SugarDrawer: A Web-Based Database Search Tool with Editing Glycan Structures.

In life science fields, database integration is progressing and contributing to collaboration between different research fields, including the glycosciences. The integration of glycan databases has greatly progressed collaboration worldwide with the development of the international glycan structure repository, GlyTouCan. This trend has increased the need for a tool by which researchers in various fields can easily search glycan structures from integrated databases. We have developed a web-based glycan structure search tool, SugarDrawer, which supports the depiction of glycans including ambiguity, such as glycan fragments which contain underdetermined linkages, and a database search for glycans drawn on the canvas. This tool provides an easy editing feature for various glycan structures in just a few steps using template structures and pop-up windows which allow users to select specific information for each structure element. This tool has a unique feature for selecting possible attachment sites, which is defined in the Symbol Nomenclature for Glycans (SNFG). In addition, this tool can input and output glycans in WURCS and GlycoCT formats, which are the most commonly-used text formats for glycan structures.

Polysaccharides from Polyporus umbellatus: A review on their extraction, modification, structure, and bioactivities.

Polyporus umbellatus (Pers.) Fries, a well-known medicinal fungus, has been reported to exhibit important functions of diuresis and dampness infiltration in traditional Chinese Medicine. Accumulating evidences have demonstrated that the P. umbellatus polysaccharides (PUPs) are the main and representative pharmacologically active ingredients and display multiple bioactivities both in vivo and in vitro methods, such as those of antioxidant, immunomodulatory, antitumor, anti-proliferative and hepatoprotective. Besides, many PUPs have been isolated from the different sources of P. umbellatus, including sclerotia, fruiting body, mycelia and fermentation liquid of this fungus. The purpose of the present review is to comprehensively and systematically reorganize the available information related to the extraction, purification, modification, structure characterization and to discuss diverse biological activities of PUPs to support their potential application value in pharmaceuticals field, functional foods and cosmetics areas. In addition, new invaluable insights on the future research with PUPs have also been proposed in the important areas of structural characterization and pharmacological activities.

Structural characterization of a polysaccharide from Radix Hedysari and its protective effects against H2O2-induced injury in human gastric epithelium cells.

The gastroprotective effects of polysaccharides had become a hot topic in the field of functional polysaccharides research. Three polysaccharides, namely HPS-80-1, HPS-80-2, and HPS-80-3 were purified by DEAE-52 column chromatography. The thermodynamic characteristics, scanning electron microscopy, and Congo red experimental results of the above polysaccharides were greatly distinctive. Then a mature GES-1 oxidative stress cell model induced by H2O2 was established to screen out subsequent research subjects. It turned out that HPS-80-1 had a desirable protective effect, which was confirmed by analyses of cell cycle & apoptosis, and oxidative stress-related factors in the cell culture media, and so on. Furthermore, Structural features demonstrated that the backbone of HPS-80-1 appeared to mainly consist of →4)-α-D-Glcp-(1→, →4,6)-ß-L-Glcp-(1→, and →6)-α-D-Galp-(1→, with branches at O-1, O-4, and O-6 position consisting of →2,4)-ß-D-Rhap-(1→, →1)-α-D-Galp-(4→, and →3,4)-α-D-Manp-(1→. It was speculated that the excellent gastric mucosal protective activity of HPS-80-1 may be due to the high amount of glucose in the backbone. In addition, it was also related to the anti-inflammatory activity and antioxidant bases such as (1 â†’ 4)-Glcp and (1 â†’ 6)-Galp in the structure of HPS-80-1. These findings provide a scientific basis for further utilization of polysaccharides from Radix Hedysari.

Effect of Fe (III), Zn (II), and Cr (III) complexation on the physicochemical properties and bioactivities of corn silk polysaccharide.

