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Find video protocols related to scientific articles indexed in Pubmed.
CD44 regulates dendrite morphogenesis through Src tyrosine kinase-dependent positioning of the Golgi apparatus.
J. Cell. Sci.
PUBLISHED: 10-11-2014
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The acquisition of proper dendrite morphology is a critical aspect of neuronal development toward the formation of a functional network. The role of the extracellular matrix and its cellular receptors in this process has remained enigmatic. We report that CD44 adhesion molecule, the main hyaluronan receptor, is localized in dendrites and plays a crucial inhibitory role in dendritic tree arborization in vitro and in vivo. This novel function is exerted by the activation of Src tyrosine kinase, leading to the alteration of Golgi apparatus morphology. The mechanism operates during normal development, but its inhibition may have a protective influence on dendritic trees under toxic conditions, in which the silencing of CD44 expression prevented dendritic shortening induced by glutamate exposure. Overall, our results indicate a novel role for CD44 as an essential regulator of dendritic arbor complexity in both health and disease.
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A compartment model of alveolar-capillary oxygen diffusion with ventilation-perfusion gradient and dynamics of air transport through the respiratory tract.
Comput. Biol. Med.
PUBLISHED: 04-21-2014
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This paper presents a model of alveolar-capillary oxygen diffusion with dynamics of air transport through the respiratory tract. For this purpose electrical model representing the respiratory tract mechanics and differential equations representing oxygen membrane diffusion are combined. Relevant thermodynamic relations describing the mass of oxygen transported into the human body are proposed as the connection between these models, as well as the influence of ventilation-perfusion mismatch on the oxygen diffusion. The model is verified based on simulation results of varying exercise intensities and statistical calculations of the results obtained during various clinical trials. The benefit of the approach proposed is its application in simulation-based research aimed to generate quantitative data of normal and pathological conditions. Based on the model presented, taking into account many essential physiological processes and air transport dynamics, comprehensive and combined studies of the respiratory efficiency can be performed. The impact of physical exercise, precise changes in respiratory tract mechanics and alterations in breathing pattern can be analyzed together with the impact of various changes in alveolar-capillary oxygen diffusion. This may be useful in simulation of effects of many severe medical conditions and increased activity level.
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Mutations in cytoplasmic dynein and its regulators cause malformations of cortical development and neurodegenerative diseases.
Biochem. Soc. Trans.
PUBLISHED: 11-22-2013
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Neurons are highly specialized for the processing and transmission of electrical signals and use cytoskeleton-based motor proteins to transport different vesicles and cellular materials. Abnormalities in intracellular transport are thought to be a critical factor in the degeneration and death of neurons in both the central and peripheral nervous systems. Several recent studies describe disruptive mutations in the minus-end-directed microtubule motor cytoplasmic dynein that are directly linked to human motor neuropathies, such as SMA (spinal muscular atrophy) and axonal CMT (Charcot-Marie-Tooth) disease or malformations of cortical development, including lissencephaly, pachygyria and polymicrogyria. In addition, genetic defects associated with these and other neurological disorders have been found in multifunctional adaptors that regulate dynein function, including the dynactin subunit p150Glued, BICD2 (Bicaudal D2), Lis-1 (lissencephaly 1) and NDE1 (nuclear distribution protein E). In the present paper we provide an overview of the disease-causing mutations in dynein motors and regulatory proteins that lead to a broad phenotypic spectrum extending from peripheral neuropathies to cerebral malformations.
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[Why do we need induced pluripotent stem cells in neurobiology?].
Postepy Biochem.
PUBLISHED: 09-19-2013
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Reprogramming of somatic cells made possible to study in vitro inaccessible human cells, such as different types of neurons. Almost immediate consequence of the emergence of this technology was the development of a number of cellular models of the nervous system diseases. They are used both to explore the cellular mechanisms of these diseases and for the development of new pharmacological strategies. Reprogrammed cells are also a potential alternative to embryonic stem cells for transplantation. This article presents the most important achievements in the use of cell reprogramming technology in neurobiology and at the same time points out the limitations of the methodology and the expected directions of its development.
