]> NIF-Quality: contains odds and ends from SAO-CORE and NIF-Cell Staining October 29, 2010 Used in various techniques, staining is the artificial coloration of a substance that enhances the contrast of tissues, genes, cells, or microorganisms(etc.), to be viewed under the microscope. In biochemistry it involves adding a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. Staining can serve the same purpose as fluorescent tagging. (Adapted from Wikipedia) Horizontal 2007-09-05 2007-09-05 Horizontal Bipolar 2007-09-05 2007-09-05 Bipolar Basket 2007-09-05 2007-09-05 Basket Chandelier 2007-09-05 2007-09-05 Chandelier Co-staining October 29, 2010 Oxidized molecular quality August 31, 2009 Jane Bugea Differential expression 135486 Expression that is increased or decreased relative to a control group at a significance level of p</=0.05. October 29, 2010 Increased expression 135147 Expression that is increased relative to a control group at a significance level of p</=0.05. October 29, 2010 Up-regulated Up-regulated expression Upregulated Upregulated expression Decreased expression 135481 Down regulated Down regulated expression Down-regulated Down-regulated expression Expression that is decreased relative to a control group at a significance level of p</=0.05. October 29, 2010 No change in expression 135746 Expression that has not reached a significance level of p</=0.05 relative to a control group. No change October 29, 2010 Increased staining 135497 October 29, 2010 Staining that is increased relative to a control group at a significance level of p</=0.05. Decreased staining 135484 October 29, 2010 Staining that is decreased relative to a control group at a significance level of p</=0.05. Differential staining 135489 October 29, 2010 Staining that is increased or decreased relative to a control group at a significance level of p</=0.05. No change in staining 135501 November 1, 2010 Staining that has not reached a significance level of p</=0.05 relative to a control group. Decreased co-staining October 29, 2010 Increased co-staining October 29, 2010 Expression level 135747 October 29, 2010 Co-expression Expression level indicated that two or more signals are expressed together in the same structure October 29, 2010 Decreased co-expression October 29, 2010 Increased co-expression October 29, 2010 Staining density November 1, 2010 Heavy staining density Heavily dense staining Heavy staining Intense staining November 11, 2010 Strong staining Very dense staining Moderate staining density Intermediate staining Moderate staining Moderately dense staining November 1, 2010 No staining Absent staining Negative staining Not detectable staining November 1, 2010 Undetectable staining Weak staining density Diffuse staining Low staining Minimally dense staining November 1, 2010 Scattered staining Weak staining Electron-dense Electron-dense January 9, 2009 Sarah M. Maynard The quality of being relatively impermeable to the electron beam of an electron microscope Demyelinated Demyelinated Loss of myelin sheath from a normally myelinated axon or dendrite March 2, 2009 Mutated March 2, 2009 Mutated Fragmented 130025 Broken into pieces Fragmented March 2, 2009 October 22, 2010 Excitatory post synaptic potential A temporay change in postsynaptic potential, usually a depolarization, which increases the likelihood of action potential discharge. This is usually due to the flow of positively charged ions into the postsynaptic cell, but can also be due to a reduction in negatively charged ionic current or the turning off of a potassium current. In common usage, the EPSP typically refers to an evoked EPSP. EPSP Excitatory post-synaptic potential Excitatory postsynaptic potential Maryann Martone May 17, 2009 Inhibitory postsynaptic potential A synaptic potential which reduces the likelihood of an action potential. Typically this is a temporay increase in postsynaptic potential, or hyperpolarization, but depolarizing or nonpolarizing potentials can also be considered inhibitory if they reduce the likelihood of action potential firing. Hyperpolarization can be the result of several ionic flows including an increase of negative charged ions into the cell, or a decrease of positively charged ions into the cell. In normal cells a Chloride conductance is the negative charge carrier and its activation is an inhibitory postsynaptic potential. IPSP