In this paper, Fe (III), Zn (II), and Cr (III) were used to complex with corn silk polysaccharide (CSP) by classical methods and CSP-Fe, CSP-Zn, and CSP-Cr were successfully synthesized, respectively. The physicochemical properties and structural features were characterized by chemical composition analysis, inductive coupled plasma-mass spectrometry (ICP-MS), ultraviolet-visible (UV-Vis) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, fourier transform infrared (FT-IR) spectroscopy, circular dichroism (CD) spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM), and differential scanning calorimetry (DSC), respectively. The antioxidant activities and inhibitory effects on α-glucosidase of CSP, CSP-Fe, CSP-Zn, and CSP-Cr were compared. The results showed that the Fe (III), Zn (II), and Cr (III) chelation could change the morphology, conformation, thermostability, and biological activities of CSP. CSP-Zn exhibited higher antioxidant activities and inhibition effects on α-glucosidase than CSP, which suggested that it could be considered as a potential candidate for developing an ingredient of functional foods for antidiabetics.

Characterization of a neutral polysaccharide from pumpkin (Cucurbita moschata Duch) with potential immunomodulatory activity.

A neutral polysaccharide designated as CMDP-1a (molecular mass 9.263 kDa) was isolated from Cucurbita moschata Duch through hot water extraction, ethanol precipitation, and column chromatography. On the basis of methylation, fourier-transform infrared, monosaccharide composition, and one- and two-dimensional nuclear magnetic resonance spectroscopy analyses, the structure of CMDP-1a was determined to be a backbone composed of α-1,4 linked glucopyranosyl residues with α-Glcp residue linkage at backbone C-6. Atomic force microscopy and scanning electron microscopy analyses revealed that CMDP-1a had a spherical conformation in solution. In immunostimulation assays, CMDP-1a promoted the proliferation of RAW 264.7 macrophages and significantly enhanced their pinocytic and phagocytic capacity. Furthermore, CMDP-1a induced the M1 polarization of original macrophages and the conversion of macrophages from M2 to M1, thereby modulating the balance of M1/M2 macrophages. These results indicated that CMDP-1a might be a potential immunomodulator for food purposes.

The Marine Polysaccharide Ulvan Confers Potent Osteoinductive Capacity to PCL-Based Scaffolds for Bone Tissue Engineering Applications.

Hybrid composites of synthetic and natural polymers represent materials of choice for bone tissue engineering. Ulvan, a biologically active marine sulfated polysaccharide, is attracting great interest in the development of novel biomedical scaffolds due to recent reports on its osteoinductive properties. Herein, a series of hybrid polycaprolactone scaffolds containing ulvan either alone or in blends with κ-carrageenan and chondroitin sulfate was prepared and characterized. The impact of the preparation methodology and the polysaccharide composition on their morphology, as well as on their mechanical, thermal, water uptake and porosity properties was determined, while their osteoinductive potential was investigated through the evaluation of cell adhesion, viability, and osteogenic differentiation of seeded human adipose-derived mesenchymal stem cells. The results verified the osteoinductive ability of ulvan, showing that its incorporation into the polycaprolactone matrix efficiently promoted cell attachment and viability, thus confirming its potential in the development of biomedical scaffolds for bone tissue regeneration applications.

Optimization of fermentation of Fomes fomentarius extracellular polysaccharide and antioxidation of derivatized polysaccharides.

Fermentation is a metabolic process that converts sugars into acids, gases, or alcohol. This process occurs in yeasts and bacteria, as well as in muscle cells when faced with a lack of oxygen. In this paper, isolation, culture, purification and extracellular polysaccharides of strain Fomes fomentarius were studied. Extraction of polysaccharides from a culture based on F. fomentarius extracellular polysaccharides, extracellular polysaccharides fermentation experiments was optimized and compared, the optimal fermentation method was obtained; extracellular polysaccharides were sulfated, phosphorylated experiments, selenium acidified, discussed the preparation of derivative polysaccharides and microscopic detection, and finally studied extracellular polysaccharides on DPPH, The scavenging ability, superoxide anion radical and hydroxyl radical scavenging ability of the derived polysaccharides were compared. The results showed that the extracellular polysaccharide and derivatized polysaccharide of F. fomentarius had certain antioxidant activity.

Single-particle cryo-EM at atomic resolution.

