ברצוננו להודות התובע קולטר (CHOP) עבור ומאפשר לנו להשתמש מיקרוסקופ 2-פוטון שלו לרכוש את 2-פוטון מהתמונות המוצגות בתחילתו של וידאו, וה &#39;טאקאנו לשיתוף איתנו המומחיות הטכנית שלו.

<ol>
	<li>Costa, M. a. r. c. e. l. l. o., Furness, J. o. h. n. . B., Llewellyn-Smith, I. J., Johnson, L. e. o. n. a. r. d. . R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> in Physiology of the Gastrointestinal Tract, edited by Leonard R. , 1-1 (1987).</li><li>Obaid, A. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatiotemporal+patterns+of+activity+in+an+intact+mammalian+network+with+single-cell+resolution:+optical+studies+of+nicotinic+activity+in+an+enteric+plexus.">Spatiotemporal patterns of activity in an intact mammalian network with single-cell resolution: optical studies of nicotinic activity in an enteric plexus.</a> J Neurosci. 19 (8), 3073-3073 (1999).</li><li>Obaid, A. L., Loew, L. M., Wuskell, J. P., Salzberg, B. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+naphthylstyryl-pyridinium+potentiometric+dyes+offer+advantages+for+neural+network+analysis.">Novel naphthylstyryl-pyridinium potentiometric dyes offer advantages for neural network analysis.</a> J. Neurosci. Methods. 134 (2), 179-179 (2004).</li><li>Hirst, G. D., McKirdy, H. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synaptic+potentials+recorded+from+neurones+of+the+submucous+plexus+of+guinea-pig+small+intestine.">Synaptic potentials recorded from neurones of the submucous plexus of guinea-pig small intestine.</a> J Physiol (Lond). 249 (2), 369-369 (1975).</li><li>Salzberg, B. M., Barker, J., McKelvy, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Current+Methods+in+Cellular+Neurobiology.">Current Methods in Cellular Neurobiology.</a> , 139-139 (1983).</li><li>Salzberg, B. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+ultra-stable+non-coherent+light+source+for+optical+measurements+in+neuroscience+and+cell+physiology.">An ultra-stable non-coherent light source for optical measurements in neuroscience and cell physiology.</a> Journal of Neuroscience Methods. 141, 165-16 (2005).</li><li>Obaid, A. L., Nelson, M. E., Lindstrom, J., Salzberg, B. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optical+studies+of+nicotinic+acetylcholine+receptor+subtypes+in+the+guinea-pig+enteric+nervous+system.">Optical studies of nicotinic acetylcholine receptor subtypes in the guinea-pig enteric nervous system.</a> J Exp Biol. 208 (Pt 15), 2981-2981 (2005).</li><li>Obaid, A. L., Zou, D. J., Rohr, S., Salzberg, B. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optical+recording+with+single+cell+resolution+from+a+simple+mammalian+nervous+system:+Electrical+activity+in+ganglia+from+the+submucous+plexus+of+the+guinea-pig+ileum.">Optical recording with single cell resolution from a simple mammalian nervous system: Electrical activity in ganglia from the submucous plexus of the guinea-pig ileum.</a> Biol. Bull. 183, 344-344 (1992).</li><li>Salzberg, B. M., Davila, H. V., Cohen, L. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optical+recording+of+impulses+in+individual+neurones+of+an+invertebrate+central+nervous+system.">Optical recording of impulses in individual neurones of an invertebrate central nervous system.</a> Nature. 246 (5434), 508-508 (1973).</li></ol>

פרוטוקול זה נכתב עם שני שערים בראש. הראשון הוא לשכנע חוקרים אחרים, בזכות ההתקדמות הטכנולוגית הרבה של העשור האחרון, הקלטה אופטית של הפעילות החשמלית באמצעות מתח רגיש צובעת הפך אחד, מתודולוגיות החזק ביותר אמינה ובמחיר סביר ללימוד רשתות נוירונים שלמים, ואכן , זה יכול להי?...

