A rapid extraction method for glycogen from formalin-fixed liver

Using molecular fine structure to identify optimal methods of extracting fungal glycogen

Glycogen is a highly branched glucose polymer that is an energy storage material in fungi and animals. Extraction of glycogen from its source in a way that minimizes its molecular degradation is essential to investigate its native structure. In this study, the following extraction methods were compared: sucrose gradient density ultracentrifugation, thermal alkali, hot alcohol and hot water extractions. Molecular-size and chain-length distributions of glycogen were measured by size-exclusion chromatography and fluorophore-assisted carbohydrate electrophoresis, respectively. These two fine-structure features are the most likely structural characteristics to be degraded during extraction. The results show that the thermal alkali, hot alcohol and hot water extractions degrade glycogen molecular size and/or chain-length distributions, and that sucrose gradient density ultracentrifugation with neither high temperature nor alkaline treatment is the most suitable method for fungal glycogen extraction.

Characterization of 3D organotypic epithelial tissues reveals tonsil-specific differences in tonic interferon signaling

Three-dimensional (3D) culturing techniques can recapitulate the stratified nature of multicellular epithelial tissues. Organotypic 3D epithelial tissue culture methods have several applications, including the study of tissue development and function, drug discovery and toxicity testing, host-pathogen interactions, and the development of tissue-engineered constructs for use in regenerative medicine. We grew 3D organotypic epithelial tissues from foreskin, cervix, and tonsil-derived primary cells and characterized the transcriptome of these in vitro tissue equivalents. Using the same 3D culturing method, all three tissues yielded stratified squamous epithelium, validated histologically using basal and superficial epithelial cell markers. The goal of this study was to use RNA-seq to compare gene expression patterns in these three types of epithelial tissues to gain a better understanding of the molecular mechanisms underlying their function and identify potential therapeutic targets for various diseases. Functional profiling by over-representation and gene set enrichment analysis revealed tissue-specific differences: i.e., cutaneous homeostasis and lipid metabolism in foreskin, extracellular matrix remodeling in cervix, and baseline innate immune differences in tonsil. Specifically, tonsillar epithelia may play an active role in shaping the immune microenvironment of the tonsil balancing inflammation and immune responses in the face of constant exposure to microbial insults. Overall, these data serve as a resource, with gene sets made available for the research community to explore, and as a foundation for understanding the epithelial heterogeneity and how it may impact their in vitro use. An online resource is available to investigate these data (https://viz.datascience.arizona.edu/3DEpiEx/).

Advanced dendritic glucan-derived biomaterials: From molecular structure to versatile applications

There is considerable interest in the development of advanced biomaterials with improved or novel functionality for diversified applications. Dendritic glucans, such as phytoglycogen and glycogen, are abundant biomaterials with highly branched three-dimensional globular architectures, which endow them with unique structural and functional attributes, including small size, large specific surface area, high water solubility, low viscosity, high water retention, and the availability of numerous modifiable surface groups. Dendritic glucans can be synthesized by in vivo biocatalysis reactions using glucosyl-1-phosphate as a substrate, which can be obtained from plant, animal, or microbial sources. They can also be synthesized by in vitro methods using sucrose or starch as a substrate, which may be more suitable for large-scale industrial production. The large numbers of hydroxyl groups on the surfaces of dendritic glucan provide a platform for diverse derivatizations, including nonreducing end, hydroxyl functionalization, molecular degradation, and conjugation modifications. Due to their unique physicochemical and functional attributes, dendritic glucans have been widely applied in the food, pharmaceutical, biomedical, cosmetic, and chemical industries. For instance, they have been used as delivery systems, adsorbents, tissue engineering scaffolds, biosensors, and bioelectronic components. This article reviews progress in the design, synthesis, and application of dendritic glucans over the past several decades.

