Mitochondrial crista morphology

(AM900087)

Structural and functional characteristics of the inward folds or cristae of the mitochondrial inner membrane including crista number, extent, and shape

Electron microscopy

Mitochondrial matrix morphology

(AM900089)

Structural and functional characteristics of the gel-like material that lies in the matrix space, or lumen, of a mitochondrion, and contains the enzymes of the tricarboxylic acid cycle

Electron microscopy

Mitochondrial number

(AM900091)

alternation in the number of the cellular organelles responsible for energy production

Electron microscopy

Basal dendritic length

(AM900100)

length of dendrites at the base of the dendritic tree

Hydrocephaly

(AM900101)

excessive accumulation of cerebrospinal fluid in the brain, especially the cerebral ventricles, often leading to increased brain size and other brain trauma

Histology

Anatomical projections and connectivity

(AM1100000)

Afferent and efferent connections and projections in all brain regions, including cortex, subcortex, midbrain, hindbrain and spino-cortical connections and the peripheral nervous system.

Immunohistochemistry; Neuronal tracing; Immunofluorescence staining; Fluorescence microscopy; Positron emission tomography (PET) imaging; Immunostaining; Diffusion weighted magnetic resonance imaging (DWI); Histological analysis; Histology; Whole-cell patch clamp; Electron microscopy

Brain anatomy

(AM1100001)

Gross or macroscopic structure of the brain

Histology; Immunohistochemistry; Nuclear staining; Magnetic resonance imaging (MRI); General observations; Microscopic analysis; Macroscopic analysis; Pathology; Electron microscopy

Brain cytoarchitecture

(AM1100002)

Arrangement and structure of neuronal cells in brain

Immunohistochemistry; Golgi-Cox staining; Electron microscopy; Nuclear size measurement; TUNEL assay; Fluorescence microscopy; Histology; Cell contour analysis; Immunostaining; Cell counting; Confocal microscopy; Timm's sulfide silver staining for metals; Cell size measurement; Stereology; Western blot; Quantitative PCR (qRT-PCR)

Brain development

(AM1100003)

Differentiation of the brain, assessed by morphology and molecular profile at different embryonic stages

Gross necroscopy; Immunohistochemistry; In situ hybridization (ISH); Immunocytochemistry; Histology; General observations; Western blot; Confocal microscopy; Gene expression microarray; RNA sequencing

Brain morphology

(AM1100004)

Structure of the brain or its regions

Histology; Electron microscopy; Macroscopic analysis; Microscopic analysis; Immunohistochemistry; Golgi-Cox staining; Voxel based morphometry; Fluorescence microscopy; Pulse-chase analysis; Histological analysis; Magnetic resonance imaging (MRI); Immunostaining; Pathology; Stereology; Diffusion tensor imaging; In situ hybridization (ISH); General observations; Western blot; Nuclear staining; Immunocytochemistry; Cell counting; Cytochrome oxidase staining; Gross necroscopy; Diffusion Tensor imaging (DTI); Photomicrographic analysis; Confocal microscopy; Whole-mount immunohistochemistry; Measurement of tissue weight

Brain size

(AM1100005)

Size of the brain, usually measured by weight or volume of extracted whole brain, but may include in vivo volume measurements using MRI

Histology; Microscopic analysis; Convex hull analysis; Gross necroscopy; Macroscopic analysis; Magnetic resonance imaging (MRI); Immunohistochemistry; Pathology; Stereology; Histological analysis; Golgi-Cox staining; Voxel based morphometry; Diffusion Tensor imaging (DTI); Measurement of tissue weight; General observations; Cranial computerized tomography (CT) scan; TUNEL assay; Nuclear staining

Cerebellar foliation

(AM1100006)

Formation and manifestation of the pattern of the ten cerebellar lobules, including midline or vermis foliation and lateral folia

Immunohistochemistry; Histology

Cerebellar morphology

(AM1100007)

Structure of the whole cerebellum, including the Purkinje cell layer, the granule cell layer, the deep cerebellar nuclei, inferior olivary nucleus (climbing fibers) and the cerebellar peduncles and their organization with respect to each other

Histology; Electron microscopy; Stereology; Immunohistochemistry; Magnetic resonance imaging (MRI)

Cortical lamination

(AM1100008)

Layered organization of the cerebral cortex into 6 laminae (layers) with specific layers enriched in neurons expressing typical genes/markers (often limited to specific layers) that identify distinctive populations of cells. In addition, laminae have differences in density, cell size and shape, input and output projections and connectivity. The layers develop in an inside-out manner, requiring large populations of migratory neural precursor cells and their development is usually studied in the embryonic stages: approximately E11-12 onwards in mouse embryos. Some of the markers specific to layers include: Ctip2, Foxp2 (layer 6),Cux1 (layer 1-2) etc

Immunohistochemistry; Immunostaining; Confocal microscopy; Histology; Nuclear staining

Cortical thickness

(AM1100009)

Thickness of cortical layers

Histology; Immunohistochemistry; Photomicrographic analysis; Magnetic resonance imaging (MRI)

