正在缓步动物抗菌肽的研究得到了校内资金来自美国中西部大学研究办公室和赞助程序 (ORSP)。ORSP 没有任何作用，研究设计、 数据收集、 分析、 解释或手稿的准备。

1.确定定义功能的蛋白质组的 <ol><li>咨询以前的出版物，以确定是否有必要考虑组的一部分的功能方面达成共识。注意到的任何不一致之处或意见研究团体之间的分歧，包括可能有助于区分另一个亚组的特点。</li>
	<li>如果以往文献不能解决最大特色，使用序列作为起点来识别保守的特点被认为集团代表。</li>
</ol> 2。收集有关序列 <ol><li>如果已编写审核，包括分析序列，所代表的集团，包括这些序列中的原始数据集。检索序列使用加入数字文献中引用和保存标准序列编辑程序中 （例如， EditSeq Lasergene 套房或的众多可供一个免费在线）。</li>
	<li>如果问题组已定义在一个结构的数据库，包括数据库列出作为组的一部分使用加入数字提供了在数据库中检索序列的序列并保存在标准序列编辑程序，如上。 
	注: 例如，分类在 CS-α β （蝎子毒素样） 超家族 SCOP 数据库中的序列可以在这里找到: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.h.c.h.html.</li> <li>执行基本本地对齐方式搜索工具 (BLAST) 14 检索公共、 在线数据库可用通过国家中心为生物技术信息中心 (NCBI) 找到可能不在文献中包含的序列或结构数据库。因为大部分完成结果、 使用这两种蛋白质爆炸 (blastp) 和翻译爆炸与蛋白 (tblastn) 查询程序;这些都可在: https://blast.ncbi.nlm.nih.gov/Blast.cgi.
	<ol><li>使用序列已知作为查询序列是感兴趣的组的一部分。复制和粘贴在顶部，搜索框中的序列或提供基因加入号码或 gi 标识符，如果可用。</li>
		<li>从下拉菜单中选择的数据库。选择非冗余蛋白质序列 (nr) 为 blastp 和表达序列标签为 tblastn.</li>
		<li>搜索结果体内设置键入有机体或分类单元的名称，从打字时出现的列表中选择的特定类群。若要添加其他有机体或类群中排除，请单击 &#34; + &#34; 按钮和另一个字段将出现。排除任何不需要的罗汗松在有机体框中键入的有机体或分类单元的名称，从同时键入，并检查显示的列表中选择 &#34; 排除 &#34; 右侧框。</li>
		<li>通过单击访问附加参数 &#34; 算法参数 &#34; 附近的页的底部。保留默认值除非有理由要改变一个参数。</li>
		单击 <li>&#34; 高炉 &#34; 按钮以运行分析; 它可能需要一些时间来显示结果。一般情况下，检索命中与预期值 （或 e-值） 的 &#34;-05 &#34; 或更好的与标准序列编辑程序中保存。
		<ol><li>如果所有点击数高于此阈值，重新运行搜索与日益增多的靶序列 （在算法参数部分） 以获得所有相关序列。</li>
		</ol></li></ol></li> <li>如有必要，修剪序列以排除不相关的信息 （例如， CS-α β 折叠仅适用于成熟肽）。识别信号肽和 pro 肽去除使用道具 15 (可用在线)，或为更复杂的信号肽预测 16 SignalP (可在线)。</li>
</ol> 3。在电子表格中基于重要特征，确定了生成引用 <ol><li>标识的组的最大特色。例如，使用 CS-α β 折叠明确建立由昆虫防御素 Phormia terraenovae ( 图 1) 8 A 的解决方案结构。
	<ol><li>这折叠包括一个小的主题，称为半胱氨酸稳定螺旋 (CSH) 17; 确定这一主题的 CXXXC （其中 X 是任何氨基酸） 上游形成两个二硫键 CXC ( 图 1、 固体粉红色线条)。 
		注: 要完成 CS-α β 母题，第三个二硫键形成从额外半胱氨酸，摆在每个半场 CSH 图案 ( 图 1，点缀粉色线) 面前。</li>