Analysis of Cell Glycogen with Quantitation and Determination of Branching Using Liquid Chromatography-Mass Spectrometry

Glycogen is a highly branched biomacromolecule that functions as a glucose buffer. It is involved in multiple diseases such as glycogen storage disorders, diabetes, and even liver cancer, where the imbalance between biosynthetic and catabolic enzymes results in structural alterations and abnormal accumulation of glycogen that can be toxic to cells. Accurate and sensitive glycogen quantification and structural determination are prerequisites for understanding the phenotypes and biological functions of glycogen under these conditions. In this research, we furthered cell glycogen characterization by presenting a highly sensitive method to measure the glycogen content and degree of branching. The method employed a novel fructose density gradient as an alternative to the traditional sucrose gradient to fractionate glycogen from cell mixtures using ultracentrifugation. Fructose was used to avoid the large glucose background, allowing the method to be highly quantitative. The glycogen content was determined by quantifying 1-phenyl-3-methyl-5-pyrazolone (PMP)-derivatized glucose residues obtained from acid-hydrolyzed glycogen using ultra-high-performance liquid chromatography/triple quadrupole mass spectrometry (UHPLC/QqQ-MS). The degree of branching was determined through linkage analysis where the glycogen underwent permethylation, hydrolysis, PMP derivatization, and UHPLC/QqQ-MS analysis. The new approach was used to study the effect of insulin on the glycogen phenotypes of human hepatocellular carcinoma (Hep G2) cells. We observed that cells produced greater amounts of glycogen with less branching under increasing insulin levels before reaching the cell's insulin-resistant state, where the trend reversed and the cells produced less but higher-branched glycogen. The advantage of this method lies in its high sensitivity in characterizing both the glycogen level and the structure of biological samples.

Characterization of 3D organotypic epithelial tissues reveals tonsil-specific differences in tonic interferon signaling

Three-dimensional (3D) culturing techniques can recapitulate the stratified nature of multicellular epithelial tissues. Organotypic 3D epithelial tissue culture methods have several applications, including the study of tissue development and function, drug discovery and toxicity testing, host-pathogen interactions, and the development of tissue-engineered constructs for use in regenerative medicine. We grew 3D organotypic epithelial tissues from foreskin, cervix, and tonsil-derived primary cells and characterized the transcriptome of these in vitro tissue equivalents. Using the same 3D culturing method, all three tissues yielded stratified squamous epithelium, validated histologically using basal and superficial epithelial cell markers. The goal of this study was to use RNA-seq to compare gene expression patterns in these three types of epithelial tissues to gain a better understanding of the molecular mechanisms underlying their function and identify potential therapeutic targets for various diseases. Functional profiling by over-representation and gene set enrichment analysis revealed tissue-specific differences: i.e. , cutaneous homeostasis and lipid metabolism in foreskin, extracellular matrix remodeling in cervix, and baseline innate immune differences in tonsil. Specifically, tonsillar epithelia may play an active role in shaping the immune microenvironment of the tonsil balancing inflammation and immune responses in the face of constant exposure to microbial insults. Overall, these data serve as a resource, with gene sets made available for the research community to explore, and as a foundation for understanding the epithelial heterogeneity and how it may impact their in vitro use. An online resource is available to investigate these data ( https://viz.datascience.arizona.edu/3DEpiEx/ ).

Liver fibrosis alters the molecular structures of hepatic glycogen

Liver fibrosis (LF) leads to liver failure and short survival. Liver glycogen is a hyperbranched glucose polymer, comprising individual β particles, which can bind together to form aggregated α particles. Glycogen functionality depends on its molecular structure. This study compared the molecular structure of liver glycogen from both LF and healthy rats, and explored underlying mechanisms for observed differences. Glycogen from both groups contained α and β particles; the LF group contained a higher proportion of β particles, with the glycogen containing fewer long chains than seen in the control group. Both glycogen branching enzyme and glycogen phosphorylase showed a significant decrease of activity in the LF group. Transcriptomics and proteomics revealed a functional deficiency of mitochondria in the LF group, which may lead to changes in glycogen structure. These results provide for the first time an understanding of how liver fibrosis affects liver glycogen metabolism and glycogen structure. HYPOTHESIS: We hypothesized that the molecular structure of liver glycogen from a rat model of liver fibrosis would be altered compared to the control group.