Dendritic architecture: spine density

(AM1100010)

Density of microscopic protrusions emerging from the dendritic branches of 'spiny' neurons, spiny neurons include the hippocampal neurons (CA1, CA3), pyramidal neurons of the motor cortex, cerebellar Purkinje neurons, and dorsal horn sensory neurons in the spinal cord. These neurons have specific spine densities with estimates randing from 1 - 10 spines per micron length of dendritic branch, which can vary depending on the type of analysis and method of visualization as well

Sholl analysis; Golgi-Cox staining; Histology; Confocal microscopy; Immunohistochemistry; Two-photon microscopy; Electron microscopy; Fluorescence microscopy; Stimulated emission depletion (STED) microscopy

DTI: fractional anisotropy or relative anisotropy in brain regions

(AM1100011)

Relative measure that represents variation between the levels of water molecule diffusion rates in different directions, in the white matter, or a measure of relative differences in the flow of water

Diffusion tensor imaging; Diffusion Tensor imaging (DTI)

Dendritic architecture: spine turnover

(AM1100012)

Dynamic gain or loss of spines over a fixed dendrite length (or number) in real time, maybe indicative of associated gain or loss of synapses or puncta

Two-photon microscopy; Whole-cell patch clamp; Histology; Whole-cell current clamp

Hippocampal morphology

(AM1100013)

Structure of the hippocampus, including the areas CA1, CA3, and the dentate gyrus and the organization of pyramidal and granule neurons

Immunohistochemistry; Histology; Magnetic resonance imaging (MRI); Magnetic resonance histology (MRH); Voxel based morphometry; Photomicrographic analysis; Sholl analysis; Immunostaining; Confocal microscopy

Hypothalamic morphology

(AM1100014)

Structure of the hypothalamus, including the supraoptic, median eminence and the posterior regions

Magnetic resonance imaging (MRI); Histology; Immunohistochemistry; In situ hybridization (ISH)

Morphology and size of anterior commissure

(AM1100015)

Structure of a round bundle of nerve fibers (white matter) that crosses the midline of the brain near the anterior limit of the third ventricle

Diffusion tensor imaging; Magnetic resonance imaging (MRI); Magnetic resonance histology (MRH); Voxel based morphometry

Morphology and size of the corpus callosum

(AM1100016)

Structure of the thick bundle of nerve fibers (white matter) comprising a commissural plate connecting the two cerebral hemispheres

Magnetic resonance imaging (MRI); Histology; Immunohistochemistry; Diffusion tensor imaging; Magnetic resonance histology (MRH); Voxel based morphometry

Morphology of cranial nerves

(AM1100017)

Structure of any of the twelve nerves that emerge from the cranium as opposed to the spinal nerves

Histology; Macroscopic analysis; Immunohistochemistry

Morphology of the basal ganglia: lentiform nucleus: globus pallidus

(AM1100018)

Size, shape and organization of the globus pallidus, part of the lentiform nucleus

Magnetic resonance histology (MRH); Voxel based morphometry; Fluorescence microscopy; Immunohistochemistry; Magnetic resonance imaging (MRI)

Neocortex morphology: size

(AM1100019)

Size or volume of the neocortex

Magnetic resonance imaging (MRI)

Morphology of the basal ganglia: striatum: caudoputamen

(AM1100020)

Size, shape and organization of the caudate-putamen nucleus

Magnetic resonance histology (MRH); Voxel based morphometry; Magnetic resonance imaging (MRI); Immunohistochemistry; Histology

Morphology of the basal ganglia: ventral striatum or nucleus accumbens

(AM1100021)

Size, shape and organization of the ventral striatum, also called nucleus accumbens

Magnetic resonance imaging (MRI); Immunohistochemistry; Histology

Morphology of the insular cortex

(AM1100022)

Structure of the region of the cerebral cortex that in mouse is located anterior to the hippocampus and parahippocampal cortices, and it is thought to be involved in cognitive function, consciousness, emotion, motor function, among other functions

Magnetic resonance imaging (MRI)

Morphology of the primary auditory cortex

(AM1100023)

Structure of the region of the cerebral cortex that receives the auditory radiation from the medial geniculate body, a thalamic cell group receiving auditory input from the cochlear nuclei in the rhombencephalon and is responsible for processing of auditory (sound) information

Magnetic resonance imaging (MRI)

Morphology of the spinal cord

(AM1100024)

Structure of the cylindrical tissue of the vertebral canal that extends from the medulla oblongata to the conus medullaris

In situ hybridization (ISH); General observations; Immunohistochemistry

Morphology of the superior and inferior colliculi

(AM1100025)

Structure of the paired superior and inferior eminences of the mesencephalic tectum that are involved in auditory and visual processing, respectively

Magnetic resonance imaging (MRI)

Myelination

(AM1100026)

Process by which myelin sheaths are formed and maintained around neurons by oligodendrocytes forming a complex multilayered membrane structure that increases the efficiency of conductance (of ions) through axons

