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We used 16S ribosomal RNA sequencing to evaluate changes in the gut microbiota of mice fed a diet supplemented with either raw or cooked beef loin powder for 9 weeks. Male BALB/c mice (n = 60) were randomly allocated to five groups: mice fed AIN-93G chow (CON), chow containing 5% (5RB) and 10% (10RB) raw beef loin powder, and chow containing 5% (5CB) and 10% (10CB) cooked beef loin powder. Dietary supplementation with both RB and CB increased the relative abundance of Clostridiales compared to the CON diet (p p = 0.018) and Lactobacillus (p = 0.001) than CON mice, and the ratio of Firmicutes/Bacteroidetes showed an increasing trend in the 10RB mice (p > 0.05). Mice fed 10CB showed a higher abundance of Peptostreptococcaceae and a lower abundance of Desulfovibrionaceae compared with the CON mice (p Bacteroides. Overall, dietary RB and CB changed the gut microbiota of mice (p

On-chip glycan biosynthesis is an effective strategy for preparing useful complex glycan sources and for preparing glycan-involved applications simultaneously. However, current methods have some limitations when analyzing biosynthesized glycans and optimizing enzymatic reactions, which could result in undefined glycan structures on a surface, leading to unequal and unreliable results. In this work, a glycan chip is developed by introducing a pH-responsive i-motif DNA linker to control the immobilization and isolation of glycans on chip surfaces in a pH-dependent manner. On-chip enzymatic glycosylations are optimized for uniform biosynthesis of cancer-associated Globo H hexasaccharide and its related complex glycans through stepwise quantitative analyses of isolated products from the surface. Successful interaction analyses of the anti-Globo H antibody and MCF-7 breast cancer cells with on-chip biosynthesized Globo H-related glycans demonstrate the feasibility of the structure-switchable DNA linker-based glycan chip platform for on-chip complex glycan biosynthesis and glycan-involved applications., Current methods for on-chip glycan biosynthesis suffer from analysing products, often resulting in poor purity and yield. Here the authors report a glycan chip developed by introducing a pH-responsive i-motif DNA linker to control the immobilization and isolation of glycans on chips.

Modeling glycan biosynthesis is becoming increasingly important due to the far-reaching implications that glycosylation can exhibit, from pathologies to biopharmaceutical manufacturing. Here we describe a stochastic simulation approach, to overcome the deterministic nature of previous models, that aims to simulate the action of glycan modifying enzymes to produce a glycan profile. This is then coupled with an approximate Bayesian computation methodology to systematically fit to empirical data in order to determine which set of parameters adequately describes the organization of enzymes within the Golgi. The model is described in detail along with a proof of concept and therapeutic applications.

The success of glycoprotein-based drugs in various disease treatments has become widespread. Frequently, therapeutic glycoproteins exhibit a heterogeneous array of glycans that are intended to mimic human glycopatterns. While immunogenic responses to biologic drugs are uncommon, enabling exquisite control of glycosylation with minimized microheterogeneity would improve their safety, efficacy and bioavailability. Therefore, close attention has been drawn to the development of glycoengineering strategies to control the glycan structures. With the accumulation of knowledge about the glycan biosynthesis enzymes, enzymatic glycan remodeling provides a potential strategy to construct highly ordered glycans with improved efficiency and biocompatibility. In this study, we quantitatively evaluate more than 30 enzymes for glycoengineering immobilized immunoglobulin G, an impactful glycoprotein class in the pharmaceutical field. We demonstrate successive glycan remodeling in a solid-phase platform, which enabled IgG glycan harmonization into a series of complex-type N-glycoforms with high yield and efficiency while retaining native IgG binding affinity.SignificanceGlycosylation plays critical functional and structural roles in protein biology. However, our understanding of how discrete glycan structures affect protein behaviors remains extremely limited due to the naturally occurring microheterogeneity. Through the use of characterized glycoengineering enzyme combination, we report a solid-phase glycan remodeling (SPGR) platform that enables efficient IgG glycan harmonization into several glycoforms of interest with high biocompatibility to the substrates. It provides an efficient strategy to screen the biological behavior of distinct glycoforms, building a fundamental understanding of glycosylation.