The three-dimensional positions of atoms in protein molecules define their structure and their roles in biological processes. The more precisely atomic coordinates are determined, the more chemical information can be derived and the more mechanistic insights into protein function may be inferred. Electron cryo-microscopy (cryo-EM) single-particle analysis has yielded protein structures with increasing levels of detail in recent years1,2. However, it has proved difficult to obtain cryo-EM reconstructions with sufficient resolution to visualize individual atoms in proteins. Here we use a new electron source, energy filter and camera to obtain a 1.7 Å resolution cryo-EM reconstruction for a human membrane protein, the ß3 GABAA receptor homopentamer3. Such maps allow a detailed understanding of small-molecule coordination, visualization of solvent molecules and alternative conformations for multiple amino acids, and unambiguous building of ordered acidic side chains and glycans. Applied to mouse apoferritin, our strategy led to a 1.22 Å resolution reconstruction that offers a genuine atomic-resolution view of a protein molecule using single-particle cryo-EM. Moreover, the scattering potential from many hydrogen atoms can be visualized in difference maps, allowing a direct analysis of hydrogen-bonding networks. Our technological advances, combined with further approaches to accelerate data acquisition and improve sample quality, provide a route towards routine application of cryo-EM in high-throughput screening of small molecule modulators and structure-based drug discovery.

Mesopolysaccharides: The extracellular surface layer of visceral organs.

The mesothelium is a dynamic and specialized tissue layer that covers the somatic cavities (pleural, peritoneal, and pericardial) as well as the surface of the visceral organs such as the lung, heart, liver, bowel and tunica vaginalis testis. The potential therapeutic manipulation of visceral organs has been complicated by the carbohydrate surface layer-here, called the mesopolysaccharide (MPS)-that coats the outer layer of the mesothelium. The traditional understanding of MPS structure has relied upon fixation techniques known to degrade carbohydrates. The recent development of carbohydrate-preserving fixation for high resolution imaging techniques has provided an opportunity to re-examine the structure of both the MPS and the visceral mesothelium. In this report, we used high pressure freezing (HPF) as well as serial section transmission electron microscopy to redefine the structure of the MPS expressed on the murine lung, heart and liver surface. Tissue preserved by HPF and examined by transmission electron microscopy demonstrated a pleural MPS layer 13.01±1.1 um deep-a 100-fold increase in depth compared to previously reported data obtained with conventional fixation techniques. At the base of the MPS were microvilli 1.1±0.35 um long and 42±5 nm in diameter. Morphological evidence suggested that the MPS was anchored to the mesothelium by microvilli. In addition, membrane pits 97±17 nm in diameter were observed in the apical mesothelial membrane. The spatial proximity and surface density (29±4.5%) of the pits suggested an active process linked to the structural maintenance of the MPS. The striking magnitude and complex structure of the MPS indicates that it is an important consideration in studies of the visceral mesothelium.

Polysaccharides from pineapple core as a canning by-product: Extraction optimization, chemical structure, antioxidant and functional properties.

Ultrasonic-assisted extraction (UAE) technique has been investigated to extract polysaccharides from pineapple core as a by-product using response surface methodology. A Box-Behnken design was employed to optimize the conditions for the maximum extraction yield of polysaccharides. The results demonstrated that the optimum extraction conditions were as follows: water/solid material ratio of 29.5 mL/g, extraction temperature of 66.3 °C and extraction time of 46.7 min. Under these conditions, the extraction yield of pineapple core polysaccharides (PCPs) was 16.7%. The structure of PCPs was analyzed by Fourier transform-infrared spectroscopy (FT-IR) analysis, X-ray diffractometry (XRD), SEM (scanning electron microscope) and gas chromatography-mass spectrometry (GC-MS). The results of thermogravimetric analysis indicated that the PCPs had a good thermal stability at temperatures below 250 °C. The extracted polysaccharides had a porous structure with rough surface. The extracted polysaccharides had strong scavenging activities on DPPH and hydroxyl radicals. Furthermore, they demonstrated interesting water-holding and fat-binding capacities (3.11 and 4.25 g/g, respectively). The results revealed that polysaccharides displayed good emulsifying and foaming properties. Overall, the findings suggest that PCPs are a promising source of antioxidants and may have potential applications in functional food industries.

An ultrasonic-extracted arabinoglucan from Tamarindus indica L. pulp: A study on molecular and structural characterizations.

