这项工作得到了 "1000plan 青年" 计划的支持, 同济大学的创业基金, 以及21607115和21777116的自然科学基金 (Lin)。

1. 斑马鱼胚胎排列模板的设计与制作
<ol><li>
设计排列模板的 12, 8, 96 井布局, 适合一个标准的96井板。使用图 1A中列出的用于上胚卡压室的尺寸 (请参阅补充文件)。
	<ol>
<li>使用在图 1B和1D中显示的用于陷井的尺寸。</li>
		<li>使用底部真空室的图 1C中的尺寸。</li>
		<li>将图 1B中的尺寸用于空气中/插座。</li>
	</ol>
</li>
	<li>使用 3 d 打印机 (0.1 mm 精度) 打印模板;有关用于打印的推荐树脂, 请参阅材料表。 注意: 推荐使用 0.1 mm 精度的3D 打印机来制作排列模板 (请参阅材料表)。模板表面的建议颜色为深灰色或黑色。</li>
</ol>2. 斑马鱼胚胎产卵
<ol><li>在产卵前的某一天放置两对雄性和雌性鱼。用透明的塑料分隔线将雄性和雌性分开。</li>
	<li>在早上摘下分隔条, 将雄性和雌性鱼混合在一起。</li>
	<li>用细网过滤器去除雄性和雌性鱼, 并收集鱼斑马的胚胎。用250毫升的鸡蛋水冲洗胚胎 (参见材料表)。</li>
	<li>用 Holtfreter 的溶液将采集到的胚胎移植到培养皿 (直径90毫米) 上 (参见材料表), 并使用显微镜去除未受精的胚胎。</li>
	<li>将胚胎放置在28.5 摄氏度的孵化器中。在 4 h 后受精 (hpf), 观察胚胎和清除任何死亡和不健康的胚胎。胚胎现在已经准备好下一步了。</li>
</ol>3. 排列模板的制备
<ol><li>用500毫升去离子水冲洗模板2–3时间, 并把它放入烘干烤箱 (45 °c) 为5分钟。</li>
	<li>用一块密封膜 (图 2, 步骤 1) 将底部腔带入磁带。</li>
	<li>通过模板底部的风口连接真空泵。 注: 推荐的真空泵最大真空度为0.1 兆帕。要注意使用的真空强度。如果负压过强, 则在密封膜上切开一个十字形孔, 以降低压力。</li>
</ol>4. 将斑马鱼胚胎排列成96井板
<ol><li>使用塑料转移吸管, 将大约150个胚胎放置到模板中, 如图 2,步骤2所示。</li>
	<li>将真空泵与风口连接, 以在步骤3.3 中密封膜密封的腔内产生负压。</li>
	<li>水平摇动整个模板, 直到每个井都有一个胚胎被包埋 (图 2,步骤 3)。 注: 如果 Holtfreter 的解决方案在每个井中被困之前都干涸了, 在诱捕室添加额外的 Holtfreter 溶液并重复此步骤。</li>
	<li>丢弃未被埋在水井中的额外 Holtfreter 的解决方案和胚胎 (图 2,步骤 4)。</li>
	<li>关闭并断开真空泵的连接。</li>
	<li>将标准的96井板倒置到模板上 (图 2,步骤 5), 同时同时旋转两个 (图 2,步骤 6)。</li>
	<li>点击模板底部或连接空气出口到压缩气体除尘可以将所有被困胚胎从模板转移到96井板 (图 2,步骤 6)。</li>
	<li>重复步骤4.1 到 4.8, 准备额外的多井板。</li>
	<li>取下密封膜, 用500毫升去离子水从上到下清洗模板3次, 供将来使用。 注: 不要使用任何有机溶剂, 如乙醇, 清洁模板。</li>
</ol>

