<meta charset="utf8"></head><body>Neurolucida 360 Kullanılarak Dendritik Omurga Analizi Protokolü

<ol>
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C., Lu, J., Zuo, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatiotemporal+dynamics+of+dendritic+spines+in+the+living+brain.">Spatiotemporal dynamics of dendritic spines in the living brain.</a> Front Neuroanat. 8, 28 (2014).</li><li>Dickstein, D. L., Weaver, C. M., Luebke, J. I., Hof, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dendritic+spine+changes+associated+with+normal+aging.">Dendritic spine changes associated with normal aging.</a> Neuroscience. 251, 21-32 (2013).</li><li>Glausier, J. R., Lewis, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dendritic+spine+pathology+in+schizophrenia.">Dendritic spine pathology in schizophrenia.</a> Neuroscience. 251, 90-107 (2013).</li><li>Phillips, M., Pozzo-Miller, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dendritic+spine+dysgenesis+in+autism+related+disorders.">Dendritic spine dysgenesis in autism related disorders.</a> Neurosci Lett. 601, 30-40 (2015).</li><li>Dorostkar, M. M., Zou, C., Blazquez-Llorca, L., Herms, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analyzing+dendritic+spine+pathology+in+alzheimer's+disease:+Problems+and+opportunities.">Analyzing dendritic spine pathology in alzheimer's disease: Problems and opportunities.</a> Acta Neuropathol. 130 (1), 1-19 (2015).</li><li>Villalba, R. M., Smith, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Loss+and+remodeling+of+striatal+dendritic+spines+in+parkinson's+disease:+From+homeostasis+to+maladaptive+plasticity.">Loss and remodeling of striatal dendritic spines in parkinson's disease: From homeostasis to maladaptive plasticity.</a> J Neural Transm (Vienna). 125 (3), 431-447 (2018).</li><li>Cheng, C., Trzcinski, O., Doering, L. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescent+labeling+of+dendritic+spines+in+cell+cultures+with+the+carbocyanine+dye+&amp;#34;dii&amp;#34.">Fluorescent labeling of dendritic spines in cell cultures with the carbocyanine dye &amp;#34;dii&amp;#34.</a> Front Neuroanat. 8, 30 (2014).</li><li>Feng, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+neuronal+subsets+in+transgenic+mice+expressing+multiple+spectral+variants+of+gfp.">Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of gfp.</a> Neuron. 28 (1), 41-51 (2000).</li><li>Baloyannis, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Staining+neurons+with+golgi+techniques+in+degenerative+diseases+of+the+brain.">Staining neurons with golgi techniques in degenerative diseases of the brain.</a> Neural Regen Res. 10 (5), 693-695 (2015).</li><li>Levet, F., Tonnesen, J., Nagerl, U. V., Sibarita, J. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SpineJ:+A+software+tool+for+quantitative+analysis+of+nanoscale+spine+morphology.">SpineJ: A software tool for quantitative analysis of nanoscale spine morphology.</a> Methods. 174, 49-55 (2020).</li><li>Peters, A., Kaiserman-Abramof, I. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+small+pyramidal+neuron+of+the+rat+cerebral+cortex.+The+perikaryon,+dendrites+and+spines.">The small pyramidal neuron of the rat cerebral cortex. The perikaryon, dendrites and spines.</a> Am J Anat. 127 (4), 321-356 (1970).</li><li>Pfeiffer, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chronic+2p-sted+imaging+reveals+high+turnover+of+dendritic+spines+in+the+hippocampus+in+vivo.">Chronic 2p-sted imaging reveals high turnover of dendritic spines in the hippocampus in vivo.</a> Elife. 7, e34700 (2018).</li><li>Harris, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure,+development,+and+plasticity+of+dendritic+spines.">Structure, development, and plasticity of dendritic spines.</a> Curr Opin Neurobiol. 9 (3), 343-348 (1999).</li><li>Hering, H., Sheng, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dendritic+spines:+Structure,+dynamics,+and+regulation.">Dendritic spines: Structure, dynamics, and regulation.