Showing papers on "Glycome published in 2004"

Glycoprofiling with micro-arrays of glycoconjugates and lectins

Abstract: To facilitate deciphering the information content in the glycome, thin film-coated photoactivatable surfaces were applied for covalent immobilization of glycans, glycoconjugates, or lectins in microarray formats. Light-induced immobilization of a series of bacterial exopolysaccharides on photoactivatable dextran-coated analytical platforms allowed covalent binding of the exopolysaccharides. Their specific galactose decoration was detected with fluorescence-labeled lectins. Similarly, glycoconjugates were covalently immobilized and displayed glycans were profiled for fucose, sialic acid, galactose, and lactosamine epitopes. The applicability of such platforms for glycan profiling was further tested with extracts of Caco2 epithelial cells. Following spontaneous differentiation or on pretreatment with sialyllactose, Caco2 cells showed a reduction of specific glycan epitopes. The changed glycosylation phenotypes coincided with altered enteropathogenic E. coli adhesion to the cells. This microarray strategy was also suitable for the immobilization of lectins through biotin-neutravidin-biotin bridging on platforms functionalized with a biotin derivatized photoactivatable dextran. All immobilized glycans were specifically and differentially detected either on glycoconjugate or lectin arrays. The results demonstrate the feasibility and versatility of the novel platforms for glycan profiling.

Glycosyltransferases encoded by viruses.

Abstract: Studies of cellular biology in recent decades have highlighted the crucial roles of glycans in numerous important biological processes, raising the concept of glycomics that is now considered as important as genomics, transcriptomics and proteomics. For millions of years, viruses have been co-evolving with their hosts. Consequently, during this co-evolution process, viruses have acquired mechanisms to mimic, hijack or sabotage host processes that favour their replication, including mechanisms to modify the glycome. The importance of the glycome in the regulation of host–virus interactions has recently led to a new concept called ‘glycovirology’. One fascinating aspect of glycovirology is the study of how viruses affect the glycome. Viruses reach that goal either by regulating expression of host glycosyltransferases or by expressing their own glycosyltransferases. This review describes all virally encoded glycosyltransferases and discusses their established or putative functions. The description of these enzymes illustrates several intriguing aspects of virology and provides further support for the importance of glycomics in biological processes.

Bioinformatics for glycomics: Status, methods, requirements and perspectives

Abstract: The term ‘glycomics’ describes the scientific attempt to identify and study all the glycan molecules – the glycome – synthesised by an organism. The aim is to create a cell-by-cell catalogue of glycosyltransferase expression and detected glycan structures. The current status of databases and bioinformatics tools, which are still in their infancy, is reviewed. The structures of glycans as secondary gene products cannot be easily predicted from the DNA sequence. Glycan sequences cannot be described by a simple linear one-letter code as each pair of monosaccharides can be linked in several ways and branched structures can be formed. Few of the bioinformatics algorithms developed for genomics/proteomics can be directly adapted for glycomics. The development of algorithms, which allow a rapid, automatic interpretation of mass spectra to identify glycan structures is currently the most active field of research. The lack of generally accepted ways to normalise glycan structures and exchange glycan formats hampers an efficient cross-linking and the automatic exchange of distributed data. The upcoming glycomics should accept that unrestricted dissemination of scientific data accelerates scientific findings and initiates a number of new initiatives to explore the data.

Extracellular virulence factors of Streptococcus pneumoniae.

Abstract: Streptococcus pneumoniae is one of the major human bacterial pathogens Current prophylactic agents against this pathogen are limited in their protective abilities and the role of therapeutics has been inadequate as resistant strains emerge The development of new and improved therapies to combat the pneumococcal disease is necessary In order to accomplish this, an understanding of the interactions between this bacterium and the host tissues is essential Such interactions largely involve extracellular virulence factors that are expressed by the pathogen to interact with the host These virulence factors include those based on sugars (glycome-based) as their building blocks, and proteins that are built from amino acids (proteome-based) The first group includes primarily the capsule, teichoic and lipoteichoic acids The second group is diverse and includes numerous surface proteins that are attached to the cell wall of pneumococci utilizing a variety of methods For the purpose of this review these surface proteins were divided into three categories, proteins bound to peptidoglycan, those bound to choline residues present on the surface of penumococci, and those bound to the lipids of the cytoplasmic membrane Both the glycome-based and protein-based virulence factors are described, analyzed, and represented graphically Whenever possible, structural properties of these molecules were introduced

Total serum protein N-glycome profiling on a capillary electrophoresis-microfluidics platform.

Abstract: We implemented 8-aminopyrene-1,3,6-trisulfonic acid (APTS)-labeled asparagine-linked glycan (N-glycan) profiling on a microfluidic electrophoresis platform. Using 11.5 cm effective length etched channels and 4% linear polyacrylamide as the separation matrix, the major N-glycans in human serum were profiled in 12 min with a resolution comparable to what is achieved for these analytes on gel-based DNA sequencers. This demonstration suggests a practical clinical application for high-speed compact analyzers which might be uniquely based on microfluidic devices.

Endothelial cells preparing to die by apoptosis initiate a program of transcriptome and glycome regulation

Abstract: SPECIFIC AIMSTo investigate changes in the transcriptome and glycome of endothelial cells (ECs) that may contribute to the apoptotic process.PRINCIPAL FINDINGS1. Partial survival factor deprivation...

