_090801 August 11, 2009 Argyrophilic Glial Inclusion Jane Bugea Glial Inclusion Glial Inclusion nlx_subcell_090802 NCI August 11, 2009 Jane Bugea Neuronal Cytoplasmic Inclusion Neuronal Cytoplasmic Inclusion nlx_subcell_090803 August 20, 2009 Cell role nlx_subcell_090901 GO_0015030 August 31, 2009 http://genetics.cwru.edu/matera3.html February 17, 2010 Coiled body Jane Bugea Cajal body nlx_subcell_091021 October 5, 2009 Sarah M. Maynard Mossy fiber rosette 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)) nlx_subcell_100203 PMID: 7477732 February 12, 2010 Grumose foamy spheroid body 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. nlx_subcell_100205 BBB Blood-brain barrier The BBB has also been defined physiologically 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. nlx_subcell_100206 February 23, 2010 F bouton 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. nlx_subcell_100207 February 23, 2010 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 nlx_subcell_100208 February 23, 2010 C bouton Synaptic bouton found in spinal cord on the soma and proximal dendrites of motor neurons nlx_subcell_100209 February 10, 2010 glial limiting membrane 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. nlx_subcell_100210 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) nlx_subcell_100307 March 17, 2010 Regional Part Of Granule Cell Axon nlx_subcell_100312 March 18, 2010 April 28, 2010 Dentate gyrus mossy fiber 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. nlx_subcell_100315 March 15, 2010 Maryann Marotone Subcellular entity subcellular_structure 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. nlx_subcell_1005001 May 11, 2010 CA3 pyramidal cell dendrite Dendrite of a hippocampal CA3 pyramidal cell nlx_subcell_1005002 May 11, 2010 dentate gyrus granule cell axonal bouton dentate gyrus mossy fiber expansion mossy fiber expansion Hippocampal mossy fiber expansion Synaptic expansion of hippocampal mossy fiber axon that makes contact with the thorny excrescences of hippocampal CA3 pyramidal cell dendrites nlx_subcell_1005003 May 11, 2010 Gemmule spine-like process found on some neurons, e.g., periglomerular cells of olfactory cortex nlx_subcell_20090101 January 9, 2009 PMID: 18026741 Sarah M. Maynard 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. Bunina Body nlx_subcell_20090102 January 9, 2009 Sarah M. Maynard 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. Pick Body nlx_subcell_20090103 January 9, 2009 PMID: 18026741 Sarah M. Maynard Skein-like Inclusion 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. Skein-like Inclusion nlx_subcell_20090104 January 9, 2009 Sarah M. Maynard Hyaline Inclusion Pale eosinophilic inclusions with halos in H&E (hematoxylin and eosin) preparations. Hyaline Inclusion nlx_subcell_20090105 January 9, 2009 Kato S. 2008 Amyotrophic lateral sclerosis models and human neuropathology: similarities and differences. Acta Neuropathol 115:97-114. page 101 Sarah M. Maynard Lewy Body-like Hyaline Inclusion 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. Lewy Body-like Hyaline Inclusion nlx_subcell_20090106 January 9, 2009 Sarah M. Maynard Transferrin Transferrin is a blood plasma protein for iron ion delivery which in humans is encoded by the TF gene. Transferrin nlx_subcell_20090201 February 12, 2009 Star-shaped Neurofibrillary Tangle Star-shaped Neurofibrillary Tangle nlx_subcell_20090202 February 12, 2009 Flame-shaped Neurofibrillary Tangle Flame-shaped Neurofibrillary Tangle nlx_subcell_20090203 February 12, 2009 Shepherd, G. M. The Synaptic organization of the brain, 5th ed., New York: Oxford University Press, 2004. 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. Climbing fiber nlx_subcell_20090204 February 12, 2009 Astrocyte Sheath Astrocyte Sheath nlx_subcell_20090205 February 23, 2009 Cytochrome c A small heme protein found loosely associated with the inner membrane of the mitochondrion. Cytochrome c nlx_subcell_20090206 February 23, 2009 Proteasome 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 nlx_subcell_20090207 February 24, 2009 Synaptophysin Synaptophysin (syp I) is a synaptic vesicle membrane protein Synaptophysin nlx_subcell_20090208 February 24, 2009 Endoneurial Space The space occupied by the endoneurium. nlx_subcell_20090209 February 27, 2009 Shepherd, G. M. The synaptic organization of the brain, 5th ed. New York: Oxford University Press, 2004 Cerebellar mossy fiber 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). Cerebellar mossy fiber nlx_subcell_20090210 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. C-fiber nlx_subcell_20090211 February 27, 2009 Calnexin 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. Calnexin nlx_subcell_20090501 May 15, 2009 Triad 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. nlx_subcell_20090502 May 16, 2009 Cerebellar glomerulus nlx_subcell_20090503 May 16, 2009 Maryann Martone 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. nlx_subcell_20090504 May 16, 2009 Shepherd, G. M. The synaptic organization of the brain, 5th ed New York: Oxford University Press, 2005 Thalamic glomerulus 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. nlx_subcell_20090505 May 17, 2009 Maryann Martone Encapsulated nerve ending Nerve ending found in skin surrounded by layers of connective tissue. nlx_subcell_20090506 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao3826089237 May 17, 2009 Axon projection Maryann Martone Axon bundle Group of myelinated or unmyelinated axons that group together. nlx_subcell_20090507 May 17, 2009 Shepherd, G. M. The synaptic organization of the brain, 5th ed New York: Oxford University Press, 2005 Ipsilateral associational-commissural projection Maryann Martone Ipsilateral associatioinal commissural projection 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. nlx_subcell_20090508 May 17, 2009 Maryann Martone Perforant path 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. nlx_subcell_20090509 May 17, 2009 Maryann Martone Schaffer collaterals Group of axons arising from hippocampal CA3 pyramidal neurons projecting to area CA1. nlx_subcell_20090510 May 19, 2009 Maryann Martone Regional Part Of Pyramidal cell axon nlx_subcell_20090511 May 19, 2009 Maryann Martone Schaffer collateral Part of axon of the CA3 pyramidal neuron that projects to hippocampal area CA1 . nlx_subcell_20090512 May 19, 2009 February 23, 2010 Maryann Martone Motor endplate Terminal ending of the axon of a motor neuron that forms a synapse onto a muscle cell. nlx_subcell_20090513 May 17, 2009 Maryann Martone Fmaid: 9672 Extracellular matrix 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. nlx_subcell_20090601 PMC2492885 June 18, 2009 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 Maryann Martone Dentate gyrus mossy fiber The granule cells give rise to distinctive unmyelinated axons referred to as mossy fibers by Ramón y Cajal. nlx_subcell_20090701 July 14, 2009 Early Endosome Small irregularly