Oligosaccharide microarrays for glycomics

Inhibitory potency of the nettle lectin on neovascularization: a biomolecule for carbohydrate-mediated targeting of angiogenesis

BACKGROUND

Current angiogenesis inhibitors target cellular vascularization processes, including proliferation, migration, and tube formation. In this study, we investigated the impact of Urtica dioica agglutinin (UDA) on the cellular vascularization process.

METHODS AND RESULTS

Various concentrations of UDA were applied to normal (HUVEC, MCF-10 A, and HDF from humans, and L-929 from mice) and cancer (A431 and U87 from humans, and 4T1 from mice) cell lines at different times. The MTT, cell migration assay, differentiation of endothelial cells, expression of VEGF-A/VEGF-R2, and integrin α2 were evaluated. The MTT results demonstrated that UDA was non-toxic to normal cells while inhibiting the growth of neoplastic cells. The migratory capacity of HUVECs and U87 glioblastoma cells was inhibited by UDA in the wound repair model. This lectin inhibited HUVEC-induced vessel sprouting in the collagen-cytodex matrix. In addition, UDA treatment reduced VEGF-integrin cross-talk in HUVECs, confirming the anti-angiogenic activity of this molecule.

CONCLUSIONS

Based on our findings, UDA may have an effect on cancer cell proliferation and vascularization events while causing minimal toxicity to normal cells via binding glyco-conjugates containing GlcNAc/man oligomers like EGFR. This is a blue clue for the angiogenesis-related therapeutic importance of UDA.

"Stuck on sugars - how carbohydrates regulate cell adhesion, recognition, and signaling"

We have explored the fundamental biological processes by which complex carbohydrates expressed on cellular glycoproteins and glycolipids and in secretions of cells promote cell adhesion and signaling. We have also explored processes by which animal pathogens, such as viruses, bacteria, and parasites adhere to glycans of animal cells and initiate disease. Glycans important in cell signaling and adhesion, such as key O-glycans, are essential for proper animal development and cellular differentiation, but they are also involved in many pathogenic processes, including inflammation, tumorigenesis and metastasis, and microbial and parasitic pathogenesis. The overall hypothesis guiding these studies is that glycoconjugates are recognized and bound by a growing class of proteins called glycan-binding proteins (GBPs or lectins) expressed by all types of cells. There is an incredible variety and diversity of GBPs in animal cells involved in binding N- and O-glycans, glycosphingolipids, and proteoglycan/glycosaminoglycans. We have specifically studied such molecular determinants recognized by selectins, galectins, and many other C-type lectins, involved in leukocyte recruitment to sites of inflammation in human tissues, lymphocyte trafficking, adhesion of human viruses to human cells, structure and immunogenicity of glycoproteins on the surfaces of human parasites. We have also explored the molecular basis of glycoconjugate biosynthesis by exploring the enzymes and molecular chaperones required for correct protein glycosylation. From these studies opportunities for translational biology have arisen, involving production of function-blocking antibodies, anti-glycan specific antibodies, and synthetic glycoconjugates, e.g. glycosulfopeptides, that specifically are recognized by GBPs. This invited short review is based in part on my presentation for the IGO Award 2019 given by the International Glycoconjugate Organization in Milan.

Plant Lectins as Medical Tools against Digestive System Cancers

Digestive system cancers-those of the esophagus, stomach, small intestine, colon-rectum, liver, and pancreas-are highly related to genetics and lifestyle. Most are considered highly mortal due to the frequency of late diagnosis, usually in advanced stages, caused by the absence of symptoms or masked by other pathologies. Different tools are being investigated in the search of a more precise diagnosis and treatment. Plant lectins have been studied because of their ability to recognize and bind to carbohydrates, exerting a variety of biological activities on animal cells, including anticancer activities. The present report integrates existing information on the activity of plant lectins on various types of digestive system cancers, and surveys the current state of research into their properties for diagnosis and selective treatment.

