Virioplankton ‘pegylation’: Use of PEG (polyethylene glycol) to concentrate and purify viruses in pelagic ecosystems

We have described the use of Polyethylene glycol (PEG) for the precipitation of natural communities of aquatic viruses, and its comparison with the usual concentration method based on ultracentrifugation. Experimental samples were obtained from different freshwater ecosystems whose trophic status varied. Based on transmission electron microscope observations and counting of phage-shaped particles, our results showed that the greatest recovery efficiency for all ecosystems was obtained when we used the PEG protocol. On average, this protocol allowed the recovery of > 2-fold more viruses, compared to ultracentrifugation. In addition, the diversity of virioplankton, based on genomic size profiling using pulsed field gel electrophoresis, was higher and better discriminated when we used the PEG method. We conclude that pegylation offers a valid, simple and cheaper alternative method to ultracentrifugation, for the concentration and the purification of pelagic viruses.     

Recovery comparison of two virus concentration methods from wastewater using cell culture and real-time PCR

Enteric viruses are shed in the feces and may be present in environmental waters. Their detection in wastewater, even at low concentration, is a major challenge. In this study, recoveries of Echovirus 7 (EV7), virions and RNA in wastewater, using virus concentration methods were determined to evaluate the detection of infectious viruses and the possibility of recovering viral genomes. Two virus concentration methods, PEG precipitation method and two-phase separation method, were applied to recovery experiments of EV7-virions from wastewater, in parallel with recovery experiments of EV7 RNA. The titration of EV7 virions was carried out by cell culture using human rhabdomyosarcoma tumor tissue and the EV7 RNA quantification was performed by real-time PCR. The mean recovery yields of EV7 virions using the PEG precipitation method and the two-phase separation method were 78.5?±?10.99 and 83.1?±?0.28?%, respectively. Besides, EV7 RNA recoveries obtained using the PEG precipitation method were four times higher than those using the two-phase separation method. According to our results, the two methods enable to concentrate both infectious viruses and viral genomes. Moreover, considering the protocol time and cost together with the ratio of the EV7 virion recovery to the EV7 RNA recovery, the two-phase separation method (83.1/2.71?%, or 30.6) seems to be more appropriate for selective concentration of viral virions than the PEG precipitation method (78.5/10.33?%, or 7.6).     

Aqueous two-phase partition of complex protein feedstocks derived from brain tissue homogenates

This study describes the application of aqueous two-phase partition using polyethylene glycol (PEG)-potassium phosphate systems for the direct recovery of proteins, and aggregates thereof, from mammalian brain tissue homogenates. Investigation of established methodologies for the purification of prion proteins (PrP) from bovine brain affected with transmissible spongiform encephalopathy (BSE) has identified an alternative purification regime based on aqueous two-phase partition. This circumvents energy-intensive and rate-limiting unit operations of ultracentrifugation conventionally used for isolation of PrP. Selectivity of various PEG-phosphate systems varied inversely with polymer molecular mass. The maximum protein recovery from bovine brain extracts was obtained with systems containing PEG 300. Manipulation of the aqueous environment, to back-extract protein product from the PEG-rich top phase into the phosphate-rich lower phase, enabled integration of ATPS with conventional hydrophobic interaction chromatography (HIC) which selectively removes obdurate contaminating proteins (i.e. ferritin).     

Size‐selective DNA separation: Recovery spectra help determine the sodium chloride (NaCl) and polyethylene glycol (PEG) concentrations required

In the presence of sodium chloride (NaCl), DNA fragments can be size‐selectively separated by varying the final concentration of polyethylene glycol (PEG). This separation strategy in combination with the use of paramagnetic particles provides a valuable platform for achieving the desired DNA size interval, which is important in automated library preparation for high‐throughput DNA sequencing. Here, we report the establishment of recovery spectra of DNA fragments that enable the determination of suitable NaCl and PEG concentrations for size‐selective separation. Firstly, at a given NaCl concentration, the recovery equation was obtained by fitting the DNA recovery ratios versus the PEG concentrations using the logistic function to determine the required parameters. Secondly, the slope function of the recovery equation was achieved by deducing its first derivative. Therefore, the recovery spectrum can be generated using the slope function based on those parameters. According to the recovery spectra of different length DNA fragments, suitable NaCl and PEG concentrations can be determined, respectively, by calculating their resolution values and recovery ratios. The strategy was effectively applied to the size‐selective separation of 532‐, 400‐, and 307‐bp fragments at the selected reagent concentrations with recoveries of 96.9, 64.7, and 85.9%, respectively. Our method enables good predictions of NaCl and PEG concentrations for size‐selective DNA separation.     

