N-glycosylation analysis of mouse immunoglobulin G isolated from dried blood spots

The association of immunoglobulin G (IgG) glycosylation changes with various human diseases and physiological conditions is well established. Since the mechanistical explanation of the regulation of IgG glycosylation and its functional role in these various states is still missing, the eyes of the biomedical community are now turned towards animal models, which enable intervention studies necessary for conclusions on causality. Mice are recognized and used as a good experimental model for human IgG glycosylation. However, smaller blood volumes, low IgG concentrations at young ages (which are most often used in mice experiments) and multiple sampling protocols during the course of longitudinal studies would profit from a robust workflow for mouse IgG glycome analysis from minute amounts of starting material, collected through a simple sampling procedure. For this purpose, we have developed a protocol for analysis of total N-glycans of IgG isolated from mouse dried blood spots (DBS), which we report here. We show that mouse DBS are a good source of material for IgG N-glycan analysis by multiplexed capillary gel electrophoresis with laser-induced fluorescence (xCGE-LIF).     

Improved sample preparation for CE-LIF analysis of plant N-glycans

In view of glycomics studies in plants, it is important to have sensitive tools that allow one to analyze and characterize the N-glycans present on plant proteins in different species. Earlier methods combined plant-based sample preparations with CE-LIF N-glycan analysis but suffered from background contaminations, often resulting in non-reproducible results. This publication describes a reproducible and sensitive protocol for the preparation and analysis of plant N-glycans, based on a combination of the 'in-gel release method' and N-glycan analysis on a multicapillary DNA sequencer. Our protocol makes it possible to analyze plant N-glycans starting from low amounts of plant material with highly reproducible results. The developed protocol was validated for different plant species and plant cells.     

N-glycan analysis by CGE-LIF: profiling influenza A virus hemagglutinin N-glycosylation during vaccine production

Glycoproteins, such as monoclonal antibodies as well as recombinant and viral proteins produced in mammalian cell culture play an important role in manufacturing of many biopharmaceuticals. To ensure consisting quality of the corresponding products, glycosylation profiles have to be tightly controlled, as glycosylation affects important properties of the corresponding proteins, including bioactivity and antigenicity. This study describes the establishment of a method for analyzing N-glycosylation patterns of mammalian cell culture-derived influenza A virus glycoproteins used in vaccine manufacturing. It comprises virus purification directly from cell culture supernatant, protein isolation, deglycosylation, and clean-up steps as well as "fingerprint" analysis of N-glycan pools by CGE-LIF, using a capillary DNA-sequencer. Reproducibility studies of CGE-LIF, virus purification, and sample preparation have been performed. For demonstrating its applicability, the method was exemplarily used for monitoring batch-to-batch reproducibility in vaccine production, with respect to the glycosylation pattern of the membrane protein hemagglutinin of influenza A/PR/8/34 (H1N1) virus. This method allows characterization of variations in protein glycosylation patterns, directly by N-glycan "fingerprint" alignment.     

A microfluidic "baby machine" for cell synchronization

Common techniques used to synchronize eukaryotic cells in the cell cycle often impose metabolic stress on the cells or physically select for size rather than age. To address these deficiencies, a minimally perturbing method known as the "baby machine" was developed previously. In the technique, suspension cells are attached to a membrane, and as the cells divide, the newborn cells are eluted to produce a synchronous population of cells in the G1 phase of the cell cycle. However, the existing "baby machine" is only suitable for cells which can be chemically attached to a surface. Here, we present a microfluidic "baby machine" in which cells are held onto a surface by pressure differences rather than chemical attachment. As a result, our method can in principle be used to synchronize a variety of cell types, including cells which may have weak or unknown surface attachment chemistries. We validate our microfluidic "baby machine" by using it to produce a synchronous population of newborn L1210 mouse lymphocytic leukemia cells in G1 phase.     

Organ weaving: woven threads and sheets as a step towards a new strategy for artificial organ development

The concept of "organ weaving" is presented, a fabrication technique that can be an attractive option for the development of artificial tissues and organs. "Living threads" are created by immersing threads that are soaked in a CaCl(2) solution into a sodium-alginate-loaded cell suspension bath, encapsulating the cells and creating a bio-friendly, easily manageable starting material for building up larger scaffold structures. Such living threads have the advantage of being a particularly mild culturing medium for mammalian cells, protecting the cells during subsequent processing steps from dehydration and other rapid changes in the chemistry of the surrounding environment. Connecting different types of threads into 3D objects gives unique opportunities to address tissue engineering challenges.     