Glycans are fundamental cellular building blocks, involved in many organismal functions. Advances in glycomics are elucidating the essential roles of glycans. Still, it remains challenging to properly analyze large glycomics datasets, since the abundance of each glycan is dependent on many other glycans that share many intermediate biosynthetic steps. Furthermore, the overlap of measured glycans can be low across samples. We address these challenges with GlyCompare, a glycomic data analysis approach that accounts for shared biosynthetic steps for all measured glycans to correct for sparsity and non-independence in glycomics, which enables direct comparison of different glycoprofiles and increases statistical power. Using GlyCompare, we study diverse N-glycan profiles from glycoengineered erythropoietin. We obtain biologically meaningful clustering of mutant cell glycoprofiles and identify knockout-specific effects of fucosyltransferase mutants on tetra-antennary structures. We further analyze human milk oligosaccharide profiles and find mother’s fucosyltransferase-dependent secretor-status indirectly impact the sialylation. Finally, we apply our method on mucin-type O-glycans, gangliosides, and site-specific compositional glycosylation data to reveal tissues and disease-specific glycan presentations. Our substructure-oriented approach will enable researchers to take full advantage of the growing power and size of glycomics data., Glycomics can uncover important molecular changes but measured glycans are highly interconnected and incompatible with common statistical methods, introducing pitfalls during analysis. Here, the authors develop an approach to identify glycan dependencies across samples to facilitate comparative glycomics.

Despite that obesity is associated with many metabolic diseases, a significant proportion (10–30 %) of obese individuals is recognized as ‘metabolically healthy obeses’ (MHOs). The aim of the current study is to characterize the gut microbiome for MHOs as compared to ‘metabolically unhealthy obeses’ (MUOs). We compared the gut microbiome of 172 MHO and 138 MUO individuals from Chongqing (China) (inclined to eat red meat and food with a spicy taste), and performed validation with selected biomarkers in 40 MHOs and 33 MUOs from Quanzhou (China) (inclined to eat seafood and food with a light/bland taste). The genera Alistipes , Faecalibacterium and Odoribacter had increased abundance in both Chongqing and Quanzhou MHOs. We also observed different microbial functions in MUOs compared to MHOs, including an increased abundance of genes associated with glycan biosynthesis and metabolism. In addition, the microbial gene markers identified from the Chongqing cohort bear a moderate accuracy [AUC (area under the operating characteristic curve)=0.69] for classifying MHOs distinct from MUOs in the Quanzhou cohort. These findings indicate that gut microbiome is significantly distinct between MHOs and MUOs, implicating the potential of the gut microbiome in stratification and refined management of obesity.

Glycobiology is an emerging field of studying glycans (sugars) and glycoconjugates that are essentially involved in almost all biological processes, from fine-tuning glycoprotein function to protein-protein interactions, signaling, immune response, host-pathogen interactions, etc. However, due to structural complexity of glycans and analytical challenges this exciting field was lagging behind other areas of biology. With technological advancements growing number of glycans’ functions are being discovered and the study of glycans is becoming a cutting-edge discipline in basic and clinical research. Despite recent developments in glycobiology field, many aspects of glycosylation process still remain unknown, both in a healthy human organism and in pathological states. Human glycome is dynamic and changes with physiological triggers, immune challenges and disease. Atypical glycosylation is consequently a subject of disease biomarker research, and a target for therapeutic interventions. On the other hand, properties of glycosylated biotherapeutics are predominantly determined by their glycans. The Role of Glycosylation in Health and Disease provides a comprehensive overview of types and functions of glycans in a healthy human organism as well as their role in pathophysiology of different diseases and efficiency of glycosylated biotherapeutics. Written by the experts in the field, this book aims to bring glycobiology field closer to students, researchers in life sciences and professionals in biopharmaceutical industry.