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Brain-derived neurotrophic factor induces matrix metalloproteinase 9 expression in neurons via the serum response factor/c-Fos pathway.
Mol. Cell. Biol.
PUBLISHED: 03-18-2013
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Brain-derived neurotrophic factor (BDNF) plays a pivotal role in the regulation of the transcription of genes that encode proplasticity proteins. In the present study, we provide evidence that stimulation of rat primary cortical neurons with BDNF upregulates matrix metalloproteinase 9 (MMP-9) mRNA and protein levels and increases enzymatic activity. The BDNF-induced MMP-9 transcription was dependent on extracellular signal-regulated kinase 1/2 (ERK1/2) pathway and c-Fos expression. Overexpression of AP-1 dimers in neurons led to MMP-9 promoter activation, with the most potent being those that contained c-Fos, whereas knockdown of endogenous c-Fos by small hairpin RNA (shRNA) reduced BDNF-mediated MMP-9 transcription. Additionally, mutation of the proximal AP-1 binding site in the MMP-9 promoter inhibited the activation of MMP-9 transcription. BDNF stimulation of neurons induced binding of endogenous c-Fos to the proximal MMP-9 promoter region. Furthermore, as the c-Fos gene is a known target of serum response factor (SRF), we investigated whether SRF contributes to MMP-9 transcription. Inhibition of SRF and its cofactors by either overexpression of dominant negative mutants or shRNA decreased MMP-9 promoter activation. In contrast, MMP-9 transcription was not dependent on CREB activity. Finally, we showed that neuronal activity stimulates MMP-9 transcription in a tyrosine kinase receptor B (TrkB)-dependent manner.
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Cyr61, a matricellular protein, is needed for dendritic arborization of hippocampal neurons.
J. Biol. Chem.
PUBLISHED: 01-28-2013
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The shape of the dendritic arbor is one of the criteria of neuron classification and reflects functional specialization of particular classes of neurons. The development of a proper dendritic branching pattern strongly relies on interactions between the extracellular environment and intracellular processes responsible for dendrite growth and stability. We previously showed that mammalian target of rapamycin (mTOR) kinase is crucial for this process. In this work, we performed a screen for modifiers of dendritic growth in hippocampal neurons, the expression of which is potentially regulated by mTOR. As a result, we identified Cyr61, an angiogenic factor with unknown neuronal function, as a novel regulator of dendritic growth, which controls dendritic growth in a ?1-integrin-dependent manner.
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A new approach to modeling of selected human respiratory system diseases, directed to computer simulations.
Comput. Biol. Med.
PUBLISHED: 01-17-2013
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This paper presents a new versatile approach to model severe human respiratory diseases via computer simulation. The proposed approach enables one to predict the time histories of various diseases via information accessible in medical publications. This knowledge is useful to bioengineers involved in the design and construction of medical devices that are employed for monitoring of respiratory condition. The approach provides the data that are crucial for testing diagnostic systems. This can be achieved without the necessity of probing the physiological details of the respiratory system as well as without identification of parameters that are based on measurement data.
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Spatiotemporal characterization of mTOR kinase activity following kainic acid induced status epilepticus and analysis of rat brain response to chronic rapamycin treatment.
PLoS ONE
PUBLISHED: 01-01-2013
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Mammalian target of rapamycin (mTOR) is a protein kinase that senses nutrient availability, trophic factors support, cellular energy level, cellular stress, and neurotransmitters and adjusts cellular metabolism accordingly. Adequate mTOR activity is needed for development as well as proper physiology of mature neurons. Consequently, changes in mTOR activity are often observed in neuropathology. Recently, several groups reported that seizures increase mammalian target of rapamycin (mTOR) kinase activity, and such increased activity in genetic models can contribute to spontaneous seizures. However, the current knowledge about the spatiotemporal pattern of mTOR activation induced by proconvulsive agents is rather rudimentary. Also consequences of insufficient mTOR activity on a status epilepticus are poorly understood. Here, we systematically investigated these two issues. We showed that mTOR signaling was activated by kainic acid (KA)-induced status epilepticus through several brain areas, including the hippocampus and cortex as well as revealed two waves of mTOR activation: an early wave (2 h) that occurs in neurons and a late wave that predominantly occurs in astrocytes. Unexpectedly, we found that pretreatment with rapamycin, a potent mTOR inhibitor, gradually (i) sensitized animals to KA treatment and (ii) induced gross anatomical changes in the brain.
