We thank Donna Epps, histologist at Institute for Genomic Biology, University of Illinois Urbana-Champaign (UIUC), for her capable technical assistance in sample preparation and sectioning. This work was supported by a research grant to B.W. Fouke from the Office of Naval Research (N00014-00-1-0609). In addition, C.A.H. Miller received grants from the UIUC Department of Geology Wanless Fellowship, UIUC Department of Geology Leighton fund and UIUC Department of Geology Roscoe Jackson fieldwork fund. Interpretations presented in this manuscript are those of the authors and may not necessarily represent those of the granting institutions. We also thank the Caribbean Research and Management of Biodiversity (Carmabi) laboratory on Cura&#231;ao for their support and collaboration in collecting the coral tissue biopsy samples. We thank Claudia Lutz, IGB Media Communication Specialist for her able language correction.

被珊瑚样品的连续块面成像试剂准备：注意 1 Preinfiltration蜡<ol><li>熔融3.6克硬脂薄片在玻璃烧杯中。在热板（60-70℃）拌匀。 </li><li>添加400毫克苏丹红四号的（最小化蜡背景荧光）。搅拌均匀，等到红色半透明的解决方案来实现的。 </li><li>新增96毫升热熔融石蜡（100％），搅拌均匀。 </li></ol> 1.2）嵌入蜡<ol><li>熔体7.2克硬脂精片的玻璃烧杯中搅拌均匀的热板（60-70℃）。 </li><li>添加0.8克苏丹四。搅拌均匀，等到红色半透明的解决方案来实现的。 </li><li>添加石蜡粒（161克），搅拌至融化石蜡完全。 </li><li>加入30克白色粒状VYBAR并在相同的烧杯中完全熔化;一旦融化，混匀。 </li><li>松散关闭有盖的玻璃瓶。将玻璃瓶在60℃对流OV烯以保持各组分在液体状态。开展这一炉的所有渗透。 </li><li>分裂200毫升红蜡的总体积中，以两片玻璃瓶每次100毫升。使用一个等分试样进行渗透，另一个用于最终嵌入。 </li></ol> 1.3）嵌入珊瑚组织的串行块面成像<ol><li> （在4-5℃，在多聚甲醛3-6个月）在磷酸盐缓冲盐水（3×5分钟）洗涤收集在字段（SI视频1），并存储在珊瑚虫和脱钙当准备进行成像。除垢在ExCal解决方案息肉24小时，或者直到为息肉是完全没有的CaCO 3。培育若干脱钙珊瑚虫为单块的25，50，75，和100％的乙醇系列，其次是1X二甲苯替代品脱水的样品。 </li><li>将处理过的息肉含100％二甲苯代替预热65℃的烘箱。樟宜孵育30分钟两次ng到新鲜的解决方案。定向成这样的息肉的息肉的顶端朝下，顶表面是尽可能平坦。 </li><li>使2解决方案：1，1:1和1:2二甲苯替代品和preinfiltration蜡（步骤1.1）在50毫升猎鹰管。 </li><li>孵育珊瑚虫与这三个浓度增加preinfiltration蜡中，随后3次温育在100％preinfiltration蜡，每次30-60分钟。 </li><li>注意：根据样品的厚度，步骤1.3.1-1.3.5可以随时间较长。 </li><li>将样品包埋蜡（见步骤1.2.6）在100％preinfiltration蜡3×孵育后。 </li><li> 30分钟后，取出嵌入蜡。更换新鲜嵌入蜡，继续培养至少4小时在65℃。 </li></ol> 1.4）在红蜡嵌入<ol><li>拍摄所述块（不锈钢托盘，其中的白色蜡放置并在其顶部的SAMPLE放置）。这是必要的，因为一旦嵌在蜡中，样品的位置将变得不可见的嵌入红蜡是不透明的。 </li><li>放置小滴的高熔点蜡围绕新的预热的不锈钢包埋模具并使其冷却。如步骤1.2.6声明倒入少量从第二个容器新鲜融化的石蜡包埋的。 </li><li>位置朝下在白蜡点很快的珊瑚虫，然后放置一个塑料的样品架的不锈钢托盘上，倒更嵌入蜡，使得蜡过来对塑料模具的表面上。 </li><li>以整个安装了65℃烘箱中，并允许它在长凳或阴凉表面冷却，直到蜡完全变硬。 </li><li>这可能需要6小时，最多两天。放置在4℃下干燥处理的冰箱挡，避光，长期储存。 </li></ol> 1.5）切片的串行块面设置<ol><li> TR即时通讯块切成1微米的部分用切片机。不收的部分，因为它们会变成粉末。请记住，我们只是成像的块面。样品在白色蜡开始消失出现。 </li><li>捕捉到光滑的块面，其中包含的样本部分被删除，每次的图像。继续下去，直到珊瑚虫消失在SI视频2。 </li><li>用FITC标记的荧光滤镜拿起自动荧光色素细胞/珊瑚虫的录制/撷取用黑白摄像机的图像。图片来自每个品种3-4脱钙核心。 </li></ol> 2，成像珊瑚在双光子荧光显微镜<ol><li>修复珊瑚虫核心，以收集（海边）网站每个包含大约10-12息肉直径约一英寸，在4％多聚甲醛，只要它们在水中收获。 </li><li>保持样品在4°C，直到成像。洗涤芯被放置在第ê同一个解决方案中的玻璃盖底部盘倒挂（0.17毫米厚）。 </li><li>利用双光子激光在使用10X（0.3 NA）的物镜780 nm激发，像3-4息肉两种不同的放大倍率（数码变焦）。珊瑚息肉形状和高度的样品（通常为1-2毫米），该成像深度之间的差异也只限于通过成像物镜的工作距离。 </li><li>使用瓦片扫描模式收集约25-100（5×5或10×10瓦）到z轴中的xy每焦平面图像和50-100的图像10或20微米的间隔，总数约为5,000-10,000的图像/珊瑚虫。 </li><li>图片三时五十七息肉领域，代表了核心和珊瑚的物种。注：2-5小时/息肉区域之间的图像采集时间不同。 </li><li>存储原始数据格式的所有图像在系统的硬盘作为LSM 5渲染3D在3D图像的分析和渲染软件。 </li></ol> 3，三维体绘制与可视化Ñ​​SBFI和双光子荧光光谱数据<ol><li>裁剪二维数据通过专注于一个单一的息肉用在程序中广场裁剪工具，以减少文件大小和编译成一个单一的TIFF文件（减小文件的大小也通过保存在8位格式的文件）的采集软件。 </li><li>在程序中了Imaris超越模块下的体积算法打开SBFI数据的汇编文件（收集步骤1.5.1）或平铺多个z栈的双光​​子光学部分（收集步骤2.1.4）。 </li><li>项目中使用了一层阴影投射在3D渲染的SBFI数据。创造一个体素是阈值化创造了坚实的表面图案（SI视频3）的等值面模式。 </li><li>使用可视化的剪取平面算法在XY，XZ的3D投影和YZ正交模式，揭示珊瑚三维结构和形状。 </li><li>在相同了Imaris程序使用关键帧动画模块的动画投影（SI六DEOS 3-7）。 </li><li>生成的视频文件，在5％的压缩和使用量生成AVI格式的影片剪辑（SI影片4和6），三维等值面和方式（SI视频5和7）。 </li></ol>