shaped intracellular vesicles to which endocytosed molecules are initially delivered (GO: 0005769). nlx_subcell_20090702 July 14, 2009 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 Endosome Late endosomes are vesicular structures that accumulate internalized components after their passage through early endosomes (GO: 0005700). nlx_subcell_20090703 July 14, 2009 Glial Cytoplasmic Inclusion Glial Cytoplasmic Inclusion sao-1046371754 uncurated 0030175 sao-1046371754 Filopodium 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) http://ccdb.ucsd.edu/SAO/images/filopodium_sw_512x512.jpg Filopodium sao-1067215520 uncurated sao-1067215520 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 Schwann Cell Paranodal Termination sao-1123256993 uncurated sao-1123256993 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-1337158144 0005575 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). Cellular Component Cell part which has a definable shape, bounded predominantly by bonafide boundaries and is countable (FMA). sao-1348591767 uncurated sao-1348591767 Branch Point Of Dendrite Branch Point Of Dendrite sao-1367457321 sao-1367457321 Mitochondrial Site Mitochondrial Site sao-1488888179 sao-1488888179 Pre-synaptic Ribbon Dense plate-like structure lying near and perpendicular to the pre-synaptic junction. Usually associated with pre-synaptic vesicles (Peters, Palay, and Webster). http://ccdb.ucsd.edu/SAO/images/pre-syn_ribbon_sw_512x512.jpg Pre-synaptic Ribbon sao-1686050947 uncurated sao-1686050947 Regional Part Of Mitochondrial Membrane Regional Part Of Mitochondrial Membrane sao-17780464455 Intercellular Gap Janction Channel Junctional complex consisting of two connexons that come together to form a communicating pore between two cells sao-1819020575 uncurated sao-1819020575 Regional Part Of Cell Component Regional Part Of Cell Component sao-1828894864 uncurated sao-1828894864 Cell Process Cell Process sao-1863852493 uncurated sao-1863852493 Glial Filament Glial Filament sao-188049490 uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 sao-188049490 May 28, 2009 Node Of Ranvier Axon 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 sao-1899375636 uncurated 0031980 sao-1899375636 Inner Mitochondrial Compartment (from Peters, Palay, and Webster) true 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. Mitochondrial Lumen sao-206157942 sao-206157942 Internode Part of nodal complex located underneath the compact myelin in between nodes of Ranvier Internode sao-234066064 sao-234066064 Paranode Region of nodal complex adjacent to the nodal region Paranode sao-250931889 uncurated sao-250931889 Neuron Protrusion Neuron Protrusion sao-3012335077 Junction Complex sao-343550527 sao-343550527 true Mitochondrial Space Spaces defined by the inner and outer mitochondrial membranes Mitochondrial Space sao-420949334 uncurated sao-420949334 Regional Part Of Neuron Process Regional Part Of Neuron Process sao-593830697 uncurated sao-593830697 Schwann Cell Myelin Sheath 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). http://ccdb.ucsd.edu/SAO/images/myelin_sheath_sw_512x512.jpg Schwann Cell Myelin Sheath sao-596411490 sao-596411490 Node Related Site Site defined with respect to the Node of Ranvier, e.g., node, paranode, juxtaparanode Node Related Site sao-699412220 uncurated sao-699412220 Regional Part Of SER Regional Part Of SER sao-820130069 uncurated sao-820130069 Pyramidal Neuronal Cell Body Pyramidal Neuronal Cell Body sao-82111036 uncurated sao-82111036 Cell Protrusion Cell Protrusion sao-867568886 sao-867568886 Neurite Neuron Process Neuron Process sao-876577163 uncurated sao-876577163 Mushroom Dendritic Spine http://ccdb.ucsd.edu/SAO/images/mush_dend_spine_sw_512x512.jpg Mushroom Dendritic Spine sao-946766835 sao-946766835 Synaptic Site Synaptic Site sao-961694769 uncurated sao-961694769 Excrescence Excrescence sao-965204139 uncurated sao-965204139 Branched Dendritic Spine http://ccdb.ucsd.edu/SAO/images/branched_dend_spine_sw_512x512.jpg Branched Dendritic Spine sao1004601938 uncurated sao1004601938 Dense Material Dense Material sao101633890 uncurated 0005829 sao101633890 C0010854 Cytosol The part of the cytoplasm that does not contain membranous or particulate subcellular components (UMLS). Cytosol sao1028571114 uncurated sao1028571114 Sorting Endosome 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. Sorting Endosome sao1036339110 uncurated 0005783 sao1036339110 C0014239 Endoplasmic Reticulum 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). http://ccdb.ucsd.edu/SAO/images/er2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/er_sw_512x512.jpg Endoplasmic Reticulum sao1037637579 sao1037637579 Membrane Cargo Refers to integral membrane proteins carried via the vesicle membrane. Membrane Cargo sao1038025871 uncurated sao1038025871 C0032592 Polyribosome 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). http://ccdb.ucsd.edu/SAO/images/polyribosome2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/polyribosome_sw_512x512.jpg Polyribosome sao1039242387 uncurated 0005802 sao1039242387 Trans Face The concave side of the Golgi apparatus, from which secretory vesicles emerge (Gene Ontology). Trans Face sao1044911821 uncurated sao1044911821 C0599444 soma Neuronal Cell Body Cell body which consists of the plasma membrane and the cytoplasm surrounding the nucleus of the neuron (FMA). Neuronal Cell Body sao1045389829 uncurated sao1045389829 Mitochondrial Membrane Mitochondrial Membrane sao1048004962 uncurated sao1048004962 C0206364 Tyrosine Kinase Receptor A class of cellular receptors that have an intrinsic protein-tyrosine kinase activity (MSH). Tyrosine Kinase Receptor sao1049471211 uncurated 0035061 sao1049471211 C0230547 Interchromatin Granule 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). Interchromatin Granule sao1049717962 uncurated sao1049717962 Regional Part Of Neuronal Cell Body Regional Part Of Neuronal Cell Body sao1071221672 uncurated 0008021 sao1071221672 C0039065 Synaptic Vesicle 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). http://ccdb.ucsd.edu/SAO/images/syn_vesicles_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/syn_vesicles_3_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/syn_vesicles_sw_512x512.jpg Synaptic Vesicle sao1074198261 sao1074198261 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 Post-synaptic Site sao1078172392 uncurated sao1078172392 Trunk Trunk sao1079900774 uncurated sao1079900774 Basal Dendrite Basilar Dendrite Basilar Dendrite sao1081228141 uncurated 0042587 sao1081228141 C0017911 Glycogen Granule 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). http://ccdb.ucsd.edu/SAO/images/glycogen_granule_sw_512x512.jpg Glycogen Granule sao109906988 uncurated sao109906988 Pinceau Fiber Dense plexus formed by the descending collaterals of cerebellar basket cells tha wrap around the Purkinje cell axonal initial segment. Pinceau Fiber sao110773650 uncurated sao110773650 