我们感谢患者参与这些实验的组织收集。国防部 OCRP 卵巢癌学院奖 (W81XWH-15-0253) 和一个试点奖从科琳的梦想基金会 Anirban k. 米特拉支持这项研究。

该议定书遵循印第安纳大学机构管理委员会的指导方针。
1. 细胞制剂
<ol><li>
人原发性间皮细胞的分离与培养
	<ol>
<li>从人网膜中分离人原发性间皮细胞 (HPMCs), 如前所述17、18和生长在完全生长培养基 [Dulbecco 的改良鹰的培养基 (DMEM) 含有10% 胎牛血清, 1%青霉素-链霉素, 1% 非必需氨基酸, 1% 维生素] 在37摄氏度和 5% CO2。 注: HPMCs 通常生长到100% 汇合处 (图 1A)。</li>
	</ol>
</li>
	<li>
卵巢癌细胞生长条件的研究
	<ol>
<li>生长 HeyA8 卵巢癌细胞在完全生长培养基在37°c 和 5% CO2。 注意: 使用 HeyA8 细胞生长到大约80% 汇合处 (图 1B)。</li>
	</ol>
</li>
</ol>2. 细胞培养
<ol><li>
近端区域性设置
	<ol>
<li>使用 Transwell 插入6井板与10微米厚的组织培养处理聚碳酸酯膜与0.4 微米毛孔 (108毛孔/cm2) 和4.67 厘米2生长区。如果需要, 可通过缩放根据生长表面积来播种的细胞数量来优化不同的插入尺寸。热完全生长培养基, 胰蛋白酶, 和磷酸盐缓冲盐水 (PBS) 到37摄氏度使用前。</li>
	</ol>
</li>
	<li>
准备插入
	<ol>
<li>要将插入膜下部表面的 HeyA8 细胞播种, 请使用无菌钳从包装中取出插入物, 并将其倒置在不育的15厘米培养皿中。</li>
		<li>使用15厘米的菜, 因为它有深度容纳倒置插入, 或替代任何适当的无菌容器。根据实验, 将所需的插入数放置在15厘米的盘子中。</li>
		<li>标签三控制和三实验条件相应地与标记在刀片的边缘。</li>
	</ol>
</li>
	<li>
准备癌细胞
	<ol>
<li>为了胰蛋白酶处理在25厘米2瓶 (~ 2 x 106细胞) 的80% 汇合处生长的 HeyA8 细胞, 添加1毫升的胰蛋白酶 (0.25%) 用于 40–60 s, 中和胰蛋白酶与6毫升完全生长培养基。</li>
		<li>将细胞以室温 (RT) 500 x g的速度离心成3分钟, 丢弃上清, 并在5毫升的完全生长培养基中并用重悬细胞颗粒。用台盼蓝染料排除法对活细胞进行计数。</li>
	</ol>
</li>
	<li>
培养癌细胞
	<ol>
<li>在完全生长培养基中悬浮10万细胞/毫升活 HeyA8 细胞。小心种子 8万 HeyA8 细胞悬浮在 800 ul 的完全生长培养基上的插入 (现在正朝上, 因为它是倒置)。</li>
		<li>种子单元格形成一个圆顶状形状, 使单元格保持在插入上 (图 1C)。从膜的中心开始, 在同心圆内向外移动, 慢慢吹打。避免超过3毫米从边缘, 以防止任何溢出的介质。 注: 种子细胞数量将取决于细胞的生长速率和实验的持续时间。对近端培养的 HeyA8 细胞数量进行了优化, 在第三天结束时, 细胞将80–90% 汇合。</li>
	</ol>
</li>
	<li>
肿瘤细胞附件
	<ol>
<li>盖上15厘米的盘子, 小心地将含有插入物的盘子移到 CO2孵化器中。在这个步骤中, 不中断插入的介质和单元格的放置非常关键。将细胞保持在37°c 4 小时, 使癌细胞附着在插入物上。</li>
	</ol>
</li>
	<li>
准备间皮细胞
	<ol>
<li>在大约 4 h 以后, 胰蛋白酶处理 HPMCs 生长在100% 汇合在 75 cm2瓶 (~ 4 x 106个细胞) 与2毫升胰蛋白酶 (0.25%) 为对的中最小和中和胰蛋白酶与12毫升完全生长培养基。</li>
