这项工作是由自然保护和私人捐助者, 资源遗留基金基金会, 戈登和贝蒂摩尔基金会, 环境防御基金, 加利福尼亚海洋赠款计划, 海洋国家合作研究计划, 和 NOAASaltonstall-肯尼迪格兰特 #13-SWR-008海洋应用研究和探索 (德克罗森, 瑞克 Botman, 安迪 Lauerman 和大卫 Jefferies) 开发, 建造和维护了视频着陆器工具。我们感谢 Jim 西格和 SeaGIS™软件的技术支持。船长和商业渔民 Tim Maricich 和船员船上的 F/V唐娜凯瑟琳提供了支持, 在部署着陆器从2012-2015。感谢所有参与视频数据收集或分析的人 (安妮 Tagini, 唐娜克莱恩, 琥珀佩恩, 布唐尼, 玛丽莎蓬, 丽贝卡米勒, 马特乙烯, 沃尔特兴奋, 史蒂夫 Rienecke, EJ 迪克, 和约翰领域)。

注意: 软件步骤的截图包括在辅助文件中。请注意, 下面介绍的软件步骤特定于所选软件 (请参见材料表)。总体方法可以扩展到任何立体软件平台。
1. 为分析准备立体摄影机素材
注意: 建议使用校准立方体进行校准。校准立方体是一个三维铝框架, 在表面上有精确定位的反射点。与校准软件一起使用时, 校准立方体比棋盘方法9更加精确和准确。
<ol><li>使用立体声校准软件校准着陆器摄像机 (图 1和图 2; 有关软件建议, 请参阅材料表。 注: 校准可在现场使用之前, 通过测量不同距离的已知大小的目标 (请参阅补充视频 1) 进行验证。在3米 (或更低) 距离的50厘米目标的平均测量误差应在已知目标长度的2% 以内。另外请注意, 给定的校准将只有在相机位置不相互改变时才有效。这是至关重要的, 以照顾和避免意外拥挤的摄像头, 直到所有的取样已经执行。</li>
	<li>使用校准的着陆器收集字段数据 (图 1,补充视频 2)。</li>
	<li>完成现场研究后, 创建一个包含视频和校准文件的新项目文件夹。 注意: 在每个项目文件夹中, 至少需要五文件: 左边和右边。Cam "校准文件, 左, 右视频文件 (。MP4 或。AVI 格式), 和物种列表 (.txt 格式)。</li>
	<li>在立体声测量软件中, 启动一个新的测量项目, 并加载适当的视频和校准文件。 注意: 所有软件步骤的截图都在辅助文件中提供。<ol>
<li>导航到 "测量" > "新测量文件"。</li>
		<li>通过导航到 "图片" > "设置图片目录" 来设置图片目录, 然后选择包含所有项目文件的文件夹。</li>
		<li>加载左摄像头 "。Cam "文件通过导航到 ' 立体声 ' > ' 相机 ' > ' 左 ' > ' 加载相机文件 ', 并选择适当的文件。</li>
		<li>重复步骤1.4.3 加载正确的相机 "。Cam "文件 注: 这些文件包含每台摄像机的校准测量 (例如、像素大小、纵横比、径向失真、decentring 失真、等), 并将用于测量鱼和计算距离照相机 (即、Z距离)。</li>
		<li>通过导航到 "图片" > "定义影片序列" 并选择左摄像机视频文件, 定义左侧视频文件的影片序列。</li>
		<li>通过选择 "图片" > "加载图片", 将左侧视频文件加载到测量软件中。 注意: 在加载视频文件之前, 请确保 "锁定" 框未选中。这允许同时加载两个视频。</li>
		<li>使用菜单 "立体声" > "图片" > "定义电影序列" 和 "立体声" > "图片" > "加载图片", 为正确的视频定义影片序列并加载视频文件。</li>
		<li>通过导航到 "测量" > "属性" > "编辑/加载物种文件" 来加载物种列表。</li>
		<li>在 "信息字段" > "编辑字段值" 下输入调查 ID 信息并保存文件以创建。EMObs 项目。</li>
	</ol>
</li>
	<li>使用 flash、喝倒彩、协调通用时间 (UTC) 标记或在两个视频中发生的任何时间特定事件同步视频。<ol>
<li>如果使用 UTC 时间戳, 请在左侧视频中向前跨帧, 直到时间戳开始新的第二个秒。其他帧向前, 直到闪光或喝倒彩发生。</li>
		<li>帧-步骤正确的视频前进, 直到时间戳完全匹配左视频。其他帧向前迈进, 直到准确的时刻, 光闪光或喝倒彩匹配左视频。 注意: 将视频同步到同一帧是很重要的。在分析过程中, 应使用视频时间戳定期检查视频同步, 以避免相机帧漂移。在视频的开始和结束时, 还可以使用拍摄的手拍, 以测试右侧和左侧的视频是否同步到同一帧。</li>
	</ol>
</li>
	<li>单击 "锁定" 按钮以确保视频一起播放并保持同步。</li>
</ol>2. 生成点计数和计算 MaxN
注意: 每条鱼最初都以2D 点标记, 以达到可能的最低分类分辨率。不确定 ID 的鱼应标明以备日后复查。
<ol><li>等待开始计数鱼直到一个完整的相机旋转结束, 以确保一个完整的360度使用。还要等到沉淀物清除 (一般 < 1-2 分钟后接触底部)。<ol>
<li>一旦着陆器开始第一次旋转, 右键单击以定义一个新的采样周期: "周期定义" > "添加新的开始时间"。输入第一个句点名称为 "01", 然后单击 "确定"。</li>
	</ol>
</li>
	<li>当着陆器转动时, 开始标记每条进入框架的鱼, 使用左摄像头的2D 点。<ol>
<li>要添加2D 点, 右键单击, 选择 "添加点", 并选择正确的物种名称。标签到尽可能最低的分类学水平, 选择 "许可证" 的未知物种, 并点击 "OK"。</li>
		<li>根据步骤2.2.1 继续标记每条新的鱼直到旋转的结论。</li>
	</ol>
</li>
	<li>对每个附加的着陆器旋转重复协议步骤 2.1-2.2-确保在每个摄像机旋转开始时定义一个新的周期。 注: 物种积累曲线被用来确定八轮换, 平均而言, 足以描述鱼类丰度在本研究。研究人员应该考虑进行初步测试, 额外的摄像机旋转, 超过更长的浸泡时间, 以确定特定生态系统内的最佳摄像机旋转次数。</li>
	<li>计算每个摄像机旋转观察到的个体的 species-specific 计数。<ol>
<li>在枚举所有旋转后, 通过导航到 "测量" > "测量摘要" > "点测量" 并将2D 点保存为 a.txt 文件, 导出2D 点。</li>
		<li>打开保存的2D.txt 点文件作为电子表格, 并创建一个物种与旋转编号的数据透视表, 通过导航到 "插入" > "数据透视表" 来汇总计数 (表 1)。为 "行标签" 和 "列标签" 的 "周期" 选择 "属和种"。</li>
	</ol>
</li>
	<li>选择具有该种最大数量的个体的摄像机旋转 (表 1), 选取每个物种的 MaxN。</li>
	<li>对于只识别属属的鱼类, 选择一个属级的 MaxN, 它是根据在该特定属中的物种数量最多的人的旋转而定的。 注意: 此步骤有助于避免计算只可识别为较高的分类组的单个鱼 (例如, 只对属或家族)。例如, 在表 1中, "旋转 1" 包含10未识别的许氏和33成员, 其中许氏属物种, 而 "旋转 3" 只包含两个身份不明的许氏许可证. 和43成员标识为物种的许氏属。因此, "旋转 3" 将用于未知的许氏的 MaxN 计数。这样, 保守的假设是, 8 的不确定的许氏在 "旋转 1" 中被识别为 "旋转 8"。</li>