	</ol></li> <li>输入这些到电子表格中定义的功能。请参见 图 2。
	<ol><li>使用列的保守的功能，并表示这些功能之间的空格。保持足够宽，以便容纳数字并确保他们有一个一致的宽度的列。设置宽度使用 &#34; 格式 |列宽度 &#34; 功能 ( 图 2，粉红色的箭头)。</li>
		<li>序列名称中使用行。</li>
		<li>当序列具有的特点，填写框中使用的填充函数 ( 图 2，粉红色广场)。功能部件之间的间距，之间的框中输入氨基酸数目并保持空缺。例如，利用昆虫防御素序列给出了包括六个半胱氨酸、 定义间距以及 C5 和 C6 之间 C2 和 C3 的引用。</li>
	</ol></li> <li>添加代表此前已建立的序列作为基于结构数据库和文学组的成员。 
	注: 例如，前面的文献和 SCOP 数据库确定列入几个群体: 昆虫防御素、 短链蝎毒素、 长链蝎毒素 MGD 1、 植物防御素、 ABFs 线虫、 果蝇， 从 drosomycins 和macins。文学也标识可能代表 18 本家族的祖先的只有四个半胱氨酸与细菌的序列。添加这些序列增加半胱氨酸在六至十参考但保持重要的结构特征 ( 图 3) 的对齐方式。
	<ol><li>若要添加一项功能，很容易定义序列 （例如，额外的半胱氨酸） 的一个子群，使用 &#34; 插入 &#34; 功能 ( 图 3，粉红色的箭头)。</li>
		<li>如果有的功能缺失从一个给定的序列，将填充框和结合代表介入氨基酸盒子。如有必要，合并单元格使用合并及居中功能 ( 图 3，粉红色的盒子)。</li>
	</ol></li> <li>继续将序列添加到的组，以更好地了解每个组的大家族中的变化。总结的群体特征，以便利比较 ( 图 4)。
	<ol><li>氨基酸之间主要特征数目变化时，使用连字符来指示一个范围，如 6-12 （6 至 12 氨基酸） 和一个斜杠，表明不是 / 或者，如 7/10 （7 或 10 氨基酸）。</li>
		<li>选择注释的序列可能有关，但不会经常发生，在引用中包括的功能的方式。例如，由于半胱氨酸是重要在这个家族中，标签附加半胱氨酸 ( 图 4，粉红色框)。</li>
	</ol></li> <li>添加 newly 确定序列到电子表格中使用既定的序列作为指南。例如，从缓步动物 （黄色） 添加序列显示缓步序列分为几个不同的家族 （ 图 5 显示摘要而不是每个层序空间用于行）。</li>
	<li>通过重新排列行 ( 图 6) 显示分类组内的变异。</li>
</ol> 4。使用改进的氨基酸排列的引用 注: 有很多的程序，可以用于多序列比对，但这个示范将使用分子进化遗传分析 (MEGA6) 19 因为它是可供免费下载。
<ol><li>下载并安装软件。</li>
	<li>通过选择开始新的对准线在巨型 &#34; 编辑/生成对齐 &#34; 下对齐选项卡选择 &#34; 创建一个新的路线 &#34; 在框中出现，请单击 &#34; OK。 &#34; 然后选择 &#34; 蛋白质。 &#34;</li>
	<li>选择 &#34; 从文件插入序列 &#34; 在 &#34; 编辑 &#34; 菜单导入序列。 
	注意: 序列将需要在 FASTA 格式导入到大型。默认情况下，使用反映不同氨基酸类型的背景颜色，但此选项可以关闭下 &#34; 显示 &#34; 菜单。</li>
	<li>一旦输入所有序列，请单击伸缩臂图标，然后 &#34; 对齐蛋白 &#34; 来对齐序列使用肌肉算法 20。 
	注: ClustalW 也是可用的。
	<ol><li>如果一个消息，说什么已经选定的持久性有机污染物和要求来选择所有，单击 &#34; OK。 &#34;</li> <li>注: 这将打开一个窗口，允许一个人能改变一些参数，但他们，才应该更改理由这样做。这种分析使用子集序列分析在先前的纸 12.</li>
	</ol></li> <li>检查对齐方式的基础的重要特征; 请注意，上面的序列的顶部栏将显示的任何列氨基酸在哪里完全保守 （*）。请参阅 图 7。请参阅初始对准显示只有三个四个保守半胱氨酸 ( 图 7，粉红色框);俯视列中，AlCRP 序列是明确未对齐 ( 图 7，粉红色的箭头)。</li>
