RNA干扰在原生动物中的应用

RNA干扰(RNAi),即由双链RNA介导的转录后基因沉默的现象,已成为分析原生动物基因功能的有效手段。现对应用RNAi研究原生动物微管蛋白的功能和基体组装、纤毛虫大核基因组重排、纤毛虫刺丝泡的发生和作用、端粒酶及细胞周期蛋白的功能等方面进行综述。     

长江洞庭湖口原生动物的生态研究

对长江洞庭湖口原生动物群落为期三年的研究结果,种类组成,季节分布、优势种类、丰度的变化等,同时还依据食性分析了各种类的功能营养类群,并对河流中原生动物地来源、长江中上游地区原生动物种类组成规律,原生动物功能营养类群和优势在在河流污染监测中的指示作用等进行了讨论。     

原生动物八肋游仆虫cDNA文库的构建

细胞内蛋白质合成过程是一个由多种蛋白质相互作用参与调节的开放系统,形成了复杂的mRNA代谢和蛋白质翻译为核心的基因表达调控的网络和信号转导途径。【目的】为了获得更多参与调节蛋白质合成终止过程的蛋白质种类和功能信息,进一步了解其中的网络和信号转导途径,本研究构建了原生动物八肋游仆虫的cDNA文库。【方法】构建过程严格遵循Clontech公司的BD MatchmakerTM Library ConstructionScreening kit提供的方案进行文库构建和筛选.【结果】首次得到了可用于筛选功能基因的原生动物纤毛虫的cDNA文库,文库滴度为2.437×107cfu/mL。利用第二类肽链释放因子为诱饵,筛选得到了一些可能与之相互作用的蛋白质,其中包括一个可能编码RNA解旋酶的基因序列。该文库为进一步筛选和研究八肋游仆虫功能基因提供了便利的平台。     

长江洞庭湖口原生动物的生态学研究

对长江洞庭湖口原生动物群落为期三年的研究结果:种类组成、季节分布、优势种类、丰度的季节变化等,同时还依据食性分析了各种类的功能营养类群,并对河流中原生动物的来源、长江中上游地区原生动物种类组成规律、原生动物功能营养类群和优势种类在河流污染监测中的指示作用等进行了讨论.       

嗜热四膜虫可变剪接基因鉴定及功能分析

可变剪接是产生蛋白质组多样性和调节基因表达的重要机制,相关研究在高等真核生物中开展较多,而在单细胞真核生物中则较少,尤其是单细胞原生动物纤毛虫中,仅有少量报道。本文基于单细胞模式原生动物嗜热四膜虫种大量转录组数据,对其可变剪接基因进行了鉴定及分析。在嗜热四膜虫中共鉴定到2 894个可变剪接位点,涉及到2 698个可变剪接基因,可分为四类。考虑到转录本拼接的准确性,选择了其中464个与基因组预测模型完全一致的可变剪接基因进行深入分析,其中生长(growth)时期、饥饿(starvation)时期、接合生殖(conjugation)时期特异性的可变剪接基因分别为49个、79个和135个。对可变剪接基因的功能进行分析表明其涉及的功能广泛且显著富集于蛋白激酶过程,提示可变剪接基因在嗜热四膜虫蛋白磷酸化和信号传导中具有重要作用。     

土壤原生动物研究方法

原生动物是土壤中形态和功能多样性高且占绝对优势的微型真核生物,在维持土壤生产力和生态系统功能上起着重要作用。随着研究方法的不断改进和创新,对土壤原生动物生态功能的认识已逐步加深。但缺乏统一且有效的定量分析方法仍是土壤原生动物生态学研究中的主要问题。本文综述相关的定量、定性以及群落结构与功能的研究方法,并着重介绍新技术方法,包括土壤定量蛋白银法、分子指纹图谱分析、同位素示踪技术,以及环境宏基因组学技术等。     

土壤原生动物群落及其生态功能

土壤原生动物是土壤微生物区系的重要组成部分。在土壤生态系统中 ,由于微生物与微动物的生命活动及其相互作用 ,从而形成了土壤的物质循环和能量转化。土壤原生动物既参与了微生物所介导的物质转化和能量循环 ,又参与了动物对微生物的捕食作用。由于原生动物具有丰富的种类和多样性以及巨大的生物量 ,所以土壤原生动物的群落及其生态功能 ,已引起了人们的广泛关注 ,并且研究理论与方法日益深入。但我国在这方面的研究报道较少 ,本文拟从群落与生态功能方面的进展做一概述。1　土壤原生动物的群落特征土壤与淡水原生动物最早是由Ａｎｔｏｎ…     