	<li>如果多个旋转对某一给定物种具有相同的 MaxN 计数, 请选择第一个旋转与 MaxN 进行3D 点测量。</li>
	<li>对于每个物种, 在 MaxN 发生的旋转中采取3D 的鱼类测量。<ol>
<li>使用在步骤 2.1-2.3 中收集的保存的2D 点, 导航到与3D 测量完全相同的鱼。</li>
		<li>放大至少 4X, 以更好地识别鱼嘴和尾鳍边缘的尖端 (图 3)。 注意: 可能有必要向前或向后帧, 以找到鱼的最佳方向的3D 测量。"最佳" 定位是在两个摄像头都能看到尾鳍的口鼻和边缘。</li>
		<li>手动点击吻口的尖端, 然后在左边的摄像头的尾巴的边缘, 然后在正确的视频重复选择相同的顺序。</li>
		<li>从下拉菜单中选择正确的物种标识, 就像在2.2.1 中那样。</li>
		<li>如果3D 长度测量不是可能的, 例如, 如果鱼的头和尾巴在两个照相机不是可看见的, 然后标记一个3D 点, 而不是左点击鱼的同样位置在左和正确录影。填写之前的信息字段, 并保留注释 "从长度测量中排除"。 注意: 不同种类的摄像机在不同的旋转过程中可能发生 MaxN;但是, 对于任何给定的物种, 测量只应在一次旋转中发生 (表 1)。</li>
	</ol>
</li>
	<li>完成对所有鱼类的3D 测量后, 导出数据 as.txt 文件进行进一步分析。<ol>
<li>导航到 "测量" > "测量摘要" > "3D 点和长度测量", 以及要导出的 save.txt 文件。</li>
	</ol>
</li>
</ol>3. species-specific 测量区域的 95% Z 距离程序
注: 95% Z 距离是一个物种在给定的研究中可以可靠地识别的平均距离的估计, 同时排除了水清澈或光照的特殊情况。这一计算考虑到了一项研究的平均海洋学条件, 每项新的研究都需要重新。
<ol><li>使用简单的引导来确定样本大小是否足够大, 以表征每个物种的可靠检测距离。<ol>
<li>对于每个样本大小类 (例如, 5 条鱼的取样大小箱), 选取1000随机抽取的样本大小, 并从样本填充中进行替换, 并计算这些1000绘制距离的平均95% 位, 并绘制结果渐近曲线。请参见补充文件 1 & 2中提供的代码。</li>
		<li>通过将实际样本大小与 95% Z 距离渐近线的样本大小进行比较, 验证是否获得了足够的样本。</li>
	</ol>
</li>
	<li>计算 95% Z 距离值为95% 位的距离-从相机测量一个物种在所有的调查。</li>
	<li>使用 95% Z 值计算每个物种的有效面积。 注: 在旋转着陆器的情况下, 95% Z 值表示被调查的一幅幅的外半径, 其内部半径由工具的物理设置和摄像机能够观察到的底座的距离决定。当着陆器旋转时, 形成一个 "甜甜圈" 形状的测量区域 (图 4)。<ol>
<li>计算被调查的区域: <img alt="Equation 1" src="/files/ftp_upload/56635/56635eq1.jpg"> 注: 例如, 一个相对较大的物种, 如 Yelloweye 石斑鱼 (许氏 ruberrimus) 的 95% Z 距离3.3 米, 有效的测量面积为 30.9 m2每个着陆器部署: 34.3 m2 (外圆)-3.4 m2 (内部圆圈) = 30.9 m2 (总计调查区域)。</li>
	</ol>
</li>
	<li>使用所调查的计算区域 (步骤 3.3.1), 将单个物种计数 (MaxN) 转换为每个可视化测量的密度估计值 (使用公式: <img alt="Equation 2" src="/files/ftp_upload/56635/56635eq2v3.jpg"> 注: 类似的程序可以用来计算体积密度, 而不是面积密度;但是, 这里没有描述这个过程。</li>
</ol><img alt="Table 1" src="/files/ftp_upload/56635/56635table1.jpg"> 表 1: 示例 MaxN 摘要表.每个物种的 MaxN 的选择是用红色和粗体文本显示的。请注意, 对于身份不明的许氏的保守 MaxN 是由确定为物种的最许氏的旋转确定的 (旋转 3)。此外, 虽然这项研究使用了八相机旋转, 但在表 1中仅显示四轮换, 以简化操作。无论旋转多少, 选择 MaxN 的过程都是相同的。
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/56635/56635fig1.jpg"> 图 1: 立体声视频着陆器。密钥硬件是编号为(1) 300 m 脐, (2)两个数字视频录像机 (DVR) 与可拆卸32GB 存储卡在防水瓶, (3)两个 LED 灯输出3000流明在色温为 5000 K, 和(4)两个摄像头, 具有620电视线 (TVL) 分辨率。<a href="//cloudflare.jove.com/files/ftp_upload/56635/56635fig1large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/56635/56635fig2.jpg"> 图 2: 校准立方体 (500 mm x 500 mm x 300 mm)。以两种不同方向显示的 "校准立方体" 的校准示例: (a)多维数据集的右侧被推向照相机, 而(B)立方体的表面与摄像机的表面平行。红色点表示此特定校准方法中使用的参考点, 并且必须始终以编号顺序标识。<a href="//cloudflare.jove.com/files/ftp_upload/56635/56635fig2large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/56635/56635fig3.jpg"> 图 3: 在许氏 miniatus上放置的3D 测量。在每个摄像头的帧中都发现了尾端的尖吻和尾部, 以便进行立体测量。<a href="//cloudflare.jove.com/files/ftp_upload/56635/56635fig3large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/56635/56635fig4.jpg"> 图 4: 着陆器工具调查的区域。着陆器工具探测到的有效面积是由最小 z 距离和每个物种的 95% z 距离限定的。请注意, 该区域在着陆器周围创建了一个 "甜甜圈" 形状的测量量。<a href="//cloudflare.jove.com/files/ftp_upload/56635/56635fig4large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>