Dried polyacrylamide gel absorption: a method for efficient elimination of the interferences from SDS-solubilized protein samples in mass spectrometry-based proteome analysis

Sample preparation holds an important place in MS-based proteome analysis. For effective proteolysis and MS analysis, it is essential to eliminate the interferences while extracting the analytes of interest from complex mixtures. To address this, herein we describe a new dried polyacrylamide gel absorption method. In this method, the protein sample prepared using high concentration of SDS was directly and completely absorbed by vacuum-dried polyacrylamide gel, and then the interfering substances including SDS and some other salts were efficiently removed by in-gel washing steps while retaining the denatured proteins in the gel, thus offering a clean environment amenable to downstream buffer exchange, proteolytic digestion and digest recovery, etc. In combination with in-gel digestion and LC-MS/MS, the newly developed method was applied to the proteome analyses of membrane-enriched fraction and whole tissue homogenate. It was demonstrated that the method is suitable for the analysis of a complex biological sample and can be widely used for sample cleanup in shotgun proteome analyses.     

High Performance Liquid Chromatography of Nucleosides in RNA and DNA

Abstract

Reversed-phase high performance liquid chromatography has been developed and used effectively as a research tool for the quantitative analysis of major and modified nucleosides present in RNAs, DNAs, and physiological fluids. Gehrke et al. (5, 6, 24, 28) have shown that RP-HPLC is especially well suited for the analysis of the array of modified nucleosides found in tRNA, as more than forty nucleosides can be resolved and quantitatively determined in a single analysis. Coupled with our rapid, quantitative and straightforward enzymatic hydrolysis protocol, RP-HPLC compositional analyses can be directly performed on microgram quantities of either unfractionated or isoaccepting tRNAs. This method is applicable to the comparison of nucleoside compositions of tRNAs from parental and mutant organisms. In addition, Gehrke and Kuo (31, 33) have developed a highly precise RP-HPLC method for the analysis of the methylated nucleoside present in DNA, 5-methyldeoxycytidine, which has been used in collaborative research to measure differences in the extent of methylation of DNA from a range of cell and tissue types and DNA sequences. The deoxyribonucleoside 3′-and 5′-monophosphates, including pm⁵dC, are also well resolved by RP-HPLC, and this separation technique should prove of value in studies on sequence methylation in DNA. RP-HPLC analysis preceded by boronate gel selective isolation of ribonucleosides gives an effective technique for the analysis of ribonucleosides in physiological fluids, and a number of publications show that urinary nucleoside levels can serve as useful indicators of neoplastic disease status.     

A self-powered "sense-act-treat" system that is based on a biofuel cell and controlled by boolean logic

Bio-logic-al: an autonomous, integrated "sense-act-treat" system that is based on an enzymatic biofuel cell has been developed. The system couples a biocomputing logic-detection method with a drug-release system to provide a logic-activated therapeutic intervention in response to a simulated abnormal physiological state, without the need for an external power source, control electronics, or microelectromechanical actuators.     

A tag-less method for direct isolation of human umbilical vein endothelial cells by gravitational field-flow fractionation

The analysis of cellular and molecular profiles represents a powerful tool in many biomedical applications to identify the mechanisms underlying the pathological changes. The improvement of cellular starting material and the maintenance of the physiological status in the sample preparation are very useful. Human umbilical vein endothelial cells (HUVEC) are a model for prediction of endothelial dysfunction. HUVEC are enzymatically removed from the umbilical vein by collagenase. This method provides obtaining a good sample yield. However, the obtained cells are often contaminated with blood cells and fibroblasts. Methods based on negative selection by in vitro passages or on the use of defined marker are currently employed to isolate target cells. However, these approaches cannot reproduce physiological status and they require expensive instrumentation. Here we proposed a new method for an easy, tag-less and direct isolation of HUVEC from raw umbilical cord sample based on the gravitational field-flow fractionation (GrFFF). This is a low-cost, fully biocompatible method with low instrumental and training investments for flow-assisted cell fractionation. The method allows obtaining pure cells without cell culture procedures as starting material for further analysis; for example, a proper amount of RNA can be extracted. The approach can be easily integrated into clinical and biomedical procedures.     