原生动物线粒体DNA的研究进展

目前已完成了多种原生动物mtDNA全序列的测定,对线粒体基因组有了较全面和深入的认识。本文总结了原生动物线粒体基因组结构、基因组成及基因表达等方面的研究进展,有助于进一步了解原始线粒体基因组的组成及其mtDNA进化,并为细胞的起源和真核生物进化的研究提供有价值的线索。     

基于克隆文库技术分析瘤棘砂壳虫的食物组成

瘤棘砂壳虫是东亚特有的原生动物,广泛分布于长江与珠江中下游以及福建地区的湖泊和水库,作为水生态系统的捕食者,在维持水生态系统的结构与功能方面发挥着重要作用。利用18S rRNA基因PCR扩增和克隆文库测序等分子生物学技术方法,从基因水平研究瘤棘砂壳虫的食物组成。结果表明:所获得的46条序列在97%相似度水平含有11类OTUs(Operational taxonomic units,操作分类单元),其中包括轮虫6个,桡足类5个,说明瘤棘砂壳虫的捕食类群以轮虫和桡足类为主,同时也证明单细胞生物可以直接以多细胞的后生动物为食。此外,通过克隆文库测序技术分析原生动物的食物组成比例,不仅是一种方便、高效、快速,重复性高的方法,同时也为分析原生动物的生态功能提供了一种新的视角。     

原生动物群落多样性变化与汉沽稳定塘水质净化效能相互关系的研究

天津汉沽生物稳定塘是近年建成并投入运行的多级污水净化系统和示范工程。论文报道了汉沽稳定塘各塘主要污染物的去除效果,重点论述了原生动物群落多样性变化及其结构和功能特征与水质净化的相互关系。研究结果表明,５个采样站原生动物群落结构与功能参数的变化与各级塘中污染物的浓度关系密切。进水口（１号站）由于各种污染物含量很高,原生动物种类数、个体数量、多样性指数ｄ值和ＰＦＵ原生动物的群集速度（功能参数）都为零。     

Receptor-mediated endocytosis of fibroblast beta-glucuronidase by peritoneal macrophages

beta-Glucuronidase secreted by mouse 3T3 fibroblasts in vitro was taken up into mouse peritoneal macrophages and into human fibroblasts by a process which was rapid and saturable. High concentrations of mannose-containing compounds inhibited uptake into macrophages but had no effect on uptake into fibroblasts. Mannose-6-phosphate inhibited uptake into both types of cell, reducing uptake into macrophages by 34% and abolishing uptake into fibroblasts completely at a concentration of 5 mM. Fructose-1-phosphate was almost equally as effective at inhibiting uptake into fibroblasts but had no effect on macrophages. Pre-treatment of beta-glucuronidase with alkaline phosphatase totally prevented its uptake into fibroblasts but had no effect on its uptake into macrophages. These results indicate that fibroblasts can secrete a lysosomal enzyme in a form recognised as a high uptake ligand not only by other fibroblasts but also by peritoneal macrophages and that endocytosis appears to be mediated by different receptors present on each type of cell. This has important implications for the potential treatment of mucopolysaccharidoses by fibroblast transplants.     

Receptor-mediated endocytosis of fibroblast β-glucuronidase by peritoneal macrophages

β-Glucuronidase secreted by mouse 3T3 fibroblasts in vitro was taken up into mouse peritoneal macrophages and into human fibroblasts by a process which was rapid and saturable. High concentrations of mannose-containing compounds inhibited uptake into macrophages but had no effect on uptake into fibroblasts. Mannose-6-phosphate inhibited uptake into both types of cell, reducing uptake into macrophages by 34% and abolishing uptake into fibroblasts completely at a concentration of 5 mM. Fructose-1-phosphate was almost equally as effective at inhibiting uptake into fibroblasts but had no effect on macrophages. Pre-treatment of β-glucuronidase with alkaline phosphatase totally prevented its uptake into fibroblasts but had no effect on its uptake into macrophages. These results indicate that fibroblasts can secrete a lysosomal enzyme in a form recognised as a high uptake ligand not only by other fibroblasts but also by peritoneal macrophages and that endocytosis appears to be mediated by different receptors present on each type of cell. This has important implications for the potential treatment of mucopolysaccharidoses by fibroblast transplants.     