<ol>
	<li>Love, M. S., Yoklavich, M. M., Thorsteinson, L. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The Rockfishes of the Northeast Pacific. , (2002).</li><li>Laidig, T. E., Watters, D. L., Yoklavich, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Demersal+fish+and+habitat+associations+from+visual+surveys+on+the+central+California+shelf.">Demersal fish and habitat associations from visual surveys on the central California shelf.</a> Estuar. Coast. Shelf Sci. 83 (4), 629-637 (2009).</li><li>Anderson, T. J., Yoklavich, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiscale+habitat+associations+of+deepwater+demersal+fishes+off+central+California.">Multiscale habitat associations of deepwater demersal fishes off central California.</a> Fish. Bull. 105 (2), 168-179 (2007).</li><li>Yoklavich, M. M., Cailliet, G. M., Sullivan, D. E., Lea, R. N., Love, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Habitat+associations+deep-water+rockfishes+a+submarine+canyon+an+example+of+a+natural+refuge.">Habitat associations deep-water rockfishes a submarine canyon an example of a natural refuge.</a> Fish. Bull. 98 (3), 625-641 (2000).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Status of the Pacific Coast Groundfish Fishery, Stock Assessment and Fishery Evaluation. , (2016).</li><li>Cappo, M., Harvey, E., Malcolm, H., Speare, P., Beumer, J. P., Grant, A., Smith, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Potential+of+video+techniques+to+monitor+diversity,+abundance+and+size+of+fish+in+studies+of+marine+protected+areas.">Potential of video techniques to monitor diversity, abundance and size of fish in studies of marine protected areas.</a> Aquatic protected areas- What works best and how do we know. , 455-464 (2003).</li><li>McLean, D. L., Green, M., Harvey, E. S., Williams, A., Daley, R., Graham, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+baited+longlines+and+baited+underwater+cameras+for+assessing+the+composition+of+continental+slope+deepwater+fish+assemblages+off+southeast+Australia.">Comparison of baited longlines and baited underwater cameras for assessing the composition of continental slope deepwater fish assemblages off southeast Australia.</a> Deep-Sea Research Part I: Oceanographic Research Papers. 98, 10-20 (2015).</li><li>Parker, D., Winker, H., 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=Insights+from+baited+video+sampling+of+temperate+reef+fishes:+How+biased+are+angling+surveys.">Insights from baited video sampling of temperate reef fishes: How biased are angling surveys.</a> Fish. Res. 179, 191-201 (2016).</li><li>Boutros, N., Shortis, M. R., Harvey, E. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparison+of+calibration+methods+and+system+configurations+of+underwater+stereo-video+systems+for+applications+in+marine+ecology.">A comparison of calibration methods and system configurations of underwater stereo-video systems for applications in marine ecology.</a> Limnol. Oceanogr. Methodss. 13 (5), 224-236 (2015).</li><li>Harvey, E. S., Cappo, M., Butler, J. J., Hall, N., Kendrick, 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=Bait+attraction+affects+the+performance+of+remote+underwater+video+stations+in+assessment+of+demersal+fish+community+structure.">Bait attraction affects the performance of remote underwater video stations in assessment of demersal fish community structure.</a> Mar. Ecol. Prog. Ser. 350, 245-254 (2007).</li><li>Watson, J. L., Huntington, B. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assessing+the+performance+of+a+cost-effective+video+lander+for+estimating+relative+abundance+and+diversity+of+nearshore+fish+assemblages.">Assessing the performance of a cost-effective video lander for estimating relative abundance and diversity of nearshore fish assemblages.</a> J. Exp. Mar. Bio. Ecol. 483, 104-111 (2016).</li><li>Easton, R. R., Heppell, S. S., Hannah, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantification+of+Habitat+and+Community+Relationships+among+Nearshore+Temperate+Fishes+Through+Analysis+of+Drop+Camera+Video.">Quantification of Habitat and Community Relationships among Nearshore Temperate Fishes Through Analysis of Drop Camera Video.</a> Mar. Coast. Fish. 7 (1), 87-102 (2015).</li><li>Hannah, R. W., Blume, M. T. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tests+of+an+experimental+unbaited+video+lander+as+a+marine+fish+survey+tool+for+high-relief+deepwater+rocky+reefs.">Tests of an experimental unbaited video lander as a marine fish survey tool for high-relief deepwater rocky reefs.</a> J. Exp. Mar. Bio. Ecol. 430, 1-9 (2012).