]> 1.2 NIF-Subcellular: contains cell parts and subcellular structures from SAO-CORE next ID: nlx_subcell_20090212 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. v1.1 (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 * Not all sao prefixed IDs are out of date or replaced by nifext. v1.2 (July, 2009) - New terms have been added since the January release (ID used: nlx_subcell_20090101 - 20090703) true Cytoskeletal system This class classifies fine under 'Constitutional part of cell', while loaded with NIF-GrossAnatomy.owl module. Synthetic Enzyme This class classifies fine under 'Enzyme', while loaded with NIF-Molecule.owl module. Protein March 18, 2009 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#sao500241072 This class classifies fine under 'Macromolecule' while loaded with NIF-Molecule.owl module. 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) February 23, 2010 Foundational Model of Anatomy Meissners corpuscle Meisner's corpuscle Meisners corpuscle Meissner's 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. tactile corpuscle 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) February 23, 2010 Foundational Model of Anatomy Merkel cell-neurite complex Merkel disk receptor Merkel's disc Merkel's disk Constitutional part of cell 2006-09-07 Bill Bug UMLS cytoskeletal system post-synaptic density true Neuropil 2006-07-15 C0228081 May 15, 2009 Neuropil 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. This class has been retired. http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBO-UBO.owl#birnlex_3 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/OBO_annotation_properties.owl#MeSH_defSource http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao205380252 true Node of Ranvier 2006-07-15 2006-09-28 C0034667 Node of Ranvier Site located at the gaps in the myelin sheaths of myelinated axons. Axon diameter is generally decreased in the nodal region, compared to the internode. Ranvier's nodes allow saltatory conduction, that is, jumping of impulses from node to node, which is faster and more energetically favorable than continuous conduction (MSH). 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 http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Sample population 2006-09-07 2006-10-09 A defined subset of a population whose spatio-temporal interactions or aggregate behavior is representative of the whole population. Bill Bug Sample population Intrinsic neuron role 2007-08-26 An interneuron participating in aneuronal circuit where all the neurons are bounded within a defined and limited region of the nervous system.(BB). Intrinsic neuron role March 31, 2009 We are leaving off "interneuron" for now, as it has different connotations in vertebrates and invertebrates http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated intrinsic neuron local circuit neuron local circuit neuron role Functional role of cell 2007-08-25 August 20, 2009 Functional role of cell 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 Functional role of nerve cell 2007-08-25 2007-08-25 Functional role of nerve cell http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Microtubule 2006-07-15 2006-09-28 C0026046 Microtubule 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/Backend/OBO_annotation_properties.owl#UMLS http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1846835077 true Neurofilament 2006-07-15 2006-09-28 Neurofilament 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 true Cytoskeletal system 2006-07-15 February 18, 2010 Maryann Martone cytoskeleton http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1635329413 true Intermediate filament 2006-07-15 2006-09-28 C0021770 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). Intermediate filament 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/OBO_annotation_properties.owl#UMLS http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao952483289 true Post synaptic density 2006-07-15 2006-09-28 BF_C000103 Post synaptic density 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 true Microfilament 2006-07-15 2006-09-28 Microfilament 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 true Parallel fiber March 17, 2010 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. Thorny excrescence Large complex spine. Each excrescence is formed by a cluster of spine heads (Amaral, 1978) May 11, 2010 The Hippocampus book by Andersen et al. Principal neuron role 2007-08-26 A principal projection neuron in a neuronal circuit whose axon extends beyond the region where its soma is located to synapse on the dendrites of cells in other regions of the nervous system (BB). 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. March 31, 2009 Principal neuron Principal neuron role Projection neuron Projection neuron role http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Glial Inclusion Argyrophilic Glial Inclusion August 11, 2009 Glial Inclusion Jane Bugea Neuronal Cytoplasmic Inclusion August 11, 2009 Jane Bugea NCI Neuronal Cytoplasmic Inclusion Cell role August 20, 2009 Cajal body August 31, 2009 Coiled body February 17, 2010 GO_0015030 Jane Bugea http://genetics.cwru.edu/matera3.html 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)) October 5, 2009 Sarah M. Maynard Grumose foamy spheroid body February 12, 2010 Grumose foamy spheroid body is a spheroidal supracellular structure with a foamy appearance in haematoxylin and eosin stains that vary from 10 to 50 microns in diameter and contain amorphous debris-like material found in the brains in certain neurodegenerative conditions. PMID: 7477732 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. BBB Blood-brain barrier The BBB has also been defined physiologically F bouton February 23, 2010 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. S bouton February 23, 2010 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 C bouton February 23, 2010 Synaptic bouton found in spinal cord on the soma and proximal dendrites of motor neurons Glia limitans February 10, 2010 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. glial limiting membrane 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) Regional Part Of Granule Cell Axon March 17, 2010 Hippocampal mossy fiber April 28, 2010 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. Dentate gyrus mossy fiber March 18, 2010 Subcellular entity Entity derived from a cell or cells. The anatomical scale of these objects roughly corresponds to that which would be visible in high resolution light microscopy or conventional electron microscopy, e.g., nanometers to microns. Example: mitochondrion, dendrite, extracellular matrix. March 15, 2010 Maryann Marotone subcellular_structure CA3 pyramidal cell dendrite Dendrite of a hippocampal CA3 pyramidal cell May 11, 2010 Hippocampal mossy fiber expansion May 11, 2010 Synaptic expansion of hippocampal mossy fiber axon that makes contact with the thorny excrescences of hippocampal CA3 pyramidal cell dendrites dentate gyrus granule cell axonal bouton