Immunohistochemistry; Histology; Immunocytochemistry; Electron microscopy; g-ratio measurement (axon diameters/fiber diameters of myelinated axons); High-performance thin-layer chromatography; General observations; Transmission electron microscopy (TEM)

Neuronal number: oxytocin expressing

(AM1100027)

Number of neurons in the hypothalamus (paraventricular nucleus) expressing the hormone and neurotransmitter oxytocin

In situ hybridization (ISH); Immunohistochemistry; Stereology

Neocortex morphology

(AM1100028)

Structure of the larger part of the mammalian cerebral cortex, distinguished from the allocortex by being composed of a larger number of nerve cells arranged in six layers

Histology; Immunohistochemistry

Neurotransporter expression

(AM1100029)

Expression of neurotransmitter transporters, which reuptake endogenous neurotransmitter molecules from the synaptic cleft back to the presynaptic axon terminal to recycle and maintain a low extracellular concentration of the neurotransmitter

Western blot; Immunocytochemistry; Fluorescence microscopy; Immunohistochemistry

Neuronal migration

(AM1100031)

Movement of immature neurons from germinal zones to specific positions where they will reside as they mature

Cell counting; Immunohistochemistry; Immunofluorescence staining; Confocal microscopy; Immunostaining; Histology; Cell migration analysis

Neuronal number

(AM1100032)

Number of neuronal cells in brain usually measured in a region of interest (ROI) with defined area or volume across the brain

Immunostaining; Histology; Immunohistochemistry; In situ hybridization (ISH); Cell counting; Nearest neighbor analysis; Immunofluorescence staining; Whole-cell patch clamp; Microscopic analysis; Stereology; General observations; Macroscopic analysis; Western blot; Fluorescence microscopy

Neuronal number: dopamine sensitive neurons: Darpp32+

(AM1100033)

Number of neurons expressing Darpp32 present in the deep cortical layers, which are dopamine-responsive excitatory neurons

Immunohistochemistry; Single-cell gene expression analysis; Cell counting

Neuronal number: dopamine sensitive neurons: Drd1+

(AM1100034)

Number of neurons expressing the Drd1 type receptors, responsive to dopamine, e.g., the striatal medium spiny neurons

Single-cell gene expression analysis; Cell counting; Fluorescence microscopy; Immunohistochemistry

Neuronal number: dopamine sensitive neurons: Drd2+

(AM1100035)

Number of neurons expressing the Drd2 type receptors, responsive to dopamine, e.g., the striatal medium spiny neurons

Fluorescence microscopy; Immunohistochemistry; Single-cell gene expression analysis; Cell counting

Neuroreceptor levels: DA

(AM1100036)

Levels (number or density) of dopamine receptors

Radioligand binding studies

Neuronal number: excitatory neurons

(AM1100037)

Number of neuronal cells that express depolarizing ligand-gated ion channels, such as the ionotropic glutamate receptor

Immunohistochemistry

Morphology and size of the optic tract: thalamic extension

(AM1100038)

Extension of axons from the optic chiasma to the lateral geniculate nucleus of the thalamus, that relays sensory stimulus arising in the retina, and forms a section of the visual pathway.

Histology

Neuronal number: inhibitory neurons

(AM1100039)

Number of neuronal cells that express hyperpolarizing ligand-gated ion channels, such as the GABA receptor

Immunohistochemistry; In situ hybridization (ISH)

Neuronal number: interneurons

(AM1100040)

Number of neurons that exclusively interact with other neurons in the brain and can be divided into many sub-populations, including the heterogenous GABAergic (GABA releasing) interneurons, that provide BOTH inhibitory and disinhibitory modulation of cortical and hippocampal circuits and contribute to the generation of oscillatory rhythms and coordinate activity of neuronal ensembles (parvalbumin positive interneurons constitute a large subset of GABAergic interneurons)

Immunohistochemistry; In situ hybridization (ISH); Fluorescence microscopy; Cell counting; Western blot; Stereology; Histology; Immunostaining; Immunocytochemistry

Neuronal number: Purkinje cells

(AM1100041)

Number of neuronal cells that are located in the interface of the molecular and granular layers of the cerebellar cortex

Histology; Immunohistochemistry; Stereology; Western blot; Fluorescence microscopy; Cell counting

Neuronal number: striatal medium spiny neurons (MSNs)

(AM1100042)

Number of the inhibitory projection neurons located in the striatum that integrate glutamatergic signals arising from the cerebral cortex and thalamus

Single-cell gene expression analysis; Cell counting

Neuroreceptor levels: glutamate receptors: AMPA receptors

(AM1100043)

Levels (number or density) of ionotropic glutamate receptors activated by AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) or receptor subunits that are ligand gated ion channels including GluRs and GluAs

Western blot; Immunohistochemistry; Fractionation; Immunostaining

Neuroreceptor levels: glutamate receptors: NMDA receptors

(AM1100044)

Levels (number or density) of ionotropic glutamate receptors activated by NMDA (N-methyl D-aspartate) or receptor subunits that are ligand gated ion channels, including the GluN receptor subtypes, NR1, NR2A, NR2B