In this study, an ultrasonic-extracted polysaccharide (nCPTP-55) was obtained with the highest yield (61.08%, w/w) from tamarind pulp, which consisted chiefly of total sugar (85.98%, w/w) with few protein (2.10%, w/w). Monosaccharide analysis showed nCPTP-55 was mainly composed of arabinose (39.19 mol%) and glucose (50.48 mol%) with negligible GlcA (2.05 mol%), indicating the neutral nature of nCPTP-55, which was further elucidated structurally via GC-MS and NMR, i.e., an arabinoglucan composed of →3)-ß-D-Glcp-(1→ backbone with only T-α-L-Araf-(1→ branched at O-4 (27.82%) and O-6 (39.99%), resulting in relatively high A/G ratio (0.68-0.70). Based on MM2 minimized energy, the 3D schematic structures of nCPTP-55 could be considered as structural basis for its conformational behavior, which was preliminarily estimated via HPSEC-MALLS as between compact sphere and loosely hyper-branched chain (ρ = 0.84). Therefore, the relationship between molecular structure and conformational behavior was basically established for nCPTP-55, which was in a bid to have a better knowledge of its structure-property and structure-bioactivity relationships potentially required for more applications in food, cosmetic and pharmaceutical fields.

Effects of ultrasound-assisted enzyme hydrolysis on the microstructure and physicochemical properties of okara fibers.

This work focuses on the effects of different ultrasound power densities on the microstructural changes and physicochemical properties of okara fibers, which are composed of carbohydrate-based polymers. Okara suspensions were treated with ultrasound at different power densities (0, 1, 2, 3, 4, and 5 W/mL) for 30 min, after which the ultrasound-treated okara were hydrolyzed by trypsin to obtain okara fibers. The ultrasound treatment of the okara fibers induced structural disorganization and changes, evidenced mainly in their morphological characteristics and their relative crystallinity degrees. Increasing the ultrasound power broke the okara fibers into flaky and stacked structures. When the ultrasound power density reached 4 W/mL, the parenchyma became compact and the hourglass structure fractured. The mean particle size of the okara fiber was reduced from 82.24 µm to 53.96 µm, and the homogeneity was enhanced significantly. The relative crystallinity of the okara fibers was reduced from 55.14% to 36.47%. The okara fiber surface charge decreased when the ultrasound power was increased. However, after ultrasound treatment at 4 W/mL (800 W), the okara fiber suspension exhibited the highest viscosity value and a higher swelling capacity, water-holding capacity, and oil-holding capacity. Therefore, the results indicated that the selection of processing conditions for okara fibers is critical and that okara fiber modification using a high ultrasound treatment might improve their use in potential applications.

Structural characteristics and anti-complement activities of polysaccharides from Sargassum hemiphyllum.

Three polysaccharides (SH-1, SH-2 and SH-3) were purified from a brown macroalgea, Sargassum hemiphyllum. The autohydrolysis products from each polysaccharide were separated to three fractions (S fractions as oligomers, L fractions as low molecular weight polysaccharides and H fractions as high molecular weight polysaccharides). Mass spectroscopy of S fractions (SH-1-S, SH-2-S and SH-3-S) showed that these three polymers all contained short stretches of sulfated fucose. The structures of L fractions (SH-1-L, SH-2-L and SH-3-L) were determined by nuclear magnetic resonance (NMR). SH-1-L was composed of two units, unit A (sulfated galactofucan) and unit B (sulfated xylo-glucuronomannan). Unit A contained a backbone of (1, 6-linked ß-D-Gal) n1, (1, 3-linked 4-sulfated α-L-Fuc) n2, (1, 3-linked 2, 4-di-sulfated α-L-Fuc) n3, (1, 4-linked α-L-Fuc) n4 and (1, 3-linked ß-D-Gal) n5, accompanied by some branches, such as sulfated fuco-oligomers, sulfated galacto-oligomers or sulfated galacto-fuco-oligomers. And unit B consisted of alternating 1, 4-linked ß-D-glucuronic acid (GlcA) and 1, 2-linked α-D-mannose (Man) with the Man residues randomly sulfated at C6 or branched with xylose (Xyl) at C3. Both SH-2-L and SH-3-L were composed of unit A and their difference was attributed to the ratio of n1: n2: n3: n4: n5. Based on monosaccharide analysis, we hypothesize that both SH-1-H and SH-2-H contained unit A and unit B while SH-3-H had a structure similar to SH-3-L. An assessment of anti-complement activities showed that the sulfated galactofucan had higher activities than sulfated galacto-fuco-xylo-glucuronomannan. These results suggest that the sulfated galactofucans might be a good candidate for anti-complement drugs.