Glycosylation is a common post-translational modification, and glycan biosynthesis is regulated by a set of ‘glycogenes’. The role of transcription factors (TFs) in regulating the glycogenes and related glycosylation pathways is largely unknown. This manuscript presents a multi-omics data-mining framework to computationally predict putative, tissue-specific TF regulators of glycosylation. It combines existing ChIP-Seq (Chromatin Immunoprecipitation Sequencing) and RNA-Seq data to suggest 22,519 potentially significant TF-glycogene relationships. This includes interactions involving 524 unique TFs and 341 glycogenes that span 29 TCGA (The Cancer Genome Atlas) cancer types. Here, TF-glycogene interactions appeared in clusters or ‘communities’, suggesting that changes in single TF expression during both health and disease may affect multiple carbohydrate structures. Upon applying the Fisher’s exact test along with glycogene pathway classification, we identify TFs that may specifically regulate the biosynthesis of individual glycan types. Integration with knowledge from the Reactome database provided an avenue to relate cell-signaling pathways to TFs and cellular glycosylation state. Whereas analysis results are presented for all 29 cancer types, specific focus is placed on human luminal and basal breast cancer disease progression. Overall, the computational predictions in this manuscript present a starting point for systems-wide validation of TF-glycogene relationships.

Glycans play key roles in biological processes. However, complex glycans are not easily accessible and affordable to support diverse functional study. In the efforts of glycan syntheses, one of the most practical approaches is the strategy that employs glycosyltransferases (GTs) – the natural catalysts for glycan biosynthesis. This chapter summarizes the synthetically useful bacterial and mammalian GTs for the preparation of glycans, with an emphasis on mammalian glycans.

Glycobiology entails the study of glycans, or carbohydrate sugar chains. Much research has been made in understanding individual glycogenes such as glycosyltransferases, and glycan structures using glycomics technologies. However, to get an overall understanding of the importance of glycosylation, current technologies are lacking, and systems biology approaches have recently been incorporated to gain better insight into glycosylation mechanisms and their applicability to biological function. Many databases organizing glycobiology data have been developed, and a variety of methods for mathematically modeling glycosylation pathways have shown to be effective. While it is known that glycans modulate signaling pathways, however, the future is wide open for systems glycobiology research.

The study of cellular glycosylation presents many challenges due, in large part, to the non-template driven nature of glycan biosynthesis and their structural complexity. Chemoenzymatic glycan labeling (CEGL) has emerged as a new technique to address the limitations of existing methods for glycan detection. CEGL combines glycosyltransferases and unnatural nucleotide sugar donors equipped with a bioorthogonal chemical tag to directly label specific glycan acceptor substrates in situ within biological samples. This article reviews the current CEGL strategies that are available to characterize cell-surface and intracellular glycans. Applications include imaging glycan expression status in live cells and tissue samples, proteomic analysis of glycoproteins, and target validation. Combined with genetic and biochemical tools, CEGL provides new opportunities to elucidate the functional roles of glycans in human health and disease.