Improved method for virological analysis of food

A single, simple method for recovering enteroviruses from several different kinds of food, such as ground beef, fish, oysters, and mussels, has been improved. First, sample contamination technique was studied. It appears that virus adsorption occurs at food pH and varies according to the kind of food and the food-virus exchange surface. Second, virus recovery was evaluated. According to the experimental results obtained, we propose the following method. Samples are submerged in 100 ml of demineralized water adjusted to pH 9 with a conductivity of 8,000 mg of NaCl per liter. Then, viruses are concentrated by ultrafiltration or by ultracentrifugation. This method was efficient for virus recovery from the four kinds of food, even in cases of very low contamination.     

Improved method for virological analysis of food.

A single, simple method for recovering enteroviruses from several different kinds of food, such as ground beef, fish, oysters, and mussels, has been improved. First, sample contamination technique was studied. It appears that virus adsorption occurs at food pH and varies according to the kind of food and the food-virus exchange surface. Second, virus recovery was evaluated. According to the experimental results obtained, we propose the following method. Samples are submerged in 100 ml of demineralized water adjusted to pH 9 with a conductivity of 8,000 mg of NaCl per liter. Then, viruses are concentrated by ultrafiltration or by ultracentrifugation. This method was efficient for virus recovery from the four kinds of food, even in cases of very low contamination.     

The use of polyethylene glycol in concentration and purification of several bovine viruses.

The polyethylene glycol (PEG) precipitation method was used for the concentration and purification of eight bovine viruses. Good results were obtained from four viruses, parainfluenza--3 virus, bovine enterovirus, bovine adenovirus, and bovine parvovirus. No satisfactory results of concentration were obtained from bovine reovirus, bovine viral diarrhea virus, and infectious bovine rhinotracheitis virus. The failure of concentration of the four viruses seems to be ascribed rather to the resuspending of virus from the virus--PEG precipitate than to the precipitation of virus from infective culture fluid. This method can be applied as the initial step to the concentration of parainfluenza--3 virus, bovine enterovirus, bovine adenovirus, and bovine parvovirus from a large volume of material, since it is simple, rapid, and inexpensive.     

Isolation and purification of bacterial ribosomes from endotoxin using polyethylene glycol

The difficulties arising in the study of the immunogenicity of bacterial ribosomes and in their possible use as vaccines are due to the fact that preparative ultracentrifugation, constituting a necessary stage in most of the methods used for the isolation of ribosomes, has a low productive capacity. To develop a more effective method for obtaining Shigella ribosomal vaccines, an attempt to use the method of precipitation with 10% polyethylene glycol (PEG), proposed by Expert-Bezan?on et al., has been made. The serological determination of O antigen has shown that nearly contained in the supernatant fluid S-30 can be detected in precipitated ribosomes. Taking into account the wide spectrum of the biological activity of bacterial endotoxin, it must be removed from the vaccine. The study has revealed that precipitation by means of ethanol (15-35%), low pH (4,2-4,7) and PEG (4-8%) can be used for this purpose. In accordance with the chosen method, the clarified material obtained by precipitation with 10% PEG is fractionated by means of 5% PEG which causes the complete precipitation of ribosomes, thus leaving endotoxin in the solution. Centrifugation in the density gradient of saccharose and electron microscopy have demonstrated that ribosomes isolated by this method possess typical sedimentation properties and structure. The yield of ribosomes is 3 times greater than that obtained by ultracentrifugation. Fractionation with PEG may be used as the method of the mass production of ribosomal vaccines.     

人脐血血浆外泌体提取方法的比较北大核心CSCD

为探寻高效且稳定的提取人脐血血浆外泌体的方法,利用超高速离心法、蔗糖垫密度梯度离心法、改良超速离心法和聚乙二醇(polyethylene glycol, PEG)沉淀法提取人脐血血浆外泌体,并比较4种方法的优劣。利用透射电镜、动态光散射技术观察外泌体的形态、结构及大小;聚氰基丙烯酸正丁酯(bicinchoninic acid, BCA)法测定外泌体蛋白总量;Western blotting检测外泌体表面标志蛋白CD63、HSP70以及外泌体阴性蛋白GM130 (高尔基标志蛋白)的表达。结果表明,与提取外泌体的“金标准”,即超高速离心法相比,蔗糖垫密度梯度离心法稳定性好,获取的外泌体粒径较均一,但操作较复杂,耗时长;改良超速离心法操作较简单,纯度较高;PEG沉淀法提取的外泌体蛋白量最高,操作时间最短,但杂质较多。结果表明,4种方法均能从人脐血血浆中获取外泌体,但在操作时间、纯度、提取量等方面存在一定差异。因此,应根据实验目的和具体要求选择合适的提取人脐血血浆外泌体的方法。     

Methods for recovering poliovirus and rotavirus from oysters.

