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Sample records for pdb carbohydrate residue

  1. Permethylation Linkage Analysis Techniques for Residual Carbohydrates

    NASA Astrophysics Data System (ADS)

    Price, Neil P. J.

    Permethylation analysis is the classic approach to establishing the position of glycosidic linkages between sugar residues. Typically, the carbohydrate is derivatized to form acid-stable methyl ethers, hydrolyzed, peracetylated, and analyzed by gas chromatography-mass spectrometry. The position of glycosidic linkages in the starting carbohydrate are apparent from the mass spectra as determined by the location of acetyl residues. The completeness of permethylation is dependent upon the choice of base catalyst and is readily confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry mass spectrometry. For the permethylation of β-cyclodextrin, Hakomori dimsyl base is shown to be superior to the NaOH-dimethyl sulfoxide system, and the use of the latter resulted in selective under-methylation of the 3-hydroxy groups. These techniques are highly applicable to residual carbohydrates from biofuel processes.

  2. CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Non-standard Residues

    PubMed Central

    Jo, Sunhwan; Cheng, Xi; Islam, Shahidul M.; Huang, Lei; Rui, Huan; Zhu, Allen; Lee, Hui Sun; Qi, Yifei; Han, Wei; Vanommeslaeghe, Kenno; MacKerell, Alexander D.; Roux, Benoît; Im, Wonpil

    2016-01-01

    CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations including free energy calculation and large-scale coarse-grained representation. Here, we describe functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator, such as ligand force field generation, incorporation of methanethiosulfonate (MTS) spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids. These new features are expected to be useful in advanced biomolecular modeling and simulation of proteins. PMID:25443960

  3. Carbohydrates

    MedlinePlus

    Carbohydrates are one of the main types of nutrients. They are the most important source of energy for your body. Your digestive system changes carbohydrates into glucose (blood sugar). Your body uses this ...

  4. Characterization of protein and carbohydrate mid-IR spectral features in crop residues

    NASA Astrophysics Data System (ADS)

    Xin, Hangshu; Zhang, Yonggen; Wang, Mingjun; Li, Zhongyu; Wang, Zhibo; Yu, Peiqiang

    2014-08-01

    To the best of our knowledge, a few studies have been conducted on inherent structure spectral traits related to biopolymers of crop residues. The objective of this study was to characterize protein and carbohydrate structure spectral features of three field crop residues (rice straw, wheat straw and millet straw) in comparison with two crop vines (peanut vine and pea vine) by using Fourier transform infrared spectroscopy (FTIR) technique with attenuated total reflectance (ATR). Also, multivariate analyses were performed on spectral data sets within the regions mainly related to protein and carbohydrate in this study. The results showed that spectral differences existed in mid-IR peak intensities that are mainly related to protein and carbohydrate among these crop residue samples. With regard to protein spectral profile, peanut vine showed the greatest mid-IR band intensities that are related to protein amide and protein secondary structures, followed by pea vine and the rest three field crop straws. The crop vines had 48-134% higher spectral band intensity than the grain straws in spectral features associated with protein. Similar trends were also found in the bands that are mainly related to structural carbohydrates (such as cellulosic compounds). However, the field crop residues had higher peak intensity in total carbohydrates region than the crop vines. Furthermore, spectral ratios varied among the residue samples, indicating that these five crop residues had different internal structural conformation. However, multivariate spectral analyses showed that structural similarities still exhibited among crop residues in the regions associated with protein biopolymers and carbohydrate. Further study is needed to find out whether there is any relationship between spectroscopic information and nutrition supply in various kinds of crop residue when fed to animals.

  5. Characterization of protein and carbohydrate mid-IR spectral features in crop residues.

    PubMed

    Xin, Hangshu; Zhang, Yonggen; Wang, Mingjun; Li, Zhongyu; Wang, Zhibo; Yu, Peiqiang