Evaluation of ion mobility-mass spectrometry for determining the isomeric heterogeneity of oligosaccharide-alditols derived from bovine submaxillary mucin

Rapid separation and independent analysis of isomeric species are needed for the structural characterization of carbohydrates in glycomics research. Ion mobility-mass spectrometry techniques were used to examine a series of isomeric neutral oligosaccharide-alditols derived from bovine submaxillary mucin. Several analytical techniques were employed: (1) off line separation of the oligosaccharide-alditol mixture by HPLC; (2) direct and rapid evaluation of isomeric heterogeneity of oligosaccharides by electrospray ionization-ion mobility-time of flight mass spectrometry; and (3) mobility-selected MS² and MS³ to evaluate isomeric mobility peaks by dual gate ion mobility-tandem mass spectrometry. Multiple isomeric ion mobility peaks were observed for the majority of oligosaccharide-alditols, which was achieved on the millisecond time scale after LC separation. Fragmentation spectra obtained from the collision-induced dissociation of isomeric precursor ions could be essentially identical, or dramatically different for a given precursor m/z using the dual-gate ion mobility quadrupole ion trap mass spectrometer. This further confirmed the need for rapid physical resolution of isomeric precursor species prior to their tandem mass spectral analysis.

Resolving structural isomers of monosaccharide methyl glycosides using drift tube and traveling wave ion mobility mass spectrometry

Monosaccharide structural isomers including sixteen methyl-D-glycopyranosides and four methyl-N-acetylhexosamines were subjected to ion mobility measurements by electrospray ion mobility mass spectrometry. Two ion mobility-MS systems were employed: atmospheric pressure drift tube ion mobility time-of-flight mass spectrometry and a Synapt G2 HDMS system which incorporates a low pressure traveling wave ion mobility separator. All the compounds were investigated as [M + Na](+) ions in the positive mode. A majority of the monosaccharide structural isomers exhibited different mobility drift times in either system, depending on differences in their anomeric and stereochemical configurations. In general, drift time patterns (relative drift times of isomers) matched between the two instruments. Higher resolving power was observed using the atmospheric pressure drift tube. Collision cross section values of monosaccharide structural isomers were directly calculated from the atmospheric pressure ion mobility experiments, and a collision cross section calibration curve was made for the traveling wave ion mobility instrument. Overall, it was demonstrated that ion mobility-mass spectrometry using either drift tube or traveling wave ion mobility is a valuable technique for resolving subtle variations in stereochemistry among the sodium adducts of monosaccharide methyl glycosides.

Preparation of a mannose-6-phosphate glycan microarray through fluorescent derivatization, phosphorylation, and immobilization of natural high-mannose N-glycans and application in ligand identification of P-type lectins

Glycan microarrays prepared by immobilization of amino-functionalized glycans on NHS-activated glass slides have been successfully used to study protein-glycan interactions. Fluorescently tagged glycans with an amino functional group can be prepared from natural glycans released from glycoproteins. These tagged glycans can be enzymatically modified with various glycosyltransferases, phosphotransferases, sulfotransferases, etc., to quickly expand the size and diversity of the tagged glycan libraries (TGLs). The TGLs, presented in the format of microarrays, provide a convenient platform for identifying the glycan ligands of glycan-binding proteins (GBPs). The chapter provides the background to prepare a defined glycan microarray and uses as an example glycans generated as phosphodiesters and phosphomonoesters of high-mannose type N-glycans. The method describes the preparation of high-mannose type glycan-AEAB conjugates (GAEABs), the purification of their phosphodiesters, and the subsequent mild acid hydrolysis to obtain corresponding phosphomonoesters. These GAEABs are covalently printed as a phosphorylated glycan microarray and used for analysis of the glycan ligand specificities of P-type lectins, such as the mannose-6-phosphate receptors (Man-6-P receptors or MPRs).

Glycan microarrays

Glycan microarrays are presentations of multiple glycans or glycoconjugates printed on a single slide for screening with glycan-binding proteins (GBPs), which include lectins, antibodies, bacteria, and viruses. Glycans derivatized with functional groups can be immobilized onto appropriately activated glass slides to generate glycan microarrays where each glycan is printed at similar concentrations. Here we describe a method for fluorescently and functionally derivatizing free reducing glycans, printing microarrays, and interrogating the microarrays with GBPs.

Differential carbohydrate binding and cell surface glycosylation of human cancer cell lines

Currently there is only a modest level knowledge of the glycosylation status of immortalised cell lines that are commonly used in cancer biology as well as their binding affinities to different glycan structures. Through use of glycan and lectin microarray technology, this study has endeavoured to define the different bindings of cell surface carbohydrate structures to glycan-binding lectins. The screening of breast cancer MDA-MB435 cells, cervical cancer HeLa cells and colon cancer Caco-2, HCT116 and HCT116-FM6 cells was conducted to determine their differential bindings to a variety of glycan and lectin structures printed on the array slides. An inverse relationship between the number of glycan structures recognised and the variety of cell surface glycosylation was observed. Of the cell lines tested, it was found that four bound to sialylated structures in initial screening. Secondary screening in the presence of a neuraminidase inhibitor (4-deoxy-4-guanidino-Neu5Ac2en) significantly reduced sialic acid binding. The array technology has proven to be useful in determining the glycosylation signatures of various cell-lines as well as their glycan binding preferences. The findings of this study provide the groundwork for further investigation into the numerous glycan-lectin interactions that are exhibited by immortalised cell lines.

