这项工作得到了传染病和微生物学、公共卫生中心的支持。作者没有收到任何其他资助这项研究。作者感谢 Drs 阿诺特, 内森. 巴赫曼和 Ranjeeta 梅农对整个基因组测序实验的专家建议和帮助。

这项研究不需要道德上的认可。
1.光滑念珠菌的亚文化和接种制备
<ol><li>选择要研究的c. 光滑隔离的面板, 其中还应包括至少一个c. 光滑美式类型区域性集合 (ATCC), 并具有已知的敏感度模式。</li>
	<li>亚文化, 通过触摸一个单一的殖民地使用无菌一次性塑料循环和裸奔到一个 Sabouraud 的葡萄糖琼脂 (不育) 板8。</li>
	<li>在35° c 的情况下孵育24-48 ĥ的纯培养基, 生长良好。</li>
</ol>2. 抗真菌药敏性的测定
<ol><li>使用无菌一次性塑料循环, 从一个新鲜的继C. 光滑隔离板上选取大约1毫米直径的4-5 菌落。重在3毫升的无菌蒸馏水中。用温和的移混合均匀的悬挂。</li>
	<li>使用密度5将单元格密度调整为0.5 麦克法兰, 该值相当于 1 x 106到 10 x 68单元格/mL。</li>
	<li>使用商业化验 (见材料表和试剂) 对所有的C. 光滑进行敏感性测试, 按照制造商的说明进行隔离。根据 CLSI 指南和准备报告 (表 1)8, 解释基于合成的抗真菌药物对菌株的敏感性。</li>
</ol>3. 基因组 DNA 提取测序
<ol><li>重在1.5 毫升的试管中, 用50毫米的 EDTA 在300µL 中, 从一个刚生长的自失能板中 loopful 出菌落。</li>
	<li>在悬浮液中加入40µL zymolyase (10 毫克/毫升), 轻轻吸管5次, 直至悬挂均匀。</li>
	<li>孵育样品在37° c 为 1-2 h 消化细胞壁。室温冷却5分钟。</li>
	<li>离心悬浮在 1.4万x g为2分钟, 然后小心地去除上清。</li>
	<li>提取 dna 提取试剂盒的基因组 dna 的指南 (见材料表)。</li>
	<li>重提取的 DNA 颗粒在50µL 10 毫米的三个缓冲 (pH 7.5-8.5), 而不是洗脱缓冲器提供的套件。</li>
	<li>通过测量 260/280 nm25的光学密度 (O. D) 来检查 DNA 的纯度。</li>
</ol>4. 基因组 DNA 定量
<ol><li>根据制造商的荧光检测指南 (见材料表), 在化验试剂盒中准备一个1x 的三 EDTA (TE) 缓冲器。</li>
	<li>通过在一次性96井板中加入2µL 至98µL 的 1x TE 化验缓冲液 (最终容积100µL, 稀释因子 1:50) 稀释 DNA 样本。此稀释步骤可以手动使用多通道吸管或自动液体处理工作站进行。</li>
	<li>通过稀释荧光检测试剂盒 (表 2) 中提供的 lambda DNA (100 µg/毫升) 来准备标准的范围, 并包括用于测量的样品。</li>
	<li>添加100µL 的荧光染料到100µL 稀释的 DNA 样品和标准的反应。在室温下孵育5分钟, 免受光照。</li>
	<li>根据制造商的指导方针测量所有样品的荧光。</li>
	<li>使用荧光读数绘制标准曲线, 并计算 DNA 样本的原始浓度。</li>
	<li>确定 dna 的体积和10毫米的三个缓冲 (pH 值 8) 来调整 dna 浓度到 0.2 ng/µL。</li>
	<li>使用自动液体处理工作站执行 DNA 稀释。这一步也可以通过手动移实现。</li>
</ol>5. DNA 文库的制备
注意: 库的准备和排序是按照制造商提供的协议和指南 (图 1A) 执行的 (请参阅材料表)。
<ol><li>Tagmentation 与 PCR 扩增
	<ol>
<li>标签一个新的96井硬壳薄墙板。</li>
		<li>添加5µL 的定量输入 DNA 在 0.2 ng/µL (总共 1 ng), 以每个样本井的板块。</li>
		<li>添加10µL 的 tagmentation 缓冲和5µL 的放大缓冲, 每一个井含有 DNA 和轻轻吸管混合。用胶板密封密封板。</li>
		<li>将盘置于热循环中, 并运行以下 PCR 程序:55 ° c 为5分钟, 并保持在10° c。当样品到达10° c 时, 立即进行中和。</li>
		<li>加入5µL 中和缓冲器, 以中和增反应, 轻轻吸管混合。密封板, 室温孵育5分钟。</li>
		<li>在样品中加入15µL 的 PCR mastermix。</li>
		<li>使用一箱索引底漆管的设置 96-井板格式, 使每个样本得到一个独特的组合索引模板的基础上 (表 3)。</li>
		<li>使用表3中模板中提供的顺序, 在索引板机架 (图 1B) 中排列索引底漆管, 并记录该模板上指数的位置。</li>
		<li>将 tagmentation 板与添加的 PCR mastermix 放在指数板架上, 并按顺序排列。</li>
		<li>将索引引物1管置于垂直排列, 并在索引架上的水平排列上索引底漆2管。使用多通道吸管, 小心地为每个样品添加5µL 的索引底漆。</li>
		<li>用新的盖子取代旧的索引管帽, 以避免指数之间的交叉污染。</li>
		<li>密封板使用 96-清楚的板封口和执行第二 PCR 如下:95 ° c 为三十年代, 12 个周期95° c 为十年代, 55 ° c 为三十年代, 72 ° c 为三十年代和72° c 为 5 min。</li>
	</ol></li>
	<li>PCR 清除
	<ol>
<li>将 pcr 产物转移到 pcr 清除, 从 tagmentation 板到深井板 (见材料表)。</li>
		<li>涡流的商业磁珠解决方案 (见材料表) 根据制造商的说明, 并添加30µL 的每个 PCR 产品的深井板。</li>
		<li>摇动在 1800 rpm 2 分钟的微振动筛板, 在室温下孵育, 无需晃动5分钟。</li>
		<li>把盘子放在一个磁性的支架上2分钟, 直到清液清除。</li>
		<li>将上清液小心地丢弃在磁性支架上。</li>
		<li>添加200µL 新鲜准备的80% 乙醇与板的磁性立场。</li>
		<li>在三十年代的磁性支架上孵育板, 小心地除去和丢弃上清, 而不干扰珠子。</li>
		<li>重复洗涤步骤, 让珠子风干15分钟. 如果有的话, 去掉多余的乙醇。</li>
		<li>从磁性支架上取下板, 并在珠子上加52.5 µL 的悬浮缓冲器。</li>
		<li>在 1800 rpm 的微振动筛上摇动盘子2分钟, 在室温下孵育2分钟而不摇晃。</li>
		<li>将盘放在磁性支架上, 使上清液清晰。</li>
		<li>使用多通道吸管, 小心地转移50µL 的上清从清理板到一个新的硬壳板。</li>
	</ol></li>
	<li>库规范化
	<ol>
<li>根据制造商的指导方针, 解冻库规范化试剂 (见材料表)。</li>