Dendritic Microtubule Dendritic Microtubule sao1111202255 sao1111202255 ribbon 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). Pre-synaptic Dense Body sao1122901839 uncurated sao1122901839 Sarah M. Maynard Dark Material 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. Dark Material sao1124888485 uncurated 0031594 sao1124888485 NMJ Neuromuscular Junction 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). Neuromuscular Junction sao113580911 uncurated sao113580911 Regional Part Of Nucleolus Regional Part Of Nucleolus sao1139385046 uncurated sao1139385046 Free Ribosome Free Ribosome sao1140587416 uncurated 0005766 sao1140587416 C0230814 Primary Lysosome A lysosome before it has fused with a vesicle or vacuole (Gene Ontology). Primary Lysosome sao1145756102 uncurated sao1145756102 May 28, 2009 Do spines only have a post synaptic density? (Maryann Martone) 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. Spine Spine sao1152983960 uncurated sao1152983960 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). Intercalated Disk sao1153182838 uncurated 0012506 sao1153182838 C1167317 Vesicle Membrane The lipid bilayer surrounding any membrane-bounded vesicle in the cell (Gene Ontology). Vesicle Membrane sao1164727693 uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao587592318 sao1164727693 C0061465 May 1, 2009 Glutamate Receptor Glutamate Receptor sao1177708494 0030120 sao1177708494 C1166749 Vesicle Coat Refers to any specialized coating present on a vesicle membrane, e.g., clathrin. Vesicle Coat sao118541872 uncurated 0005921 sao118541872 C0206117 Gap Junction 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). http://ccdb.ucsd.edu/SAO/images/gap_junction_sw_512x512.jpg Gap Junction sao1186327184 uncurated 0000262 sao1186327184 C1166687 Mitochondrial Chromosome A chromosome found in the mitochondrion of a eukaryotic cell (Gene Ontology). Mitochondrial Chromosome sao1186642361 uncurated 0043218 sao1186642361 Oligodendrocyte 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). Oligodendrocyte Compact Myelin sao1186862860 uncurated sao1186862860 Basal Pole Of Neuron Portion of a cell soma closest to the point where the basilar dendrite emerges. Basal Pole Of Neuron sao1189060993 graph position temporary uncurated sao1189060993 is this the same as what is now termed the peripheral astrocyte process? Vellous Process Refers to the fine, veil-like terminal processes of protoplasmic astrocytes. Vellous Process sao118944228 graph position temporary 0005758 sao118944228 C1166886 true 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. Mitochondrial Intermembrane Space The region between the inner and outer lipid bilayers of the mitochondrial envelope. (Gene Ontology). Mitochondrial Intermembrane Space sao1191319089 uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 sao1191319089 May 28, 2009 Juxta Paranode Axon Region of axon immediately adjacent to the paranode. Juxta Paranode Axon sao1196688972 BF_C000103 0014069 sao1196688972 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). http://ccdb.ucsd.edu/SAO/images/psd_sw_512x512.jpg Post-synaptic Density sao11978067 uncurated 0005932 sao11978067 C0230744 Basal Body 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). http://ccdb.ucsd.edu/SAO/images/basal_bodies_sw_512x512.jpg Basal Body sao120573470 uncurated sao120573470 Inclusion Body Cellular Inclusion A nuclear or cytoplasmic aggregate of stainable substances, usually proteins. Cellular Inclusion sao120818728 uncurated sao120818728 Lumenal Surface Lumenal Surface sao1210952635 uncurated sao1210952635 Nucleolus-associated Heterochromatin Dense particles of heterochromatin, consisting of a loosely twisted strang ~600 A thick, found associated with the nucleolus (Palay and Chan-Palay, 1974). Nucleolus-associated Heterochromatin sao1211023249 uncurated 0030425 sao1211023249 C0011305 Dendrite 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). 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. http://ccdb.ucsd.edu/SAO/images/dend_ccdb_512x512.jpg Dendrite sao1217793903 uncurated sao1217793903 C0230580 Pars Granulosa 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 sao1232858786 uncurated sao1232858786 Thin Dendritic Spine http://ccdb.ucsd.edu/SAO/images/thin_dend_spine_sw_512x512.jpg Thin Dendritic Spine sao1241866791 uncurated 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 sao1243595998 uncurated 0045334 sao1243595998 Clathrin Coated Endocytic Vesicle A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology). http://ccdb.ucsd.edu/SAO/images/clath_coated_endocy_vesicle_sw_512x512.jpg Clathrin Coated Endocytic Vesicle sao124393998 uncurated sao124393998 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 sao1253297813 uncurated sao1253297813 Glial Subcompartment Glial Subcompartment sao1279474730 uncurated 0043209 sao1279474730 C0026973 Oligodendrocyte Myelin Sheath 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). Oligodendrocyte Myelin Sheath sao128470897 uncurated sao128470897 Sub-surface Cisternae 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 Sub-surface Cisternae sao1289190043 uncurated sao1289190043 Cellular Space Anatomical space occurring within a cell, usually formed by intracellular membranes. Cellular Space sao1289741256 uncurated 0005741 sao1289741256 C0230839 Mitochondrial Membrane Outer The membrane on the outer surface of the mitochondrion, interfacing with the cell cytoplasm (Gene Ontology). http://ccdb.ucsd.edu/SAO/images/mito_outer_memb_ccdb_512x512.jpg Mitochondrial Membrane Outer sao1291545653 uncurated sao1291545653 Membrane Bound Ribosome A ribosome that is attached to a intracellular membrane. Does not itself have a membrane surrounding it. Membrane Bound Ribosome sao1299635018 uncurated sao1299635018 Maryann Martone 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 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 Cell Cell Contact Zone sao1311109124 uncurated sao1311109124 Electrical Synapse Electrotonic Synapse 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). http://ccdb.ucsd.edu/SAO/images/electrotonic_syn_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/sym_synapse_sw_512x512.jpg Electrotonic Synapse sao1316272517 uncurated 0005883 sao1316272517 C0027834 Neurofilament 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). http://ccdb.ucsd.edu/SAO/images/neurofilament_sw_512x512.jpg Neurofilament sao1329750433 uncurated sao1329750433 Membrane Surface Membrane Surface sao1340260079 uncurated sao1340260079 April 28, 2010 dendritic tuft Tuft The terminal specialization found in some types of dendrites consisting of numerous small terminal branches, giving the dendrite a tufted appearance. Tuft sao1342297498 sao1342297498 Sarah M. Maynard Amyloid Fibril A fibril composed of amyloid protein. http://ccdb.ucsd.edu/SAO/images/amyloid_filament_sw_512x512.jpg Amyloid Fibril sao1354781919 uncurated sao1354781919 Paranodal loop Oligodendrocyte 