Characterization of Polysaccharides Extracted from Pulps and Seeds of Crataegus azarolus L. var. aronia: Preliminary Structure, Antioxidant, Antibacterial, α-Amylase, and Acetylcholinesterase Inhibition Properties.

Polysaccharides from the pulps (CAP) and seeds (CAS) of Crataegus azarolus L. var. aronia were extracted by hot water method. Both polysaccharides were characterized by scanning electron microscopy (SEM), Congo red test, FT-IR spectroscopy, and their antioxidant, α-amylase, antiacetylcholinesterase, and antibacterial activities were evaluated. CAP showed the highest total carbohydrate (82.35%) and uronic acid (29.39%) contents. The Congo red test revealed the lack of triple-helical conformation for both polysaccharides. The comparison of both infrared spectra indicated similar patterns with the presence of typical bands of polysaccharides. However, the microstructure of both samples indicated differences when analyzed by SEM. CAP displayed higher antioxidant, α-amylase, and acetylcholinesterase inhibitory activities. Besides, CAP showed the strongest antimicrobial effects against seven microorganisms and, notably, the Gram-positive bacteria. Overall, the results suggest that polysaccharides from C. azarolus L. var. aronia may be considered as novel sources of antioxidants and recommended as enzyme inhibitory agents in food and pharmaceutical industries.

Using a novel polysaccharide BM2 produced by Bacillus megaterium strain PL8 as an efficient bioflocculant for wastewater treatment.

In this study, the purification and characterization of a novel polysaccharide-based bioflocculant BM2 produced by a bacterium Bacillus megaterium strain PL8 with self-flocculating property were investigated. The results showed that BM2 was an acidic polysaccharide composed of Gal, GalUA, Glc, GlcUA and Man at a molar ratio of 45.1: 33.8:9.3:9.2:2.4, respectively. The molecular weight of BM2 was 4.55 × 106 Da. BM2 had high flocculation efficiencies across a wide pH ranged from 4 to 11 and a wide temperature ranged from 20 to 100 °C towards kaolin clay. BM2 was a cation-independent bioflocculant which could achieve high flocculation activity without the addition of other cations. Adsorption bridging was the main mechanism in the flocculation process of BM2 towards kaolin clay. The BM2 also displayed a high removal efficiency in terms of Congo red (88.14%) and Pb2+ ions (82.64%). These results suggested that BM2 had a great potential as an efficient bioflocculant candidate in wastewater treatment.

Atomic force microscopy imaging of delignified secondary cell walls in liquid conditions facilitates interpretation of wood ultrastructure.

Deep understanding of the physicochemical and structural characteristics of wood at the nanoscale is essential for improving wood usage in biorefining and advancing new high performance materials design. Herein, we use in situ atomic force microscopy and a simple delignification treatment to elucidate the nanoscale architecture of individual secondary cell wall layers. Advantages of this approach are: (i) minimal sample preparation that reduces the introduction of potential artifacts; (ii) prevention of structural rearrangements due to dehydration; (iii) increased accessibility to structural details masked by the lignin matrix; and (iv) possibility to complement results with other analytical techniques without sample manipulation. The methodology permits the visualization of parallel and helicoidally arranged microfibril aggregates in the S1 layer and the determination of lignin contribution to microfibril aggregates forming S2 layers. Cellulose and hemicelluloses constitute the core of the aggregates with a mean diameter of approximately 19 nm, and lignin encloses the core forming single structural entities of about 30 nm diameter. Furthermore, we highlight the implications of sample preparation and imaging parameters on the characterization of microfibril aggregates by AFM.