Polioviruses and rotaviruses are potential indicators of sewage pollution of water and shellfish. Several methods for detecting these viruses in oysters were assessed. Elution-precipitation involving Catfloc for clarification and skim milk for subsequent flocculation resulted in the recovery of an average of 79% of poliovirus type 1 and 37% of rotavirus SA-11 from oyster homogenates inoculated with low numbers of these viruses. Adsorption-elution-precipitation did not improve the recovery of poliovirus and was detrimental to the recovery of rotavirus. Ultrafiltration or ultracentrifugation resulted in improved recovery of rotavirus but also in higher toxicity of oyster extracts to cell cultures. We recommend the use of the described elution-precipitation method for detecting viral pollutants in sample of oysters.     

Methods for recovering poliovirus and rotavirus from oysters

Polioviruses and rotaviruses are potential indicators of sewage pollution of water and shellfish. Several methods for detecting these viruses in oysters were assessed. Elution-precipitation involving Catfloc for clarification and skim milk for subsequent flocculation resulted in the recovery of an average of 79% of poliovirus type 1 and 37% of rotavirus SA-11 from oyster homogenates inoculated with low numbers of these viruses. Adsorption-elution-precipitation did not improve the recovery of poliovirus and was detrimental to the recovery of rotavirus. Ultrafiltration or ultracentrifugation resulted in improved recovery of rotavirus but also in higher toxicity of oyster extracts to cell cultures. We recommend the use of the described elution-precipitation method for detecting viral pollutants in sample of oysters.     

A new method for the determination of critical polyethylene glycol concentration for selective precipitation of DNA fragments

Separation strategies based on size-selective precipitation of DNA fragments with polyethylene glycol (PEG) have been used for achieving desired DNA interval in automated sample preparation for next-generation sequencing. By varying PEG concentration, DNA fragments of different sizes can be precipitated onto surfaces of carboxyl-coated paramagnetic particles selectively, and therefore, the desired DNA interval can be obtained. However, one of the crucial points in this approach is to determine the critical PEG concentration for DNA fragment of a certain size. The aim of this work was to develop a convenient and reliable method for accurately determining the critical PEG concentration. In our method, at a fixed concentration of sodium chloride (NaCl), recovered DNA samples obtained with different PEG concentrations were directly quantified, and their concentrations as a function of the PEG concentration were fitted by the logistic function. The critical PEG value was easily and accurately determined from the fitted logistic function. The repeatability and stability of the critical PEG value were assessed, showing an excellent reliability of the method. Based on this method, critical PEG values of different-size DNA fragments were determined at different NaCl concentrations. The effectiveness of the method was also demonstrated by selective precipitation of DNA fragments.     

Precipitation of S,M, X and Y potato viruses by polyethyleneglycols with different molecular weights

The minimum concentration of polyethyleneglycol (PEG) with molecular weights 4000, 6000, and 15000 necessary for precipitation of S, M, X and Y potato viruses was determined. An excessive amount of PEG causes the precipitation of other protein compounds from potato leaf cell sap. In order to obtain highly purified samples, it is necessary to use just the minimum sufficient amount of PEG. Using the minimum quantity of PEG is, also, advisable from an economical point of view. The minimum concentration of PEG of given molecular weight differs for different potato disease viruses. The concentration of PEG necessary for precipitation of a given potato virus depends on the molecular weight of PEG used—4000, 6000 and 15000. As the molecular weight increases, the concentration of PEG necessary for precipitation decreases.     

Purification of filamentous plant viruses by thin layer centrifugation.

The construction of a modified thin layer ultracentrifuge rotor is described. This rotor was used in the purification of five filamentous plant viruses, viz. TMV, SCMV, PVX, SGV and YMC. The purification and concentration of these viruses in their monomeric forms is hazardous when conventional "tube" rotors are used since they invariably result in dissociation and aggregation of the virus particles. Using the thin layer rotor these infective agents may be concentrated in volumes of fluid equal to approximately 1% of the starting suspension and not as pellets obtained after ultracentrifugation is conventional "tube" rotors. Electron microscopy revealed that the virus particles concentrated by thin layer centrifugation were not aggregated and that only few fragments of the virus filaments were present in the final preparations.     