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		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>Medium 199</td>
<td>&nbsp;</td>
<td>Sigma, St. Louis, MO</td>
<td>M3769</td>
<td>With Earle&#x2019;s salts Without L-Glutamine, Phenol Red and Sodium Bicarbonate</td>
</tr>
<tr>
<td>Sylgard</td>
<td>&nbsp;</td>
<td>Dow Corning Corp., Midland, MI</td>
<td>184 silicone elastomer kit</td>
<td>&nbsp;</td>
<tr>
<td>Insect pins used for dissection</td>
<td>&nbsp;</td>
<td>F.S.T., Foster City, CA</td>
<td>26001-30</td>
<td>&nbsp;</td>
<tr>
<td>Dumont forceps</td>
<td>&nbsp;</td>
<td>F.S.T., Foster City, CA</td>
<td>11203-23 or 11200-33</td>
<td>&nbsp;</td>
<tr>
<td>Moria MC19/B Pascheff-Wolff Spring Scissors</td>
<td>&nbsp;</td>
<td>F.S.T., Foster City, CA</td>
<td>15371-92</td>
<td>&nbsp;</td>
<tr>
<td>Pins to hold the tissue during the experiment</td>
<td>&nbsp;</td>
<td>Seirin Corp., Shizuoka, Japan</td>
<td>Seirin Spinex</td>
<td>&nbsp;</td>
<tr>
<td>Collagenase VII</td>
<td>&nbsp;</td>
<td>Sigma, St. Louis, MO</td>
<td>C0773</td>
<td>&nbsp;</td>
<tr>
<td>Protease IX</td>
<td>&nbsp;</td>
<td>Sigma, St. Louis, MO</td>
<td>P6141</td>
<td>&nbsp;</td>
<tr>
<td>Fetal Bovine Serum</td>
<td>&nbsp;</td>
<td>Invitrogen, Carlsbad, CA</td>
<td>10439-016</td>
<td>&nbsp;</td>
<tr>
<td>PenStrep</td>
<td>&nbsp;</td>
<td>GIBCO, BRL</td>
<td>15140</td>
<td>&nbsp;</td>
<tr>
<td>L-Glutamine 100X</td>
<td>&nbsp;</td>
<td>GIBCO, BRL</td>
<td>25030</td>
<td>&nbsp;</td>
<tr>
<td>Nifedipine</td>
<td>&nbsp;</td>
<td>Sigma, St. Louis, MO</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Di-4-ANEPPDHQ</td>
<td>&nbsp;</td>
<td>Molecular Probes, Eugene, OR</td>
<td>D36802</td>
<td>&nbsp;</td>
<tr>
<td>4-Channel Stimulus Generator</td>
<td>&nbsp;</td>
<td>Multi Channel System MCS GmbH, Reutlingen, Germany</td>
<td>2000 Series</td>
<td>&nbsp;</td>
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<td>Peristaltic pump</td>
<td>&nbsp;</td>
<td>Rainin, Woburn, MA</td>
<td>2-channel Dinamax RP-1</td>
<td>&nbsp;</td>
<tr>
<td>High-speed camera</td>
<td>&nbsp;</td>
<td>RedShirtImaging, LLC Decatur, GA</td>
<td>NeuroCCD-SM</td>
<td>&nbsp;</td>
<tr>
<td>1:10 demagnifier / relay lens</td>
<td>&nbsp;</td>
<td>Optem, Qioptiq Linos, Inc., Rochester, NY</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Upright microscope</td>
<td>&nbsp;</td>
<td>Olympus Optical Co., Tokyo, Japan</td>
<td>BX61TRF</td>
<td>&nbsp;</td>
<tr>
<td>Gibraltar fixed stage with motorized X-Y translator</td>
<td>&nbsp;</td>
<td>Gibraltar, Burleigh Instruments, EXFO, Quebec, Canada</td>
<td>PSSG--BX2</td>
<td>&nbsp;</td>
<tr>
<td>Linear matrix electrodes</td>
<td>&nbsp;</td>
<td>FHC, Inc., Bowdoin, ME</td>
<td>Custom made</td>
<td>&nbsp;</td>
<tr>
<td>Active vibration-isolation table</td>
<td>&nbsp;</td>
<td>Halcyonics,Inc., Menlo Park, CA</td>
<td>Micro 60</td>
<td>&nbsp;</td>
<tr>
<td>Ultra-low-ripple feedback stabilized power supply</td>
<td>&nbsp;</td>
<td>Kepco, Flushing, NY</td>
<td>ATE 75-15M</td>
<td>&nbsp;</td>
<tr>
<td>Heat filter</td>
<td>&nbsp;</td>
<td>Schott Optical Glass, Duryea, PA</td>
<td>KG-1</td>
<td>&nbsp;</td>
<tr>
<td>High-Q interference filter</td>
<td>&nbsp;</td>
<td>Chroma, Inc., Rockingham, VT</td>
<td>HQ530/50</td>
<td>&nbsp;</td>
<tr>
<td>Dichroic mirror</td>
<td>&nbsp;</td>
<td>Chroma, Inc., Rockingham, VT</td>
<td>565 nm (50% transmission)</td>
<td>&nbsp;</td>
<tr>
<td>Long-pass filter</td>
<td>&nbsp;</td>
<td>Chroma, Inc., Rockingham, VT</td>
<td>HQ572LP</td>
<td>&nbsp;</td>
<tr>
<td>Acoustic curtains</td>
<td>&nbsp;</td>
<td>Acoustical Surfaces, Inc.</td>
<td>BSC-25</td>
<td>&nbsp;</td>
<tr>
<td>Neuroplex</td>
<td>&nbsp;</td>
<td>RedShirtImaging, Inc., Decatur, GA</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>IDL</td>
<td>&nbsp;</td>
<td>ITT Visual Information Solutions, Boulder, CO</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>High-resolution CCD camera, with its own camera controller</td>
<td>&nbsp;</td>
<td>Hamamatsu Photonics, KK, Hamamatsu City, Japan</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Frame-grabber for high-resolution camera</td>
<td>&nbsp;</td>
<td>Data Translation, Marlboro, MA</td>
<td>DT3120K-1</td>
<td>&nbsp;</td>
<tr>
<td>Imaging software for high-resolution camera</td>
<td>&nbsp;</td>
<td>Data Translation, Marlboro, MA</td>
<td>Global Lab Image/2</td>
<td>&nbsp;</td>		</tbody>
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optical recording of electrical activity in guinea-pig enteric networks using voltage-sensitive dyes