</li><li>Starr, R. M., Gleason, M. G., 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=Targeting+Abundant+Fish+Stocks+while+Avoiding+Overfished+Species:+Video+and+Fishing+Surveys+to+Inform+Management+after+Long-Term+Fishery+Closures.">Targeting Abundant Fish Stocks while Avoiding Overfished Species: Video and Fishing Surveys to Inform Management after Long-Term Fishery Closures.</a> Plos One. 11 (12), 0168645 (2016).</li><li>Love, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Certainly more than you want to know about the fishes of the Pacific Coast: a postmodern experience. , (2011).</li><li>Campbell, M. D., Pollack, A. G., Gledhill, C. T., Switzer, T. S., DeVries, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+relative+abundance+indices+calculated+from+two+methods+of+generating+video+count+data.">Comparison of relative abundance indices calculated from two methods of generating video count data.</a> Fish. Res. 170, 125-133 (2015).</li><li>Cappo, M., Speare, P., De'ath, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+baited+remote+underwater+video+stations+(BRUVS)+and+prawn+(shrimp)+trawls+for+assessments+of+fish+biodiversity+in+inter-reefal+areas+of+the+Great+Barrier+Reef+Marine+Park.">Comparison of baited remote underwater video stations (BRUVS) and prawn (shrimp) trawls for assessments of fish biodiversity in inter-reefal areas of the Great Barrier Reef Marine Park.</a> J. Exp. Mar. Bio. Ecol. 302 (2), 123-152 (2004).</li><li>Schobernd, Z. H., Bacheler, N. M., Conn, P. B., Trenkel, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Examining+the+utility+of+alternative+video+monitoring+metrics+for+indexing+reef+fish+abundance.">Examining the utility of alternative video monitoring metrics for indexing reef fish abundance.</a> Can. Jour. Fish. Aquat. Sci. 71 (3), 464-471 (2014).</li><li>Hansen, M. J., Schorfhaar, R. G., Selgeby, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gill-Net+Saturation+by+Lake+Trout+in+Michigan+Waters+of+Lake+Superior.">Gill-Net Saturation by Lake Trout in Michigan Waters of Lake Superior.</a> North Am. J. Fish. Manag. 18 (4), 847-853 (1998).</li><li>Dauk, P. C., Schwarz, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Catch+estimation+in+the+presence+of+declining+catch+rate+due+to+gear+saturation.">Catch estimation in the presence of declining catch rate due to gear saturation.</a> Biometrics. 57 (1), 287-293 (2001).</li><li>Hilborn, R., Walters, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Quantitative Fisheries Stock Assessment Choice, Dynamics and uncertainty. , (1992).</li><li>Erisman, B. E., Allen, L. G., Claisse, J. T., Pondella, D. J., Miller, E. F., Murray, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+illusion+of+plenty:+hyperstability+masks+collapses+in+two+recreational+fisheries+that+target+fish+spawning+aggregations.">The illusion of plenty: hyperstability masks collapses in two recreational fisheries that target fish spawning aggregations.</a> Can. Jour. Fish. Aquat. Sci. 68, 1705-1716 (2011).</li><li>Buckland, S. T., Anderson, D. R., Burnham, K. P., Laake, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Distance Sampling: Estimating abundance of biological populations. , (1993).</li><li>Ronconi, R. A., Burger, A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Estimating+seabird+densities+from+vessel+transects:+Distance+sampling+and+implications+for+strip+transects.">Estimating seabird densities from vessel transects: Distance sampling and implications for strip transects.</a> Aquat. Bio. 4 (3), 297-309 (2008).</li><li>Caselle, J. E., Rassweiler, A., Hamilton, S. L., Warner, R. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recovery+trajectories+of+kelp+forest+animals+are+rapid+yet+spatially+variable+across+a+network+of+temperate+marine+protected+areas+Recovery+trajectories+of+kelp+forest+animals+are+rapid+yet+spatially+variable+across+a+network+of+temperate+marine+protected.">Recovery trajectories of kelp forest animals are rapid yet spatially variable across a network of temperate marine protected areas Recovery trajectories of kelp forest animals are rapid yet spatially variable across a network of temperate marine protected.</a> Nat. Publ. Gr. , 1-14 (2015).</li><li>Starr, R. M., Wendt, D. E., 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=Variation+in+Responses+of+Fishes+across+Multiple+Reserves+within+a+Network+of+Marine+Protected+Areas+in+Temperate+Waters.">Variation in Responses of Fishes across Multiple Reserves within a Network of Marine Protected Areas in Temperate Waters.</a> Plos One. 10 (3), 0118502 (2015).</li><li>Lester, S., Halpern, B., 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=Biological+effects+within+no-take+marine+reserves:+a+global+synthesis.">Biological effects within no-take marine reserves: a global synthesis.</a> Mar. Ecol. Prog. Ser. 384, 33-46 (2009).</li></ol>

