Name: an optogenetic method to control and analyze gene expression patterns in cell-to-cell interactions
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这项工作得到了 JST (人工智能) 的支持, 进化科学和技术的核心研究 (JPMJCR12W2 (警服)), 为创新领域的科学研究提供资助 (教育部、文化部、体育、科学和技术部 (下个), 日本26119708 (人工智能) 和 16H06480 (警服)), 科学研究 (a) (日本促进科学学会 (jsp) 24240049 (警服)) 和年轻科学家 (A) (jsp 15H05326 (人工智能)) 和一个资助为创新领域的科学研究 "荧光"现场成像" 的下个, 日本和平台的动态方法的生活系统从下个, 日本。

1. Tol2 系统生成稳定的细胞系
<ol><li>
将 Tol2-based optogenetic 模块的染质粒向量 (图 1A) 与 transposase (Tol2) 表达式向量 (pCAGGS-mT2TP) 结合到 C2C12 单元格中。在所有步骤中, 培养细胞与 DMEM 培养基补充10% 胎牛血清 (血清) 和青霉素-链霉素在37°c (表 1), 在存在 5% CO2, 否则表示。
	<ol>
<li>将 trypsinized 单元格计数为单元格计数器, 并将 5 x 104 C2C12 单元格中的每个井在 12-井板中, 在转染前一天。</li>
		<li>用 pAI218 试剂共染0.375 微克的 Tol2-based optogenetic 载体 (pAI177 或 pAI170), 0.125 微克的药物选择载体 (pCAGGS-mT2TP) 和0.5 微克的 lipofection 载体。</li>
		<li>胰蛋白酶处理转染的细胞, 并将其板成100毫米的培养皿后的一天。</li>
		<li>交换培养基为转染的细胞到培养基补充100毫克/毫升潮霉素。</li>
		<li>培养细胞3天, 以消除未转染的细胞。请注意, 中等变化是不必要的。</li>
	</ol>
</li>
	<li>胰蛋白酶处理转染细胞, 并纯化细胞的数量, 表达荧光蛋白的选择。对于携带 pAI177 的接收细胞, 将分选门设置为绿色 PE 通道, 以净化 mCherry 阳性细胞种群。对于携带 pAI218 的光敏发件人细胞, 将分拣门设置为 APC 通道以净化 iRFP713-positive 细胞种群。</li>
	<li>选)采用标准方法建立克隆细胞种群, 如有限稀释或单细胞分选。</li>
</ol>2. 在人口层面评价工程细胞的光敏感度
注: 本部分描述了一种通过生化检测 (如 qPCR 和西方印迹) 检查 Dll1 配体蛋白在蓝光照射下动态诱导的协议。
<ol><li>设置两种类型的孵化器, 有或没有光源的光诱发条件或暗条件, 分别。设置光强度的蓝色 LED 反式照明灯, 如图 1B所示, 使用测光表。程序的定时和光照持续时间通过将控制脚本加载到单板微控制器, 允许可编程的照明计划 (图 1C)。</li>
	<li>使用单元格计数器计数 trypsinized 单元格, 1.0 x 105感光发件人细胞携带 pAI218 和 pAI170 在35毫米直径的塑料培养皿上 (超过12个盘子为光情况和1盘为黑暗的情况) 和设置菜在单独的孵化器为黑暗/光的条件。设置餐具后, 保持孵化器的门关闭, 直到收集细胞裂解物。</li>
	<li>电镀后一天半, 开始照明 (细胞预计将超过80% 汇合)。不要把细胞暴露在光线下, 以避免不良的照片刺激。 注意: 照明的时间表取决于实验的目的。请注意, 持续光照条件 (e. g. 1 分钟持续时间和10分钟间隔, 40 µmol/米2/s 光强度) 足以进行简单的照片感应检查, 而且强光照射对细胞有害。因此, 请确保选择的光照的无害参数。</li>
	<li>电镀后约2天, 用30分钟间隔制备细胞裂解液。将样品碟从孵化器移到冰上, 并开始准备细胞裂解物进行进一步分析。</li>