מערכת העצבים enteric (ENS) היא רשת עצמאי המזוהה עם פונקציות, מסוגל לבצע התנהגויות מורכבות בבידוד. הנוירונים שלה (10-25 מיקרומטר קוטר) מסודרים plexuses כי מוגבלים מטוסים שונים של דופן המעי<sup&gt; 1</sup&gt;; מקלעת myenteric ניתן למצוא בין שכבות השריר האורך מעגליות, ואת מקלעת submucous בין שכבת השריר עגולים רירית. מאז מערכות עבור מפעיל plexuses אלה (הובלת אפיתל, תאים האנדוקרינית, אלמנטים החיסונית, כלי דם ושרירים חלקים) כלולים גם בתוך קיר הבטן, חצי שלם ההכנות יכול להיות גזור כי לשמר רכיבים בודדים של רפלקס מסלולים שונים. ההתנהגות של מערכות מפעיל נשלטת על ידי plexuses submucous ו myenteric הפועל קונצרט. לכן, ידע מפורט של אינטראקציות הסינפטית בתוך ובין הגרעינים, ואת התקשורת בין plexuses, הוא חיוני להבנת תפקוד תקין של מערכת העיכול. ENS, כמו מערכת העצבים תמים, הוא מודל ניסיוני ייחודי שבו ניתן לתאם אירועים מולקולריים הסלולר עם ההתנהגות החשמלית של הרשת העצבית ותפוקות הפיזיולוגי שלה. בגלל ארגון מעין דו מימדי של plexuses שלה, ENS הוא גם מתאים במיוחד ללימוד רשתות עצביות באמצעות מספר רב של טכניקות הקלטה אופטית אתר המעסיקות מתח רגיש צבעים<sup&gt; 2,7,8,9</sup&gt;. נדגים כאן את השימוש חדש יחסית naphthylstyryl-pyridinium צבען (di-4-ANEPPDHQ)<sup&gt; 3</sup&gt; זה מציע יתרונות רבים על פני קודמיו, כולל phototoxicity נמוך מאוד, קצב איטי של הפנמה, ואת היציבות הכימית מדהים. הפועל בשיתוף עם מצלמה המאפשרת משנה אלפית שנייה זמן רזולוציה, צבע זה מאפשר לנו לנטר את הפעילות החשמלית של כל הנוירונים בתחום של נוף עם רזולוציה מרחבית מקסימלית של ~ 2.5 מיקרומטר בהגדלה 100x. בהגדלה נמוכה (10X או 20X), להקריב את ההחלטה תא בודד הוא פיצוי לזכות בפרספקטיבה, חושף את המורכבות של המעגלים בין ganglionic.