Optimization of liver glycogen extraction when considering the fine molecular structure

Liver glycogen is a branched glucose polymer that functions as a blood-sugar buffer in animals. Previous studies have shown that glycogen's molecular structure affects its properties. This makes it important to develop a technique that extracts and purifies a representative sample of glycogen. Here we aim to optimize the sucrose density gradient centrifugation method for preserving glycogen's molecular structure by varying the density of the sucrose solution. The preservation of glycogen's structure involves: 1) minimizing molecular damage and 2) obtaining a structurally representative sample of glycogen. The addition of a 10-minute boiling step was also tested as a means for denaturing any glycogen degrading enzymes. Lower sucrose concentrations and the introduction of the boiling step were shown to be beneficial in obtaining a more structurally representative sample, with the preservation of smaller glycogen particles and decreased glycogen chain degradation.

The importance of glycogen molecular structure for blood glucose control

Type 2 diabetes incidence continues to increase rapidly. This disease is characterized by a breakdown in blood glucose homeostasis. The impairment of glycemic control is linked to the structure of glycogen, a highly branched glucose polymer. Liver glycogen, a major controller of blood sugar, comprises small β particles which can link together to form larger α particles. These degrade to glucose more slowly than β particles, enabling a controlled release of blood glucose. The α particles in diabetic mice are however easily broken down into β particles, which degrade more quickly. Because this may lead to higher blood glucose, understanding this diabetes-associated breakdown of α-particle molecular structure may help in the development of diabetes therapeutics. We review the extraction of liver glycogen, its molecular structure, and how this structure is affected by diabetes and then use this knowledge to make postulates to guide the development of strategies to help mitigate type 2 diabetes.

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Diabetes involves uncontrolled blood glucose levels

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Liver glycogen acts as a blood glucose buffer

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Diabetes can lead to molecularly fragile liver glycogen particles

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Molecularly fragile liver glycogen may exacerbate poor blood glucose control

Metformin and Berberine suppress glycogenolysis by inhibiting glycogen phosphorylase and stabilizing the molecular structure of glycogen in db/db mice

Glycogen is a branched glucose polymer involved in sustaining blood glucose homeostasis. Liver glycogen comprises α particles (up to 300 nm in diameter) made of joined β particles (∼20 nm in diameter). Glycogen α particles in a mouse model for diabetes are molecularly fragile, breaking down into smaller β particles more readily than in healthy mice. Glycogen phosphorylase (GP), a rate-limiting enzyme in glycogen degradation, is overexpressed in diabetic mice. This study shows that Metformin and Berberine, two common drugs, two common drugs used to treat diabetes, are able to revert the liver glycogen of diabetic mice to the stable structure seen in non-diabetic mice. It is also shown that these drugs reduce the GP level via the cAMP/PKA signaling pathway in diabetic livers and decrease the affinity of GP with the glycogen of db/db mice. These effects of these drugs may slow down the degradation of liver glycogen and improve glucose homeostasis.

Glycogen as a Building Block for Advanced Biological Materials

Biological nanoparticles found in living systems possess distinct molecular architectures and diverse functions. Glycogen is a unique biological polysaccharide nanoparticle fabricated by nature through a bottom-up approach. The biocatalytic synthesis of glycogen has evolved over time to form a nanometer-sized dendrimer-like structure (20-150 nm) with a highly branched surface and a dense core. This makes glycogen markedly different from other natural linear or branched polysaccharides and particularly attractive as a platform for biomedical applications. Glycogen is inherently biodegradable, nontoxic, and can be functionalized with diverse surface and internal motifs for enhanced biofunctional properties. Recently, there has been growing interest in glycogen as a natural alternative to synthetic polymers and nanoparticles in a range of applications. Herein, the recent literature on glycogen in the material-based sciences, including its use as a constituent in biodegradable hydrogels and fibers, drug delivery vectors, tumor targeting and penetrating nanoparticles, immunomodulators, vaccine adjuvants, and contrast agents, is reviewed. The various methods of chemical functionalization and physical assembly of glycogen nanoparticles into multicomponent nanodevices, which advance glycogen toward a functional therapeutic nanoparticle from nature and back again, are discussed in detail.

