Assay for Rab geranylgeranyltransferase using size exclusion chromatography

A simple chromatographic assay for Rab geranylgeranyltransferase (Rab GGTase) has been developed. The method involves separation of the reaction mixture on a Sephadex G-25 superfine minicolumn. Addition of 2-propanol to the assay results in substantial (approximately 90%) decline of formation of noncovalent lipid-protein complexes, increasing reproducibility and reliability of the method. The activity of Rab prenyltransferase was measured in crude and partially purified enzyme preparations from wheat seedlings; measurements for several other plants and rat brain cytosol fractions are also presented. This method can be routinely applied to evaluate the activity of different protein prenyltransferases.     

Multidimensional proteomics of human serum using parallel chromatography of native constituents and microplate technology

A versatile, multidimensional, and non-denaturing proteome separation procedure using microplate technology is presented, yielding a digitized image of proteome composition. In the first dimension, the sample under study is separated into 96 fractions by size exclusion chromatography (SEC). In the second dimension, the fractions of the first dimension are transferred by the liquid-handling device CyBi-Well (CyBio AG, Jena, Germany) to 96 parallel anion exchange chromatography columns. In this way the proteins are conserved in their native states and are distributed in 2400 liquid fractions with high recovery rates and sufficient reproducibility. The resulting fractions are subjected to protein quantitation and identification. Spectrophotometrical and immunological methods and enzyme activity measurements are used for quantitation. To identify proteins, the fractions are subjected to MALDI-MS, and their tryptic digests to both MALDI- and LC-ESI-MS/MS. All preparation steps except the first are applied in parallel to sets of multiples of 96 samples. The procedure may be refined by adding more separation steps and may be adapted to various protein amounts and to various proteomes. Moreover, the method offers the opportunity to investigate functional protein complexes. The method was applied to separate the normal human serum proteome. Within 255 fractions exhibiting the highest protein concentrations, 742 proteins were identified by LC-ESI-MS/MS peptide sequence tags.     

Frozen tissue can provide reproducible proteomic results of subcellular fractionation

Differential detergent fractionation (DDF) is frequently used to partition fresh cells and tissues into distinct compartments. We have tested whether DDF can reproducibly extract and fractionate cellular protein components from frozen tissues. Frozen kidneys were sequentially extracted with three different buffer systems. Analysis of the three fractions with liquid chromatography–tandem mass spectrometry (LC–MS/MS) identified 1693 proteins, some of which were common to all fractions and others of which were unique to specific fractions. Normalized spectral index (SI_N) values obtained from these data were compared to evaluate both the reproducibility of the method and the efficiency of enrichment. SI_N values between replicate fractions demonstrated a high correlation, confirming the reproducibility of the method. Correlation coefficients across the three fractions were significantly lower than those for the replicates, supporting the capability of DDF to differentially fractionate proteins into separate compartments. Subcellular annotation of the proteins identified in each fraction demonstrated a significant enrichment of cytoplasmic, cell membrane, and nuclear proteins in the three respective buffer system fractions. We conclude that DDF can be applied to frozen tissue to generate reproducible proteome coverage discriminating subcellular compartments. This demonstrates the feasibility of analyzing cellular compartment-specific proteins in archived tissue samples with the simple DDF method.     

Combinatorial use of offline SCX and online RP-RP liquid chromatography for iTRAQ-based quantitative proteomics applications

Extensive front-end separation is usually required for complex samples in bottom-up proteomics to alleviate the problem of peptide undersampling. Isobaric Tags for Relative and Absolute Quantification (iTRAQ)-based experiments have particularly higher demands, in terms of the number of duty cycles and the sensitivity, to confidently quantify protein abundance. Strong cation exchange (SCX)/reverse phase (RP) liquid chromatography (LC) is currently used routinely to separate iTRAQ-labeled peptides because of its ability to simultaneously clean up the iTRAQ reagents and byproducts and provide first-dimension separation; nevertheless, the low resolution of SCX means that peptides can be redundantly sampled across fractions, leading to loss of usable duty cycles. In this study, we explored the combinatorial application of offline SCX fractionation with online RP-RP applied to iTRAQ-labeled chloroplast proteins to evaluate the effect of three-dimensional LC separation on the overall performance of the quantitative proteomics experiment. We found that the higher resolution of RP-RP can be harnessed to complement SCX-RP and increase the quality of protein identification and quantification, without significantly impacting instrument time and reproducibility.     