dentate gyrus mossy fiber expansion mossy fiber expansion Gemmule May 11, 2010 spine-like process found on some neurons, e.g., periglomerular cells of olfactory cortex Bunina Body Bunina Body Bunina bodies are small eosinphilic granular inclusions that are 1-3 microns in diameter in the anterior horn cells, appearing either singly or in a group. Sometimes they are arranded in small beaded chains. They stain bright red with hematoxylin and eosin (H&E) staining, deep blue with phospotungstic acid hematoxylin and blue with Luxol fast blue. They express cystatin C and consist of electron-dense amorphous material that contains tubules or vesicular structures. The amorphous material frequently includes a cytoplasmis island containing neurofilaments and other micro-organelles. January 9, 2009 PMID: 18026741 Sarah M. Maynard Pick Body January 9, 2009 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 Sarah M. Maynard Skein-like Inclusion 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. Hyaline Inclusion Hyaline Inclusion January 9, 2009 Pale eosinophilic inclusions with halos in H&E (hematoxylin and eosin) preparations. 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. January 9, 2009 Kato S. 2008 Amyotrophic lateral sclerosis models and human neuropathology: similarities and differences. Acta Neuropathol 115:97-114. page 101 Lewy Body-like Hyaline Inclusion Sarah M. Maynard Transferrin 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. Star-shaped Neurofibrillary Tangle February 12, 2009 Star-shaped Neurofibrillary Tangle Flame-shaped Neurofibrillary Tangle February 12, 2009 Flame-shaped Neurofibrillary Tangle 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 February 12, 2009 Shepherd, G. M. The Synaptic organization of the brain, 5th ed., New York: Oxford University Press, 2004. Astrocyte Sheath Astrocyte Sheath February 12, 2009 Cytochrome c A small heme protein found loosely associated with the inner membrane of the mitochondrion. Cytochrome c February 23, 2009 Proteasome 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. Synaptophysin February 24, 2009 Synaptophysin Synaptophysin (syp I) is a synaptic vesicle membrane protein Endoneurial Space February 24, 2009 The space occupied by the endoneurium. 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 February 27, 2009 Shepherd, G. M. The synaptic organization of the brain, 5th ed. New York: Oxford University Press, 2004 C-fiber C-fiber February 27, 2009 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. Calnexin 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. February 27, 2009 Triad May 15, 2009 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. Cerebellar glomerulus May 16, 2009 Olfactory glomerulus Glomerulus located in the olfactory bulb formed by the incoming axons of olfactory receptor cells synapsing onto the dendritic branches of one or more mitral cells. The olfactory glomerulus is roughly spherical and is partially or wholly encapsulated by glial processes. Maryann Martone May 16, 2009 Thalamic glomerulus May 16, 2009 Shepherd, G. M. The synaptic organization of the brain, 5th ed New York: Oxford University Press, 2005 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. Encapsulated nerve ending Maryann Martone May 17, 2009 Nerve ending found in skin surrounded by layers of connective tissue. Axon bundle Axon projection Group of myelinated or unmyelinated axons that group together. Maryann Martone May 17, 2009 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao3826089237 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. Ipsilateral associational-commissural projection Maryann Martone May 17, 2009 Shepherd, G. M. The synaptic organization of the brain, 5th ed New York: Oxford University Press, 2005 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. Maryann Martone May 17, 2009 Schaffer collaterals Group of axons arising from hippocampal CA3 pyramidal neurons projecting to area CA1. Maryann Martone May 17, 2009 Regional Part Of Pyramidal cell axon Maryann Martone May 19, 2009 Schaffer collateral Maryann Martone May 19, 2009 Part of axon of the CA3 pyramidal neuron that projects to hippocampal area CA1 . Motor endplate February 23, 2010 Maryann Martone May 19, 2009 Terminal ending of the axon of a motor neuron that forms a synapse onto a muscle cell. 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. Fmaid: 9672 Maryann Martone May 17, 2009 Dentate gyrus mossy fiber Granule cell axons June 18, 2009 Maryann Martone PMC2492885 PMID PMC2492885 The dentate gyrus: fundamental neuroanatomical organization (dentate gyrus for dummies) by David G. Amaral, Helen E. Scharfman, and Pierre Lavenex The granule cells give rise to distinctive unmyelinated axons referred to as mossy fibers by Ramón y Cajal. Early Endosome July 14, 2009 Small irregularly shaped intracellular vesicles to which endocytosed molecules are initially delivered (GO: 0005769). Late Endosome July 14, 2009 Late endosomes are vesicular structures that accumulate internalized components after their passage through early endosomes (GO: 0005700). 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 Glial Cytoplasmic Inclusion Glial Cytoplasmic Inclusion July 14, 2009 Filopodium 0030175 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 sao-1046371754 uncurated 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-1067215520 uncurated Schwann Cell Compact Myelin 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). sao-1123256993 uncurated Cellular Component 0005575 Cell part which has a definable shape, bounded predominantly by bonafide boundaries and is countable (FMA). 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). Branch Point Of Dendrite Branch Point Of Dendrite sao-1348591767 uncurated Mitochondrial Site Mitochondrial Site sao-1367457321 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). Pre-synaptic Ribbon http://ccdb.ucsd.edu/SAO/images/pre-syn_ribbon_sw_512x512.jpg sao-1488888179 Regional Part Of Mitochondrial Membrane Regional Part Of Mitochondrial Membrane sao-1686050947 uncurated Intercellular Gap Janction Channel Junctional complex consisting of two connexons that come together to form a communicating pore between two cells Regional Part Of Cell Component Regional Part Of Cell Component sao-1819020575 uncurated Cell Process Cell Process sao-1828894864 uncurated Glial Filament Glial Filament sao-1863852493 uncurated Node Of Ranvier Axon 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. http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 sao-188049490 uncurated Mitochondrial Lumen 0031980 Inner Mitochondrial Compartment (from Peters, Palay, and Webster) 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-1899375636 true uncurated Internode Internode Part of nodal complex located underneath the compact myelin in between nodes of Ranvier sao-206157942 Paranode Paranode Region of nodal complex adjacent to the nodal region sao-234066064 Neuron Protrusion Neuron Protrusion sao-250931889 uncurated Junction Complex