Watch this Scientific Journal Video about Optical Recording of Electrical Activity in Guinea-pig Enteric Networks using Voltage-sensitive Dyes at JoVE.com

Optical Recording of Electrical Activity in Guinea-pig Enteric Networks using Voltage-sensitive Dyes

פרוטוקול זה מדגים כיצד מתח רגיש צבעים לאפשר הקלטה אופטית של הפעילות החשמלית של רשתות עצביות שלמים כגון plexuses של מערכת חזירי הים העצבים enteric, עם רזולוציה מתכווננת אשר נע בין חד תאים למעגל רב ganglionic.

הקלטה אופטית של הפעילות החשמלית גינאה חזיר רשתות enteric באמצעות מתח רגיש צבעים

The enteric nervous system (ENS) is a self-contained network with identified functions, capable of performing complex behaviors in isolation. Its neurons ...

optical-recording-electrical-activity-guinea-pig-enteric-networks

Research

JoVE Journal

Biology

9.9K Views.  University of Pennsylvania-School of Medicine. פרוטוקול זה מדגים כיצד מתח רגיש צבעים לאפשר הקלטה אופטית של הפעילות החשמלית של רשתות עצביות שלמים כגון plexuses של מערכת חזירי הים העצבים enteric, עם רזולוציה מתכווננת אשר נע בין חד תאים למעגל רב ganglionic.

Video: Optical Recording of Electrical Activity in Guinea-pig Enteric Networks using Voltage-sensitive Dyes

Labeling Stem Cells with Fluorescent Dyes for non-invasive Detection with Optical Imaging

Optical imaging (OI) is an easy, fast and inexpensive tool for in vivo monitoring of new stem cell based therapies. The technique is based on ex vivo labeling of stem cells with a fluorescent dye, subsequent intravenous injection of the labeled cells and visualization of their accumulation in specific target organs or pathologies. The presented technique demonstrates how we label human mesenchymal stem cells (hMSC) by simple incubation with the lipophilic fluorescent dye DiD (C67H103CIN2O3S) and how we label human embryonic stem cells (hESC) with the FDA approved fluorescent dye Indocyanine Green (ICG). The uptake mechanism is via adherence and diffusion of the lypophilic dye across the phospholipid cell membrane bilayer. The labeling efficiency is usually improved if the cells are incubated with the dye in serum-free media as opposed to incubation in serum-containing media. Furthermore, the addition of the transfection agent Protamine Sulfate significantly improves contrast agent uptake.

This video shows techniques for labeling of human embryonic stem cells and mesenchymal stem cells with fluorescent dyes. This technique can be used for an in vivo tracking of transplanted stem cells with optical imaging and for histopathological correlations with fluorescence microscopy.

תיוג בתאי גזע עם צבעי ניאון על איתור פולשני עם דימות אופטי

Optical imaging (OI) is an easy, fast and inexpensive tool for in vivo monitoring of new stem cell based therapies. The technique is based on ex vivo ...

Proper Care and Cleaning of the Microscope

Keeping the microscope optics clean is important for high-quality imaging. Dust, fingerprints, excess immersion oil, or mounting medium on or in a microscope causes reduction in contrast and resolution. DIC is especially sensitive to contamination and scratches on the lens surfaces. This protocol details the procedure for keeping the microscope clean.

Keeping the microscope optics clean is important for high-quality imaging. Dust, fingerprints, excess immersion oil, or mounting medium on or in a microscope causes reduction in contrast and resolution. DIC is especially sensitive to contamination and scratches on the lens surfaces. This protocol details the procedure for keeping the microscope clean.