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The authors declare no conflict of interests.

珊瑚礁研究是一个高度跨学科的研究工作，包括分析，同时物理，化学和生物现象工作在海洋环境。复杂的珊瑚礁生态系统的研究中上下文框架（ 图10）中的“十国”，因此最好的完成。此图编制说明，珊瑚生态系统涵盖了广泛的空间尺寸（10-9至10 5米）。此外，这次演习表明地球生物学在中间长度比例为1毫米1厘米分析是结合现场和实验室分析所需的桥梁。十大框架...

全球变暖和相应的环境变化都直接影响热带海洋珊瑚1-4的健康和分布。多重影响正在被观察到，包括珊瑚白化和传染病5-6的出现。然而，未来的珊瑚应对这些环境威胁更准确的预测将需要进行组织学“基线”成立，它定义了组织形态和细胞的组成和分布“看起来健康”的珊瑚。反过来，“影响”珊瑚然后可以定量比较。此外，该基线应建立在外表健康的珊瑚在各种环境条件下，使“健康反应”也可以跨越环境梯度来衡量。由于对建立这一基础的第一步，高分辨率3D已开展研究如何看起来健康的珊瑚虫组织形态和细胞成分响应增加水深（WD）和随附的跌幅在阳光辐照度。结果可以用来确定珊瑚适应更全面的机械理解，以及深入了解珊瑚共生演进和捕光增强。 石珊瑚（ 石珊瑚 ）是殖民地的海洋无脊椎动物中发挥主机到复杂的组合等微生物，统称为珊瑚holobiont 7-10。在本研究中所进行的研究旨在利用一套先进的成像技术，同时跟踪随水深组织颜料和看起来健康的宿主珊瑚共生的虫黄藻的变化。这将建立所需要的比较组织细胞的“基线”跨越水深梯度看起来健康的珊瑚，并作为珊瑚老天指标LTH 10。珊瑚色素，称为色素细胞 ，起到吸收，反射，散射，折射，衍射，或与入射太阳辐射11以其他方式干扰。虫黄藻，色素细胞内共生关系，使中高屋建瓴捕光优化和骨骼成长战略的协同进化，以及营养的可塑性（移喂养策略回来的往复从自养到异养）的珊瑚动物12。 库拉索岛南部的加勒比海岛国（荷属安的列斯以前部分）位于委内瑞拉以北约为65公里，东西走向的阿鲁巴岛香格里拉Blanquilla群岛（ 图1A）内。库拉索岛的70公里长的南海岸包含一个连续的现代化和中新世-上新世-更新世-全新世古岸珊瑚礁道13,14。年平均海温的变化库拉索岛约3℃的nually，从一月下旬最低26℃，最高29℃，在九月初，有27.5±0.5ºC的年平均温度（NOAA海温资料集2000-2010）。珊瑚礁的Playa Kalki（12°22&#39;31.63“N，69°09&#39;29.62”W），躺在库拉索（ 图1A）的西北尖端，被选为抽样，因为它之前已经充分研究和在这个位置上的海洋生态系统正沐浴在清新无污染海水中7,15-19。 。两个密切相关的石珊瑚物种，M. annularis和M faveolata，被选择用于实验和分析在本研究中，因为每个物种：（1）相对于所述货架断和上礁道呈现明显不同的和不重叠的等深线分布相关的碳酸盐沉积的沉积环境（M. annularis范围= 0-10米的WD; 米faveolata范围= 10-20米WD 20; 图1B，2A和2B）; （2）在整个加勒比海21一 ​​个共同的珊瑚礁框架构建;和（3）具有充分研究的生态，生理和进化关系22。 现场取样本研究采用离岸滩Kalki库拉索岛的标准水肺潜水技术进行的。浅到深的水中测深断面成立跨架子跑了，过了保质突破，并进入深水区前礁环境。显然，健康的珊瑚头，然后确定了采样沿着这条测深断面，其中包括：（1）三个人约1米直径的珊瑚M的头annularis，所有这些都是以5m水深度（WD）; （2）三个独立的约1米直径的珊瑚M的头所有这些faveolata，是在12米WD。光合有效辐射（PAR）的测定为33-36％的PAR为5m的WD和18-22％的PAR以10米的WD。采样是在1月​​进行，当海温为26℃时的水深均5米和12米每六珊瑚头进行采样，一式三份，在同等空间位置（ 即约45°北纬每六个半球状珊瑚头）。每个单独的样本包括收集与清洗拱冲，一个直径为2.5厘米的珊瑚组织构架核心活检。三珊瑚组织，骨骼活检取样标准潜水用戴手套的手从每个珊瑚头（从9 米annularis为5m的WD殖民地，从9 米faveolata在12米WD）。后立即收集在深度，每个活检核心样品置于无菌50毫升聚丙烯离心管中，螺旋盖密封，并返回到表面。海水从每个离心管中倾出，每个核心活检后，浸渍，储存，并在4％多聚甲醛输送。 23-30的进行。这些研究大多利用光/光镜带任何荧光或明场技术。然而，研究已经在利用扫描电子串行块面成像，在过去的31超高放大倍率进行。在本研究中，修饰SBFI协议已被开发用于与施加到珊瑚首次。由于M。 annularis和M。 faveolata珊瑚虫是1-2毫米的厚度，没有任何的常规光显微技术将能够穿透珊瑚息肉组织的整个厚度。因此，我们有专门为珊瑚样本设计SBFI样品制备协议。此外，我们的定制设计了立体支架，该机动化地在X和Y两个方向上移动。该装置采用的样本的块面的图像，而不是使用常规的切片在显微镜的前收集的部分。我们还介绍了另一种非线性光学双光子显微技术将图像的同一珊瑚虫整个珊瑚组织的整个厚度。这克服了由SBFI在脱钙的术语，并且可以由样品制备（脱水）和处理协议来诱导组织的形态和容积（收缩）的变化的可能性，所施加的限制。此外，从珊瑚排放剖面，光谱分辨识别色素细胞和虫黄藻光合作用的高峰排放量和变化。这些结果在使用该方法的情况下和其有关的采集时间个别的优点，分析时间，并解决精细结构细节不损害str中的能力进行了评价珊瑚组织uctural完整性。