		<li>离心细胞在 500 x g在 RT 3 分钟, 并用重悬细胞颗粒在10毫升的完全生长培养基, 并计数的活细胞使用台盼蓝染料排除方法。</li>
	</ol>
</li>
	<li>
将间皮细胞播种
	<ol>
<li>在完全生长培养基中悬浮30万细胞/毫升活 HPMCs。将2.5 毫升新鲜完整的生长介质添加到6井板的每一个井中。小心地把15厘米的盘子里装有插入物的生物安全罩。使用无菌钳, 翻转插入和放置在6井板的井, 使其直立, 与 HeyA8 细胞附着在较低的表面浸入完全生长介质 (图 1C)。</li>
		<li>种子 45万 HPMCs 悬浮在1.5 毫升的生长培养基内的插入与 HeyA8 细胞附着在表面上面对井底 (图 1C) 或插入没有任何 HeyA8 细胞的 HPMC 控制。添加1.5 毫升的生长培养基, 没有细胞的 HeyA8 控制。</li>
	</ol>
</li>
	<li>
成长的近端文化
	<ol>
<li>让近端文化生长在 CO2孵化器在37°c 和 5% CO2为 72 h。如有需要, 可按如下方式补充介质。<ol>
<li>对于内插入, 删除750µL 和添加750µL 新鲜完整的生长培养基。</li>
			<li>对于插入的外部 (6 井板), 去除1毫升和增加1毫升新鲜完全生长培养基。1毫升的选择是为了方便改变的媒介在一步。如果需要, 可以删除1.25 毫升, 取而代之。</li>
		</ol>
</li>
	</ol>
</li>
	<li>
收集单元格
	<ol>
<li>在近端培养72小时后采集细胞。在这一步骤中特别小心, 以防止交叉污染的 HeyA8 细胞和 HPMCs. 胰蛋白酶处理细胞, 离心, 并溶解颗粒, 而不是株溶藻细胞膜上的细胞, 以防止交叉污染。</li>
	</ol>
</li>
	<li>
Trypsinizing 细胞
	<ol>
<li>用 1x PBS 冲洗插入件的两侧。</li>
		<li>将插入件转移到新井中, 加入胰蛋白酶。加入0.5 毫升的胰蛋白酶到内插入, 并添加2毫升胰蛋白酶到6井板, 以胰蛋白酶处理癌细胞附着在下部的插入。在37摄氏度孵育2分钟的盘子。</li>
	</ol>
</li>
	<li>
中和胰蛋白酶
	<ol>
<li>加入1毫升的完全生长培养基内的插入, 以中和的胰蛋白酶, 吸管向上和向下, 然后采取细胞和转移到一个标记的收集管。添加额外的2毫升完整的生长培养基, 完全中和。应注意不要在吹打时刺穿细胞膜, 以防止细胞交叉污染。</li>
		<li>要收集插入底部的单元格, 请将步骤12.2 中添加的2毫升胰蛋白酶移到下表面 2–3x, 使细胞落入6井板的底部。将该板块底部的胰蛋白酶与6毫升的生长培养基中和, 将该板块的内容转移到标记的收集管上。</li>
	</ol>
</li>
	<li>
收集和株溶藻细胞
	<ol>
<li>离心细胞在 500 x g 3 分钟, 并吸入介质。并用重悬和溶解以0.7 毫升苯酚-硫氰酸胍为基础的裂解试剂进行 RNA 提取。使用任何合适的工具包隔离 RNA。</li>
	</ol>
</li>
</ol>3. 定量实时聚合酶链反应
注: 以下步骤描述了定量的实时聚合酶链反应 (qPCR), 以研究基因表达的变化, 由于近端培养。
<ol><li>从 RNA 样品中制备 qPCR 的 cDNA。使用任何合适的逆转录酶与相应的缓冲和随机引物, 以确保所有 mRNA 的反向转录 (见材料表)。</li>
	<li>通过 qPCR 与甘油 3-磷酸脱氢酶 (GAPDH) 作为内部控制, 评估纤维连接蛋白 (FN1) 和 e-钙黏蛋白 (CDH1) mRNA 表达水平的变化和转化生长因子 beta 1 (TGFβ1)。可以使用标准化的商用基因表达化验 (见材料表) 或设计底漆。</li>
	<li>比较近端培养中的 HeyA8 细胞与 HPMCs 的 HeyA8 控制和近端培养的 HPMCs 与 HPMC 的对照。</li>
</ol>