טיפול ניקוי נאות של המיקרוסקופ

Keeping the microscope optics clean is important for high-quality imaging. Dust, fingerprints, excess immersion oil, or mounting medium on or in a ...

Selective Labelling of Cell-surface Proteins using CyDye DIGE Fluor Minimal Dyes

Surface  proteins are central to the cell's ability to react to its environment and to interact with neighboring cells. They are known to be inducers of almost all intracellular signaling. Moreover, they play an important role in environmental adaptation and drug treatment, and are often involved in disease pathogenesis and pathology (1). Protein-protein interactions are intrinsic to signaling pathways, and to gain more insight in these complex biological processes, sensitive and reliable methods are needed for studying cell surface proteins. Two-dimensional (2-D) electrophoresis is used extensively for detection of biomarkers and other targets in complex protein samples to study differential changes. Cell surface proteins, partly due to their low abundance (1 2% of cellular proteins), are difficult to detect in a 2-D gel without fractionation or some other type of enrichment. They are also often poorly represented in 2-D gels due to their hydrophobic nature and high molecular weight (2). In this study, we present a new protocol for intact cells using CyDye  DIGE Fluor minimal dyes for specific labeling and detection of this important group of proteins. The results showed specific labeling of a large number of cell surface proteins with minimal labeling of intracellular proteins. This protocol is rapid, simple to use, and all three CyDye DIGE Fluor minimal dyes (Cy 2, Cy 3 and Cy 5) can be used to label cell-surface proteins. These features allow for multiplexing using the 2-D Fluorescence Difference Gel Electrophoresis (2-D DIGE) with Ettan  DIGE technology and analysis of protein expression changes using DeCyder  2-D Differential Analysis Software. The level of cell-surface proteins was followed during serum starvation of CHO cells for various lengths of time (see Table 1). Small changes in abundance were detected with high accuracy, and results are supported by defined statistical methods.

A simple and specific method was demonstrated for fluorescent labeling and enhanced detection of cell surface proteins without a fractionation step. Differential abundance in cell surface proteins was analyzed using two-dimensional (2-D) electrophoresis and Ettan&#x2122; DIGE technology.

Labelling סלקטיבי של חלבונים על פני קרום התא באמצעות CyDye DIGE צבעים פלואוריד מינימלי

Surface  proteins are central to the cell's ability to react to its environment and to interact with neighboring cells. They are known to be inducers of ...

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Phenotypes are determined by a complex series of physical (e.g. protein-protein) and functional (e.g. gene-gene or genetic) interactions (GI)1. While physical interactions can indicate which bacterial proteins are associated as complexes, they do not necessarily reveal pathway-level functional relationships1. GI screens, in which the growth of double mutants bearing two deleted or inactivated genes is measured and compared to the corresponding single mutants, can illuminate epistatic dependencies between loci and hence provide a means to query and discover novel functional relationships2. Large-scale GI maps have been reported for eukaryotic organisms like yeast3-7, but GI information remains sparse for prokaryotes8, which hinders the functional annotation of bacterial genomes. To this end, we and others have developed high-throughput quantitative bacterial GI screening methods9, 10.
Here, we present the key steps required to perform quantitative E. coli Synthetic Genetic Array (eSGA) screening procedure on a genome-scale9, using natural bacterial conjugation and homologous recombination to systemically generate and measure the fitness of large numbers of double mutants in a colony array format. Briefly, a robot is used to transfer, through conjugation, chloramphenicol (Cm) - marked mutant alleles from engineered Hfr (High frequency of recombination) 'donor strains' into an ordered array of kanamycin (Kan) - marked F- recipient strains. Typically, we use loss-of-function single mutants bearing non-essential gene deletions (e.g. the 'Keio' collection11) and essential gene hypomorphic mutations (i.e. alleles conferring reduced protein expression, stability, or activity9, 12, 13) to query the functional associations of non-essential and essential genes, respectively. After conjugation and ensuing genetic exchange mediated by homologous recombination, the resulting double mutants are selected on solid medium containing both antibiotics. After outgrowth, the plates are digitally imaged and colony sizes are quantitatively scored using an in-house automated image processing system14. GIs are revealed when the growth rate of a double mutant is either significantly better or worse than expected9. Aggravating (or negative) GIs often result between loss-of-function mutations in pairs of genes from compensatory pathways that impinge on the same essential process2. Here, the loss of a single gene is buffered, such that either single mutant is viable. However, the loss of both pathways is deleterious and results in synthetic lethality or sickness (i.e. slow growth). Conversely, alleviating (or positive) interactions can occur between genes in the same pathway or protein complex2 as the deletion of either gene alone is often sufficient to perturb the normal function of the pathway or complex such that additional perturbations do not reduce activity, and hence growth, further. Overall, systematically identifying and analyzing GI networks can provide unbiased, global maps of the functional relationships between large numbers of genes, from which pathway-level information missed by other approaches can be inferred9.