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Coral Tissue Skeleton</td>
			<td>None</td>
			<td>None</td>
			<td>2.5 cm Biopsy from natural habitat</td>
		</tr>
		<tr>
			<td>Arch Punch Coring Device</td>
			<td>C.S. Osborne and Company</td>
			<td>No. 149</td>
			<td>For Coral biopsy collection</td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Electron Microscopy Sciences</td>
			<td>RT 15700</td>
			<td>16% Pre-diluted</td>
		</tr>
		<tr>
			<td>Histoclear/Safeclear II</td>
			<td>Electron Microscopy Sciences</td>
			<td>RT 64111-04</td>
			<td>Non-Toxic alternate to Xylene, Dehydration and Deparafinization</td>
		</tr>
		<tr>
			<td>Xylene and Ethanol</td>
			<td>Fisher Scientific</td>
			<td>Fisher Scientific</td>
			<td>Dehydration</td>
		</tr>
		<tr>
			<td>Paraffin Wax</td>
			<td>Richard Allen Scientific</td>
			<td>Type H REF 8338</td>
			<td>Infiltration solution</td>
		</tr>
		<tr>
			<td>Vybar</td>
			<td>The Candle Maker</td>
			<td>None</td>
			<td>Component of Red Wax</td>
		</tr>
		<tr>
			<td>Stearin</td>
			<td>The Candle Maker</td>
			<td>None</td>
			<td>Component of Red Wax</td>
		</tr>
		<tr>
			<td>Sudan IV</td>
			<td>Fisher Chemical</td>
			<td>S667-25</td>
			<td>Red Wax-Opaque background</td>
		</tr>
		<tr>
			<td>Wheat Germ Agglutinin (WGA)</td>
			<td>Life Technologies</td>
			<td>W32466</td>
			<td>For labeling&#160; Coral Mucus</td>
		</tr>
		<tr>
			<td>Prolong Gold</td>
			<td>Life Technologies</td>
			<td>P36095</td>
			<td>Anti-fade mounting media</td>
		</tr>
		<tr>
			<td>Fluoro Dish</td>
			<td>World Precision Instruments</td>
			<td>FD-35-100</td>
			<td>For two-photon imaging</td>
		</tr>
		<tr>
			<td>XY Motor, Driver and Controller</td>
			<td>Lin Engineering</td>
			<td>211-13-01R0, R325, R256-RO</td>
			<td>XY Translational Movement</td>
		</tr>
		<tr>
			<td>Hot Plate</td>
			<td>Corning</td>
			<td>DC-220</td>
			<td>Melting all wax</td>
		</tr>
		<tr>
			<td>Convection Oven</td>
			<td>Yamato</td>
			<td>DX-600</td>
			<td>Infiltration and Embedding</td>
		</tr>
		<tr>
			<td>Tissue Processor</td>
			<td>Leica</td>
			<td>ASP 300</td>
			<td>Dehydration, Infiltration</td>
		</tr>
		<tr>
			<td>Microtome</td>
			<td>Leica</td>
			<td>RM2055</td>
			<td>Disposable knifes</td>
		</tr>
		<tr>
			<td>Stereo Microscope</td>
			<td>Carl Zeiss</td>
			<td>Stereolumar V 12</td>
			<td>1.5x (30 mm WD) Objective</td>
		</tr>
		<tr>
			<td>Fluorescence Microscope with ApoTome</td>
			<td>Carl Zeiss</td>
			<td>Axiovert M 200, ApoTome I System</td>
			<td>Imaging thin section of a polyp: Zooxanthellae</td>
		</tr>
		<tr>
			<td>Axiocam camera</td>
			<td>Carl Zeiss</td>
			<td>MRm</td>
			<td>Monochrome camera 1388x1040 pixels</td>
		</tr>
		<tr>
			<td>Axiovision Software</td>
			<td>Carl Zeiss</td>
			<td>Version 4.8</td>
			<td>Image acquisition program</td>
		</tr>
		<tr>
			<td>Two-Photon Laser</td>
			<td>Spectraphysics</td>
			<td>Maitai eHP, pulsed laser (70 fs)</td>
			<td>With DeepSee module</td>
		</tr>
		<tr>
			<td>Laser Scanning Microscope</td>
			<td>Carl Zeiss</td>
			<td>LSM 710 with Spectral Detector</td>
			<td>34 channel PMT detection</td>
		</tr>
		<tr>
			<td>Zen Software</td>
			<td>Carl Zeiss</td>
			<td>2010 or above</td>
			<td>for two-photon and spectral image acquisition</td>
		</tr>
		<tr>
			<td>Imaris Suite Software</td>
			<td>Bitplane, Inc.,</td>
			<td>Version 7.0 or above</td>
			<td>3D Volume, Iso-surface Rendering, Visualization</td>
		</tr>
	</tbody>
</table>

multimodal optical microscopy methods reveal polyp tissue morphology and structure in caribbean reef building corals