A generic building block for C- and N-terminal protein-labeling and protein-immobilization

Expressed protein ligation (EPL) and bioconjugation based on the maleimide group (MIC-conjugation) provide powerful tools for protein modification. In the light of the importance of site-selectively modified proteins for the study of protein function, a flexible method for the introduction of tags and reporter groups into the C-terminus of proteins employing EPL and MIC-conjugation was developed. We describe the solid-phase synthesis of a generic building block, equipped with fluorescence markers or different functional groups. This generic building block allows for a flexible incorporation of different tags into proteins and was used for the introduction of fluorescence markers into the C-terminus of Rab and Ras GTPases by EPL or MIC-conjugation techniques. In addition, a building block appropriately modified for the incorporation of an azide into proteins was synthesized. Azide-functionalized Ras protein was immobilized on a phosphane-modified surface by means of Staudinger ligation providing a highly chemoselective ligation method for the immobilization of proteins.     

Tetraspan cargo adaptors usher GPI-anchored proteins into multivesicular bodies

Ubiquitinated membrane proteins are sorted into intralumenal endosomal vesicles on their way for degradation in lysosomes. Here we summarize the discovery of the Cos proteins, which work to organize and segregate ubiquitinated cargo prior to its incorporation into intralumenal vesicles of the multivesicular body (MVB). Importantly, cargoes such as GPI-anchored proteins (GPI-APs) that cannot undergo ubiquitination, rely entirely on Cos proteins for sorting into intralumenal vesicles using the same pathway that depends on ESCRTs and ubiquitin ligases that typical polytopic membrane proteins do. Here we show Cos proteins provide functions as not only adaptor proteins for ubiquitin ligases, but also as cargo carriers that can physically usher a variety of other proteins into the MVB pathway. We then discuss the significance of this new sorting model and the broader implications for this cargo adaptor mechanism, whereby yeast Cos proteins, and their likely animal analogs, provide a ubiquitin sorting signal in trans to enable sorting of a membrane protein network into intralumenal vesicles.     

Compartmentation of phosphorylated precursors of phospholipid biosynthesis in cultured neuroblastoma cells

The continuous turnover of membrane phospholipids requires a steady supply of biosynthetic precursors. We evaluated the effects of decreasing extracellular Na+ concentration on phospholipid metabolism in cultured neuroblastoma (N1E 115) cells. Incubating cultures with 145 to 0 mM NaCl caused a concentration-dependent inhibition of [32P]phosphate uptake into the water-soluble intracellular pool and incorporation into phospholipid. Phospholipid classes were differentially affected; [32P]phosphate incorporated into phosphati-dylethanolamine (PE) and phosphatidylcholine (PC) was consistently less than into phosphatidylinositol (PI) and phosphatidylserine (PS). This could not be attributed to decreased phospholipid synthesis since under identical conditions, there was no effect on arachidonic acid or ethanolamine incorporation, and choline utilization for PC synthesis was increased. The effect of Na+ was highly specific since reducing phosphate uptake to a similar extent by incubating cultures in a phosphate-deficient medium containing Na+ did not alter the relative distribution of [32P]phosphate in phospholipid. Of several cations tested only Li+ could partially (50%) replace Na+. Incubation in the presence of ouabain or amiloride had no effect on [32P]phosphate incorporation into phospholipid. The differential effects of low Na+ on [32P]phosphate incorporation into PI relative to PC and PE suggests preferential compartmentation of [32P]phosphate into ATP in pools used for phosphatidic acid synthesis and relatively less in ATP pools used for synthesis of phosphocholine and phosphoethanolamine, precursors of PC and PE, respectively. This suggestion of heterogeneous and distinct pools of ATP for phospholipid biosynthesis, and of potential modulation by Na+ ion, has important implications for understanding intracellular regulation of metabolism.     