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Systematic, large-scale synthetic genetic (gene-gene or epistasis) interaction screens can be used to explore genetic redundancy and pathway cross-talk. Here, we describe a high-throughput quantitative synthetic genetic array screening technology, termed eSGA that we developed for elucidating epistatic relationships and exploring genetic interaction networks in Escherichia coli.

מיפוי רשתות פונקציונליות חיידקיים ומסלולים ב<em&gt; חיידקי Escherichia</em&gt; באמצעות מערכים גנטיים סינטטיים

Phenotypes  are determined by a complex series of physical (e.g. protein-protein) and  functional (e.g. gene-gene or genetic) interactions (GI)1. While ...

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

DNA nanotechnology requires large amounts of highly pure DNA as an engineering material. Plasmid DNA could meet this need since it is replicated with high fidelity, is readily amplified through bacterial culture and can be stored indefinitely in the form of bacterial glycerol stocks. However, the double-stranded nature of plasmid DNA has so far hindered its efficient use for construction of DNA nanostructures or devices that typically contain single-stranded or branched domains. In recent work, it was found that nicked double stranded DNA (ndsDNA) strand displacement gates could be sourced from plasmid DNA. The following is a protocol that details how these ndsDNA gates can be efficiently encoded in plasmids and can be derived from the plasmids through a small number of enzymatic processing steps. Also given is a protocol for testing ndsDNA gates using fluorescence kinetics measurements. NdsDNA gates can be used to implement arbitrary chemical reaction networks (CRNs) and thus provide a pathway towards the use of the CRN formalism as a prescriptive molecular programming language. To demonstrate this technology, a multi-step reaction cascade with catalytic kinetics is constructed. Further it is shown that plasmid-derived components perform better than identical components assembled from synthetic DNA.

This protocol describes a method for deriving DNA strand displacement gates from plasmids and testing them using fluorescence kinetics measurements. Gates can be modularly composed into multi-component systems to approximate the behavior of formal chemical reaction networks (CRN), demonstrating a new use for CRNs as a molecular programming language.

גדיל DNA עקירת עיר רשתות תגובת השרשת כימית המופק מפלסמיד

DNA nanotechnology requires large amounts of highly pure DNA as an engineering material. Plasmid DNA could meet this need since it is replicated with high ...

Drosophila Preparation and Longitudinal Imaging of Heart Function In Vivo Using Optical Coherence Microscopy (OCM)

Longitudinal study of the heartbeat in small animals contributes to understanding structural and functional changes during heart development. Optical coherence microscopy (OCM) has been demonstrated to be capable of imaging small animal hearts with high spatial resolution and ultrahigh imaging speed. The high image contrast and noninvasive properties make OCM ideal for performing longitudinal studies without requiring tissue dissections or staining. Drosophila has been widely used as a model organism in cardiac developmental studies due to its high number of orthologous human disease genes, its similarity of molecular mechanisms and genetic pathways with vertebrates, its short life cycle, and its low culture cost. Here, the experimental protocols are described for the preparation of Drosophila and optical imaging of the heartbeat with a custom OCM system throughout the life cycle of the specimen. By following the steps provided in this report, transverse M-mode and 3D OCM images can be acquired to conduct longitudinal studies of the Drosophila cardiac morphology and function. The en face and axial sectional OCM images and the heart rate (HR) and cardiac activity period (CAP) histograms, were also shown to analyze the heart structural changes and to quantify the heart dynamics during Drosophila metamorphosis, combined with the videos constructed with M-mode images to trace cardiac activity intuitively. Due to the genetic similarity between Drosophila and vertebrates, longitudinal study of heart morphology and dynamics in fruit flies could help reveal the origins of human heart diseases. The protocol here would provide an effective method to perform a wide range of studies to understand the mechanisms of cardiac diseases in humans.