一个集成的成像技术套件已经被应用来确定三维（3D）的形态学和细胞息肉组织结构，包括加勒比礁珊瑚Montastraea annularis和M. faveolata。这些方法包括荧光显微技术（FM），串行块面成像（SBFI），和双光子激光扫描共聚焦显微镜（TPLSM）。 SBFI提供物理切片后深层组织成像;它详细说明了组织表面纹理和三维可视化到组织的深度超过2毫米。组织细胞结构的互补性调频和TPLSM产量的超高分辨率图像。结果：（1）确定的个别珊瑚虫的外壁和先前未报告叶形组织的形态（2）创建的色素细胞和藻类状藻虫黄内共生体的三维分布和组织密度的第一表面上的地图。光谱吸收豌豆500 nm和675 nm的KS，分别提示M. annularis和M。 faveolata包含相似类型的叶绿素和色素细胞的。然而，M annularis和M。 faveolata呈现的组织密度，对这些关键细胞成分的三维分布显著差异。本研究着重于影像学方法表明SBFI是对脱钙珊瑚组织大型毫米级样品的分析非常有用。免费FM和TPLSM揭示nondecalcified珊瑚组织样本中的细胞分布和密度微妙的亚毫米尺度的变化。该TPLSM技术能提供：（1）微创样品制备，（2）优良的光学切片的能力，以及（3）最小的光的吸收和散射，同时仍允许深部组织成像。

定制设计的SBFI设备（专门针对本研究制造; 图3）产生的第一个详细的三维数字高程外表面质感的米和形态的地图（数字高程模型） annularis和M。 faveolature珊瑚虫（ 图4和SI视频1-2）。此得到的珊瑚组织同心地从每个息肉（ 图4B，4D和4E）的中心向外辐射的先前未描述的堆叠凸起的图像。这些瓣沿堆叠组织覆盖中小学骨骼隔的最高...

Watch this Scientific Journal Video about Multimodal Optical Microscopy Methods Reveal Polyp Tissue Morphology and Structure in Caribbean Reef Building Corals at JoVE.com

Multimodal Optical Microscopy Methods Reveal Polyp Tissue Morphology and Structure in Caribbean Reef Building Corals

一个集成的成像技术套件已经被应用于确定息肉形态学和组织结构在加勒比海珊瑚Montastraea annularis和M. faveolata。荧光，串行块面，和双光子激光扫描共聚焦显微术已经确定叶形结构，息肉墙壁，和估计的色素细胞和虫黄藻密度和分布。

多模态光学显微镜方法在加勒比海礁珊瑚显示息肉组织形态和结构

An integrated suite of imaging techniques has been applied to determine the three-dimensional (3D) morphology and cellular structure of polyp tissues ...

multimodal-optical-microscopy-methods-reveal-polyp-tissue-morphology

Research

JoVE Journal

Environment

12.2K 次观看.  University of Illinois at Urbana-Champaign. 一个集成的成像技术套件已经被应用于确定息肉形态学和组织结构在加勒比海珊瑚Montastraea annularis和M. faveolata。荧光，串行块面，和双光子激光扫描共聚焦显微术已经确定叶形结构，息肉墙壁，和估计的色素细胞和虫黄藻密度和分布。 

视频: Multimodal Optical Microscopy Methods Reveal Polyp Tissue Morphology and Structure in Caribbean Reef Building Corals

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 ...

科研

环境科学

Methods of Soil Resampling to Monitor Changes in the Chemical Concentrations of Forest Soils

Recent soils research has shown that important chemical soil characteristics can change in less than a decade, often the result of broad environmental changes. Repeated sampling to monitor these changes in forest soils is a relatively new practice that is not well documented in the literature and has only recently been broadly embraced by the scientific community. The objective of this protocol is therefore to synthesize the latest information on methods of soil resampling in a format that can be used to design and implement a soil monitoring program. Successful monitoring of forest soils requires that a study unit be defined within an area of forested land that can be characterized with replicate sampling locations. A resampling interval of 5 years is recommended, but if monitoring is done to evaluate a specific environmental driver, the rate of change expected in that driver should be taken into consideration. Here, we show that the sampling of the profile can be done by horizon where boundaries can be clearly identified and horizons are sufficiently thick to remove soil without contamination from horizons above or below. Otherwise, sampling can be done by depth interval. Archiving of sample for future reanalysis is a key step in avoiding analytical bias and providing the opportunity for additional analyses as new questions arise.