Lectin microarrays for glycomic analysis

Glycomics is the study of comprehensive structural elucidation and characterization of all glycoforms found in nature and their dynamic spatiotemporal changes that are associated with biological processes. Glycocalyx of mammalian cells actively participate in cell-cell, cell-matrix, and cell-pathogen interactions, which impact embryogenesis, growth and development, homeostasis, infection and immunity, signaling, malignancy, and metabolic disorders. Relative to genomics and proteomics, glycomics is just growing out of infancy with great potential in biomedicine for biomarker discovery, diagnosis, and treatment. However, the immense diversity and complexity of glycan structures and their multiple modes of interactions with proteins pose great challenges for development of analytical tools for delineating structure function relationships and understanding glyco-code. Several tools are being developed for glycan profiling based on chromatography, mass spectrometry, glycan microarrays, and glyco-informatics. Lectins, which have long been used in glyco-immunology, printed on a microarray provide a versatile platform for rapid high throughput analysis of glycoforms of biological samples. Herein, we summarize technological advances in lectin microarrays and critically review their impact on glycomics analysis. Challenges remain in terms of expansion to include nonplant derived lectins, standardization for routine clinical use, development of recombinant lectins, and exploration of plant kingdom for discovery of novel lectins.

Protein microarrays for genome-wide posttranslational modification analysis

Protein microarray technology has emerged as a powerful tool for comparing binding interactions, expression level, substrate specificities, and posttranslational modifications (PTMs) of different proteins in a parallel and high-throughput manner. The ability to immobilize proteins to a solid surface and register the specific address of each protein has bridged major limitations for investigating the proteome in biological samples, namely, the wide dynamic range of protein concentrations and the perturbation of the physical and chemical properties of proteins by their modification. Recent advances introduced the use of functional mammalian cell extracts to assay PTMs under different cellular conditions. This assay offers a new approach for performing large-scale complex biochemical analysis of protein modifications. Here, we review studies of PTM profiling using protein microarrays and discuss the limitations and potential applications of the system. We believe that the information generated from such proteomic studies may be of significant value in our elucidation of the molecular mechanisms that govern human physiology.

Photo-click immobilization of carbohydrates on polymeric surfaces--a quick method to functionalize surfaces for biomolecular recognition studies

Methods to rapidly functionalize specific polymeric surfaces with alkynes, which can subsequently be linked to azide-containing carbohydrates, are presented. The methods comprise two main concepts: azide photoligation and Cu-catalyzed azide-alkyne cycloaddition. 2-Azidoethyl-functionalized alpha-D-mannopyranoside was synthesized and covalently attached to alkyne-functionalized polymeric surfaces using the techniques. The protein recognition properties of the carbohydrate-presenting surfaces were evaluated using quartz crystal microbalance biosensor instrumentation.

Modification of exopolysaccharide composition and production by three cyanobacterial isolates under salt stress

BACKGROUND, AIM, AND SCOPE

Polysaccharides are renewable resources representing an important class of polymeric materials of biotechnological interest, offering a wide variety of potentially useful products to mankind. Exopolysaccharides (EPSs) of microbial origin with a novel functionality, reproducible physico-chemical properties, stable cost and supply, became a better alternative to polysaccharides of algal origin. EPSs are believed to protect bacterial cells from desiccation, heavy metals or other environmental stresses, including hostimmune responses, and to produce biofilms, thus enhancing the cells chances of colonising special ecological niches. One of the most important stress factor is salt stress for microorganisms. The present investigation is aimed to determine correlation between salt resistance and EPS production by three cyanobacterial isolates (Synechocystis sp. BASO444, Synechocystis sp. BASO507 and Synechocystis sp. BASO511). It is also aimed to investigate the effect of salt concentrations on EPS production by cyanobacteria and effect of salt on monosaccharide composition of EPS.

MATERIALS AND METHODS

Cyanobacterial isolates were identified by 16 S rRNA analysis. Its salt (NaCl) tolerance and association with exopolysaccharides (EPSs) production in three cyanobacterial isolates were investigated. Also, EPS was analysed by HPLC for monomer characterization.