</ol>3. 人口水平动态发件人-接收器分析: PMT 对光刺激时细胞反应的实时监测
<ol><li>用标准方法胰蛋白酶处理和计数发送方和接收单元的数字。准备1毫升的混合悬浮液的总体积 2.5 x 104接收机和 1.25 x 105发件人单元 (1:5 比率)。 注意: 2:1、1:1 或1:2 发件人-接收器比率还可以使用 1.5 x 105的总单元格数。10
</li>
	<li>24井黑板各井中的板块混合单元, 培养基中含有1毫米荧光素的培养基。</li>
	<li>对平板阅读器中的细胞进行荧光素酶检测, 并确认输出信号对记录系统不太高。 注: 如果输出信号高于 1 x 106光子计数/秒, 则它们可能已饱和。在这种情况下, 将荧光素的浓度降低到最佳值, 以便输出信号低于 1 x 10 6 光子计数/秒.</li>
	<li>在录音系统上设置车牌, 然后启动录制程序 (图 1D)。例如, 设置录音后, 在18小时开始照明。 注意: 时间滤波, 如 detrending 信号的运动平均和 Savitzky-Golay 滤波, 对于波形和峰值检测的可视化是有用的。</li>
</ol>4. 单细胞水平动态发件人-接收器检测: Optogenetic 摄动控制下单细胞反应的实时成像
<ol><li>板 0.5 x 105接收机和 2.5 x 105发件人单元格到27毫米直径-玻璃基35毫米直径菜肴。确保正确调整混合比率和总细胞数 (细胞密度)。</li>
	<li>电镀后的一天, 交换介质与2毫升的记录介质 (苯酚-红色自由 DMEM 培养基补充5% 的血清, 青霉素-链霉素和1毫米荧光素), 并设置玻璃基盘在显微镜上。如有必要, 用 PBS (-) 冲洗死细胞的碎片。 注意: 最好在黑暗条件下执行此步骤。</li>
	<li>在37摄氏度和 5% CO2上安装一个环境室的倒置显微镜。</li>
	<li>设置一个冷却的 CCD 相机。确保 CCD 传感器的温度降低到目标值 (通常为-90 摄氏度)。</li>
	<li>
在自动采集软件中设置 "多维 Timelapse" 窗口的参数, 以5分钟间隔和288倍以上 (一夜录音) 捕捉图像。
	<ol>
<li>打开 "多维 Timelapse" 窗口, 从下拉菜单中选择一个发光通道和一个慢速 50 kHz 读出模式, 并设置 4 x 4 binning, 其曝光率为4分钟。确保读出模式设置为慢速50赫模式, 这对于减少读出的噪声以检测弱发光的生物发光光至关重要。</li>
		<li>打开 "多维 Timelapse" 窗口, 从下拉菜单中选择 "荧光通道" 和 "快速 1 MHz 读出" 模式, 并设置 2 x 2 binning 和 400 ms 曝光。确保读出模式设置为快速 1 MHz 模式, 以减少荧光成像所需的时间。</li>
		<li>通过单击 "获取" 按钮开始定时记录。</li>
	</ol>
</li>
	<li>用图像分析软件从时间推移电影中提取出发光通道的单细胞痕迹, 如下所示。首先, 将图像数据导入图像分析软件, 使发光和荧光叠加图像。对于发光图像, 通过比较在世俗相邻图像中像素的强度, 将像素值替换为上一个和下一个帧的时间平均值 (实现为 "SpikeNoise 过滤器"), 删除来自宇宙射线的热像素,将这些已处理的图像应用于空间平滑滤镜, 并从每个帧中减去外场视图的背景像素值。然后, 在每个时间点确定荧光图像上每个单元格的 "感兴趣区域" (roi), 将 roi 应用于发光图像, 并测量每个 ROI 的发光强度。</li>
</ol>

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我们展示了一种控制基因表达动力学的方法, 周期为2到3小时。这个时间尺度比其他传统系统中的周期要短得多, 包括 LightOn 系统和原始的系统。达到超时间尺度的关键参数是光诱导的分子产物、基因和蛋白质的半衰期。这些动力学参数可能取决于细胞类型和种类。为调整动力学, 替换 Hes1 3 ' UTR 序列与其他是一个直接向前的方式, 因为它不改变目标蛋白质的序列和作用。为了寻求其他 3 ' UTRs 获得理...