Analytical Procedures for the Sequential Extraction of 14C-Labeled Constituents from Leaves, Bark and Wood of Cottonwood Plants

A procedure for the extraction, separation, and measurement of photosynthetically fixed ¹⁴C in up to 8 chemical fractions (CHCl), amino acids, organic acids, sugars, protein, starch, hemicellulose, and residue) from small samples (1 to 100 mg) of cottonwood (Populus deltoides Bartr.) leaf material is described. The different chemical fractions are extracted in a sequence of chemical, ion exchange, and enzymatic steps. The ¹⁴C-activity in these major fractions is then determined with liquid scintillation spectrometry. These major fractions (e.g., sugars, amino acids, organic acids) can be further separated into their individual chemical components by standard thin-layer or gas- chromatographic methods for quantitative analysis if specific activities are desired. The major advantage of the procedure is that many chemical fractions can be sequentially separated with good reproducibility from a small amount of plant material without transfer of the material from the original homogenizer or centrifuge tube.     

Ultrastructural studies of peripheral blood lymphocytes in T cell-depleted rabbits

Summary Density separation of purified peripheral blood leucocytes from T-cell depleted rabbits on a linear Ficoll-metrizoate gradient has been applied to obtain different leucocyte fractions. Two lymphocyte fractions separated on density seem to have different characteristics, both morphologically and immunologically. In this study these two fractions have been characterized ultrastructurally by using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and a relationship has been established between the surface architecture (SEM), the cell size (SEM/TEM) and surface-Ig/C₃-receptors (LM, light microscopy). Finally three types of lymphocytes have been described in the two lymphocyte fractions separated on density. Morphometric information such as cell size, cell shape, eu-/heterochromatin ratio in the nucleus and the nucleus-/cell ratio have been correlated to the stage of activation of the B lymphocyte in a representative density separation.     

Laboratory database to manage electrophoresis and chromatography separations and the associated samples

A database was developed to store, organize, and retrieve the data associated with electrophoresis and chromatography separations. It allows laboratories to store extensive data on separation techniques (analytical and preparative). The data for gel electrophoresis includes gel composition, staining methods, electric fields, analysis, and samples loaded. The database stores data on chromatography conditions, the samples used, and the fractions collected. The data structure of this database was designed to maintain the link between samples (including fractions) from chromatography separations and their analysis by gel electrophoresis. The database will allow laboratories to organize and maintain a large amount of separation and sample data in a uniform data environment. It will facilitate the retrieval of the separation history of important samples and the separation conditions used.     

温度梯度凝胶电泳技术及应用

温度梯度凝胶电泳（TGGE）是一种用于检测核酸序列变异和点突变的电泳方法.该法利用不同构象的核酸分子具有不同的变性温度（T_m)来进行分离.TGGE方法具有分辨能力高、重复性好和节省时间的特点,可广泛应用于分子生物学研究领域.     

Purification of plant complex protein extracts in non-denaturing conditions by in-solution isoelectric focusing

An alternative approach for plant complex protein extracts pre-purification by in-solution isoelectric focusing in non-denaturing conditions is presented. The separation of biologically active proteins, in narrow ranges of isoelectric point (pI) was obtained by a modified OFFGEL electrophoresis. Two different water-soluble protein extracts from Phragmites leaves were fractionated into 24 fractions within a 3–10 pI range at 10 °C in the absence of denaturing/reducing agents. One-dimensional electrophoretic analysis revealed different protein distribution patterns and the effective fractionation of both protein extracts. Peroxidase activity of each fraction confirmed that proteins remained active and pre-purification occurred. Biological triplicates assured the needed reproducibility.     

Gradient fractionation of cycling and resting cells monitored by BrdUrd incorporation

A number of techniques are currently employed for the fractionation of heterogeneous cell populations or for the separation of cells in different phases of their cycle. With the development of osmotically inert colloidal silica particles media, density gradient centrifugation became an established method for the separation and purification of cells and subcellular particles. We have applied this technique to the separation of cycling from resting Friend erythroleukemia cells, to obtain purified populations for further biological assays. The flow cytometric analysis of DNA content of the different fractions obtained by the gradient and stained with Propidium Iodide (PI), showed the S compartment highly concentrated in the 1.073/77 g/ml interface, while the upper levels of the gradient were highly enriched of cells in G1 phase. Moreover, the dual parameter analysis of DNA content by means of Bromodeoxyuridine (BrdUrd) incorporation and PI staining, showed that part of the cells in the 1.067/73 fraction represented the early S phase even if their DNA level, measured on the basis of PI fluorescence was within the diploid cell cluster. This method seems to be suitable to obtain pure cell fractions even when dealing with numerically large populations.     

