Size-dependent trajectories of DNA macromolecules due to insulative dielectrophoresis in submicrometer-deep fluidic channels.

In this paper, we demonstrate for the first time that insulative dielectrophoresis can induce size-dependent trajectories of DNA macromolecules. We experimentally use lambda (48.5 kbp) and T4GT7 (165.6 kbp) DNA molecules flowing continuously around a sharp corner inside fluidic channels with a depth of 0.4 mum. Numerical simulation of the electrokinetic force distribution inside the channels is in qualitative agreement with our experimentally observed trajectories. We discuss a possible physical mechanism for the DNA polarization and dielectrophoresis inside confining channels, based on the observed dielectrophoresis responses due to different DNA sizes and various electric fields applied between the inlet and the outlet. The proposed physical mechanism indicates that further extensive investigations, both theoretically and experimentally, would be very useful to better elucidate the forces involved at DNA dielectrophoresis. When applied for size-based sorting of DNA molecules, our sorting method offers two major advantages compared to earlier attempts with insulative dielectrophoresis: Its continuous operation allows for high-throughput analysis, and it only requires electric field strengths as low as approximately 10 Vcm.

松科nrDNA 的进化研究Evolution of nuclear ribosomal DNA in Pinaceae

核核糖体DNA（nrDNA）已被作为一个重要的标记，用于推断很多分类等级上的系统发育关系。相对于在被子植物中的快速致同进化，nrDNA在裸子植物中的致同进化速率低，且ITS和5S-NTS区有着较大的长度变异，这种现象在松科植物中尤为明显。在本研究中，我们克隆并测定了银杉属的5S rDNA以及冷杉属、银杉属、雪松属、油杉属、长苞铁杉属、金钱松属与铁杉属的ITS序列。基于获得的新数据，再结合前人报导的其它属的数据，我们探讨了如下四个问题： （1）松科 nrDNA ITS1 亚重复单位的组成、分布及进化;（2）ITS1区的长度变异与亚重复单位数目的关系以及它们的系统学意义;（3）松科ITS1的二级结构特征;（4）银杉5S rDNA编码区及非转录间隔区的结构特征。主要研究结果如下： 1. ITS区的序列分析ITS区的克隆及序列分析发现：（1） 松科ITS1的长度变异范围为 944-3271 bp, 这是目前已报导的真核生物中属间ITS变异最大的类群之一;（2） 所有松科植物的ITS区域都包含亚重复单位，亚重复单位的数目从2到9，并且这些亚重复单位可分为两种类型，即不含保守核心序列（5’-GGCCACCCTAGTC ） 的长亚重复单位（LSR）和含上述保守核心序列的短亚重复单位（SSR）;（3） ITS1区的巨大长度变异主要归因于亚重复单位的数量变异; （4） ITS1区的GC含量与 它的序列长度和亚重复单位的数目有一定关系，并能够提供一些系统发育信息，特别是支持云杉属、松属和银杉属三者具有很近的亲缘关系。 2. ITS1亚重复单位的系统发育分析为了研究亚重复单位的进化关系，我们用最大似然法和最大简约法构建了松科ITS1亚重复单位的系统发育树。结果表明：（1）在ML和MP树中可发现有共同的五个分支; （2） 银杉比松科其它属拥有更多的SSR，且该属的所有9个SSR在系统树中构成一个单系支，表明它们是在银杉属内发生重复的;（3）一些SSR在属间和种间具有同源性，可为nrDNA ITS 的进化历史以及松科的系统发育 研究提供重要信息;（4）亚重复单位的多次重复以及伴随的重组可能是导致LSR 和SSR在松科不同属中分布式样不同的原因。 3. 松科ITS1的二级结构 用 Mfold 3.2 软件对松科所有11个属的ITS1区进行了二级结构预测，共获得了563个最低自由能折叠。结合以前关于松科二级结构的报导，我们分析的结果表明：（1） 松科ITS1的二级结构主要由几个延展的发夹结构组成;（2） 构象的复杂性与亚重复的数目呈正相关;（3）配对的亚重复单位通常在保守核心区（5’-GGCCACCCTAGTC ） 处有部分重叠，并且构成一个长茎，而其它的亚重复单位通常会自身折叠，且保守核心区的部分出现在发夹结构的环中。 4. 银杉5S rDNA 序列分析 我们对来自银杉不同群体的3个个体的5S rDNA进行了克隆，共获得 45 条序列，分析结果表明：（1） 绝大多数银杉5S rDNA编码区长度为120 bp, 以GGG 开头，以CTC结尾，编码区出现的碱基替代主要为转换;（2） 银杉与其它裸子植物相比，5S rDNA基因编码区具很高的相似性（90-99%）; （3）间隔区含有一个poly-C和一个poly-T结构、两个TC丰富区以及五个GC丰富区。根据长度和序列特征，银杉的5S rDNA间隔区可分为三种类型：Type A 长751-764 bp，Type B 长770-807 bp （含一个32 bp的插入），Type C 长581-594 bp; （5）长间隔区（Type A，Type B ）中含有两个148-175 bp的串联亚重复单位，该亚重复单位与短间隔区（Type C ）中的一段143 bp的序列具有较高的相似性（56.0-66.8%）。 5. 银杉5S rRNA的二级结构 Mfold 3.2 预测结果表明：（1）银杉5S rRNA二级结构包括5个双螺旋区（干区）（Ⅰ-Ⅴ）、2个发夹结构环区（C和D）、3个中间环区（B1、B2 和 E）和1个铰链区（A）, 铰链区为三个双螺旋的结合处;（2） 二级结构中的环区通常比双螺旋区更加保守;（3）在5个双螺旋中，I 和 IV 区有较高的碱基替代率。