	<li>要摆脱我的大差距和保守的 C，突出显示的短划线和新闻 &#34; 删除 &#34; 的关键。不突出任何氨基酸，或他们将同时删除。</li>
	<li>移动到右边的氨基酸，突出显示，按空间栏
	<ol><li>注 AlCRP 现在已经对齐结构半胱氨酸和 C 最后的 CXXXC 主题守恒整个对齐 ( 图 8)。调整对齐方式，有必要优先序列的最重要特点。</li>
	</ol></li></ol> 5。比较组确定使用从系统发育分析结果与参考 <ol><li>从初步的路线，确定哪些序列应包含在系统发育分析; 对于少量的序列，这一步可能是不必要的。
	<ol><li>保留对齐文件包含所有的序列，但系统发育分析，将删除冗余序列 （ 图 9，粉红色框显示对的冗余序列）。</li>
		<li>如果数据集包含大量的序列，运行初步分析和选择代表从群体总是形成分支。</li>
	</ol></li> <li>确定最佳的氨基酸替代模式。
	<ol><li>出口巨型格式 （在数据选项卡） 中的对齐方式。</li>
		<li>转到模型菜单并选择 &#34; 找到最佳 DNA/蛋白质模型。 &#34; 选择刚刚保存的文件并打开它; 这将打开一个窗口，可以更改某些参数。</li>
		<li>使用默认参数，除非有理由去改变它们。单击 &#34; 计算 &#34; 开始分析。</li>
	</ol></li> <li>运行的最大似然 (ML) 分析在巨型。
	<ol><li>选择 &#34; 构建/测试最大似然树 &#34; 从发展史上菜单。</li>
		<li>选择确定的模型是最适合的数据从步 5.2 (输出就能替代模型，最好 &#34; 率网站 &#34; 参数)。</li>
		<li>选择 1,000 引导复制以获得对树的支持措施。</li>
		单击 <li>&#34; 计算 &#34; 运行分析;巨型有 &#34; 树资源管理器 &#34; 可视化树。</li>
	</ol></li> <li>MrBayes 开放源码软件 21 运行贝叶斯分析。 
	注: MrBayes 手册是也可从本网站。这只提供基本步骤并不是进行贝叶斯系统发育分析的综合指南。
	<ol><li>将巨型对齐在波普 (Nexus) 格式导出到 MrBayes 程序相同的文件夹中。</li>
		<li>开放 MrBayes 和类型 &#34; exe 文件名 &#34; (例如， &#34; exe Alignment.nex &#34;)。</li>
		<li>指定的模型和分析参数。选择在步骤 5.2 中指定的任一模型或选择 &#34; 混合 &#34; 设置，会尝试各种型号和报告在树上与最好的后验概率模型的频率 (prset aamodelpr = 混合)。类型 &#34; showmodel &#34; 报告当前的模型设置和 &#34; 帮助 mcmc &#34; 显示当前参数设置，与每个的简要说明。</li>
		<li>设置的数代使用 &#34; mcmcp ngen = &#34; 命令 （100 万是典型）。</li>
		<li>型 &#34; mcmc &#34; 开始分析。</li>
		<li>代数目已完成时，程序会要求要添加更多的后代。如果分裂频率平均标准偏差均小于 0.1，键入 no。如果它是高于 0.1，分析应该再继续下去，或一些参数应改变 （见手册 》）。</li>
		<li>使用 &#34; sumt &#34; 命令以生成树文件。</li>
		<li>完成分析并生成共识树之后，可以在忐忑不安中查看树 (可在线)。</li>
	</ol></li> <li>比较，树木可以看到是否方法生成一致的结果。 
	注意: 一些序列并不提供大量的信息: 树可能不是很好的解决和分公司，可能有极少的支持 ( 图 10)。</li>
	<li>把确定使用引用来看看是否系统发育分析支持这些群体的群体树木比作。</li>
</ol>