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 Oligodendrocyte Paranodal Termination sao1362520468 uncurated 0030139 sao1362520468 C0887883 Endocytic Vesicle A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology). Endocytic Vesicle sao1371347282 uncurated 0005743 sao1371347282 C0230840 Mitochondrial Membrane Inner 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). http://ccdb.ucsd.edu/SAO/images/mito_inner_memb_ccdb_512x512.jpg Mitochondrial Membrane Inner sao1376748732 uncurated sao1376748732 Ensheathing Process Refers to the process of the Schwann cell that surrounds an unmyelinated axon or cell soma. http://ccdb.ucsd.edu/SAO/images/ensheath_process_sw_512x512.jpg Ensheathing Process sao1379604862 uncurated 0042599 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). Lamellar Body sao138219748 uncurated sao138219748 Vesicular Component Vesicular Component sao1382918459 uncurated 0030143 sao1382918459 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). Inter-Golgi Transport Vesicle sao138430598 uncurated sao138430598 Nematosome 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) Nematosome sao1395777368 sao1395777368 Intercellular Junction Intercellular Junction sao1397492660 uncurated 0005605 sao1397492660 C0242195 Basal Lamina A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix (Gene Ontology). Basal Lamina sao1400623473 uncurated sao1400623473 fascia adhaerens Zonula Adhaerens Adherent, symmetrical junction characterized by widened extracellular space and filamentous material (Peters, Palay and Webster, 1991). http://ccdb.ucsd.edu/SAO/images/zonula_adherens_sw_512x512.jpg Zonula Adhaerens sao1425028079 uncurated 0005616 sao1425028079 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). http://ccdb.ucsd.edu/SAO/images/extracell_space_sw_512x512.jpg Extracellular Space sao1429207766 uncurated 0005840 sao1429207766 C0035553 Ribosome 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). http://ccdb.ucsd.edu/SAO/images/ribosomes_sw_512x512.jpg Ribosome sao1447478620 uncurated sao1447478620 Pial Endfoot Pial Endfoot sao1455064842 sao1455064842 Vesicle Subcomponent Vesicle Subcomponent sao1455996588 uncurated 0005652 sao1455996588 C1136039 Nuclear Lamina 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). 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). Nuclear Lamina sao1456184038 uncurated 0043228 sao1456184038 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). Non Membrane Bound Organelle sao1470121605 uncurated sao1470121605 Active Zone Cytomatrix Filamentous matrix immediately internal to the plasma membrane docking zone (Zhai and Bellen, 2004). Active Zone Cytomatrix sao1470140754 uncurated sao1470140754 Axon Collateral Smaller branches of an axon that emanate from the main axon cylinder. Axon Collateral sao1490223249 sao1490223249 Need to determine whether this should be a part of a vesicle; I think it shouldn't be Vesicle Cargo Refers to the contents contained in the vesicle. Vesicle Cargo sao1499850686 uncurated sao1499850686 Nuclear Subcomponent Nuclear Subcomponent sao1506103497 uncurated sao1506103497 Mixed Synapse Existence of both chemical and electrotonic synapses at the same interface (Peters, Palay and Webster, 1991). Synaptic contact characterized by both electrical and chemical synaptic junctions. Mixed Synapse sao1507566336 sao1507566336 Post-synaptic Component Post-synaptic Component sao1514682949 uncurated sao1514682949 Cytoplasmic Surface Cytoplasmic Surface sao1524397168 sao1524397168 Junctional Site Junctional Site sao1531915298 uncurated sao1531915298 Amorphous Vesicle 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 sao1536532595 uncurated sao1536532595 Sessile Dendritic Spine Sessile Dendritic Spine sao1539965131 uncurated 0043226 sao1539965131 C0029219 Organelle 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 sao1546288504 uncurated sao1546288504 Regional Part Of Golgi Regional Part Of Golgi sao1547508851 uncurated 0031904 sao1547508851 endosome lumen Endosomal Lumen The volume enclosed by the membranes of an endosome (Gene Ontology). Endosomal Lumen sao1549842807 uncurated 0005767 sao1549842807 C0230815 Secondary Lysosome Vacuole formed by the fusion of a lysosome with an organelle (autosome) or with a primary phagosome (Gene Ontology). Secondary Lysosome sao1570660411 uncurated sao1570660411 Tubular Endosome 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 sao1571698684 uncurated sao1571698684 Barr Body Barr Body sao1573004591 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 sao1573004591 It is not clear whether peripheral astrocyte process only refers to the processes surrounding synapses or also refers to the endfeet 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. Peripheral Astrocyte Process sao1579007712 uncurated sao1579007712 Cell Interior Cell Interior sao1586851177 uncurated sao1586851177 Regional Part Of Basket cell axon Terminal pre-synaptic ending of an axon or axon collateral. Regional Part Of Basket Cell Axon sao1588493326 uncurated 0005884 sao1588493326 C0025979 Actin Filament 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). http://ccdb.ucsd.edu/SAO/images/act_filament_sw_512x512.jpg Actin Filament sao1590928667 uncurated sao1590928667 Regional Part Of Spiny Dendrite Regional Part Of Spiny Dendrite sao1594955670 uncurated sao1594955670 Dendritic Growth Cone http://ccdb.ucsd.edu/SAO/images/dend_growth_cone_sw_512x512.jpg Dendritic Growth Cone sao1596955044 uncurated 0030868 sao1596955044 SER Membrane The lipid bilayer surrounding the smooth endoplasmic reticulum (Gene Ontology). SER Membrane sao1596975044 uncurated sao1596975044 Main Axon Used to refer to the main axonal trunk, as opposed to the collaterals. Main Axon sao1612527463 uncurated 0005637 sao1612527463 Nuclear Inner Membrane The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope (Gene Ontology). Nuclear Inner Membrane sao1615953555 uncurated 0000785 sao1615953555 C0008546 Chromatin The ordered and organized complex of DNA and protein that forms the chromosome (Gene Ontology). Chromatin sao1617136075 uncurated 0005640 sao1617136075 Nuclear Outer Membrane 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). Nuclear Outer Membrane sao1630537580 uncurated sao1630537580 Astrocyte Process Refers to processes of astrocytes extending from the cell soma that wrap around neurons and conform to cellular components in the neuropil. http://ccdb.ucsd.edu/SAO/images/astrocyte_process_sw_512x512.jpg Astrocyte Process sao1634374950 uncurated sao1634374950 Hypolemmal Cisternae 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 sao1635329413 uncurated sao1635329413 Cytoskeletal Element Cytoskeletal Element sao1642494436 uncurated sao1642494436 Recurrent Collateral Axon collateral that ramifies in the area of the soma of the cell of origin. Recurrent Collateral sao1642908940 uncurated sao1642908940 neck pedicle Spine Neck Spine Neck sao1663586795 C0007603 uncurated 0005886 sao1663586795 cell membrane Plasma