Saline-saturated DMSO-EDTA as a storage medium for microbial DNA analysis from coral mucus swab samples

The mucus surface layer of corals plays a number of integral roles in their overall health and fitness. This mucopolysaccharide coating serves as vehicle to capture food, a protective barrier against physical invasions and trauma, and serves as a medium to host a community of microorganisms distinct from the surrounding seawater. In healthy corals the associated microbial communities are known to provide antibiotics that contribute to the coral’s innate immunity and function metabolic activities such as biogeochemical cycling. Culture-dependent (Ducklow and Mitchell, 1979; Ritchie, 2006) and culture-independent methods (Rohwer, et al., 2001; Rohwer et al., 2002; Sekar et al., 2006; Hansson et al., 2009; Kellogg et al., 2009) have shown that coral mucus-associated microbial communities can change with changes in the environment and health condition of the coral. These changes may suggest that changes in the microbial associates not only reflect health status but also may assist corals in acclimating to changing environmental conditions. With the increasing availability of molecular biology tools, culture-independent methods are being used more frequently for evaluating the health of the animal host. Although culture-independent methods are able to provide more in-depth insights into the constituents of the coral surface mucus layer’s microbial community, their reliability and reproducibility rely on the initial sample collection maintaining sample integrity. In general, a sample of mucus is collected from a coral colony, either by sterile syringe or swab method (Woodley, et al., 2008), and immediately placed in a cryovial. In the case of a syringe sample, the mucus is decanted into the cryovial and the sealed tube is immediately flash-frozen in a liquid nitrogen vapor shipper (a.k.a., dry shipper). Swabs with mucus are placed in a cryovial, and the end of the swab is broken off before sealing and placing the vial in the dry shipper. The samples are then sent to a laboratory for analysis. After the initial collection and preservation of the sample, the duration of the sample voyage to a recipient laboratory is often another critical part of the sampling process, as unanticipated delays may exceed the length of time a dry shipper can remain cold, or mishandling of the shipper can cause it to exhaust prematurely. In remote areas, service by international shipping companies may be non-existent, which requires the use of an alternative preservation medium. Other methods for preserving environmental samples for microbial DNA analysis include drying on various matrices (DNA cards, swabs), or placing samples in liquid preservatives (e.g., chloroform/phenol/isoamyl alcohol, TRIzol reagent, ethanol). These methodologies eliminate the need for cold storage, however, they add expense and permitting requirements for hazardous liquid components, and the retrieval of intact microbial DNA often can be inconsistent (Dawson, et al., 1998; Rissanen et al., 2010). A method to preserve coral mucus samples without cold storage or use of hazardous solvents, while maintaining microbial DNA integrity, would be an invaluable tool for coral biologists, especially those in remote areas. Saline-saturated dimethylsulfoxide-ethylenediaminetetraacetic acid (20% DMSO-0.25M EDTA, pH 8.0), or SSDE, is a solution that has been reported to be a means of storing tissue of marine invertebrates at ambient temperatures without significant loss of nucleic acid integrity (Dawson et al., 1998, Concepcion et al., 2007). While this methodology would be a facile and inexpensive way to transport coral tissue samples, it is unclear whether the coral microbiota DNA would be adversely affected by this storage medium either by degradation of the DNA, or a bias in the DNA recovered during the extraction process created by variations in extraction efficiencies among the various community members. Tests to determine the efficacy of SSDE as an ambient temperature storage medium for coral mucus samples are presented here.