Western blot; Semi-quantitative PCR (qRT-PCR); Whole-cell patch clamp; Quantitative PCR (qRT-PCR); Histology; Immunohistochemistry

Number of oligodendrocytes

(AM1100045)

Number of cells of the central nervous system that form the insulating myelin sheath of axons in the central nervous system

Immunohistochemistry

Piriform cortex morphology

(AM1100046)

Structure of the subdivision of the laminated olfactory cortex with only three main layers that receive monosynaptic input from the olfactory bulb via the lateral olfactory tract

Histology

Post-synaptic density size

(AM1100047)

Size or thickness of the protein dense specialized structure attached to the post-synaptic membrane at the synapse

Electron microscopy

Post-synaptic density size: excitatory synapses

(AM1100048)

Size or thickness of the protein dense specialized structure attached to the post-synaptic membrane at the excitatory synapse, which is typically glutamatergic

Electron microscopy; Western blot; Transmission electron microscopy (TEM)

Post-synaptic density size: inhibitory synapses

(AM1100049)

Size or thickness of the protein dense specialized structure attached to the post-synaptic membrane at the inhibitory synapse, which is typically GABAergic

Electron microscopy

Neuronal size: active neurons

(AM1100050)

Soma size of neurons that are active in a network. Active neurons appear to have a larger soma so this maybe used as an indicator of activity level.

Immunohistochemistry

Size of cerebral ventricles: lateral ventricle

(AM1100051)

Size of the largest ventricle or fluid filled space in the brain, the lateral ventricle, which present in each hemisphere

Stereology; General observations; Histology; Magnetic resonance imaging (MRI); Immunohistochemistry

Somatosensory cortical map architecture

(AM1100052)

Structure of the area of the postcentral gyrus and central sulcus that is involved in somatic sensation

Immunohistochemistry; Histology; Nuclear staining

Spinal nerve branch point morphology

(AM1100053)

Structure of any of the 31 paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment

Immunohistochemistry

Structural dendritic plasticity

(AM1100054)

Structural plasticity determines the formation and removal of synapses, which in turn depend on addition or removal of dendritic spines where they form, depending on environmental cues and the strength of activation of synapses and associated neurons. Both Hebbian and homeostatic structural plasticity have been observed in dendritic spines.

Whole-cell patch clamp; Golgi-Cox staining; Two-photon microscopy

Synapse density

(AM1100055)

Number of density of synapses, the membrane junction sites of nerve cells to a target cell body or dendrite of another nerve cell, an effector cell, or a sensory receptor cell

Histology; Electron microscopy; Immunostaining; Immunohistochemistry; Immunofluorescence staining; Golgi-Cox staining; Cell counting; Fluorescence microscopy; Stereology

Synapse density: excitatory

(AM1100056)

Number or density of excitatory synapses usually located on tips of dendrites using glutamate as the neurotransmitter. Excitatory synapses are much more common in the brain than inhibitory synapses

Immunohistochemistry; Two-photon microscopy; Fluorescence microscopy; Transmission electron microscopy (TEM); Electron microscopy; Whole-cell patch clamp

Neuronal number: neuroendocrine cells

(AM1100057)

The number of neuroendocrine cells in the the paraventricular, supraoptic and arcuate nuclei.

Immunohistochemistry

Synaptic morphology

(AM1100058)

Structure of the membrane junction site of a nerve cell to a target cell, such as another nerve cell, an effector cell, or a sensory receptor cell

Immunohistochemistry; Western blot; Electron microscopy; Immunofluorescence staining; Array tomography; Histology; Confocal microscopy

Synaptic neuroreceptors

(AM1100059)

Number or density of neurotransmistter receptors, which are localized to the synapse in the post synaptic neurons

Western blot; Immunohistochemistry; Whole-cell patch clamp

Thalamic morphology

(AM1100060)

Structure of the large ovoid mass of paired bodies containing mostly grey matter and forming part of the lateral wall of the third ventricle of the brain

Histology; Magnetic resonance imaging (MRI); Cell counting; Magnetic resonance histology (MRH); Voxel based morphometry

Dendritic architecture: dendritic tree complexity

(AM1100061)

Structure of dendritic branching or arborization which strongly modulates the shape of the action potential onset at the axon initial segment; it is increased in neurons with larger dendritic surface area

Golgi-Cox staining; Confocal microscopy; Immunofluorescence staining; Sholl analysis; Histology; Immunohistochemistry; Immunocytochemistry; Fluorescence microscopy; Electron microscopy

Axonal architecture: branch length

(AM1100062)

Length of axonal branches measured from branch point to terminal end.