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作者没有什么可透露的。

了解细胞间分泌和 juxtacrine 信号的机制对于培养对正常组织稳态和疾病状况的更好的认识是至关重要的,7,8。大多数分泌信号的研究是通过收集条件培养基从一个细胞类型和使用它来治疗其他细胞类型。这种方法在其固有的简单性方面具有优势。然而, 它并没有准确地重述细胞微环境中分泌因子的局部浓度, 或所涉及因素的产生和消耗的动力学。虽然前者...

癌细胞与肿瘤微环境的相互作用在肿瘤进展中的作用已经得到了很好的确立, 并已成为癌症生物学研究的主要重点1。在伤口愈合、免疫应答、血管生成、干细胞龛位和发育过程中, 双向信号的相似情况是至关重要的,2、3、4、5、6,7,8. 在所有这些生物过程中, 一个共同的主题是细胞以各种方式对其微环境中的细胞外信号作出反应, 这决定了体细胞的命运、组织生理学和疾病进展。因此, 重点日益转向发展对这种细胞通讯所涉及的机制的更好的了解。大多数这种相互作用涉及细胞之间的分泌或 juxtacrine 信号。分泌信号涉及特定信号因子的分泌由一个细胞, 这是由相应的受体在附近的另一个细胞感知, 触发反应, 在它9,10, 而 juxtacrine信号要求两个细胞的细胞成分之间的直接接触涉及11,12。
这种信号是组织稳态以及肿瘤微环境中的重要组成部分。癌细胞从肿瘤基质细胞中的分泌和 juxtacrine 因子中受益, 包括肿瘤相关的成纤维细胞 (咖啡馆)、免疫细胞和脂肪瘤13、14、15、16。分泌信号可以由生长因子、细胞因子、趋化因子等介导, 而 juxtacrine 信号则包括在凹槽信号中并列配体和受体, 或整合与其各自的相互作用细胞外基质蛋白。我们已经证明了卵巢癌细胞与咖啡馆在肿瘤进展和转移中相互作用的重要性14。同样, 转移卵巢癌细胞与覆盖转移部位的间皮细胞的相互作用, 调节癌细胞的关键 microRNAs 和转录因子, 促进转移性殖民化17,18。
大多数关于分泌信号的研究涉及使用从一个细胞类型收集的条件培养基来治疗第二细胞类型。虽然这种方法已被广泛使用, 但它并没有有效地复制在接收细胞微环境中分泌因子的局部高浓度水平。它也无法重现由一个细胞产生的分泌因子连续流动的动力学, 相邻细胞接收。分泌信号是有效的短距离, 因为分泌因子是在所需浓度仅在源细胞附近, 并倾向于扩散和稀释, 随着距离的增加。这种局部高浓度的分泌因子对于触发受体细胞的反应至关重要。此外, 受体细胞的反应也依赖于新分泌因子的平衡, 以及它们在受体细胞中的退化、束缚和内化以及从源细胞扩散的持续损耗。条件培养基可以集中在微环境中存在的较高的局部浓度, 但不能准确地复制准确的浓度。此外, 它不能模仿生产的自然动力学和所涉及的因素的耗尽。为了更准确地复制分泌信号并将其与 juxtacrine 信号机制分开, 我们设计了一种新的近距离培养方法, 它涉及在多孔膜的任一表面上生长两种细胞类型。毛孔小到足以防止 juxtacrine 相互作用, 但允许在局部高浓度下交换分泌因子。这样, 系统就保留了生产的动力学和分泌因素的损耗。

<table>
	<tbody>
		<tr>
			<td>24 mm Transwell permeable support with 0.4 &#181;m Pore Polycarbonate Membrane Insert</td>
			<td>Corning (Costar)</td>
			<td>3412</td>
			<td>&#8226; 10 &#181;m thick translucent polycarbonate membrane 
			&#8226; Treated for optimal cell attachment 
			&#8226; Packaged 6 inserts in a 6 well plate, 4 plates per case 
			&#8226; Membrane must be stained for cell visibility 
			&#8226; Sterilized by gamma radiation</td>
		</tr>
		<tr>
			<td>6 well plate</td>
			<td>Corning (Falcon)</td>
			<td>353046</td>
			<td>Flat Bottom, TC-treated, sterile, with Lid</td>
		</tr>
		<tr>
			<td>15 cm culture dish</td>
			<td>Corning (Falcon)</td>
			<td>353025</td>
			<td>Sterile, TC-treated Cell Culture Dish</td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Corning (Cellgro)</td>
			<td>10-013-CV</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin Streptomycin</td>
			<td>Corning</td>
			<td>30-002-CI</td>
			<td></td>
		</tr>
		<tr>
			<td>MEM Nonessential amino acids</td>
			<td>Corning (Cellgro)</td>
			<td>25-025-CI</td>
			<td></td>
		</tr>
		<tr>
			<td>MEM Vitamins</td>
			<td>Corning (Cellgro)</td>
			<td>25-020-CI</td>
			<td></td>
		</tr>
		<tr>
			<td>0.25% Trypsin, 2.21 mM EDTA</td>
			<td>Corning</td>
			<td>25-053-CI</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>Atlanta Biologicals</td>
			<td>S11150</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipets</td>
			<td></td>
			<td></td>
			<td>Any make is fine</td>
		</tr>
		<tr>
			<td>CO2 Incubator</td>
			<td></td>
			<td></td>
			<td>Any make is fine</td>
		</tr>
		<tr>
			<td>Biosafety level II cabinet</td>
			<td></td>
			<td></td>
			<td>Any make is fine</td>
		</tr>
		<tr>
			<td>FN1 TaqMan Gene Expression Assay</td>
			<td>ThermoFisher Scientific</td>
			<td>Hs01549976_m1</td>
			<td></td>
		</tr>
		<tr>
			<td>TGFB1 TaqMan Gene Expression Assay</td>
			<td>ThermoFisher Scientific</td>
			<td>Hs00998133_m1</td>
			<td></td>
		</tr>
		<tr>
			<td>CDH1 TaqMan Gene Expression Assay</td>
			<td>ThermoFisher Scientific</td>
			<td>Hs01023895_m1</td>
			<td></td>
		</tr>
		<tr>
			<td>GAPDH TaqMan Gene Expression Assay</td>
			<td>ThermoFisher Scientific</td>
			<td>Hs99999905_m1</td>
			<td></td>
		</tr>
		<tr>
			<td>miRNeasy mini RNA isolation Kit</td>
			<td>Qiagen</td>
			<td>217004</td>
			<td></td>
		</tr>
		<tr>
			<td>High-Capacity cDNA Reverse Transcription Kit</td>
			<td>ThermoFisher Scientific</td>
			<td>43-688-13</td>
			<td></td>
		</tr>
		<tr>
			<td>HeyA8 ovarian cancer cells</td>
			<td>Obtained from Ernst Lengyel Lab, University of Chicago</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>TGF&#946; Neutralizing Antibody</td>
			<td>R&#38;D Systems</td>
			<td>MAB1835-100</td>
			<td></td>
		</tr>
	</tbody>
</table>