<ol>
	<li>Howe, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+zebrafish+reference+genome+sequence+and+its+relationship+to+the+human+genome.">The zebrafish reference genome sequence and its relationship to the human genome.</a> Nature. 496 (7446), 498-503 (2013).</li><li>Leslie, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Zebrafish+larvae+could+help+to+personalize+cancer+treatments.">Zebrafish larvae could help to personalize cancer treatments.</a> Science. 357 (6353), 745-745 (2017).</li><li>Lin, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Understanding+the+Transformation,+Speciation,+and+Hazard+Potential+of+Copper+Particles+in+a+Model+Septic+Tank+System+Using+Zebrafish+to+Monitor+the+Effluent.">Understanding the Transformation, Speciation, and Hazard Potential of Copper Particles in a Model Septic Tank System Using Zebrafish to Monitor the Effluent.</a> ACS Nano. 9 (2), 2038-2048 (2015).</li><li>Lin, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aspect+ratio+plays+a+role+in+the+hazard+potential+of+ceo2+nanoparticles+in+mouse+lung+and+zebrafish+gastrointestinal+tract.">Aspect ratio plays a role in the hazard potential of ceo2 nanoparticles in mouse lung and zebrafish gastrointestinal tract.</a> ACS Nano. 8 (5), 4450-4464 (2014).</li><li>Baraban, S. C., Dinday, M. T., Hortopan, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drug+screening+in+Scn1a+zebrafish+mutant+identifies+clemizole+as+a+potential+Dravet+syndrome+treatment.">Drug screening in Scn1a zebrafish mutant identifies clemizole as a potential Dravet syndrome treatment.</a> Nature Communications. 4, (2013).</li><li>Lin, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High+content+screening+in+zebrafish+speeds+up+hazard+ranking+of+transition+metal+oxide+nanoparticles.">High content screening in zebrafish speeds up hazard ranking of transition metal oxide nanoparticles.</a> ACS Nano. 5 (9), 7284-7295 (2011).</li><li>Kuipers, J., Kalicharan, R. D., Wolters, A. H. G., van Ham, T. J., Giepmans, B. N. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-scale+Scanning+Transmission+electron+microscopy+(nanotomy)+of+healthy+and+injured+zebrafish+brain.">Large-scale Scanning Transmission electron microscopy (nanotomy) of healthy and injured zebrafish brain.</a> Journal of Visualized Experiments. (111), (2016).</li><li>Liu, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+Phenotype+Recognition+for+Zebrafish+Embryo+Based+In+vivo+High+Throughput+Toxicity+Screening+of+Engineered+Nano-Materials.">Automated Phenotype Recognition for Zebrafish Embryo Based In vivo High Throughput Toxicity Screening of Engineered Nano-Materials.</a> PLoS One. 7 (4), (2012).</li><li>Tu, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automatic+Categorization+and+Scoring+of+Solid,+Part-Solid+and+Non-Solid+Pulmonary+Nodules.">Automatic Categorization and Scoring of Solid, Part-Solid and Non-Solid Pulmonary Nodules.</a> in CT Images with Convolutional Neural Network. Scientific Reports. 7, 8533 (2017).</li><li>Mandrell, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+zebrafish+chorion+removal+and+single+embryo+placement:+optimizing+throughput+of+zebrafish+developmental+toxicity+screens.">Automated zebrafish chorion removal and single embryo placement: optimizing throughput of zebrafish developmental toxicity screens.</a> Journal of Laboratory Automation. 17 (1), 66-74 (2012).</li><li>Lin, S., Zhao, Y., Nel, A. E., Lin, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Zebrafish:+An+in+vivo+model+for+nano+EHS+studies.">Zebrafish: An in vivo model for nano EHS studies.</a> Small. 9 (9-10), 1608-1618 (2013).</li></ol>

作者在所描述的 3 d 打印模板上填写了一项专利。

该协议中有两个关键步骤需要密切注意, 以成功地实施 3 d 打印模板排列斑马鱼胚胎。
排列模板设计中最重要的因素是诱捕井。为了确保每个井中只有一个胚胎被困, 人们应该密切关注压井的直径和深度, 以及通孔的直径。建议的直径在一个典型的胚胎 (包括绒毛膜) 直径的1.5 到2倍之内。诱捕井的深度应在典型胚胎 (包括绒毛膜) 直径的2倍以内, 以避免在同一井中堆积胚胎。通?...

