Nonenzymatic release of free reducing glycans from glycosphingolipids

A major limitation in studying the structures and functions of glycans in glycosphingolipids is the difficulty in releasing free glycans for analysis and derivatization. Here we show that reducing glycans can be released nonenzymatically from glycosphingolipids after a brief treatment with ozone followed by heating in neutral aqueous buffer (pHs 6.0-8.0). The released free reducing glycans are then available for glycomic analyses, including fluorescent labeling, permethylation, and mass spectrometry. This procedure is simple and highly efficient, with no base-catalyzed "peeling" reaction by-products observed.     

Versatile fluorescent derivatization of glycans for glycomic analysis

The new field of functional glycomics encompasses information about both glycan structure and recognition by carbohydrate-binding proteins (CBPs) and is now being explored through glycan array technology. Glycan array construction, however, is limited by the complexity of efficiently generating derivatives of free, reducing glycans with primary amines for conjugation. Here we describe a straightforward method to derivatize glycans with 2,6-diaminopyridine (DAP) to generate fluorescently labeled glycans (glycan-DAP conjugates or GDAPs) that contain a primary amine for further conjugation. We converted a wide variety of glycans, including milk sugars, N-glycans, glycosaminoglycans and chitin-derived glycans, to GDAPs, as verified by HPLC and mass spectrometry. We covalently conjugated GDAPs to N-hydroxysuccinimide (NHS)-activated glass slides, maleimide-activated protein, carboxylated microspheres and NHS-biotin to provide quantifiable fluorescent derivatives. All types of conjugated glycans were well-recognized by appropriate CBPs. Thus, GDAP derivatives provide versatile new tools for biologists to quantify and covalently capture minute quantities of glycans for exploring their structures and functions and generating new glycan arrays from naturally occurring glycans.     

Shotgun glycomics: a microarray strategy for functional glycomics

Major challenges of glycomics are to characterize a glycome and identify functional glycans as ligands for glycan-binding proteins (GBPs). To address these issues we developed a general strategy termed shotgun glycomics. We focus on glycosphingolipids (GSLs), a class of glycoconjugates that is challenging to study, recognized by toxins, antibodies and GBPs. We derivatized GSLs extracted from cells with a heterobifunctional fluorescent tag suitable for covalent immobilization. We separated fluorescent GSLs by multidimensional chromatography, quantified them and coupled them to glass slides to create GSL shotgun microarrays. Then we interrogated the microarrays with cholera toxin, antibodies and sera from individuals with Lyme disease to identify biologically relevant GSLs that we subsequently characterized by mass spectrometry. Shotgun glycomics incorporating GSLs and potentially glycoprotein-derived glycans is an approach for accessing the complex glycomes of animal cells and is a strategy for focusing structural analyses on functionally important glycans.     

Tools for glycomics: relative quantitation of glycans by isotopic permethylation using 13CH3I

Analysis of oligosaccharides by mass spectrometry (MS) has enabled the investigation of the glycan repertoire of organisms with high resolution and sensitivity. It is difficult, however, to correlate the expression of glycosyltransferases with the glycan structures present in a particular cell type or tissue because the use of MS for quantitative purposes has significant limitations. For this reason, in order to develop a technique that would allow relative glycan quantification by MS analysis between two samples, a procedure was developed for the isotopic labeling of oligosaccharides with (13)C-labeled methyl iodide using standard permethylation conditions. Separate aliquots of oligosaccharides from human milk were labeled with (12)C or (13)C methyl iodide; the labeled and non-labeled glycans were mixed in known proportions, and the mixtures analyzed by MS. Results indicated that the isotopic labeling described here was capable of providing relative quantitative data with a dynamic range of at least two orders of magnitude, adequate linearity, and reproducibility with a coefficient of variation that was 13% on average. This procedure was used to analyze N-linked glycans released from various mixtures of glycoproteins, such as alpha-1 acid glycoprotein, human transferrin, and bovine fetuin, using MS techniques that included matrix assisted laser desorption ionization-time of flight MS and electrospray ionization with ion cyclotron resonance-Fourier transformation MS. The measured (12)C:(13)C ratios from mixtures of glycans permethylated with either (12)CH(3)I or (13)CH(3)I were consistent with the theoretical proportions. This technique is an effective procedure for relative quantitative glycan analysis by MS.     

Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy

Several chronic viral infections (such as HIV and hepatitis C virus) are highly prevalent and are a serious health risk. The adaptation of animal viruses to the human host, as recently exemplified by influenza viruses and the severe acute respiratory syndrome coronavirus, is also a continuous threat. There is a high demand, therefore, for new antiviral lead compounds and novel therapeutic concepts. In this Review, an original therapeutic concept for suppressing enveloped viruses is presented that is based on a specific interaction of carbohydrate-binding agents (CBAs) with the glycans present on viral-envelope glycoproteins. This approach may also be extended to other pathogens, including parasites, bacteria and fungi.     

Dual-gradient high-performance liquid chromatography for identification of cytosolic high-mannose-type free glycans

It has been shown that free oligosaccharides derived from N-linked glycans accumulate in the cytosol of animal cells. Most of the glycans have only a single GlcNAc at their reducing termini (Gn1 glycans), whereas the original N-glycans retain N,N′-diacetylchitobiose at their reducing termini (Gn2 glycans). Under the conditions of high-performance liquid chromatography (HPLC) mapping established for pyridylamine (PA)-labeled Gn2 N-glycans, Gn1 glycans are not well retained on reversed-phase HPLC, making simultaneous analysis of Gn1 and Gn2 glycans problematic. We introduced a dual gradient (i.e., pH and butanol gradient) for the separation of Gn1 and Gn2 glycans in a single reversed-phase HPLC. Determination of elution time for various standard Gn2 high-mannose-type glycans, as well as Gn1 glycans found in the cytosol of animal cells, showed that elution of Gn1 and Gn2 glycans could be separated. Sufficient separation for most of the structural isomers could be achieved for Gn1 and Gn2 glycans. This HPLC, therefore, is a powerful method for identification of the structures of PA-labeled glycans, especially Gn1-type glycans, isolated from the cytosol of animal cells.     

Enantiomeric determination of amphetamines: exploring a novel one-step solid-phase microextraction-based approach

The recent advances in fiber manufacturing technology, solid-phase microextraction (SPME) is now widely studied for its effectiveness for the pretreatment of various categories of samples. This study explores a novel SPME approach for enantiomeric analysis of amphetamines, in which absorption/derivatization are accomplished in one step. Specifically, (S)-(-)-N-(Trifluoroacetyl)-prolyl chloride was adopted as the chiral derivatizing reagent and added directly into the sample matrix. Analytical parameters, such as temperature, absorption/desorption duration, and the amount of derivatizing reagent, were studied to determine their effects on the yield of analytes. The derivatization products resulting from this study show excellent desorption characteristics on the polydimethylsiloxane-coated fiber adopted in this study. Optimal operational parameters (absorption: 70 degrees C for 10 min; injection: 250 degrees C for 5 min) cause minimal negative impact on the fiber, allowing repeated use of the fiber for more than 30 times. For quantitation, data were collected under selected ion monitoring (SIM) mode using m/z 237 and 251 to designate derivatized amphetamine and methamphetamine. This method was evaluated and proved to be effective in (a) quantitative determination of the enantiomeric pairs of amphetamine and methamphetamine--in terms of repeatability, linearity, and limits of detection and quantitation; and (b) generating case-specimen data comparable to those derived from a conventional Liquid-liquid extraction approach. Good linearity for the calibration curves were established in the range of 1000-50 ng/mL for both analytes. The limits of detection for these analytes were 30 ng/mL.     

A self-cleavable sortase fusion for one-step purification of free recombinant proteins

A new protein fusion system has been developed to generate free recombinant protein in a single affinity chromatographic step. The key component in the fusion is the catalytic core of sortase A from Staphylococcus aureus (SrtAc), which recognizes and cleaves the Thr-Gly bond at an LPXTG sequence with moderate activity. The fusion here consists of an N-terminal His6 tag, SrtAc, and an LPETG linker followed by protein of interest at the C-terminus. The fusion protein is expressed in Escherichia coli and purified by immobilized metal-ion affinity chromatography (IMAC). The immobilized fusion then undergoes on-column SrtAc-mediated cleavage at the LPETG site in the presence of Ca2+ and/or triglycine. The target protein with an extra N-terminal glycine is released from the fusion while the N-terminal portion remains bound to the column. Because the cleavage enzyme SrtAc is co-expressed as a fusion with the target protein, the purification system eliminates exogenous proteolysis. This purification approach is simple, robust, inexpensive, time saving, and allows purification of free recombinant protein via one-step chromatography.     