Inhibitory post synaptic potential Inhibitory post-synaptic potential Maryann Martone May 17, 2009 Resting Membrane potential A quality inhering in a cell's plasma membrane by virtue of the electric potential difference across it during the resting state of the cell. This resting state usually implies that the potassium current dominates membrane potential. Maryann Martone May 17, 2009 Evoked Excitatory post synaptic potential An EPSP that was evoked by an action potential invading a presynaptic axon. This is as opposed to a spontaneous EPSP. Evoked EPSP Maryann Martone May 17, 2009 Spontaneous Excitatory post synaptic potential An EPSP that is elicited by the random fusion of a synaptic vesicle, in contrast to an evoked EPSP. Maryann Martone May 17, 2009 mEPSP mini miniature EPSP sEPSP Evoked inhibitory postsynaptic potential An IPSP that is the result of an action potential invading a presynaptic inhibitory axon, as opposed to a spontaneous IPSP Evoked inhibitory post synaptic potential Evoked inhibitory post-synaptic potential Maryann Martone May 17, 2009 evoked IPSP Spontaneous Inhibitory postsynaptic potential An IPSP that is the result of a spontaneous fusion of a vessicle, as opposed to an evoked IPSP Maryann Martone May 17, 2009 Spontaneous inhibitory post synaptic potential Spontaneous inhibitory post-synaptic potential mIPSP mini IPSP miniature IPSP sIPSP Event related potential ERP ERPs Maryann Martone May 17, 2009 May 3, 2010 Soma Quality Shape descriptors that have been applied to the cell soma of nerve cells. The shape generally does not take into account processes extending from the soma. Soma Quality sao-1126011106 Pyramidal Generally triangular-shaped soma with a dendrite emerging from the apical pole and basilar dendrites emerging from two or more basal poles Pyramidal curation complete sao-1465673360 Basal Basal sao-282380853 uncurated NIF-Quality Retired class Retired classes from NIF-Quality Morphological Quality Morphological Quality sao1057800815 uncurated Axocruciform Axocruciform Synaptic arrangement where the axon courses orthogonal to and forms a synapse with a portion of dendrite. sao1062287912 uncurated Microtubule Polarity Microtubule Polarity Microtubules are characterized by a + and a - end and may be oriented with respect to the soma (origin) in either + to - or - to +. sao107236050 uncurated Filopodial Dendritic specialization that is typically long and has a darker cytoplasm than spines. Additionally, filopodia usually end in a pointy rather than a bulbous head, and can be much longer than mature dendritic spines. Filopodial sao1141340175 uncurated Random No particular orientation. Random sao1143221302 uncurated Condensed Condensed Morphological state characterized by a contracted matrix and expanded intracristal space; observed experimentally when added ADP is used up (Mannella et al., 2001). sao1152497626 uncurated Attachment Attachment C0923872 sao1179195262 uncurated Bouton Quality Bouton Quality Refers to the morphology of a bouton. sao1189513296 uncurated Connectivity C0925206 Connectivity sao1211239798 uncurated Length Length sao1217691568 uncurated Half Life Half Life Measure of turnover. sao124571525 uncurated Indented Indented Nucleus with one or more indentations in the nuclear membrane. sao1277586470 uncurated Cell Morphological Quality Cell Morphological Quality sao1278200674 Fused Vesicle Fused Vesicle Omega profile Synaptic vesicle that is fused to the pre-synaptic membrane, forming the characteristic omega profile. sao128105491 uncurated Aspiny Dendrite Quality A dendrite characterized by few or no recognizable dendritic spines. Aspiny Aspiny sao128827344 uncurated Sparsely Spiny Dendrite Quality Characterized by a low density of dendritic spines. Sparsely Spiny Sparsely Spiny sao1288413465 uncurated Synaptic Configuration Arrangement of pre- and post-synaptic components. Synaptic Configuration sao1289583168 uncurated Microtubule Mediated Motility Microtubule Mediated Motility Refers to the transport of a structure via microtubules and microtubule-associated motors. sao1301290450 Motility Motility Refers to the ability of structures to move about the cell. sao1330317521 Cross Section Diameter Minor Cross Section Diameter Minor Minimum diameter of a cross section through structure. sao136816674 uncurated Junctional Continuity Indicates that two