Immunofluorescence staining

Neuroreceptor levels: serotonin

(AM1100063)

Levels (number or density) of serotonin receptors

Immunofluorescence staining; Autoradiographic analysis; High-performance liquid chromatography (HPLC); High-performance liquid chromatography with electrochemical detection (HPLC-EC); Radial maze test

Perineuronal net morphology

(AM1100064)

Structure of the reticular complex or specialized extracellular matrix found in the central nervous system, surrounding the cell bodies of many neurons, and extend along the dendrites and around mature synapses

Immunohistochemistry; Electron microscopy

Synapse density: inhibitory

(AM1100065)

Number or density of inhibitory synapses that use GABA or glycine and are located in the shaft of a dendrite or on the cell body of the postsynaptic neuron

Immunostaining; Immunohistochemistry; Electron microscopy; Histology; Fluorescence microscopy

Cerebellar morphology: granule cell layer thickness

(AM1100066)

Thickness of the inner (in adults) or outer (in pups till P21) granule cell layer in the cerebellum

Histology

Cerebellar morphology: molecular layer thickness

(AM1100067)

Thickness of the molecular layer of the cerebellum containing most of the axons and nerve terminals

Histology; Immunohistochemistry; Immunostaining

Neuronal cytoskeletal organization

(AM1100068)

Organization of any component of the neuronal cytokeleton including neurofilaments

Immunohistochemistry

Dendritic architecture: spine morphology

(AM1100069)

Morphogenetic characteristics of dendritic spines including head and neck length or thickness; changes to which regulate electrical compartmentalization of postsynaptic signals, maybe measured using compartmentalization factor (VL/A, V being head volume, L being neck length and A cross sectional area of the neck)

Golgi-Cox staining; Confocal microscopy; Immunohistochemistry; Electron microscopy; Stimulated emission depletion (STED) microscopy

Cell proliferation: neural precursors

(AM1100071)

Number of neurons or neuronal precursors undergoing cell cycle in the adult or developing brain (also measured usually in a ROI)

Whole-mount immunohistochemistry; Immunostaining; EdU incorporation; Immunohistochemistry; Immunofluorescence staining; Golgi-Cox staining; Pulse-chase analysis

Prefrontal cortex morphology

(AM1100072)

Size and structural organization of the prefrontal cortex, including the frontal association areas (overlaps with neocortex morphology, differentiated based on type of analysis)

Diffusion Tensor imaging (DTI)

Olfactory bulb morphology

(AM1100073)

Size and structural organization of the olfactory bulb that is arranged into 6 layers: the external most olfactory sensory neurons makes synapses in the glomerular layer with the heterogenous juxtaglomerular cells(periglomerular and superficial short-axon cells) present in this layer, the external plexiform layer contains the tufted cells, while the layer beneath contains the mitral cells forming the mitral cell layer. The innermost two layers are inner plexiform layer (mainly containes nerve endings) and the granule cell layer containing granule cells

Diffusion Tensor imaging (DTI); Gross necroscopy; Magnetic resonance histology (MRH); Voxel based morphometry

Morphology of the amygdala

(AM1100074)

Size and structural organization of the amygdala located in the frontal portion of the temporal lobe

Magnetic resonance histology (MRH); Voxel based morphometry; Immunohistochemistry; Magnetic resonance imaging (MRI)

Morphology and size of stria terminalis

(AM1100075)

Size and structure of the band of fibers or white matter tract that projects from the amygdala caudally. It follows a semicircular path following the lateral ventricle and continues anteriorly in the junction of the caudate nucleus and the thalamus, further projecting on to the anterior hypothalamus and the ventromedial nucleus of the hypothalamus as well

Magnetic resonance imaging (MRI); Magnetic resonance histology (MRH); Voxel based morphometry

Morphology and size of the optic tract

(AM1100076)

Size and structure of the optic tract that is formed after the optic nerves leaving the retina cross the optic chiasm. The optic tract wraps around the midbrain to reach the lateral geniculate nucleus (LGN) where all the axons synapse.

Histology; Magnetic resonance histology (MRH); Voxel based morphometry

Morphology and size of fimbria

(AM1100077)

Size and structure of the band of fibers or white matter tract called fimbria that is formed medially by the convergence of fibers from the alveus that has efferent fibers emerging directly from the hippocampus (the alveus gives rise to the fimbria)

Magnetic resonance histology (MRH); Voxel based morphometry; Magnetic resonance imaging (MRI)

Morphology and size of fornix

(AM1100078)

Size and structure of the C shaped white matter tract fornix, which is formed by the fimbria as the fimbria of each hippocampus thickens posteriorly. It is the main efferent system of the hippocampus and has four parts: crura, hippocampal commissure, body and columns. At the anterior commissure the fornix divides into posterior and anterior fibers that end at the mammillary body (hypothalamus) and the septal region or nucleus accumbens, repectively

Magnetic resonance histology (MRH); Voxel based morphometry

Neuroreceptor levels: glutamate receptors: mGluR

(AM1100079)

Levels (number or density) of metabotropic glutamate receptors or receptor subunits that are members of the G-protein-coupled receptor family and act to modulate cell excitablility and synaptic transmission via secondary messenger signaling pathway, activated by their ligand L-glutamate , including all mGluRs: group I (mGluR1 and mGLuR5), group II (mGluR2, mGluR3, GRM3A2, GRM3A4, GRM3A2A3), group III (mGluR4, mGluR, mGluR7, mGluR8)