Microwave-assisted extraction of solanesol from tobacco leaves

Solanesol is the starting material for many high-value biochemicals, including co-enzyme Q10 and Vitamin K analogues. In the present study, a microwave-assisted extraction (MAE) technique has been developed for the fast extraction of solanesol from tobacco leaves. Compared to heat-reflux extraction, MAE reduced extraction time and obtained higher percentage extracted of solanesol. The effect of microwave on cell destruction of plant material was observed by scanning electron microscopy (SEM). The microwave-assisted extraction efficiency was further improved by adding NaOH into the extraction solvent, and the maximum percentage extracted of solanesol reached 0.91% (weight solanesol/weight tobacco) in 40 min at an optimum NaOH concentration of 0.05 M. The developed MAE integrated with saponification process provided an efficient method for solanesol recovery from tobacco leaf materials, and it also alleviated emulsification in the following separation and purification procedure as well.     

Tris(hydroxymethyl)aminomethane-functionalized silica particles and their application for hydrophilic interaction chromatography

A new method is presented for synthesizing a highly hydrophilic silica-based material for use in hydrophilic interaction chromatography. Porous silica particles used as a starting substrate were modified with 3-bromopropyl trichlorosilane and grafted with glycidyl methacrylate by controlled ("living") atom transfer radical polymerization in order to introduce an oxirane-carrying reactive tentacle layer on the silica surface. The grafted material was thereafter subject to an oxirane ring opening reaction with tris(hydroxy-methyl)aminomethane in dimethylformamide to yield a polymer-bound equivalent of the well known and highly hydrophilic "TRIS" buffering substance. Chemical characterization was done by diffuse reflectance FT-IR, X-ray photoelectron spectroscopy, elemental analysis, and (1)H NMR. Porosity and surface area examination was done with Brunauer-Emmett-Teller. Chromatographic application of the material was evaluated by separations of nucleic bases, small organic acids, and common nucleotides under mixed hydrophilic interaction chromatography and weak anion exchange conditions.     

Sample preparation by in-gel digestion for mass spectrometry-based proteomics

The proteomic characterization of proteins and protein complexes from cells and cell organelles is the next challenge for investigation of the cell. After isolation of the cell compartment, three steps have to be performed in the laboratory to yield information about the proteins present. The protein mixtures must be separated into single species, broken down into peptides, and, finally, identified by mass spectrometry. Most scientists engaged in proteomics separate proteins by electrophoresis. For characterization and identification of proteomes, mass spectrometry of peptides is the method of choice. To combine electrophoresis and mass spectrometry, sample preparation by “in-gel digestion” has been developed. Many procedures are available for in-gel digestion, which inspired us to review in-gel digestion approaches. Figure Classical in-gel digestion process for a protein band stained with CBB. Protein bands are cut from the polyacrylamide gel (1). CBB molecules (blue circles) bound to the protein are released by iterative incubation in a buffered organic solvent system (2). To increase digestion efficiency and sequence coverage proteins are reduced (3) and alkylated (4). Proteins are subsequently digested with proteolytic enzymes (scissors symbols), typically trypsin (5). Trypsin cleaves at the amino acid residues arginine (R) and lysine (K). The resulting peptides (A, B, and C) are extracted from the polyacrylamide matrix (6). The peptide solution can be further purified for analysis by mass spectrometry (Section “Concentration and desalting of peptides”)     

One step microelectroelution concentration method for efficient coupling of sodium dodecylsulfate gel electrophoresis and matrix-assisted laser desorption time-of-flight mass spectrometry for protein analysis

The coupling of the widely used separation technique of conventional sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) with the mass accuracy measurement capability of mass Spectrometry (MS) provides a very powerful analytical technique. However, at present, there is no simple, definitive method for coupling the two methods. Typically, separated proteins are extracted from the gel, either as the native protein or as a peptide mixture after in-gel proteolytic digestion, and then analyzed by mass Spectrometry. However, the various extraction techniques described previously have been labor intensive and require a large number of steps. The mass Spectrometry analysis of very low concentrations of in vivo derived proteins requires minimum sample handling and on-line concentration. Therefore, we have developed an efficient microelectroelution technique that is applied in a single step manner and contains an on-line concentration device. Initial results from this system have shown a high efficiency of analyte elution from the gel and a simple, robust technique for the coupling of SDS-containing gels with MALDI-TOF-MS analysis and a capability of analyzing proteins at the subpicomole level.     