Mitochondrial Space Mitochondrial Space Spaces defined by the inner and outer mitochondrial membranes sao-343550527 true Regional Part Of Neuron Process Regional Part Of Neuron Process sao-420949334 uncurated 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). Schwann Cell Myelin Sheath http://ccdb.ucsd.edu/SAO/images/myelin_sheath_sw_512x512.jpg sao-593830697 uncurated Node Related Site Node Related Site Site defined with respect to the Node of Ranvier, e.g., node, paranode, juxtaparanode sao-596411490 Regional Part Of SER Regional Part Of SER sao-699412220 uncurated Pyramidal Neuronal Cell Body Pyramidal Neuronal Cell Body sao-820130069 uncurated Cell Protrusion Cell Protrusion sao-82111036 uncurated Neuron Process Neurite Neuron Process sao-867568886 Mushroom Dendritic Spine Mushroom Dendritic Spine http://ccdb.ucsd.edu/SAO/images/mush_dend_spine_sw_512x512.jpg sao-876577163 uncurated Synaptic Site Synaptic Site sao-946766835 Excrescence Excrescence sao-961694769 uncurated Branched Dendritic Spine Branched Dendritic Spine http://ccdb.ucsd.edu/SAO/images/branched_dend_spine_sw_512x512.jpg sao-965204139 uncurated Dense Material Dense Material sao1004601938 uncurated Cytosol 0005829 C0010854 Cytosol The part of the cytoplasm that does not contain membranous or particulate subcellular components (UMLS). sao101633890 uncurated 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 sao1028571114 uncurated Endoplasmic Reticulum 0005783 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 sao1036339110 uncurated Membrane Cargo Membrane Cargo Refers to integral membrane proteins carried via the vesicle membrane. sao1037637579 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). C0032592 Polyribosome http://ccdb.ucsd.edu/SAO/images/polyribosome2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/polyribosome_sw_512x512.jpg sao1038025871 uncurated Trans Face 0005802 The concave side of the Golgi apparatus, from which secretory vesicles emerge (Gene Ontology). Trans Face sao1039242387 uncurated Neuronal Cell Body C0599444 Cell body which consists of the plasma membrane and the cytoplasm surrounding the nucleus of the neuron (FMA). Neuronal Cell Body sao1044911821 soma uncurated Mitochondrial Membrane Mitochondrial Membrane sao1045389829 uncurated Tyrosine Kinase Receptor A class of cellular receptors that have an intrinsic protein-tyrosine kinase activity (MSH). C0206364 Tyrosine Kinase Receptor sao1048004962 uncurated Interchromatin Granule 0035061 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). C0230547 Interchromatin Granule sao1049471211 uncurated Regional Part Of Neuronal Cell Body Regional Part Of Neuronal Cell Body sao1049717962 uncurated Synaptic Vesicle 0008021 C0039065 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). Synaptic Vesicle 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 sao1071221672 uncurated Post-synaptic Site Before replacing the is_Location_Of property with RO's contained_in and the site_Contained_In property with RO's contained_in, we had the two restrictions: 1) is_Location_Of some Post-synaptic Density and 2) site_Contained_In some Post-synatpic Density. Thus, now we just have one restriction: contained_in some Post-synaptic Density. Post-synaptic Site sao1074198261 Trunk Trunk sao1078172392 uncurated Basilar Dendrite Basal Dendrite Basilar Dendrite sao1079900774 uncurated Glycogen Granule 0042587 C0017911 Cytoplasmic bead-like structures of animal cells, visible by electron microscope. Each granule is a functional unit with the biosynthesis and catabolism of glycogen being catalyzed by enzymes bound to the granule surface (Gene Ontology). Appears as small, electron dense particles 20-40 nm in diameter. Glycogen is difficult to fix in vivo so amounts may be underestimated (Peters, Palay and Webster). Glycogen Granule http://ccdb.ucsd.edu/SAO/images/glycogen_granule_sw_512x512.jpg sao1081228141 uncurated Pinceau Fiber Dense plexus formed by the descending collaterals of cerebellar basket cells tha wrap around the Purkinje cell axonal initial segment. Pinceau Fiber sao109906988 uncurated Dendritic Microtubule Dendritic Microtubule sao110773650 uncurated 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 ribbon sao1111202255 Dark Material 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. Sarah M. Maynard sao1122901839 uncurated Neuromuscular Junction 0031594 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). sao1124888485 uncurated Regional Part Of Nucleolus Regional Part Of Nucleolus sao113580911 uncurated Free Ribosome Free Ribosome sao1139385046 uncurated Primary Lysosome 0005766 A lysosome before it has fused with a vesicle or vacuole (Gene Ontology). C0230814 Primary Lysosome sao1140587416 uncurated Spine Do spines only have a post synaptic density? (Maryann Martone) May 28, 2009 Spine 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. sao1145756102 uncurated Intercalated Disk Contact site between adjacent cells in cardiac muscle fibers. When observing tissue through a microscope, this is an identifying feature of cardiac muscle.It holds the myofibrils together and permits easy transfer of excitation (depolarization). Intercalated Disk sao1152983960 uncurated Vesicle Membrane 0012506 C1167317 The lipid bilayer surrounding any membrane-bounded vesicle in the cell (Gene Ontology). Vesicle Membrane sao1153182838 uncurated Glutamate Receptor C0061465 Glutamate Receptor May 1, 2009 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao587592318 sao1164727693 uncurated Vesicle Coat 0030120 C1166749 Refers to any specialized coating present on a vesicle membrane, e.g., clathrin. Vesicle Coat sao1177708494 Gap Junction 0005921 Any specialized areas of the plasma membranes of adjacent cells where the membranes are 2-4 nm apart and penetrated by a connexon (Gene Ontology). C0206117 Gap Junction http://ccdb.ucsd.edu/SAO/images/gap_junction_sw_512x512.jpg sao118541872 uncurated Mitochondrial Chromosome 0000262 A chromosome found in the mitochondrion of a eukaryotic cell (Gene Ontology). C1166687 Mitochondrial Chromosome sao1186327184 uncurated Oligodendrocyte Compact Myelin 0043218 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). sao1186642361 uncurated Basal Pole Of Neuron Basal Pole Of Neuron Portion of a cell soma closest to the point where the basilar dendrite emerges. sao1186862860 uncurated Vellous Process Refers to the fine, veil-like terminal processes of protoplasmic astrocytes. Vellous Process graph position temporary is this the same as what is now termed the peripheral astrocyte process? sao1189060993 uncurated Mitochondrial Intermembrane Space 0005758 C1166886 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). graph position temporary sao118944228 true Juxta Paranode Axon Juxta Paranode Axon May 28, 2009 Region of axon immediately adjacent to the paranode. http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 sao1191319089 uncurated Post-synaptic Density 0014069 BF_C000103 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 sao1196688972 