    2014-08-14

    To the best of our knowledge, a few studies have been conducted on inherent structure spectral traits related to biopolymers of crop residues. The objective of this study was to characterize protein and carbohydrate structure spectral features of three field crop residues (rice straw, wheat straw and millet straw) in comparison with two crop vines (peanut vine and pea vine) by using Fourier transform infrared spectroscopy (FTIR) technique with attenuated total reflectance (ATR). Also, multivariate analyses were performed on spectral data sets within the regions mainly related to protein and carbohydrate in this study. The results showed that spectral differences existed in mid-IR peak intensities that are mainly related to protein and carbohydrate among these crop residue samples. With regard to protein spectral profile, peanut vine showed the greatest mid-IR band intensities that are related to protein amide and protein secondary structures, followed by pea vine and the rest three field crop straws. The crop vines had 48-134% higher spectral band intensity than the grain straws in spectral features associated with protein. Similar trends were also found in the bands that are mainly related to structural carbohydrates (such as cellulosic compounds). However, the field crop residues had higher peak intensity in total carbohydrates region than the crop vines. Furthermore, spectral ratios varied among the residue samples, indicating that these five crop residues had different internal structural conformation. However, multivariate spectral analyses showed that structural similarities still exhibited among crop residues in the regions associated with protein biopolymers and carbohydrate. Further study is needed to find out whether there is any relationship between spectroscopic information and nutrition supply in various kinds of crop residue when fed to animals.

  6. Carbohydrates.

    PubMed

    Cocinero, Emilio J; Çarçabal, Pierre

    2015-01-01

    Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).

  7. Analysis of carbohydrate residues on recombinant human thyrotropin receptor.

    PubMed

    Oda, Y; Sanders, J; Roberts, S; Maruyama, M; Kiddie, A; Furmaniak, J; Smith, B R

    1999-06-01

    An investigation of the sugar groups on recombinant human TSH receptors (TSHR) expressed in CHO-K1 cells and solubilized with detergents is described. Western blotting studies with TSHR monoclonal antibodies showed that the receptor was present principally as two bands with approximate molecular masses of 120 and 100 kDa. Further blotting studies using lectins and/or involving treatment with different glycosidases indicated that the 100-kDa band contained about 16 kDa of high mannose-type sugars, and the 120-kDa band contained about 33 kDa of complex-type sugars. It was possible to separate the 120- and 100-kDa components of the TSHRs by lectin affinity chromatography. In particular, Galanthus nivalis lectin, which binds high mannose-type sugars, bound the 100-kDa band, but not the 120-kDa band, whereas Datura stramonium lectin, which binds complex-type sugars, bound the 120-kDa band, but not the 100-kDa band. 125I-Labeled TSH binding studies with the various lectin column fractions showed that TSH-binding activity was principally associated with the complex-type sugar containing the 120-kDa form of the receptor rather than the high mannose-containing 100-kDa form. During peptide chain glycosylation, high mannose-type sugar residues are attached first and then modified by the formation of complex type structures to form the mature glycoprotein. Our data suggest that in the case of the TSH receptor, this type of posttranslational processing has an important role in forming the TSH-binding site.

  8. Application of sedimentary carbohydrate residues in a study of organic facies and natural gas occurrences

    NASA Astrophysics Data System (ADS)

    Swain, F. M.

    Recent aquatic environments and resulting organic facies can be characterized by types and amounts of carbohydrate residues. Characteristics are based on source organisms, degree and type of degradation, and reactions with associated compounds in the mineral-kerogen-humus complex. Selected modern environments are typified by the following presently known carbohydrate suites: (1) deep sea, mid-Pacific, mid-Atlantic Oceans—glucose, galactose, furfurals, low total carbohydrates (TC); (2) deep gulf, Gulf of California—glu, gal, xylose, mannose, furfurals, moderate to high TC; (3) continental shelf, eastern North America—glu, xyl, gal, furfurals, high TC; (5) oligotrophic lake, Minnesota—furfurals, low TC; (6) eutrophic lake, Minnesota—glu, xyl, arabinose, gal, rhamnose, man, ribose, furfurals, glucuronic acid, high TC; (7) bog, Minnesota—glu, ara, xyl, gal, man, rib, very high TC. Polysaccharides are rare to absent in modern deep sea deposits but have been found in Lower Quaternary and younger deep gulf sediments. Cellulose, alpha- and beta-amylose and laminaran are common in shallow marine and lacustrine sediments. Methane, derived from both terrestrial and aquatic higher plant residues is high in yield in freshwater marshes and bogs and in eutrophic lake sediments, moderate in salt-water marshes and estuaries and relatively low in offshore marine sediments. Nitrogen and carbon dioxide are the commonest non-hydrocarbon gases. In many samples studied, xylans appear to predominate over other plant polysaccharide as methane sources. Carbohydrate residues in ancient rocks, based on examples from North America, show a tentative, but as yet poorly investigated, relationship to environmental organic facies and should prove to be useful in natural gas exploration.