		<li>从清理盘转移20µL 到新的深井板。</li>
		<li>加45µL 磁珠悬浮液, 用平板封口机封板。</li>
		<li>在 1800 rpm 的微振动筛上摇动盘子30分钟。这种潜伏期是至关重要的, 不应超过。</li>
		<li>将板放在磁性支架上2分钟, 确认清液已清除 (图 1B)。</li>
		<li>在一个适当的危险废物容器中除去并丢弃上清液, 而该板仍在磁架上。</li>
		<li>从磁性支架上取下盘子, 用45µL 洗涤缓冲器清洗珠子。</li>
		<li>在 1800 rpm 为5分钟的微振动筛上用洗涤缓冲器摇动盘子。</li>
		<li>将板放在磁性支架上2分钟, 当它变清晰时丢弃上清。</li>
		<li>从磁性支架上取下板, 再用洗涤缓冲器重复洗涤。</li>
		<li>从磁性支架上取下板, 并加入30µL 0.1 N 氢氧化钠。</li>
		<li>摇动板与 0.1 N 氢氧化钠在一个微振动筛在 1800 rpm 5 分钟, 并把板上的磁性立场为2分钟或直到液体是明确的。</li>
		<li>将30µL 的洗脱缓冲液添加到新的96井硬壳薄墙最终规范化的库板中。</li>
		<li>将30µL 上清液从正常化板转移到最终规范化的库板, 使最终体积60µL。现在, 这些库已准备就绪, 可以进行排序。</li>
	</ol></li>
	<li>qPCR 法测定 DNA 文库浓度
	<ol>
<li>根据制造商的指南, 解冻 qPCR 套件中提供的 mastermix、底漆和标准 (见材料表)。</li>
		<li>结合 PCR 试剂 mastermix 和 qPCR 试剂盒中提供的底漆, 按照制造商的说明和等分可以存储在-20 ° c。</li>
		<li>为了确定 dna 库的浓度, 通过执行1:100 稀释 (1.5 µL 脱氧核糖核酸库到148.5 µL 三缓冲), 然后1:80 稀释 (2 µL 从1:100 到158µL 三缓冲), 使脱氧核糖核酸图书馆的1/8000 稀释使用10毫米三个缓冲 (pH 8)。</li>
		<li>摇动稀释板在 700 rpm 至少1分钟, 然后离心机在 14000 x g为1分钟。</li>
		<li>通过混合4µL 稀释 dna 库或 dna 标准和16µL mastermix, 制备20µL 的最终 PCR 反应。</li>
		<li>执行 PCR 以下制造商的设置在 thermocycler:95 ° c 为 5 min, 35 周期95° c 为三十年代和60° c 为四十五年代, 并且最后65° c 到95° c 为融解曲线分析。</li>
		<li>从 qPCR thermocycler 中获取样本 DNA 库和标准的 Ct 值。</li>
		<li>从标准的 Ct 值生成标准曲线 (图 2)。定义上和下 QC 范围由±3周期的平均值。例如, 如果平均 Ct 值是13周期, 那么 QC 范围是在16和10周期之间。</li>
		<li>根据标准曲线和 Ct 值确定个体和平均库浓度 (ALC)。</li>
		<li>确定要使用的总计库 (PAL) 的体积, 根据下面给出的计算结果, 考虑到目标库的浓度介于 1.4-1.8 pM 之间。 注意:从 qPCR = ALC 获得的平均图书馆浓度;汇总库 (PAL) = ALC/2;变性 pal (达尔) = pal * 0.666 根据与缓冲混合的达尔的体积, 是将库的浓度添加到流单元中。例如, 如果将库的65µL 添加到835µL 的缓冲区中, 则从该稀释 (Dil 1) 195 添加到1300年的总容量µL: (65/900) * dnPAL = Dil1 Dil1 * (195/1300) = 最终浓度 (应介于 1.4-1.8 pM 之间)</li>
	</ol></li>
</ol>6. 台式排序器中的库池和初始排序
<ol><li>根据制造商的指导方针, 解冻试剂盒。从4° c 的存储中取出一个新的流动单元, 并在测序前至少30分钟将室温带入房间温度。使用前取出缓冲盒和 prechill 测序缓冲器 (见资料表)。</li>
	<li>通过混合5µL 库 (1 nM) 和5µL 0.2 N 氢氧化钠, 准备一个控制库。在室温下进行5分钟的涡旋和孵育, 将控制库变性成单股。</li>
	<li>添加5µL 200 毫米的三盐酸, pH 7 和涡流。添加235µL prechilled 测序缓冲器并轻轻混合。总容量是250µL 与控制图书馆最后的集中在晚上20点。</li>
	<li>通过将每个样本库的5µL 传输到一个单一的 low-bind 1.5 mL 管中, 将每一个采样文库的序列从最终规范化的库板中进行排序。</li>
	<li>添加30µL 的共用库和30µL 的 0.2 N 氢氧化钠, 变性图书馆在另一个低绑定管。</li>
	<li>涡 low-bind 管和孵化5分钟的室温变性图书馆成单股。</li>
	<li>添加30µL 200 毫米的三盐酸, pH 7 到管与变性库中和反应。</li>
	<li>添加65µL 的中和变性图书馆悬浮和835µL 的 pre-chilled 测序缓冲和旋涡混合好。</li>
	<li>在最后的低束缚管结合以下: 195 µL 从中立的变性图书馆, 1.30 µL 的控制库和1103.70 µL 的测序缓冲器。正确混合。</li>
	<li>将最终的库组合 (1300 µL) 加载到试剂盒上的指定位置。</li>
	<li>设置排序运行通过输入项目和样本详细信息在排序器指定的网站遵循的准则。</li>
	<li>按照指导方针开始测序。台式排序器中的负载流单元、带库的试剂盒和缓冲盒。</li>
	<li>记录顺序中使用的所有试剂盒和墨盒的批号。</li>
</ol>7. 从测序网站下载数据
<ol><li>按照制造商在网站上提供的说明下载 FASTQ 文件。</li>
	<li>为一个良好的质量运行检查百分比 Q30 是≥75% 和集群密度是介于 170-280 k/mm2与最佳在 200-210 k/毫米2 (表 4)。</li>
</ol>8. 测序数据分析
<ol><li>将已测序样本的 FASTQ 文件导入数据分析集成软件包 (见资料表)。</li>
	<li>通过使用表5中列出的设置, 在软件中添加功能, 即修剪、映射到参考 (选择参考基因组)、局部重新排列和变体分析 (图 3a), 创建一个排序工作流。</li>
	<li>通过选择单个示例或一批示例 FASTQ 文件并将输出文件保存在指定的示例文件夹中来运行工作流。</li>
	<li>生成序列覆盖率深度、映射区域和基因组中结构变量列表的报告 (图 3B)。</li>
	<li>使用结构变量列表搜索同义单核苷酸多态性 (snp) 的基因赋予抗药性和毒力。</li>
	<li>通过列出 SNP 位置、基因和耐药或易感菌株的数量来准备报告 (表 6)。</li>
</ol>