Peptidomic analysis of the larval Drosophila melanogaster central nervous system by two-dimensional capillary liquid chromatography quadrupole time-of-flight mass spectrometry

Peptides are the largest class of signalling molecules found in animals. Nevertheless, in most proteomic studies peptides are overlooked since they literally fall through the mazes of the net. In analogy with proteomics technology, where all proteins expressed in a cell or tissue are analyzed, the peptidomic approach aims at the simultaneous visualization and identification of the whole peptidome of a cell or tissue, i.e. all expressed peptides with their post-translational modifications. In this paper we describe the analysis of the larval fruit fly central nervous system using two-dimensional capillary liquid chromatography/quadrupole time-of-flight tandem mass spectrometry (LC/Q-TOF-MS/MS. Using the central nervous systems of only 50 larval Drosophila as starting material, we identified 38 peptides in a single analysis, 20 of which were not detected in a previous study that reported on the one-dimensional capillary LC/MS/MS analysis of the same tissue. Among the 38 sequenced peptides, some originate from precursors, such as the tachykinin and the IFamide precursor that were entirely missed in the first study. This clearly demonstrates that the two-dimensional capillary LC approach enhances the coverage of the peptidomic analysis.     

Solid-phase methylamidation for sialoglycomics by MALDI-MS

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been a major approach for glycan analysis. However, the preferential cleavage of the sialic acid moiety by in- and post-source decay influences the determination of sialylated glycans by MALDI-MS. Many chemical derivatization methods were introduced to stabilize the sialylated glycan during MALDI-MS. Among current derivatization methods, methylamidation is a promising means for simultaneous analysis of natural sialylated glycans regardless of their sialic acid linkage types. Here, a novel derivatization method was developed, in which proteins were conjugated on the solid-phase support in order to stabilize the sialic acids by methylamidation and to reduce sample loss and contamination during the derivatization process. This derivatization strategy was used to investigate N-glycans from fetuin, a glycoprotein containing different types of complex N-glycans. The developed method was also applied to the N-glycan profiling of human serum from patients and healthy volunteers. Results were consistent with N-glycan profiling by HPLC-fluorescence detection. This new method provided a sensitive, simple, and robust approach for profiling glycan structures of complex samples.     

A new approach for the removal of protein impurities from purified biologicals using combinatorial solid-phase ligand libraries

The removal of last impurity traces from a purified protein is generally called polishing. It is an important step in downstream processing since protein impurities may generate undesirable side effects when the preparation is intended for research, diagnostic and more importantly therapeutic applications. Polishing is generally achieved by using orthogonal separation methods to previous steps, the most common being gel permeation chromatography. In spite of its polishing effectiveness, this technique suffers from a poor separation capacity and modest productivity as a result of low speed. Other approaches, for instance, based on anion exchange or on hydrophobic chromatography, that may be optimized for a given process cannot be used as generic methods. This document reports for the first time the use of a combinatorial solid-phase peptide library as a general method for the removal of impurity traces. Several examples of impurity trace removal are reported; starting material is either a pure protein spiked with serum proteins or with Escherichia coli extracts or current purified proteins still containing a small percentage of impurities. Among polished proteins are recombinant human albumin expressed in Pichia pastoris and human transferrin purified from whole plasma. This new method is used in neutral or even physiological pH and ionic strength conditions, with a remarkable capability to remove impurities. The process is as rapid as current adsorption chromatography procedures usable for the removal of a large number of protein impurities, with each one present in small amounts, such as host cell proteins.     