Progress in glycoscience is hampered by a lack of well-defined complex oligosaccharide standards that are needed to fabricate the next generation of microarrays, to develop analytical protocols to determine exact structures of isolated glycans, and to elucidate pathways of glycan biosynthesis. We describe here a chemoenzymatic methodology that makes it possible, for the first time, to prepare any bi-, tri-, and tetra-antennary asymmetric N-glycan from a single precursor. It is based on the chemical synthesis of a tetra-antennary glycan that has N-acetylglucosamine (GlcNAc), N-acetyllactosamine (LacNAc), and unnatural Galα(1,4)-GlcNAc and Manβ(1,4)-GlcNAc appendages. Mammalian glycosyltransferases recognize only the terminal LacNAc moiety as a substrate, and thus this structure can be uniquely extended. Next, the β-GlcNAc terminating antenna can be converted into LacNAc by galactosylation and can then be enzymatically modified into a complex structure. The unnatural α-Gal and β-Man terminating antennae can sequentially be decaged by an appropriate glycosidase to liberate a terminal β-GlcNAc moiety, which can be converted into LacNAc and then elaborated by a panel of glycosyltransferases. Asymmetric bi- and triantennary glycans could be obtained by removal of a terminal β-GlcNAc moiety by treatment with β-N-acetylglucosaminidase and selective extension of the other arms. The power of the methodology is demonstrated by the preparation of an asymmetric tetra-antennary N-glycan found in human breast carcinoma tissue, which represents the most complex N-glycan ever synthesized. Multistage mass spectrometry of the two isomeric triantennary glycans uncovered unique fragment ions that will facilitate identification of exact structures of glycans in biological samples.

Glycosylation refers to the covalent attachment of sugar residues to a protein or lipid, and the biological importance of this modification has been widely recognized. While glycosylation in mammals is being extensively investigated, lower level animals such as invertebrates have not been adequately interrogated for their glycosylation. The rich diversity of invertebrate species, the increased database of sequenced invertebrate genomes and the time and cost efficiency of raising and experimenting on these species have enabled a handful of the species to become excellent model organisms, which have been successfully used as tools for probing various biologically interesting problems. Investigation on invertebrate glycosylation, especially on model organisms, not only expands the structural and functional knowledgebase, but also can facilitate deeper understanding on the biological functions of glycosylation in higher organisms. Here, we reviewed the research advances in invertebrate glycosylation, including N- and O-glycosylation, glycosphingolipids and glycosaminoglycans. The aspects of glycan biosynthesis, structures and functions are discussed, with a focus on the model organisms Drosophila and Caenorhabditis . Analytical strategies for the glycans and glycoconjugates are also summarized.

Phosphoglycosyl transferases (PGTs) initiate the biosynthesis of both essential and virulence-associated bacterial glycoconjugates including lipopolysaccharide, peptidoglycan and glycoproteins. PGTs catalyze the transfer of a phosphosugar moiety from a nucleoside diphosphate sugar to a polyprenol phosphate, to form a membrane-bound polyprenol diphosphosugar product. PGTs are integral membrane proteins, which include between 1 and 11 predicted transmembrane domains. Despite this variation, common motifs have been identified in PGT families through bioinformatics and mutagenesis studies. Bacterial PGTs represent important antibacterial and virulence targets due to their significant role in initiating the biosynthesis of key bacterial glycoconjugates. Considerable effort has gone into mechanistic and inhibition studies for this class of enzymes, both of which depend on reliable, high-throughput assays for easy quantification of activity. This review summarizes recent advances made in the characterization of this challenging but important class of enzymes., National Institutes of Health (Grant GM-039334)

Results from recent studies are breaking the paradigm that all viruses depend on their host machinery to glycosylate their proteins. Chloroviruses encode several genes involved in glycan biosynthesis and some of their capsid proteins are decorated with N-linked oligosaccharides with unique features. Here we describe the elucidation of the N-glycan structure of an unusual chlorovirus, NE-JV-1, that belongs to the Pbi group. The host for NE-JV-1 is the zoochlorella Micractinium conductrix. Spectroscopic analyses established that this N-glycan consists of a core region that is conserved in all of the chloroviruses. The one difference is that the residue 3OMe-L-rhamnose is acetylated at the O-2 position in a non-stoichiometric fashion.

