| Trypanosomatid, fluorescence-based in vitro U-insertion/U-deletion RNA-editing (FIDE)
|
|
Author:
Date:
2021-03-05
[Abstract] Gene expression within the mitochondria of African trypanosomes and other protozoan organisms relies on a nucleotide-specific RNA-editing reaction. In the process exclusively uridine (U)-nucleotides are site-specifically inserted into and deleted from sequence-deficient primary transcripts to convert them into translatable mRNAs. The reaction is catalyzed by a 0.8 MDa multiprotein complex termed the editosome. Here we describe an improved in vitro test to quantitatively explore the catalytic activity of the editosome. The assay uses synthetic, fluorophore-derivatized oligoribonucleotides as editing substrates, which enable the automated electrophoretic separation of the reaction products by capillary electrophoresis (CE) coupled to laser-induced fluorescence (LIF) detection systems. The ...
[摘要] [摘要]非洲锥虫和其他原生动物生物线粒体内的基因表达依赖于核苷酸特异性的RNA编辑反应。在该过程中，仅将尿苷（U）-核苷酸位点特异性插入序列不足的初级转录物中，并从中缺失，以将其转化为可翻译的mRNA。该反应由0.8 MDa的多蛋白复合物催化，该复合物被称为编辑体。在这里我们描述了一种改进的体外试验，以定量探索Editosome的催化活性。该测定使用合成的，荧光团衍生的寡核糖核苷酸 作为编辑底物，可通过耦合到激光诱导荧光（LIF）检测系统的毛细管电泳（CE）自动分离反应产物。该测定法功能强大，只需要纳克级的材料，并且通过使用多毛细管CE / LIF仪器，可以高度平行的方式进行测定。进一步的改进包括使用硫代磷酸酯修饰的，因此具有RNase耐性的底物RNA，以及用于同时监测U插入和U缺失反应的多重型荧光团标记策略。该测定方法对于研究酶体的机理和酶学是有用的。ħ H但是，它也可以在高通量执行以筛选RNA编辑特异性抑制剂。
图形摘要：
基于荧光的体外U插入/ U缺失RNA编辑（FIDE）分析的特征
[背景]中的RNA编辑反应动质体原生动物如非洲锥虫和利什曼原虫表示一个信使的最显着的转录后修饰（米）的RNA（综述Göringer ...
|
|
|
| Electron Tomography to Study the Three-dimensional Structure of Plasmodesmata in Plant Tissues–from High Pressure Freezing Preparation to Ultrathin Section Collection
|
|
Author:
Date:
2018-01-05
[Abstract] Plasmodesmata (PD) are nanometric (~20 nm wide) membrane lined pores encased in the cell walls of the adjacent plant cells. They allow the cells to exchange all types of molecules ranging from nutrients like sugar, hormones, to RNAs and various proteins. Unfortunately, they are also hijacked by phyto-viruses, enabling them to spread from cell-to-cell and then systematically throughout the whole plant. Their central position in plant biology makes it crucial to understand their physiology and especially link their function to their structure. Over the past 50 years, electron microscopists have observed them and attempted to ultrastructurally characterize them. They laid the foundation of what is known about these pores (Tilney et al., 1991; Ding et al., 1992; Oparka and ...
[摘要] Plasmodesmata（PD）是包裹在相邻植物细胞的细胞壁中的纳米（〜20nm宽）膜衬里的孔。它们允许细胞交换从糖，激素，RNA到各种蛋白质等营养物质的所有类型的分子。不幸的是，它们也被植物病毒劫持，使它们从细胞间传播，然后在整个植物体系中传播。它们在植物生物学中的核心地位使得理解其生理机制，尤其是将其功能与其结构联系起来至关重要。在过去的50年中，电子显微镜观察家们已经观察到了这些现象，并试图用超微结构来表征它们。他们为已知的这些毛孔奠定了基础（Tilney等人，1991; Ding等人，1992; Oparka和Roberts，2001; Nicolas等人， et al。，2017a）。
尽管三维电子显微镜（3D-EM）爆炸，PD超微结构仍然不支持这种技术。第一个技术难点是在尽可能接近原生状态的情况下处理它们。其次，由于染色/固定试剂穿透率差，其体积增大，含水量高以及存在酸性液泡，植物样品显示自己难以加工。最重要的是，它们在细胞壁上的独特位置和它们的纳米尺寸使得难以方便地染色以便看到这些孔隙的内部运作。
这里我们详细描述Nicolas et al。（2017b）中使用的协议，对PD进行细节化处理，并生成高分辨率的X线断层图。
【背景】高压冻结（HPF）依赖于样品中存在的水的玻璃化。通过以足够高的冷冻速度（10 ...
|
|
|
| Pit Assay to Measure the Bone Resorptive Activity of Bone Marrow-derived Osteoclasts
|
|
Author:
Date:
2016-06-20
[Abstract] Although it is possible to use a tartrate-resistant acid phosphatase (TRAP) stain to assist in identifying osteoclasts, a separate method is needed to determine the bone resorption activity of osteoclasts. Since osteoclasts leave “pits” after bone matrix resorption (Charles et al., 2014), it is possible to stain pits as a method of measuring osteoclast bone resorption activity. The pit assay protocol enables researchers to stain bony slices that were co-cultured with osteoclasts with toluidine blue in order to allow the visualization, capture, and analysis of osteoclast resorptive activity based on the number, size and depth of pits (Zhou et al., 2015). The pit assay protocol is separated into three sequential stages: Preparation of bone slices (1); preparation of ...
[摘要] 尽管可以使用抗酒石酸盐的酸性磷酸酶（TRAP）染色来辅助鉴定破骨细胞，但是需要单独的方法来确定破骨细胞的骨吸收活性。 由于破骨细胞在骨基质吸收之后离开"凹陷"（Charles等人，2014），因此可以将斑点染色作为测量破骨细胞骨吸收活性的方法。 坑测定方案使研究人员能够将与破骨细胞与甲苯胺蓝共培养的骨切片染色，以便基于坑的数量，尺寸和深度可视化，捕获和分析破骨细胞再吸收活性（Zhou等人， et al。，2015）。 坑测定方案分为三个连续阶段：骨切片的制备（1）; 制备破骨细胞前体（Ross等人，2006; Teitelbaum等人，2000）（2）和骨吸收坑测定（3）。
|
|
|