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作者没有相互竞争的金融利益, 也没有利益冲突的披露。

本研究确定了在光滑中 WGS 引导检测耐药性的可行性、近似时间线和精密度。图书馆准备和测序的周转时间为四天, 报告分析结果1/2 天。这与培养皿和桑格测序中的药敏测定方法相比, 至少有相当数量的样品。大约 30-90 C. 光滑基因组可以根据测序流细胞容量进行测序, 80-100% 测序覆盖率。由于测序是在 in-house WGS 实验室设置, 因此本研究的成本/资源需求相当于桑格测序和探测器分析的当前成本, 估计每样成本为 AUD 80-100。所有分离株的易感性是由一个商业化验试剂盒确定的, 用阅读镜目视阅读。从蓝色到粉红色的比色生长指标的变化表明, 文化的生长。在一系列粉红色 (生长) 井之后, MIC 被读为第一个蓝色井, 即抗真菌剂的最低浓度, 它能极大地抑制生长。对于 WGS, 基因组 DNA 库是用图书馆准备工具包准备的。隔离图书馆的数量由 qPCR。定量的图书馆汇集在一起为最后测序奔跑执行在台式排序器。
在我们的分析中, 存在的 snp 基因中的抗性在菌株中的相关性很好与高架的体外MIC 对药物。FKS1 中的突变S629P和FKS2中的 S663P 明显与对棘的抵抗有关。两个突变是已知的授予表型电阻29,30。同时基因组全序列测序也揭示了与 5-嘧啶 (基因FCY2) 和唑电阻 (CgPDR1, CgCDR1和CgFLR1) 相关的基因突变, 它们通过激活与抵抗相关联。过度表达为射流泵26,27,28。然而, 与唑和 5-嘧啶抗性相关的基因突变的影响31需要通过额外的功能分析来证实, 以评估基因表达水平。有趣的是, 在所有隔离32,33的单元格壁 adhesins 中也发现了大量的 snp。黏附基因的变异EPA6,编码生物膜形成, 相对地频繁地发生了33。此外, 孤立 CMRL-3, CMRL-4 和 CMRL-8 缺乏突变唑抗性基因没有记录的 snp 在EPA1和EPA624,34。然而, 总的来说, 在 adhesins 和药物的多态性的 snp 之间没有特定的联系, 因为包括的测试菌株数量很少。
WGS 在临床真菌的实施, 要求实施稳健的质量管理体系。高质量的基因组 DNA 和质量控制检查点, 伴随着实验中的每一步, 对于一个好的 WGS 结果是必不可少的。C. 光滑样本 DNA 的纯度可通过紫外线吸收法 (260/280 nm 和 260/230 nm25的吸光度) 进行验证。在我们的经验中, 对于C. 光滑DNA, 260/280 预计将在建议的范围内 1.8-2 和260/230 之间 2-2. 2。如果 DNA 提取物不符合这些质量要求, 可以进行乙醇沉淀的额外纯化。Tagmentation 是一个必要的步骤, 添加独特的条形码序列称为指数引物, 以便能够区分多个样本在排序 (复用)。因此, 在索引过程中, 必须格外小心, 以避免索引管和样品之间的交叉污染, 以保持指数的唯一性。序列化的规范化确保了在样本 DNA 库中出现的任何可能在测序数据中引入偏差的差异被消除。使用基于微珠的清理的正常化步骤通常允许删除多余的 DNA 库碎片, 以及在库准备过程中可能出现的库大小的变化。因此, 30 分钟的孵化是关键的最佳簇密度。在测序过程中, 由大量放大产生的样本库的克隆簇密度, 影响数据质量, 如 Q30 分数和总数据输出。虽然 underclustering 可能会提供较高的数据质量, 但也会导致较低的数据输出, 而 overclustering 低的 Q30 分数。在 PCR 清理和规范化过程中, DNA 库应无磁珠残留, 从而影响测序数据质量。QPCR 应该至少在几个具有代表性的样本库上进行, 包括一个参考应变作为正控制 (在这种情况下,光滑的 ATCC 应变) 从一组特定的索引。平均 Ct 值应介于 15-18 周期之间。此范围内的任何样本都被认为是可以接受的排序运行。然而, 如果 Ct 值在这个范围之外, qPCR 应该被重复。由于低质量输入 DNA 或在库准备过程中出现错误, qPCR 有时会失败。根据正向控制的计算结果, 建立了能产生良好序列数据的库的最小集中度。利用从 qPCR 获得的库的平均浓度, 可以计算要添加的最终库的数量。这应该产生建议的最后图书馆集中在 1.4-1.8 pM 之间。对于c. 光滑库, 使用c. 光滑ATCC 隔离的已建立的 Ct 范围介于16-18 周期, 平均库集中范围为 300-500 pM。在 200-250 K/mm2之间的簇密度范围内, 共用变性 DNA 库的相应体积范围为60-65 µL。
在进一步分析之前, 应 demultiplexed 序列数据文件。这可以通过排序到他们的各自的图书馆使用他们的条形码在排序之后发生了。在进行数据分析之前, 可以对 FASTQ 文件进行质量修整的可选步骤。使用在标准软件包中创建的自定义工作流分析 WGS 中的分离器的序列读取。这允许修剪低质量的读取, 然后映射到参考念珠菌基因组。参考基因组, CBS138, 从念珠菌基因组数据库 (CGD) 下载, 并链接到分析之前的工作流程。在念珠菌基因组中存在 dna 重复 (例如, 黏附基因有 dna 重复) 可能会使 short-read 序列和 SNP 调用的排列复杂化。这可以通过对映射序列进行额外的局部重新调整来改进。工作流的输出是一个结构变体列表, 它提供带有同义和同义 SNP 位置和覆盖率的带注释的基因。这是用来确定 snp 基因的兴趣和准备最后的分析报告的孤立 (表 6)。
我们的研究和方法的一些局限性应该得到承认。我们的报告是基于少数的隔离和没有标准的真菌 resistome 数据库的临床真菌。虽然桑格 DNA 测序目前更易于临床实验室, 但它的能力有限, 同时检测多基因突变, 赋予耐药性的念珠菌许可证. (> 20 FKS突变仅棘抵抗)。随着病理学服务的整合和降低测序成本, 在桑格测序中使用 WGS 的实用性可能会增加。然而, 一个重要的考虑是最初的实验室设置和成本的 WGS 仪器的实施以及 end-user 培训的实验室人员。长期成本主要包括采购测序试剂盒和附件。如果 WGS 仪器不 in-house, 则应期待额外费用和更高的价格。此外, DNA 重复序列在基因组中的存在可能使 short-read 序列和 SNP 调用的排列复杂化。使用 long-read 技术测序的高质量参考基因组的可用性将有助于保持 SNP 鉴定的质量。
在未来, WGS 有望通过快速跟踪报告时间来提高临床治疗的效果, 该诊断设置可轻松访问并由临床医生20,22进行解释。这可以实现与开发的策划和最新的 WGS 抗真菌药物抗药性数据库的新的和验证性突变推断抗真菌耐药性。随着已知表型药物敏感性的临床相关酵母的更多基因组可供分析, 有可能发现新的抗真菌药物耐药性的标记和机制。这些进展将大大减少因多重耐药性和药物毒性而导致的治疗失败的风险。最后, 下一代排序与适当的质量管理协议, 使基因组范围内的突变, 赋予抗性在念珠菌光滑, 可以增加表型测试在真菌实验室。临床相关的念珠菌的快速基因组测序所提供的洞察力可以从根本上改变我们对不同种类抗真菌药物耐药性机制的认识, 改善对侵袭性患者的管理真菌疾病。