斑马鱼作为一种流行的模型生物, 广泛应用于医学和毒物学领域1,2,3,4。与体外平台相比, 斑马鱼提供了更大的生物复杂性, 即一个或两种细胞无法提供。除了作为一个整体的生物模型, 斑马鱼的巨大繁殖力, 快速和同时胚胎发育, 和高器官半透明已经给这个模型独特的优势, 用于大规模毒性或药物/复合筛查5。一双成年斑马鱼每周生产的数以百计的胚胎超过了其他所有的动物模型, 并使其适合高通量筛选。
一个典型的筛选程序使用斑马鱼涉及大量的手工工作, 如成年斑马鱼产卵, 胚胎选择, 并排列胚胎进入适当的容器, 他们通过水浸泡暴露。对胚胎的发育进行监测, 可观察到的端点, 如死亡率、孵化率和异常, 通常是手动评估的, 并作为化学品毒性的初步鉴定或指示药物或化合物。为了加快筛选程序, 前面已经探讨了自动成像和计算机辅助图像分析等方法。例如, 具有高含量成像能力的显微镜已经适应了从96/384 井板6的不同发育阶段对斑马鱼胚胎进行自动亮场或荧光成像。微流控装置与显微镜结合使用, 用于定位斑马鱼幼虫通过当前操作的大脑神经元的成像7。与传统的手工操作相比, 这些方法可以显著提高图像获取的效率。此外, 在生成大量图像的同时, 还开发了图像分析工具以加快数据处理速度, 如刘et和 Tu et . 所示。8,9。
随着成像和图像分析的吞吐量水平的提高, 显而易见的是, 筛查速率限制的步骤在于准备用于暴露的斑马鱼胚胎, 这通常意味着将它们排列到96或384井板中。为解决这一瓶颈步骤, Mandrell 开发了视觉导引机器人. 10和美国11以前替换手动处理, 但这些工具相当复杂, 并且有一个深入的学习曲线来实现这些技术。因此, 提供一种易于使用的方法成为进一步提高斑马鱼筛查吞吐量水平的一个重要因素, 是这项工作的主要目标。
在这项工作中, 我们设计和制造了一个胚胎排列模板3D 打印。这种排列模板的设计, 以诱捕斑马鱼胚胎进入水井, 符合标准的96井板。而不是选择胚胎和排列他们一个一个一个一个, 你可以执行胚胎诱捕和阵列所有96胚胎成一个多层板一次。使用这个模板和下面的协议, 你可以显著提高排列胚胎的效率到多层板, 这将在短期内提高筛选能力至少比手工操作。下面描述的协议包括排列模板、斑马鱼产卵、胚胎采集和排列的总体设计。图 1显示了排列模板的总体设计。图 2显示了使用部件3和4中描述的模板的分步协议概述。

<table border="0" cellpadding="0" cellspacing="0" width="1557">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Zebrafish Facility</td>
			<td style="width:425px;">Shanghai Haisheng Biotech Co., Ltd.</td>
			<td style="width:229px;">Z-A-S5</td>
			<td style="width:429px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Mating box</td>
			<td style="width:425px;">Shanghai Haisheng Biotech Co., Ltd.</td>
			<td style="width:229px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Wash Bottle, 500 ml</td>
			<td style="width:425px;">Sangon Biotech</td>
			<td style="width:229px;">F505001-0001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium chloride</td>
			<td style="width:425px;">Vetec</td>
			<td style="width:229px;">V900058-500G</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Potassium Chloride</td>
			<td style="width:425px;">Sinopharm Chemical Reagent Co.,Ltd</td>
			<td style="width:229px;">10016318</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Calcium chloride</td>
			<td style="width:425px;">Sinopharm Chemical Reagent Co.,Ltd</td>
			<td style="width:229px;">20011160</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium bicarbonate&#160;</td>
			<td style="width:425px;">Vetec</td>
			<td style="width:229px;">v900182-500G</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Methylene Blue Hydrate</td>
			<td style="width:425px;">TCI</td>
			<td style="width:229px;">M0501</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Hydrochloric acid</td>
			<td style="width:425px;">Sinopharm Chemical Reagent Co.,Ltd</td>
			<td style="width:229px;">10011008</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Sea Salts</td>
			<td>Instant Ocean</td>
			<td style="width:229px;">SS15-10</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pipetter</td>
			<td style="width:425px;">Fisherbrand</td>
			<td style="width:229px;">13-675M</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Controlled Drop Pasteur Pipet</td>
			<td style="width:425px;">Fisherbrand</td>
			<td style="width:229px;">13-678-30</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Microscope</td>
			<td style="width:425px;">OLYMPUS</td>
			<td style="width:229px;">SZ61</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Biochemical incubator</td>
			<td>Shanghai Yiheng Scientific Instrument Co., Ltd.</td>
			<td>LRH-250</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">3D printer</td>
			<td>UnionTech</td>
			<td>Lite600</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Photosensitive resin</td>
			<td>UnionTech</td>
			<td>UTR9000</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Vacuum pump</td>
			<td>Shanghai Yukang Scientific Instrument Co., Ltd.</td>
			<td>SHB-IIIA</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Adhesive PCR Plate Seals</td>
			<td style="width:425px;">Solarbio</td>
			<td style="width:229px;">YA0245</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">96 well plate</td>
			<td style="width:425px;">Costar</td>
			<td style="width:229px;">3599</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Multi 8-channel pipette 30 - 300 &#956;l</td>
			<td style="width:425px;">Eppendorf</td>
			<td style="width:229px;">3122000.051</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Compressed Gas Duster</td>
			<td style="width:425px;">Shanghai Zhantu Chemical Co., Ltd.</td>
			<td style="width:229px;">ST1005</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">DI Water</td>
			<td style="width:425px;">Thermo</td>
			<td style="width:229px;">GenPure Pro UV/UF</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">Drying oven</td>
			<td style="width:425px;">Shanghai Yiheng Scientific Instrument Co., Ltd.</td>
			<td style="width:229px;">BPG-9106A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:475px;">System water</td>
			<td style="width:425px;"></td>
			<td style="width:229px;"></td>
			<td style="width:429px;">Water out of the facility&#8217;s water system</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:475px;">Egg water</td>
			<td style="width:425px;"></td>
			<td style="width:229px;"></td>
			<td style="width:429px;">Dilute 60mg &#8220;Instant Ocean&#8221; sea salts and 0.25 mg/L methylene blue in 1 L DI water</td>
		</tr>
		<tr height="116">
			<td height="116" style="height:116px;width:475px;">Holtfreter&#8217;s solution</td>
			<td style="width:425px;"></td>
			<td style="width:229px;"></td>
			<td style="width:429px;">Dissolve 7.0 g Sodium chloride (NaCl), 0.4 g Sodium bicarbonate (NaHCO3), 0.1 g Potassium Chloride (KCl), 0.235 g Calcium chloride (CaCl2.2H2O) in 1.9 L DI water. Adjust pH to 7 using HCl and adjust volume to 2 L using Di water</td>
		</tr>
	</tbody>
</table>