Basal Body 0005932 A short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium or flagellum that is similar in structure to a centriole. The basal body serves as a nucleation site for axoneme growth (Gene Ontology). Basal Body C0230744 http://ccdb.ucsd.edu/SAO/images/basal_bodies_sw_512x512.jpg sao11978067 uncurated Cellular Inclusion A nuclear or cytoplasmic aggregate of stainable substances, usually proteins. Cellular Inclusion Inclusion Body sao120573470 uncurated Lumenal Surface Lumenal Surface sao120818728 uncurated 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 sao1210952635 uncurated Dendrite 0030425 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). C0011305 Dendrite 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 sao1211023249 uncurated Pars Granulosa C0230580 Nucleolar compartment consisting of large numbers of small, extremely dense granules 150-300 A in diameter, suspended in a matting of fine filaments (Palay and Chan-Palay, 1974). Pars Granulosa sao1217793903 uncurated Thin Dendritic Spine Thin Dendritic Spine http://ccdb.ucsd.edu/SAO/images/thin_dend_spine_sw_512x512.jpg sao1232858786 uncurated Large Vesicle Large Vesicle Vesicles of same size and content of coated vesicles; posited by Clooney et al. (2002) to represent coated vesicles after uncoating. sao1241866791 uncurated Clathrin Coated Endocytic Vesicle 0045334 A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology). Clathrin Coated Endocytic Vesicle http://ccdb.ucsd.edu/SAO/images/clath_coated_endocy_vesicle_sw_512x512.jpg sao1243595998 uncurated Endoplasmic Reticulum Exit Site 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). sao124393998 uncurated Glial Subcompartment Glial Subcompartment sao1253297813 uncurated Oligodendrocyte Myelin Sheath 0043209 An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system (Gene Ontology). C0026973 Oligodendrocyte Myelin Sheath sao1279474730 uncurated 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). Sub-surface Cisternae http://ccdb.ucsd.edu/SAO/images/cisternae_sw_512x512.jpg sao128470897 uncurated Cellular Space Anatomical space occurring within a cell, usually formed by intracellular membranes. Cellular Space sao1289190043 uncurated Mitochondrial Membrane Outer 0005741 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 sao1289741256 uncurated Membrane Bound Ribosome A ribosome that is attached to a intracellular membrane. Does not itself have a membrane surrounding it. Membrane Bound Ribosome sao1291545653 uncurated Cell Cell Contact Zone 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 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 sao1299635018 uncurated Electrotonic Synapse 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 sao1311109124 uncurated Neurofilament 0005883 A type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter (Gene Ontology). C0027834 Neurofilament http://ccdb.ucsd.edu/SAO/images/neurofilament_sw_512x512.jpg sao1316272517 uncurated Membrane Surface Membrane Surface sao1329750433 uncurated Tuft April 28, 2010 The terminal specialization found in some types of dendrites consisting of numerous small terminal branches, giving the dendrite a tufted appearance. Tuft dendritic tuft sao1340260079 uncurated Amyloid Fibril A fibril composed of amyloid protein. Amyloid Fibril Sarah M. Maynard http://ccdb.ucsd.edu/SAO/images/amyloid_filament_sw_512x512.jpg sao1342297498 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 Paranodal loop sao1354781919 uncurated Endocytic Vesicle 0030139 A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology). C0887883 Endocytic Vesicle sao1362520468 uncurated Mitochondrial Membrane Inner 0005743 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 sao1371347282 uncurated Ensheathing Process 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 sao1376748732 uncurated Lamellar Body 0042599 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). sao1379604862 uncurated Vesicular Component Vesicular Component sao138219748 uncurated Inter-Golgi Transport Vesicle 0030143 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 sao1382918459 uncurated 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 sao138430598 uncurated Intercellular Junction Intercellular Junction sao1395777368 Basal Lamina 0005605 A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix (Gene Ontology). Basal Lamina C0242195 sao1397492660 uncurated Zonula Adhaerens Adherent, symmetrical junction characterized by widened extracellular space and filamentous material (Peters, Palay and Webster, 1991). Zonula Adhaerens fascia adhaerens http://ccdb.ucsd.edu/SAO/images/zonula_adherens_sw_512x512.jpg sao1400623473 uncurated Extracellular Space 0005616 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 sao1425028079 uncurated Ribosome 0005840 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). C0035553 Ribosome http://ccdb.ucsd.edu/SAO/images/ribosomes_sw_512x512.jpg sao1429207766 uncurated Pial Endfoot Pial Endfoot sao1447478620 uncurated Vesicle Subcomponent Vesicle Subcomponent sao1455064842 Nuclear Lamina 0005652 C1136039 Meshwork of extremely fine filaments composed of polypeptides called lamins that run parallel with the inner surface of the nuclear envelope (Peters, Palay and Webster, 1991). Nuclear Lamina 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). sao1455996588 uncurated Non Membrane Bound Organelle 0043228 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). sao1456184038 uncurated Active Zone Cytomatrix Active Zone Cytomatrix Filamentous matrix immediately internal to the plasma membrane docking zone (Zhai and Bellen, 2004). sao1470121605 uncurated Axon Collateral Axon Collateral Smaller branches of an axon that emanate from the main axon cylinder. sao1470140754 uncurated Vesicle Cargo Need to determine whether this should be a part of a vesicle; I think it shouldn't be Refers to the contents contained in the vesicle. Vesicle Cargo sao1490223249 Nuclear Subcomponent Nuclear Subcomponent sao1499850686 uncurated Mixed Synapse Existence of both chemical and electrotonic synapses at the same interface (Peters, Palay and Webster, 1991). Mixed Synapse Synaptic contact characterized by both electrical and chemical synaptic junctions. sao1506103497 uncurated Post-synaptic Component Post-synaptic Component sao1507566336 Cytoplasmic Surface Cytoplasmic Surface sao1514682949 uncurated Junctional Site Junctional Site sao1524397168 Amorphous Vesicle 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. sao1531915298 uncurated Sessile Dendritic Spine Sessile Dendritic Spine sao1536532595 uncurated Organelle 0043226 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). sao1539965131 uncurated Regional Part Of Golgi Regional Part Of Golgi sao1546288504 uncurated Endosomal Lumen 0031904 Endosomal Lumen The volume enclosed by the membranes of an endosome (Gene Ontology). endosome lumen sao1547508851 uncurated Secondary Lysosome 0005767 C0230815 Secondary Lysosome Vacuole formed by the fusion of a lysosome with an organelle (autosome) or with a primary phagosome (Gene Ontology). sao1549842807 uncurated 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 sao1570660411 uncurated Barr Body Barr Body sao1571698684 uncurated Peripheral Astrocyte Process It is not clear whether peripheral astrocyte process only refers to the processes surrounding synapses or also refers to the endfeet Peripheral Astrocyte Process Thin terminal processes of astrocytes found in sheathing, axon terminals, blood vessels, and pial surface of the brain. 