肠道病毒71型感染前后宿主细胞蛋白质组的二维液相色谱分离和比较

以肠道病毒71型及其宿主细胞为研究主体,建立了一种二维液相色谱分离和分析比较病毒感染前后细胞蛋白表达谱的方法。该方法以高效液相色谱(HPLC)为技术平台,对细胞裂解物先后进行一维色谱聚焦分离和二维反相色谱分离。利用ProteoVue软件将二维色谱数据转换成模拟胶图,再利用DeltaVue软件对感染前后的宿主蛋白表达谱进行比较和分析,找出差异蛋白。二维液相色谱分离法能够根据蛋白的等电点和疏水性建立精确的细胞蛋白表达图谱,每0．2个pH为一个收集区段,在pH8．5～3．9的范围内可见蛋白条带约1200条。该方法良好的重现性、自动化以及结果分析的简易化,使之在细胞表达谱差异显示中的应用潜力巨大,并且为研究病毒与宿主相互作用提供了新的方法和思路。     

Inter Subject Variability and Reproducibility of Diffusion Tensor Imaging within and between Different Imaging Sessions

The aim of these studies was to provide reference data on intersubject variability and reproducibility of diffusion tensor imaging. Healthy volunteers underwent imaging on two occasions using the same 3T Siemens Verio magnetic resonance scanner. At each session two identical diffusion tensor sequences were obtained along with standard structural imaging. Fractional anisotropy, apparent diffusion coefficient, axial and radial diffusivity maps were created and regions of interest applied in normalised space. The baseline data from all 26 volunteers were used to calculate the intersubject variability, while within session and between session reproducibility were calculated from all the available data. The reproducibility of measurements were used to calculate the overall and within session 95% prediction interval for zero change. The within and between session reproducibility data were lower than the values for intersubject variability, and were different across the brain. The regional mean (range) coefficient of variation figures for within session reproducibility were 2.1 (0.9–5.5%), 1.2 (0.4–3.9%), 1.2 (0.4–3.8%) and 1.8 (0.4–4.3%) for fractional anisotropy, apparent diffusion coefficient, axial and radial diffusivity, and were lower than between session reproducibility measurements (2.4 (1.1–5.9%), 1.9 (0.7–5.7%), 1.7 (0.7–4.7%) and 2.4 (0.9–5.8%); p<0.001). The calculated overall and within session 95% prediction intervals for zero change were similar. This study provides additional reference data concerning intersubject variability and reproducibility of diffusion tensor imaging conducted within the same imaging session and different imaging sessions. These data can be utilised in interventional studies to quantify change within a single imaging session, or to assess the significance of change in longitudinal studies of brain injury and disease.     

Chemical and biochemical variation in animal manure solids separated using different commercial separation technologies

Chemical and biochemical properties were investigated in 47 solids collected from commercial solids separation plants separating liquid manure into a nutrient-rich solid fraction and a nutrient-poor liquid fraction. The samples originated from five different types of separation technologies, separating primarily swine manure and anaerobically digested manure. The largest variations in measured chemical and biochemical characteristics between samples from the five different separation technologies were found for ash, total P, total C, DM and C distribution in the biochemical fractions (neutral detergent solubles (NDS), hemicellulose, cellulose and lignin). Principal component analysis (PCA) of the data obtained showed that the chemical and biochemical characteristics of the solids were dependent on the type of technology used for separation.     

Immunoreactive evidence of beta-endorphin and methionine-enkephalin-Arg-Gly-Leu in human tooth pulp

For the first time, beta-endorphin-like immunoreactivity (BE-LI) has been measured in human tooth pulp. Separation of peptides from pulp tissue was achieved by acid extraction followed by chromatographic separation through a Sep-Pak disposable cartridge. Reversed phase high performance liquid chromatographic (RP-HPLC) was performed on the peptide-rich fractions for further peptide separation. Radioreceptor assay (RRA) data of the HPLC fractions was used to construct a profile of opioid-receptor active peptides. Radioimmunoassay (RIA) data provided further information. Following acute mechanical stress, a monotonic decrease in BE-LI concentrations was evident according to a four bicuspid extraction order.     

Gradient fractionation of cycling and resting cells monitored by BrdUrd incorporation

Summary A number of techniques are currently employed for the fractionation of heterogeneous cell populations or for the separation of cells in different phases of their cycle. With the development of osmotically inert colloidal silica particles media, density gradient centrifugation became an established method for the separation and purification of cells and subcellular particles. We have applied this technique to the separation of cycling from resting Friend erythroleukemia cells, to obtain purified populations for further biological assays. The flow cytometric analysis of DNA content of the different fractions obtained by the gradient and stained with Propidium lodide (PI), showed the S compartment highly concentrated in the 1.073/77g/ml interface, while the upper levels of the gradient were highly enriched of cells in G₁ phase. Moreover, the dual parameter analysis of DNA content by means of Bromodeoxyuridine (BrdUrd) incorporation and PI staining, showed that part of the cells in the 1.067/73 fraction represented the early S phase even if their DNA level, measured on the basis of PI fluorescence was within the diploid cell cluster. This method seems to be suitable to obtain pure cell fractions even when dealing with numerically large populations.     