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F., 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=Gapped+BLAST+and+PSI-BLAST:+a+new+generation+of+protein+database+search+programs.">Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.</a> Nucleic Acids Res. 25 (17), 3389-3402 (1997).</li><li>Zhang, Z., 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=Protein+sequence+similarity+searches+using+patterns+as+seeds.">Protein sequence similarity searches using patterns as seeds.</a> Nucleic Acids Res. 26 (17), 3986-3990 (1998).</li></ol>

作者没有透露。

命名组内的蛋白质标准应该是明确的但事实并非总是如此。在许多实验室使用各种各样的生物，导致在不同系统中的术语，以及不同程度的表征，研究了有 CS-α β 折叠的序列。企图强加一个完全新的命名法是不合理的会导致大量的混乱时以前文献。参考编号系统可以蛋白质名称用于澄清其与家族的特征。
组蛋白的明确标准的命名和分类将不可能受益于生成参考在电子表格中?...

蛋白质的名称应该反映是特征及与其他蛋白质的关系。不幸的是，名称通常会发现当时被分配，并且，随着研究的继续，较大范围的理解可能更改。如果蛋白质被独立地识别由多个实验室，变化在命名或被认为是明确分配名称时的特点和充足地不再区分蛋白质的名称，这会导致多个名称从别人。
无脊椎动物防御提供很好的例子，变性的命名和分类。第一次的无脊椎动物防御宗从昆虫，和名称"昆虫防御素"，提出了基于感知的同源性为哺乳动物防御素1，2。长期防御素仍然使用，即使它是现在很清楚那无脊椎动物及哺乳动物防御素不共享一个共同的祖先3，4。根据物种，"防御"无脊椎动物可能有六个或八个半胱氨酸 （即形成三个或四个二硫键） 和各种抗菌活性。防止局势进一步复杂化，具有相同特征的蛋白质称为防御素是不总是"防御，"如最近发现的 cremycins 从秀丽 remanei5。此外，无脊椎动物大防御素是更有可能进化有关脊椎动物 β-防御素比到其他无脊椎动物防御6。尽管这样，研究人员有时依赖名称"防御"确定哪些序列应列入分析时。
结构的研究揭示昆虫防御素与蝎子毒素7，之间的相似性和 CS-α β 折叠随后成立作为昆虫防御8的定义结构特征。这折叠结构蛋白质分类 (SCOP) 数据库中9，目前包括五个家庭定义蝎子毒素样 （CS-α β） 超家族: 昆虫防御素、 短链蝎毒素、 长链蝎毒素，MGD 1 （从软体动物） 和植物防御素。这个家族是最近描述的独联体防御4和蛋白酶基因 3D 数据库10，11超 3.30.30.10 家族的代名词。从繁多的无脊椎动物类群、 植物和真菌显示的名称包含这折叠的蛋白质显然无关的半胱氨酸数量的抗菌活性或键合模式、 进化历史12的研究。
缺乏一致性和明确的标准，使它具有挑战性进行命名和分类在这个家族中的新发现序列。比较此超家族蛋白的主要障碍是半胱氨酸的编号对每个单独序列 （每个序列中的第一个半胱氨酸是 C1），没有办法解释的结构的作用。这意味着只有序列与相同数量的半胱氨酸可以进行比较。还有小序列保守性非半胱氨酸形成 CS-α β 折叠，使线路及系统发育分析困难。通过开发划分结构功能优先级编号系统，可以更轻松地比较和对齐家族序列。保守的特点，以及那些定义分组，可以快速，可视化和新序列可以更轻松地放入适当的上下文。
本文使用一个电子表格软件 （如Excel） 来生成参考编号系统的 CS-α β 超家族。它显示如何这澄清序列之间的比较，并将其应用于新的 CS-α β 序列确定从缓步动物。使用 CS-α β 超家族作为一个例子，是写议定书 》 提供指导，当使用序列的兴趣;然而，它不是要具体到这个家族或富含半胱氨酸序列。此方法可能会最有用的蛋白质，有独立研究在不同类群和 （或） 有小的整体序列同源性，与离散性的特征，不可能很容易识别的分子分析软件组。此方法要求一些先验的决定，有关重要的功能，所以它将有限的公共事业，如果没有重要的特点，确定了。主要的目标是展示如何可以实现一个简单的可视化的序列关系。这然后可以用于通知序列比对和分析，但如果对齐方式和分析的主要目标，条形码方法会有更多的容量，为自动化13个合适的选择。当前方法的线性形式，显示每个肽的特点，所以它不会有助于直接可视化的三维结构。

<table width="573">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="42">
			<td height="42" style="width:216px;height:42px;">BLAST webpage</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">https://blast.ncbi.nlm.nih.gov/Blast.cgi</td>
		</tr>
		<tr height="21">
			<td height="21" style="width:216px;height:21px;">EditSeq (Lasergene suite)</td>
			<td style="width:71px;">DNASTAR</td>
			<td style="width:119px;"></td>
			<td style="width:167px;">https://www.dnastar.com/t-allproducts.aspx</td>
		</tr>
		<tr height="21">
			<td height="21" style="width:216px;height:21px;">Excel 2013</td>
			<td style="width:71px;">Microsoft</td>
			<td style="width:119px;"></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="63">
			<td height="63" style="width:216px;height:63px;">FigTree</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">&#160;http://tree.bio.ed.ac.uk/software/figtree/</td>
		</tr>
		<tr height="21">
			<td height="21" style="width:216px;height:21px;">MEGA</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td>www.megasoftware.net</td>
		</tr>
		<tr height="42">
			<td height="42" style="width:216px;height:42px;">MrBayes</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">http://mrbayes.sourceforge.net/</td>
		</tr>
		<tr height="42">
			<td height="42" style="width:216px;height:42px;">SCOP database</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">http://scop.mrc-lmb.cam.ac.uk/scop/</td>
		</tr>
	</tbody>
</table>

creating and applying a reference to facilitate the discussion and classification of proteins in a diverse group

研究了在不同的实验室使用不同生物体的相关的蛋白可能缺乏统一的制度的命名和分类，制作困难，讨论组作为一个整体并放置到适当的上下文的新序列。发展优先重要序列特征的引用有关的结构和 （或) 活动可用于除规定名称向不同的蛋白质组中添加一些相干。本文使用的半胱氨酸稳定 α 螺旋 （CS-α β） 超家族作为一个例子显示如何在电子表格软件中生成的引用可以澄清现有蛋白超家族成员之间的关系，以及促进新的加法序列。它还演示如何引用可以帮助完善中常用的软件，系统发育分析的有效性的影响生成的序列比对。引用的使用可能会对于蛋白质组包含高度不同的序列，从广泛的类群，具有各种功能，不充分的分子分析捕捉到最有帮助。

序列在文献报道的 CS-α β 超家族中的组如图 4所示。半胱氨酸配对的基础，每个序列的编号表明五个基本组 (表 1，中间列)。第一小组有六个半胱氨酸，从三个二硫键债券，包括昆虫、 蛛形纲动物、 软体动物、 线虫、 真菌从序列。组 2、 3 和 4 已形成四个二硫键的 8 半胱氨酸。第二组包括昆虫、 蜘蛛纲动物和植物序列;第 3 组包括蛛形?...