  9. Electron Microscope Characterization of Carbohydrate Residues on the Body Wall of Xiphinema index.

    PubMed

    Spiegal, Y; Robertson, W M; Himmelhoch, S; Zuckerman, B M

    1983-10-01

    The location of carbohydrate moieties on the outer cuticle of Xiphinema index was examined by electron microcopy using several different reagents: a) The periodic acid-thiosemicarbazide-silver proteinate reaction was used as a general stain for carbohydrates. In sectioned material it stained the canal system and deeper layers of the cuticle as well as the outer surface, b) Cationized ferritin at pH 2.5, which identifies carboxyl and sulfate groups, was used to identify sialic acid residues and also labelled parts of the canal system, c) Ferritin-goat anti rabbit IgG coupled to a DNP ligand was used to label either sialyl or galactosyl/N-acetyl-D-galactosaminyl residues, d) Ferritin hydrazide, a new reagent, was used for the ultrastructural localization of glyco-conjugates. Reagents c) (with appropriate antisera) and d) were applied only to the outer surfaces of the cuticle; they showed that sialic acid residues were concentrated mainly on the outer body wall of the head, the lips, oral opening, amphid apertures, and outer surface of protruded odontostyles. Ferritin distribution was not altered by pretreatment with neurantinidase. Galactose oxidase treatments revealed galactose/N-acetyl-D-galactosamine residues along the entire body wall. These results confirmed earlier findings obtained by fluorescence microscopy.

  10. A series of PDB-related databanks for everyday needs.

    PubMed

    Touw, Wouter G; Baakman, Coos; Black, Jon; te Beek, Tim A H; Krieger, E; Joosten, Robbie P; Vriend, Gert

    2015-01-01

    We present a series of databanks (http://swift.cmbi.ru.nl/gv/facilities/) that hold information that is computationally derived from Protein Data Bank (PDB) entries and that might augment macromolecular structure studies. These derived databanks run parallel to the PDB, i.e. they have one entry per PDB entry. Several of the well-established databanks such as HSSP, PDBREPORT and PDB_REDO have been updated and/or improved. The software that creates the DSSP databank, for example, has been rewritten to better cope with π-helices. A large number of databanks have been added to aid computational structural biology; some examples are lists of residues that make crystal contacts, lists of contacting residues using a series of contact definitions or lists of residue accessibilities. PDB files are not the optimal presentation of the underlying data for many studies. We therefore made a series of databanks that hold PDB files in an easier to use or more consistent representation. The BDB databank holds X-ray PDB files with consistently represented B-factors. We also added several visualization tools to aid the users of our databanks.

  11. Functional Role of Carbohydrate Residues in Human Immunoglobulin G and Therapeutic Monoclonal Antibodies.

    PubMed

    Dorokhov, Y L; Sheshukova, E V; Kosobokova, E N; Shindyapina, A V; Kosorukov, V S; Komarova, T V

    2016-08-01

    Therapeutic monoclonal antibodies (TMA) provide an important means for treating diseases that were previously considered untreatable. Currently more than 40 full-size TMAs created primarily based on immunoglobulin G1 are widely used for treating various illnesses. Glycosylation of TMA is among other numerous factors that affect their biological activity, effector functions, immunogenicity, and half-life in the patient's serum. The importance of carbohydrate residues for activity of human serum immunoglobulin and TMA produced in animal cells is considered in this review, with emphasis given to N-glycosylation of the Fc fragment of the antibody. PMID:27677552

  12. Selenium Protects Retinal Cells from Cisplatin-Induced Alterations in Carbohydrate Residues

    PubMed Central

    Akşit, Dilek; Yazıcı, Alper; Akşit, Hasan; Sarı, Esin S.; Yay, Arzu; Yıldız, Onur; Kılıç, Adil; Ermiş, Sıtkı S.; Seyrek, Kamil