a 3-dimensional (3d)-printed template for high throughput zebrafish embryo arraying

斑马鱼是全球公认的淡水有机体, 经常用于发展生物学、环境毒理学和人类疾病相关的研究领域。由于其独特的特点, 包括大的繁殖力, 胚胎半透明, 快速和同时发展,等, 斑马鱼胚胎经常被用于对化学品进行大规模毒性评估和药物/复合筛查。一个典型的筛选程序涉及成年斑马鱼产卵, 胚胎选择, 并排列胚胎成多井板块。从那里, 胚胎受到接触和化学的毒性, 或者药物/化合物的有效性可以根据表型观察相对快速地评估。在这些过程中, 胚胎排列是限制吞吐量水平的最耗时和最耗费劳力的步骤之一。在本协议中, 我们提出了一种创新的方法, 使用一个 3 d 打印排列模板加上真空操作, 以加快这一艰巨的步骤。此处的协议描述了排列模板的总体设计, 详细的实验设置和分步过程, 随后有代表性的结果。在实施时, 这种方法应证明是有益的, 以斑马鱼胚胎作为测试对象的各种研究应用。

图 3显示了典型的 3 d 打印的排列模板。本模板采用光敏树脂为原料, 由3D 打印机制成;用一层黑色颜料, 可以更好地对比胚胎的颜色。96口井 (12 8) 的位置设计为符合标准96井板。同样, 384 (24 乘 16) 井模板也可以使用相同的方法设计和制作。向上的房间稍大于标准的96井板, 以提供一个更好的配件。凹槽也被设计用来在排列期间容纳额外的胚胎。
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A 3-dimensional 3D-printed Template for High Throughput Zebrafish Embryo Arraying

在这里, 我们提出了一个设计和制造斑马鱼胚胎排列模板的协议, 然后详细的程序, 使用这种模板, 高吞吐量斑马鱼胚胎排列成96井板。

3维 (3 d) 印制的高吞吐量斑马鱼胚胎排列模板

The zebrafish is a globally recognized fresh water organism frequently used in developmental biology, environmental toxicology, and human disease related ...

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A 3-dimensional (3D)-printed Template for High Throughput Zebrafish Embryo Arraying

6.7K 次观看.  Tongji University. 在这里, 我们提出了一个设计和制造斑马鱼胚胎排列模板的协议, 然后详细的程序, 使用这种模板, 高吞吐量斑马鱼胚胎排列成96井板。

视频: A 3-dimensional 3D-printed Template for High Throughput Zebrafish Embryo Arraying

Determination of Microbial Extracellular Enzyme Activity in Waters, Soils, and Sediments using High Throughput Microplate Assays