Effect of Sclerin on Amino Acid Incorporation into Mitochondria Isolated from Rat Liver

Though sclerin (SCL) stimulated amino acid incorporation into the protein fraction of post mitochondrial supernatant of rat liver homogenate, it had no effect on the incorporation into the isolated mitochondria at pH 7.2, despite of its stimulating effect on mitochondrial oxidative phosphorylation. SCL stimulated amino acid incorporation into the mitochondria at pH 6.1, and to some extent maintained the activity on that in mitochondria during aging in hypotonic Tris-HCl buffer (pH 7.2). Since SCL prevented leakage of amino acids from the mitochondria into these buffers, it was suggested that SCL may protect a structure of mitochondrial membrane which appeared to have a significance on transport of amino acids. In liver slices, SCL stimulated amino acid incorporation only into the extra-mitochondrial fraction for the first 3 min, but gradually turned to stimulate incorporation into mitochondria within 30 min.     

Forward rate constants for receptor clusters. Variational methods for upper and lower bounds

We are interested in the effect of receptor clustering on k+, the diffusion-limited forward rate constant for the binding of a ligand to a cell surface receptor. Here we estimate the reduction in k+ when receptors are clustered in various configurations. We obtain two alternative expressions for the flux of ligands into receptors distributed on a surface. Next we show through a variational principle that these provide both upper and lower bounds on the flux when evaluated for trial concentration functions which satisfy only the boundary conditions of the Laplace equation. We use an analogy with electrostatics to calculate rigorous bounds within approx. 10% of the exact result for a variety of planar clusters of hemispherical receptor sites. We also obtain an exact result for the flux into a spheroidal receptor and use this result to obtain bounds on the flux into certain receptor clusters.     

Microfluidic delivery of small molecules into mammalian cells based on hydrodynamic focusing

Microfluidics-based cell assays offer high levels of automation and integration, and allow multiple assays to be run in parallel, based on reduced sample volumes. These characteristics make them attractive for studies associated with drug discovery. Controlled delivery of drug molecules or other exogenous materials into cells is a critical issue that needs to be addressed before microfluidics can serve as a viable platform for drug screening and studies. In this study, we report the application of hydrodynamic focusing for controlled delivery of small molecules into cells immobilized on the substrate of a microfluidic device. We delivered calcein AM which was permeant to the cell membrane into cells, and monitored its enzymatic conversion into fluorescent calcein during and after the delivery. Different ratios of the sample flow to the side flow were tested to determine how the conditions of hydrodynamic focusing affected the delivery. A 3D numerical model was developed to help understand the fluid flow, molecular diffusion due to hydrodynamic focusing in the microfluidic channel. The results from the simulation indicated that the calcein AM concentration on the outer surface of a cell was determined by the conditions of hydrodynamic focusing. By comparing the results from the simulation with those from the experiment, we found that the calcein AM concentration on the cell outer surface correlated very well with the amount of the molecules delivered into the cell. This suggests that hydrodynamic focusing provides an effective way for potentially quantitative delivery of exogenous molecules into cells at the single cell or subcellular level. We expect that our technique will pave the way to high-throughput drug screening and delivery on a microfluidic platform.     

Engineered Saccharomyces cerevisiae strain for improved xylose utilization with a three-plasmid SUMO yeast expression system

A three-plasmid yeast expression system utilizing the portable small ubiquitin-like modifier (SUMO) vector set combined with the efficient endogenous yeast protease Ulp1 was developed for production of large amounts of soluble functional protein in Saccharomyces cerevisiae. Each vector has a different selectable marker (URA, TRP, or LEU), and the system provides high expression levels of three different proteins simultaneously. This system was integrated into the protocols on a fully automated plasmid-based robotic platform to screen engineered strains of S. cerevisiae for improved growth on xylose. First, a novel PCR assembly strategy was used to clone a xylose isomerase (XI) gene into the URA-selectable SUMO vector and the plasmid was placed into the S. cerevisiae INVSc1 strain to give the strain designated INVSc1-XI. Second, amino acid scanning mutagenesis was used to generate a library of mutagenized genes encoding the bioinsecticidal peptide lycotoxin-1 (Lyt-1) and the library was cloned into the TRP-selectable SUMO vector and placed into INVSc1-XI to give the strain designated INVSc1-XI-Lyt-1. Third, the Yersinia pestis xylulokinase gene was cloned into the LEU-selectable SUMO vector and placed into the INVSc1-XI-Lyt-1 yeast. Yeast strains expressing XI and xylulokinase with or without Lyt-1 showed improved growth on xylose compared to INVSc1-XI yeast.