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NMDA receptor activation suppresses microtubule growth and spine entry.
J. Neurosci.
PUBLISHED: 06-03-2011
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Dynamic microtubules are important to maintain neuronal morphology and function, but whether neuronal activity affects the organization of dynamic microtubules is unknown. Here, we show that a protocol to induce NMDA-dependent long-term depression (LTD) rapidly attenuates microtubule dynamics in primary rat hippocampal neurons, removing the microtubule-binding protein EB3 from the growing microtubule plus-ends in dendrites. This effect requires the entry of calcium and is mediated by activation of NR2B-containing NMDA-type glutamate receptor. The rapid NMDA effect is followed by a second, more prolonged response, during which EB3 accumulates along MAP2-positive microtubule bundles in the dendritic shaft. MAP2 is both required and sufficient for this activity-dependent redistribution of EB3. Importantly, NMDA receptor activation suppresses microtubule entry in dendritic spines, whereas overexpression of EB3-GFP prevents NMDA-induced spine shrinkage. These results suggest that short-lasting and long-lasting changes in dendritic microtubule dynamics are important determinants for NMDA-induced LTD.
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Zipcode binding protein 1 regulates the development of dendritic arbors in hippocampal neurons.
J. Neurosci.
PUBLISHED: 04-08-2011
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The pattern of dendritic branching, together with the density of synapses and receptor composition, defines the electrical properties of a neuron. The development of the dendritic arbor and its additional stabilization are highly orchestrated at the molecular level and are guided by intrinsic mechanisms and extracellular information. Although protein translation is known to contribute to these processes, the role of its local component has not been fully explored. For local translation, mRNAs are transported to dendrites in their dormant form as ribonucleoparticles (RNPs). We hypothesized that disturbing spatial mRNA distribution via RNP targeting may result in severe underdevelopment of the dendritic arbor. Zipcode binding protein 1 (ZBP1) controls ?-actin mRNA transport and translation in dendrites. We showed that proper cellular levels of ZBP1, its ability to engage in mRNA binding, and Src-dependent release of mRNA cargo from ZBP1 are vital for dendritic arbor development in cultured rat hippocampal neurons. Moreover, ?-actin overexpression significantly alleviated the effects of ZBP1 knockdown. These results suggest that ZBP1-dependent dendritic mRNA transport contributes to proper dendritic branching.
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CLIP-170 and IQGAP1 cooperatively regulate dendrite morphology.
J. Neurosci.
PUBLISHED: 03-25-2011
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Dendritic arbors are compartments of neurons dedicated to receiving synaptic inputs. Their shape is an outcome of both the intrinsic genetic program and environmental signals. The microtubules and actin cytoskeleton are both crucial for proper dendritic morphology, but how they interact is unclear. The present study demonstrates that microtubule plus-end tracking protein CLIP-170 and actin-binding protein IQGAP1 regulate dendrite morphology of rat neurons by coordinating the interaction between microtubules and the actin cytoskeleton. Moreover, we show that mTOR kinase interacts with CLIP-170 and is needed for efficient formation of a protein complex containing CLIP-170 and IQGAP1. Dynamic microtubules, CLIP-170, and IQGAP1 are required for proper dendritic arbor morphology and PI3K-mTOR-induced increase in dendritic arbor complexity. Moreover, CLIP-170 and IQGAP1 knockdown modulates dendritic arbor growth via regulation of the actin cytoskeleton. We postulate that mTOR controls dendritic arbor morphology by enhancing cross talk between dynamic microtubules and actin through CLIP-170 and IQGAP1.
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2-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family.
Nucleic Acids Res.