RESULTS

Increased EPS production was associated with NaCl tolerance. The most tolerant isolate, Synechocystis sp. BASO444, secreted the most EPS (500 mg/L). EPS production by Synechocystis sp. BASO444, Synechocystis sp. BASO507 and Synechocystis sp. BASO511 was investigated following exposure to 0.2 and 0.4 M NaCl. Also, flasks containing medium without NaCl were inoculated in the same manner to serve as controls. The monosaccharide compositions of EPS produced by the three isolates following exposure to 0.2 M NaCl were analysed by HPLC. Control EPS of BASO444 was composed of glucose (97%) and galacturonic acid (3%). The composition of BASO511 (control) was glucose (95%), xylose (4.80%), arabinose (0.13%), glucuronic acid (0.03%) and galacturonic acid (0.04%). However, the composition of BASO507 (control) was glucose (0.98%), xylose (98.00%), arabinose (1.00%), glucuronic acid (0.01%) and galacturonic acid (0.01%). In the presence of 0.2 M NaCl, EPS compositions and ratios of three cyanobacterial isolates changed.

DISCUSSION

Although hyperproduction of EPS in response to starvation, antiviral activity, thickening agent and cosmetic industry for product formulations has been reported for cyanobacteria, the effect of NaCl on EPS production in cyanobacteria is not a popular area of study. There are no clear reports correlating EPS production and NaCl tolerance. The gap in the data about the effect of NaCl on cyanobacterial EPS production was filled by this investigation, and the results of our study have important implications in both the industrial and environmental arenas.

CONCLUSIONS

Our results indicate that 1) exposure to elevated concentrations of NaCl affects the composition of EPS produced by Synechocystis sp. BASO444, Synechocystis sp. BASO507 and Synechocystis sp. BASO511, and 2) there is a correlation between NaCl tolerance and EPS production in some cyanobacteria.

RECOMMENDATIONS AND PERSPECTIVES

Differences in the monosaccharide composition and ratios of EPS may promote NaCl tolerance in these microorganisms. As well, these alternative composition polysaccharides may be important for industrial applications.

Quantitative microarray analysis of intact glycolipid-CD1d interaction and correlation with cell-based cytokine production

The protein CD1d binds self and foreign glycolipids for presentation to CD1-restricted T cells by means of TCR recognition and activates T(H)1 and T(H)2 chemokine release. In this study, a variety of glycolipid ligands were attached to a microarray surface and their binding with dimeric CD1d was investigated. An alpha-galactosyl ceramide (alpha-GalCer) bearing a carbamate group at the 6'-OH position was tethered to the surface, and the dissociation constant on surface with CD1d was determined to reflect the multivalent interaction. Competition assays were then used to determine the dissociation constants (Ki) of new and intact glycolipids in solution. The 4-fluorophenyloctanoyl-modified alpha-GalCer (18) was found to bind most strongly with CD1d (Ki 0.21 microM), 2 orders of magnitude stronger than alpha-GalCer and more than three times more selective than alpha-GalCer for IFN-gamma release from NKT cells. Various alpha-GalCer analogues were analyzed, and the results showed that the binding affinity of glycolipids to CD1d correlates well with IFN-gamma production but poorly with IL-4 secretion by NKT cells, suggesting that tighter binding ligands could bias cytokine release through the T(H)1 pathway.

Application of carbohydrate microarray technology for the detection of Burkholderia pseudomallei, Bacillus anthracis and Francisella tularensis antibodies

We developed a microarray platform by immobilizing bacterial 'signature' carbohydrates onto epoxide modified glass slides. The carbohydrate microarray platform was probed with sera from non-melioidosis and melioidosis (Burkholderia pseudomallei) individuals. The platform was also probed with sera from rabbits vaccinated with Bacillus anthracis spores and Francisella tularensis bacteria. By employing this microarray platform, we were able to detect and differentiate B. pseudomallei, B. anthracis and F. tularensis antibodies in infected patients, and infected or vaccinated animals. These antibodies were absent in the sera of naïve test subjects. The advantages of the carbohydrate microarray technology over the traditional indirect hemagglutination and microagglutination tests for the serodiagnosis of melioidosis and tularemia are discussed. Furthermore, this array is a multiplex carbohydrate microarray for the detection of all three biothreat bacterial infections including melioidosis, anthrax and tularemia with one, multivalent device. The implication is that this technology could be expanded to include a wide array of infectious and biothreat agents.