Polysaccharide extracted from Huperzia serrata using response surface methodology and its biological activity.

In this study, Huperzia serrata polysaccharide (HSP) fraction was isolated using response surface methodology (RSM) and Box-Behnken design (BBD). The extraction time, temperature and ratio of water to raw material were employed effects. And properties of four polysaccharide (60%-HSP, 70%-HSP, 80%-HSP and 90%-HSP) were evaluated. The results indicated that the optimal extraction conditions were the following: 3.07 h, 49.46 °C and a liquid material ratio of 20.73:1. The four HSP presented irregular aggregation of shape. And all HSP exhibited antioxidant and anticancer activities.

Cell Wall Composition and Ultrastructural Immunolocalization of Pectin and Arabinogalactan Protein during Olea europaea L. Fruit Abscission.

Cell wall modification is integral to many plant developmental processes where cells need to separate, such as abscission. However, changes in cell wall composition during natural fruit abscission are poorly understood. In olive (Olea europaea L.), some cultivars such as 'Picual' undergo massive natural fruit abscission after fruit ripening. This study investigates the differences in cell wall polysaccharide composition and the localization of pectins and arabinogalactan protein (AGP) in the abscission zone (AZ) during cell separation to understand fruit abscission control in 'Picual' olive. To this end, immunogold labeling employing a suite of monoclonal antibodies to cell wall components (JIM13, LM5, LM6, LM19 and LM20) was investigated in olive fruit AZ. Cell wall polysaccharide extraction revealed that the AZ cell separation is related to the de-esterification and degradation of pectic polysaccharides. Moreover, ultrastructural localization showed that both esterified and unesterified homogalacturonans (HGs) localize mainly in the AZ cell walls, including the middle lamella and tricellular junction zones. Our results indicate that unesterified HGs are likely to contribute to cell separation in the olive fruit AZ. Similarly, immunogold labeling demonstrated a decrease in both galactose-rich and arabinose-rich pectins in AZ cell walls during ripe fruit abscission. In addition, AGPs were localized in the cell wall, plasma membrane and cytoplasm of AZ cells with lower levels of AGPs during ripe fruit abscission. This detailed temporal profile of the cell wall polysaccharide composition, and the pectins and AGP immunolocalization in the olive fruit AZ, offers new insights into cell wall remodeling during ripe fruit abscission.

Ascorbic acid induced degradation of polysaccharide from natural products: a review.

Polysaccharide derived from natural products has a wide range of sources and mild properties, and exhibit various bioactivities. Ascorbic acid is one of the most important nutrients in fruits and vegetables, as well as their products. Ascorbic acid and polysaccharide coexist in many systems during food production and processing. Many studies have found that ascorbic acid at low concentrations degrades polysaccharide derived from natural products via hydroxyl radical. In this paper, the research progress on ascorbic acid induced polysaccharide degradation is summarized from four aspects: mechanism of action, analytical methods, influencing factors and bioactivity of degradation products. It is expected to provide a theoretical basis for further research.

Structure and morphology of cellulose fibers in garlic skin.

The knowledge of the texture and morphology of cellulose is essential for reliable modelling of cell growth and mechanical resistance of vegetal systems. Microscopic observations on thin layers of the skin of Allium sativum have shown elongated structures (i.e. cellulose fibers) imbedded in a matrix of more or less rounded cells. Examination by an optical polarizing microscope (OPM) has shown an intermittent high and low birefringence along fibers. Transversal regions with a reduced brightness along fibers are expected to contain a higher amount of amorphous lignin, hemicelluloses and waxes, some of which might also be birefringent, but at a much lower degree than cellulose. Scanning electron microscopy (SEM) has also evidenced an alternating growth of the fibers. Moreover, the negative sign of birefringence suggests a parallel orientation of cellulose nanofibrils transversally to the fiber axis. The characteristic modulation of intensity along lignocellulosic fibers can be due to variation of the cellulose concentration or orientation, perhaps caused by circadian cycles of temperature and light during growth. Indeed, imperfect orthogonal light can be totally reflected at the interface between regions with different values of the refractive index, contributing to the optical effect of banding.