a proximal culture method to study paracrine signaling between cells

细胞间相互作用在许多生物学过程中起着重要作用, 包括肿瘤进展、免疫反应、血管生成和发育。分泌或 juxtacrine 信号介导这种相互作用。使用条件中等和共培养研究是区分这两种相互作用的最常见的方法。然而, 在分泌相互作用过程中, 局部高浓度分泌因子在微环境中的作用不是通过条件培养基准确概括的, 因此可能导致不精确的结论。为了克服这一问题, 我们设计了一种近端培养方法来研究分泌信号。两种细胞生长在10µm 厚的聚碳酸酯膜的任何表面, 0.4 µm 毛孔。毛孔允许交换分泌因子, 同时抑制 juxtacrine 信号。可以在端点收集和裂解细胞, 以确定分泌信号的影响。除了允许分泌因子的局部浓度梯度外, 这种方法还能经受长时间的培养以及抑制剂的使用的实验。利用这种方法研究卵巢癌细胞与转移部位间皮细胞的相互作用, 可以适应任何两种黏附细胞类型, 研究分泌信号在各个领域的应用,包括肿瘤微环境、免疫学和发育。

转移卵巢癌细胞在腹膜腔内的转移部位出现间皮细胞19。生产分泌和 juxtacrine 与间皮细胞的相互作用有助于诱导卵巢癌细胞的适应性反应, 从而成功转移17,18,20,21.为了检验近端培养方法的有效性, 我们测试了 HeyA8 卵巢癌细胞与 HPMCs 的分泌相互作用。以前有报?...

Watch this Scientific Journal Video about A Proximal Culture Method to Study Paracrine Signaling Between Cells at JoVE.com

A Proximal Culture Method to Study Paracrine Signaling Between Cells

分泌和 juxtacrine 细胞相互作用在许多生物学过程中起着重要作用, 包括肿瘤的进展、免疫反应、血管生成和发育。在这里, 一种近端培养方法用于研究分泌信号, 其中的分泌因子的局部浓度保持, 而防止直接细胞接触。

一种研究细胞间分泌信号的近距离培养方法

Intercellular interactions play an important role in many biological processes, including tumor progression, immune responses, angiogenesis, and ...

a-proximal-culture-method-to-study-paracrine-signaling-between-cells

Universidad de Cartagena UDEC

Research

JoVE Journal

Biology

9.4K 次观看.  Indiana University School of Medicine. 分泌和 juxtacrine 细胞相互作用在许多生物学过程中起着重要作用, 包括肿瘤的进展、免疫反应、血管生成和发育。在这里, 一种近端培养方法用于研究分泌信号, 其中的分泌因子的局部浓度保持, 而防止直接细胞接触。

视频: A Proximal Culture Method to Study Paracrine Signaling Between Cells

Testing Visual Sensitivity to the Speed and Direction of Motion in Lizards

Testing visual sensitivity in any species provides basic information regarding behaviour, evolution, and ecology. However, testing specific features of the visual system provide more empirical evidence for functional applications. Investigation into the sensory system provides information about the sensory capacity, learning and memory ability, and establishes known baseline behaviour in which to gauge deviations (Burghardt, 1977). However, unlike mammalian or avian systems, testing for learning and memory in a reptile species is difficult. Furthermore, using an operant paradigm as a psychophysical measure of sensory ability is likewise as difficult. Historically, reptilian species have responded poorly to conditioning trials because of issues related to motivation, physiology, metabolism, and basic biological characteristics. Here, I demonstrate an operant paradigm used a novel model lizard species, the Jacky dragon (Amphibolurus muricatus) and describe how to test peripheral sensitivity to salient speed and motion characteristics. This method uses an innovative approach to assessing learning and sensory capacity in lizards. I employ the use of random-dot kinematograms (RDKs) to measure sensitivity to speed, and manipulate the level of signal strength by changing the proportion of dots moving in a coherent direction. RDKs do not represent a biologically meaningful stimulus, engages the visual system, and is a classic psychophysical tool used to measure sensitivity in humans and other animals. Here, RDKs are displayed to lizards using three video playback systems. Lizards are to select the direction (left or right) in which they perceive dots to be moving. Selection of the appropriate direction is reinforced by biologically important prey stimuli, simulated by computer-animated invertebrates.