The spatiotemporal regulation of light-gated ion channels is a powerful tool to study physiological pathways and develop personalized theranostic modalities. So far, most existing light-gated channels are limited by their action spectra in the ultraviolet (UV) or visible region. Simple and innovative strategies for the specific attachment of photoswitches on the cell surface without modifying or genetically encoding channel structures, and more importantly, that enable the remote activation of ion-channel functions within near-infrared (NIR) spectral window in living systems, remain a challenging concern. Herein, metabolic glycan biosynthesis is used to achieve site-specific covalent attachment of near-infrared-light-mediated lanthanide-doped upconversion nanocrystals (UCNs) to the cell surface through copper-free click cyclization. Upon irradiation with 808 nm light, the converted emission at 480 nm could activate a light-gated ion channel, channelrhodopsins-2 (ChR2), and thus remotely control the cation influx. This unique strategy provides valuable insights on the specific regulation membrane-associated activities in vivo.

HNK-1 糖鎖は神経系に高発現しており、記憶学習やスパイン構造の成熟に深く関与している。その構造はN- アセチルラクトサミンの非還元末端に硫酸化グルクロン酸が付加した(HSO3)-3GlcA β 1-3Gal β 1-4GlcNAc-) 特徴的なもので、生合成の中心となるのは二種のグルクロン酸転移酵素と硫酸基転移酵素である。我々は、これら転移酵素の活性が細胞内においてどのような機構で調節され、HNK-1 糖鎖の発現がどのように制御されているかに着目した。その結果、これら転移酵素群が複合体を形成して効率的に糖鎖生合成を行っていること、また厳密な細胞内局在制御により生合成活性が調節されていることなどを明らかにした。これらの事実は、HNK-1 糖鎖の発現が合成酵素の多面的な活性調節機構により厳密に制御されることを示唆している。

Glycosylation is an essential form of post-translational modification that regulates intracellular and extracellular processes. Regrettably, conventional biochemical and genetic methods often fall short for the study of glycans, because their structures are often not precisely defined at the genetic level. To address this deficiency, chemists have developed technologies to perturb glycan biosynthesis, profile their presentation at the systems level, and perceive their spatial distribution. These tools have identified potential disease biomarkers and ways to monitor dynamic changes to the glycome in living organisms. Still, glycosylation remains the underexplored frontier of many biological systems. In this Account, we focus on research in our laboratory that seeks to transform the study of glycan function from a challenge to routine practice. In studies of proteins and nucleic acids, functional studies have often relied on genetic manipulations to perturb structure. Though not directly subject to mutation, we can determine glycan structure-function relationships by synthesizing defined glycoconjugates or by altering natural glycosylation pathways. Chemical syntheses of uniform glycoproteins and polymeric glycoprotein mimics have facilitated the study of individual glycoconjugates in the absence of glycan microheterogeneity. Alternatively, selective inhibition or activation of glycosyltransferases or glycosidases can define the biological roles of the corresponding glycans. Investigators have developed tools including small molecule inhibitors, decoy substrates, and engineered proteins to modify cellular glycans. Current approaches offer a precision approaching that of genetic control. Genomic and proteomic profiling form a basis for biological discovery. Glycans also present a rich matrix of information that adapts rapidly to changing environs. Glycomic and glycoproteomic analyses via microarrays and mass spectrometry are beginning to characterize alterations in glycans that correlate with disease. These approaches have already identified several cancer biomarkers. Metabolic labeling can identify recently synthesized glycans and thus directly track glycan dynamics. This approach can highlight changes in physiology or environment and may be more informative than steady-state analyses. Together, glycomic and metabolic labeling techniques provide a comprehensive description of glycosylation as a foundation for hypothesis generation. Direct visualization of proteins via the green fluorescent protein (GFP) and its congeners has revolutionized the field of protein dynamics. Similarly, the ability to perceive the spatial organization of glycans could transform our understanding of their role in development, infection, and disease progression. Fluorescent tagging in cultured cells and developing organisms has revealed important insights into the dynamics of these structures during growth and development. These results have highlighted the need for additional imaging probes.