entities share a continuous space but that the continuity is formed through a specialized junctional component, e.g., gap junction. Junctional Continuity sao1374293695 uncurated Spine Quality Refers to the morphological type of a spine. Spine Quality sao1436578787 uncurated Clustered Clustered sao1475145503 uncurated Density Density sao1510923311 uncurated Mitochondrial Quality Mitochondrial Quality Refers to the morphology of mitochondria. sao1562245920 uncurated Symmetrical Gray's Type 2 Symmetrical Type of chemical synapse characterized by a thin post-synaptic density relatively equal in density to the pre-synaptic specialization giving the junction a symmetric appearance. This type of synapse is also characterized by flattened or pleiomorphic vesicles in the pre-synaptic terminal when fixed with aldehydes. curation complete sao1583093969 see example at: http://synapse-web.org/anatomy/chemical/symh.htm Oval Generally rounded shape, where the minimum and maximum dimensions produce a roughly egg-shape. Oval core:definition incomplete sao1595237779 Thin Characterized by the length being greater than the diameter of the neck, with the diameter of the head being similar to that of the neck (Harris et. al 1992). Thin sao1643644091 uncurated In Vitro In Vitro Indicates that the feature was observed in cells in culture or in isolated subcellular fractions. sao1649728317 Fast Frozen Freeze Substituted Fast Frozen Freeze Substituted Indicates that feature was described in tissue prepared by fast freezing followed by freeze substitution. sao1693353776 Living Animal Indicates that the feature was observed in the living animal. Living Animal sao1694199019 Apical Apical sao1703115805 uncurated Varicose Dendrite Quality Characterized by numerous swellings or varicosities along their length. Varicose Dendrite Varicose Dendrite sao1706854098 uncurated Chemical Synapse Quality Chemical Synapse Quality core:definition incomplete http://ccdb.ucsd.edu/SAO/images/asym_synpase_sw_512x512.jpg sao1746643703 Varicose Axon Varicose Axon sao1746802704 Terminal Bouton Terminal Bouton http://ccdb.ucsd.edu/SAO/images/terminal_bouton_sw_512x512.jpg sao1757774791 uncurated Distance From Soma Distance From Soma Distance, usually in linear microns, from soma where a feature is observed. sao1779606731 uncurated Flattened Characterized by a flattened shape in glutaraldehyde fixed tissue. Flattened sao1785495506 uncurated Stubby Characterized by the diameter of the neck being similar to that of the head (Harris et. al 1992). Stubby sao1786354232 uncurated Surface Area Surface Area sao1788621392 uncurated Functional State Differentiates among different functional states of a cell or cell component, e.g., activated microglia, interphase nucleus, orthodox mitochondria. Functional State sao1802798922 Cristae Quality Cristae Quality Refers to the morphology of mitochondrial cristae. sao1843037539 uncurated Smooth Membrane Characterized by a nuclear membrane with no indentations. Smooth Membrane sao1845602529 uncurated Vesicle Quality Refers to the morphology of a vesicle. Vesicle Quality sao1863391630 uncurated Configuration Configuration Refers to a specialized arrangements of a cellular component or other structure that is characteristic of a given region, e.g., bundled microtubules. sao18717211 uncurated Dendrite Quality Characterization based on high or low density of classical spines on dendrites. Dendrite Quality sao1959705051 uncurated Experimental Condition All experimental entities will be ported into a separate ontology based on OBI Experimental Condition Indicates the experimental conditions under which a feature was observed. sao1960697157 uncurated Volume Volume sao196989303 uncurated Mushroom Characterized by the diameter of the head being much greater than that of the neck (Harris et. al 1992). Mushroom sao1983595164 uncurated Lamellar Lamellar Refers to cristae with a flattened, extended appearance. sao1995010823 uncurated Pedunculated May need to do more reading to determine whether this should be a parent of mushroom and thin. Pedunculated Type of spine characterized by a narrow neck of varying length attached to an expanded head (Jones and Powell 1969). It appears from the core:definition given by these authors that the thin and mushroom shaped categories are both included as subclasses of pedunculated. graph position temporary