细胞对细胞的通信在胚胎模式的发展过程中起着至关重要的作用。在脊椎动物胚胎中, 称为胚胎背部的 metameric 结构沿前后体轴形成, 在时间保持时钟的控制下精确的时间精度, 称为分段时钟 1.在此过程中, 一组 presomitic 胚层 (PSM) 单元格以同步方式定期转换为胚胎背部。这一过程涉及同步振荡基因表达和 PSM 细胞, 振荡的阶段形成相同的胚胎背部。在小鼠中振荡基因表达的周期约为2至3小时, 斑马鱼中约30分钟。当离解时, PSM 单元格会丢失同步2、3, 但当重新聚合时, 它们可以自组织并恢复人口同步4, 这表明单元格耦合是同步振荡.
广泛的努力表明, 信号分子在三角洲凹槽通路是紧密相连的同步振荡的分割时钟基因。无论是药理抑制剂或凹槽信号的基因突变 desynchronize 的振荡器的数量。在斑马鱼中, 凹槽信号元件 (如 DeltaC、DeltaD 和 Notch1a) 的突变体显示异步振荡5,6。在小鸡或小鼠胚胎中, 不仅有凹槽配体 Delta-like1 (Dll1), 而且还需要有凹槽调制器 (Lfng), 同步振荡7,8,9。然而, 由于基因调控动力学的常规扰动的时间分辨率不足以研究这种分子在细胞到细胞间的动态信息传递的功能能力, 因此很难检测2–3 h (超节律) 的尺度过程。
我们最近开发了一种综合的方法来控制和监测哺乳动物细胞中的基因表达模式10。该技术使超时间尺度上周期性光照对基因表达脉冲的诱导。该协议代表了在细胞间通信的环境下, 通过活细胞发光监测来建立光敏细胞线和观察细胞动态反应的方法。该方法适用于其它许多信号通路的分析。

<table><tbody><tr><td>FACS</td><td>Becton, Dickinson and Company</td><td>FACSAriaII SORP</td><td></td></tr><tr><td>Camera</td><td>Andor</td><td>iKon M-934</td><td></td></tr><tr><td>Microscope</td><td>Olympus</td><td>IX-81 ZDC</td><td></td></tr><tr><td>PMT device</td><td>Churitsu eletric corp.</td><td>CL24B-LIC/B</td><td></td></tr><tr><td>Blue LED illuminator</td><td>OptoCode</td><td>LEDB-SBOXH</td><td></td></tr><tr><td>DMEM</td><td>Nacalai</td><td>08459-35</td><td></td></tr><tr><td>Penicillin-streptomycin</td><td>Nacalai</td><td>26253-84</td><td></td></tr><tr><td>Fetal bovine serum</td><td>Sigma</td><td>172012</td><td></td></tr><tr><td>KRYSTAL24 (black 24 well plate )</td><td>Hi-tech</td><td>303012</td><td></td></tr><tr><td>D-Luciferin Potassium Salt</td><td>Nacalai</td><td>20028-24</td><td></td></tr><tr><td>Light meter</td><td>LI-COR Biosciences</td><td>LI-250A</td><td></td></tr><tr><td>anti-HA-Peroxidase antibody</td><td>Roche</td><td>clone 3F10</td><td></td></tr><tr><td>anti-Actin-Peroxidase antibody</td><td>Wako</td><td>clone 2F3</td><td></td></tr></tbody></table>

an optogenetic method to control and analyze gene expression patterns in cell-to-cell interactions

细胞应适当地对世俗变化的环境作出反应, 而这种情况受周围细胞各种因素的影响。凹槽信号通路是细胞间通信必不可少的分子机制之一, 在胚胎的正常发育中起着关键作用。这一途径涉及细胞对细胞传递的振荡信息与超的节奏, 但尽管分子生物学技术的进展, 它一直是挑战, 以阐明多细胞相互作用对振荡基因的影响动力学.在这里, 我们提出一个协议, 允许 optogenetic 控制和实时监测的基因表达模式, 在一个精确的时间方式。该方法成功地揭示了凹槽信号的胞内细胞和细胞间周期输入 entrain 在单细胞分辨率下的频率调谐和相移的固有振荡。该方法适用于分析各种信号通路的动态特性, 为多细胞系统动态基因表达程序的功能意义测试提供了独特的平台。

我们适应了 LightOn 系统11,12, 这使得在哺乳动物细胞中的照片诱导的基因表达, 研究的基因振荡器与 2-到 3-小时周期性。该系统包括两部分: 光诱导转录激活剂 hGAVPO 和一个无人机启动盒, 以推动转录的任意基因的兴趣。为了加速光诱导基因表达的脉动动力学, 波利亚 Hes1 3 ' UTR 取代了无人参与启动盒中的序列, 缩短了小鼠成纤维细?...