NBD-isocolcemid-tubulin interaction: a novel one-step reaction involving no conformational adjustment of reactants

Isocolcemid, a colcemid analogue in which the positions of the C-ring methoxy and carbonyl are exchanged, is virtually inactive in binding to tubulin and inhibiting the formation of microtubule assembly. We have found that the substitution of a NBD group in the side chain of the B-ring of isocolcemid can reverse the effect of these structural alterations (at the C-ring) and the newly synthesized NBD-isocolcemid restores the lost biological activity. It inhibits microtubule assembly with an IC(50) of 12 microM and competes efficiently with [(3)H]colchicine, for binding to tubulin. NBD-isocolcemid has two binding sites on tubulin; one is characterized by fast binding, whereas the binding to the other site is slow. These two sites are independent and unrelated to each other. Colchicine and its analogues compete with NBD-isocolcemid for the slow site. Association and dissociation rate constants for the fast site, obtained from the stopped-flow measurements, are (7.37 +/- 0. 70) x 10(5) M(-1) s(-1) and 7.82 +/- 2.74 s(-1), respectively. While the interaction of colchicine and its analogues with tubulin involves two steps, NBD-isocolcemid binding to tubulin at the slow site has been found to be a one-step reaction. This is evident from the linear dependence of the observed rate constant (k(obs)) with both NBD-isocolcemid and tubulin concentrations. The interaction of NBD-isocolcemid with tubulin does not involve the conformational change of NBD-isocolcemid, as is evident from the unchanged CD spectra of the drug. The absence of enhanced GTPase activity of tubulin and the native-like protease cleavage pattern of the NBD-isocolcemid-tubulin complex suggest an unaltered conformation of tubulin upon NBD-isocolcemid binding to it as well. Implications of this on the mechanism of polymerization inhibition have been discussed.     

Heterobifunctionalized tetraethylene glycol: A spacer for surface attachment of viral peptide epitopes for ELISA and derivatization of membrane modifying peptides

New hydrophilic linkers of the formula Fmoc- NHCH2CH2COO(CH2CH2O)4X (X = COCH2CH2COOH Fmoc-Ats (2), X = CONHCH2COOH Fmoc-Atg (4), and X = CONHCH2CH2COOH Fmoc-Ata (5)) have been prepared by heterobifunctional modification of tetraethylene glycol as starting material. These linkers represent a useful tool for solid phase peptide synthesis according to Fmoc/tBu strategy. Two examples are presented to illustrate the applicability of these building blocks: (i) spacing between biotin and a peptide epitope of the hepatitis C virus and evaluation in a biotin- streptavidin ELISA, and (ii) coupling of the new linker to the N- and C-terminus of the peptide antibiotic alamethicin to show eventual influences on the peptide's -helical conformation.     

Heterobifunctionalized tetraethylene glycol: A spacer for surface attachment of viral peptide epitopes for ELISA and derivatization of membrane modifying peptides

Summary New hydrophilic linkers of the formula Fmoc-NHCH₂CH₂COO(CH₂CH₂O)₄X (X=COCH₂CH₂COOH Fmoc-Ats (2), X=CONHCH₂COOH Fmoc-Atg (4) and X=CONHCH₂CH₂COOH Fmoc-Ata (5) have been prepared by heterobifunctional modification of tetraethylene glycol as starting material. These linkers represent a useful tool for solid phase peptide synthesis according to Fmoc/tBu strategy. Two examples are presented to illustrate the applicability of these building blocks: (i) spacing between biotin and a peptide epitope of the hepatitis C virus and evaluation in a biotin-streptavidin ELISA, and (ii) coupling of the new linker to the N- and C-terminus of the peptide antibiotic alamethicin to show eventual influences on the peptide's α-helical conformation.     