Watch this Scientific Journal Video about Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group at JoVE.com

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

创建和应用的参考，以便不同的组中的蛋白质分类与探讨

本议定书的目标是制定一个基准不同蛋白质缺乏连贯一致的命名和分类标准的组中。此引用有助于分析和小组讨论作为一个整体，可采用除规定名称。

Related proteins that have been studied in different labs using varying organisms may lack a uniform system of nomenclature and classification, making it ...

creating-applying-reference-to-facilitate-discussion-classification

Research

JoVE Journal

Behavior

7.0K 次观看.  Midwestern University. 本议定书的目标是制定一个基准不同蛋白质缺乏连贯一致的命名和分类标准的组中。此引用有助于分析和小组讨论作为一个整体，可采用除规定名称。

视频: Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

The Crossmodal Congruency Task as a Means to Obtain an Objective Behavioral Measure in the Rubber Hand Illusion Paradigm

The rubber hand illusion (RHI) is a popular experimental paradigm. Participants view touch on an artificial rubber hand while the participants' own hidden hand is touched. If the viewed and felt touches are given at the same time then this is sufficient to induce the compelling experience that the rubber hand is one's own hand. The RHI can be used to investigate exactly how the brain constructs distinct body representations for one's own body. Such representations are crucial for successful interactions with the external world. To obtain a subjective measure of the RHI, researchers typically ask participants to rate statements such as "I felt as if the rubber hand were my hand". Here we demonstrate how the crossmodal congruency task can be used to obtain an objective behavioral measure within this paradigm.
The variant of the crossmodal congruency task we employ involves the presentation of tactile targets and visual distractors. Targets and distractors are spatially congruent (i.e. same finger) on some trials and incongruent (i.e. different finger) on others. The difference in performance between incongruent and congruent trials - the crossmodal congruency effect (CCE) - indexes multisensory interactions. Importantly, the CCE is modulated both by viewing a hand as well as the synchrony of viewed and felt touch which are both crucial factors for the RHI.
The use of the crossmodal congruency task within the RHI paradigm has several advantages. It is a simple behavioral measure which can be repeated many times and which can be obtained during the illusion while participants view the artificial hand. Furthermore, this measure is not susceptible to observer and experimenter biases. The combination of the RHI paradigm with the crossmodal congruency task allows in particular for the investigation of multisensory processes which are critical for modulations of body representations as in the RHI.

We demonstrate how an objective measure can be employed in the widely employed rubber hand illusion paradigm. This measure is obtained by modifying the well-established crossmodal congruency task. This task allows the investigation of multisensory processes which are critical for modulations of body representations as in the rubber hand illusion.

一致性的任务作为一种手段来获取目标行为的措施中的橡胶手错觉范式Crossmodal

The rubber hand illusion (RHI) is a popular experimental paradigm. Participants view touch on an artificial rubber hand while the participants' own hidden ...

科研

行为学

Uncovering Beat Deafness: Detecting Rhythm Disorders with Synchronized Finger Tapping and Perceptual Timing Tasks

A set of behavioral tasks for assessing perceptual and sensorimotor timing abilities in the general population (i.e., non-musicians) is presented here with the goal of uncovering rhythm disorders, such as beat deafness. Beat deafness is characterized by poor performance in perceiving durations in auditory rhythmic patterns or poor synchronization of movement with auditory rhythms (e.g., with musical beats). These tasks include the synchronization of finger tapping to the beat of simple and complex auditory stimuli and the detection of rhythmic irregularities (anisochrony detection task) embedded in the same stimuli. These tests, which are easy to administer, include an assessment of both perceptual and sensorimotor timing abilities under different conditions (e.g., beat rates and types of auditory material) and are based on the same auditory stimuli, ranging from a simple metronome to a complex musical excerpt. The analysis of synchronized tapping data is performed with circular statistics, which provide reliable measures of synchronization accuracy (e.g., the difference between the timing of the taps and the timing of the pacing stimuli) and consistency. Circular statistics on tapping data are particularly well-suited for detecting individual differences in the general population. Synchronized tapping and anisochrony detection are sensitive measures for identifying profiles of rhythm disorders and have been used with success to uncover cases of poor synchronization with spared perceptual timing. This systematic assessment of perceptual and sensorimotor timing can be extended to populations of patients with brain damage, neurodegenerative diseases (e.g., Parkinson&#8217;s disease), and developmental disorders (e.g., Attention Deficit Hyperactivity Disorder).