作者没有透露

传统的 MaxN 度量是基于在调查过程中计算出有保证的最小数量的个人的想法。如果在单个视频帧中同时显示一定数量的鱼, 则不会有任何更少的当前, 但由于鱼是移动和异分布的, 因此在单个视频帧中同时看到所有个人的可能性很低.因此, 传统的 MaxN 可能会低估真正的鱼丰度16,17。此外, 已证明传统的 MaxN 可能显示非线性的负偏置关系与增加鱼丰度<sup class...

在美国太平洋沿岸, 许多对商业和休闲底层渔业很重要的物种 (例如, 石斑鱼复合体 (许氏) 和蛇 (Ophiodon 细长)) 都与浮雕, hard-bottom 栖息地1,2,3,4,5。立体声视频下降相机是一个有吸引力的非工具, 使用在岩石生境由于相对容易和简单的操作。各种立体声摄像系统已经开发并部署在南半球, 浅水生态系统6,7,8,9,10, 以及最近, 视频降摄相机作为一种管理工具, 在太平洋沿岸的深海岩石礁环境中获得了牵引力11,12,13。我们试图通过使用立体声摄像系统 (以下简称 "着陆器") 来修改这些现有的立体相机设计, 以便更有效地描述太平洋沿岸浮雕海底的鱼类种群 (见表材料)。使用的着陆器与现有的视频系统不同, 因为摄像头安装在一个中央旋转杆上, 在下落位置14允许完全360°覆盖海底。着陆器每分钟完成一次完全旋转, 这使我们能够快速地描述一个地区的丰度和群落组成, 并获得相同级别的统计能力, 减少登陆者的部署。(有关着陆器配置的详细信息, 请参见斯塔尔 (2016)14 。研究系统的初步试验表明, 在我们的调查中, 八的摄影机旋转足以描述物种丰度和丰富程度。这一决定是通过观察物种丰度和鱼类密度在较长的下降中的收益递减而作出的。我们建议在任何新的系统中进行一项包括更长浸泡时间在内的试验性研究, 以确定特定生态系统/研究物种的最佳浸泡时间。
通过使用配对立体摄像机, 可以计算每个视频测量的总测量面积和绝对鱼密度;然而, 使用旋转相机需要修改传统的鱼类计数指标。固定视频系统通常使用 "MaxN" 作为部署610上的鱼类的保守计数。传统的 MaxN 描述了一个特定物种的鱼的最大数量在一个单一的视频帧一起观察, 以避免重复计数一条鱼已经离开并返回到帧。因此, MaxN 已经估计出已知存在的鱼的最小数量, 并且可能会低估真正的鱼丰度6,10。MaxN 指标被重新定义, 以代表在每一个摄像机的旋转中看到的最大数量的鱼。
对以前的立体声视频方法进行的第二次修改是考虑到各种大小、颜色和形状的种类具有不同的最大可靠识别距离的事实。例如, 像O. 细长这样的大型物种具有明显的细长形状, 而且与小型和隐蔽的物种 (如 Squarespot 石斑鱼 (许氏 hopkinsi) 相比, 可以可靠地识别出更大的距离。这些不同的最大可探测范围改变了着陆器为每个物种取样的有效面积。因为立体声摄像机允许我们将每条鱼放在三维空间中, 精确度很高, 你可以确定每条鱼的测量距离 (即, "Z 距离", 它的命名为 "z-axis", 这是垂直于相机之间绘制的直线。对于每个物种, 95% 的所有个体被观察到的距离 (以后 "95% Z 距离") 被认为是测量区域的半径, 并被用来计算调查的总面积。除 species-specific 特性外, 可还会受到水浊度等环境条件的影响。由于这些因素在时间和空间上都有变化, 所以仅在聚合中使用 95% Z 统计数据是很重要的。虽然对于大型样品来说是非常准确的, 但在调查的地区, 任何一项单项调查都可能有所不同。
下面详述的协议提供了如何创建和使用这些指标的指导。虽然重点是在太平洋沿岸的深水岩石栖息地的特点, 该方法所描述的修改 MaxN 计数很容易适用于任何旋转落相机系统。对鱼类种群进行定性所需的摄像机旋转数量将取决于当地的生态系统动态, 但修改后的 MaxN 的概念化将保持不变。同样, 虽然我们使用3D 摄影测量软件来分析立体声视频, 但是, 只要在三维空间中的鱼的精确位置是可能的, 这里描述的技术很容易在软件平台上应用。此外, 在未来的研究中, 应用 95% Z 距离值的方法可以考虑 species-specific 范围的可探测性和更准确地计算鱼类丰度。

<table border="0" cellpadding="0" cellspacing="0" style="width:877px;" width="876">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="84">
			<td height="84" style="height:84px;width:201px;">calibration cube</td>
			<td style="width:193px;">SeaGIS</td>
			<td style="width:279px;">http://www.seagis.com.au/hardware.html</td>
			<td style="width:204px;">1000x1000x500 mm is the preferred dimensions. Other methods of calibration are available.&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:201px;">CAL calibration software</td>
			<td style="width:193px;">SeaGIS</td>
			<td style="width:279px;">http://www.seagis.com.au/bundle.html</td>
			<td style="width:204px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:201px;">EventMeasure stereo measurement software</td>
			<td style="width:193px;">SeaGIS</td>
			<td style="width:279px;">http://www.seagis.com.au/event.html</td>
			<td style="width:204px;"></td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:201px;">Statistical software</td>
			<td style="width:193px;">R Core Team 2017 (v. 3.4.0)</td>
			<td style="width:279px;"></td>
			<td style="width:204px;">Bootstrapping code can be found: https://github.com/rfields2017/JoVE-Bootstrap-Function</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:201px;">Spreadsheet Software</td>
			<td style="width:193px;">Microsoft Excel</td>
			<td style="width:279px;"></td>
			<td style="width:204px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:201px;">2&#160; waterproof cameras</td>
			<td style="width:193px;">Deep Sea Power and Light</td>
			<td style="width:279px;"></td>
			<td style="width:204px;">HD quality preferred</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:201px;">2 depth rated, waterproof lights</td>
			<td style="width:193px;">Deep Sea Power and Light : 3000 lumen LED with 5000k color temperature</td>
			<td style="width:279px;"></td>
			<td style="width:204px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:201px;">DVR recorder</td>
			<td style="width:193px;">Stack LTD DVR</td>
			<td style="width:279px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:201px;">standard PC</td>
			<td style="width:193px;"></td>
			<td style="width:279px;"></td>
			<td>Windows 10 preferred OS</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:201px;">rotating Lander platform</td>
			<td style="width:193px;">Marine Applied Research and Engineering (MARE)</td>
			<td style="width:279px;"></td>
			<td></td>
		</tr>
	</tbody>
</table>

development of new methods for quantifying fish density using underwater stereo-video tools