sao2045795635 Asymmetrical Asymmetrical Gray's Type 1 Type of chemical synapse characterized by a pronounced and relatively thick post-synaptic density compared to the pre-synaptic specialization giving the junction an asymmetrical appearance. This type of synapse is also characterized by round, clear vesicles in the pre-synaptic terminal. curation complete sao2047438300 see example at: http://synapse-web.org/anatomy/chemical/asymh.htm Atlas Location Atlas Location graph position temporary sao2052625281 Radial Radial sao2077793822 uncurated Rosette Rosette sao2082026326 uncurated Axon Quality Axon Quality Refers to the morphology of an axon. sao2088691397 uncurated Speed Speed sao2102170307 uncurated Tubular Refers to crisate with a roughly circular profile in cross section. Tubular sao2110170574 uncurated Spacing Refers to the average distance between features. Spacing sao2126482353 uncurated Plus To Minus Plus To Minus sao2139310701 uncurated Synaptic Connectivity Implies that a morphologically identified synapse exists between two cell components where release of transmitter from cell influences cell B. Synaptic Connectivity sao223845603 uncurated Branched Spine Branched Spine Characterized by two or more heads (Harris et. al 1992) that emerge from the same origin (Sorra KE and Harris KM, 2000). sao268063700 uncurated Orientation Orientation Refers to the "entities of reference" (FMA). Location may be defined by qualitative coodrinates or absolute coordinates. sao271899308 uncurated Measurement Measurement sao279801585 uncurated Bundled Bundled When several members of a class occur tightly apposed to one another or attached to one another in identifiable bundles. sao296309608 uncurated Lobulated Lobulated Nucleus with heavily indented nuclear membrane, giving the appearance of one or more lobes. sao301169922 uncurated Cell Body Referent Polarity Cell Body Referent Polarity sao311075036 uncurated Stacked Stacked sao3169628 uncurated Population Quality Descriptive terms pertaining to a population of objects. Population Quality Sarah M. Maynard sao336034368 uncurated Nucleus Quality Maryann Martone Nucleus Quality The shape of the nucleus, e.g., round, lobulated, indented sao343486489 uncurated Polarity Need to define property with "reference point" Polarity sao349337269 uncurated Orthodox Morphological state characterized by an expanded matrix space and contracted intracristal space; observed experimentally when ADP is added (Mannella et al., 2001). Orthodox sao358853874 uncurated Aggregated Aggregated Formed into a body or mass. Sarah M. Maynard sao3710738764 uncurated Misfolded Misfolded Pertains to formation of protein aggregates. There are varying degrees of "misfolded". Sarah M. Maynard sao4092866126 uncurated Concentrated Concentrated Indicates a group of objects exist in a large amount in a particular area. Sarah M. Maynard sao4152363223 uncurated Globular Globe-shaped; having the form of a ball or sphere. Globular Sarah M. Maynard sao4253573122 uncurated Longitudinal Longitudinal Oriented parallel to the long axis. sao430240391 uncurated Spherical Lewy Body Generally round shape where minimum diameter and maximum diameter are roughly the same. Sarah M. Maynard Spherical Lewy Body sao4459136323 uncurated Accumulated 130027 Accumulated Indicates an increased number of objects that implies that the increase is due to a failure to break down or remove extra objects. October 22, 2010 Sarah M. Maynard sao4531544124 uncurated Smooth Nucleus with smooth membrane and no large folds or lobules. Smooth sao47950958 uncurated Branched Branched sao497641585 uncurated Phosphorylated Indicates a phosphate (PO4) added to protein molecule or small molecule. Phosphorylated Sarah M. Maynard sao4985712724 uncurated Filamentous Filamentous Having a thread-like quality; consisting of filaments. Sarah M. Maynard sao5221865117 uncurated Activated Activated Microglial activation, e.g., in brain injury, is characterized by enlargement, changes in shape, and increased synthesis of cytokines such as IL-1. There are three subtypes: primed, enlarged, phagocytic Sarah M. Maynard Sheng JG et al. 1997. Neuritic plaque evolution in Alzheimer's disease is accompanied by transition of activated microglia from primed to enlarged to phagocytic forms. Acta Neuropathol 94:1-5. sao5413665309 uncurated Adjacency Adjacency C0923871 Two