    2016-01-01

    Background: Investigate alterations in the expression and localization of carbohydrate units in rat retinal cells exposed to cisplatin toxicity. Aims: The aim of the study was to evaluate putative protective effects of selenium on retinal cells subjected to cisplatin. Study Design: Animal experiment. Methods: Eighteen healthy Wistar rats were divided into three equal groups: 1. Control, 2. Cisplatin and 3. Cisplatin+selenium groups. After anesthesia, the right eye of each rat was enucleated. Results: Histochemically, retinal cells of control groups reacted with α-2,3-bound sialic acid-specific Maackia amurensis lectin (MAA) strongly, while cisplatin reduced the staining intensity for MAA. However, selenium administration alleviated the reducing effect of cisplatin on the binding sites for MAA in retinal cells. The staining intensity for N-acetylgalactosamine (GalNAc residues) specific Griffonia simplicifolia-1 (GSL–1) was relatively slight in control animals and cisplatin reduced this slight staining for GSL-1 further. Selenium administration mitigated the reducing effect of cisplatin on the binding sites for GSL-1. A diffuse staining for N-acetylglucosamine (GlcNAc) specific wheat germ agglutinin (WGA) was observed throughout the retina of the control animals. In particular, cells localized in the inner plexiform and photoreceptor layers are reacted strongly with WGA. Compared to the control animals, binding sites for WGA in the retina of rats given cisplatin were remarkably decreased. However, the retinal cells of rats given selenium reacted strongly with WGA. Conclusion: Cisplatin reduces α-2,3-bound sialic acid, GlcNAc and GalNAc residues in certain retinal cells. However, selenium alleviates the reducing effect of cisplatin on carbohydrate residues in retinal cells.

  13. Selenium Protects Retinal Cells from Cisplatin-Induced Alterations in Carbohydrate Residues

    PubMed Central

    Akşit, Dilek; Yazıcı, Alper; Akşit, Hasan; Sarı, Esin S.; Yay, Arzu; Yıldız, Onur; Kılıç, Adil; Ermiş, Sıtkı S.; Seyrek, Kamil

    2016-01-01

    Background: Investigate alterations in the expression and localization of carbohydrate units in rat retinal cells exposed to cisplatin toxicity. Aims: The aim of the study was to evaluate putative protective effects of selenium on retinal cells subjected to cisplatin. Study Design: Animal experiment. Methods: Eighteen healthy Wistar rats were divided into three equal groups: 1. Control, 2. Cisplatin and 3. Cisplatin+selenium groups. After anesthesia, the right eye of each rat was enucleated. Results: Histochemically, retinal cells of control groups reacted with α-2,3-bound sialic acid-specific Maackia amurensis lectin (MAA) strongly, while cisplatin reduced the staining intensity for MAA. However, selenium administration alleviated the reducing effect of cisplatin on the binding sites for MAA in retinal cells. The staining intensity for N-acetylgalactosamine (GalNAc residues) specific Griffonia simplicifolia-1 (GSL–1) was relatively slight in control animals and cisplatin reduced this slight staining for GSL-1 further. Selenium administration mitigated the reducing effect of cisplatin on the binding sites for GSL-1. A diffuse staining for N-acetylglucosamine (GlcNAc) specific wheat germ agglutinin (WGA) was observed throughout the retina of the control animals. In particular, cells localized in the inner plexiform and photoreceptor layers are reacted strongly with WGA. Compared to the control animals, binding sites for WGA in the retina of rats given cisplatin were remarkably decreased. However, the retinal cells of rats given selenium reacted strongly with WGA. Conclusion: Cisplatin reduces α-2,3-bound sialic acid, GlcNAc and GalNAc residues in certain retinal cells. However, selenium alleviates the reducing effect of cisplatin on carbohydrate residues in retinal cells. PMID:27606141

  14. Bioethanol production from carbohydrate-enriched residual biomass obtained after lipid extraction of Chlorella sp. KR-1.

    PubMed

    Lee, Ok Kyung; Oh, You-Kwan; Lee, Eun Yeol

    2015-11-01

    The residual biomass of Chlorella sp. KR-1 obtained after lipid extraction was used for saccharification and bioethanol production. The carbohydrate was saccharified using simple enzymatic and chemical methods using Pectinex at pH 5.5 and 45°C and 0.3N HCl at 121°C for 15min with 76.9% and 98.2% yield, respectively, without any pretreatment. The residual biomass contained 49.7% carbohydrate consisting of 82.4% fermentable sugar and 17.6% non-fermentable sugar, which is valuable for bioethanol fermentation. Approximately 98.2% of the total carbohydrate was converted into monosaccharide (fermentable+non-fermentable sugar) using dilute acid saccharification. The fermentable sugar was subsequently fermented to bioethanol through separate hydrolysis and fermentation with a fermentation yield of 79.3%. Overall, 0.4g ethanol/g fermentable sugar and 0.16g ethanol/g residual biomass were produced.