Much of the nutrient cycling and carbon processing in natural environments occurs through the activity of extracellular enzymes released by microorganisms. Thus, measurement of the activity of these extracellular enzymes can give insights into the rates of ecosystem level processes, such as organic matter decomposition or nitrogen and phosphorus mineralization. Assays of extracellular enzyme activity in environmental samples typically involve exposing the samples to artificial colorimetric or fluorometric substrates and tracking the rate of substrate hydrolysis. Here we describe microplate based methods for these procedures that allow the analysis of large numbers of samples within a short time frame. Samples are allowed to react with artificial substrates within 96-well microplates or deep well microplate blocks, and enzyme activity is subsequently determined by absorption or fluorescence of the resulting end product using a typical microplate reader or fluorometer. Such high throughput procedures not only facilitate comparisons between spatially separate sites or ecosystems, but also substantially reduce the cost of such assays by reducing overall reagent volumes needed per sample.

Microplate based procedures are described for the colorimetric or fluorometric analysis of extracellular enzyme activity. These procedures allow for the rapid assay of such activity in large numbers of environmental samples within a manageable time frame.

在使用高通量微孔板测定水，土壤，沉积物和微生物测定胞外酶活性的

Much of the nutrient cycling and carbon  processing in natural environments occurs through the activity of extracellular  enzymes released by ...

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环境科学

High-throughput Fluorometric Measurement of Potential Soil Extracellular Enzyme Activities

Microbes in soils and other environments produce extracellular enzymes to depolymerize and hydrolyze organic macromolecules so that they can be assimilated for energy and nutrients. Measuring soil microbial enzyme activity is crucial in understanding soil ecosystem functional dynamics. The general concept of the fluorescence enzyme assay is that synthetic C-, N-, or P-rich substrates bound with a fluorescent dye are added to soil samples. When intact, the labeled substrates do not fluoresce. Enzyme activity is measured as the increase in fluorescence as the fluorescent dyes are cleaved from their substrates, which allows them to fluoresce. Enzyme measurements can be expressed in units of molarity or activity. To perform this assay, soil slurries are prepared by combining soil with a pH buffer. The pH buffer (typically a 50 mM sodium acetate or 50 mM Tris buffer), is chosen for the buffer&#39;s particular acid dissociation constant (pKa) to best match the soil sample pH. The soil slurries are inoculated with a nonlimiting amount of fluorescently labeled (i.e. C-, N-, or P-rich) substrate. Using soil slurries in the assay serves to minimize limitations on enzyme and substrate diffusion. Therefore, this assay controls for differences in substrate limitation, diffusion rates, and soil pH conditions; thus detecting potential enzyme activity rates as a function of the difference in enzyme concentrations (per sample).
Fluorescence enzyme assays are typically more sensitive than spectrophotometric (i.e. colorimetric) assays,&#160;but can suffer from interference caused by impurities and the instability of many fluorescent compounds when exposed to light; so caution is required when handling fluorescent substrates. Likewise, this method only assesses potential enzyme activities under laboratory conditions when substrates are not limiting. Caution should be used when interpreting the data representing cross-site comparisons with differing temperatures or soil types, as in situ soil type and temperature can influence enzyme kinetics.

To measure potential rates of soil extracellular enzyme activities, synthetic substrates that are bound to a fluorescent dye are added to soil samples. Enzyme activity is measured as the fluorescent dye is released from the substrate by an enzyme-catalyzed reaction, where higher fluorescence indicates more substrate degradation.

潜在土壤胞外酶活性的高通量荧光测量

Microbes in soils and other environments produce extracellular enzymes to depolymerize and hydrolyze organic macromolecules so that they can be ...

Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

Structural determination of proteins is rather challenging for proteins with molecular masses between 40 - 200 kDa. Considering that more than half of natural proteins have a molecular mass between 40 - 200 kDa1,2, a robust and high-throughput method with a nanometer resolution capability is needed. Negative staining (NS) electron microscopy (EM) is an easy, rapid, and qualitative approach which has frequently been used in research laboratories to examine protein structure and protein-protein interactions. Unfortunately, conventional NS protocols often generate structural artifacts on proteins, especially with lipoproteins that usually form presenting rouleaux artifacts. By using images of lipoproteins from cryo-electron microscopy (cryo-EM) as a standard, the key parameters in NS specimen preparation conditions were recently screened and reported as the optimized NS protocol (OpNS), a modified conventional NS protocol 3 . Artifacts like rouleaux can be greatly limited by OpNS, additionally providing high contrast along with reasonably high&#8208;resolution (near 1 nm) images of small and asymmetric proteins. These high-resolution and high contrast images are even favorable for an individual protein (a single object, no average) 3D reconstruction, such as a 160 kDa antibody, through the method of electron tomography4,5. Moreover, OpNS can be a high&#8208;throughput tool to examine hundreds of samples of small proteins. For example, the previously published mechanism of 53 kDa cholesteryl ester transfer protein (CETP) involved the screening and imaging of hundreds of samples 6. Considering cryo-EM rarely successfully images proteins less than 200 kDa has yet to publish any study involving screening over one hundred sample conditions, it is fair to call OpNS a high-throughput method for studying small proteins. Hopefully the OpNS protocol presented here can be a useful tool to push the boundaries of EM and accelerate EM studies into small protein structure, dynamics and mechanisms.