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. This comes from derouiche et al. J. Physol. Paris 2002 96:177 PubMedID:12445894 graph position temporary sao1573004591 Cell Interior Cell Interior sao1579007712 uncurated Regional Part Of Basket cell axon Regional Part Of Basket Cell Axon Terminal pre-synaptic ending of an axon or axon collateral. sao1586851177 uncurated Actin Filament 0005884 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). Actin Filament C0025979 http://ccdb.ucsd.edu/SAO/images/act_filament_sw_512x512.jpg sao1588493326 uncurated Regional Part Of Spiny Dendrite Regional Part Of Spiny Dendrite sao1590928667 uncurated Dendritic Growth Cone Dendritic Growth Cone http://ccdb.ucsd.edu/SAO/images/dend_growth_cone_sw_512x512.jpg sao1594955670 uncurated SER Membrane 0030868 SER Membrane The lipid bilayer surrounding the smooth endoplasmic reticulum (Gene Ontology). sao1596955044 uncurated Main Axon Main Axon Used to refer to the main axonal trunk, as opposed to the collaterals. sao1596975044 uncurated Nuclear Inner Membrane 0005637 Nuclear Inner Membrane The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope (Gene Ontology). sao1612527463 uncurated Chromatin 0000785 C0008546 Chromatin The ordered and organized complex of DNA and protein that forms the chromosome (Gene Ontology). sao1615953555 uncurated Nuclear Outer Membrane 0005640 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). sao1617136075 uncurated Astrocyte Process 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 sao1630537580 uncurated Hypolemmal Cisternae 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). sao1634374950 uncurated Cytoskeletal Element Cytoskeletal Element sao1635329413 uncurated Recurrent Collateral Axon collateral that ramifies in the area of the soma of the cell of origin. Recurrent Collateral sao1642494436 uncurated Spine Neck Spine Neck neck pedicle sao1642908940 uncurated Plasma Membrane 0005886 C0007603 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). cell membrane 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 sao1663586795 uncurated Regional Part Of Spine Apparatus Regional Part Of Spine Apparatus sao1682692988 uncurated Endosomal Subcomponent Endosomal Subcomponent sao1683772610 uncurated Calyx Of Held Calyx Of Held sao1684283879 uncurated Nuclear Membrane 0031965 C0028584 Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space (Gene Ontology). Nuclear Membrane sao1687101204 uncurated Nucleus 0005634 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). C0007610 Nucleus http://ccdb.ucsd.edu/SAO/images/nucleus_sw_512x512.jpg sao1702920020 uncurated Endosome 0005768 A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation (GO). C0034850 Endosome sao1720343330 uncurated Dendritic Tree BF_C000102 Dendritic Tree The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches. sao172297168 uncurated Pre-synaptic Grid A hexagonal array of electron dense particles attched to the cyotplasmic face of the presynaptic membrane, revealed by staining with ethanolic phosphotungstic acid (Peters, Palay and Webster, 1991). Pre-synaptic Grid sao1730664005 uncurated Orthogonal Array Orthogonal Array Square arrays of closely spaced intramembrane particles, 4-6 nm in size seen in astrocyte processes, now known to contain aquaporins. sao1747012216 square array uncurated 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 sao1749953771 uncurated Axon 0030424 Axon C0004461 Cell appendage of a neuron that consists of an axon hillock, an axon proper, axon collaterals and an axon terminal (FMA) Fiber May 5, 2010 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 sao1770195789 uncurated Synaptic Component Synaptic Component sao1784069613 Regional Part Of Myelinated Axon May 28, 2009 Regional Part Of Myelinated Axon This class has been retired. http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao183270081 sao1791490892 true uncurated Dendritic Spine 0043197 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 sao1799103720 uncurated Mitochondrial Matrix 0005759 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). sao1804523077 uncurated Cytoplasmic Vesicle 0031410 A vesicle formed of membrane or protein, found in the cytoplasm of a cell (Gene Ontology). Cytoplasmic Vesicle sao180601769 uncurated Glial Limiting Endfoot 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. sao181458425 uncurated RER Lumen 0048237 RER Lumen The volume enclosed by the membranes of the rough endoplasmic reticulum (Gene Ontology). rough endoplasmic reticulum lumen sao1819509473 uncurated Nucleolus 0005730 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). C0007609 Nucleolus http://ccdb.ucsd.edu/SAO/images/nucleoli_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/nucleolus_sw_512x512.jpg sao1820400233 uncurated Axonal Spine Axonal Spine Refers to spine that originates from the axon, usually the initial segment (Peters, Palay and Webster, 1991). sao18239917 uncurated Crista Junction Crista Junction Tubular structures of relatively uniform size that connect mitochondrial cristae to the inner mitchondrial membrane (Perkins and Ellisman, 2003). sao1825845900 uncurated Subregional Part Of Neuron Process Subcompartment of a compartment. Subregional Part Of Neuron Process sao183270081 uncurated Pars Fibrosa C0230581 Pars Fibrosa Portion of the nucleolus composed of densely matted filaments with scattered dark granules (Palay and Chan-Palay, 1974). sao1841764412 uncurated SER Subcomponent SER Subcomponent sao1842028314 uncurated Inner Bounding Mitochondrial Membrane Inner Bounding Mitochondrial Membrane Part of mitochondrial inner membrane that runs parallel to the outer mitochondrial membrane sao18461326 uncurated Microtubule 0005874 Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle (Gene Ontology). C0026046 Microtubule http://ccdb.ucsd.edu/SAO/images/microtubules_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/microtubules_sw_512x512.jpg sao1846835077 uncurated Bridge Contact Site 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). sao1858501007 uncurated Mitochondrion 0005739 A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration (Gene Ontology). C0026237 Mitochondrion http://ccdb.ucsd.edu/SAO/images/mito_ccdb_512x512.jpg http://ccdb.ucsd.edu/SAO/images/mito_sw_512x512.jpg mitochondria sao1860313010 uncurated Microtubule Fascicle Microtubule Fascicle Refers to a bundle of closely apposed microtubules running parallel to each other. sao1872343973 uncurated Synaptic Bouton