Comprehensive native glycan profiling with isomer separation and quantitation for the discovery of cancer biomarkers

Glycosylation is highly sensitive to the biochemical environment and has been implicated in many diseases including cancer. Glycan compositional profiling of human serum with mass spectrometry has already identified potential biomarkers for several types of cancer and diseases; however, composition alone does not fully describe glycan stereo- and regioisomeric diversity. The vast structural heterogeneity of glycans presents a formidable analytical challenge. We have developed a method to identify and quantify isomeric native glycans using nanoflow liquid chromatography (nano-LC)/mass spectrometry. A microfluidic chip packed with graphitized carbon was used to chromatographically separate the glycans. To determine the utility of this method for structure-specific biomarker discovery, we analyzed serum samples from two groups of prostate cancer patients with different prognoses. More than 300 N-glycan species (including isomeric structures) were identified, corresponding to over 100 N-glycan compositions. Statistical tests established significant differences in glycan abundances between patient groups. This method provides comprehensive, selective, and quantitative glycan profiling.     

Aqueous fluoride and the preparation of [99mTc(CO)3(OH2)3]+ and 99mTc-carborane complexes

A method for the preparation of eta5-metallocarborane complexes of technetium-99m in water was developed. The key to the procedure is the use of aqueous sodium or potassium fluoride, which prevents premature degradation of the Tc(I) starting material used to prepare the carborane complexes. Solid-phase extraction was used to purify Tc-metallocarboranes derived from both ortho and meta isomers, which were isolated in good to excellent yields in high radiochemical purities. In conjunction with these studies, a series of fluoride-based "kits" were developed to produce the key precursor [99mTc(CO)3(H2O)3]+ in the absence of any other stabilizing ligand. Using this approach, [99mTc(CO)3(H2O)3]+ could be prepared directly from 99mTcO4- under a range of pH values, including neutral pH, which affords the opportunity to develop one-pot labeling procedures for base-sensitive targeting vectors.     

Patterning the surface cytophobicity of an albumin-physisorbed substrate by electrochemical means

Spatiotemporal control of surface properties under physiological conditions such as those found in culture media is an important technique in fundamental cell biology, tissue engineering, and cell-based bioelectronics. To this end, we have developed a mild, wet cellular micropatterning technique. The principle of the technique is based on the fact that the cell-repellant property of the albumin-coated substrate rapidly switches to cell-adhesive upon exposure to the reactive oxidizing agent, electrochemically generated hypobromous acid. Herein, we report the effect of the hypobromous acid on serum albumin physisorbed on a hydrophobic substrate. It was found that albumin molecules detach from the substrate by application of the oxidizing agent, resulting in exposure of the underlying hydrophobic surface to the liquid phase. The adsorption of extracellular matrix proteins such as fibronectin onto the hydrophobic surface induces cell adhesion and growth.     

Enhanced Detection of Ubiquitin Isopeptides Using Reductive Methylation

Identification of ubiquitination (Ub) sites is of great interest due to the critical roles that the modification plays in cellular regulation. Current methods using mass spectrometry rely upon tryptic isopeptide diglycine tag generation followed by database searching. We present a novel approach to ubiquitin detection based upon the dimethyl labeling of isopeptide N-termini glycines. Ubiquitinated proteins were digested with trypsin and the resulting peptide mixture was derivatized using formaldehyde-D2 solution and sodium cyanoborohydride. The dimethylated peptide mixtures were next separated by liquid chromatography and analyzed on a quadrupole-TOF based mass spectrometer. Diagnostic b2′ and a1′ ions released from the isopeptide N-terminus upon collision-induced dissociation (CID) were used to spectrally improve the identification of ubiquitinated isopeptides. Proof of principle was established by application to a ubiquitinated protein tryptic digest spiked into a six-protein mix digest background. Extracted ion chromatograms of the a1′ and b2′ diagnostic product ions from the diglycine tag resulted in a significant reduction in signal complexity and demonstrated a selectivity towards the identification of diglycine branched isopeptides. The method was further shown to be capable of identifying diglycine isopeptides resulting from in-gel tryptic digests of ubiquitin enriched material from a His-Ub transfected cell line. We envisage that these ions may be utilized in global ubiquitination studies with post-acquisition MS/MS (or MSe) data interrogation on high resolution hybrid mass spectrometers.