Membrane 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_memb2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/plas_memb_3_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/plas_memb_sw_512x512.jpg Plasma Membrane sao1682692988 uncurated sao1682692988 Regional Part Of Spine Apparatus Regional Part Of Spine Apparatus sao1683772610 uncurated sao1683772610 Endosomal Subcomponent Endosomal Subcomponent sao1684283879 uncurated sao1684283879 Calyx Of Held Calyx Of Held sao1687101204 uncurated 0031965 sao1687101204 C0028584 Nuclear Membrane Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space (Gene Ontology). Nuclear Membrane sao1702920020 uncurated 0005634 sao1702920020 C0007610 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). http://ccdb.ucsd.edu/SAO/images/nucleus_sw_512x512.jpg Nucleus sao1720343330 uncurated 0005768 sao1720343330 C0034850 Endosome A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation (GO). Endosome sao172297168 BF_C000102 uncurated sao172297168 Dendritic Tree The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches. Dendritic Tree sao1730664005 uncurated sao1730664005 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). Pre-synaptic Grid sao1747012216 uncurated sao1747012216 square array Orthogonal Array Square arrays of closely spaced intramembrane particles, 4-6 nm in size seen in astrocyte processes, now known to contain aquaporins. Orthogonal Array sao1749953771 uncurated sao1749953771 Tail Portion 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). Tail Portion sao1770195789 uncurated 0030424 sao1770195789 C0004461 May 5, 2010 Fiber Axon Cell appendage of a neuron that consists of an axon hillock, an axon proper, axon collaterals and an axon terminal (FMA) 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). http://ccdb.ucsd.edu/SAO/images/axon_sw_512x512.jpg Axon sao1784069613 sao1784069613 Synaptic Component Synaptic Component sao1791490892 uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao183270081 sao1791490892 May 28, 2009 This class has been retired. Regional Part Of Myelinated Axon true Regional Part Of Myelinated Axon sao1799103720 uncurated 0043197 sao1799103720 C0872341 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). http://ccdb.ucsd.edu/SAO/images/dend_spine_ccdb_512x512.jpg http://ccdb.ucsd.edu/SAO/images/dend_spine_sw_512x512.jpg Dendritic Spine sao1804523077 uncurated 0005759 sao1804523077 C0230843 Mitochondrial Matrix 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 sao180601769 uncurated 0031410 sao180601769 Cytoplasmic Vesicle A vesicle formed of membrane or protein, found in the cytoplasm of a cell (Gene Ontology). Cytoplasmic Vesicle sao181458425 uncurated sao181458425 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 sao1819509473 uncurated 0048237 sao1819509473 rough endoplasmic reticulum lumen RER Lumen The volume enclosed by the membranes of the rough endoplasmic reticulum (Gene Ontology). RER Lumen sao1820400233 uncurated 0005730 sao1820400233 C0007609 Nucleolus 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/nucleoli_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/nucleolus_sw_512x512.jpg Nucleolus sao18239917 uncurated sao18239917 Axonal Spine Refers to spine that originates from the axon, usually the initial segment (Peters, Palay and Webster, 1991). Axonal Spine sao1825845900 uncurated sao1825845900 Crista Junction Tubular structures of relatively uniform size that connect mitochondrial cristae to the inner mitchondrial membrane (Perkins and Ellisman, 2003). Crista Junction sao183270081 uncurated sao183270081 Subregional Part Of Neuron Process Subcompartment of a compartment. Subregional Part Of Neuron Process sao1841764412 uncurated sao1841764412 C0230581 Pars Fibrosa Portion of the nucleolus composed of densely matted filaments with scattered dark granules (Palay and Chan-Palay, 1974). Pars Fibrosa sao1842028314 uncurated sao1842028314 SER Subcomponent SER Subcomponent sao18461326 uncurated sao18461326 Inner Bounding Mitochondrial Membrane Part of mitochondrial inner membrane that runs parallel to the outer mitochondrial membrane Inner Bounding Mitochondrial Membrane sao1846835077 uncurated 0005874 sao1846835077 C0026046 Microtubule 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). http://ccdb.ucsd.edu/SAO/images/microtubules_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/microtubules_sw_512x512.jpg Microtubule sao1858501007 uncurated sao1858501007 Bridge Contact Site 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 sao1860313010 uncurated 0005739 sao1860313010 C0026237 mitochondria Mitochondrion 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). http://ccdb.ucsd.edu/SAO/images/mito_ccdb_512x512.jpg http://ccdb.ucsd.edu/SAO/images/mito_sw_512x512.jpg Mitochondrion sao1872343973 uncurated sao1872343973 Microtubule Fascicle Refers to a bundle of closely apposed microtubules running parallel to each other. Microtubule Fascicle sao187426937 uncurated sao187426937 Synaptic Bouton Terminal pre-synaptic ending of an axon or axon collateral. http://ccdb.ucsd.edu/SAO/images/syn_bouton_sw_512x512.jpg Synaptic Bouton sao1877927224 uncurated sao1877927224 Apical Pole Of Neuron Portion of a cell soma closest to the point where the apical dendrite emerges. Apical Pole Of Neuron sao1881364067 uncurated 0005791 sao1881364067 C0230779 Nissl substance Rough Endoplasmic Reticulum 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). Rough Endoplasmic Reticulum sao1884931180 uncurated sao1884931180 Ribbon Synapse 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 sao1890444066 uncurated sao1890444066 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) Schwann Cell Microvillus sao1894609662 uncurated sao1894609662 Sarah M. Maynard Regional Part Of Lewy Body Regional Part Of Lewy Body sao1908934319 uncurated sao1908934319 Intranuclear Membrane Space The space between the inner and outer nuclear membranes Intranuclear Membrane Space sao1911631652 uncurated sao1911631652 Pre-synaptic Active Zone Component Pre-synaptic Active Zone Component sao1922892319 core:definition incomplete 0005911 sao1922892319 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. Intercellular Junction Site The site of cell-cell contact containing a morphologically identified junctional complex joining the two cells. Intercellular Junction Site sao1925368674 uncurated sao1925368674 Pinocytic Vesicle Pinocytic Vesicle sao1933817066 uncurated sao1933817066 MAC mitochondrial-associated adherens complex Mitochondrial Adhaerens Complex 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). Mitochondrial Adhaerens Complex sao1938587839 core:definition incomplete sao1938587839 2007-02-23 Subplasmalemmal Coating 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 Subplasmalemmal Coating sao1939999134 uncurated 0005923 sao1939999134 tight junction Zonula Occludens 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). Zonula Occludens sao1943947957 uncurated