Repeated soil sampling has recently been shown to be an effective way to monitor forest soil change over years and decades. To support its use, a protocol is presented that synthesizes the latest information on soil resampling methods to aid in the design and implementation of successful soil monitoring programs.

土壤重采样的方法监控森林土壤的化学浓度的变化

Recent soils research has shown that important chemical soil characteristics can change in less than a decade, often the result of broad environmental ...

Building Double-decker Traps for Early Detection of Emerald Ash Borer

Emerald ash borer (EAB) (Agrilus planipennis Fairmaire), the most destructive forest insect to have invaded North America, has killed hundreds of millions of forest and landscape ash (Fraxinus spp.) trees. Several artificial trap designs to attract and capture EAB beetles have been developed to detect, delineate, and monitor infestations. Double-decker (DD) traps consist of two corrugated plastic prisms, one green and one purple, attached to a 3 m tall polyvinyl chloride (PVC) pipe supported by a t-post. The green prism at the top of the PVC pipe is baited with cis-3-hexenol, a compound produced by ash foliage. Surfaces of both prisms are coated with sticky insect glue to capture adult EAB beetles. Double-decker traps should be placed near ash trees but in open areas, exposed to sun. Double-decker trap construction and placement are presented here, along with a summary of field experiments demonstrating the efficacy of DD traps in capturing EAB beetles. In a recent study in sites with relatively low EAB densities, double-decker traps captured significantly more EAB than green or purple prism traps or green funnel traps, all of which are designed to be suspended from a branch in the canopy of ash trees. A greater percentage of double decker traps were positive, i.e., captured at least one EAB, than the prism traps or funnel traps that were hung in ash tree canopies.

Effective traps to attract and capture the emerald ash borer (EAB) are a key element of detecting and managing this invasive pest. Double-decker traps, placed in full sun near ash trees, incorporate visual and olfactory cues and were more likely to capture EAB than other trap designs in field trials.

建筑双层疏水阀早期检测翡翠灰螟

Emerald ash borer (EAB) (Agrilus planipennis Fairmaire), the most destructive forest insect to have invaded North America, has killed hundreds of millions ...

Bioindication Testing of Stream Environment Suitability for Young Freshwater Pearl Mussels Using In Situ Exposure Methods

Knowledge of habitat suitability for freshwater mussels is an important step in the conservation of this endangered species group. We describe a protocol for performing in situ juvenile exposure tests within oligotrophic river catchments over one-month and three-month periods. Two methods (in both modifications) are presented to evaluate the juvenile growth and survival rate. The methods and modifications differ in value for the locality bioindication and each has its benefits as well as limitations. The sandy cage method works with a large set of individuals, but only some of the individuals are measured and the results are evaluated in bulk. In the mesh cage method, the individuals are kept and measured separately, but a low individual number is evaluated. The open water exposure modification is relatively easy to apply; it shows the juvenile growth potential of sites and can also be effective for water toxicity testing. The within-bed exposure modification needs a high workload but is closer to the conditions of a natural juvenile environment and it is better for reporting the real suitability of localities. On the other hand, more replications are needed in this modification due to its high-hyporheic environment variability.

Bioindication Testing of Stream Environment Suitability for Young Freshwater Pearl Mussels Using In Situ Exposure Methods

In situ bioindications enable determination of the suitability of an environment for endangered mussel species. We describe two methods based on the juvenile exposure of freshwater pearl mussels in cages to oligotrophic river habitats. Both methods are implemented in variants for open water and hyporheic water environments.

用原位曝光法测定淡水珍珠贻贝 Bioindication 的流环境适宜性

Knowledge of habitat suitability for freshwater mussels is an important step in the conservation of this endangered species group. We describe a protocol ...