Identification of a novel type of spacer element required for imprinting in fission yeast

Asymmetrical segregation of differentiated sister chromatids is thought to be important for cellular differentiation in higher eukaryotes. Similarly, in fission yeast, cellular differentiation involves the asymmetrical segregation of a chromosomal imprint. This imprint has been shown to consist of two ribonucleotides that are incorporated into the DNA during lagging-strand synthesis in response to a replication pause, but the underlying mechanism remains unknown. Here we present key novel discoveries important for unravelling this process. Our data show that cis-acting sequences within the mat1 cassette mediate pausing of replication forks at the proximity of the imprinting site, and the results suggest that this pause dictates specific priming at the position of imprinting in a sequence-independent manner. Also, we identify a novel type of cis-acting spacer region important for the imprinting process that affects where subsequent primers are put down after the replication fork is released from the pause. Thus, our data suggest that the imprint is formed by ligation of a not-fully-processed Okazaki fragment to the subsequent fragment. The presented work addresses how differentiated sister chromatids are established during DNA replication through the involvement of replication barriers.     

A novel method for the analysis of platelet-activating factor: direct derivatization of glycerophospholipids

A novel, facile, and sensitive method for the quantitative and complete structure-proof analysis of platelet-activating factor (PAF) and other glycerophospholipids is described. 1-O-Alkyl/acyl-2-acyl-3-glycerophospholipids were treated with heptafluorobutyric anhydride in a one-step reaction to yield 1-O-alkyl/acyl-2-acyl-3-heptafluorobutyroyl-sn-glycerols as gas-liquid chromatography (GLC)-compatible derivatives. Furthermore, the components of the polar head group were also analyzed from the aqueous extract of the same reaction mixture as t-butyldimethylsilyl derivatives. Thus, this new method eliminates the need for phospholipase C treatment and subsequent purification procedures. Moreover, the direct derivatization of PAF homologs and analogs with hepatofluorobutyric anhydride does not result in positional isomerization of the product, providing increased specificity for gas-liquid chromatography-mass spectrometric (MS) analysis. It has also been shown that the heptafluorobutyroyl (HFB) derivative can easily be converted to the respective t-butyldimethylsilyl analog in a one-step reaction using t-butyldimethylsilyl chloride/imidazole reagent. Analogous to the formation of heptafluorobutyroyl derivatives, PAF also was reacted with pentafluorobenzoyl chloride to generate the pentafluorobenzoyl derivative. Therefore, this method has wide applicability for the formation of GLC-compatible derivatives of various glycerophospholipids. Our successful HFB derivatization and GLC-MS detection of subnanogram quantities of PAF indicate that this analytical procedure will greatly facilitate complete and quantitative identification of each of the molecular species of biologically derived PAF.     

新型柱前衍生试剂分析草甘膦的高效液相色谱研究

以2,5-二甲氧基苯磺酰氯(DMOSC)为柱前衍生化试剂,建立了柱前衍生草甘膦的紫外检测反相高效液相色谱法,并优化了衍生化条件,得最佳条件:衍生温度35℃,时间15 min,pH 10.0,草甘膦与DMOSC的摩尔比为1∶6。HPLC分析条件:采用Kromasil C18柱,流速1.0 mL/min,柱温30℃,检测波长220 nm,流动相为甲醇-乙腈-磷酸盐缓冲溶液(0.02 mol/L、pH 5.5),三者的体积比为15∶5∶80。结果表明:草甘膦质量浓度在5~100μg/mL范围内线性关系良好,相关系数为0.996 2,检测限为0.067μg/mL。实验表明该方法反应条件温和,灵敏度高,衍生产物稳定。     

Catabolism of glycoprotein glycans. Characterization of a lysosomal endo-N-acetyl-beta-D-glucosaminidase specific for glycans with a terminal chitobiose residue

An endo-N-acetyl-beta-D-glucosaminidase active towards oligosaccharides with a reducing terminal [bis(N-acetylglucosamine)]residue has been characterized in rat liver. The primary structure of its reaction products was determined using high-resolution 1H-NMR spectroscopy. The enzyme is predominantly located in the lysosomal fraction, presents a maximum of activity at pH 3.5 and is completely inactive towards conjugated glycans, i.e. glycoproteins and glycopeptides as well as on glycoasparagines. These results support the existence of a new pathway for the degradation of glycoprotein glycans inside the lysosome. In particular, this enzymic activity may be the origin of oligosaccharides bearing a single terminal reducing N-acetylglucosamine residue which are excreted in the urine of patients with various exoglycosidase deficiencies.     