Synaptic Bouton Terminal pre-synaptic ending of an axon or axon collateral. http://ccdb.ucsd.edu/SAO/images/syn_bouton_sw_512x512.jpg sao187426937 uncurated Apical Pole Of Neuron Apical Pole Of Neuron Portion of a cell soma closest to the point where the apical dendrite emerges. sao1877927224 uncurated Rough Endoplasmic Reticulum 0005791 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). sao1881364067 uncurated Ribbon Synapse 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) sao1884931180 uncurated Schwann Cell Microvillus Schwann Cell Microvillus Small finger-like extension of the Schwann cell that contact the nodal membrane but are not closely apposed to each other like the paranodal lops (Sosinsky et al., 2005) sao1890444066 uncurated Regional Part Of Lewy Body Regional Part Of Lewy Body Sarah M. Maynard sao1894609662 uncurated Intranuclear Membrane Space Intranuclear Membrane Space The space between the inner and outer nuclear membranes sao1908934319 uncurated Pre-synaptic Active Zone Component Pre-synaptic Active Zone Component sao1911631652 uncurated Intercellular Junction Site 0005911 Intercellular Junction Site The Cell_Cell_Contact_Zone and the Intercellular_Junction are not the same. The junction only refers to the bridging complex and not the larger region where the junction resides. The intercellular_Junction is part of a larger cell-cell contact zone. The cell-cell contact zone may also contain additional junctions and cellular machinery related to the function of the junction. The site of cell-cell contact containing a morphologically identified junctional complex joining the two cells. core:definition incomplete sao1922892319 Pinocytic Vesicle Pinocytic Vesicle sao1925368674 uncurated 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). MAC Mitochondrial Adhaerens Complex mitochondrial-associated adherens complex sao1933817066 uncurated Subplasmalemmal Coating 2007-02-23 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 core:definition incomplete sao1938587839 Zonula Occludens 0005923 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 sao1939999134 tight junction uncurated 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 sao1943947957 uncurated Schaffer Collateral Axon collateral of CA3 pyramidal neurons that project to CA1 and synapse in the zona radiatum. Schaffer Collateral sao1950673097 uncurated Regional Part Of Schwann Cell Regional Part Of Schwann Cell sao195217619 uncurated Golgi Lumen Golgi Lumen sao1956231674 uncurated Macular Adhaerentia Look into the relationship of Macular and zonula adhaerentia and determine whether they are all subclasses of adhaerent junction Macular Adhaerentia sao1956738165 uncurated Coated Pit 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). sao1969557946 uncurated Cell Regional Part Aggregate Object Cell Regional Part Aggregate Object sao1970895398 Regional Part Of Epithelial Cell C0932419 Regional Part Of Epithelial Cell sao1974433376 uncurated 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) C0025979 Microfilament sao2006047981 uncurated Axon Terminal Axon Terminal The distal terminations of axons which are specialized for the release of neurotransmitters. Also included are varicosities along the course of axons which have similar specializations and also release transmitters. Presynaptic terminals in both the central and peripheral nervous systems are included (MSH). http://ccdb.ucsd.edu/SAO/images/axon_term_sw_512x512.jpg sao2007137787 uncurated Age Associated Age Associated Need to look this one up and see what this really meant. sao2017162875 uncurated Regional Part Of RER 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). sao2019617624 uncurated 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 sao2031592629 uncurated Dendritic Shaft 0043198 BF_C000106 Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines (Gene Ontology). Dendritic Shaft http://ccdb.ucsd.edu/SAO/images/dend_shaft_ccdb_512x512.jpg sao2034472720 uncurated Active Zone Plasma Membrane Active Zone Plasma Membrane Plasma membrane juxtaposed to the PSD where synaptic vesicle fusion occurs (Zhai and Bellen, 2004). sao2038461087 uncurated Axonal Growth Cone Axonal Growth Cone sao203987954 uncurated Multivesicular Body 0005771 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). C0230825 Multivesicular Body http://ccdb.ucsd.edu/SAO/images/multives_bodies_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/mutlivesicular_body_sw_512x512.jpg sao2045955158 uncurated Somatic Spine Somatic Spine Spine emanating from the cell soma. http://ccdb.ucsd.edu/SAO/images/somatic_spine_sw_512x512.jpg sao2048514053 uncurated Perivascular Endfoot Perivascular Endfoot We are unclear why this is causing an inconsistency error. sao2048701763 uncurated 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). C0228081 Neuropil http://ccdb.ucsd.edu/SAO/images/neuropil_sw_512x512.jpg sao205380252 uncurated Vascular Endfoot Vascular Endfoot http://ccdb.ucsd.edu/SAO/images/vasc_endfoot_sw_512x512.jpg sao2064469343 uncurated Pre-synaptic Site Pre-synaptic Site sao2108323256 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 sao2114874506 uncurated Mesaxon 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). sao2127666702 uncurated Spine Mat 2007-02-09 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). Maryann Martone Spine Mat sao2128156969 Extracellular Surface Extracellular Surface sao2135015805 uncurated Nuclear Pore 0005643 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). C0028587 Nuclear Pore http://ccdb.ucsd.edu/SAO/images/nucl_pore_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/nucl_pore_sw_512x512.jpg sao220861693 uncurated Vesicle 0031982 Any small, fluid-filled, spherical organelle enclosed by membrane or protein (Gene Ontology). C0042219 Vesicle sao221389602 uncurated Population 2006-09-07 A collection of independent organismal entities engaged in some form of spatio-temporal interaction or aggregate behavior Bill Bug Population sao2254405550 uncurated 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 Sarah M. Maynard sao2409833926 uncurated Synaptic Cleft 0043083 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 sao243541954 uncurated Neurotubule Neurotubule Refers to a microtubule found in a nerve cell. The term "neurotubule" may now be obselete; however, it was used in earlier findings. sao248349196 uncurated Axolemma 0030673 Axolemma The plasma membrane of an axon; it is a specialized trilaminar random mosaic of protein molecules floating within a fluid matrix of highly mobile phospholipid molecules, 7-8 nm in thickness (Gene Ontology). sao250772229 uncurated 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. Schmidtt-Lanterman Cleft http://ccdb.ucsd.edu/SAO/images/Schmidtt-Lanterman_cleft_sw_512x512.jpg sao254777664 uncurated Initial Segment 0043194 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 sao256000789 uncurated Puncta Adhaerentia A small version of the zonula adharens type junction, characterized by a symmetrical