Drosophila Preparation and Longitudinal Imaging of Heart Function In Vivo Using Optical Coherence Microscopy OCM

Here, the experimental protocols are described for preparing Drosophila at different developmental stages and performing longitudinal optical imaging of Drosophila heartbeats using a custom optical coherence microscopy (OCM) system. The cardiac morphological and dynamical changes can be quantitatively characterized by analyzing the heart structural and functional parameters from OCM images.

הכנת תסיסנית והדמיה אורכית תפקוד הלב in vivo באמצעות מיקרוסקופית קוהרנטיות אופטית (OCM)

Longitudinal study of the heartbeat in small animals contributes to understanding structural and functional changes during heart development. Optical ...

Photodiode-Based Optical Imaging for Recording Network Dynamics with Single-Neuron Resolution in Non-Transgenic Invertebrates

The development of transgenic invertebrate preparations in which the activity of specifiable sets of neurons can be recorded and manipulated with light represents a revolutionary advance for studies of the neural basis of behavior. However, a downside of this development is its tendency to focus investigators on a very small number of &#8220;designer&#8221; organisms (e.g., C. elegans and Drosophila), potentially negatively impacting the pursuit of comparative studies across many species, which is needed for identifying general principles of network function. The present article illustrates how optical recording with voltage-sensitive dyes in the brains of non-transgenic gastropod species can be used to rapidly (i.e., within the time course of single experiments) reveal features of the functional organization of their neural networks with single-cell resolution. We outline in detail the dissection, staining, and recording methods used by our laboratory to obtain action potential traces from dozens to ~150 neurons during behaviorally relevant motor programs in the CNS of multiple gastropod species, including one new to neuroscience &#8211; the nudibranch Berghia stephanieae. Imaging is performed with absorbance voltage-sensitive dyes and a 464-element photodiode array that samples at 1,600 frames/second, fast enough to capture all action potentials generated by the recorded neurons. Multiple several-minute recordings can be obtained per preparation with little to no signal bleaching or phototoxicity. The raw optical data collected through the methods described can subsequently be analyzed through a variety of illustrated methods. Our optical recording approach can be readily used to probe network activity in a variety of non-transgenic species, making it well suited for comparative studies of how brains generate behavior.

This protocol presents a method for imaging neuronal population activity with single-cell resolution in non-transgenic invertebrate species using absorbance voltage-sensitive dyes and a photodiode array. This approach enables a rapid workflow, wherein imaging and analysis can be pursued over the course of a single day.

הדמיה אופטית מבוססת פוטודיודה להקלטת דינמיקה ברשת עם רזולוציית נוירון יחיד בבלתי חוליות לא מהונדסים

The development of transgenic invertebrate preparations in which the activity of specifiable sets of neurons can be recorded and manipulated with light ...

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

The root microbiome plays an important role in plant growth and environmental adaptation. Network analysis is an important tool for studying communities, which can effectively explore the interaction relationship or co-occurrence model of different microbial species in different environments. The purpose of this manuscript is to provide details on how to use the weighted correlation network algorithm to analyze different co-occurrence networks that may occur in microbial communities due to different ecological environments. All analysis of the experiment is performed in the WGCNA package. WGCNA is an R package for weighted correlation network analysis. The experimental data used to demonstrate these methods were microbial community data from the NCBI (National Center for Biotechnology Information) database for three niches of the rice (Oryza sativa) root system. We used the weighted correlation network algorithm to construct co-abundance networks of microbial community in each of the three niches. Then, differential co-abundance networks among endosphere, rhizoplane and rhizosphere soil were identified. In addition, the core genera in network were obtained by the "WGCNA" package, which plays an important regulated role in network functions. These methods enable researchers to analyze the response of microbial network to environmental disturbance and verify different microbial ecological response theories. The results of these methods show that the significant differential microbial networks identified in the endosphere, rhizoplane and rhizosphere soil of rice.

