私達は私達が私たちと彼の技術的な専門知識を共有するための2光子ビデオの冒頭に示されている画像、およびH.高野を取得するために彼の2光子顕微鏡を使用できるようにするためのDAコールターを（CHOP）に感謝いたします。

<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>

このプロトコルは、二つの目標を念頭に書かれています。最初のものは、過去10年間の多くの技術的進歩、電位感受性色素を用いて電気的活性の光記録のおかげで無傷の神経ネットワークを研究するための最も強力な、信頼性と手頃な方法論の一つとなっている、という他の研究者を説得することです。確かに、それは簡単に控えめなリソースを持つ実験室でも実装することができます。第?...

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		<thead>
		<tr>
		<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>
<tr>
<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>
		</table>
		</div>

optical recording of electrical activity in guinea-pig enteric networks using voltage-sensitive dyes

腸神経系（ENSは）分離して複雑な動作を行うことのできる識別機能を持つ自己完結型のネットワークです。その神経細胞（直径10〜25μmであるが）腸壁の異なる平面に限定されている神経叢に配置されています<sup&gt; 1</sup&gt;、筋層間神経叢は、縦と円形の筋層、及び円形の筋層と粘膜との間の粘膜下神経叢との間で見つけることができます。これらの神経叢（上皮、内分泌細胞、免疫要素、血管や平滑筋の輸送）のためのエフェクターシステムはまた、腸壁内に含まれているので、半無傷の調製物は、異なる反射経路の個々のコンポーネントを保持することを解剖することができます。エフェクターシステムの動作は、コンサートで行動する粘膜下と筋層間神経叢によって制御されます。したがって、神経節内との間に、と神経叢の間の通信のシナプスの相互作用の詳細な知識は、正常な胃腸機能を理解するために不可欠です。 ENSは、無傷の神経系として、1つは神経回路網とその生理的な出力の電気的挙動を分子や細胞のイベントを関連付けることのできるユニークな実験的なモデルです。ため、その神経叢の準2次元組織から、ENSは、特によく電位感受性色素を採用し、複数のサイト光記録技術を用いたニューラルネットワークの学習に適しています<sup&gt; 2,7,8,9</sup&gt;。我々はここでは比較的新しいnaphthylstyryl - ピリジニウム染料（ジ-4 - ANEPPDHQ）の使用を説明します<sup&gt; 3</sup&gt;非常に低い光毒性、内在化の速度が遅い、と顕著な化学的安定性を含む、その前任者以上の複数の利点を、提供している。サブミリ秒の時間分解能を可能にするカメラと組み合わせて使用​​すると、この色素は、私たちは、100Xの倍率で〜2.5μmの最大限の空間分解能と視野内のすべてのニューロンの電気的活動を監視することができます。低倍率（10倍または20倍）で、単一セルの分解能の犠牲は間神経節回路の複雑さを明らかに、視点の利得によって補償されます。

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

電位感受性色素は、その単一細胞から複数の神経節の回路への範囲は調整可能な解像度と、そのようなモルモット腸神経系の神経叢としてそのままニューラルネットワークからの電気活動の光学的記録を有効にする方法このプロトコルは示しています。

電位感受性色素を用いてモルモット腸ネットワークにおける電気活動の光学的記録

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 ビュー.  University of Pennsylvania-School of Medicine. 電位感受性色素は、その単一細胞から複数の神経節の回路への範囲は調整可能な解像度と、そのようなモルモット腸神経系の神経叢としてそのままニューラルネットワークからの電気活動の光学的記録を有効にする方法このプロトコルは示しています。

ビデオ: 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.

光イメージングによる非侵襲的検出のための蛍光色素で標識幹細胞

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 ...

生物学

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.

顕微鏡の適切な手入れとクリーニング

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

Phase Contrast and Differential Interference Contrast (DIC) Microscopy

Phase-contrast microscopy is often used to produce contrast for transparent, non light-absorbing, biological specimens. The technique was discovered by Zernike, in 1942, who received the Nobel prize for his achievement. DIC microscopy, introduced in the late 1960s, has been popular in biomedical research because it highlights edges of specimen structural detail, provides high-resolution optical sections of thick specimens including tissue cells, eggs, and embryos and does not suffer from the  phase halos  typical of phase-contrast images. This protocol highlights the principles and practical applications of these microscopy techniques.