Recent progress in the structure of glycogen serving as a durable energy reserve in bacteria

Glycogen is conventionally considered as a transient energy reserve that can be rapidly synthesized for glucose accumulation and mobilized for ATP production. However, this conception is not completely applicable to prokaryotes due to glycogen structural heterogeneity. A number of studies noticed that glycogen with small average chain length g_c in bacteria has the potential to degrade slowly, which might prolong bacterial environment survival. This phenomenon was previously examined and later formulated as the durable energy storage mechanism hypothesis. Although recent research has been warming to the hypothesis, experimental validation is still missing at current stage. In this review, we summarized recent progress of the hypothesis, provided a supporting mathematical model, and explored the technical pitfalls that shall be avoided in glycogen study.

Is liver glycogen fragility a possible drug target for diabetes?

Liver glycogen α particles are molecularly fragile in diabetic mice, and readily form smaller β particles, which degrade more rapidly to glucose. This effect is well associated with the loss of blood-glucose homeostasis in diabetes. The biological mechanism of such fragility is still unknown; therefore, there are perceived opportunities that could eventually lead to new means to manage type 2 diabetes. The hierarchical structures of glycogen particles are controlled by the underlying biosynthesis/degradation process that involves various enzymes, including, for example, glycogen synthase (GS) and glycogen-branching enzyme (GBE). Recent studies have shown that fragile glycogen α particles in diabetic mice have longer chains and a higher molecular density compared to wild-type mice, indicating an enhanced enzymatic activity ratio of GS to GBE in diabetes. Furthermore, it has been shown that with an improved blood glucose homeostasis, the glycogen fragility in diabetic mice can be restored by treatment with active ingredients from traditional Chinese medicine, yet the underlying mechanism is unknown. In this review, we summarize recent advances in understandings glycogen fragility from the perspectives of glycogen biosynthesis/degradation, glycogen hierarchical structures, and its relation to diabetes. Importantly, we for the first time set GS/GBE activity ratio as the therapeutic target for diabetes.

Glucose and glycogen in the diabetic kidney: Heroes or villains?

Glucose metabolism in the kidney is currently foremost in the minds of nephrologists, diabetologists and researchers globally, as a result of the outstanding success of SGLT2 inhibitors in reducing renal and cardiovascular disease in individuals with diabetes. However, these exciting data have come with the puzzling but fascinating paradigm that many of the beneficial effects on the kidney and cardiovascular system seem to be independent of the systemic glucose lowering actions of these agents. This manuscript places into context an area of research highly relevant to renal glucose metabolism, that of glycogen accumulation and metabolism in the diabetic kidney. Whether the glycogen that abnormally accumulates is pathological (the villain), is somehow protective (the hero) or is inconsequential (the bystander) is a research question that may provide insight into the link between diabetes and diabetic kidney disease.

Molecular Structure of Glycogen in Escherichia coli

Glycogen, a randomly branched glucose polymer, provides energy storage in organisms. It forms small β particles which in animals bind to form composite α particles, which give better glucose release. Simulations imply β particle size is controlled only by activities and sizes of glycogen biosynthetic enzymes and sizes of polymer chains. Thus, storing more glucose requires forming more β particles, which are expected to sometimes form α particles. No α particles have been reported in bacteria, but the extraction techniques might have caused degradation. Using milder glycogen extraction techniques on Escherichia coli, transmission electron microscopy and size-exclusion chromatography showed α particles, consistent with this hypothesis for α-particle formation. Molecular density and size distributions show similarities with animal glycogen, despite very different metabolic processes. These general polymer constraints are such that any organism which needs to store and then release glucose will have similar α and β particle structures: a type of convergent evolution.