Behavioral tasks that allow for the assessment of perceptual and sensorimotor timing abilities in the general population (i.e., non-musicians) are presented. Synchronization of finger tapping to the beat of an auditory stimuli and detecting rhythmic irregularities provides a means of uncovering rhythm disorders.

揭开节拍耳聋:检测节律紊乱与同步手指敲击和感知定时任务

A set of behavioral tasks for assessing perceptual and sensorimotor timing abilities in the general population (i.e., non-musicians) is presented here ...

Using the Threat Probability Task to Assess Anxiety and Fear During Uncertain and Certain Threat

Fear of certain threat and anxiety about uncertain threat are distinct emotions with unique behavioral, cognitive-attentional, and neuroanatomical components. Both anxiety and fear can be studied in the laboratory by measuring the potentiation of the startle reflex. The startle reflex is a defensive reflex that is potentiated when an organism is threatened and the need for defense is high. The startle reflex is assessed via electromyography (EMG) in the orbicularis oculi muscle elicited by brief, intense, bursts of acoustic white noise (i.e., &#8220;startle probes&#8221;). Startle potentiation is calculated as the increase in startle response magnitude during presentation of sets of visual threat cues that signal delivery of mild electric shock relative to sets of matched cues that signal the absence of shock (no-threat cues). In the Threat Probability Task, fear is measured via startle potentiation to high probability (100% cue-contingent shock; certain) threat cues whereas anxiety is measured via startle potentiation to low probability (20% cue-contingent shock; uncertain) threat cues. Measurement of startle potentiation during the Threat Probability Task provides an objective and easily implemented alternative to assessment of negative affect via self-report or other methods (e.g., neuroimaging) that may be inappropriate or impractical for some researchers. Startle potentiation has been studied rigorously in both animals (e.g., rodents, non-human primates) and humans which facilitates animal-to-human translational research. Startle potentiation during certain and uncertain threat provides an objective measure of negative affective and distinct emotional states (fear, anxiety) to use in research on psychopathology, substance use/abuse and broadly in affective science. As such, it has been used extensively by clinical scientists interested in psychopathology etiology and by affective scientists interested in individual differences in emotion.

Potentiation of the startle reflex is measured via electromyography of the orbicularis oculi muscle during low (uncertain) and high (certain) probability electric shock threat in the Threat Probability Task. This provides an objective measure of distinct negative emotional states (fear/anxiety) for research on psychopathology, substance use/abuse, and broad affective science.

使用威胁概率任务，以评估焦虑和恐惧在不确定性和一定的威胁

Fear of certain threat and anxiety about uncertain threat are distinct emotions with unique behavioral, cognitive-attentional, and neuroanatomical ...

The Modified Hole Board - Measuring Behavior, Cognition and Social Interaction in Mice and Rats

This protocol describes the modified hole board (mHB), which combines features from a traditional hole board and open field and is designed to measure multiple dimensions of unconditioned behavior in small laboratory mammals (e.g., mice, rats, tree shrews and small primates). This paradigm is a valuable alternative for the use of a behavioral test battery, since a broad behavioral spectrum of an animal&#8217;s behavioral profile can be investigated in one single test.
The apparatus consists of a box, representing the &#8216;protected&#8217; area, separated from a group compartment. A board, on which small cylinders are staggered in three lines, is placed in the center of the box, representing the &#8216;unprotected&#8217; area of the set-up. The cognitive abilities of the animals can be measured by baiting some cylinders on the board and measuring the working and reference memory. Other unconditioned behavior, such as activity-related-, anxiety-related- and social behavior, can be observed using this paradigm. Behavioral flexibility and the ability to habituate to a novel environment can additionally be observed by subjecting the animals to multiple trials in the mHB, revealing insight into the animals&#8217; adaptive capacities.
Due to testing order effects in a behavioral test battery, na&#239;ve animals should be used for each individual experiment. By testing multiple behavioral dimensions in a single paradigm and thereby circumventing this issue, the number of experimental animals used is reduced. Furthermore, by avoiding social isolation during testing and without the need to food deprive the animals, the mHB represents a behavioral test system, inducing if any, very low amount of stress.

This protocol describes the modified hole board, which is a behavioral test set-up that comprises the characteristics of an open field and a traditional hole board. This set-up enables the differential analysis of unconditioned behavior of small laboratory mammals as well as the analysis of cognitive abilities.

修改后的孔板 - 测量行为，认知和社会互动小鼠和大鼠

This protocol describes the modified hole board (mHB), which combines features from a traditional hole board and open field and is designed to measure ...