The filamentous soil bacteria of the genus Streptomyces are commercially exploited for the production of a wide range of natural products such as antibiotics, anticancer agents and immunosuppressants. Additionally, there is a strong interest in the use of these bacteria for the production of industrial proteins. Optimal production of these secondary metabolites and enzymes is tightly coupled to morphology. However, relatively little is known about the genetic determinants influencing the morphology of streptomycetes in liquid-grown cultures. The work presented in this thesis focuses on the formation of extracellular macromolecules and their influence on morphogenesis, with a special emphasis on the role of the cellulose synthase-like protein CslA and the radical copper oxidase GlxA in the production of a tip-localized glycan. This research is of fundamental importance for understanding the determinants of growth and development of this multicellular model organism, and at the same time may help us to further optimize their exploitation for the industrial production of secondary metabolites and enzymes.

To evaluate the qualitative and quantitative changes in N-linked glycosylation, which occurred in association with diethyl nitrosamine-induced hepatocellular carcinoma (HCC) in rodents.Liver tissues of (1) normal (non-tumor-bearing) rats; and (2) tumor-bearing rats; were collected and were used for histological and GlycanMap analyses. Briefly, GlycanMap analysis is a high-throughput assay that provides a structural and quantitative readout of protein-associated glycans using a unique, automated 96-well assay technology coupled to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and custom bioinformatics. Histopathological studies were carried out to ensure the development of HCC in the tested animals.The N-glycomic analysis revealed 5 glycans; Glc₁Man₉GlcNAc₂, Gal₂Man₃GlcNac₄Fuc₁Neu₁, Man₄GlcNac₂, Gal₂Man₃GlcNac₄Neu₃OAc₃, and Man₃GlcNac₅ Fuc₁, which showed significant changes in rat HCC tissues when compared with normal liver tissues. Four glycans were increased (P0.05) and Glc₁Man₉GlcNAc₂ was decreased (5.89 ± 0.45 vs 3.54 ± 0.21, P0.01) in HCC tissues compared to normal liver tissues. An increase (66.5 ± 1.05 vs 62.7 ± 1.1, P0.05) in high-mannose structures in HCC rats was observed compared to normal rats. Importantly, HCC rats showed an increase (P0.05) in both tumor-associated carbohydrates and in branched glycans. The changes in glycans correlated well with glycan flow changes reported in the glycan biosynthetic pathway, which indicates the importance of enzyme activities involved in glycan synthesis at different subcellular localizations.The reported HCC-associated changes in glycan flow and subcellular localization explain the increase in high mannose glycans and siayl Lewis glycans common in HCC liver tissues.

The carbohydrate moieties displayed by pathogenic protozoan parasites exhibit many unusual structural features and their expression is often developmentally regulated. These unique structures suggest a specific relationship between such carbohydrates and parasite pathogenicity. Studies of infected humans indicate that immune responses to protozoan parasites are elicited by glycan determinants on cell-surface or secreted molecules. Infections by protozoa are a major worldwide health problem, and no vaccines or efficacious treatments exist to date. Recent progress has been made in elucidating the structure and function of carbohydrates displayed by major protozoan parasites that infect man. These structures can be used as prototypes for the chemical or combined chemo-enzymatic synthesis of new compounds for diagnosis and vaccine development, or as inhibitors specifically designed to target parasite glycan biosynthesis.

The polypeptide N-α-acetylgalactosaminyltransferases (ppGalNAcTs) play a key role in mucin-type O-linked glycan biosynthesis by installing the intial GalNAc residue on the protein scaffold. The preferred substrates and functions of the >20 isoforms in mammals are not well understood. However, current data suggest that glycosylated mucin domains are created by the successive, often hierarchical, action of several specific ppGalNAcTs. Herein we analyzed the glycopeptide substrate preferences of several ppGalNAcT family members using a library screening approach. A 56-member glycopeptide library designed to reflect a diversity of glycan clustering was assayed for substrate activity with ppGalNAcT isoforms using an azido-ELISA. The data suggest that the ppGalNAcTs can be classified into at least four types, which working together, are able to produce densely glycosylated mucin glycoproteins.