sao1943947957 Peg And Socket Contact 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). Peg And Socket Contact sao1950673097 uncurated sao1950673097 Schaffer Collateral Axon collateral of CA3 pyramidal neurons that project to CA1 and synapse in the zona radiatum. Schaffer Collateral sao195217619 uncurated sao195217619 Regional Part Of Schwann Cell Regional Part Of Schwann Cell sao1956231674 uncurated sao1956231674 Golgi Lumen Golgi Lumen sao1956738165 uncurated sao1956738165 Look into the relationship of Macular and zonula adhaerentia and determine whether they are all subclasses of adhaerent junction Macular Adhaerentia Macular Adhaerentia sao1969557946 uncurated sao1969557946 C0009143 Coated Pit Specialized sites on the plasma membrane exhibiting a clathrin coat; likely vesicles in the process of pinching off (Conner and Schmid, 2003). Coated Pit sao1970895398 sao1970895398 Cell Regional Part Aggregate Object Cell Regional Part Aggregate Object sao1974433376 uncurated sao1974433376 C0932419 Regional Part Of Epithelial Cell Regional Part Of Epithelial Cell sao2006047981 uncurated sao2006047981 C0025979 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) Microfilament sao2007137787 uncurated sao2007137787 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). http://ccdb.ucsd.edu/SAO/images/axon_term_sw_512x512.jpg Axon Terminal sao2017162875 uncurated sao2017162875 Need to look this one up and see what this really meant. Age Associated Age Associated sao2019617624 uncurated sao2019617624 Regional Part Of RER 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 sao2031592629 uncurated sao2031592629 Neurosecretory Vesicle 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 sao2034472720 BF_C000106 uncurated 0043198 sao2034472720 Dendritic Shaft Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines (Gene Ontology). http://ccdb.ucsd.edu/SAO/images/dend_shaft_ccdb_512x512.jpg Dendritic Shaft sao2038461087 uncurated sao2038461087 Active Zone Plasma Membrane Plasma membrane juxtaposed to the PSD where synaptic vesicle fusion occurs (Zhai and Bellen, 2004). Active Zone Plasma Membrane sao203987954 uncurated sao203987954 Axonal Growth Cone Axonal Growth Cone sao2045955158 uncurated 0005771 sao2045955158 C0230825 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). http://ccdb.ucsd.edu/SAO/images/multives_bodies_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/mutlivesicular_body_sw_512x512.jpg Multivesicular Body sao2048514053 uncurated sao2048514053 Somatic Spine Spine emanating from the cell soma. http://ccdb.ucsd.edu/SAO/images/somatic_spine_sw_512x512.jpg Somatic Spine sao2048701763 uncurated sao2048701763 We are unclear why this is causing an inconsistency error. Perivascular Endfoot Perivascular Endfoot sao205380252 uncurated sao205380252 C0228081 Neuropil 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). http://ccdb.ucsd.edu/SAO/images/neuropil_sw_512x512.jpg Neuropil sao2064469343 uncurated sao2064469343 Vascular Endfoot http://ccdb.ucsd.edu/SAO/images/vasc_endfoot_sw_512x512.jpg Vascular Endfoot sao2108323256 sao2108323256 Pre-synaptic Site Pre-synaptic Site sao2114874506 uncurated sao2114874506 Membrane Stack 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 sao2127666702 uncurated sao2127666702 Mesaxon 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). Mesaxon sao2128156969 sao2128156969 2007-02-09 Maryann Martone 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). Spine Mat sao2135015805 uncurated sao2135015805 Extracellular Surface Extracellular Surface sao220861693 uncurated 0005643 sao220861693 C0028587 Nuclear Pore 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 http://ccdb.ucsd.edu/SAO/images/nucl_pore_sw_512x512.jpg Nuclear Pore sao221389602 uncurated 0031982 sao221389602 C0042219 Vesicle Any small, fluid-filled, spherical organelle enclosed by membrane or protein (Gene Ontology). Vesicle sao2254405550 uncurated sao2254405550 2006-09-07 Bill Bug Population A collection of independent organismal entities engaged in some form of spatio-temporal interaction or aggregate behavior Population sao2409833926 uncurated sao2409833926 Sarah M. Maynard Neurofibrillary Tangle 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. Neurofibrillary Tangle sao243541954 uncurated 0043083 sao243541954 C0682685 Synaptic Cleft The narrow gap that separates the presynaptic and postsynaptic membranes, into which a neurotransmitter is released (Gene Ontology). http://ccdb.ucsd.edu/SAO/images/syn_cleft_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/syn_cleft_sw_512x512.jpg Synaptic Cleft sao248349196 uncurated sao248349196 Neurotubule Refers to a microtubule found in a nerve cell. The term "neurotubule" may now be obselete; however, it was used in earlier findings. Neurotubule sao250772229 uncurated 0030673 sao250772229 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). Axolemma sao254777664 uncurated sao254777664 Schmidtt-Lanterman Cleft 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. http://ccdb.ucsd.edu/SAO/images/Schmidtt-Lanterman_cleft_sw_512x512.jpg Schmidtt-Lanterman Cleft sao256000789 uncurated 0043194 sao256000789 Initial Segment 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). http://ccdb.ucsd.edu/SAO/images/init_seg_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/init_seg_sw_512x512.jpg Initial Segment sao257629430 uncurated sao257629430 Puncta Adhaerentia 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 Puncta Adhaerentia sao273773228 BF_C000112 uncurated sao273773228 Apical Dendrite Apical Dendrite sao280355188 uncurated sao280355188 Regional Part Of Axon Regional Part Of Axon sao28175134 uncurated sao28175134 Terminal Specialization Terminal Specialization sao289211478 uncurated sao289211478 Chemical Synapse Chemical Synapse sao295057932 uncurated sao295057932 Dendriole Dendriole sao3089754107 sao3089754107 RER Membrane RER Membrane sao317384566 uncurated sao317384566 Stubby Dendritic Spine http://ccdb.ucsd.edu/SAO/images/stubby_dend_spine_sw_512x512.jpg Stubby Dendritic Spine sao333328131 uncurated 0030061 sao333328131 C0230844 Cristae Any of the inward folds of the mitochondrial inner membrane. (Gene Ontology) http://ccdb.ucsd.edu/SAO/images/cristae_ccdb_512x512.jpg Cristae sao340271629 uncurated sao340271629 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 sao3826089237 uncurated sao3826089237 Sarah Maynard Aggregate Object Aggregate Object sao386529203 sao386529203 Pre-synaptic Component Pre-synaptic Component sao388182739 graph position temporary uncurated sao388182739 Endfoot Terminal process of astrocyte abutting non-neuronal surfaces in the brain. Endfoot sao401910342 uncurated sao401910342 Somatic Portion Portion of the tanycyte that lies within the ependyma and contains the nucleus (Peters, Palay and Webster, 1991). Somatic Portion sao403156667 uncurated sao403156667 Docked Vesicle Synaptic vesicle docked at the pre-synaptic active zone. Docked Vesicle sao4040591221 