Fabrication of Anisotropic Polymeric Artificial Antigen Presenting Cells for CD8+ T Cell Activation

Artificial antigen presenting cells (aAPC) are a promising platform for immune modulation due to their potent ability to stimulate T cells. Acellular substrates offer key advantages over cell-based aAPC, including precise control of signal presentation parameters and physical properties of the aAPC surface to modulate its interactions with T cells. aAPC constructed from anisotropic particles, particularly ellipsoidal particles, have been shown to be more effective than their spherical counterparts at stimulating T cells due to increased binding and larger surface area available for T cell contact, as well as reduced nonspecific uptake and enhanced pharmacokinetic properties. Despite increased interest in anisotropic particles, even widely accepted methods of generating anisotropic particles such as thin-film stretching can be challenging to implement and use reproducibly.
To this end, we describe a protocol for the rapid, standardized fabrication of biodegradable anisotropic particle-based aAPC with tunable size, shape, and signal presentation for T cell expansion ex vivo or in vivo, along with methods to characterize their size, morphology, and surface protein content, and to assess their functionality. This approach to fabricating anisotropic aAPC is scalable and reproducible, making it ideal for generating aAPC for &#34;off-the-shelf&#34; immunotherapies.

Here, we present a protocol to quickly and reproducibly generate biologically inspired, biodegradable articifical antigen presenting cells (aAPC) with tunable size, shape, and surface protein presentation for T cell expansion ex vivo or in vivo.

CD8+ T 细胞活化的各向异性聚合物人工抗原呈现细胞的制备

Artificial antigen presenting cells (aAPC) are a promising platform for immune modulation due to their potent ability to stimulate T cells. Acellular ...

Automated 3D Optical Coherence Tomography to Elucidate Biofilm Morphogenesis Over Large Spatial Scales

Biofilms are a most successful microbial lifestyle and prevail in a multitude of environmental and engineered settings. Understanding biofilm morphogenesis, that is the structural diversification of biofilms during community assembly, represents a remarkable challenge across spatial and temporal scales. Here, we present an automated biofilm imaging system based on optical coherence tomography (OCT). OCT is an emerging imaging technique in biofilm research. However, the amount of data that currently can be acquired and processed hampers the statistical inference of large scale patterns in biofilm morphology. The automated OCT imaging system allows covering large spatial and extended temporal scales of biofilm growth. It combines a commercially available OCT system with a robotic positioning platform and a suite of software solutions to control the positioning of the OCT scanning probe, as well as the acquisition and processing of 3D biofilm imaging datasets. This setup allows the in situ and non-invasive automated&#160;monitoring of biofilm development and may be further developed to couple OCT imaging with macrophotography and microsensor profiling.

Microbial biofilms form complex architectures at interphases and develop into highly scale-dependent spatial patterns. Here, we introduce an experimental system (hard- and software) for the automated acquisition of 3D optical coherence tomography (OCT) datasets. This toolset allows the non-invasive and multi-scale characterization of biofilm morphogenesis in space and time.

自动 3D 光学相干断层扫描，以在大型空间尺度上阐明生物膜变形

Biofilms are a most successful microbial lifestyle and prevail in a multitude of environmental and engineered settings. Understanding biofilm ...

Split Point Analysis and Uncertainty Quantification of Thermal-Optical Organic/Elemental Carbon Measurements

Researchers from myriad fields frequently seek to quantify and classify concentrations of carbonaceous aerosols as organic carbon (OC) or elemental carbon (EC). This is commonly accomplished using thermal-optical OC/EC analyzers (TOAs), which enable measurement via controlled thermal pyrolysis and oxidation under specific temperature protocols and within constrained atmospheres. Several commercial TOAs exist, including a semi-continuous instrument that enables on-line analyses in the field. This instrument employs an in-test calibration procedure that requires relatively frequent calibration. This article details a calibration protocol for this semi-continuous TOA and presents an open-source software tool for data analysis and rigorous Monte Carlo quantification of uncertainties. Notably, the software tool includes novel means to correct for instrument drift and identify and quantify the uncertainty in the OC/EC split point. This is a significant improvement on the uncertainty estimation in the manufacturer&#8217;s software, which ignores split point uncertainty and otherwise uses fixed equations for relative and absolute errors (generally leading to under-estimated uncertainties and often yielding non-physical results as demonstrated in several example data sets). The demonstrated calibration protocol and new software tool enabling accurate quantification of combined uncertainties from calibration, repeatability, and OC/EC split point are shared with the intent of assisting other researchers in achieving better measurements of OC, EC, and total carbon mass in aerosol samples.

This article presents a protocol and software tool for the quantification of uncertainties in the calibration and data analysis of a semi-continuous thermal-optical organic/elemental carbon analyzer.