Photoenhancement of transfection efficiency using novel cationic lipids having a photocleavable spacer

New cationic lipids having an o-nitrobenzyl moiety as a photocleavable spacer between its hydrophilic and hydrophobic region were synthesized. To improve the efficiency of transfection with lipoplexes, after transfecting the cationic lipid aggregate/DNA complex, photoirradiation was performed. Photochemical decomposition of lipids would not only make the vector's membrane unstable to facilitate the fusion with endocytic vesicles, but also promote dissociation of cationic lipid-DNA complex, thus aiding the escape of DNA from the endocytic vesicles. Using a luciferase gene as a model, we show that UV irradiation of photoresponsive lipoplex-treated COS-1 cells induces a substantial increase in the efficiency of transfection. Herein, we show a novel photoresponsive gene delivery system.     

Sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking

Two major emerging bands (a 350-bp band and a 650-bp band) within the RISA (ribosomal intergenic spacer analysis) profile of a soil bacterial community spiked with Hg(II) were selected for further identification of the populations involved in the response of the community to the added metal. The bands were cut out from polyacrylamide gels, cloned, characterized by restriction analysis, and sequenced for phylogenetic affiliation of dominant clones. The sequences were the intergenic spacer between the rrs and rrl genes and the first 130 nucleotides of the rrl gene. Comparison of sequences derived from the 350-bp band to The GenBank database permitted us to identify the bacteria as being mostly close relatives to low G+C firmicutes (Clostridium-like genera), while the 650-bp band permitted us to identify the bacteria as being mostly close relatives to beta-proteobacteria (Ralstonia-like genera). Oligonucleotide probes specific for the identified dominant bacteria were designed and hybridized with the RISA profiles derived from the control and spiked communities. These studies confirmed the contribution of these populations to the community response to the metal. Hybridization of the RISA profiles from subcommunities (bacterial pools associated with different soil microenvironments) also permitted to characterize the distribution and the dynamics of these populations at a microscale level following mercury spiking.     

GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans

Mass spectrometry is the main analytical technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensitivity and the ability to handle complex mixtures of different glycan variations. Determination of glycan structures from analysis of MS data is a major bottleneck in high-throughput glycomics projects, and robust solutions to this problem are of critical importance. However, all the approaches currently available have inherent restrictions to the type of glycans they can identify, and none of them have proved to be a definitive tool for glycomics. GlycoWorkbench is a software tool developed by the EUROCarbDB initiative to assist the manual interpretation of MS data. The main task of GlycoWorkbench is to evaluate a set of structures proposed by the user by matching the corresponding theoretical list of fragment masses against the list of peaks derived from the spectrum. The tool provides an easy to use graphical interface, a comprehensive and increasing set of structural constituents, an exhaustive collection of fragmentation types, and a broad list of annotation options. The aim of GlycoWorkbench is to offer complete support for the routine interpretation of MS data. The software is available for download from: http://www.eurocarbdb.org/applications/ms-tools.     

Advanced microscale bioreactor system: a representative scale-down model for bench-top bioreactors

In recent years, several automated scale-down bioreactor systems have been developed to increase efficiency in cell culture process development. ambr™ is an automated workstation that provides individual monitoring and control of culture dissolved oxygen and pH in single-use, stirred-tank bioreactors at a working volume of 10–15 mL. To evaluate the ambr™ system, we compared the performance of four recombinant Chinese hamster ovary cell lines in a fed-batch process in parallel ambr™, 2-L bench-top bioreactors, and shake flasks. Cultures in ambr™ matched 2-L bioreactors in controlling the environment (temperature, dissolved oxygen, and pH) and in culture performance (growth, viability, glucose, lactate, Na⁺, osmolality, titer, and product quality). However, cultures in shake flasks did not show comparable performance to the ambr™ and 2-L bioreactors.