High-throughput screening of monoclonal antibodies against plant cell wall glycans by hierarchical clustering of their carbohydrate microarray binding profiles

Antibody-producing hybridoma cell lines were created following immunisation with a crude extract of cell wall polymers from the plant Arabidopsis thaliana. In order to rapidly screen the specificities of individual monoclonal antibodies (mAbs), their binding to microarrays containing 50 cell wall glycans immobilized on nitrocellulose was assessed. Hierarchical clustering of microarray binding profiles from newly produced mAbs, together with the profiles for mAbs with previously defined specificities allowed the rapid assignments of mAb binding to antigen classes. mAb specificities were further investigated using subsequent immunochemical and biochemical analyses and two novel mAbs are described in detail. mAb LM13 binds to an arabinanase-sensitive pectic epitope and mAb LM14, binds to an epitope occurring on arabinogalactan-proteins. Both mAbs display novel patterns of recognition of cell walls in plant materials.

Quantifiable fluorescent glycan microarrays

A glycan microarray was developed by using 2,6-diaminopyridine (DAP) as a fluorescent linker and printing of the glycan-DAP conjugates (GDAPs) on epoxy-activated glass slides. Importantly, all coupled GDAPs showed a detectable level of concentration-dependent GDAP fluorescence under blue laser excitation (495 nm) that can be used for both grid location and on-slide quantification. A glycan array including a large number of GDAP's derived from natural and commercially available free glycans was constructed and glycan interactions with various plant lectins were investigated. In addition, binding parameters of lectins to glycans were obtained by varying both the amount of GDAPs on the array and the lectin concentration in analyses. These data demonstrate the general utility of GDAP microarrays for functional glycomic analyses and for determining binding parameters of glycan binding proteins (GBPs).

Glyco-array technology for efficient monitoring of plant cell wall glycosyltransferase activities

The plant cell wall is a complex network of polysaccharides. The diversity in the linkage types connecting all monosaccharides within these polysaccharides would need a large set of glycosyltransferases to catalyze their formation. Development of a methodology that would allow monitoring of glycosyltransferase activities in an easy and high-throughput manner would help assign biochemical functions, and understand their roles in building this complex network. A microarray-based method was optimized for testing glycosyltransferases involved in plant wall biosynthesis using an alpha(1,2)fucosyltransferase involved in xyloglucan biosynthesis. The method is simple, sensitive, and easy to implement in any lab. Tamarind xyloglucan polymer and trimer, and a series of cello-oligosaccharides were immobilized on a thin-coated photo-activable glass slide. The slide with the attached sugars was then used to estimate the incorporation of [(14)C]Fuc onto xyloglucan polymer and trimer. [(14)C]-radiolabel incorporation is revealed with a standard phosphoimager scanner, after exposure of the glycochip to a phosphor screen and detection. The method proved to be sensitive enough to detect as low as 45 cpm/spot. Oriented anchoring of small oligosaccharides (trimer) was required for optimal transferase activities. The glycochip was also used to monitor and estimate xyloglucan fucosyltransferase activity in detergent-solubilized crude extracts from pea microsomes that are known to contain this enzyme activity. Our data indicate that the methodology can be used for efficient and rapid monitoring of glycosyltransferase activities involved in plant wall polysaccharides biosynthesis.

Recent developments in sample preparation for chromatographic analysis of carbohydrates

Carbohydrates are a very important group of compounds due to their roles as structural materials, sources of energy, biological functions and environmental analytes; they are characterized by their structural diversity and the high number of isomers they present. While many advances have been made in carbohydrate analysis, the sample preparation remains difficult. This review aims to summarize the most important treatments which have been recently developed to be applied prior to the analysis of carbohydrates by chromatographic techniques. Due to the multiplicity of structures and matrices, many different techniques are required for clean-up, fractionation and derivatization. A number of new techniques which could be potentially adequate for carbohydrate characterization have also been revised.