Testing visual sensitivity in lizards using an operant conditioning paradigm that employs video playback of random-dot kinematograms and computer-generated invertebrates.

测试的速度和运动方向的视觉灵敏度在蜥蜴

Testing visual sensitivity in any species provides basic information regarding behaviour, evolution, and ecology. However, testing specific features of ...

科研

生物学

Method for Culture of Early Chick Embryos ex vivo (New Culture)

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying  the formation and patterning of brain, neural tube, somite and heart primordia. Applications of chick embryo culture include electroporation of DNA or RNA constructs in order to analyze gene function, grafts of growth factor coated beads such as FGFs and BMPs , as well as whole mount in situ hybridization and immunohistochemistry. This video demonstrates the different steps in chick embryo culture; First, the embryo is explanted in saline. Then, the embryo is centered on a glass ring. The membranes surrounding the embryo are lifted along the walls of the ring. The ring is then placed in a culture dish containing a pool of albumine. The culture dish is sealed and placed in a humid chamber, where the embryo is cultured for up to 24 hrs. Finally, the embryo is removed from the ring, fixed and processed for further applications. A troubleshooting guide is also presented.

Method for Culture of Early Chick Embryos ex vivo New Culture

This video demonstrates New culture, a method by which chick embryos are cultured outside the egg for up to 24 hr. This method enables one to study early development (primitive streak to 14 som.), a period corresponding to E7-9 in mouse. Applications of this technique include electroporation, in situ hybridization and immunohistochemistry.

文化早期鸡胚体外（新文化）的方法

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ...

A high-throughput method to globally study the organelle morphology in S. cerevisiae

High-throughput methods to examine protein localization or organelle morphology is an effective tool for studying protein interactions and can help achieve an comprehensive understanding of molecular pathways. In Saccharomyces cerevisiae, with the development of the non-essential gene deletion array, we can globally study the morphology of different organelles like the endoplasmic reticulum (ER) and the mitochondria using GFP (or variant)-markers in different gene backgrounds. However, incorporating GFP markers in each single mutant individually is a labor-intensive process. Here, we describe a procedure that is routinely used in our laboratory. By using a robotic system to handle high-density yeast arrays and drug selection techniques, we can significantly shorten the time required and improve reproducibility. In brief, we cross a GFP-tagged mitochondrial marker (Apc1-GFP) to a high-density array of 4,672 nonessential gene deletion mutants by robotic replica pinning.  Through diploid selection, sporulation, germination and dual marker selection, we recover both alleles. As a result, each haploid single mutant contains Apc1-GFP incorporated at its genomic locus. Now, we can study the morphology of mitochondria in all non-essential mutant background. Using this high-throughput approach, we can conveniently study and delineate the pathways and genes involved in the inheritance and the formation of organelles in a genome-wide setting.

GFP-fusion proteins are widely used to visualize organelles by confocal microscopy. However, screening for mutations that affect the morphology of organelles generally requires individual mutagenesis and is time consuming. Here, we demonstrate a method to simultaneously incorporate organelle-GFP markers in almost 5,000 non-essential genes in yeast.

一种高通量的方法，在全球范围内研究在酿酒酵母中的细胞器形态

High-throughput methods to examine protein localization or organelle morphology is an effective tool for studying protein interactions and can help ...

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

The three-dimensional folding of chromosomes compartmentalizes the genome and and can bring distant functional elements, such as promoters and enhancers, into close spatial proximity 2-6. Deciphering the relationship between chromosome organization and genome activity will aid in understanding genomic processes, like transcription and replication. However, little is known about how chromosomes fold. Microscopy is unable to distinguish large numbers of loci simultaneously or at high resolution. To date, the detection of chromosomal interactions using chromosome conformation capture (3C) and its subsequent adaptations required the choice of a set of target loci, making genome-wide studies impossible 7-10.
We developed Hi-C, an extension of 3C that is capable of identifying long range interactions in an unbiased, genome-wide fashion. In Hi-C, cells are fixed with formaldehyde, causing interacting loci to be bound to one another by means of covalent DNA-protein cross-links. When the DNA is subsequently fragmented with a restriction enzyme, these loci remain linked. A biotinylated residue is incorporated as the 5' overhangs are filled in. Next, blunt-end ligation is performed under dilute conditions that favor ligation events between cross-linked DNA fragments. This results in a genome-wide library of ligation products, corresponding to pairs of fragments that were originally in close proximity to each other in the nucleus. Each ligation product is marked with biotin at the site of the junction. The library is sheared, and the junctions are pulled-down with streptavidin beads. The purified junctions can subsequently be analyzed using a high-throughput sequencer, resulting in a catalog of interacting fragments.
Direct analysis of the resulting contact matrix reveals numerous features of genomic organization, such as the presence of chromosome territories and the preferential association of small gene-rich chromosomes. Correlation analysis can be applied to the contact matrix, demonstrating that the human genome is segregated into two compartments: a less densely packed compartment containing open, accessible, and active chromatin and a more dense compartment containing closed, inaccessible, and inactive chromatin regions. Finally, ensemble analysis of the contact matrix, coupled with theoretical derivations and computational simulations, revealed that at the megabase scale Hi-C reveals features consistent with a fractal globule conformation.