On the Origin of Glycome and Saccharide Recognition

Abstract: Lectin Affinity Chromatography as a Tool to Differentiate Erythropoietin (EPO) and its analogues : abstract

Managing and analyzing carbohydrate data

Abstract: One of the most vital molecules in multicellular organisms is the carbohydrate, as it is structurally important in the construction of such organisms. In fact, all cells in nature carry carbohydrate sugar chains, or glycans, that help modulate various cell-cell events for the development of the organism. Unfortunately, informatics research on glycans has been slow in comparison to DNA and proteins, largely due to difficulties in the biological analysis of glycan structures. Our work consists of data engineering approaches in order to glean some understanding of the current glycan data that is publicly available. In particular, by modeling glycans as labeled unordered trees, we have implemented a tree-matching algorithm for measuring tree similarity. Our algorithm utilizes proven efficient methodologies in computer science that has been extended and developed for glycan data. Moreover, since glycans are recognized by various agents in multicellular organisms, in order to capture the patterns that might be recognized, we needed to somehow capture the dependencies that seem to range beyond the directly connected nodes in a tree. Therefore, by defining glycans as labeled ordered trees, we were able to develop a new probabilistic tree model such that sibling patterns across a tree could be mined. We provide promising results from our methodologies that could prove useful for the future of glycome informatics.

Sugar Chains in Cell Adhesion and Cell Division-Comparative Glycomics Throwing Light on Glycobiology

Abstract: ABH式血液型抗原は何の生理学的機能もないと考えられてきた。Xenopus laevis のCa2+依存性細胞間接着を研究している時、私達は血液型B型抗原を付加されたGPIアンカー型レクチンとB型糖鎖を付加された複合糖質が初期胚の細胞接着を引きおこしていることを発見した。マウスの初期胚では、B型血液型抗原ではなく、Lewis x 血液型物質が付加された分子が、コンパクションにおいて同様の機能を果たしている。どのようにして細胞表面の細胞接着に働いているグリコームの発現パターンがこの二つの種で進化してきたのであろうか?線虫 Caenorhabditis elegans においてはコンドロイチンプロテオグリカンの鎖が細胞分裂の完了に必須の役割を果たしている。胚細胞表面のコンドロイチンが減少するとみたところ細胞分裂が逆行する現象がひきおこされる。細胞質分裂と染色体の分配が異常になり、胚細胞は死亡する。高等動物においてもコンドロイチンは同様な役割を細胞分裂において果たしているのだろうか? あるいは、コンドロイチンの役割は異なる糖鎖によってとってかわられているのだろうか? これら二つの例から分かるように、様々な生物のグリコーム間の比較は、糖鎖生物学における様々な仮説を生み出す大変強力な手法ということができる。ゲノムDNA配列の解読の完了によって、バイオインフォマティックスと機能グリコミックスの手法をもちいてグリコームの進化を研究することができる時代がようやくおとずれてきたの考えられる。

The Automation of Glycopeptide Discovery in HighThroughput MS/MS Data

Abstract: Glycosylation, the addition of one or more carbohydrates molecules to a protein, is crucial for many cellular processes. Aberrant glycosylation is a key marker for various diseases such as cancer and rheumatoid arthritis. It has also recently been discovered that glycosylation is important in the ability of the Human Immunodeficiency Virus (HIV) to evade recognition by the immune system. Given the importance of glycosylation in disease, major efforts are underway in life science research to investigate the glycome, the entire glycosylation profile of an organelle, cell or tissue type. To date, little bioinformatics research has been performed in glycomics due to the complexity of glycan structures and the low throughput of carbohydrate analysis. Recent advances in mass spectrometry (MS) have greatly facilitated the analysis of the glycome. Increasingly, this technology is preferred over traditional methods of carbohydrate analysis which are often laborious and unsuitable for low abundance glycoproteins. When subject to mass spectrometry with collision-induced dissociation, glycopeptides produce characteristic MS/MS spectra that can be detected by visual inspection. However, given the high volume of data output from proteome studies today, manually

Glycome: a medical paradigm.

Abstract: The folk cures of early society have become the Complementary and Alternative Medicine of today. Basic science has unlocked many secrets of early herbal compounds and therapies. Computer science has aided in the opening of a new frontier called Glycobiology, the study of saccharides (sugars). This body of knowledge, known as the Glycome, may be the last frontier in medicine’s quest for health.

Strategies for the Development of Nucleic Acid Probes for WMD Agents

Abstract: Distinguishing a particular microorganism from all others demands finding a target sequence that is unique for that organism, is conserved in all members of that species or strain, and has limited or no plasticity. Such targets can be a nucleic acid sequence, constitutive protein, or an antigenic epitope. The target can be probed with PCR-based, immunochemical, or mass spectroscopy assays. Genomics has played an important role in developing new generations of probes. The genomes of an organisms of which is the nucleic acid content has been sequenced and annotated is of invaluable aid in the identifications of targets. Post genomic disciplines such as proteomics and glycomics are and will usher in a new generation probes. The proteome can be defined as a set of proteins produced by an organism under a defined set of conditions.The presence of a protein is the ultimate proof that a gene is being expressed. The glycome represents the glycan groups or saccharide chains attached to proteins or lipids. Surface proteins (S-layer) are ideal targets. Since they are often found at the surface of a cell they are probed with antibodies without breaking the cell.

Glycome analysis by oligosaccharide profiling using liquid chromatography/mass spectrometry

Abstract: Liquid chromatography/mass spectrometry equipped with a graphitized carbon column is useful for the simultaneous analysis of oligosaccharides By using capillary column and nanoelectrospray ion source, the method can be used for the oligosaccharide profiling of sub microgram quantities of glycoproteins This oligosaccharide profiling is expected to be a powerful tool for the glycome analysis We demonstrate a potential application of oligosaccharide profiling in glycomics with two examples, the structural analysis of N-linked oligosaccharides from a gel-separated glycoprotein, and the differential analysis of N-linked oligosaccharides in cells