念珠菌光滑是一种日益受到重视的病原体, 其重要性作为一个物种, 它对唑以及最近的棘1、2、3进行了抵抗。不同于二倍体的c. 白念珠菌,光滑的单倍体基因组可能允许它获得突变和更容易地发展多重耐药性。两个药物类的共同抵抗也被报告了4。因此, 早期评估的抗真菌药敏性和检测耐药性在C. 光滑是至关重要的正确的, 有针对性的治疗, 以及在抗真菌的情况下, 以限制驱动器的抗菌素耐药性1,5,6. 建立一个有效的工作流程, 快速检测耐药菌株中的抗性生物标志物的验证性突变, 也有助于改善处方决定和临床结局。
抗真菌药易感性通常通过测量最小的抑制浓度 (MIC) 来评估, 这被定义为最低的药物浓度, 从而导致微生物的生长与无药物的生长相比显著降低。控制.临床和实验室标准研究所 (CLSI) 和欧洲抗菌药易感性检测委员会 (EUCAST) 有标准化的易感性测试方法, 以使 MIC 测定更准确和一致的7, 8。然而, 抗真菌 MIC 的效用仍然有限, 特别是对棘, 特别是在实验室比较, 在不同的方法和条件使用9。也有不确定的相关的中等收入与反应的棘治疗和无法区分重量 (或易感) 菌株与那些窝藏 FKS 突变 (棘耐药菌株)10,11。尽管有验证性基因 PCRs 和桑格测序的抗真菌抵抗标志, 结果的实现往往延迟, 由于缺乏同时检测多电阻标记5,12。因此, 在整个基因组 sequencing-based 分析的支持下, 同时检测基因组不同位置的抗性突变, 比目前的方法具有明显的优势。
整个基因组测序 (WGS) 已成功地实施, 以跟踪疾病传播在爆发期间, 以及在细菌和病毒的基因组范围内的风险评估和耐药性测试的方法13。核酸测序技术的最新进展使病原体的全基因组测序 (WGS) 在技术上和经济上都是可行的。DNA 测序提供了重要的优势比其他方法的病原体鉴定和定性在微生物学实验室使用14,15,16。首先, 它提供了一个具有高吞吐量、速度和质量的通用解决方案。测序可以应用于任何微生物, 并允许在地方或区域实验室的规模经济。其次, 它以 "经得起未来考验" 的方式生产数据, 可以在国家和国际两级进行比较。最后, WGS 在医学中的潜在效用已经通过包含参考基因组的公共数据库的快速增长而得到了增强, 这可以与包含其他临床和流行病学元数据的等效数据库相链接17 ,18。
最近的研究表明, WGS 用于鉴定临床分离的念珠菌的抗真菌性标志物的效用。10,19,20. 这主要是由于高通量台式器的可用性, 建立了生物信息学管道, 降低了测序的成本21,22。真菌 WGS 对桑格测序的优势在于, WGS 允许在一次运行中对多个基因组进行测序。此外, WGS 的念珠菌基因组可以识别药物靶点的新突变, 跟踪遗传进化, 以及临床相关序列类型的出现20,22,23。最重要的是, 在固有的多药耐药性的情况下, WGS 可以帮助及早发现治疗选择前的抗性突变22,24。
在这里, 我们研究了 WGS 的可行性筛选的突变相关的耐药性不同类别的抗真菌药物。我们提出了从 end-user 和诊断真菌实验室角度实施 WGS 的方法。我们在这项分析中包括三分离对培养从三独立的临床病例, 其中体外抗棘和 5-嘧啶在经过一段时间的抗真菌治疗后发展。