uncurated sao4040591221 Sarah M. Maynard has Regional Part some Regional_Part_of_Lewy_Body restriction violated because Cortical Lewy Body lacks halo. Cortical Lewy Body Lesion that is less well defined than a Classical Lewy Body and lacks a halo. Cortical Lewy Body sao413722576 uncurated sao413722576 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. Peri Cellular Basket sao414196390 uncurated 0043227 sao414196390 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 sao420754792 uncurated sao420754792 Regional Part Of Dendrite Regional Part Of Dendrite sao427941916 graph position temporary 0005918 sao427941916 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 Septate Junction sao445019788 uncurated 0005922 sao445019788 C0230609 Wikipedia hemichannel, connexon complex 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. Connexon sao445485807 uncurated 0000791 sao445485807 euchromatin Extended Chromatin A dispersed and relatively uncompacted form of chromatin (Gene Ontology). Extended Chromatin sao447856407 uncurated sao447856407 Contact Site Sites of close apposition of the inner and outer mitochondrial membrane (Perkins and Frey, 2000). Contact Site sao451912436 uncurated 0005794 sao451912436 C0018042 golgi cisternae Golgi Apparatus 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) http://ccdb.ucsd.edu/SAO/images/golgi_app_sw_512x512.jpg Golgi Apparatus sao452970150 umls_ID: C0230664 Membrane Receptor Membrane Receptor sao4749542545 uncurated sao4749542545 Sarah M. Maynard Classical Lewy Body 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. Classical Lewy Body sao478230652 uncurated sao478230652 Granular Vesicle Vesicle of varying size, but usually larger than 45 nm, that has an electron dense "granular" core, associated with noradrenergic and peptidergic cells. Granular Vesicle sao4785563283 uncurated sao4785563283 Sarah M. Maynard Amyloid Aggregate Insoluble fibrous protein aggregation sharing specific structural traits. Amyloid Aggregate sao488120195 uncurated sao488120195 Calyx Calyx sao4933778419 uncurated sao4933778419 there are two morphological types: classical (brain stem) and cortical Lewy bodies Sarah M. Maynard Lewy Body 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. Lewy Body sao494258938 uncurated 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). Active Zone Dense Projection sao499555322 uncurated 0005777 sao499555322 C0752063 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). Resembles lysosomes in appearance (Peters, Palay and Webster, 1991). According to the latter, peroxisome is synonymous with microbodies. Peroxisome sao505137457 uncurated 0016604 sao505137457 C0230595 Nuclear Body Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins (Gene Ontology). Nuclear Body sao5051906853 uncurated sao5051906853 Sarah M. Maynard This is a placeholder. Fibril A minute fibril or filament. Fibril sao506721981 uncurated sao506721981 Laminated Body Laminated Body sao508165343 uncurated sao508165343 Supracellular Structure Supra Cellular Structure A morphological or functional domain formed by parts of two or more cells, e.g., neuropil, dendritic bundles. Supra Cellular Structure sao508958414 uncurated sao508958414 true Intracristal Space The space bounded by the cristae membrane Intracristal Space sao517367952 sao517367952 Endocytic Zone 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 sao553711217 sao553711217 Spine Related Site Spine Related Site sao553737851 uncurated sao553737851 Spinule http://ccdb.ucsd.edu/SAO/images/spinule_sw_512x512.jpg Spinule sao561419532 uncurated sao561419532 Golgi Lamellae Golgi Lamellae sao571652273 uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#birnlex_1152_2 sao571652273 C0034667 May 16, 2009 This class has been retired. Node Of Ranvier true 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). Node Of Ranvier sao5764355747 uncurated sao5764355747 Halo Sarah M. Maynard Corona The periphery of the Lewy Body. In Parkinson's Disease, it contains sperical accumulations of filaments arrange in a loose, radiating array. Corona sao577473346 uncurated sao577473346 Vesicle Other Category for vesicles observed in electron micrographs with unknown function. Vesicle Other sao581845896 uncurated 0000792 sao581845896 heterochromatin Condensed Chromatin A compact and highly condensed form of chromatin (Gene Ontology). Chromatin that are agglomerated into irregular masses, some attached to the nuclear envelope. Condensed Chromatin sao585356902 uncurated 0005764 sao585356902 C0024369 Lysosome 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 sao587592318 uncurated sao587592318 C0034828 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 sao587858733 uncurated sao587858733 June 22, 2009 I'm not sure whether this should be a type of neuropil or a type of synaptic complex. (Maryann Martone) Glomerulus 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 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. Glomerulus sao601362597 uncurated 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. Lewy Neurite sao624292949 uncurated sao624292949 Golgi Subcomponent Golgi Subcomponent sao627227260 uncurated 0043203 sao627227260 C0228079 Axon Hillock 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). Axon Hillock sao628508602 uncurated sao628508602 Cellular Subcomponent Cellular Subcomponent sao632188024 uncurated sao632188024 Cis Face Cis Face sao6433132645 sao6433132645 Cellular Membrane Cellular Membrane sao6587439252 uncurated sao6587439252 Sarah M. Maynard Core The center portion of the Lewy Body. In Parkinson's Disease, it contains a matted meshwork of filaments. Core sao6603990120 sao6603990120 PHF Sarah M. Maynard Paired Helical Filament Two threads of tau protein that are wound around each other. Paired Helical Filament sao661522542 uncurated 0005654 sao661522542 C0682537 Nucleoplasm That part of the nuclear content other than the chromosomes or the nucleolus (Gene Ontology). Nucleoplasm sao666410040 uncurated sao666410040 Mitochondrial Subcomponent Mitochondrial Subcomponent sao671419673 uncurated sao671419673 Microvilli http://ccdb.ucsd.edu/SAO/images/microvilli_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/microvilli_sw_512x512.jpg Microvilli sao685712019 uncurated sao685712019 Regional Part Of Astrocyte Regional Part Of Astrocyte sao694815499 uncurated sao694815499 Coated Tip Coated tips of tubular endosomes that appear to be vesicles in the process of budding off (Clooney et al., 2002). Coated Tip sao700839054 sao700839054 Need to determine what is the proper relationships between an electrotonic synapse and a gap junction Gap Junction Plaque 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 sao7016027781 uncurated sao7016027781 Sarah M. Maynard Protein Aggregate An insoluble mass of misfolded proteins. Protein Aggregate sao707332678 uncurated sao707332678 Axon Microtubule Fascicle Refers to the bundled configuration of microtubules in the axon hillock and