Phase Contrast and Differential Interference Contrast DIC Microscopy

This protocol highlights the principles and practical applications of Phase and Differential Interference Contrast (DIC) Microscopy

位相コントラストおよび微分干渉コントラスト（DIC）顕微鏡

Phase-contrast microscopy is often used to produce contrast for transparent, non light-absorbing, biological specimens. The technique was discovered by ...

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.

CyDye DIGEフルーア最小限の色素を用いた細胞表面タンパク質の選択的ラベリング

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 ...

Bioengineering Human Microvascular Networks in Immunodeficient Mice

The future of tissue engineering and cell-based therapies for tissue regeneration will likely rely on our ability to generate functional vascular networks in vivo. In this regard, the search for experimental models to build blood vessel networks in vivo is of utmost importance 1. The feasibility of bioengineering microvascular networks in vivo was first shown using human tissue-derived mature endothelial cells (ECs) 2-4; however, such autologous endothelial cells present problems for wide clinical use, because they are difficult to obtain in sufficient quantities and require harvesting from existing vasculature. These limitations have instigated the search for other sources of ECs. The identification of endothelial colony-forming cells (ECFCs) in blood presented an opportunity to non-invasively obtain ECs 5-7. We and other authors have shown that adult and cord blood-derived ECFCs have the capacity to form functional vascular networks in vivo 7-11. Importantly, these studies have also shown that to obtain stable and durable vascular networks, ECFCs require co-implantation with perivascular cells. The assay we describe here illustrates this concept: we show how human cord blood-derived ECFCs can be combined with bone marrow-derived mesenchymal stem cells (MSCs) as a single cell suspension in a collagen/fibronectin/fibrinogen gel to form a functional human vascular network within 7 days after implantation into an immunodeficient mouse. The presence of human ECFC-lined lumens containing host erythrocytes can be seen throughout the implants indicating not only the formation (de novo) of a vascular network, but also the development of functional anastomoses with the host circulatory system. This murine model of bioengineered human vascular network is ideally suited for studies on the cellular and molecular mechanisms of human vascular network formation and for the development of strategies to vascularize engineered tissues.

Here, we describe a methodology to deliver human cord blood-derived endothelial colony-forming cells (ECFCs) and bone marrow-derived mesenchymal stem cells (MSCs), embedded in a collagen/fibronectin gel, subcutaneously into immunodeficient mice. This cell/gel combination generates a human vascular network that connects with the mouse vasculature.

免疫不全マウスにおける生体工学ヒト微小血管ネットワーク

The future of tissue engineering and cell-based therapies for tissue regeneration will likely rely on our ability to generate functional vascular networks ...

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.

細菌機能ネットワークとPathwaysでのマッピング<em&gt;大腸菌</em&gt;合成遺伝子配列を用いて

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.

実装化学反応ネットワーク用プラスミド由来のDNA鎖置換ゲイツ

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 ...

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes

In this protocol, we demonstrate a method for the synthesis of 2&#39;-alkyne modified deoxyribonucleic acid (DNA) strands by automated solid phase synthesis using standard phosphoramidite chemistry. Oligonucleotides are post-synthetically labeled by two new photostable cyanine dyes using copper-catalyzed click-chemistry. The synthesis of both donor and acceptor dye is described and is performed in three consecutive steps. With the DNA as the surrounding architecture, these two dyes undergo an energy transfer when they are brought into close proximity by hybridization. Therefore, annealing of two single stranded DNA strands is visualized by a change of fluorescence color. This color change is characterized by fluorescence spectroscopy but can also be directly observed by using a handheld ultraviolet (UV) lamp. The concept of a dual fluorescence color readout makes these oligonucleotide probes excellent tools for molecular imaging especially when the described photostable dyes are used. Thereby, photobleaching of the imaging probes is prevented, and biological processes can be observed in real time for a longer time period.

Photostable cyanine dyes are attached to oligonucleotides to monitor hybridization by energy transfer.

光安定シアニン色素を用いた波長シフトDNAハイブリダイゼーションプローブの合成

In this protocol, we demonstrate a method for the synthesis of 2&#39;-alkyne modified deoxyribonucleic acid (DNA) strands by automated solid phase ...

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.

ショウジョウバエの調製と光コヒーレンス顕微鏡を用いてin vivoで心機能の縦イメージング（OCM）

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

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.

重み付け相関ネットワークに基づく異なる生息地における根内微生物叢の発散

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