在鱼类生态学研究中使用摄像系统继续作为一种可行的、非的测量鱼长和估计鱼类丰度的方法而得到牵引。我们开发和实施了一个旋转的立体声视频相机工具, 涵盖了一个完整的360度采样, 这将最大程度的采样努力相比, 固定相机工具。各种研究都详细说明了静态、立体摄像系统的能力, 以获得高度精确和精确的鱼类测量;这里的重点是开发方法方法, 用旋转摄像系统来量化鱼的密度。第一种方法是发展对公制 MaxN 的修改, 这通常是在给定的相机测量中观察到的最小鱼数的保守计数。我们重新定义 MaxN 是在任何给定的摄像机系统旋转中观察到的最大鱼数。当采取预防措施, 以避免重复计数, 这种方法的 MaxN 可能更准确地反映真正的丰度比从固定相机。其次, 因为立体声视频允许鱼在三维空间中被映射, 所以每条鱼的距离相机的精确估计可以得到。通过使用观察到的距离的95% 位数从照相机建立 species-specific 区域勘测, 我们解释了不同在可探测性之间, 并且避免稀释密度估计用最大距离一个种类是观察.对这一系列可探测性的核算是准确估计鱼类丰度的关键。这种方法将促进旋转立体视频工具在应用科学和管理环境中的集成。

在2013和2014之间, 我们进行了816调查与旋转立体声视频着陆器 (图 1) 沿中央加利福尼亚海岸和收集 MaxN 和 95% Z 距离 (图 4) 数据在超过20种。由于物种的大小、形状和颜色的相互作用 (图 5), 在有效检测到的物种范围内存在明显的模式。例如, 标志石斑鱼 (许氏 rubrivinctus) 在其两侧有明显的条纹, 允许在?...

Watch this Scientific Journal Video about Development of New Methods for Quantifying Fish Density Using Underwater Stereo-video Tools at JoVE.com

Development of New Methods for Quantifying Fish Density Using Underwater Stereo-video Tools

我们描述了一种新的计数鱼类, 并估计相对丰度 (MaxN) 和鱼类密度使用旋转立体摄像系统。我们还演示了如何使用距离相机 (Z 距离), 以估计 species-specific 可探测性。

利用水下立体视频工具量化鱼类密度的新方法研究进展

The use of video camera systems in ecological studies of fish continues to gain traction as a viable, non-extractive method of measuring fish lengths and ...

development-new-methods-for-quantifying-fish-density-using-underwater

Research

JoVE Journal

Environment

9.2K 次观看.  Moss Landing Marine Laboratories. 我们描述了一种新的计数鱼类, 并估计相对丰度 (MaxN) 和鱼类密度使用旋转立体摄像系统。我们还演示了如何使用距离相机 (Z 距离), 以估计 species-specific 可探测性。

视频: Development of New Methods for Quantifying Fish Density Using Underwater Stereo-video Tools

Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses

Setaria viridis is an emerging model system for C4 grasses. It is closely related to the bioenergy feed stock switchgrass and the grain crop foxtail millet. Recently, the 510 Mb genome of foxtail millet, S. italica, has been sequenced 1,2 and a 25x coverage genome sequence of the weedy relative S. viridis is in progress. S. viridis has a number of characteristics that make it a potentially excellent model genetic system including a rapid generation time, small stature, simple growth requirements, prolific seed production 3 and developed systems for both transient and stable transformation 4. However, the genetics of S. viridis is largely unexplored, in part, due to the lack of detailed methods for performing crosses. To date, no standard protocol has been adopted that will permit rapid production of seeds from controlled crosses.
The protocol presented here is optimized for performing genetic crosses in S. viridis, accession A10.1. We have employed a simple heat treatment with warm water for emasculation after pruning the panicle to retain 20-30 florets and labeling of flowers to eliminate seeds resulting from newly developed flowers after emasculation. After testing a series of heat treatments at permissive temperatures and varying the duration of dipping, we have established an optimum temperature and time range of 48 &deg;C for 3-6 min. By using this method, a minimum of 15 crosses can be performed by a single worker per day and an average of 3-5 outcross progeny per panicle can be recovered. Therefore, an average of 45-75 outcross progeny can be produced by one person in a single day. Broad implementation of this technique will facilitate the development of recombinant inbred line populations of S. viridis X S. viridis or S. viridis X S. italica, mapping mutations through bulk segregant analysis and creating higher order mutants for genetic analysis.

Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses

We have developed a methodology for performing crosses in Setaria viridis (S. viridis). The method involves pruning the panicle prior to a hot water treatment to kill viable pollen. Crosses are performed following a well-controlled growth regime and typically result in the recovery of 1 to 7 cross-pollinated seed/s per panicle.

方法中进行杂交<em&gt;狗尾草</em&gt;，新模型体系的草

Setaria viridis is an emerging model system for C4 grasses. It is closely related to the bioenergy feed stock switchgrass and the grain crop foxtail ...