adherent point between two cells. Puncta Adhaerentia http://ccdb.ucsd.edu/SAO/images/puncta_adherens_sw_512x512.jpg sao257629430 uncurated Apical Dendrite Apical Dendrite BF_C000112 sao273773228 uncurated Regional Part Of Axon Regional Part Of Axon sao280355188 uncurated Terminal Specialization Terminal Specialization sao28175134 uncurated Chemical Synapse Chemical Synapse sao289211478 uncurated Dendriole Dendriole sao295057932 uncurated RER Membrane RER Membrane sao3089754107 Stubby Dendritic Spine Stubby Dendritic Spine http://ccdb.ucsd.edu/SAO/images/stubby_dend_spine_sw_512x512.jpg sao317384566 uncurated Cristae 0030061 Any of the inward folds of the mitochondrial inner membrane. (Gene Ontology) C0230844 Cristae http://ccdb.ucsd.edu/SAO/images/cristae_ccdb_512x512.jpg sao333328131 uncurated Regional Part Of Cell 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 sao340271629 uncurated Aggregate Object Aggregate Object Sarah Maynard sao3826089237 uncurated Pre-synaptic Component Pre-synaptic Component sao386529203 Endfoot Endfoot Terminal process of astrocyte abutting non-neuronal surfaces in the brain. graph position temporary sao388182739 uncurated Somatic Portion Portion of the tanycyte that lies within the ependyma and contains the nucleus (Peters, Palay and Webster, 1991). Somatic Portion sao401910342 uncurated Docked Vesicle Docked Vesicle Synaptic vesicle docked at the pre-synaptic active zone. sao403156667 uncurated Cortical Lewy Body Cortical Lewy Body Lesion that is less well defined than a Classical Lewy Body and lacks a halo. Sarah M. Maynard has Regional Part some Regional_Part_of_Lewy_Body restriction violated because Cortical Lewy Body lacks halo. sao4040591221 uncurated Peri Cellular Basket 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. sao413722576 uncurated Membrane Bound Organelle 0043227 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). sao414196390 uncurated Regional Part Of Dendrite Regional Part Of Dendrite sao420754792 uncurated Septate Junction 0005918 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 graph position temporary sao427941916 Connexon 0005922 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. C0230609 Connexon Wikipedia hemichannel, connexon complex sao445019788 uncurated Extended Chromatin 0000791 A dispersed and relatively uncompacted form of chromatin (Gene Ontology). Extended Chromatin euchromatin sao445485807 uncurated Contact Site Contact Site Sites of close apposition of the inner and outer mitochondrial membrane (Perkins and Frey, 2000). sao447856407 uncurated Golgi Apparatus 0005794 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) C0018042 Golgi Apparatus golgi cisternae http://ccdb.ucsd.edu/SAO/images/golgi_app_sw_512x512.jpg sao451912436 uncurated Membrane Receptor Membrane Receptor umls_ID: C0230664 Classical Lewy Body 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. Sarah M. Maynard sao4749542545 uncurated Granular Vesicle 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. sao478230652 uncurated Amyloid Aggregate Amyloid Aggregate Insoluble fibrous protein aggregation sharing specific structural traits. Sarah M. Maynard sao4785563283 uncurated Calyx Calyx sao488120195 uncurated Lewy Body 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. Sarah M. Maynard sao4933778419 there are two morphological types: classical (brain stem) and cortical Lewy bodies uncurated Active Zone Dense Projection Active Zone Dense Projection Electron dense projection extending from the cytomatrix into the cytoplasm on which synaptic vesicles are tethered (Zhai and Bellen, 2004). sao494258938 uncurated Peroxisome 0005777 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). C0752063 Peroxisome Resembles lysosomes in appearance (Peters, Palay and Webster, 1991). According to the latter, peroxisome is synonymous with microbodies. sao499555322 uncurated Nuclear Body 0016604 C0230595 Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins (Gene Ontology). Nuclear Body sao505137457 uncurated Fibril A minute fibril or filament. Fibril Sarah M. Maynard This is a placeholder. sao5051906853 uncurated Laminated Body Laminated Body sao506721981 uncurated Supra Cellular Structure A morphological or functional domain formed by parts of two or more cells, e.g., neuropil, dendritic bundles. Supra Cellular Structure Supracellular Structure sao508165343 uncurated Intracristal Space Intracristal Space The space bounded by the cristae membrane sao508958414 true uncurated Endocytic Zone 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). sao517367952 Spine Related Site Spine Related Site sao553711217 Spinule Spinule http://ccdb.ucsd.edu/SAO/images/spinule_sw_512x512.jpg sao553737851 uncurated Golgi Lamellae Golgi Lamellae sao561419532 uncurated Node Of Ranvier C0034667 May 16, 2009 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). This class has been retired. http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#birnlex_1152_2 sao571652273 true uncurated Corona Corona Halo Sarah M. Maynard The periphery of the Lewy Body. In Parkinson's Disease, it contains sperical accumulations of filaments arrange in a loose, radiating array. sao5764355747 uncurated Vesicle Other Category for vesicles observed in electron micrographs with unknown function. Vesicle Other sao577473346 uncurated Condensed Chromatin 0000792 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 heterochromatin sao581845896 uncurated Lysosome 0005764 Any of a group of related cytoplasmic, membrane bound organelles that are found in most animal cells and that contain a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions (Gene Ontology). C0024369 Lysosome sao585356902 uncurated Neurotransmitter receptor role C0034828 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 sao587592318 uncurated Glomerulus Glomerulus I'm not sure whether this should be a type of neuropil or a type of synaptic complex. (Maryann Martone) June 22, 2009 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. sao587858733 uncurated 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 sao601362597 uncurated Golgi Subcomponent Golgi Subcomponent sao624292949 uncurated Axon Hillock 0043203 Axon Hillock C0228079 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). sao627227260 uncurated Cellular Subcomponent Cellular Subcomponent sao628508602 uncurated Cis Face Cis Face sao632188024 uncurated Cellular Membrane Cellular Membrane sao6433132645 Core Core Sarah M. Maynard The center portion of the Lewy Body. In Parkinson's Disease, it contains a matted meshwork of filaments. sao6587439252 uncurated Paired Helical Filament PHF Paired Helical Filament Sarah M. Maynard Two threads of tau protein that are wound around each other. sao6603990120 Nucleoplasm 0005654 C0682537 Nucleoplasm That part of the nuclear content other than the chromosomes or the nucleolus (Gene Ontology). sao661522542 uncurated Mitochondrial Subcomponent Mitochondrial Subcomponent sao666410040 uncurated Microvilli Microvilli