Glycogen structure in type 1 diabetic mice: Towards understanding the origin of diabetic glycogen molecular fragility

Glycogen is a complex branched glucose polymer. Liver glycogen in db/db mouse, a type-2 diabetic mouse model, has been found to be more molecularly fragile than in healthy mice. Size-exclusion chromatography was employed in this study to investigate the molecular structure of liver glycogen in two types of type 1 diabetic mouse models (NOD and C57BL/6J mice), sacrificed at various times throughout the diurnal cycle, and the fragility of liver glycogen after exposure to a hydrogen-bond disruptor were tested. Type 1 diabetic mice exhibit a similar glycogen fragility with that observed for db/db mice. This eliminates many of the potential causes for glycogen molecular fragility; the most likely explanation is that it is caused by high blood-glucose level and/or insulin deficiency, both phenotypes being common to both type 1 and type 2 diabetic mice. This result suggests ways towards new drug targets for the management of diabetes.

Proteomic Investigation of the Binding Agent between Liver Glycogen β Particles

Glycogen is a highly branched glucose polymer which plays an important role in glucose storage and the maintenance of blood sugar homeostasis. The dimeric protein glycogenin can self-glucosylate to act as a primer for glycogen synthesis, eventually resulting in small (∼20 nm diameter) glycogen β particles with a dimer of glycogenin at their core. In the liver, glycogen is also found in the form of α particles: large bound composites of many β particles. Here, we provide evidence using qualitative and quantitative proteomics and size-exclusion chromatography from healthy rat, mouse, and human liver glycogen that glycogenin is the binding agent linking β particles together into α particles.

Diurnal changes of glycogen molecular structure in healthy and diabetic mice

Glycogen is a complex branched glucose polymer functioning as a blood-sugar reservoir in animals. Liver glycogen β particles can bind together to form α particles, which have a slower enzymatic degradation to glucose. The linkage between β particles in α particles in diabetic liver breaks (is fragile) in dimethyl sulfoxide (DMSO), a H-bond disruptor, consistent with blood-sugar homeostasis loss in diabetes. We examined diurnal changes in the molecular structure of healthy and diabetic mouse-liver glycogen. Healthy mouse glycogen was fragile to DMSO during glycogen synthesis but not degradation; diabetic glycogen was always fragile. Two alternative mechanisms for this are suggested: healthy glycogen is fragile when formed and becomes stable during subsequent degradation, a process damaged in diabetes; alternatively, there are two types of glycogen: one compact but fragile and the other loose but non-fragile. This suggests potential types of diabetes drug targets through modifying the activities of glycogen synthesis enzymes.

Sirtuins in the phylum Basidiomycota: A role in virulence in Cryptococcus neoformans

Virulence of Cryptococcus neoformans is regulated by a range of transcription factors, and is also influenced by the acquisition of adaptive mutations during infection. Beyond the temporal regulation of virulence factor production by transcription factors and these permanent microevolutionary changes, heritable epigenetic modifications such as histone deacetylation may also play a role during infection. Here we describe the first comprehensive analysis of the sirtuin class of NAD+ dependent histone deacetylases in the phylum Basidiomycota, identifying five sirtuins encoded in the C. neoformans genome. Each sirtuin gene was deleted and a wide range of phenotypic tests performed to gain insight into the potential roles they play. Given the pleiotropic nature of sirtuins in other species, it was surprising that only two of the five deletion strains revealed mutant phenotypes in vitro. However, cryptic consequences of the loss of each sirtuin were identified through whole cell proteomics, and mouse infections revealed a role in virulence for SIR2, HST3 and HST4. The most intriguing phenotype was the repeated inability to complement mutant phenotypes through the reintroduction of the wild-type gene. These data support the model that regulation of sirtuin activity may be employed to enable a drastic alteration of the epigenetic landscape and virulence of C. neoformans.