Western blot; Immunostaining; Quantitative PCR (qRT-PCR); Immunohistochemistry

Synaptic morphology: synaptic cleft length

(AM1100080)

Distance between the pre- and post- synaptic membranes which indicates the type of synapse and the time required for synaptic vesicles to diffuse from the presynaptic membrane to the post-synaptic membrane

Electron microscopy; Transmission electron microscopy (TEM)

Synaptic morphology: active zone

(AM1100081)

During synaptic transmission synaptic vesicles, carrying neurotransmitters, dock and fuse with the presynaptic membrane to release neurotransmitters into the synaptic cleft at regions called active zones, the area of which indicates the degree of acitivity of the synapse

Transmission electron microscopy (TEM); Immunohistochemistry; Electron microscopy; Immunofluorescence staining; Western blot; Quantitative PCR (qRT-PCR)

Neuroreceptor levels: TrkB

(AM1100082)

Levels (number or density) of the BDNF receptor TrkB

Immunohistochemistry; Western blot

Neuroreceptor levels: Oxt

(AM1100083)

Levels (number or density) of oxytocin receptors

Radioligand binding studies

Myelination: PNS

(AM1100084)

Formation of myelin sheaths around neurons by Schwann cells in the peripheral nervous system

Electron microscopy; g-ratio measurement (axon diameters/fiber diameters of myelinated axons)

Neuronal number: laryngeal premotor neurons

(AM1100085)

Neurons in the primary motor cortex in mice that are connected to the functioning of larynx to produce song behavior, present in M1 layer V. These have been recently found to exist and be connected to the brainstem vocal motor neurons (nucleus ambiguous or Amb), be functionally active during USV song (call) behavior, while also projecting to the anterior striatum and thalamus (Gustavo et al PlosONE 2012).

Immunohistochemistry

Cell proliferation: neural precursors: granule cell precursors

(AM1100086)

Proliferation of granule cell precursors in the external granular layer (EGL) of the developing cerebellum before and upto 3 weeks after birth

Immunohistochemistry

Size of cerebral ventricles

(AM1100087)

Size of the all ventricles or fluid filled spaces in the brain

Magnetic resonance imaging (MRI); General observations

Size of cerebral ventricles: third ventricle

(AM1100088)

Size of the third ventricle or fluid filled space in the brain

Magnetic resonance imaging (MRI)

Neuronal size

(AM1100089)

Size of neuronal soma, measured in a specific neuronal type

Immunostaining; Confocal microscopy; Immunohistochemistry; Immunofluorescence staining

Dendritic architecture: dendritic length

(AM1100090)

Length of dendrites, in a specific neuronal type

Golgi-Cox staining; Immunohistochemistry; Electron microscopy; Sholl analysis; Histology; Immunofluorescence staining

Neuronal number: enteric neurons: dopaminergic

(AM1100091)

Number of enteric neurons that produce dopamine in the gastrointestinal tract, mostly found in the submucosal and myenteric plexuses . Maybe measured as density, using markers like tyrosine hydroxylase (TH)

Immunocytochemistry

Neuronal number: enteric neurons: CGRP+

(AM1100092)

Number of enteric neurons that are positive for calcitonin gene related peptide (CGRP) expression in the gastrointestinal tract. The gene for Beta CGRP is expressed in distinct regions of the gastrointestinal tract, including the myenteric and submucosal plexuses of the small and large intestine.

Immunocytochemistry

Neuronal number: enteric neurons: gabaergic

(AM1100093)

Number of enteric neurons that produce gamma aminobutyric acid (GABA) in the gastrointestinal system, GABA is found in several types of enteric neurons including Dogiel type I and Dogiel type II and myenteric plexus

Immunocytochemistry

Neuronal number: enteric neurons: serotonergic

(AM1100094)

Number of enteric neurons that synthesize serotonin using tryptophan hydroxylase 2 (these are different from enterochromaffin cells that also produce serotonin)

Immunocytochemistry

Neuroreceptor levels: histamine receptors: H2R

(AM1100095)

Levels (number or density) of H2R histamine receptors

In situ hybridization (ISH); Radioligand binding studies

Neuroreceptor levels: histamine receptors: H3R

(AM1100096)

Levels (number or density) of H3R histamine receptors

Radioligand binding studies

Neuroreceptor levels: CRH

(AM1100097)

Levels (number or density) of corticotropin releasing hormone receptors

Quantitative PCR (qRT-PCR)

Neuronal number: enteric neurons

(AM1100098)

Number of enteric neurons in the gastrointestinal tract, mostly found in the submucosal and myenteric plexuses

In situ hybridization (ISH); Immunocytochemistry; Immunofluorescence staining

Neuroreceptor levels: GABA-R: GABAa

(AM1100099)

Levels (number or density) of receptors for the neurotransmitter, gamma-aminobutyric acid (GABA). or receptor subunits that form the heteropentameric GABAa receptors associated with chloride channels in different regions of the CNS, these including the alpha, beta, gamma subtypes