Applying Stereotactic Injection Technique to Study Genetic Effects on Animal Behaviors

Stereotactic injection is a useful technique to deliver high titer lentiviruses to targeted brain areas in mice. Lentiviruses can either overexpress or knockdown gene expression in a relatively focused region without significant damage to the brain tissue. After recovery, the injected mouse can be tested on various behavioral tasks such as the Open Field Test (OFT) and the Forced Swim Test (FST). The OFT is designed to assess locomotion and the anxious phenotype in mice by measuring the amount of time that a mouse spends in the center of a novel open field. A more anxious mouse will spend significantly less time in the center of the novel field compared to controls. The FST assesses the anti-depressive phenotype by quantifying the amount of time that mice spend immobile when placed into a bucket of water. A mouse with an anti-depressive phenotype will spend significantly less time immobile compared to control animals. The goal of this protocol is to use the stereotactic injection of a lentivirus in conjunction with behavioral tests to assess how genetic factors modulate animal behaviors.

Stereotactic injection of lentiviruses expressing cDNAs or shRNAs can modulate gene expression in specific brain areas of mice. Here, we present a protocol to combine stereotactic injections with behavioral tasks, such as the Open Field Test (OFT) and the Forced Swim Test (FST).

应用立体定向注射技术在研究动物行为的遗传效应

Stereotactic injection is a useful technique to deliver high titer lentiviruses to targeted brain areas in mice. Lentiviruses can either overexpress or ...

The Social Dimension of Stress: Experimental Manipulations of Social Support and Social Identity in the Trier Social Stress Test

In many situations humans are influenced by the behavior of other people and their relationships with them. For example, in stressful situations supportive behavior of other people as well as positive social relationships can act as powerful resources to cope with stress. In order to study the interplay between these variables, this protocol describes two effective experimental manipulations of social relationships and supportive behavior in the laboratory. In the present article, these two manipulations are implemented in the Trier Social Stress Test (TSST)&#8212;a standard stress induction paradigm in which participants are subjected to a simulated job interview. More precisely, we propose (a) a manipulation of the relationship between different protagonists in the TSST by making a shared social identity salient and (b) a manipulation of the behavior of the TSST-selection committee, which acts either supportively or unsupportively. These two experimental manipulations are designed in a modular fashion and can be applied independently of each other but can also be combined. Moreover, these two manipulations can also be integrated into other stress protocols and into other standardized social interactions such as trust games, negotiation tasks, or other group tasks.

Previous research on the social dimension of stress has focused on two important variables: social identity and social support. This protocol introduces an effective experimental manipulation of these two social variables and describes their implementation in a standard stress induction paradigm (Trier Social Stress Test).

应力的社会问题:社会支持和社会认同的特里尔社会的实验操作压力测试

In many situations humans are influenced by the behavior of other people and their relationships with them. For example, in stressful situations ...

Psychophysical Tracking Method to Measure Taste Preferences in Children and Adults

The Monell two-series, forced-choice, paired-comparison tracking method provides a reliable measure of sweet taste preferences from childhood to adulthood. The method, which is identical for children, adolescents, and adults, is of short duration (&#60; 15 min), does not rely on sustained attention or place demands on memory (which would yield spurious age differences), and minimizes the impact of language development, making this method amenable to the cognitive limitations of pediatric populations. In this whole-mouth tasting method, subjects are asked to taste (without swallowing) pairs of solutions of different sucrose concentrations and to point to the solution they prefer. Each subsequent pair contains the participant&#39;s preceding preferred concentration and an adjacent stimulus concentration. The procedure continues until the subject chooses either a given concentration of sucrose when paired with both a higher and a lower concentration, or the highest or lowest concentration two consecutive times. Subjects are prevented from reaching response criteria on the basis of first or second position bias by the two-series design of the method, which counterbalances the order of solution presentation within each pair between the series (the weaker concentration is presented first in Series 1, second in Series 2). The geometric mean of the two sucrose concentrations chosen in Series 1 and 2 is an estimate of the participant&#39;s most preferred level of sucrose. Sucrose preference as determined with this laboratory-based measure has been shown to be associated with preference for sugars in foods and beverages and with taste receptor genotype, family history of alcoholism, and race/ethnicity, as well as depressive symptomatology among pediatric populations. The method has real-world relevance and has been applied to determine most preferred level of other tastes (e.g., salt), making it a valuable psychophysical tool.

Sweet taste has powerful hedonic appeal among people of all ages, particularly children. Described herein is a reliable and valid method that can be used to determine the level of sweetness most preferred, making it a valuable psychophysical tool for scientists.

心理跟踪方法来衡量儿童和成人的口味偏好

The Monell two-series, forced-choice, paired-comparison tracking method provides a reliable measure of sweet taste preferences from childhood to ...