A new non-degradative method to purify glycogen

Liver glycogen, a complex branched glucose polymer containing a small amount of protein, is important for maintaining glucose homeostasis (blood-sugar control) in humans. It has recently been found that glycogen molecular structure is impaired in diabetes. Isolating the carbohydrate polymer and any intrinsically-attached protein(s) is an essential prerequisite for studying this structural impairment. This requires an effective, non-degradative and efficient purification method to exclude the many other proteins present in liver. Proteins and glycogen have different ranges of molecular sizes. Despite the plethora of proteins that might still be present in significant abundance after other isolation techniques, SEC (size exclusion chromatography, also known as GPC), which separates by molecular size, should separate those extraneous to glycogen from glycogen with any intrinsically associated protein(s). A novel purification method is developed for this, based on preparative SEC following sucrose gradient centrifugation. Proteomics is used to show that the new method compares favourably with current methods in the literature.

Molecular Structure of Human-Liver Glycogen

Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets.

Acid hydrolysis and molecular density of phytoglycogen and liver glycogen helps understand the bonding in glycogen α (composite) particles

Phytoglycogen (from certain mutant plants) and animal glycogen are highly branched glucose polymers with similarities in structural features and molecular size range. Both appear to form composite α particles from smaller β particles. The molecular size distribution of liver glycogen is bimodal, with distinct α and β components, while that of phytoglycogen is monomodal. This study aims to enhance our understanding of the nature of the link between liver-glycogen β particles resulting in the formation of large α particles. It examines the time evolution of the size distribution of these molecules during acid hydrolysis, and the size dependence of the molecular density of both glucans. The monomodal distribution of phytoglycogen decreases uniformly in time with hydrolysis, while with glycogen, the large particles degrade significantly more quickly. The size dependence of the molecular density shows qualitatively different shapes for these two types of molecules. The data, combined with a quantitative model for the evolution of the distribution during degradation, suggest that the bonding between β into α particles is different between phytoglycogen and liver glycogen, with the formation of a glycosidic linkage for phytoglycogen and a covalent or strong non-covalent linkage, most probably involving a protein, for glycogen as most likely. This finding is of importance for diabetes, where α-particle structure is impaired.

Molecular structure of glycogen in diabetic liver

Liver glycogen (involved in maintaining blood-sugar levels) is a hyperbranched glucose polymer containing β particles (diameter ~20 nm), which can form composite α particles (diameter ~50-300 nm), and includes a small but significant amount of bound protein. Size distributions of glycogen from livers of healthy and diabetic mice were examined using size-exclusion chromatography with two separate eluents: aqueous eluent and dimethylsulfoxide (DMSO) eluent. Morphologies were examined with transmission electron microscopy. Diabetic glycogen (DG) exhibited many α particles in the mild water-based solvent, but in DMSO, which breaks H bonds, these degraded to β particles; α particles however were always present in healthy glycogen (HG). This DG fragility shows the binding of β into α particles is different in HG and DG. The diabetic α particle fragility may be involved with the uncontrolled blood-sugar release symptomatic of diabetes: small β particles degrade more easily to glucose than α particles. This has implications for diabetes management.

Evolutionary Engineering Improves Tolerance for Replacement Jet Fuels in Saccharomyces cerevisiae

Monoterpenes are liquid hydrocarbons with applications ranging from flavor and fragrance to replacement jet fuel. Their toxicity, however, presents a major challenge for microbial synthesis. Here we evolved limonene-tolerant Saccharomyces cerevisiae strains and sequenced six strains across the 200-generation evolutionary time course. Mutations were found in the tricalbin proteins Tcb2p and Tcb3p. Genomic reconstruction in the parent strain showed that truncation of a single protein (tTcb3p(1-989)), but not its complete deletion, was sufficient to recover the evolved phenotype improving limonene fitness 9-fold. tTcb3p(1-989) increased tolerance toward two other monoterpenes (β-pinene and myrcene) 11- and 8-fold, respectively, and tolerance toward the biojet fuel blend AMJ-700t (10% cymene, 50% limonene, 40% farnesene) 4-fold. tTcb3p(1-989) is the first example of successful engineering of phase tolerance and creates opportunities for production of the highly toxic C10 alkenes in yeast.