</a> Nat Rev Neurosci. 2 (12), 880-888 (2001).</li><li>Jontes, J. D., Smith, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Filopodia,+spines,+and+the+generation+of+synaptic+diversity.">Filopodia, spines, and the generation of synaptic diversity.</a> Neuron. 27 (1), 11-14 (2000).</li><li>Pchitskaya, E., Bezprozvanny, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dendritic+spines+shape+analysis-classification+or+clusterization?+Perspective.">Dendritic spines shape analysis-classification or clusterization? Perspective.</a> Front Synaptic Neurosci. 12, 31 (2020).</li><li>Berry, K. P., Nedivi, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spine+dynamics:+Are+they+all+the+same.">Spine dynamics: Are they all the same.</a> Neuron. 96 (1), 43-55 (2017).</li><li>Rodriguez, A., Ehlenberger, D. B., Dickstein, D. L., Hof, P. R., Wearne, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+three-dimensional+detection+and+shape+classification+of+dendritic+spines+from+fluorescence+microscopy+images.">Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images.</a> PLoS One. 3 (4), e1997 (2008).</li><li>Swanger, S. A., Yao, X., Gross, C., Bassell, G. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+4D+analysis+of+dendritic+spine+morphology:+Applications+to+stimulus-induced+spine+remodeling+and+pharmacological+rescue+in+disease+model.">Automated 4D analysis of dendritic spine morphology: Applications to stimulus-induced spine remodeling and pharmacological rescue in disease model.</a> Mol Brain. 4, 38 (2011).</li><li>Basu, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+3-D+morphometric+analysis+of+individual+dendritic+spines.">Quantitative 3-D morphometric analysis of individual dendritic spines.</a> Sci Rep. 8 (1), 3545 (2018).</li><li>Ekaterina, P., Peter, V., Smirnova, D., Vyacheslav, C., Ilya, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spinetool+is+an+open-source+software+for+analysis+of+morphology+of+dendritic+spines.">Spinetool is an open-source software for analysis of morphology of dendritic spines.</a> Sci Rep. 13 (1), 10561 (2023).</li><li>Li, B. Z., Sumera, A., Booker, S. A., Mccullagh, E. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Current+best+practices+for+analysis+of+dendritic+spine+morphology+and+number+in+neurodevelopmental+disorder+research.">Current best practices for analysis of dendritic spine morphology and number in neurodevelopmental disorder research.</a> ACS Chem Neurosci. 14 (9), 1561-1572 (2023).</li><li>Dickstein, D. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automatic+dendritic+spine+quantification+from+confocal+data+with+Neurolucida+360.">Automatic dendritic spine quantification from confocal data with Neurolucida 360.</a> Curr Protoc Neurosci. 77, 1-21 (2016).</li><li>Gage, G. J., Kipke, D. R., Shain, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole+animal+perfusion+fixation+for+rodents.">Whole animal perfusion fixation for rodents.</a> J Vis Exp. (65), e3564 (2012).</li><li>Parajuli, L. K., Koike, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional+structure+of+dendritic+spines+revealed+by+volume+electron+microscopy+techniques.">Three-dimensional structure of dendritic spines revealed by volume electron microscopy techniques.</a> Front Neuroanat. 15, 627368 (2021).</li><li>Ferreira, J. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Distance-dependent+regulation+of+NMDAR+nanoscale+organization+along+hippocampal+neuron+dendrites.">Distance-dependent regulation of NMDAR nanoscale organization along hippocampal neuron dendrites.</a> Proc Natl Acad Sci U S A. 117 (39), 24526-24533 (2020).</li><li>Megias, M., Emri, Z. s., Freund, T. F., Gulyas, A. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Total+number+and+distribution+of+inhibitory+and+excitatory+synapses+on+hippocampal+ca1+pyramidal+cells.">Total number and distribution of inhibitory and excitatory synapses on hippocampal ca1 pyramidal cells.</a> Neuroscience. 102 (3), 527-540 (2001).</li><li>Katz, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synapse+distribution+suggests+a+two-stage+model+of+dendritic+integration+in+ca1+pyramidal+neurons.">Synapse distribution suggests a two-stage model of dendritic integration in ca1 pyramidal neurons.</a> Neuron. 63 (2), 171-177 (2009).</li><li>Bourne, J., Harris, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Do+thin+spines+learn+to+be+mushroom+spines+that+remember.">Do thin spines learn to be mushroom spines that remember.</a> Curr Opin Neurobiol. 17 (3), 381-386 (2007).</li><li>Runge, K., Cardoso, C., De Chevigny, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dendritic+spine+plasticity:+Function+and+mechanisms.">Dendritic spine plasticity: Function and mechanisms.</a> Front Synaptic Neurosci. 12, 36 (2020).</li><li>Tonnesen, J., Katona, G., Rozsa, B., Nagerl, U. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spine+neck+plasticity+regulates+compartmentalization+of+synapses.">Spine neck plasticity regulates compartmentalization of synapses.</a> Nat Neurosci. 17 (5), 678-685 (2014).</li><li>Mattila, P. K., Lappalainen, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Filopodia:+Molecular+architecture+and+cellular+functions.">Filopodia: Molecular architecture and cellular functions.</a> Nat Rev Mol Cell Biol. 9 (6), 446-454 (2008).</li><li>Grutzendler, J., Kasthuri, N., Gan, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Long-term+dendritic+spine+stability+in+the+adult+cortex.">Long-term dendritic spine stability in the adult cortex.</a> Nature. 420 (6917), 812-816 (2002).</li></ol>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>518F Immersion Oil</td>
			<td>Zeiss</td>
			<td>444960-0000-000</td>
			<td></td>
		</tr>
		<tr>
			<td>Cryostat</td>
			<td>Leica</td>
			<td>CM3050S</td>
			<td>For slice preparation</td>
		</tr>
		<tr>
			<td>Fine Forceps</td>
			<td>FST</td>
			<td>11150-10</td>
			<td></td>
		</tr>
		<tr>
			<td>Hemostat Forceps</td>
			<td>FST</td>
			<td>13020-12</td>
			<td></td>
		</tr>
		<tr>
			<td>Large Surgical Scissors</td>
			<td>FST</td>
			<td>14002-16</td>
			<td></td>
		</tr>
		<tr>
			<td>LSM 880 Confocal Microscope</td>
			<td>Zeiss</td>
			<td>LSM 880</td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope Cover Glass</td>
			<td>Fisherbrand</td>
			<td>12-541-035</td>
			<td></td>
		</tr>
		<tr>
			<td>Mini-Peristaltic Pump II</td>
			<td>Harvard Apparatus</td>
			<td>70-2027</td>
			<td>For perfusions</td>
		</tr>
		<tr>
			<td>Neurolucida 360</td>
			<td>MBF Bioscience</td>
			<td>v2022.1.1</td>
			<td>Spine Analysis Software</td>
		</tr>
		<tr>
			<td>Neurolucida Explorer</td>
			<td>MBF Bioscience</td>
			<td>v2022.1.1</td>
			<td>Spine Analysis Software</td>
		</tr>
		<tr>
			<td>OCT Compound</td>
			<td>Sakura Finetek</td>
			<td>4583</td>
			<td>For cryostat sectioning</td>
		</tr>
		<tr>
			<td>Paraformaldehyde (37%)</td>
			<td>Fisherbrand</td>
			<td>F79-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Plan-Apochromat 63x/1.40 Oil DIC</td>
			<td>Zeiss</td>
			<td>440762-9904-000</td>
			<td></td>
		</tr>
		<tr>
			<td>Scalpel Blade</td>
			<td>FST</td>
			<td>10022-00</td>
			<td></td>
		</tr>
		<tr>
			<td>Small Surgical Scissors</td>
			<td>FST</td>
			<td>14060-09</td>
			<td></td>
		</tr>
		<tr>
			<td>Spatula&#160;</td>
			<td>FST</td>
			<td>10091-12</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>FIsherbrand</td>
			<td>S5-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Superfrost Plus Microslides</td>
			<td>Diagger</td>
			<td>ES4951+</td>
			<td></td>
		</tr>
		<tr>
			<td>Vectashield HardSet Mounting Medium</td>
			<td>Vector Laboratories</td>
			<td>H-1400-10</td>
			<td></td>
		</tr>
	</tbody>
</table>