噬菌体434单链阻遏蛋白的高亲和力DNA结合序列的设计和筛选

一． 设计和筛选单链阻遏蛋白的高亲和力DNA结合序列 　　单链阻遏蛋白RRTRES是噬菌体434阻遏蛋白的衍生物，它是噬菌体434阻 遏蛋白的N端DBD(1-69位氨基酸)组成的共价二聚体。这个单链分子有两个DBD，一个是野生型噬菌体434的DBD-R，另一个是突变了的DBD - RTRES，二者用重组接头以头接尾的方式连接起来。在RTRES的α3-螺旋中．1、1、2、5位氨基酸与DNA识别紧密相关，它们分别为T、R、E、S。为了筛选出突变的RTRES的DNA结合位点，设计了核心序列为CATACAAGAAAGNNNNNNTTTATG随机DNA库，通过RRTRES与随机DNA库的体外结合和循环筛选。将筛选到的群体克隆并测序。通过与单链阻遏蛋白RRTRES的亲和力测定，对每一个筛选到的序列进行特性分析。结果表明，当结合位点（上述划线部分）为TTAC或TTCC时为最适操纵区序列。它们与单链阻遏蛋白RRTRES的亲和力很高，Kd值在1-10pM的范围。其中随机部分为TTTACG的操纵区与RRTRES的亲和力最高，Kd值约为lpM;当结合位点为TTAC时，平均Kd值为3pM：当结合位点为 TTCC时，Kd值在5-lOpM之间。天然噬菌体434阻遏蛋白与其操纵区的亲和力的Kd值在nM数量级，与之相比，所筛选操纵区的亲和力明显提高。此外，亲和力大小还受到结合位点两侧的碱基的影响，特别是5'位碱基的影响。 　　表达纯化同源双突变的单链阻遏蛋白RTRESRTRE'根据RTRES的以上识别特一点，设计了一系列新的操纵区序列，它们的共有序列为GTAAGAAARNTTACN，或GGAAGAAARNTTCCN，并测定它们与RTRES RTRE之间的结合特异性。结果表明，它们可被RTRES RTRES特异识别，且亲和力也很高，Kd值在5-40pM之间。其中GTAAGAAAGTTTACG与RTRES RTRES之间结合的Kd值约为5pM。同样，表达了异源双突变的单链阻遏蛋白R*RTRES，然而它与 设计的相关操纵区的亲和力并不很高，Kd值约为lOOpM。利用本工作中的随机筛选和合理设计的原则，得到了新的具有特异性识别和高亲和力的蛋白一DNA相互作用。这个方法可望用于其他DBP的新的结合特异性的筛选。 二． 非同位素的方法筛选单链阻遏蛋白的最佳DNA结合序列初探 　　克隆和表达了带半胱氨酸尾的单链阻遏蛋白，利用已包被了马来酰胺的活性板可以与自由巯基结合的特性，将蛋白固定在活性板表面。体外筛选RTRES RTRES的最佳DNA结合序列，得到了一些与RTRES RTRES结合的序列，但Kd值nM数量级。此方法需进一步优化。