科研

环境科学

A Fish-feeding Laboratory Bioassay to Assess the Antipredatory Activity of Secondary Metabolites from the Tissues of Marine Organisms

Marine chemical ecology is a young discipline, having emerged from the collaboration of natural products chemists and marine ecologists in the 1980s with the goal of examining the ecological functions of secondary metabolites from the tissues of marine organisms. The result has been a progression of protocols that have increasingly refined the ecological relevance of the experimental approach. Here we present the most up-to-date version of a fish-feeding laboratory bioassay that enables investigators to assess the antipredatory activity of secondary metabolites from the tissues of marine organisms. Organic metabolites of all polarities are exhaustively extracted from the tissue of the target organism and reconstituted at natural concentrations in a nutritionally appropriate food matrix. Experimental food pellets are presented to a generalist predator in laboratory feeding assays to assess the antipredatory activity of the extract. The procedure described herein uses the bluehead, Thalassoma bifasciatum, to test the palatability of Caribbean marine invertebrates; however, the design may be readily adapted to other systems. Results obtained using this laboratory assay are an important prelude to field experiments that rely on the feeding responses of a full complement of potential predators. Additionally, this bioassay can be used to direct the isolation of feeding-deterrent metabolites through bioassay-guided fractionation. This feeding bioassay has advanced our understanding of the factors that control the distribution and abundance of marine invertebrates on Caribbean coral reefs and may inform investigations in diverse fields of inquiry, including pharmacology, biotechnology, and evolutionary ecology.

This bioassay employs a model predatory fish to assess the presence of feeding-deterrent metabolites from organic extracts of the tissues of marine organisms at natural concentrations using a nutritionally comparable food matrix.

了鱼喂食实验室生物测定，从海洋生物的组织评估次生代谢产物的Antipredatory活动

Marine chemical ecology is a young discipline, having emerged from the collaboration of natural products chemists and marine ecologists in the 1980s with ...

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 ...

Protocols for Quantifying Transferable Pesticide Residues in Turfgrass Systems

Plant canopies in established turfgrass systems can intercept an appreciable amount of sprayed pesticides, which can be transferred through various routes onto humans. For this reason, transferable pesticide residue experiments are required for registration and re-registration by the United States Environmental Protection Agency (USEPA). Although such experiments are required, limited specificity is required pertaining to experimental approach. Experimental approaches used to assess pesticide transfer to humans including hand wiping with cotton gloves, modified California roller (moving a roller of known mass over cotton cloth) and soccer ball roll (ball wrapped with sorbent strip) over three treated turfgrass species (creeping bentgrass, hybrid bermudagrass and tall fescue maintained at 0.4, 5 and 9 cm, respectively) are presented. The modified California roller is the most extensively utilized approach to date, and is best suited for use at low mowing heights due to its reproducibility and large sampling area. The soccer ball roll is a less aggressive transfer approach; however, it mimics a very common occurrence in the most popular international sport, and has many implications for nondietary pesticide exposure from hand-to-mouth contact. Additionally, this approach may be adjusted for other athletic activities with limited modification. Hand wiping is the best approach to transfer pesticides at higher mowing heights, as roller-based approaches can lay blades over; however, it is more subjective due to more variable sampling pressure. Utility of these methods across turfgrass species is presented, and additional considerations to conduct transferable pesticide residue research in turfgrass systems are discussed.

Transferable pesticide residue experiments in turfgrass systems are integral components of human risk exposure assessments. Experimental approaches to measure transferable residues should be adjusted to the human interaction of interest and turfgrass system dynamics. Three transferable pesticide residue protocols are presented and the suitability across three turfgrass systems is discussed.

协议在草坪系统量化转换农药残留

Plant canopies in established turfgrass systems can intercept an appreciable amount of sprayed pesticides, which can be transferred through various routes ...

High-pressure, High-temperature Deformation Experiment Using the New Generation Griggs-type Apparatus

In order to address geological processes at great depths, rock deformation should ideally be tested at high pressure (&#62; 0.5 GPa) and high temperature (&#62; 300 &#176;C). However, because of the low stress resolution of current solid-pressure-medium apparatuses, high-resolution measurements are today restricted to low-pressure deformation experiments in the gas-pressure-medium apparatus. A new generation of solid-medium piston-cylinder (&#34;Griggs-type&#34;) apparatus is here described. Able to perform high-pressure deformation experiments up to 5 GPa and designed to adapt an internal load cell, such a new apparatus offers the potential to establish a technological basis for high-pressure rheology. This paper provides video-based detailed documentation of the procedure (using the &#34;conventional&#34; solid-salt assembly) to perform high-pressure, high-temperature experiments with the newly designed Griggs-type apparatus. A representative result of a Carrara marble sample deformed at 700 &#176;C, 1.5 GPa and 10-5 s-1 with the new press is also given. The related stress-time curve illustrates all steps of a Griggs-type experiment, from increasing pressure and temperature to sample quenching when deformation is stopped. Together with future developments, the critical steps and limitations of the Griggs apparatus are then discussed.

Rock deformation needs to be quantified at high pressure. A description of the procedure to perform deformation experiments in a newly designed solid-medium Griggs-type apparatus is here given. This provides technological basis for future rheological studies at pressures up to 5 GPa.

新一代格雷型装置高压高温变形试验

In order to address geological processes at great depths, rock deformation should ideally be tested at high pressure (&#62; 0.5 GPa) and high temperature ...

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 ...

Necropsy-based Wild Fish Health Assessment

Anthropogenic influences from increased nutrients and chemical contaminants, to habitat alterations and climate change, can have significant effects on fish populations. Adverse effects monitoring, utilizing biomarkers from the organismal to the molecular level, can be used to assess the cumulative effects on fishes and other organisms. Fish health has been used worldwide as an indicator of aquatic ecosystem health. The necropsy-based fish health assessment provides data on visible abnormalities and lesions, parasites, condition and organosomatic indices. These can be compared by site, season and sex, as well as temporally, to document change over time. Severity ratings can be assigned to various observations to calculate a fish health index for more quantitative assessment. A drawback of the necropsy-based assessment is that it is based on visual observations and condition factors, which are not as sensitive as tissue and subcellular biomarkers for sublethal effects. Additionally, it is rarely possible to identify causes or risk factors associated with observed abnormalities. So, for instance a raised lesion or "tumor" on the fins, lips or body surface may be a neoplasm. However, it could also be a response to a parasite, chronic inflammation or hyperplasia of normal cells in response to an irritant. Conversely, neoplasms, certain parasites, other infectious agents and many tissue changes are not visible and so may be underestimated. However, during the necropsy-based assessment, blood (plasma), tissues for histopathology (microscopic pathology), genomics and other molecular analyses, and otoliths for aging can be collected. These downstream analyses, together with geospatial analyses, habitat assessments, water quality and contaminant analyses can all be important in comprehensive ecosystem evaluations.