http://ccdb.ucsd.edu/SAO/images/microvilli_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/microvilli_sw_512x512.jpg sao671419673 uncurated Regional Part Of Astrocyte Regional Part Of Astrocyte sao685712019 uncurated Coated Tip Coated Tip Coated tips of tubular endosomes that appear to be vesicles in the process of budding off (Clooney et al., 2002). sao694815499 uncurated 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 Need to determine what is the proper relationships between an electrotonic synapse and a gap junction sao700839054 Protein Aggregate An insoluble mass of misfolded proteins. Protein Aggregate Sarah M. Maynard sao7016027781 uncurated Axon Microtubule Fascicle Axon Microtubule Fascicle Refers to the bundled configuration of microtubules in the axon hillock and initial segment. sao707332678 uncurated Smooth Endoplasmic Reticulum 0005790 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 sao710427438 uncurated 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. C0230810 Spine Apparatus http://ccdb.ucsd.edu/SAO/images/spine_app_2_sw_512x512.jpg http://ccdb.ucsd.edu/SAO/images/spine_app_3_sw_512x512.jpg sao725931194 uncurated Dense Body An electron dense body, some of which contain granules (Peters, Palay and Webster (1991) Dense Body Not clear if this should be described as an organelle or an inclusion. graph position temporary sao730872736 Pinceau 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. sao732341560 uncurated Alpha-Synuclein Fibril 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. Sarah M. Maynard sao7474011676 uncurated Collagen Fibril Collagen Fibril Delicate fibrils of collagen in connective tissue. It is composed of molecules of tropocollagen aggregated in linear array. Sarah M. Maynard sao7547390221 uncurated Filament Filament 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 sao7561423738 uncurated Juxtaparanode Juxtaparanode Region of nodal complex adjacent to the paranode sao758620702 Dense Core Vesicle 40-60 nm vesicle containing an electron dense granule, 15-20 nm in diameter (Peters, Palay and Webster, 1991). C0887944 Dense Core Vesicle http://ccdb.ucsd.edu/SAO/images/dense_core_vesicle_sw_512x412.jpg sao772007592 uncurated Cilium 0005929 C0008778 Cilia arising from neurons have been described in many different regions of the nervous system. Neuronal cilia have a "9+0" pattern, that is, they are missing the central pair of microtubules that characterizes most cilia (Peters, Palay and Webster, 1991). Cilium http://ccdb.ucsd.edu/SAO/images/cilium_sw_512x512.jpg sao787716553 uncurated Pre-synaptic Active Zone 0048786 A specialized presynaptic plasma membrane region where synaptic vesicles dock and fuse (Gene Ontology). Pre-synaptic Active Zone http://ccdb.ucsd.edu/SAO/images/active_zone_sw_512x512.jpg sao792027222 uncurated Nissl Body Nissl Body Stacks of rough endoplasmic reticulum that stain intensely with basophilic dyes. sao793088923 uncurated Vesicle Lumen 0031983 The volume enclosed by the membrane or protein that forms a vesicle (Gene Ontology). Vesicle Lumen sao797538226 uncurated Golgi-associated Vesicle 0005798 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). C0230767 Golgi-associated Vesicle sao819927218 uncurated Internode Axon Internode Axon May 28, 2009 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 sao830092290 uncurated Intracellular Membrane Intracellular Membrane sao830981606 uncurated Regional Part Of Oligodendrocyte Regional Part Of Oligodendrocyte sao831502550 uncurated 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 Autophagolysosome, degrading autophagic vacuole (AVd) Sarah M. Maynard sao8444068431 uncurated Regional Part Of Neuron Regional Part Of Neuron neuron compartment sao864921383 uncurated Regional Part Of Spine Regional Part Of Spine sao866168499 uncurated 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 Sarah M. Maynard autophagic vacuole, initial autophagic vacuole (AVi) sao8663416959 uncurated Nodal Complex Nodal Complex http://ccdb.ucsd.edu/SAO/images/node_ccdb_512x512.jpg sao873654461 Regional Part Of Tanycyte Regional Part Of Tanycyte sao877341397 uncurated Clathrin Coat 0030118 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). C1166728 Clathrin Coat sao879919129 uncurated Dendritic Branch Dendritic Branch Refers to dendrites arising from another dendrite. sao884265541 uncurated Transport Vesicle 0030133 Any of the vesicles of the constitutive secretory pathway, which carry cargo from the ER to the Golgi, between Golgi cisternae, and to destinations within or outside the cell (Gene Ontolgoy). C0887882 Transport Vesicle sao885490876 secretory vesicle uncurated Regional Part Of Glial Cell Regional Part Of Glial Cell sao895885284 uncurated 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 sao901230115 Extracellular Structure Extracellular Structure Sarah M. Maynard Structure that exists outside the cell. sao9117790637 uncurated Plaque A formation or growth of cells. Plaque Sarah M. Maynard sao9137852997 uncurated Synapse 0045202 Synapse The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell; the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane (Gene Ontology). sao914572699 uncurated 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 sao924713546 uncurated SER Lumen 0048238 SER Lumen The volume enclosed by the membranes of the smooth endoplasmic reticulum (Gene Ontology). sao927884761 smooth endoplasmic reticulum lumen uncurated Paranode Axon May 28, 2009 Paranode Axon http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao1791490892 sao936144858 uncurated 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 sao937871668 uncurated Trans Golgi Network 0005802 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). C0887838 Trans Golgi Network sao9456487 uncurated Centriole 0005814 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). C0007708 Centriole http://ccdb.ucsd.edu/SAO/images/centriole_sw_512x512.jpg sao95019936 uncurated 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 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. sao9515821206 uncurated Intermediate Filament 0005882 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). C0021770 Intermediate Filament sao952483289 uncurated Spine Head Spine Head sao952643730 uncurated 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 Sarah M. Maynard sao9537723288 uncurated 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. Sarah M. Maynard Senile Plaque We are not sure if there is a distinction between Neuritic plaque and Senile plaque. amyloid plaques, senile druse, braindruse http://ccdb.ucsd.edu/SAO/images/senile_plaque_sw_512x512.jpg sao9615155060 uncurated 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 sao967812059 uncurated Lumen Cargo Lumen Cargo Refers to cargo carried in the lumen of the vesicle; may be crystalized or otherwise bound, e.g., insulin. sao976831666 Endosomal Membrane Endosomal Membrane sao978443756 uncurated Cell Component Aggregate Object Cell Component Aggregate Object sao991156472 true SNpc