The Hi-C method allows unbiased, genome-wide identification of chromatin interactions (1). Hi-C couples proximity ligation and massively parallel sequencing. The resulting data can be used to study genomic architecture at multiple scales: initial results identified features such as chromosome territories, segregation of open and closed chromatin, and chromatin structure at the megabase scale.

嗨 - C：一个方法研究基因组的三维架构。

The three-dimensional folding of chromosomes compartmentalizes the genome and and can bring distant functional elements, such as promoters and enhancers, ...

A System for Culturing Iris Pigment Epithelial Cells to Study Lens Regeneration in Newt

Salamanders like newt and axolotl possess the ability to regenerate many of its lost body parts such as limbs, the tail with spinal cord, eye, brain, heart, the jaw 1. Specifically, newts are unique for its lens regeneration capability. Upon lens removal, IPE cells of the dorsal iris transdifferentiate to lens cells and eventually form a new lens in about a month 2,3. This property of regeneration is never exhibited by the ventral iris cells. The regeneration potential of the iris cells can be studied by making transplants of the in vitro cultured IPE cells. For the culture, the dorsal and ventral iris cells are first isolated from the eye and cultured separately for a time period of 2 weeks (Figure 1). These cultured cells are reaggregated and implanted back to the newt eye. Past studies have shown that the dorsal reaggregate maintains its lens forming capacity whereas the ventral aggregate does not form a lens, recapitulating, thus the in vivo process (Figure 2) 4,5. This system of determining regeneration potential of dorsal and ventral iris cells is very useful in studying the role of genes and proteins involved in lens regeneration.

In newt, the lens regenerates always from the dorsal iris by transdifferentiation of the iris pigmented epithelial cells (IPEs). Here we describe a procedure to culture dorsal and ventral newt IPE cells and their implantation to the newt eye. The implanted cells are then studied by tissue sectioning and immunohistochemistry.

一个系统为培养虹膜色素上皮细胞，研究蝾螈镜头再生

Salamanders like newt and axolotl possess the ability to regenerate many of its lost body parts such as limbs, the tail with spinal cord, eye, brain, ...

A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica

Wild-type I. cylindrica (cogongrass) is one of the top ten worst invasive plants in the world, negatively impacting agricultural and natural resources in 73 different countries throughout Africa, Asia, Europe, New Zealand, Oceania and the Americas1-2. Cogongrass forms rapidly-spreading, monodominant stands that displace a large variety of native plant species and in turn threaten the native animals that depend on the displaced native plant species for forage and shelter. To add to the problem, an ornamental variety [I. cylindrica var. koenigii (Retzius)] is widely marketed under the names of Imperata cylindrica 'Rubra', Red Baron, and Japanese blood grass (JBG). This variety is putatively sterile and noninvasive and is considered a desirable ornamental for its red-colored leaves. However, under the correct conditions, JBG can produce viable seed (Carol Holko, 2009 personal communication) and can revert to a green invasive form that is often indistinguishable from cogongrass as it takes on the distinguishing characteristics of the wild-type invasive variety4 (Figure 1). This makes identification using morphology a difficult task even for well-trained plant taxonomists. Reversion of JBG to an aggressive green phenotype is also not a rare occurrence. Using sequence comparisons of coding and variable regions in both nuclear and chloroplast DNA, we have confirmed that JBG has reverted to the green invasive within the states of Maryland, South Carolina, and Missouri. JBG has been sold and planted in just about every state in the continental U.S. where there is not an active cogongrass infestation. The extent of the revert problem in not well understood because reverted plants are undocumented and often destroyed.
Application of this molecular protocol provides a method to identify JBG reverts and can help keep these varieties from co-occurring and possibly hybridizing. Cogongrass is an obligate outcrosser and, when crossed with a different genotype, can produce viable wind-dispersed seeds that spread cogongrass over wide distances5-7. JBG has a slightly different genotype than cogongrass and may be able to form viable hybrids with cogongrass. To add to the problem, JBG is more cold and shade tolerant than cogongrass8-10, and gene flow between these two varieties is likely to generate hybrids that are more aggressive, shade tolerant, and cold hardy than wild-type cogongrass. While wild-type cogongrass currently infests over 490 million hectares worldwide, in the Southeast U.S. it infests over 500,000 hectares and is capable of occupying most of the U.S. as it rapidly spreads northward due to its broad niche and geographic potential3,7,11. The potential of a genetic crossing is a serious concern for the USDA-APHIS Federal Noxious Week Program. Currently, the USDA-APHIS prohibits JBG in states where there are major cogongrass infestations (e.g., Florida, Alabama, Mississippi). However, preventing the two varieties from combining can prove more difficult as cogongrass and JBG expand their distributions. Furthermore, the distribution of the JBG revert is currently unknown and without the ability to identify these varieties through morphology, some cogongrass infestations may be the result of JBG reverts. Unfortunately, current molecular methods of identification typically rely on AFLP (Amplified Fragment Length Polymorphisms) and DNA sequencing, both of which are time consuming and costly. Here, we present the first cost-effective and reliable PCR-based molecular genotyping method to accurately distinguish between cogongrass and JBG revert.