Behavioral Disturbances: An Innovative Approach to Monitor the Modulatory Effects of a Nutraceutical Diet

In dogs, diets are often used to modulate behavioral disturbances related to chronic anxiety and stress caused by intense and restless activity. However, the traditional ways to monitor behavioral changes in dogs are complicated and not efficient. In the current clinical evaluation, a new, simple monitoring system was used to assess the effectiveness of a specific diet in positively modulating the intense and restless activity of 24 dogs of different ages and breeds. This protocol describes how to easily and rapidly evaluate improvement in a set of symptoms related to generalized anxiety by using a specific sensor, a mobile phone app, a wireless router, and a computer. The results showed that dogs treated with specific diets showed significant improvement in the times spent active and at rest after 10 days (p &lt; 0.01 and p &lt; 0.05, respectively). These dogs also showed an overall significant improvement in clinical and behavioral symptoms. A specific sensor, along with its related hardware, was demonstrated to successfully monitor behavioral changes relating to movement in dogs.

We report a simple approach to evaluate the effectiveness of a specific diet in positively modulating the daily activity and clinical and behavioral symptoms of dogs with evident behavioral disturbances.

行为障碍:一个创新的方法来监控保健品饮食的调节作用

In dogs, diets are often used to modulate behavioral disturbances related to chronic anxiety and stress caused by intense and restless activity. However, ...

Using a Virtual Store As a Research Tool to Investigate Consumer In-store Behavior

People&#39;s responses to products and/or choice environments are crucial to understanding in-store consumer behaviors. Currently, there are various approaches (e.g., surveys or laboratory settings) to study in-store behaviors, but the external validity of these is limited by their poor capability to resemble realistic choice environments. In addition, building a real store to meet experimental conditions while controlling for undesirable effects is costly and highly difficult. A virtual store developed by virtual reality techniques potentially transcends these limitations by offering the simulation of a 3D virtual store environment in a realistic, flexible, and cost-efficient way. In particular, a virtual store interactively allows consumers (participants) to experience and interact with objects in a tightly controlled yet realistic setting. This paper presents the key elements of using a desktop virtual store to study in-store consumer behavior. Descriptions of the protocol steps to: 1) build the experimental store, 2) prepare the data management program, 3) run the virtual store experiment, and 4) organize and export data from the data management program are presented. The virtual store enables participants to navigate through the store, choose a product from alternatives, and select or return products. Moreover, consumer-related shopping behaviors (e.g., shopping time, walking speed, and number and type of products examined and bought) can also be collected. The protocol is illustrated with an example of a store layout experiment showing that shelf length and shelf orientation influence shopping- and movement-related behaviors. This demonstrates that the use of a virtual store facilitates the study of consumer responses. The virtual store can be especially helpful when examining factors that are costly or difficult to change in real life (e.g., overall store layout), products that are not presently available in the market, and routinized behaviors in familiar environments.

This paper describes the use of a desktop virtual store to create virtual shopping environments to investigate in-store consumer behavior. A description of the protocol to build and run experiments, example results from an experiment concerning store layout, and important considerations when conducting virtual store experiments are presented.

使用虚拟商店作为调查消费者店内行为的研究工具

People&#39;s responses to products and/or choice environments are crucial to understanding in-store consumer behaviors. Currently, there are various ...

Using the FishSim Animation Toolchain to Investigate Fish Behavior: A Case Study on Mate-Choice Copying In Sailfin Mollies

Over the last decade, employing computer animations for animal behavior research has increased due to its ability to non-invasively manipulate the appearance and behavior of visual stimuli, compared to manipulating live animals. Here, we present the FishSim Animation Toolchain, a software framework developed to provide researchers with an easy-to-use method for implementing 3D computer animations in behavioral experiments with fish. The toolchain offers templates to create virtual 3D stimuli of five different fish species. Stimuli are customizable in both appearance and size, based on photographs taken of live fish. Multiple stimuli can be animated by recording swimming paths in a virtual environment using a video game controller. To increase standardization of the simulated behavior, the prerecorded swimming path may be replayed with different stimuli. Multiple animations can later be organized into playlists and presented on monitors during experiments with live fish.
In a case study with sailfin mollies (Poecilia latipinna), we provide a protocol on how to conduct a mate-choice copying experiment with FishSim. We utilized this method to create and animate virtual males and virtual model females, and then presented these to live focal females in a binary choice experiment. Our results demonstrate that computer animation may be used to simulate virtual fish in a mate-choice copying experiment to investigate the role of female gravid spots as an indication of quality for a model female in mate-choice copying.
Applying this method is not limited to mate-choice copying experiments but can be used in various experimental designs. Still, its usability depends on the visual capabilities of the study species and first needs validation. Overall, computer animations offer a high degree of control and standardization in experiments and bear the potential to &#39;reduce&#39; and &#39;replace&#39; live stimulus animals as well as to &#39;refine&#39; experimental procedures.

Using the FishSim Animation Toolchain to Investigate Fish Behavior: A Case Study on Mate-Choice Copying In Sailfin Mollies

Using the novel FishSim Animation Toolchain, we present a protocol for non-invasive visual manipulation of public information in the context of mate-choice copying in sailfin mollies. FishSim Animation Toolchain provides an easy-to-use framework for the design, animation and presentation of computer-animated fish stimuli for behavioral experiments with live test fish.