<table border="0" cellpadding="0" cellspacing="0" style="width:991px;" width="989">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">DensiCHECK Plus</td>
			<td style="width:183px;">BioM&#233;rieux Inc</td>
			<td style="width:151px;">K083536</td>
			<td style="width:383px;">Densitometer used for McFarland readings</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:275px;">Sensititre YeastOne</td>
			<td style="width:183px;">TREK Diagnostic Systems, Thermo Scientific</td>
			<td style="width:151px;">YO10</td>
			<td style="width:383px;">Commercial susceptibility assay plate with standard antifungal drugs.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:275px;">Fisherbrand Disposable Inoculating Loops and Needles</td>
			<td style="width:183px;">Fisher Scientific, Thermo Fisher Scientific</td>
			<td style="width:151px;">22-363-605</td>
			<td style="width:383px;">Disposable plastic loops can be used directly from package. No flaming required.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:275px;">Eppendorf Safe-Lock microcentrifuge tubes</td>
			<td style="width:183px;">Sigma Aldrich, Merck</td>
			<td style="width:151px;">T2795&#160;&#160;&#160;</td>
			<td style="width:383px;">Volume 2.0 mL, natural 
			&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:275px;">ZYMOLYASE 20T from Arthrobacter luteus</td>
			<td style="width:183px;">MP Biomedicals, LLC</td>
			<td style="width:151px;">8320921</td>
			<td style="width:383px;">Used for cell wall lysis of fungal isolate before 
			DNA extraction</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">Wizard Genomic DNA Purification Kit&#160;</td>
			<td style="width:183px;">Promega&#160;</td>
			<td style="width:151px;">A1120</td>
			<td>Does 100 DNA extractions</td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:275px;">Quant-iT PicoGreen dsDNA Assay Kit</td>
			<td style="width:183px;">Thermo Fisher Scientific</td>
			<td style="width:151px;">P7589</td>
			<td style="width:383px;">&#160;Picogreen reagent referred to as fluorescent dye in the protocol. 
			Includes Lambda DNA standard and picogreen reagent for assay.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">Nextera XT DNA Sample Preparation Kit</td>
			<td style="width:183px;">Illumina</td>
			<td style="width:151px;">FC-131-1096</td>
			<td style="width:383px;">Includes Box 1 and Box 2&#160; reagents for 96 samples</td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:275px;">Nextera XT Index Kit v2</td>
			<td style="width:183px;">Illumina</td>
			<td style="width:151px;">FC-131-2001, 
			FC-131-2002, 
			FC-131-2003, 
			FC-131-2004</td>
			<td style="width:383px;">Index set A 
			Index set B 
			Index set C 
			Index set D</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">NextSeq 500/550 High Output Kit v2&#160;</td>
			<td style="width:183px;">Illumina</td>
			<td style="width:151px;">FC-404-2004</td>
			<td>300 cycles, More than 250 samples per kit</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">NextSeq 500 Mid Output v2 Kit</td>
			<td style="width:183px;">Illumina</td>
			<td style="width:151px;">FC-404-2003</td>
			<td>300 cycles, More than 130 samples per kit</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">PhiX Control Kit</td>
			<td style="width:183px;">Illumina</td>
			<td style="width:151px;">FC-110-3001</td>
			<td style="width:383px;">To arrange indices from Index kit in order</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">TruSeq Index Plate Fixture Kit</td>
			<td style="width:183px;"></td>
			<td style="width:151px;">FC-130-1005</td>
			<td>&#160;2 Fixtures</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:275px;">KAPA Library Quantification Kit 
			for Next-Generation Sequencing</td>
			<td style="width:183px;">KAPA Biosystems</td>
			<td style="width:151px;">KK4824</td>
			<td>Includes premade standards, primers and MasterMix</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:275px;">Janus NGS Express Liquid handling system&#160;</td>
			<td style="width:183px;">PerkinElmer</td>
			<td style="width:151px;">YJS4NGS</td>
			<td>Used for DNA dilutions during sequencing</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">&#160;0.8 mL Storage Plate</td>
			<td style="width:183px;">Thermo Scientific</td>
			<td style="width:151px;">AB0765B</td>
			<td style="width:383px;">MIDI Plate for DNA Library cleanup and 
			normalisation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Agencourt AMPure XP</td>
			<td style="width:183px;">Beckman Coulter</td>
			<td style="width:151px;">A63881</td>
			<td>&#160;Magnetic beads in solution for library purification</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">Magnetic Stand-96</td>
			<td style="width:183px;">Thermo Fisher Scientific</td>
			<td style="width:151px;">AM10027</td>
			<td>Used for magnetic bead based DNA purification</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">OrbiShaker MP&#160;</td>
			<td style="width:183px;">Benchmark Scientific</td>
			<td style="width:151px;">BT1502</td>
			<td>96-well plate shaker with 4 platforms</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">Hard Shell PCR Plate</td>
			<td style="width:183px;">BioRad</td>
			<td style="width:151px;">HSP9601</td>
			<td>Thin Wall, 96 Well</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">LightCycler 480 Instrument II&#160;</td>
			<td style="width:183px;">Roche&#160;</td>
			<td style="width:151px;">5015278001</td>
			<td>Accomodates 96 well plate</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:275px;">Microseal &#39;B&#39; PCR Plate Sealing Film, adhesive, optical&#160;</td>
			<td style="width:183px;">BioRad</td>
			<td style="width:151px;">&#160;MSB1001</td>
			<td>Clear 96-well plate sealers</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">CLC Genomics Workbench</td>
			<td style="width:183px;">Qiagen</td>
			<td style="width:151px;">CLCBio</td>
			<td>Software for data analysis, Version 8</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:275px;">NextSeq500 instrument</td>
			<td style="width:183px;">Illumina&#160;</td>
			<td style="width:151px;">Illumina&#160;</td>
			<td>Benchtop Sequencer used for next generation sequencing</td>
		</tr>
	</tbody>
</table>

whole genome sequencing of candida glabrata for detection of markers of antifungal drug resistance

光滑念珠菌可以快速获得导致耐药性的突变, 特别是对唑和棘。基因突变的识别是必不可少的, 因为检测到的电阻体外往往与临床失败相关。我们研究了使用全基因组测序 (WGS) 进行基因组分析抗真菌药物耐药性的可行性, 在C. 光滑中。目的是 torecognize 执行 WGS 的推动因素和障碍, 并衡量其有效性。本文概述了关键的质量控制检查点和 WGS 方法的基本组成部分, 以研究与降低抗真菌药易感性相关的遗传标记。它还估计了数据分析的准确性和测试的转过来时间。
通过抗真菌药敏试验测定了12例临床和一 ATCC光滑的表型敏感性。其中包括三个隔离对, 来自三患者, 在药物最小抑制浓度上升。在两对, 每对的第二个隔离开发了抵抗对棘。第三对的第二个分离开发了抵抗对 5-嘧啶。其余组成的易感性和唑耐药菌株。在抗棘、唑和 5-嘧啶抗性的基因中, 单核苷酸多态 (snp) 通过 WGS 的下一代测序, 在耐药菌株中得到证实。识别抗 真菌抗性基因的非同义 snp, 如FKS1、 FKS2、 CgPDR1、CgCDR1和FCY2 。总的来说, 平均98% 的 WGS 读取的C. 光滑孤立映射到参考基因组, 大约有75倍的读深度覆盖率。周转时间和费用与桑格测序相媲美。
总之, 在不需要多重 PCR/DNA 测序反应的情况下, WGS 的C. 光滑是可行的, 可以揭示抗性不同抗真菌药物类的临床重要基因突变。这是一个积极的步骤, 建立 WGS 能力的临床实验室, 同时检测抗真菌耐药性授予替代品。

Watch this Scientific Journal Video about Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance at JoVE.com

Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance

这项研究实施了全基因组测序分析的基因突变, 赋予抗真菌药物耐药性的念珠菌光滑。对棘、唑和 5-嘧啶的耐光滑的菌株进行了测序, 以说明方法。分离株的敏感性分布与基因特异性突变模式的存在或缺失相关。

念珠菌光滑全基因组测序检测抗真菌耐药性标志物

Candida glabrata can rapidly acquire mutations that result in drug resistance, especially to azoles and echinocandins. Identification of genetic mutations ...