PUBLISHED: 02-09-2011
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The 5 cap of human messenger RNA consists of an inverted 7-methylguanosine linked to the first transcribed nucleotide by a unique 5-5 triphosphate bond followed by 2-O-ribose methylation of the first and often the second transcribed nucleotides, likely serving to modify efficiency of transcript processing, translation and stability. We report the validation of a human enzyme that methylates the ribose of the second transcribed nucleotide encoded by FTSJD1, henceforth renamed HMTR2 to reflect function. Purified recombinant hMTr2 protein transfers a methyl group from S-adenosylmethionine to the 2-O-ribose of the second nucleotide of messenger RNA and small nuclear RNA. Neither N(7) methylation of the guanosine cap nor 2-O-ribose methylation of the first transcribed nucleotide are required for hMTr2, but the presence of cap1 methylation increases hMTr2 activity. The hMTr2 protein is distributed throughout the nucleus and cytosol, in contrast to the nuclear hMTr1. The details of how and why specific transcripts undergo modification with these ribose methylations remains to be elucidated. The 2-O-ribose RNA cap methyltransferases are present in varying combinations in most eukaryotic and many viral genomes. With the capping enzymes in hand their biological purpose can be ascertained.
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Distinct molecular regulation of glycogen synthase kinase-3alpha isozyme controlled by its N-terminal region: functional role in calcium/calpain signaling.
J. Biol. Chem.
PUBLISHED: 01-25-2011
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Glycogen synthase kinase-3 (GSK-3) is expressed as two isozymes ? and ?. They share high similarity in their catalytic domains but differ in their N- and C-terminal regions, with GSK-3? having an extended glycine-rich N terminus. Here, we undertook live cell imaging combined with molecular and bioinformatic studies to understand the distinct functions of the GSK-3 isozymes focusing on GSK-3? N-terminal region. We found that unlike GSK-3?, which shuttles between the nucleus and cytoplasm, GSK-3? was excluded from the nucleus. Deletion of the N-terminal region of GSK-3? resulted in nuclear localization, and treatment with leptomycin B resulted in GSK-3? accumulation in the nucleus. GSK-3? rapidly accumulated in the nucleus in response to calcium or serum deprivation, and accumulation was strongly inhibited by the calpain inhibitor calpeptin. This nuclear accumulation was not mediated by cleavage of the N-terminal region or phosphorylation of GSK-3?. Rather, we show that calcium-induced GSK-3? nuclear accumulation was governed by GSK-3? binding with as yet unknown calpain-sensitive protein or proteins; this binding was mediated by the N-terminal region. Bioinformatic and experimental analyses indicated that nuclear exclusion of GSK-3? was likely an exclusive characteristic of mammalian GSK-3?. Finally, we show that nuclear localization of GSK-3? reduced the nuclear pool of ?-catenin and its target cyclin D1. Taken together, these data suggest that the N-terminal region of GSK-3? is responsible for its nuclear exclusion and that binding with a calcium/calpain-sensitive product enables GSK-3? nuclear retention. We further uncovered a novel link between calcium and nuclear GSK-3?-mediated inhibition of the canonical Wnt/?-catenin pathway.
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The dissection of transcriptional modules regulated by various drugs of abuse in the mouse striatum.
Genome Biol.
PUBLISHED: 02-09-2010
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Various drugs of abuse activate intracellular pathways in the brain reward system. These pathways regulate the expression of genes that are essential to the development of addiction. To reveal genes common and distinct for different classes of drugs of abuse, we compared the effects of nicotine, ethanol, cocaine, morphine, heroin and methamphetamine on gene expression profiles in the mouse striatum.
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Biochemical characterization and expression analysis of a novel EF-hand Ca2+ binding protein calmyrin2 (Cib2) in brain indicates its function in NMDA receptor mediated Ca2+ signaling.
Arch. Biochem. Biophys.