Quantitative PCR (qRT-PCR); Western blot; Autoradiographic analysis

Morphology of the spinal cord: sensory and motor tracts

(AM1100100)

Structure and arrangement of white matter tracts found in the spinal cord, which carry sensory information to the spinal cord and the brain (i.e., spinocerebellar tract, spinothalamic tract), these are the ascending tracts, whereas the tracts that relay motor responses originating in the brain or spinal cord itself (i.e., corticospinal tract, subsconscious motor tracts that includes vestibulospinal tract etc.) are the descending tracts

Histology

Neuronal morphology: axonal structure

(AM1100101)

Internal structure of the axonal projections (nerve fibers) from a neuron (excludes myelination as that is an external structure component synthesized by glial cells)

Histology; Confocal microscopy; Electron microscopy

Neuroreceptor levels: gastrin related peptide receptor (GRPR)

(AM1100102)

Levels (number or density; mRNA or protein levels) of gastrin related peptide receptor (GRPR) in neurons

Semi-quantitative PCR (qRT-PCR)

Neuroreceptor levels: epidermal growth factor receptor (EGFR)

(AM1100103)

Levels (number or density; mRNA or protein levels) of Epidermal growth factor receptor (EGFR) in neurons

Semi-quantitative PCR (qRT-PCR)

Neuronal number: serotonergic

(AM1100104)

Number of neurons expressing tryptophan hydroxylase, a marker for serotonergic neurons

Immunofluorescence staining; Immunohistochemistry

Brain cytoarchitecture: cortical patches

(AM1100105)

Patches of disorganized cortical cytoarchitecture during embryonic development and adulthood manifested as a loss of the cortical-layer-specific markers special AT-rich sequence-binding protein 2 (SATB2) and T-brain-1 (TBR1).

Immunohistochemistry

Glial morphology

(AM1100106)

Morphology and number of glial cells

Confocal microscopy

Axonal architecture: branch number

(AM1100107)

Number of axonal branches that allow a single neuron to connect to multiple synaptic targets, or form multiple synapses with a single target (such as a muscle fiber at the neromuscular junction).

Immunofluorescence staining; Immunostaining

Synapse density: mature boutons

(AM1100108)

Number of mature boutons

Immunostaining; Immunohistochemistry

Synapse density: satellite boutons

(AM1100109)

Number of satellite boutons

Immunostaining

Notochord morphogenesis

(AM1100110)

The morphogenetic process by which the notochord, a mesoderm-derived structure located ventral of the developing neural tube, is generated and organized. The notochord serves as a core around which other mesodermal cells form the vertebrae.

Microscopic analysis; General observations

Morphology of optic lobes

(AM1100111)

Size and organization of the optic lobes in Drosophila. Optic lobes are the largest structures in the fly brain containing the lamina, medulla and the lobula complex, which itself is made of the lobula and the lobula plate. The optic lobes develop from neuroepithelia: the inner proliferation center (IPC) and outer proliferation center (OPC)

General observations; Histology

Mushroom body development: mushroom body size

(AM1100112)

The process whose specific outcome is the progression of the mushroom body over time, from its formation to the mature structure. The mushroom body is composed of the prominent neuropil structures of the insect central brain, thought to be crucial for olfactory associated learning. These consist mainly of a bulbous calyx and tightly packaged arrays of thin parallel fibers of the Kenyon cells.

Mushroom body development: neuropil volume

(AM1100113)

The process whose specific outcome is the progression of the mushroom body over time, from its formation to the mature structure. The mushroom body is composed of the prominent neuropil structures of the insect central brain, thought to be crucial for olfactory associated learning. These consist mainly of a bulbous calyx and tightly packaged arrays of thin parallel fibers of the Kenyon cells.

Mushroom body development: kenyon cell: cell cluster volume

(AM1100114)

The process whose specific outcome is the progression of the mushroom body over time, from its formation to the mature structure. The mushroom body is composed of the prominent neuropil structures of the insect central brain, thought to be crucial for olfactory associated learning. These consist mainly of a bulbous calyx and tightly packaged arrays of thin parallel fibers of the Kenyon cells.

Mushroom body development: kenyon cell: cell size

(AM1100115)

The process whose specific outcome is the progression of the mushroom body over time, from its formation to the mature structure. The mushroom body is composed of the prominent neuropil structures of the insect central brain, thought to be crucial for olfactory associated learning. These consist mainly of a bulbous calyx and tightly packaged arrays of thin parallel fibers of the Kenyon cells.

Morphology of telencephalon

(AM1100121)

Size and organization of the adult telencephalon (zebrafish) constituting the anterial and dorsal forebrain neuromere

Histology

Morphology of optic tectum

(AM1100122)

Size and organization of the optic tectum, part of midbrain, in zebrafish it acts as the main visual processor

Histology

Cerebellar morphology: corpus cerebelli

(AM1100123)

Size and organization of corpus cerebelli (Cce), one of three parts of a teleost (zebrafish) cerebellum

Histology

Axonal architecture: axonal branch number

(AM1100124)

Number of axonal branches, cytoplasmic extensions that contain synaptic terminals.