A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica

We provide a cost-effective and rapid molecular genotyping protocol that employs variety-specific PCR primers that target DNA sequence differences within the chloroplast trnL-F spacer region to differentiate between varieties of Imperata cylindrica (cogongrass) that cannot be distinguished by morphology alone. These varieties include the federally listed noxious weed, cogongrass and closely-related, wide-spread ornamental variety, I. cylindrica var. koenigii (Japanese blood grass).

一个基于PCR的基因分型方法来区分野生型和观赏品种白茅</em

Wild-type I. cylindrica (cogongrass) is one of the top ten worst invasive plants in the world, negatively impacting agricultural and natural resources in ...

Visualization of Vascular Ca2+ Signaling Triggered by Paracrine Derived ROS

Oxidative stress has been implicated in a number of pathologic conditions including ischemia/reperfusion damage and sepsis. The concept of oxidative stress refers to the aberrant formation of ROS (reactive oxygen species), which include O2&bull;-, H2O2, and hydroxyl radicals. Reactive oxygen species influences a multitude of cellular processes including signal transduction, cell proliferation and cell death1-6. ROS have the potential to damage vascular and organ cells directly, and can initiate secondary chemical reactions and genetic alterations that ultimately result in an amplification of the initial ROS-mediated tissue damage. A key component of the amplification cascade that exacerbates irreversible tissue damage is the recruitment and activation of circulating inflammatory cells. During inflammation, inflammatory cells produce cytokines such as tumor necrosis factor-&alpha; (TNF&alpha;) and IL-1 that activate endothelial cells (EC) and epithelial cells and further augment the inflammatory response7. Vascular endothelial dysfunction is an established feature of acute inflammation. Macrophages contribute to endothelial dysfunction during inflammation by mechanisms that remain unclear. Activation of macrophages results in the extracellular release of O2&bull;- and various pro-inflammatory cytokines, which triggers pathologic signaling in adjacent cells8. NADPH oxidases are the major and primary source of ROS in most of the cell types. Recently, it is shown by us and others9,10 that ROS produced by NADPH oxidases induce the mitochondrial ROS production during many pathophysiological conditions. Hence measuring the mitochondrial ROS production is equally important in addition to measuring cytosolic ROS. Macrophages produce ROS by the flavoprotein enzyme NADPH oxidase which plays a primary role in inflammation. Once activated, phagocytic NADPH oxidase produces copious amounts of O2&bull;- that are important in the host defense mechanism11,12. Although paracrine-derived O2&bull;- plays an important role in the pathogenesis of vascular diseases, visualization of paracrine ROS-induced intracellular signaling including Ca2+ mobilization is still hypothesis. We have developed a model in which activated macrophages are used as a source of O2&bull;- to transduce a signal to adjacent endothelial cells. Using this model we demonstrate that macrophage-derived O2&bull;- lead to calcium signaling in adjacent endothelial cells.

Visualization of Vascular Ca2+ Signaling Triggered by Paracrine Derived ROS

An efficient method to gain insights into visualizing the paracrine-derived ROS induction of endothelial Ca2+ signaling is described. This method takes advantage of measuring paracrine derived ROS triggered Ca2+ mobilization in vascular endothelial cells in a co-culture model.

血管钙的可视化 2 +信号旁分泌源性活性氧引发

Oxidative stress has been implicated in a number of pathologic conditions including ischemia/reperfusion damage and sepsis. The concept of oxidative ...

A High-content Imaging Workflow to Study Grb2 Signaling Complexes by Expression Cloning