Aqueous two-phase systems containing urea: influence on phase separation and stabilization of protein conformation by phase components.

During recombinant Escherichia coli fermentation with high expression levels, inclusion bodies are often formed. Aqueous two-phase systems have been used in the presence of urea for the initial recovery steps. To investigate phase behavior of such systems we determined phase diagrams of poly(ethylene glycol) (PEG)/sodium sulfate/urea/water and PEG/dextran T-500 (DEX)/urea/phosphate buffer/water at different concentrations of urea and different molecular weight of PEG. PEG/Na2SO4 aqueous two-phase systems could be obtained including up to 30% w/w urea at 25 degrees C and PEG/dextran T-500 up to 35% w/w urea. The binodial was displaced toward higher concentrations with increasing urea concentrations. The partition coefficient of urea was near unity. An unstable mutant of T4-lysozyme with an amino acid replacement in the core (V149T) was used to analyze the effect of phase components on the conformation of the enzyme. We showed that partitioning of tryptophan was not dependent on the concentration of urea in the phase system.     

噬菌体浓缩方法的比较

目的：对不同噬菌体浓缩方法进行比较。方法：采用PEG沉淀、PEG反透析、阴阳离子结合树脂、超滤等5种方法对T4、T7、N4等3类噬菌体进行浓缩对比试验;在此基础上,用浓缩效果较好的方法对土壤和河道污水样本中的噬菌体进行浓缩,观察浓缩效果。结果：上述5种方法对3类噬菌体均有浓缩效果;超滤的浓缩效果最好,其次是PEG反透析,PEG沉淀没有很好的浓缩效果;河水样本中噬菌体的回收率比土壤样本高。结论：可通过PEG反透析、超滤或两者相结合的方法,得到高浓度的有活性的噬菌体。     

HAV病毒液的3种浓缩方法比较

目的:对HAV病毒液的3种常见浓缩方法进行分析比较,为HAV病毒研究及规模化疫苗生产提供参考。方法:使用MILLIPORE PELLICON超滤、PEG 6000沉淀、蔗糖-甘油垫三种方法对纯化HAV病毒液进行浓缩,用ELISA方法对浓缩液进行抗原滴度检测,计算不同浓缩方法的回收率。结果:HAV病毒液经过7次超滤循环浓缩,平均回收率为86%;PEG浓缩方法回收率平均72.5%;蔗糖-甘油离心浓缩方法平均回收率53.3%。结论:蔗糖/甘油超离心法,集纯化浓缩一体,适用于样品量较少,需要高浓度样品的试验;PEG浓缩得率适中,操作简单,应用范围较广;超滤膜浓缩在大规模疫苗生产或样品量较大时适用,但需控制样品浓度及浓缩倍数不能太高,以免样品损失。     

HAV病毒液的3种浓缩方法比较

目的：对HAV病毒液的3种常见浓缩方法进行分析比较,为HAV病毒研究及规模化疫苗生产提供参考。方法：使用MILLIPOREPELLICON超滤、PEG6000沉淀、蔗糖．甘油垫三种方法对纯化HAV病毒液进行浓缩,用ELISA方法对浓缩液进行抗原滴度检测,计算不同浓缩方法的回收率。结果：HAV病毒液经过7次超滤循环浓缩,平均回收率为86％;PEG浓缩方法回收率平均72．5％;蔗糖．甘油离心浓缩方法平均回收率53．3％。结论：蔗糖／甘油超离心法,集纯化浓缩一体,适用于样品量较少,需要高浓度样品的试验;PEG浓缩得率适中,操作简单,应用范围较广;超滤膜浓缩在大规模疫苗生产或样品量较大时适用,但需控制样品浓度及浓缩倍数不能太高。以免样品损失。     

19. Purification of Filamentous Plant Viruses by Thin Layer Centrifugation (Applied to TMV,SCMV, PVX,SCV, and YMC Viruses)

ABSTRACT

The construction of a modified thin layer ultracentrifuge rotor is described. This rotor was used in the purification of five filamentous plant viruses, viz. TMV, SCMV, PVX, SCV and YMC. The purification and concentration of these viruses in their monomeric forms is hazardous when conventional "tube" rotors are used since they invariably result in dissociation and aggregation of the virus particles. Using the thin layer rotor these infective agents may be concentrated in volumes of fluid equal to approximately 1% of the starting suspension and not as pellets obtained after ultracentrifugation in conventional "tube" rotors. Electron microscopy revealed that the virus particles concentrated by thin layer centrifugation were not aggregated and that only few fragments of the virus filaments were present in the final preparations.