Isolation of plasma membranes from cultured glioma cells and application to evaluation of membrane sphingomyelin turnover

A rapid and reliable method for the isolation of plasma membranes and microsomes of high purity and yield from cultured glioma cells is described. The procedure involves disruption by N2 cavitation, preliminary separation by centrifugation in Tricine buffer, and final separation on a gradient formed from 40% Percoll at pH 9.3. Enzyme and chemical markers indicated greater than 60% yield with six- to eightfold enrichment for plasma membranes and greater than 25% yield with three- to fourfold enrichment for a microsomal fraction consisting mainly of endoplasmic reticulum. The final fractions were obtained with high reproducibility in less than 1 h from the time of cell harvesting. Application of this procedure to human fibroblasts in culture is assessed. The isolation procedure was applied to investigations of synthesis and turnover of sphingomyelin and phosphatidylcholine in plasma membranes of glioma cells following incubation for 4-24 h with [methyl-3H]choline. These studies indicated that radioactivity from phosphatidylcholine synthesized in microsomes from exogenous choline may serve as a precursor of the head-group of sphingomyelin accumulating in the plasma membrane.     

Proteome profile of human urine with two-dimensional liquid phase fractionation

Two-dimensional liquid chromatography separation (2-DL), based on chromatofocusing for first dimension and hydrophobicity for second, can be used as a complementary method to two-dimensional gel electrophoresis (2-DE). A platform now available, ProteomeLab PF 2D provided by Beckman Coulter, (Fullerton, CA, USA), assembles these methods in automation. This system was applied to resolve large numbers of urine proteins. Reproducibility and sensitivity in protein resolution were evaluated in this study using urines collected from male blood donors. About 1000 peaks were detected at a pH range of 4.0-8.5 by applying 1 mg of proteins. Furthermore, the same fractions showing peaks with high absorbance intensities in second dimension were collected and subjected to matrix-assisted laser desorption/ionization-time of flight/mass spectrometry analysis for identification. The results showed that the 2-DL provides high reproducibility of two-dimensional protein map, and lends fractions to subsequent mass spectrometry analysis without the further need for extraction or solubilization of samples as required for spots excised from 2-DE gels. In addition, this system also allows to separate particularly proteins with 40-9 kDa molecular weight.     

Solids and nutrients removals from the liquid fraction of swine slurry through screening and flocculation treatment and influence of these processes on anaerobic biodegradability

A correct separation of solids from liquid fraction is crucial for a successful treatment of swine manure. For this reason an in-depth study of flocculant addition on different livestock wastewaters was carried out. Two flushed swine manure matrices, namely the mixture from nursery and feeder-to-finish pigs and the feeder-to-finish slurry alone, were tested for solids and nutrients removals from liquid fractions. The separation techniques applied were sieving and flocculation. A range of 80-200 ppm of polyacrylamide (PAM) followed by screening was employed in the case of flocculation treatment. The best results were observed when using the highest PAM dose in the matrix correspondent to the mixture of slurries. The removal rates in the liquid fraction were 73% for total solids, 87% for volatile solids, 98% for suspended total and volatile solids, 71% for chemical oxygen demand, 40% for total Kjeldahl nitrogen, and 34% for soluble phosphorus. Once the best PAM dose (120 ppm) was chosen, an anaerobic biodegradability study was performed in order to check the increase of methane production in the separated fractions by using the flocculant and the screen. The assay determined that the solid fractions biodegradability was constant at 79%. Meanwhile for the liquid fractions, an increase of 9% points was achieved with PAM-amendment when compared with 82% reached for the liquid fraction obtained by screening.     

Differentiation of endopeptidases and aminopeptidases by high-performance liquid chromatography of reaction products from chromogenic peptide p-nitroanilines as substrates

A method for differentiating endopeptidases and aminopeptidases on the basis of substrate specificity is presented. Various synthetic chromogenic substrates, succinyl-(Ala)3-p-nitroaniline, succinyl-(Ala)2-p-nitroaniline, (Ala)3-p-nitroaniline, and (Ala)2-p-nitroaniline, were incubated with various peptidases and the incubation mixtures were directly analyzed by high-performance liquid chromatography to determine the splitting patterns of these substrates by the enzymes. The substrates and hydrolyzed products containing the chromophore were separated on a reverse-phase column under isocratic conditions, and the chromophore was specifically detected in the effluent fractions by absorbance measurement at 314 nm. Endopeptidases, leucine aminopeptidase, and dipeptidyl aminopeptidase showed different patterns of cleavage of the substrates. This simple and rapid high-performance liquid chromatographic procedure is suitable for identifying the above activities in different fractions obtained during separation and purification studies. The same approach was applied to the simultaneous determination of three types of endopeptidase activities in rat tissues based on the ability of the enzymes to hydrolyze different sites in succinyl-(Ala)3-p-nitroaniline.