PUBLISHED: 01-30-2009
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Calmyrin2 (CaMy2, Cib2) is a novel EF-hand calcium-binding protein found recently in skeletal muscles. CaMy2 mRNA was also detected in brain, but nothing is known about CaMy2 protein localization and properties in the brain. We report cloning and characterization of CaMy2 in rat brain: its expression pattern, intracellular localization and biochemical features. CaMy2 binds Ca2+ and exhibits Ca2+/conformational switch. Moreover, CaMy2 undergoes N-myristoylation without Ca2+/myristoyl switch, is membrane-associated and localizes in neurons together with Golgi apparatus and dendrite markers. CaMy2 transcript and protein are present mainly in the hippocampus and cortex. In cultured hippocampal neurons, CaMy2 is induced upon neuronal activation. Most prominent increase in CaMy2 protein (7-fold), and mRNA (2-fold) occurs upon stimulation of NMDA receptor (NMDAR). The induction is blocked by translation inhibitors, specific antagonists of NMDAR, the Ca2+-chelator BAPTA, and inhibitors of ERK1/2 and PKC, kinases transmitting NMDAR-linked Ca2+ signal. Our results show that CaMy2 level is controlled by NMDAR and Ca2+ and suggest CaMy2 role in Ca2+ signaling underlying NMDAR activation.
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Dynamic microtubules regulate dendritic spine morphology and synaptic plasticity.
Neuron
PUBLISHED: 01-17-2009
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Dendritic spines are the major sites of excitatory synaptic input, and their morphological changes have been linked to learning and memory processes. Here, we report that growing microtubule plus ends decorated by the microtubule tip-tracking protein EB3 enter spines and can modulate spine morphology. We describe p140Cap/SNIP, a regulator of Src tyrosine kinase, as an EB3 interacting partner that is predominantly localized to spines and enriched in the postsynaptic density. Inhibition of microtubule dynamics, or knockdown of either EB3 or p140Cap, modulates spine shape via regulation of the actin cytoskeleton. Fluorescence recovery after photobleaching revealed that EB3-binding is required for p140Cap accumulation within spines. In addition, we found that p140Cap interacts with Src substrate and F-actin-binding protein cortactin. We propose that EB3-labeled growing microtubule ends regulate the localization of p140Cap, control cortactin function, and modulate actin dynamics within dendritic spines, thus linking dynamic microtubules to spine changes and synaptic plasticity.
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Beyond control of protein translation: what we have learned about the non-canonical regulation and function of mammalian target of rapamycin (mTOR).
Biochim. Biophys. Acta
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Mammalian target of rapamycin (mTOR) is a serine-threonine kinase involved in almost every aspect of mammalian cell function. This kinase was initially believed to control protein translation in response to amino acids and trophic factors, and this function has become a canonical role for mTOR. However, mTOR can form two separate protein complexes (mTORCs). Recent advances clearly demonstrate that both mTORCs can respond to various stimuli and change myriad cellular processes. Therefore, our current view of the cellular roles of TORCs has rapidly expanded and cannot be fully explained without appreciating recent findings about the new modes of mTOR regulation and identification of non-canonical effectors of mTOR that contribute to transcription, cytoskeleton dynamics, and membrane trafficking. This review discusses the molecular details of these newly discovered non-canonical functions that allow mTORCs to control the cellular environment at multiple levels. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
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Functional anatomy of neural circuits regulating fear and extinction.
Proc. Natl. Acad. Sci. U.S.A.
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The memory of fear extinction is context dependent: fear that is suppressed in one context readily renews in another. Understanding of the underlying neuronal circuits is, therefore, of considerable clinical relevance for anxiety disorders. Prefrontal cortical and hippocampal inputs to the amygdala have recently been shown to regulate the retrieval of fear memories, but the cellular organization of these projections remains unclear. By using anterograde tracing in a transgenic rat in which neurons express a dendritically-targeted PSD-95:Venus fusion protein under the control of a c-fos promoter, we found that, during the retrieval of extinction memory, the dominant input to active neurons in the lateral amygdala was from the infralimbic cortex, whereas the retrieval of fear memory was associated with greater hippocampal and prelimbic inputs. This pattern of retrieval-related afferent input was absent in the central nucleus of the amygdala. Our data show functional anatomy of neural circuits regulating fear and extinction, providing a framework for therapeutic manipulations of these circuits.