  15. PDB to AMPL Conversion

    2002-09-01

    PDB to AMPL Conversion was written to convert protein data base files to AMPL files. The protein data bases on the internet contain a wealth of information about the structue and makeup of proteins. Each file contains information derived by one or more experiments and contains information on how the experiment waw performed, the amino acid building blocks of each chain, and often the three-dimensional structure of the protein extracted from the experiments. The waymore » a protein folds determines much about its function. Thus, studying the three-dimensional structure of the protein is of great interest. Analysing the contact maps is one way to examine the structure. A contact map is a graph which has a linear back bone of amino acids for nodes (i.e., adjacent amino acids are always connected) and vertices between non-adjacent nodes if they are close enough to be considered in contact. If the graphs are similar then the folds of the protein and their function should also be similar. This software extracts the contact maps from a protein data base file and puts in into AMPL data format. This format is designed for use in AMPL, a programming language for simplifying linear programming formulations.« less

  16. Bioethanol production from carbohydrate-enriched residual biomass obtained after lipid extraction of Chlorella sp. KR-1.

    PubMed

    Lee, Ok Kyung; Oh, You-Kwan; Lee, Eun Yeol

    2015-11-01

    The residual biomass of Chlorella sp. KR-1 obtained after lipid extraction was used for saccharification and bioethanol production. The carbohydrate was saccharified using simple enzymatic and chemical methods using Pectinex at pH 5.5 and 45°C and 0.3N HCl at 121°C for 15min with 76.9% and 98.2% yield, respectively, without any pretreatment. The residual biomass contained 49.7% carbohydrate consisting of 82.4% fermentable sugar and 17.6% non-fermentable sugar, which is valuable for bioethanol fermentation. Approximately 98.2% of the total carbohydrate was converted into monosaccharide (fermentable+non-fermentable sugar) using dilute acid saccharification. The fermentable sugar was subsequently fermented to bioethanol through separate hydrolysis and fermentation with a fermentation yield of 79.3%. Overall, 0.4g ethanol/g fermentable sugar and 0.16g ethanol/g residual biomass were produced. PMID:26218538

  17. Increase in the carbohydrate content of the microalgae Spirulina in culture by nutrient starvation and the addition of residues of whey protein concentrate.

    PubMed

    Vieira Salla, Ana Cláudia; Margarites, Ana Cláudia; Seibel, Fábio Ivan; Holz, Luiz Carlos; Brião, Vandré Barbosa; Bertolin, Telma Elita; Colla, Luciane Maria; Costa, Jorge Alberto Vieira

    2016-06-01

    Non-renewable sources that will end with time are the largest part of world energy consumption, which emphasizes the necessity to develop renewable sources of energy. This necessity has created opportunities for the use of microalgae as a biofuel. The use of microalgae as a feedstock source for bioethanol production requires high yields of both biomass and carbohydrates. With mixotrophic cultures, wastewater can be used to culture algae. The aim of the study was to increase the carbohydrate content in the microalgae Spirulina with the additions of residues from the ultra and nanofiltration of whey protein. The nutrient deficit in the Zarrouk medium diluted to 20% and the addition of 2.5% of both residue types led to high carbohydrate productivity (60 mg L(-1) d(-1)). With these culture conditions, the increase in carbohydrate production in Spirulina indicated that the conditions were appropriate for use with microalgae as a feedstock in the production of bioethanol.

  18. Facilitating the enzymatic saccharification of pulped bamboo residues by degrading the remained xylan and lignin-carbohydrates complexes.

    PubMed

    Huang, Caoxing; He, Juan; Li, Xin; Min, Douyong; Yong, Qiang

    2015-09-01

    Kraft pulping was performed on bamboo residues and its impact on the chemical compositions and the enzymatic digestibility of the samples were investigated. To improve the digestibility of sample by degrading the xylan and lignin-carbohydrates complexes (LCCs), xylanase and α-L-arabinofuranosidase (AF) were supplemented with cellulase. The results showed more carbohydrates were remained in the samples pulped with low effective alkali (EA) charge, compared to conventional kraft pulping. When 120 IU/g xylanase and 15 IU/g AF were supplemented with 20 FPU/g cellulase, the xylan degradation yield of the sample pulped with 12% EA charge increased from 68.20% to 88.35%, resulting in an increased enzymatic saccharification efficiency from 58.98% to 83.23%. The amount of LCCs in this sample decreased from 8.63/100C9 to 2.99/100C9 after saccharification with these enzymes. The results indicated that degrading the remained xylan and LCCs in the pulp could improve its enzymatic digestibility.

  19. ccPDB: compilation and creation of data sets from Protein Data Bank

    PubMed Central

    Singh, Harinder; Chauhan, Jagat Singh; Gromiha, M. Michael; Raghava, Gajendra P. S.