More than half of proteins are small proteins (molecular mass &#60;200 kDa) that are challenging for both electron microscope imaging and three-dimensional reconstructions. Optimized negative staining is a robust and high-throughput protocol to obtain high contrast and relatively high resolution (~1 nm) images of small asymmetric proteins or complexes under different physiological conditions.

优化负染:通过电子显微镜检查小和不对称蛋白结构的高通量协议

Structural determination of proteins is rather challenging for proteins with molecular masses between 40 - 200 kDa. Considering that more than half of ...

Semi-High Throughput Screening for Potential Drought-tolerance in Lettuce (Lactuca sativa) Germplasm Collections

This protocol describes a method by which a large collection of the leafy green vegetable lettuce (Lactuca sativa L.) germplasm was screened for likely drought-tolerance traits. Fresh water availability for agricultural use is a growing concern across the United States as well as many regions of the world. Short-term drought events along with regulatory intervention in the regulation of water availability coupled with the looming threat of long-term climate shifts that may lead to reduced precipitation in many important agricultural regions has increased the need to hasten the development of crops adapted for improved water use efficiency in order to maintain or expand production in the coming years. This protocol is not meant as a step-by-step guide to identifying at either the physiological or molecular level drought-tolerance traits in lettuce, but rather is a method developed and refined through the screening of thousands of different lettuce varieties. The nature of this screen is based in part on the streamlined measurements focusing on only three water-stress indicators: leaf relative water content, wilt, and differential plant growth following drought-stress. The purpose of rapidly screening a large germplasm collection is to narrow the candidate pool to a point in which more intensive physiological, molecular, and genetic methods can be applied to identify specific drought-tolerant traits in either the lab or field. Candidates can also be directly incorporated into breeding programs as a source of drought-tolerance traits.

Semi-High Throughput Screening for Potential Drought-tolerance in Lettuce Lactuca sativa Germplasm Collections

This protocol was developed to screen a large germplasm collection of the leafy vegetable lettuce (Lactuca sativa L.) for drought-tolerance, in order to identify a small candidate pool of lettuce for use in physiological, molecular, and genetic studies to identify underlying drought-tolerance traits along with breeding programs.

半高通量筛选潜在的抗干旱的生菜（<em&gt;莴苣</em&gt;）种质资源

This protocol describes a method by which a large collection of the leafy green vegetable lettuce (Lactuca sativa L.) germplasm was screened for likely ...

High-throughput Screening of Recalcitrance Variations in Lignocellulosic Biomass: Total Lignin, Lignin Monomers, and Enzymatic Sugar Release

The conversion of lignocellulosic biomass to fuels, chemicals, and other commodities has been explored as one possible pathway toward reductions in the use of non-renewable energy sources. In order to identify which plants, out of a diverse pool, have the desired chemical traits for downstream applications, attributes, such as cellulose and lignin content, or monomeric sugar release following an enzymatic saccharification, must be compared. The experimental and data analysis protocols of the standard methods of analysis can be time-consuming, thereby limiting the number of samples that can be measured. High-throughput (HTP) methods alleviate the shortcomings of the standard methods, and permit the rapid screening of available samples to isolate those possessing the desired traits. This study illustrates the HTP sugar release and pyrolysis-molecular beam mass spectrometry pipelines employed at the National Renewable Energy Lab. These pipelines have enabled the efficient assessment of thousands of plants while decreasing experimental time and costs through reductions in labor and consumables.

Plant cell wall structure and chemistry traits are evaluated to identify ideal feedstocks for biofuels and bio-materials. Standard methods have limitations when applied to large data sets. These high-throughput pretreatment, enzyme saccharification, and pyrolysis-molecular beam mass spectrometry methods compare large numbers of biomass samples with decreased experimental time and cost.