entities are considered to be adjacent if they have no overlapping (shared) boundaries and parts and not other anatomical entity is interposed between them. The adjacency relationship is symmetrical (adapted from FMA). sao542191739 uncurated Fusiform Elongated shape that tapers at both ends Fusiform Spindle curation complete sao542875575 Single Indicates that the feature exists in isolation, e.g., single filaments as opposed to bundled filaments. Single sao548826380 uncurated Molecular Quality Descriptive terms pertaining to molecular qualities. Molecular Quality Sarah M. Maynard sao5798413869 uncurated Simple Fingerlike evaginations that extend from the dendrite that are filled with fluffy filamentous material, characteristic of some neurons like motor neurons (Peters, Palay and Webster, 1991). Simple sao614188547 uncurated Radius Radius sao632949619 uncurated Nonactivated A microglia that is not activated. Nonactivated Sarah M. Maynard sao6363641087 uncurated Spiny Dendrite Quality Characterized by a high density of dendritic spines. Spiny Spiny sao638749545 uncurated Molecular Configuration Molecular Configuration Sarah M. Maynard We need to consult the protein community to find the most accurate location for Molecular Configuration. sao6450066368 uncurated Actin Based Motility Actin Based Motility Mobility that is mediated by the actin cytoskeleton. sao656094176 Minus To Plus Minus To Plus sao675186109 uncurated Transverse Oriented orthogonal to the long axis. Transverse sao679027665 uncurated Granule Granule http://ccdb.ucsd.edu/SAO/images/granule_sw_512x512.jpg sao6934064108 small numerous cell uncurated Spatial Relationship Spatial Relationship These relationships are modeled after the spatial relationships contained in the FMA. sao723896903 uncurated Anatomical Pattern Anatomical Pattern sao732945962 uncurated Pathological Cellular inclusions associated with pathological conditions. Pathological sao74391158 uncurated Tufted Dendrite Quality Characterized by a terminal tuft. Tufted Tufted sao754373097 uncurated Distal End Distal End Ending of a process furthest from the cell soma. sao783483540 uncurated En Passant En Passant http://ccdb.ucsd.edu/SAO/images/en_passant_bouton_sw_512x512.jpg sao809320003 uncurated Proximal End Ending of a process closest to the cell soma. Proximal End sao812067870 uncurated Acute Slice Acute Slice sao819188787 Cross Section Diameter Major Cross Section Diameter Major Maximum diameter of a cross section through structure, assumed to be the maximum diameter in the case of spherical structures like vesicles. Use this field when entering only a single cross section value where the structure is assumed to be spherical. sao824839913 uncurated Nitrated Combined, or impregnated, with nitric acid, or some of its compounds. Nitrated Sarah M. Maynard sao8314803620 uncurated Pleomorphic Characterized by many shapes in glutaraldehyde fixed tissue. Pleomorphic sao854959971 uncurated Width Width sao888175480 uncurated In Vivo In Vivo Indicates that a feature was described in intact tissue. sao897115057 Functional Quality for Microglia Functional Quality for Microglia Sarah M. Maynard Terms to describe the functional state of microglia. We are not sure this is exactly how to solve this issue. Do we want this to be a state quality? sao9222381184 uncurated Stellate Generally star shaped multipoloar cell shpae with spherically extending processes Stellate sao9271919883 uncurated Ubiquinated Pertains to the post-translational modification of a protein by the covalent attachment of one or more ubiquitin monomers. This labels proteins for proteasomal degradation and controls the stability, function, and intracellular localization of a wide variety of proteins. Protein ubiquitination is the process by which one or more ubiquitin moieties are added to a protein. (Gene Ontology) Sarah M. Maynard Ubiquinated Ubiquitylation sao9291838256 uncurated Sessile Also refers to a stubby spine. Sessile sao941226261 uncurated Spherical Generally round shape where minimum diameter and maximum diameter are roughly the same Spherical curation complete sao957949983 Round Clear Round Clear sao967304317 uncurated Continuity C0934150 Continuity sao969067581 uncurated Lewy Body Quality Labels that refer to the morphological characteristics of a Lewy Body. Lewy Body Quality Sarah M. Maynard sao9946511970 uncurated