New Trends in Immunoassays

This article takes a special focus on signal amplification technologies in immunoassays and new generations of lateral-flow assays. Novel signal amplification technologies based either on new classes of biofunctional nanocrystals consisting of releasable fluorophores or on aggregation-induced emission (AIE) can improve the sensitivity and the limits of detection in immunoassays. A bio-barcode assay also allows signal amplification by utilizing antibody-coated magnetic beads to concentrate the analytes and antibody-coated gold nanoparticle probes to carry with a large number of oligonucleotides. These innovative technologies boost the development of immunoassays. Growth in rapid immunoassay is fueled by the increasing number of diabetics, the globalization of infectious diseases and the surge in cardiovascular and other chronic diseases as well as other chronic conditions. Rapid, near patient, decentralized, point-of-care (POC) tests are emerging as a tool for more efficient diagnosis and patient evaluation. Technological innovations in lateral-flow assays have enabled a move to bring testing closer to the patient. A novel "digital-style" lateral-flow assay provides semi-quantitative results by simply counting the number of red lines in the test without any expensive reading instrument. An immuno-threshold-based assay can give a signal directly proportional to the concentration of a hapten to prevent confusion on interpretation of the test results. In addition, POC tests become more meaningful to healthcare professionals by combining the benefits of new technologies to provide quantitative results. A molecular compact disc provides a high-resolution imaging capability that can identify and quantify many different antigens simultaneously in highly complex immunoassays. Further advances in immunoassays will bring diagnostic testing even closer to the patient, and can help physicians to monitor diseases that require immediate test results, thereby enhancing the quality of patient care.

Partial characterization of extracellular polysaccharides from cyanobacteria

Four cyanobacterial strains, Cyanothece sp., Oscillatoria sp., Nostoc sp. and Nostoc carneum were studied for physico-chemical characterization of extracellular polysaccharide (EPS) secreted during the controlled growth condition. Hydrolyzed EPSs showed the compositional involvement of four sugar moieties viz. mannose, glucose, xylose and ribose in varying combinations. Infrared spectra of EPSs showed a specific absorbance of O-H stretching at 3448-3400 cm(-1), asymmetrical-symmetrical C-H stretching at 2924 and 2854 cm(-1) and a bending vibration of C-H at 1400-1380 cm(-1). Absorbance at 1259 and 1140 cm(-1) with Cyanothece sp. EPS, indicated the presence of sulfur containing functional group. Thermal gravimetric analysis and differential scanning calorimetric analysis confirmed the polysaccharides thermal stability as high as around 250 degrees C. In the presence of 0.1 M NaCl aqueous solution, the intrinsic viscosity of polysaccharides from Oscillatoria sp. and Nostoc sp. decreased 1.6 fold, whereas, 3-5 fold reduction in intrinsic viscosity was observed with commercially available guar and xanthan gum.

Carbohydrate Microarrays: Survey of Fabrication Techniques

Carbohydrate microarrays are being developed in order to decipher the information content of the glycome. This postgenomic activity is necessary because of the complexity of protein biosynthesis and post-translational modifications that cannot currently be detected at the genome level. This review looks, in detail, at the experimental approaches that have been taken in the fabrication and preparation of carbohydrate microarrays, glycan arrays and glyco-chips. Tether structures, glycan solution preparation, detection methods and applications have been gathered together in a tabular format.

Microarray technology in obstetrics and gynecology: a guide for clinicians

Microarrays can be constructed with dozens to millions of probes on their surface to allow high-throughput analyses of many biologic processes to be performed simultaneously on the same sample. Microarrays are now widely used for gene expression analysis, deoxyribonucleic acid resequencing, single-nucleotide polymorphism genotyping, and comparative genomic hybridization. Microarray technology is accelerating research in many fields and now microarrays are moving into clinical application. This review discusses the emerging role of microarrays in molecular diagnostics, pathogen detection, oncology, and pharmacogenomics.

Polysaccharide microarray technology for the detection of Burkholderia pseudomallei and Burkholderia mallei antibodies

A polysaccharide microarray platform was prepared by immobilizing Burkholderia pseudomallei and Burkholderia mallei polysaccharides. This polysaccharide array was tested with success for detecting B. pseudomallei and B. mallei serum (human and animal) antibodies. The advantages of this microarray technology over the current serodiagnosis of the above bacterial infections were discussed.

Design of carbohydrate multiarrays

Recently, microarray technology has increasingly been widely applied in glycobiology. This technology has rather evident potential advantages: unlimited number of carbohydrate ligands coated onto one small sized chip, enormously low consumption of both carbohydrate ligands and carbohydrate-binding proteins to be tested, etc. Literature data demonstrate that three approaches are used for glycoarray design. The first one is based on the physical adsorption of glycomolecules on a surface (as in a common ELISA), the second one-on covalent immobilization, and the third one-on a streptavidin-biotin system. In all of the described methods, carbohydrate ligands were placed on chips as a 2D monolayer and high sensitivity was achieved due to fluorescent detection. Notably, a tendency of stepping from model chips toward real multiarrays, where the number of carbohydrate ligands can be up to two hundred, has been observed the last 2 years, this already producing a number of interesting findings when studying carbohydrate-binding proteins. In 2005 new construction, 3D glycochip was described, where 150 mum diameter polyacrylamide gel elements serve as microreactors instead of 2D dots. As a result of the 3D placement of a ligand, two orders of magnitude increase of its density is possible, this providing principal signal improvement during fluorescent detection and increasing method sensitivity. At the same time, carbohydrate consumption is low, i.e., approximately 1 pmol per gel element. Copolymerization chemistry enables the immobilization of several glycomolecule classes to the gel, in particular, aminospacered oligosaccharides, polyacrylamide conjugates, and even 2-aminopyridine derivatives of oligosaccharides, which are widely used in the structural analysis of glycoprotein N-chains.