initial segment. Axon Microtubule Fascicle sao710427438 uncurated 0005790 sao710427438 C0230789 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 Smooth Endoplasmic Reticulum sao725931194 uncurated sao725931194 C0230810 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_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/spine_app_3_sw_512x512.jpg Spine Apparatus sao730872736 graph position temporary sao730872736 Not clear if this should be described as an organelle or an inclusion. Dense Body An electron dense body, some of which contain granules (Peters, Palay and Webster (1991) Dense Body sao732341560 uncurated sao732341560 Pinceau 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 sao7474011676 uncurated sao7474011676 Sarah M. Maynard Alpha-Synuclein Fibril 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. Alpha-Synuclein Fibril sao7547390221 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 sao7561423738 uncurated sao7561423738 Protein Filament Sarah M. Maynard 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 Filament Filament sao758620702 sao758620702 Juxtaparanode Region of nodal complex adjacent to the paranode Juxtaparanode sao772007592 uncurated sao772007592 C0887944 Dense Core Vesicle 40-60 nm vesicle containing an electron dense granule, 15-20 nm in diameter (Peters, Palay and Webster, 1991). http://ccdb.ucsd.edu/SAO/images/dense_core_vesicle_sw_512x412.jpg Dense Core Vesicle sao787716553 uncurated 0005929 sao787716553 C0008778 Cilium 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). http://ccdb.ucsd.edu/SAO/images/cilium_sw_512x512.jpg Cilium sao792027222 uncurated 0048786 sao792027222 Pre-synaptic Active Zone A specialized presynaptic plasma membrane region where synaptic vesicles dock and fuse (Gene Ontology). http://ccdb.ucsd.edu/SAO/images/active_zone_sw_512x512.jpg Pre-synaptic Active Zone sao793088923 uncurated sao793088923 Nissl Body Stacks of rough endoplasmic reticulum that stain intensely with basophilic dyes. Nissl Body sao797538226 uncurated 0031983 sao797538226 Vesicle Lumen The volume enclosed by the membrane or protein that forms a vesicle (Gene Ontology). Vesicle Lumen sao819927218 uncurated 0005798 sao819927218 C0230767 Golgi-associated Vesicle 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 sao830092290 uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 sao830092290 May 28, 2009 Internode Axon Internode Axon sao830981606 uncurated sao830981606 Intracellular Membrane Intracellular Membrane sao831502550 uncurated sao831502550 Regional Part Of Oligodendrocyte Regional Part Of Oligodendrocyte sao8444068431 uncurated sao8444068431 Autophagolysosome, degrading autophagic vacuole (AVd) Sarah M. Maynard Autolysosome 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. Autolysosome sao864921383 uncurated sao864921383 neuron compartment Regional Part Of Neuron Regional Part Of Neuron sao866168499 uncurated sao866168499 Regional Part Of Spine Regional Part Of Spine sao8663416959 uncurated sao8663416959 autophagic vacuole, initial autophagic vacuole (AVi) Sarah M. Maynard Autophagosome 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. Autophagosome sao873654461 sao873654461 Nodal Complex http://ccdb.ucsd.edu/SAO/images/node_ccdb_512x512.jpg Nodal Complex sao877341397 uncurated sao877341397 Regional Part Of Tanycyte Regional Part Of Tanycyte sao879919129 uncurated 0030118 sao879919129 C1166728 Clathrin Coat 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 sao884265541 uncurated sao884265541 Dendritic Branch Refers to dendrites arising from another dendrite. Dendritic Branch sao885490876 uncurated 0030133 sao885490876 C0887882 secretory vesicle 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). Transport Vesicle sao895885284 uncurated sao895885284 Regional Part Of Glial Cell Regional Part Of Glial Cell sao901230115 sao901230115 Neck Portion 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 sao9117790637 uncurated sao9117790637 Sarah M. Maynard Extracellular Structure Structure that exists outside the cell. Extracellular Structure sao9137852997 uncurated sao9137852997 Sarah M. Maynard Plaque A formation or growth of cells. Plaque sao914572699 uncurated 0045202 sao914572699 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 sao924713546 uncurated sao924713546 Terminal Loop Portion of myelin-forming Schwann cell consisting of terminal cytoplasmic extensions adhered to the axon at the beginning and end of the myelin sheath. Terminal Loop sao927884761 uncurated 0048238 sao927884761 smooth endoplasmic reticulum lumen SER Lumen The volume enclosed by the membranes of the smooth endoplasmic reticulum (Gene Ontology). SER Lumen sao936144858 uncurated http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 sao936144858 May 28, 2009 Paranode Axon Paranode Axon sao937871668 uncurated sao937871668 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) Spiny Bracelet Of Nageotte sao9456487 uncurated 0005802 sao9456487 C0887838 Trans Golgi Network 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). Trans Golgi Network sao95019936 uncurated 0005814 sao95019936 C0007708 Centriole 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). http://ccdb.ucsd.edu/SAO/images/centriole_sw_512x512.jpg Centriole sao9515821206 uncurated sao9515821206 Sarah M. Maynard 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. Neuritic 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 sao952483289 uncurated 0005882 sao952483289 C0021770 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). Intermediate Filament sao952643730 uncurated sao952643730 Spine Head Spine Head sao9537723288 uncurated sao9537723288 Sarah M. Maynard Neuropil Thread Abnormal structures located in distal dendrites. Filamentous bundles made up of straight and paried helical filaments which contain ubiquitin and tau. Neuropil Thread sao9615155060 uncurated sao9615155060 amyloid plaques, senile druse, braindruse Sarah M. Maynard We are not sure if there is a distinction between Neuritic plaque and Senile plaque. 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. http://ccdb.ucsd.edu/SAO/images/senile_plaque_sw_512x512.jpg Senile Plaque sao967812059 uncurated sao967812059 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 sao976831666 sao976831666 Lumen Cargo Refers to cargo carried in the lumen of the vesicle; may be crystalized or otherwise bound, e.g., insulin. Lumen Cargo sao978443756 uncurated sao978443756 Endosomal Membrane Endosomal Membrane sao991156472 sao991156472 Cell Component Aggregate Object true Cell Component Aggregate Object dcmitype:Image snap:MaterialEntity snap:ObjectAggregate snap:ObjectBoundary snap:Role snap:Site foaf:Document 1.3 (May 2012) NIF-Subcellular: contains cell parts and subcellular structures from SAO-CORE and Gene Ontology Cellular Component (GO-CC) next ID: nlx_subcell_20090212 1.3 (May 2012) 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. 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)