Watch this Scientific Journal Video about An Optogenetic Method to Control and Analyze Gene Expression Patterns in Cell-to-cell Interactions at JoVE.com

An Optogenetic Method to Control and Analyze Gene Expression Patterns in Cell-to-cell Interactions

本文提出了一种通过 optogenetic 控制和实时监测基因表达来分析振荡信息的细胞间传递的协议。这种方法为测试多细胞系统动态基因表达程序的功能意义提供了一个独特的平台。

细胞间相互作用中基因表达模式的控制与分析的 Optogenetic 方法

Cells should respond properly to temporally changing environments, which are influenced by various factors from surrounding cells. The Notch signaling ...

an-optogenetic-method-to-control-analyze-gene-expression-patterns

Universidad San Sebastian

Research

JoVE Journal

Genetics

7.6K 次观看.  Kyoto University. 本文提出了一种通过 optogenetic 控制和实时监测基因表达来分析振荡信息的细胞间传递的协议。这种方法为测试多细胞系统动态基因表达程序的功能意义提供了一个独特的平台。

视频: An Optogenetic Method to Control and Analyze Gene Expression Patterns in Cell-to-cell Interactions

Lentivirus-mediated Genetic Manipulation and Visualization of Olfactory Sensory Neurons in vivo

Development of a precise olfactory circuit relies on accurate projection of olfactory sensory neuron (OSN) axons to their synaptic 
targets in the olfactory bulb (OB). The molecular mechanisms of OSN axon growth and targeting are not well understood. Manipulating gene expression and subsequent 
visualizing of single OSN axons and their terminal arbor morphology have thus far been challenging. To study gene function at the single cell level within a specified 
time frame, we developed a lentiviral based technique to manipulate gene expression in OSNs in vivo. Lentiviral particles are delivered to OSNs by microinjection 
into the olfactory epithelium (OE). Expression cassettes are then permanently integrated into the genome of transduced OSNs. Green fluorescent protein expression 
identifies infected OSNs and outlines their entire morphology, including the axon terminal arbor. Due to the short turnaround time between microinjection and 
reporter detection, gene function studies can be focused within a very narrow period of development. With this method, we have detected GFP expression within as 
few as three days and as long as three months following injection. We have achieved both over-expression and shRNA mediated knock-down by lentiviral microinjection. 
This method provides detailed morphologies of OSN cell bodies and axons at the single cell level in vivo, and thus allows characterization of candidate gene function 
during olfactory development.

Lentivirus-mediated Genetic Manipulation and Visualization of Olfactory Sensory Neurons in vivo

We present a lentiviral technique for genetic manipulation and visualization of single olfactory sensory neuron axon and its terminal arborization in vivo.

嗅觉感官神经元的慢病毒介导的遗传操作和可视化在体内</em

Development of a precise olfactory circuit relies on accurate projection of olfactory sensory neuron (OSN) axons to their synaptic 
targets in the ...

科研

神经科学

Light-mediated Reversible Modulation of the Mitogen-activated Protein Kinase Pathway during Cell Differentiation and Xenopus Embryonic Development

Kinase activity is crucial for a plethora of cellular functions, including cell proliferation, differentiation, migration, and apoptosis. During early embryonic development, kinase activity is highly dynamic and widespread across the embryo. Pharmacological and genetic approaches are commonly used to probe kinase activities. Unfortunately, it is challenging to achieve superior spatial and temporal resolution using these strategies. Furthermore, it is not feasible to control the kinase activity in a reversible fashion in live cells and multicellular organisms. Such a limitation remains a bottleneck for achieving a quantitative understanding of kinase activity during development and differentiation. This work presents an optogenetic strategy that takes advantage of a bicistronic system containing photoactivatable proteins Arabidopsis thaliana cryptochrome 2 (CRY2) and the N-terminal domain of cryptochrome-interacting basic-helix-loop-helix (CIBN). Reversible activation of the mitogen-activated protein kinase (MAPK) signaling pathway is achieved through light-mediated protein translocation in live cells. This approach can be applied to mammalian cell cultures and live vertebrate embryos. This bicistronic system can be generalized to control the activity of other kinases with similar activation mechanisms and can be applied to other model systems.