Multiplexed protein measurement: technologies and applications of protein and antibody arrays

The ability to measure the abundance of many proteins precisely and simultaneously in experimental samples is an important, recent advance for static and dynamic, as well as descriptive and predictive, biological research. The value of multiplexed protein measurement is being established in applications such as comprehensive proteomic surveys, studies of protein networks and pathways, validation of genomic discoveries and clinical biomarker development. As standards do not yet exist that bridge all of these applications, the current recommended best practice for validation of results is to approach study design in an iterative process and to integrate data from several measurement technologies. This review describes current and emerging multiplexed protein measurement technologies and their applications, and discusses the remaining challenges in this field.

Protein-detecting microarrays: current accomplishments and requirements

The sequencing of the human genome has been successfully completed and offers the chance of obtaining a large amount of valuable information for understanding complex cellular events simply and rapidly in a single experiment. Interestingly, in addressing these proteomic studies, the importance of protein-detecting microarray technology is increasing. In the coming few years, microarray technology will become a significantly promising and indispensable research/diagnostic tool from just a speculative technology. It is clear that the protein-detecting microarray is supported by three independent but strongly related technologies (surface chemistry, detection methods, and capture agents). Firstly, a variety of surface-modification methodologies are now widely available and offer site-specific immobilization of capture agents onto surfaces in such a way as to keep the native conformation and activity. Secondly, sensitive and parallel detection apparatuses are being developed to provide highly engineered microarray platforms for simultaneous data acquisition. Lastly, in the development of capture agents, antibodies are now probably the most prominent capture agents for analyzing protein abundances. Alternative scaffolds, such as phage-displayed antibody and protein fragments, which provide the advantage of increasing diversity of proteinic capture agents, however, are under development. An approach involving recombinant proteins fused with affinity tag(s) and coupled with a highly engineered surface chemistry will provide simple production protocols and specific orientations of capture agents on the microarray formats. Peptides and other small molecules can be employed in screening highly potent ligands as well as in measuring enzymatic activities. Protein-detecting microarrays supported by the three key technologies should contribute in accelerating diagnostic/biological research and drug discovery.

Microarrays meet the Voltaire challenge: Drug discovery on a chip?

The co-emergence of microarray technologies with systems oriented approaches to discovery is testament to the technological and conceptual advancements of recent years. By providing a platform for massively parallelized reductionism, microarrays are enabling us to examine the functional features of diverse classes of bio-system components in a contextually meaningful manner. Yet, to provide economic impact, future development of these technologies demands intimate alignment with the goal of producing safer and more efficacious drugs.:

On-bead synthesis and binding assay of chemoselectively template-assembled multivalent neoglycopeptides

The investigation of recognition events between carbohydrates and proteins, especially the control of how spatial factors and binding avidity are correlated in, remains a great interest for glycomics. Therefore, the development of efficient methods for the rapid evaluation of new ligands such as multivalent glycoconjugates is essential for diverse diagnostic or therapeutic applications. In this paper we describe the synthesis of chemoselectively-assembled multivalent neoglycopeptides and the subsequent recognition assay on a solid support. Aminooxylated carbohydrates (betaLac-ONH(2) 4, alphaGalNAc-ONH(2) 9 and alphaMan-ONH(2) 13) have been prepared as carbohydrate-based recognition elements and assembled as clusters onto a cyclopeptidic scaffold by an oxime-based strategy in solid phase. Further binding tests between lectins and beads of resin derivatized with neoglycopeptides displaying clustered lactoses, N-acetylgalactoses and mannoses (18-20) have shown specific recognition and enhanced affinity through multivalent interactions, suggesting that the local density of carbohydrate-based ligands at the bead surface is crucial to improve the interaction of proteins of weak binding affinity. This solid phase strategy involving both molecular assembly and biological screening provides a rapid and efficient tool for various applications in glycomics.