whole-genome-sequencing-candida-glabrata-for-detection-markers

Nanyang Technological University

Research

JoVE Journal

Medicine

Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance

13.6K 次观看.  Westmead Hospital. 这项研究实施了全基因组测序分析的基因突变, 赋予抗真菌药物耐药性的念珠菌光滑。对棘、唑和 5-嘧啶的耐光滑的菌株进行了测序, 以说明方法。分离株的敏感性分布与基因特异性突变模式的存在或缺失相关。

视频: Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance

Intraoperative Detection of Subtle Endometriosis: A Novel Paradigm for Detection and Treatment of Pelvic Pain Associated with the Loss of Peritoneal Integrity

Endometriosis is a common disease affecting 40 to 70% of reproductive-aged women with chronic pelvic pain (CPP) and/or infertility. The purpose of this study was to demonstrate the use of a blue dye (methylene blue) to stain peritoneal surfaces during laparoscopy (L/S) to detect the loss of peritoneal integrity in patients with pelvic pain and suspected endometriosis. Forty women with CPP and 5 women without pain were evaluated in this pilot study. During L/S, concentrated dye was sprayed onto peritoneal surfaces, then aspirated and rinsed with Lactated Ringers solution. Areas of localized dye uptake were evaluated for the presence of visible endometriotic lesions. Areas of intense peritoneal staining were resected and some fixed in 2.5% buffered gluteraldehyde and examined by scanning (SEM) electron microscopy. Blue dye uptake was more common in women with endometriosis and chronic pelvic pain than controls (85% vs. 40%). Resection of the blue stained areas revealed endometriosis by SEM and loss of peritoneal cell-cell contact compared to normal, non-staining peritoneum. Affected peritoneum was associated with visible endometriotic implants in most but not all patients. Subjective pain relief was reported in 80% of subjects. Based on scanning electron microscopy, we conclude that endometrial cells extend well beyond visible implants of endometriosis and appear to disrupt the underlying mesothelium. Subtle lesions of endometriosis could therefore cause pelvic pain by disruption of peritoneal integrity, allowing menstrual or ovulatory blood and associated pain factors access to underlying sensory nerves. Complete resection of affected peritoneum may provide a better long-term treatment for endometriosis and CPP. This simple technique appears to improve detection of subtle or near invisible endometriosis in women with CPP and minimal visual findings at L/S and may serve to elevate diagnostic accuracy for endometriosis at laparoscopy.

Loss of peritoneal integrity provides a new paradigm to understand and treat chronic pelvic pain in women with mild forms of endometriosis and can be easily detected using intraoperative instillation of dye at the time of laparoscopy.

术中的微妙的子宫内膜异位症的检测:A新型范式为相关联的与的的腹膜的完整性之亏损盆腔疼痛的的的的检测和治疗的

Endometriosis is a  common disease affecting 40 to 70% of reproductive-aged women with chronic  pelvic pain (CPP) and/or infertility. The purpose of this ...

科研

医学

Cerenkov Luminescence Imaging (CLI) for Cancer Therapy Monitoring

In molecular imaging, positron emission tomography (PET) and optical imaging (OI) are two of the most important and thus most widely used modalities1-3. PET is characterized by its excellent sensitivity and quantification ability while OI is notable for non-radiation, relative low cost, short scanning time, high throughput, and wide availability to basic researchers. However, both modalities have their shortcomings as well. PET suffers from poor spatial resolution and high cost, while OI is mostly limited to preclinical applications because of its limited tissue penetration along with prominent scattering optical signals through the thickness of living tissues.
 Recently a bridge between PET and OI has emerged with the discovery of Cerenkov Luminescence Imaging (CLI)4-6. CLI is a new imaging modality that harnesses Cerenkov Radiation (CR) to image radionuclides with OI instruments. Russian Nobel laureate Alekseyevich Cerenkov and his colleagues originally discovered CR in 1934. It is a form of electromagnetic radiation emitted when a charged particle travels at a superluminal speed in a dielectric medium7,8. The charged particle, whether positron or electron, perturbs the electromagnetic field of the medium by displacing the electrons in its atoms. After passing of the disruption photons are emitted as the displaced electrons return to the ground state. For instance, one 18F decay was estimated to produce an average of 3 photons in water5. 
 Since its emergence, CLI has been investigated for its use in a variety of preclinical applications including in vivo tumor imaging, reporter gene imaging, radiotracer development, multimodality imaging, among others4,5,9,10,11. The most important reason why CLI has enjoyed much success so far is that this new technology takes advantage of the low cost and wide availability of OI to image radionuclides, which used to be imaged only by more expensive and less available nuclear imaging modalities such as PET.
 Here, we present the method of using CLI to monitor cancer drug therapy. Our group has recently investigated this new application and validated its feasibility by a proof-of-concept study12. We demonstrated that CLI and PET exhibited excellent correlations across different tumor xenografts and imaging probes. This is consistent with the overarching principle of CR that CLI essentially visualizes the same radionuclides as PET. We selected Bevacizumab (Avastin; Genentech/Roche) as our therapeutic agent because it is a well-known angiogenesis inhibitor13,14. Maturation of this technology in the near future can be envisioned to have a significant impact on preclinical drug development, screening, as well as therapy monitoring of patients receiving treatments.

Cerenkov Luminescence Imaging CLI for Cancer Therapy Monitoring

Use of Cerenkov Luminescence Imaging (CLI) for monitoring preclinical cancer treatment is described here. This method takes advantage of Cerenkov Radiation (CR) and optical imaging (OI) to visualize radiolabeled probes and thus provides an alternative to PET in preclinical therapeutic monitoring and drug screening.

癌症治疗监测的切伦科夫发光成像（CLI）

In  molecular imaging, positron emission tomography (PET) and optical imaging (OI)  are two of the most important and thus most widely used modalities1-3. ...

Identification of Sleeping Beauty Transposon Insertions in Solid Tumors using Linker-mediated PCR