Light-mediated Reversible Modulation of the Mitogen-activated Protein Kinase Pathway during Cell Differentiation and Xenopus Embryonic Development

This protocol describes an optogenetic strategy to modulate mitogen-activated protein kinase (MAPK) activity during cell differentiation and Xenopus embryonic development. This method allows for the reversible activation of the MAPK signaling pathway in mammalian cell culture and in multicellular live organisms, like Xenopus embryos, with high spatial and temporal resolution.

在细胞分化过程中光介导的可逆调节丝裂原活化蛋白激酶途径<em&gt;爪蟾</em&gt;胚胎发育

Kinase activity is crucial for a plethora of cellular functions, including cell proliferation, differentiation, migration, and apoptosis. During early ...

发育生物学

A Method for High Fidelity Optogenetic Control of Individual Pyramidal Neurons In vivo

Optogenetic methods have emerged as a powerful tool for elucidating neural circuit activity underlying a diverse set of behaviors across a broad range of species. Optogenetic tools of microbial origin consist of light-sensitive membrane proteins that are able to activate (e.g., channelrhodopsin-2, ChR2) or silence (e.g., halorhodopsin, NpHR) neural activity ingenetically-defined cell types over behaviorally-relevant timescales. We first demonstrate a simple approach for adeno-associated virus-mediated delivery of ChR2 and NpHR transgenes to the dorsal subiculum and prelimbic region of the prefrontal cortex in rat. Because ChR2 and NpHR are genetically targetable, we describe the use of this technology to control the electrical activity of specific populations of neurons (i.e., pyramidal neurons) embedded in heterogeneous tissue with high temporal precision. We describe herein the hardware, custom software user interface, and procedures that allow for simultaneous light delivery and electrical recording from transduced pyramidal neurons in an anesthetized in vivo preparation. These light-responsive tools provide the opportunity for identifying the causal contributions of different cell types to information processing and behavior.

A Method for High Fidelity Optogenetic Control of Individual Pyramidal Neurons In vivo

The recent development of neuroscience tools that combine genetics and optics, termed "optogenetics", enables control over neural circuit activity with an unprecedented level of spatial and temporal resolution. Here we provide a protocol for integrating in vivo recording with optogenetic manipulation of genetically-defined subsets of prefrontal cortical and subicular pyramidal neurons.

单个锥体神经元的高保真光遗传学控制方法<em&gt;在体内</em

Optogenetic methods  have emerged as a powerful tool for elucidating neural circuit activity  underlying a diverse set of behaviors across a broad range ...

Bioluminescent Optogenetics 2.0: Harnessing Bioluminescence to Activate Photosensory Proteins In Vitro and In Vivo

Bioluminescence - light emitted by a luciferase enzyme oxidizing a small molecule substrate, a luciferin - has been used in vitro and in vivo to activate light-gated ion channels and pumps in neurons. While this bioluminescent optogenetics (BL-OG) approach confers a chemogenetic component to optogenetic tools, it is not limited to use in neuroscience. Rather, bioluminescence can be harnessed to activate any photosensory protein, thus enabling the manipulation of a multitude of light-mediated functions in cells. A variety of luciferase-luciferin pairs can be matched with photosensory proteins requiring different wavelengths of light and light intensities.
Depending on the specific application, efficient light delivery can be achieved by using luciferase-photoreceptor fusion proteins or by simple co-transfection. Photosensory proteins based on light-dependent dimerization or conformational changes can be driven by bioluminescence to effect cellular processes from protein localization, regulation of intracellular signaling pathways to transcription. The protocol below details the experimental execution of bioluminescence activation in cells and organisms and describes the results using bioluminescence-driven recombinases and transcription factors. The protocol provides investigators with the basic procedures for carrying out bioluminescent optogenetics in vitro and in vivo. The described approaches can be further extended and individualized to a multitude of different experimental paradigms.