Immunohistochemistry; Fluorescence microscopy

Axon architecture: axon length

(AM1100125)

Length of axon

Immunohistochemistry; Fluorescence microscopy

Synapse density: synaptic bouton number

(AM1100126)

Number of synaptic boutons, specialized area within the axon of the presynaptic cell that contains neurotransmitters enclosed in synaptic vesicles.

Immunohistochemistry; Fluorescence microscopy

Neuronal number: histamine

(AM1100127)

Number or density of neurons producing or storing histamine

Neuronal number: dopaminergic

(AM1100128)

Number or density of neurons producing dopamine

Neuroreceptor levels: histamine receptors: H1R

(AM1100129)

Levels of histamine receptor H1R expressed in neurons

Dendritic architecture: dendritic thickness

(AM1100130)

Thickness or width of dendrites in a specific neuron type

Golgi-Cox staining; Immunohistochemistry; Electron microscopy; Sholl analysis; Histology; Immunofluorescence staining

Neuroreceptor levels: vasopressin

(AM1100131)

Levels (number or density) of vasopressin receptors

Neuronal morphology

(AM1100132)

Overall structural characteristics of neurons as detected by histological or immunohistochemical assays

Anatomical projections and connectivity: neuromuscular junctions

(AM1100133)

The junction between the axon of a motor neuron and a muscle fiber.

Confocal microscopy

Axonal architecture: defasciculation

(AM1100134)

Separation of axons away from a bundle of axons known as a fascicle.

Confocal microscopy

Blood brain barrier permeability

(AM1100135)

Specialized packing of cells in the brain to prevent the passage of most molecules from the circulating blood into the brain, with the exception of lipid soluble molecules or those that are actively transported.

Blood brain barrier integrity test

Neuroreceptor levels: acetylcholine

(AM1100136)

Levels of acetylcholine receptors, nicotinic or ionotropic (nAChR) and muscarinic or metabotropic (mAChR), expressed in neurons

Neuronal number: sensory

(AM1100137)

Number of sensory neurons

Glial number

(AM1100138)

The absolute or relative number of glia in a defined region or the multiplication or reproduction of glial cells by cell division, resulting in the expansion of the glial population.

Morphology of the external capsule

(AM1100139)

Morphology of the area of white matter fiber tracts in the brain that run between the most lateral segment of the lentiform nucleus and the claustrum; the white matter of the external capsule contains fibers known as corticocortical association fibers which are responsible for connecting the cerebral cortex to another cortical area

Morphology of the internal capsule

(AM1100140)

Morphology of the area of white matter in the brain that lies between the lenticular and caudate nuclei, and contains a group of myelinated ascending and descending axonal fiber tracts that connects the cerebral cortex to the brain stem and spinal cord

Neuroreceptor levels: estrogen

(AM1100141)

Expression levels or numbers of estrogen receptors

Western blot

Neuronal differentiation

(AM1100142)

abnormality in the process whereby neural stem cells acquire specialized structural and functional features that characterize them as neurons

Neuronal specification

(AM1100143)

defects in the developmental patterning of neurons resulting in ectopic placement, decreased numbers or absence of mature neurons

Microglial number

(AM1100144)

atypical production of or inability to produce the small, migratory, phagocytic, interstitial cells derived from myeloid progenitor cells and found in the parenchyma of the central nervous system

Immunohistochemistry

Microglial morphology

(AM1100145)

any structural anomaly of microglia that are scavengers, engulfing dead cells and other debris

Immunohistochemistry

Neuronal degeneration

(AM1100146)

a retrogressive impairment of function or destruction of neural tissue

Immunohistochemistry

Radial glial cell number

(AM1100147)

anomaly in the number of the supporting cells of the developing central nervous system that guide neuronal migration during development and exchange metabolites with developing and migrating neurons; these cells differentiate into astrocytes and some neuronal types in the adult

Immunohistochemistry

Astrocyte number

(AM1100148)

reduction in the number of the large neuroglial (macroglial) cells in the central nervous system

Immunohistochemistry

Morphology of neuromuscular junction

(AM1100149)

structural characteristics of the membrane to membrane contact of a motor axon and a muscle myofiber that is responsible for the transmission of nerve impulses

Immunofluorescence staining

Motor neuron morphology

(AM1100150)

structural chanacteristics of cells that innervate an effector (muscle or glandular) tissue and are responsible for transmission of motor impulses

Immunofluorescence staining

Astrocyte morphology

(AM1100151)

structural characteristics of the large neuroglial (macroglial) cells in the central nervous system, astrocytes are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier; astrocytes regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury

Immunohistochemistry

Myelination: node of Ranvier morphology

(AM1100152)

Structure of the short unmyelinated segments of an axon between myelinated segments, where voltage gated channels accumulate and regenerate an action potential as it is conducted along the axon

Dendritic architecture: dendritic orientation

(AM1100153)

Orientation or direction of growth of dendrites in a specific neuron type

Neuronal number: retinal ganglion cells

(AM1500032)

Number of retinal ganglion cells in the retina

Histology