Genomic, proteomic, transcriptomic, and epigenomic analyses of human tumors indicate that there are thousands of anomalies within each cancer genome compared to matched normal tissue. Based on these analyses it is evident that there are many undiscovered genetic drivers of cancer1. Unfortunately these drivers are hidden within a much larger number of passenger anomalies in the genome that do not directly contribute to tumor formation. Another aspect of the cancer genome is that there is considerable genetic heterogeneity within similar tumor types. Each tumor can harbor different mutations that provide a selective advantage for tumor formation2. Performing an unbiased forward genetic screen in mice provides the tools to generate tumors and analyze their genetic composition, while reducing the background of passenger mutations. The Sleeping Beauty (SB) transposon system is one such method3. The SB system utilizes mobile vectors (transposons) that can be inserted throughout the genome by the transposase enzyme. Mutations are limited to a specific cell type through the use of a conditional transposase allele that is activated by Cre Recombinase. Many mouse lines exist that express Cre Recombinase in specific tissues. By crossing one of these lines to the conditional transposase allele (e.g. Lox-stop-Lox-SB11), the SB system is activated only in cells that express Cre Recombinase. The Cre Recombinase will excise a stop cassette that blocks expression of the transposase allele, thereby activating transposon mutagenesis within the designated cell type. An SB screen is initiated by breeding three strains of transgenic mice so that the experimental mice carry a conditional transposase allele, a concatamer of transposons, and a tissue-specific Cre Recombinase allele. These mice are allowed to age until tumors form and they become moribund. The mice are then necropsied and genomic DNA is isolated from the tumors. Next, the genomic DNA is subjected to linker-mediated-PCR (LM-PCR) that results in amplification of genomic loci containing an SB transposon. LM-PCR performed on a single tumor will result in hundreds of distinct amplicons representing the hundreds of genomic loci containing transposon insertions in a single tumor4. The transposon insertions in all tumors are analyzed and common insertion sites (CISs) are identified using an appropriate statistical method5. Genes within the CIS are highly likely to be oncogenes or tumor suppressor genes, and are considered candidate cancer genes. The advantages of using the SB system to identify candidate cancer genes are: 1) the transposon can easily be located in the genome because its sequence is known, 2) transposition can be directed to almost any cell type and 3) the transposon is capable of introducing both gain- and loss-of-function mutations6. The following protocol describes how to devise and execute a forward genetic screen using the SB transposon system to identify candidate cancer genes (Figure 1).

Identification of Sleeping Beauty Transposon Insertions in Solid Tumors using Linker-mediated PCR

A method of identifying unknown drivers of carcinogenesis using an unbiased approach is described. The method uses the Sleeping Beauty transposon as a random mutagen directed to specific tissues. Genomic mapping of transposon insertions that drive tumor formation identifies novel oncogenes and tumor suppressor genes

鉴定<em&gt;睡美人</em&gt;转座子插入连接器介导的PCR实体瘤

Genomic, proteomic, transcriptomic, and epigenomic analyses of human tumors indicate that there are thousands of anomalies within each cancer genome ...

An Orthotopic Murine Model of Human Prostate Cancer Metastasis

Our laboratory has developed a novel orthotopic implantation model of human prostate cancer (PCa). As PCa death is not due to the primary tumor, but rather the formation of distinct metastasis, the ability to effectively model this progression pre-clinically is of high value. In this model, cells are directly implanted into the ventral lobe of the prostate in Balb/c athymic mice, and allowed to progress for 4-6 weeks. At experiment termination, several distinct endpoints can be measured, such as size and molecular characterization of the primary tumor, the presence and quantification of circulating tumor cells in the blood and bone marrow, and formation of metastasis to the lung. In addition to a variety of endpoints, this model provides a picture of a cells ability to invade and escape the primary organ, enter and survive in the circulatory system, and implant and grow in a secondary site. This model has been used effectively to measure metastatic response to both changes in protein expression as well as to response to small molecule therapeutics, in a short turnaround time.

This orthotopic model of human prostate cancer allows for quantification of tumor size, circulating tumor cells, and formation of distinct metastasis to the lung. As cells must escape the primary organ, enter the blood stream, and implant into a secondary site, this model effectively recapitulates the scenario in humans.

人类前列腺癌转移的原位小鼠模型

Our laboratory has developed a novel orthotopic implantation model of  human prostate cancer (PCa). As PCa death is not due to the primary tumor, but  ...

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings

HIV-1 drug resistance has the potential to seriously compromise the effectiveness and impact of antiretroviral therapy (ART). As ART programs in sub-Saharan Africa continue to expand, individuals on ART should be closely monitored for the emergence of drug resistance. Surveillance of transmitted drug resistance to track transmission of viral strains already resistant to ART is also critical. Unfortunately, drug resistance testing is still not readily accessible in resource limited settings, because genotyping is expensive and requires sophisticated laboratory and data management infrastructure. An open access genotypic drug resistance monitoring method to manage individuals and assess transmitted drug resistance is described. The method uses free open source software for the interpretation of drug resistance patterns and the generation of individual patient reports. The genotyping protocol has an amplification rate of greater than 95% for plasma samples with a viral load &#62;1,000 HIV-1 RNA copies/ml. The sensitivity decreases significantly for viral loads &#60;1,000 HIV-1 RNA copies/ml. The method described here was validated against a method of HIV-1 drug resistance testing approved by the United States Food and Drug Administration (FDA), the Viroseq genotyping method. Limitations of the method described here include the fact that it is not automated and that it also failed to amplify the circulating recombinant form CRF02_AG from a validation panel of samples, although it amplified subtypes A and B from the same panel.

Drug resistance testing for HIV-1 infected individuals failing antiretroviral therapy (ART) can guide future therapies and improve treatment outcomes. Optimizing individual and population health outcomes in high HIV prevalence but resource-limited settings will ultimately require affordable and accessible drug resistance genotyping and interpretation methods.

对于资源有限设置一个负担得起的HIV-1耐药性监测方法

HIV-1 drug resistance has the potential to seriously compromise the effectiveness and impact of antiretroviral therapy (ART). As ART programs in ...

Collection and Extraction of Saliva DNA for Next Generation Sequencing

The preferred source of DNA in human genetics research is blood, or cell lines derived from blood, as these sources yield large quantities of high quality DNA. However, DNA extraction from saliva can yield high quality DNA with little to no degradation/fragmentation that is suitable for a variety of DNA assays without the expense of a phlebotomist and can even be acquired through the mail. However, at present, no saliva DNA collection/extraction protocols for next generation sequencing have been presented in the literature. This protocol optimizes parameters of saliva collection/storage and DNA extraction to be of sufficient quality and quantity for DNA assays with the highest standards, including microarray genotyping and next generation sequencing.

DNA extraction from saliva can provide a readily available source of high molecular weight DNA, with little to no degradation/fragmentation. This protocol provides optimized parameters for saliva collection/storage and DNA extraction to be of sufficient quality and quantity for downstream DNA assays with high quality requirements.

收集和唾液DNA提取用于新一代测序

The preferred source of DNA in human genetics research is blood, or cell lines derived from blood, as these sources yield large quantities of high quality ...