Bioluminescent Optogenetics 2.0: Harnessing Bioluminescence to Activate Photosensory Proteins In Vitro and In Vivo

Bioluminescence-light emitted by a luciferase enzyme oxidizing a small-molecule substrate, a luciferin-can be harnessed to activate photosensory proteins, thereby adding another dimension to light stimulation and enabling the manipulation of a multitude of light-mediated functions in cells across temporal and spatial scales.

生物发光光遗传学2.0:利用生物发光在体外和体内激活光敏蛋白

Bioluminescence - light emitted by a luciferase enzyme oxidizing a small molecule substrate, a luciferin - has been used in vitro and in vivo to activate ...

生物化学

Design and Implementation of an Automated Illuminating, Culturing, and Sampling System for Microbial Optogenetic Applications

Optogenetic systems utilize genetically-encoded proteins that change conformation in response to specific wavelengths of light to alter cellular processes. There is a need for culturing and measuring systems that incorporate programmed illumination and stimulation of optogenetic systems. We present a protocol for building and using a continuous culturing apparatus to illuminate microbial cells with programmed doses of light, and automatically acquire and analyze images of cells in the effluent. The operation of this apparatus as a chemostat allows the growth rate and the cellular environment to be tightly controlled. The effluent of the continuous cell culture is regularly sampled and the cells are imaged by multi-channel microscopy. The culturing, sampling, imaging, and image analysis are fully automated so that dynamic responses in the fluorescence intensity and cellular morphology of cells sampled from the culture effluent are measured over multiple days without user input. We demonstrate the utility of this culturing apparatus by dynamically inducing protein production in a strain of Saccharomyces cerevisiae engineered with an optogenetic system that activates transcription.

We designed a continuous culturing apparatus for use with optogenetic systems to illuminate cultures of microbes and regularly image cells in the effluent with an inverted microscope. The culturing, sampling, imaging, and image analysis are fully automated so that dynamic responses to illumination can be measured over several days.

设计和自动照明，培养和取样系统实现微生物光遗传学的应用

Optogenetic systems utilize genetically-encoded proteins that change conformation in response to specific wavelengths of light to alter cellular ...

生物工程

研究斑马鱼光遗传学信号转导操作的发育

Optogenetic Signaling Activation in Zebrafish Embryos

Signaling pathways orchestrate fundamental biological processes, including development, regeneration, homeostasis, and disease. Methods to experimentally manipulate signaling are required to understand how signaling is interpreted in these wide-ranging contexts. Molecular optogenetic&#160;tools can provide reversible, tunable manipulations of signaling pathway activity with a high degree of spatiotemporal control and have been applied in vitro, ex vivo, and in vivo. These tools couple light-responsive protein domains, such as the blue light homodimerizing light-oxygen-voltage sensing (LOV) domain, with signaling effectors to confer light-dependent experimental control over signaling. This protocol provides practical guidelines for using the LOV-based bone morphogenetic protein (BMP) and Nodal signaling activators bOpto-BMP and bOpto-Nodal in the optically accessible early zebrafish embryo. It describes two control experiments: A quick phenotype assay to determine appropriate experimental conditions, and an immunofluorescence assay to directly assess signaling. Together, these control experiments can help establish a pipeline for using optogenetic tools in early zebrafish embryos. These strategies provide a powerful platform to investigate the roles of signaling in development, health, and physiology.

作者聚焦：操纵斑马鱼胚胎中的信号转导以解码细胞命运决定 

Optogenetic manipulation of signaling pathways can be a powerful strategy to investigate how signaling is decoded in development, regeneration, homeostasis, and disease. This protocol provides practical guidelines for using light-oxygen-voltage sensing domain-based Nodal and bone morphogenic protein (BMP) signaling activators in the early zebrafish embryo.

斑马鱼胚胎中的光遗传学信号激活

Signaling pathways orchestrate fundamental biological processes, including development, regeneration, homeostasis, and disease. Methods to experimentally ...