Plant metabolomics: potential for practical operation

In the postgenomic era, metabolomics is expected to be the newest useful omics science for functional genomics. However, in plant science, the present metabolomics technology cannot be considered a universal tool to perfectly elucidate perturbations imposed on sample plants although this is desired by plant physiologists. Despite it being an immature technology, metabolomics has already been used as a powerful tool for precise phenotyping, particularly for industrial application. Metabolomics is the best technology for the analysis of large mutant or transgenic libraries of model experimental plants, such as Arabidopsis, rice, etc. Here, we review the applications and technical problems of metabolomics. We also suggest the potential of metabolomics for plant post-genomic science.

Carbochips: a new energy for old biobuilders

Microarray technology has come of age for use in high-throughput operations and large-scale studies. It allows rapid and simultaneous detection of thousands of parameters within a single experiment. Recent developments in the field of carbohydrate microarray technology facilitate applications for different types of protein–carbohydrate interactions. These developments included capture molecule immobilization, surface engineering and detection strategies to analyze entire glycomes and glycosylation in vertebrate systems, the most common post-translational modification.

Synthesis of multitopic neoglycopeptides displaying recognition and detection motifs

We describe herein the synthesis of cyclic decapeptide template displaying clustered carbohydrate recognition motifs and detection agent on spatially separated domains. Such multitopic labeled neoglycopeptides represent attractive tools for binding assays with carbohydrate binding proteins in glycomic research.

New Methods for the Generation of Carbohydrate Arrays on Glass Slides and Their Evaluation

Glycosides, having spacers functionalized with an aldehyde or a carboxylic group, were immobilized through reductive amination or amidation, respectively, onto amino-functionalized glass slides. Hybridization experiments with lectins exhibited very little nonspecific protein binding, hence precluding the necessity for the blocking of unreacted functional groups on the glass slide. The covalency and the concentration dependency of the sugar ligation to the glass slide were demonstrated; the reversibility and the selectivity of lectin-carbohydrate interactions were shown.

Microarrays – status and prospects

Microarrays have become an extremely important research tool for life science researchers and are also beginning to be used in diagnostic, treatment and monitoring applications. This article provides a detailed description of microarrays prepared by in situ synthesis, deposition using microspotting methods, nonplanar bead arrays, flow-through microarrays, optical fiber bundle arrays and nanobarcodes. The problems and challenges in the development of microarrays, development of standards and diagnostic microarrays are described. Tables summarizing the vendor list of various derivatized microarray surfaces, commercially sold premade microarrays, bead arrays and unique microarray products in development are also included.

Interaction assay of oligosaccharide with lectins using glycosylasparagine

Glycosyl amino acids having natural glycan were useful for the interaction assay of oligosaccharides. A glycochip containing the whole structure of an oligosaccharide was easily prepared by the immobilization of the glycosyl amino acid. Furthermore, fluorescence probes were introduced into the glycosyl amino acid while maintaining the whole structure of oligosaccharide. By using these labeled oligosaccharides, fluorescence polarization (FP) and fluorescence correlation spectroscopy (FCS) analyzed the carbohydrate-lectin interaction in a solution assay system.

A metabolic labeling approach toward proteomic analysis of mucin-type O-linked glycosylation

Mucin-type O-linked glycoproteins are involved in a variety of biological interactions in higher eukaryotes. The biosynthesis of these glycoproteins is initiated by a family of polypeptide N-acetyl-alpha-galactosaminyltransferases (ppGalNAcTs) that modify proteins in the secretory pathway. The lack of a defined consensus sequence for the ppGalNAcTs makes the prediction of mucin-type O-linked glycosylation difficult based on primary sequence alone. Herein we present a method for labeling mucin-type O-linked glycoproteins with a unique chemical tag, the azide, which permits their selective covalent modification from complex cell lysates. From a panel of synthetic derivatives, we identified an azido GalNAc analog (N-azidoacetylgalactosamine, GalNAz) that is metabolized by numerous cell types and installed on mucin-type O-linked glycoproteins by the ppGalNAcTs. The azide serves as a bioorthogonal chemical handle for selective modification with biochemical or biophysical probes using the Staudinger ligation. The approach was validated by labeling a recombinant glycoprotein that is known to possess O-linked glycans with GalNAz. In addition, GalNAz efficiently labeled mucin-type O-linked glycoproteins expressed at endogenous levels. The ability to label mucin-type O-linked glycoproteins with chemical tags should facilitate their identification by proteomic strategies.