dendritic spine quantification using an automatic three-dimensional neuron reconstruction software

Dendritic spines are protrusions of dendrites often comprising the post-synaptic site of glutamatergic synapses1,2. Dendritic spines are of particular interest in the field of synaptic plasticity. Spines are often altered when synaptic strength changes, becoming larger and stronger in long-term synaptic potentiation or smaller and weaker in long-term synaptic depression3,4,5,6,7. Beyond synaptic plasticity, the profile of dendritic spines changes throughout the lifespan. In early development, there is a period of dendritic spine formation and growth, followed by dendritic spine pruning until reaching a steady state8,9,10. In the aging brain, spine loss accompanies brain shrinkage and cognitive decline11. Additionally, many neurological, neurodegenerative, and psychiatric disorders are characterized by aberrant dendritic spines. Multiple brain regions in individuals affected with schizophrenia have fewer dendritic spines, likely resulting from altered synaptic pruning12. Autism spectrum disorders are also characterized by dendritic spine pathologies13. Dendritic spine loss is a hallmark of both Alzheimer&#39;s and Parkinson&#39;s disease14,15. Given the wide array of research topics encompassing investigations into dendritic spine properties, techniques for accurate spine quantification are of paramount importance.
Staining, i.e., the Golgi method, or labeling neurons via dye filling or expressing fluorescent proteins are common methods for dendritic spine visualization16,17,18. Once visualized, spines can be analyzed with a variety of free and commercially available software clients. The desired output of the analysis is an important factor in determining which software will be of the most use. Fiji is a viable software option for questions centered around dendritic spine density. However, this technique largely relies on time consuming manual counting that can introduce the potential for bias. New plugins such as SpineJ allow for automatic quantification, additionally allowing for more accurate spine neck analysis19. A drawback of these approaches is the loss of a three-dimensional analysis for determining spine volume, as SpineJ is limited to two-dimensional image stacks. Additionally, obtaining spine subtype information becomes challenging via these processes. The four predominant spine subtypes, thin, mushroom, stubby, and filopodia, all connote individual functions and are largely classified via morphology20. Thin spines are characterized by an elongated neck and defined head21. Mushroom spines have a much larger and pronounced spine head22. Stubby spines are short and have little variance between head and neck23. Filopodia are immature spines with a long, thin neck and no obviously observable head24. While classification provides valuable information, spines exist on a continuum of dimensions. Classification into categories is based on ranges of morphological measurements25,26. Manually measuring spines for classification compounds the logistical burden for researchers in this approach.
Other software options focusing specifically on three-dimensional dendritic spine analysis are better suited for investigations into spine volume and subtype properties27,28,29,30,31. Despite the difficulty presented by three-dimensional analysis, such as poor z-plane resolution and smear, these software options allow for reliable three-dimensional reconstruction of dendrites and dendritic spines in a user-guided semi-automated fashion. Automatic classification of identified spines into their subtypes is also a feature present in some of these spine analysis software packages. This can ameliorate concerns of potential workload and experimental bias. Neurolucida 360 is one commercially available software allowing for reliable and reproducible three-dimensional dendritic spine identification and classification32. Here, we present a comprehensive protocol to effectively prepare fixed tissue, acquire images, and ultimately quantify and classify dendritic spines using this software.

<meta charset="utf8"></head><body>Yazar Spotlight: Hipokampus CA1 apikal dendritlerinde dengeli manuel ve otomatik değerlendirme için dendritik omurga analizinin optimize edilmesi

Otomatik Üç Boyutlu Nöron Rekonstrüksiyon Yazılımı Kullanılarak Dendritik Omurga Ölçümü

The scope of our research is to examine the structural profile of dendritic spines in the hippocampus, specifically the CA-one apical dendrite. Through this, we're trying to answer questions centered around how different inputs to different parts of the same dendrite can be encoded at the cellular level. One challenge is obtaining high resolution images of dendritic spines for spine analysis.Once you have these images, the method to most accurately and reliably analyze spines in a fashion that isn't overly burdensome for the researcher presents an additional challenge. A balance must be struck between the two components. This protocol offers a happy medium between fully manual and fully automated dendritic spine analysis.Our protocol reduces the burden of manually counting individual spines. Additionally, the 3D reconstruction makes it possible to obtain spine volume. Classify the spines at the subtypes automatically.

Synaptic connections allow for the exchange and processing of information between neurons. The post-synaptic site of excitatory synapses is often formed ...

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Research

Dendritic Spine Quantification Using an Automatic Three-Dimensional Neuron Reconstruction Software

JoVE Journal

Neuroscience

1.1K Görüntüleme.  National Institutes of Health. Araştırmamızın kapsamı, hipokampustaki dendritik dikenlerin, özellikle CA-one apikal dendritin yapısal profilini incelemektir. Bu sayede, aynı dendritin farklı bölümlerine yapılan farklı girdilerin hücresel düzeyde nasıl kodlanabileceğine odaklanan soruları yanıtlamaya çalışıyoruz. Zorluklardan biri, omurga analizi için dendritik dikenlerin yüksek çözünürlüklü görüntülerini elde etmektir.Bu görüntülere sahip olduğu...

Video: Yazar Spotlight: Hipokampus CA1 apikal dendritlerinde dengeli manuel ve otomatik değerlendirme için dendritik omurga analizinin optimize edilmesi