总木质素，木质素单体，和酶促糖推出:顽拗变奏曲在木质纤维素生物质的高通量筛选

The conversion of lignocellulosic biomass to fuels, chemicals, and other commodities has been explored as one possible pathway toward reductions in the ...

RGB and Spectral Root Imaging for Plant Phenotyping and Physiological Research: Experimental Setup and Imaging Protocols

Better understanding of plant root dynamics is essential to improve resource use efficiency of agricultural systems and increase the resistance of crop cultivars against environmental stresses. An experimental protocol is presented for RGB and hyperspectral imaging of root systems. The approach uses rhizoboxes where plants grow in natural soil over a longer time to observe fully developed root systems. Experimental settings are exemplified for assessing rhizobox plants under water stress and studying the role of roots. An RGB imaging setup is described for cheap and quick quantification of root development over time. Hyperspectral imaging improves root segmentation from the soil background compared to RGB color based thresholding. The particular strength of hyperspectral imaging is the acquisition of chemometric information on the root-soil system for functional understanding. This is demonstrated with high resolution water content mapping. Spectral imaging however is more complex in image acquisition, processing and analysis compared to the RGB approach. A combination of both methods can optimize a comprehensive assessment of the root system. Application examples integrating root and aboveground traits are given for the context of plant phenotyping and plant physiological research. Further improvement of root imaging can be obtained by optimizing RGB image quality with better illumination using different light sources and by extension of image analysis methods to infer on root zone properties from spectral data.

An experimental protocol is presented for assessment of soil grown plant root systems with RGB and hyperspectral imaging. Combination of RGB image time series with chemometric information from hyperspectral scans optimizes insights into plant root dynamics.

RGB 和光谱根成像植物表型和生理研究: 实验装置和成像协议

Better understanding of plant root dynamics is essential to improve resource use efficiency of agricultural systems and increase the resistance of crop ...

Basic Research in Plasma Medicine - A Throughput Approach from Liquids to Cells

In plasma medicine, ionized gases with temperatures close to that of vertebrate systems are applied to cells and tissues. Cold plasmas generate reactive species known to redox regulate biological processes in health and disease. Pre-clinical and clinical evidence points to beneficial effects of plasma treatment in the healing of chronic ulcer of the skin. Other emerging topics, such as plasma cancer treatment, are receiving increasing attention. Plasma medical research requires interdisciplinary expertise in physics, chemistry, and biomedicine. One goal of plasma research is to characterize plasma-treated cells in a variety of specific applications. This includes, for example, cell count and viability, cellular oxidation, mitochondrial activity, cytotoxicity and mode of cell death, cell cycle analysis, cell surface marker expression, and cytokine release. This study describes the essential equipment and workflows required for such research in plasma biomedicine. It describes the proper operation of an atmospheric pressure argon plasma jet, specifically monitoring its basic emission spectra and feed gas settings to modulate reactive species output. Using a high-precision xyz-table and computer software, the jet is hovered in millisecond-precision over the cavities of 96-well plates in micrometer-precision for maximal reproducibility. Downstream assays for liquid analysis of redox-active molecules are shown, and target cells are plasma-treated. Specifically, melanoma cells are analyzed in an efficient sequence of different consecutive assays but using the same cells: measurement of metabolic activity, total cell area, and surface marker expression of calreticulin, a molecule important for the immunogenic cell death of cancer cells. These assays retrieve content-rich biological information about plasma effects from a single plate. Altogether, this study describes the essential steps and protocols for plasma medical research.

A high-throughput cold physical plasma treatment protocol of liquids and cells is shown. It involves setting up different feed gas compositions for plasma ignition, measuring the plasma&#39;s emission spectra, and the subsequent analysis of liquids and cellular activity after plasma treatment.

等离子体医学基础研究--从液体到细胞的吞吐量方法

In plasma medicine, ionized gases with temperatures close to that of vertebrate systems are applied to cells and tissues. Cold plasmas generate reactive ...

High-throughput, Microscale Protocol for the Analysis of Processing Parameters and Nutritional Qualities in Maize (Zea mays L.)