Network analysis was applied to evaluate the association of various ecological microbial communities, such as soil, water and rhizosphere. Presented here is a protocol on how to use the WGCNA algorithm to analyze different co-occurrence networks that may occur in the microbial communities due to different ecological environments.

סטייה של מיקרוביוטה שורש בבתי גידול שונים המבוססת על רשתות מתאם משוקללים

The root microbiome plays an important role in plant growth and environmental adaptation. Network analysis is an important tool for studying communities, ...

Isolation of Retinal Pigment Epithelial Cells from Guinea Pig Eyes

This protocol describes the isolation of cells of the retinal pigment epithelium (RPE) from the eyes of young pigmented guinea pigs for potential application in molecular biology studies, including gene expression analyses. In the context of eye growth regulation and myopia, the RPE likely plays a role as a cellular relay for growth modulatory signals, as it is located between the retina and the two walls of the eye, such as the choroid and sclera. While protocols for isolating the RPE have been developed for both chicks and mice, these protocols have proven not to be directly translatable to the guinea pig, which has become an important and widely used mammalian myopia model. In this study, molecular biology tools were used to examine the expression of specific genes to confirm that the samples were free of contamination from the adjacent tissues. The value of this protocol has already been demonstrated in an RNA-Seq study of RPE from young pigmented guinea pigs exposed to myopia-inducing optical defocus. Beyond eye growth regulation, this protocol has other potential applications in studies of retinal diseases, including myopic maculopathy, one of the leading causes of blindness in myopes, in which the RPE has been implicated. The main advantage of this technique is that it is relatively simple and&#160;once perfected, yields high-quality RPE samples suitable for molecular biology studies, including RNA analysis.

We describe a simple and efficient method for isolating cells of the retinal pigment epithelium (RPE) cells from the eyes of young pigmented guinea pigs. This procedure allows for follow-up molecular biology studies on the isolated RPE, including gene expression analyses.

בידוד תאי אפיתל פיגמנט ברשתית מעיני חזיר גינאה

This protocol describes the isolation of cells of the retinal pigment epithelium (RPE) from the eyes of young pigmented guinea pigs for potential ...

כימות מיטופגיה ב- C. elegans וקו תאים של סרטן הכבד

Detection of Mitophagy in Caenorhabditis elegans and Mammalian Cells Using Organelle-Specific Dyes

Mitochondria are essential for various biological functions, including energy production, lipid metabolism, calcium homeostasis, heme biosynthesis, regulated cell death, and the generation of reactive oxygen species (ROS). ROS are vital for key biological processes. However, when uncontrolled, they can lead to oxidative injury, including mitochondrial damage. Damaged mitochondria release more ROS, thereby intensifying cellular injury and the disease state. A homeostatic process named mitochondrial autophagy (mitophagy) selectively removes damaged mitochondria, which are then replaced by new ones. There are multiple mitophagy pathways, with the common endpoint being the breakdown of the damaged mitochondria in lysosomes. 
Several methodologies, including genetic sensors, antibody immunofluorescence, and electron microscopy, use this endpoint to quantify mitophagy. Each method for examining mitophagy has its advantages, such as specific tissue/cell targeting (with genetic sensors) and great detail (with electron microscopy). However, these methods often require expensive resources, trained personnel, and a lengthy preparation time before the actual experiment, such as for creating transgenic animals. Here, we present a cost-effective alternative for measuring mitophagy using commercially available fluorescent dyes targeting mitochondria and lysosomes. This method effectively measures mitophagy in the nematode Caenorhabditis elegans and human liver cells, which indicates its potential efficiency in other model systems.

מחבר זרקור: זיהוי מיטופגיה בתאי Caenorhabditis elegans ובתאי יונקים באמצעות צבעים ספציפיים לאברונים  

Exploring mitophagy through electron microscopy, genetic sensors, and immunofluorescence requires costly equipment, skilled personnel, and a significant time investment. Here, we demonstrate the efficacy of a commercial fluorescence dye kit in quantifying the mitophagy process in both Caenorhabditis elegans and a liver cancer cell line.

איתור מיטופגיה בתאי Caenorhabditis elegans ובתאי יונקים באמצעות צבעים ספציפיים לאברונים

Mitochondria are essential for various biological functions, including energy production, lipid metabolism, calcium homeostasis, heme biosynthesis, ...