Early Detection of Drug-Induced Renal Hemodynamic Dysfunction Using Sonographic Technology in Rats

The kidney normally functions to maintain hemodynamic homeostasis and is a major site of damage caused by drug toxicity. Drug-induced nephrotoxicity is estimated to contribute to 19- 25% of all clinical cases of acute kidney injury (AKI) in critically ill patients. AKI detection has historically relied on metrics such as serum creatinine (sCr) or blood urea nitrogen (BUN) which are demonstrably inadequate in full assessment of nephrotoxicity in the early phase of renal dysfunction. Currently, there is no robust diagnostic method to accurately detect hemodynamic alteration in the early phase of AKI while such alterations might actually precede the rise in serum biomarker levels. Such early detection can help clinicians make an accurate diagnosis and help in in decision making for therapeutic strategy. Rats were treated with Cisplatin to induce AKI. Nephrotoxicity was assessed for six days using high-frequency sonography, sCr measurement and upon histopathology of kidney. Hemodynamic evaluation using 2D and Color-Doppler images were used to serially study nephrotoxicity in rats, using the sonography. Our data showed successful drug-induced kidney injury in adult rats by histological examination. Color-Doppler based sonographic assessment of AKI indicated that resistive-index (RI) and pulsatile-index (PI) were increased in the treatment group; and peak-systolic velocity (mm/s), end-diastolic velocity (mm/s) and velocity-time integral (VTI, mm) were decreased in renal arteries in the same group. Importantly, these hemodynamic changes evaluated by sonography preceded the rise of sCr levels. Sonography-based indices such as RI or PI can thus be useful predictive markers of declining renal function in rodents. From our sonography-based observations in the kidneys of rats that underwent AKI, we showed that these noninvasive hemodynamic measurements may consider as an accurate, sensitive and robust method in detecting early stage kidney dysfunction. This study also underscores the importance of ethical issues associated with animal use in research.

Early stage hemodynamic dysfunction is critical to the development of kidney disease. Yet, detection methodologies are limited. Recent advances in sonography provide a noninvasive, accurate option for early detection of kidney injury. This study outlines a step-by-step, sonographic methodology for detecting kidney dysfunction using a drug-induced nephrotoxicity rat model.

大鼠使用超声技术药物引起的肾血流动力学障碍的早期检测

The kidney normally functions to maintain hemodynamic homeostasis and is a major site of damage caused by drug toxicity. Drug-induced nephrotoxicity is ...

Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms

Although targeted therapies are initially effective, resistance inevitably emerges. Several methods, such as genetic analysis of resistant clinical specimens, have been applied to uncover these resistance mechanisms to facilitate follow-up care. Although these approaches have led to clinically relevant discoveries, difficulties in attaining the relevant patient material or in deconvoluting the genomic data collected from these specimens have severely hampered the path towards a cure. To this end, we here describe a tool for expeditious discovery that may guide improvement in first-line therapies and alternative clinical management strategies. By coupling preclinical in vitro or in vivo drug selection with next-generation sequencing, it is possible to identify genomic structural variations and/or gene expression alterations that may serve as functional drivers of resistance. This approach facilitates the spontaneous emergence of alterations, enhancing the probability that these mechanisms may be observed in the patients. In this protocol we provide guidelines to maximize the potential for uncovering single nucleotide variants that drive resistance using adherent lines.

Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms

Drug resistance to targeted therapeutics is widespread and the need to identify mechanisms of resistance--prior to or following clinical onset--is critical for guiding alternative clinical management strategies. Here, we present a protocol to couple derivation of drug-resistant lines in vitro with sequencing to expedite discovery of these mechanisms.

实施<em&gt;体外</em&gt;耐药性检测:最大化的潜力，揭开临床有关的耐药机制

Although targeted therapies are initially effective, resistance inevitably emerges. Several methods, such as genetic analysis of resistant clinical ...

A Cell Culture Model of Resistance Arteries

The myoendothelial junction (MEJ), a unique signaling microdomain in small diameter resistance arteries, exhibits localization of specific proteins and signaling processes that can control vascular tone and blood pressure. As it is a projection from either the endothelial or smooth muscle cell, and due to its small size (on average, an area of ~1 &#181;m2), the MEJ is difficult to study in isolation. However, we have developed a cell culture model called the vascular cell co-culture (VCCC) that allows for in vitro MEJ formation, endothelial cell polarization, and dissection of signaling proteins and processes in the vascular wall of resistance arteries. The VCCC has a multitude of applications and can be adapted to suit different cell types. The model consists of two cell types grown on opposite sides of a filter with 0.4 &#181;m pores in which the in vitro MEJs can form. Here we describe how to create the VCCC via plating of cells and isolation of endothelial, MEJ, and smooth muscle fractions, which can then be used for protein isolation or activity assays. The filter with intact cell layers can be fixed, embedded, and sectioned for immunofluorescent analysis. Importantly, many of the discoveries from this model have been confirmed using intact resistance arteries, underscoring its physiological relevance.

A cell culture model of resistance arteries is described, allowing for the dissection of signaling pathways in endothelium, smooth muscle, or between endothelium and smooth muscle (the myoendothelial junction). The selective application of agonists or protein isolation, electron microscopy, or immunofluorescence can be utilized using this cell culture model.

阻力动脉的细胞培养模型

The myoendothelial junction (MEJ), a unique signaling microdomain in small diameter resistance arteries, exhibits localization of specific proteins and ...

Optimized LC-MS/MS Method for the High-throughput Analysis of Clinical Samples of Ivacaftor, Its Major Metabolites, and Lumacaftor in Biological Fluids of Cystic Fibrosis Patients

Defects in the cystic fibrosis trans-membrane conductance regulator (CFTR) are the cause of cystic fibrosis (CF), a disease with life-threatening pulmonary manifestations. Ivacaftor (IVA) and ivacaftor-lumacaftor (LUMA) combination are two new breakthrough CF drugs that directly modulate the activity and trafficking of the defective CFTR-protein. However, there is still a dearth of understanding on pharmacokinetic/pharmacodynamic parameters and the pharmacology of ivacaftor and lumacaftor. The HPLC-MS technique for the simultaneous analysis of the concentrations of ivacaftor, hydroxymethyl-ivacaftor, ivacaftor-carboxylate, and lumacaftor in biological fluids in patients receiving standard ivacaftor or ivacaftor-lumacaftor combination therapy has previously been developed by our group and partially validated to FDA standards. However, to allow the high-throughput analysis of a larger number of patient samples, our group has optimized the reported method through the use of a smaller pore size reverse-phase chromatography column (2.6 &#181;m, C8 100 &#197;; 50 x 2.1 mm) and a gradient solvent system (0-1 min: 40% B; 1-2 min: 40-70% B; 2-2.7 min: held at 70% B; 2.7-2.8 min: 70-90% B; 2.8-4.0 min: 90% B washing; 4.0-4.1 min: 90-40% B; 4.1-6.0 min: held at 40% B) instead of an isocratic elution. The goal of this study was to reduce the HPLC-MS analysis time per sample dramatically from ~15 min to only 6 min per sample, which is essential for the analysis of a large amount of patient samples. This expedient method will be of considerable utility for studies into the exposure-response relationships of these breakthrough CF drugs.

Ivacaftor and ivacaftor-lumacaftor combination are two new CF drugs. However, there is still a dearth of understanding on their PK/PD and pharmacology. We present an optimized HPLC-MS technique for the simultaneous analysis of ivacaftor and its major metabolites, and lumacaftor.