Maize is an important grain crop in the United States and worldwide. However, maize grain must be processed prior to human consumption. Furthermore, whole grain composition and processing characteristics vary among maize hybrids and can impact the quality of the final processed product. Therefore, in order to produce healthier processed food products from maize, it is necessary to know how to optimize processing parameters for particular sets of germplasm to account for these differences in grain composition and processing characteristics. This includes a better understanding of how current processing techniques impact the nutritional quality of the final processed food product. Here, we describe a microscale protocol that both simulates the processing pipeline to produce cornflakes from large flaking grits and allows for the processing of multiple grain samples simultaneously. The flaking grits, the intermediate processed products, or final processed product, as well as the corn grain itself, can be analyzed for nutritional content as part of a high-throughput analytical pipeline. This procedure was developed specifically for incorporation into a maize breeding research program, and it can be modified for other grain crops. We provide an example of the analysis of insoluble-bound ferulic acid and p-coumaric acid content in maize. Samples were taken at five different processing stages. We demonstrate that sampling can take place at multiple stages during microscale processing, that the processing technique can be utilized in the context of a specialized maize breeding program, and that, in our example, most of the nutritional content was lost during food product processing.

High-throughput, Microscale Protocol for the Analysis of Processing Parameters and Nutritional Qualities in Maize Zea mays L.

Here, we present a microscale protocol for processing grain samples and for incorporating this microscale approach into a high-throughput analytical pipeline. This is a higher throughput adaptation of currently available protocols.

玉米加工参数和营养品质分析的高通量、微尺度协议 (玉蜀黍)

Maize is an important grain crop in the United States and worldwide. However, maize grain must be processed prior to human consumption. Furthermore, whole ...

Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures

Natural organic matter (NOM) is composed of a highly complex mixture of thousands of organic compounds which, historically, proved difficult to characterize. However, to understand the thermodynamic and kinetic controls on greenhouse gas (carbon dioxide [CO2] and methane [CH4]) production resulting from the decomposition of NOM, a molecular-level characterization coupled with microbial proteome analyses is necessary. Further, climate and environmental changes are expected to perturb natural ecosystems, potentially upsetting complex interactions that influence both the supply of organic matter substrates and the microorganisms performing the transformations. A detailed molecular characterization of the organic matter, microbial proteomics, and the pathways and transformations by which organic matter is decomposed will be necessary to predict the direction and magnitude of the effects of environmental changes. This article describes a methodological throughput for comprehensive metabolite characterization in a single sample by direct injection Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), gas chromatography mass spectrometry (GC-MS), nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography mass spectrometry (LC-MS), and proteomics analysis. This approach results in a fully-paired dataset which improves statistical confidence for inferring pathways of organic matter decomposition, the resulting CO2 and CH4 production rates, and their responses to environmental perturbation. Herein we present results of applying this method to NOM samples collected from peatlands; however, the protocol is applicable to any NOM sample (e.g., peat, forested soils, marine sediments, etc.).

This protocol describes a single throughput for complementary analytical and omics techniques culminating in a fully-paired characterization of natural organic matter and microbial proteomics in different ecosystems. This approach permits robust comparisons for identifying metabolic pathways and transformations important for describing greenhouse gas production and predicting responses to environmental change.

用于表征复杂天然有机物混合物的单吞吐量互补高分辨率分析技术

Natural organic matter (NOM) is composed of a highly complex mixture of thousands of organic compounds which, historically, proved difficult to ...

Evaluation of the Productivity of Social Wasp Colonies (Vespinae) and an Introduction to the Traditional Japanese Vespula Wasp Hunting Technique

For vespine wasps, colony productivity is typically estimated by counting the number of larval cells. This paper presents an improved method that enables researchers to estimate more accurately the number of adults produced, counting the number of meconia (the stools left in the cells by wasp larvae when pupating into adults, per 100 cells) in each comb. This method can be applied before or after colony collapse (i.e., in active or inactive nests). The paper also describes how to locate wild Vespula wasp colonies by &#34;flagging&#34; wasp baits and chasing the wasp collecting them, using a method traditionally performed by local people in central Japan (as illustrated in the associated video). The Vespula chasing method described has several advantages: it is easy to reinitiate the chase from a point where the forager flying back to the nest was lost, and it is easy to pinpoint the nest location as marked wasps often lose their flag at the nest entrance. These methods for estimating colony productivity and collecting nests can be valuable for researchers studying social wasps.

Evaluation of the Productivity of Social Wasp Colonies Vespinae and an Introduction to the Traditional Japanese Vespula Wasp Hunting Technique

This methodological paper evaluates the productivity of a social wasp colony by examining the number of meconia per 100 cells of comb, to estimate the total number of adults the wasps produced. The associated video describes how to search for Vespula wasp nests, a method developed by amateur wasp chasers.

社会黄蜂群落（韦皮纳）生产力评价及日本传统黄蜂狩猎技术简介

For vespine wasps, colony productivity is typically estimated by counting the number of larval cells. This paper presents an improved method that enables ...