The surfaces of all living cells are decorated with branched sugar polymers known as glycans. These information-rich structures confer cells with a recognizable molecular identity, and underlie many specific cell-cell interactions. Analytic methods - including NMR, mass-spectrometry, and glycan arrays - now permit the routine profiling of glycans associated with various cells or proteins. This has stimulated efforts to build comprehensive and searchable glycan databases. However, from an informatics perspective glycans present multiple challenges. First, whereas nucleotide and amino acid chains are efficiently represented as strings, sugars can polymerize into complex tree-like objects. The potential combinatorial space of glycans is therefore much larger than that of proteins. Second, many specific molecular interactions appear to be mediated by groups of closely-related glycan variants rather than by a single well-defined structure. This phenomenon of “micro-heterogeneity” makes it difficult to rigorously characterize the glycan repertoire of a cell. In this workshop, I will use ideas from algorithmic self-assembly to show that glycan structure and diversity are best understood through the lens of glycan biosynthesis. I will demonstrate that a specific glycan structure is the outcome of glycosyltransferase enzymes acting according to simple rules in a specific order, like workers on a factory floor. Errors in this process produce a well-defined spectrum of glycan by-products, precisely matching the observed micro-heterogeneity in real glycan profiles. This predictive theoretical framework allows us to use glycans as sensitive cell-biological probes. It provides a unifying perspective within which the rich and growing datasets of glycan structures can be organized and fully utilized.

The biological study of O-linked glycosylation is particularly problematic, as chemical tools to control this modification are lacking. An inhibitor of the UDP-GlcNAc 4-epimerase that synthesizes UDP-GalNAc, the donor initiating O-linked glycosylation, would be a powerful reagent for reversibly inhibiting O-linked glycosylation. We synthesized a 1338 member library of uridine analogs directed to the epimerase by virtue of substrate mimicry. Screening of the library identified an inhibitor with a K(i) value of 11 microM. Tests against related enzymes confirmed the compound's specificity for the UDP-GlcNAc 4-epimerase. Inhibitors of a key step of O-linked glycan biosynthesis can be discovered from a directed library screen. Progeny thereof may be powerful tools for controlling O-linked glycosylation in cells.

Glycan biosynthesis is a complex and highly non-linear process requiring a large number of diverse proteins (glycosyltransferases, glycosidases and sugar nucleotide transporters) to act in accord. ...

Summary: Systems glycobiology studies the interaction of various pathways that regulate glycan biosynthesis and function. Software tools for the construction and analysis of such pathways are not yet available. We present GNAT, a platform-independent, user-extensible MATLAB-based toolbox that provides an integrated computational environment to construct, manipulate and simulate glycans and their networks. It enables integration of XML-based glycan structure data into SBML (Systems Biology Markup Language) files that describe glycosylation reaction networks. Curation and manipulation of networks is facilitated using class definitions and glycomics database query tools. High quality visualization of networks and their steady-state and dynamic simulation are also supported. Availability: The software package including source code, help documentation and demonstrations are available at http://sourceforge.net/projects/gnatmatlab/files/. Contact: neel@buffalo.edu or gangliu@buffalo.edu

Here, we determined the staining properties of Balamuthia mandrillaris cysts, and assessed the effect of 2, 6-dichlorobenzonitrile (DCB), a cellulose synthesis inhibitor, and calcofluor white, a brightening agent, on its encystment. Periodic acid-Schiff reagent stained the inner wall intensely and middle and outer walls weakly suggesting that the cyst wall of B. mandrillaris may contain glycans. Furthermore, cysts, but not trophozoites, fluoresced when stained with calcofluor white. Calcofluor white and DCB, a cellulose synthesis inhibitor, inhibited B. mandrillaris encystment. This is the first report suggesting possible glycan biosynthesis in B. mandrillaris encystment, and this pathwaymay provide a potentially useful drug target and help improve treatment.