Signal transduction by growth factor receptors is essential for cells to maintain proliferation and differentiation and requires tight control. Signal transduction is initiated by binding of an external ligand to a transmembrane receptor and activation of downstream signaling cascades. A key regulator of mitogenic signaling is Grb2, a modular protein composed of an internal SH2 (Src Homology 2) domain flanked by two SH3 domains that lacks enzymatic activity. Grb2 is constitutively associated with the GTPase Son-Of-Sevenless (SOS) via its N-terminal SH3 domain. The SH2 domain of Grb2 binds to growth factor receptors at phosphorylated tyrosine residues thus coupling receptor activation to the SOS-Ras-MAP kinase signaling cascade. In addition, other roles for Grb2 as a positive or negative regulator of signaling and receptor endocytosis have been described. The modular composition of Grb2 suggests that it can dock to a variety of receptors and transduce signals along a multitude of different pathways1-3.
	Described here is a simple microscopy assay that monitors recruitment of Grb2 to the plasma membrane. It is adapted from an assay that measures changes in sub-cellular localization of green-fluorescent protein (GFP)-tagged Grb2 in response to a stimulus4-6. Plasma membrane receptors that bind Grb2 such as activated Epidermal Growth Factor Receptor (EGFR) recruit GFP-Grb2 to the plasma membrane upon cDNA expression and subsequently relocate to endosomal compartments in the cell. In order to identify in vivo protein complexes of Grb2, this technique can be used to perform a genome-wide high-content screen based on changes in Grb2 sub-cellular localization. The preparation of cDNA expression clones, transfection and image acquisition are described in detail below. Compared to other genomic methods used to identify protein interaction partners, such as yeast-two-hybrid, this technique allows the visualization of protein complexes in mammalian cells at the sub-cellular site of interaction by a simple microscopy-based assay. Hence both qualitative features, such as patterns of localization can be assessed, as well as the quantitative strength of the interaction.

A high-content screening method for the identification of novel signaling competent transmembrane receptors is described. This method is amenable to large-scale automation and allows predictions about in vivo protein binding and the sub-cellular localization of protein complexes in mammalian cells.

一个高含量的成像流程研究Grb2的信号复合体的表达克隆

Signal  transduction by growth factor receptors is essential for cells to maintain  proliferation and differentiation and requires tight control. Signal  ...

A Novel Ex vivo Culture Method for the Embryonic Mouse Heart

Developmental studies in the mouse are hampered by the inaccessibility of the embryo during gestation. Thus, protocols to isolate and culture individual organs of interest are essential to provide a method of both visualizing changes in development and allowing novel treatment strategies. To promote the long-term culture of the embryonic heart at late stages of gestation, we developed a protocol in which the excised heart is cultured in a semi-solid, dilute Matrigel. This substrate provides enough support to maintain the three-dimensional structure but is flexible enough to allow continued contraction. In brief, hearts are excised from the embryo and placed in a mixture of cold Matrigel diluted 1:1 with growth medium. After the diluted Matrigel solidifies, growth medium is added to the culture dish. Hearts excised as late as embryonic day 16.5 were viable for four days post-dissection. Analysis of the coronary plexus shows that this method does not disrupt coronary vascular development. Thus, we present a novel method for long-term culture of embryonic hearts.

A Novel Ex vivo Culture Method for the Embryonic Mouse Heart

Developmental studies in the mouse are hampered by the inaccessibility of the embryo during gestation. To promote the long-term culture of the embryonic heart at late stages of gestation, we developed a protocol in which the excised heart is cultured in a semi-solid, dilute Matrigel.

一种新型的<em&gt;体外</em小鼠胚胎心脏的培养方法

Developmental studies in the mouse are hampered  by the inaccessibility of the embryo during gestation. Thus, protocols to  isolate and culture individual ...

Mechanical Stimulation-induced Calcium Wave Propagation in Cell Monolayers: The Example of Bovine Corneal Endothelial Cells

Intercellular communication is essential for the coordination of physiological processes between cells in a variety of organs and tissues, including the brain, liver, retina, cochlea and vasculature. In experimental settings, intercellular Ca2+-waves can be elicited by applying a mechanical stimulus to a single cell. This leads to the release of the intracellular signaling molecules IP3 and Ca2+ that initiate the propagation of the Ca2+-wave concentrically from the mechanically stimulated cell to the neighboring cells. The main molecular pathways that control intercellular Ca2+-wave propagation are provided by gap junction channels through the direct transfer of IP3 and by hemichannels through the release of ATP. Identification and characterization of the properties and regulation of different connexin and pannexin isoforms as gap junction channels and hemichannels are allowed by the quantification of the spread of the intercellular Ca2+-wave, siRNA, and the use of inhibitors of gap junction channels and hemichannels. Here, we describe a method to measure intercellular Ca2+-wave in monolayers of primary corneal endothelial cells loaded with Fluo4-AM in response to a controlled and localized mechanical stimulus provoked by an acute, short-lasting deformation of the cell as a result of touching the cell membrane with a micromanipulator-controlled glass micropipette with a tip diameter of less than 1 &mu;m. We also describe the isolation of primary bovine corneal endothelial cells and its use as model system to assess Cx43-hemichannel activity as the driven force for intercellular Ca2+-waves through the release of ATP. Finally, we discuss the use, advantages, limitations and alternatives of this method in the context of gap junction channel and hemichannel research.

Intercellular Ca2+-waves are driven by gap junction channels and hemichannels. Here, we describe a method to measure intercellular Ca2+-waves in cell monolayers in response to a local single-cell mechanical stimulus and its application to investigate the properties and regulation of gap junction channels and hemichannels.

机械刺激引起的钙波传播的细胞单层:牛角膜内皮细胞的例子

Intercellular communication is essential for the coordination of physiological processes between cells in a variety of organs and tissues, including the ...

一种研究细胞间分泌信号的近距离培养方法

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