热光学有机/元素碳测量的分割点分析与不确定性定量

Researchers from myriad fields frequently seek to quantify and classify concentrations of carbonaceous aerosols as organic carbon (OC) or elemental carbon ...

Leaf Area Index Estimation Using Three Distinct Methods in Pure Deciduous Stands

Accurate estimations of leaf area index (LAI), defined as half of the total leaf surface area per unit of horizontal ground surface area, are crucial for describing the vegetation structure in the fields of ecology, forestry, and agriculture. Therefore, procedures of three commercially used methods (litter traps, needle technique, and a plant canopy analyzer) for performing LAI estimation were presented step-by-step. Specific methodological approaches were compared, and their current advantages, controversies, challenges, and future perspectives were discussed in this protocol. Litter traps are usually deemed as the reference level. Both the needle technique and the plant canopy analyzer (e.g., LAI-2000) frequently underestimate LAI values in comparison with the reference. The needle technique is easy to use in deciduous stands where the litter completely decomposes each year (e.g., oak and beech stands). However, calibration based on litter traps or direct destructive methods is necessary. The plant canopy analyzer is a commonly used device for performing LAI estimation in ecology, forestry, and agriculture, but is subject to potential error due to foliage clumping and the contribution of woody elements in the field of view (FOV) of the sensor. Eliminating these potential error sources was discussed. The plant canopy analyzer is a very suitable device for performing LAI estimations at the high spatial level, observing a seasonal LAI dynamic, and for long-term monitoring of LAI.

An accurate estimation of leaf area index (LAI) is crucial for many models of material and energy fluxes within plant ecosystems and between an ecosystem and the atmospheric boundary layer. Therefore, three methods (litter traps, needle technique, and PCA) for taking precise LAI measurements were in the presented protocol.

在纯落叶支架中使用三种截然不同的方法估算叶面积指数

Accurate estimations of leaf area index (LAI), defined as half of the total leaf surface area per unit of horizontal ground surface area, are crucial for ...

Fluorescently Labeled Bacteria as a Tracer to Reveal Novel Pathways of Organic Carbon Flow in Aquatic Ecosystems

Elucidating trophic interactions, such as predation and its effects, is a frequent task for many researchers in ecology. The study of microbial communities has many limitations, and determining a predator, prey, and predatory rates is often difficult. Presented here is an optimized method based on the addition of fluorescently labelled prey as a tracer, which allows for reliable quantitation of the grazing rates in aquatic predatory eukaryotes and estimation of nutrient transfer to higher trophic levels.

Presented here is a protocol for a single-cell, epifluorescence microscopy-based technique to quantify grazing rates in aquatic predatory eukaryotes with high precision and taxonomic resolution.

荧光标记细菌作为追踪器揭示水生生态系统中有机碳流动的新途径

Elucidating trophic interactions, such as predation and its effects, is a frequent task for many researchers in ecology. The study of microbial ...

Standardized Methods for Measuring Induction of the Heat Shock Response in Caenorhabditis elegans

The heat shock response (HSR) is a cellular stress response induced by cytosolic protein misfolding that functions to restore protein folding homeostasis, or proteostasis. Caenorhabditis elegans occupies a unique and powerful niche for HSR research because the HSR can be assessed at the molecular, cellular, and organismal levels. Therefore, changes at the molecular level can be visualized at the cellular level and their impacts on physiology can be quantitated at the organismal level. While assays for measuring the HSR are straightforward, variations in the timing, temperature, and methodology described in the literature make it challenging to compare results across studies. Furthermore, these issues act as a barrier for anyone seeking to incorporate HSR analysis into their research. Here, a series of protocols is&#160;presented for measuring induction of the HSR in a robust and reproducible manner with RT-qPCR, fluorescent reporters, and an organismal thermorecovery assay. Additionally, we show that a widely used thermotolerance assay is not dependent on the well-established master regulator of the HSR, HSF-1, and therefore should not be used for HSR research. Finally, variations in these assays found in the literature are discussed and best practices are proposed to help standardize results across the field, ultimately facilitating neurodegenerative disease, aging, and HSR research.

Standardized Methods for Measuring Induction of the Heat Shock Response in Caenorhabditis elegans

Here, standardized protocols are presented to assess induction of the heat shock response (HSR) in Caenorhabditis elegans using RT-qPCR at the molecular level, fluorescent reporters at the cellular level, and thermorecovery at the organismal level.

卡诺哈布迪蒂斯精英热休克反应的测量诱导标准化方法

The heat shock response (HSR) is a cellular stress response induced by cytosolic protein misfolding that functions to restore protein folding homeostasis, ...