Reliably Engineering and Controlling Stable Optogenetic Gene Circuits in Mammalian Cells

Reliable gene expression control in mammalian cells requires tools with high fold change, low noise, and determined input-to-output transfer functions, regardless of the method used. Toward this goal, optogenetic gene expression systems have gained much attention over the past decade for spatiotemporal control of protein levels in mammalian cells. However, most existing circuits controlling light-induced gene expression vary in architecture, are expressed from plasmids, and utilize variable optogenetic equipment, creating a need to explore characterization and standardization of optogenetic components in stable cell lines. Here, the study provides an experimental pipeline of reliable gene circuit construction, integration, and characterization for controlling light-inducible gene expression in mammalian cells, using a negative feedback optogenetic circuit as a case example. The protocols also illustrate how standardizing optogenetic equipment and light regimes can reliably reveal gene circuit features such as gene expression noise and protein expression magnitude. Lastly, this paper may be of use for laboratories unfamiliar with optogenetics who wish to adopt such technology. The pipeline described here should apply for other optogenetic circuits in mammalian cells, allowing for more reliable, detailed characterization and control of gene expression at the transcriptional, proteomic, and ultimately phenotypic level in mammalian cells.

Reliably controlling light-responsive mammalian cells requires the standardization of optogenetic methods. Toward this goal, this study outlines a pipeline of gene circuit construction, cell engineering, optogenetic equipment operation, and verification assays to standardize the study of light-induced gene expression using a negative-feedback optogenetic gene circuit as a case study.

可靠地工程和控制哺乳动物细胞中稳定的光遗传学基因回路

Reliable gene expression control in mammalian cells requires tools with high fold change, low noise, and determined input-to-output transfer functions, ...

Combining Optogenetics with Artificial microRNAs to Characterize the Effects of Gene Knockdown on Presynaptic Function within Intact Neuronal Circuits

The purpose of this protocol is to characterize the effect of gene knockdown on presynaptic function within intact neuronal circuits. We describe a workflow on how to combine artificial microRNA (miR)-mediated RNA interference with optogenetics to achieve selective stimulation of manipulated presynaptic boutons in acute brain slices. The experimental approach involves the use of a single viral construct and a single neuron-specific promoter to drive the expression of both an optogenetic probe and artificial miR(s) against presynaptic gene(s). When stereotactically injected in the brain region of interest, the expressed construct makes it possible to stimulate with light exclusively the neurons with reduced expression of the gene(s) under investigation. This strategy does not require the development and maintenance of genetically modified mouse lines and can in principle be applied to other organisms and to any neuronal gene of choice. We have recently applied it to investigate how the knockdown of alternative splice isoforms of presynaptic P/Q-type voltage-gated calcium channels (VGCCs) regulates short-term synaptic plasticity at CA3 to CA1 excitatory synapses in acute hippocampal slices. A similar approach could also be used to manipulate and probe the neuronal circuitry in vivo.

This protocol provides a workflow on how to combine artificial microRNA-mediated RNA interference with optogenetics to stimulate specifically presynaptic boutons with reduced expression of selective gene(s) within intact neuronal circuits.

光遗传学与人工 microRNAs 相结合对完整神经元回路中基因击倒对突触前功能的影响

The purpose of this protocol is to characterize the effect of gene knockdown on presynaptic function within intact neuronal circuits. We describe a ...

细胞间相互作用中基因表达模式的控制与分析的 Optogenetic 方法

摘要

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此视频中的章节

嗅觉感官神经元的慢病毒介导的遗传操作和可视化在体内

在细胞分化过程中光介导的可逆调节丝裂原活化蛋白激酶途径

单个锥体神经元的高保真光遗传学控制方法

生物发光光遗传学2.0:利用生物发光在体外和体内激活光敏蛋白

设计和自动照明，培养和取样系统实现微生物光遗传学的应用

斑马鱼胚胎中的光遗传学信号激活

斑马鱼胚胎中的光遗传学信号激活

斑马鱼胚胎中的光遗传学信号激活

可靠地工程和控制哺乳动物细胞中稳定的光遗传学基因回路

光遗传学与人工 microRNAs 相结合对完整神经元回路中基因击倒对突触前功能的影响