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Mammalian target of rapamycin complex 1 (mTORC1) and 2 (mTORC2) control the dendritic arbor morphology of hippocampal neurons.
J. Biol. Chem.
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Dendrites are the main site of information input into neurons. Their development is a multistep process controlled by mammalian target of rapamycin (mTOR) among other proteins. mTOR is a serine/threonine protein kinase that forms two functionally distinct complexes in mammalian cells: mTORC1 and mTORC2. However, the one that contributes to mammalian neuron development remains unknown. This work used short hairpin RNA against Raptor and Rictor, unique components of mTORC1 and mTORC2, respectively, to dissect mTORC involvement in this process. We provide evidence that both mTOR complexes are crucial for the proper dendritic arbor morphology of hippocampal neurons. These two complexes are required for dendritic development both under basal conditions and upon the induction of mTOR-dependent dendritic growth. We also identified Akt as a downstream effector of mTORC2 needed for proper dendritic arbor morphology, the action of which required mTORC1 and p70S6K1.
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Total-tau in cerebrospinal fluid of patients with multiple sclerosis decreases in secondary progressive stage of disease and reflects degree of brain atrophy.
Ups. J. Med. Sci.
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Tau protein is a potential marker of neuronal damage. The aim of the study is to investigate its potential role as a marker of brain atrophy in multiple sclerosis (MS).
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Sub-micrometer particles produced by a low-powered AC electric arc in liquids.
J Nanosci Nanotechnol
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The article presents the report of the production of composites of sub-micrometer metal particles in matrix consisted of the metal compounds by means of an AC electric arc in water and paraffin solutions using electrodes carbon-metal and metal-metal (metal: Ni, Fe, Co, Cu). The advantage of this method is the low electric power (from 5 to 10 W) needed in comparison to standard DC arc-discharge methods (0.8 to 3 kW). This method enables the production of particles from conductive material also in wide range of temperature and in solvent which could be either transparent to light or opaque. Moreover the solvent can be electrolyte or insulating liquid. The microstructure of the composite layer was investigated by scanning electron microscopy (SEM), Electron Probe Microanalysis (EPMA) and X-ray. During particles production in water metal oxides were created. Additionally using cobalt-copper, nickel-copper as couple electrodes, insoluble in water copper (II) hydroxide crystal grains were created additionally which crystals shape was depended on transition metal. For iron-copper couple electrodes system the copper (II) hydroxide was not formed. Experiments with sequence production of Ni and Fe particles with C electrode assisting in molten paraffin let to obtain both Ni and Fe particles surrounded by paraffin. After solidification the material was insulator but if locally magnetic field influenced on the liquid solution in that place after solidification a new composite was created which was electric current conductor with resistivity around 0.1 omega x m, was attracted by magnetic field and presented magneto resistance around 0.4% in changing magnetic field in a range 150 mT. After mixing the concentrated paraffin with normal paraffin resistivity of the mixture increased and it became photosensitive and created small voltage under light influence.
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Developmental plasticity of the dendritic compartment: focus on the cytoskeleton.
Adv. Exp. Med. Biol.
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Plasticity, the ability to undergo lasting changes in response to a stimulus, is an important attribute of neurons. It allows proper development and underlies learning, memory, and the recovery of the nervous system after severe injuries. Often, an outcome of neuronal plasticity is a structural plasticity manifested as a change of neuronal morphology. In this chapter, we focus on the structural plasticity of dendritic arbors and spines during development. Dendrites receive and compute synaptic inputs from other neurons. The number of dendrites and their branching pattern are strictly correlated with the function of a particular neuron and the geometry of the connections it receives. The development of proper dendritic tree morphology depends on the interplay between genetic programming and extracellular signals. Spines are tiny actin-rich dendritic protrusions that harbor excitatory synapses. No consensus has been reached regarding how dendritic spines form, and several models of spine morphogenesis exist. Nevertheless, most researchers agree that spinogenesis is an important target for structural plasticity. In this chapter, we discuss examples of such plasticity and describe the principles and molecular mechanisms underlying this process, focusing mostly on the regulation of the cytoskeleton during dendrito- and spinogenesis.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.