The health of wild fishes can be used as an indicator of aquatic ecosystem health. Necropsy-based fish health assessments provide documentation of visible lesions or abnormalities, data used to calculate condition indices as well as the opportunity to collect tissues for microscopic evaluation, gene expression and other more in-depth analyses.

基于尸检的野生鱼类健康评估

Anthropogenic influences from increased nutrients and chemical contaminants, to habitat alterations and climate change, can have significant effects on ...

A New Portable In Vitro Exposure Cassette for Aerosol Sampling

This protocol introduces a new in vitro exposure system, capable of being worn, including its characterization and performance. Air-liquid interface (ALI) in vitro exposure systems are often large and bulky, making transport to the field and operation at the source of emission or within the breathing zone difficult. Through miniaturization of these systems, the lab can be brought to the field, expediting processing time and providing a more appropriate exposure method that does not alter the aerosol prior to contacting the cells. The Portable In vitro Exposure Cassette (PIVEC) adapts a 37 mm filter cassette to allow for in vitro toxicity testing outside of a traditional laboratory setting. The PIVEC was characterized using three sizes of copper nanoparticles to determine deposition efficiency based on gravimetric and particle number concentration analysis. Initial cytotoxicity experiments were performed with exposed lung cells to determine the ability of the system to deposit particles while maintaining cell viability. The PIVEC provides a similar or increased deposition efficiency when comparing to available perpendicular flow in vitro exposure devices. Despite the lower sample throughput, the small size gives some advantages to the current in vitro ALI exposure systems. These include the ability to be worn for personal monitoring, mobility from the laboratory to the source of emission, and the option to set-up multiple systems for spatial resolution while maintaining a lower user cost. The PIVEC is a system capable of collecting aerosols in the field and within the breathing zone onto an air-interfaced, in vitro model.

A New Portable In Vitro Exposure Cassette for Aerosol Sampling

Here, we present a protocol to perform portable cellular aerosol exposures and measure cellular response. The method uses cells, grown at the air-liquid interface, mimicking in vivo physiology. Cellular response to copper nanoparticle aerosols was observed as oxidative stress through reactive oxygen species generation and cytotoxicity as lactate dehydrogenase release.

一种用于气溶胶取样的新型便携式体外曝光盒

This protocol introduces a new in vitro exposure system, capable of being worn, including its characterization and performance. Air-liquid interface (ALI) ...

Combined Size and Density Fractionation of Soils for Investigations of Organo-Mineral Interactions

Combined size and density fractionation (CSDF) is a method used to physically separate soil into fractions differing in particle size and mineralogy. CSDF relies on sequential density separation and sedimentation steps to isolate (1) the free light fraction (uncomplexed organic matter), (2) the occluded light fraction (uncomplexed organic matter trapped in soil aggregates) and (3) a variable number of heavy fractions (soil minerals and their associated organic matter) differing in composition. Provided that the parameters of the CSDF (dispersion energy, density cut-offs, sedimentation time) are properly selected, the method yields heavy fractions of relatively homogeneous mineral composition. Each of these fractions is expected to have a different complexing ability towards organic matter, rendering this a useful method to isolate and study the nature of organo-mineral interactions. Combining density and particle size separation brings an improved resolution compared to simple size or density fractionation methods, allowing the separation of heavy components according to both mineralogy and size (related to surface area) criteria. As is the case for all physical fractionation methods, it may be considered as less disruptive or aggressive than chemically-based extraction methods. However, CSDF is a time-consuming method and furthermore, the quantity of material obtained in some fractions can be limiting for subsequent analysis. Following CSDF, the fractions may be analyzed for mineralogical composition, soil organic carbon concentration and organic matter chemistry. The method provides quantitative information about organic carbon distribution within a soil sample and brings light to the sorptive capacity of the different, naturally-occurring mineral phases, thus providing mechanistic information about the preferential nature of organo-mineral interactions in soils (i.e., which minerals, what type of organic matter).

Combined size and density fractionation (CSDF) is a method to physically separate soil into fractions differing in texture (particle size) and mineralogy (density). The purpose is to isolate fractions with different reactivities towards soil organic matter (SOM), in order to better understand organo-mineral interactions and SOM dynamics.

土壤联合粒径与密度的分离研究

Combined size and density fractionation (CSDF) is a method used to physically separate soil into fractions differing in particle size and mineralogy. CSDF ...

A Method for Quantifying Foliage-Dwelling Arthropods

Terrestrial arthropods play an important role in our environment. Quantifying arthropods in a way that allows for a precise index or estimates of density requires a method with high detection probability and a known sampling area. While most described methods provide a qualitative or semi-quantitative estimate adequate for describing species presence, richness, and diversity, few provide an adequately consistent detection probability and known or consistent sampling areas to provide an index or estimate with adequate precision to detect differences in abundance across environmental, spatial, or temporal variables. We describe how to quantify leaf-dwelling arthropods by sealing the leaves and end of branches in a bag, clipping and freezing the bagged material, and rinsing the previously frozen material in water to separate arthropods from the substrate and quantify them. As we demonstrate, this method can be used at a landscape scale to quantify leaf-dwelling arthropods with adequate precision to test for and describe how spatial, temporal, environmental, and ecological variables influence arthropod richness and abundance. This method allowed us to detect differences in density, richness, and diversity of leaf-dwelling arthropods among 5 genera of trees commonly found in southeastern deciduous forests.

We describe how to quantify leaf dwelling arthropods by sealing the leaves and end of branches in a bag, clipping and freezing the bagged material, and rinsing the previously frozen material in water to separate arthropods from the substrate for quantification.

定量叶类节肢动物的方法

Terrestrial arthropods play an important role in our environment. Quantifying arthropods in a way that allows for a precise index or estimates of density ...