    2012-01-01

    ccPDB (http://crdd.osdd.net/raghava/ccpdb/) is a database of data sets compiled from the literature and Protein Data Bank (PDB). First, we collected and compiled data sets from the literature used for developing bioinformatics methods to annotate the structure and function of proteins. Second, data sets were derived from the latest release of PDB using standard protocols. Third, we developed a powerful module for creating a wide range of customized data sets from the current release of PDB. This is a flexible module that allows users to create data sets using a simple six step procedure. In addition, a number of web services have been integrated in ccPDB, which include submission of jobs on PDB-based servers, annotation of protein structures and generation of patterns. This database maintains >30 types of data sets such as secondary structure, tight-turns, nucleotide interacting residues, metals interacting residues, DNA/RNA binding residues and so on. PMID:22139939

  20. Reversible and irreversible cross-linking of immunoglobulin heavy chains through their carbohydrate residues.

    PubMed Central

    Heimgartner, U; Kozulić, B; Mosbach, K

    1990-01-01

    After periodate oxidation and incubation with a dihydrazide, cross-linking of the two heavy chains of immunoglobulins G from several species proceeds specifically through their oligosaccharides. We have used malonic acid dihydrazide, adipic acid dihydrazide and dithiodipropionic acid dihydrazide. The last compound is introduced in this work as a cleavable-carbohydrate-specific cross-linker. It was found that in rabbit and human immunoglobulins the degree of cross-linking was strongly dependent on the oxidation conditions but only very weakly dependent on the concentration and size of the dihydrazides. Papain cleavage of the cross-linked rabbit IgG indicated that the cross-linking occurred predominantly, if not exclusively, in the Fc region, probably through the two glycans linked to Asn-297 in the CH2 domain of each of the two heavy chains. The immunoglobulins from sheep, pig, goat and guinea pig show a comparable cross-linking pattern, indicating that the sugar chains from these immunoglobulins have a spatial structure closely related to that of rabbit and human IgG. When dithiodipropionic acid dihydrazide was used as the cross-linker, the cross-link could be cleaved by mercaptoethanol. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. PMID:2111130

  1. Analysis and validation of carbohydrate three-dimensional structures

    SciTech Connect

    Lütteke, Thomas

    2009-02-01

    The article summarizes the information that is gained from and the errors that are found in carbohydrate structures in the Protein Data Bank. Validation tools that can locate these errors are described. Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein–carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein–carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures.

  2. Novel temperature-responsive polymer brushes with carbohydrate residues facilitate selective adhesion and collection of hepatocytes

    NASA Astrophysics Data System (ADS)

    Idota, Naokazu; Ebara, Mitsuhiro; Kotsuchibashi, Yohei; Narain, Ravin; Aoyagi, Takao

    2012-12-01

    Temperature-responsive glycopolymer brushes were designed to investigate the effects of grafting architectures of the copolymers on the selective adhesion and collection of hypatocytes. Homo, random and block sequences of N-isopropylacrylamide and 2-lactobionamidoethyl methacrylate were grafted on glass substrates via surface-initiated atom transfer radical polymerization. The galactose/lactose-specific lectin RCA120 and HepG2 cells were used to test for specific recognition of the polymer brushes containing galactose residues over the lower critical solution temperatures (LCSTs). RCA120 showed a specific binding to the brush surfaces at 37 °C. These brush surfaces also facilitated the adhesion of HepG2 cells at 37 °C under nonserum conditions, whereas no adhesion was observed for NIH-3T3 fibroblasts. When the temperature was decreased to 25 °C, almost all the HepG2 cells detached from the block copolymer brush, whereas the random copolymer brush did not release the cells. The difference in releasing kinetics of cells from the surfaces with different grafting architectures can be explained by the correlated effects of significant changes in LCST, mobility, hydrophilicity and mechanical properties of the grafted polymer chains. These findings are important for designing ‘on-off’ cell capture/release substrates for various biomedical applications such as selective cell separation.

  3. Increase in the carbohydrate content of the microalgae Spirulina in culture by nutrient starvation and the addition of residues of whey protein concentrate.

    PubMed

    Vieira Salla, Ana Cláudia; Margarites, Ana Cláudia; Seibel, Fábio Ivan; Holz, Luiz Carlos; Brião, Vandré Barbosa; Bertolin, Telma Elita; Colla, Luciane Maria; Costa, Jorge Alberto Vieira

    2016-06-01

    Non-renewable sources that will end with time are the largest part of world energy consumption, which emphasizes the necessity to develop renewable sources of energy. This necessity has created opportunities for the use of microalgae as a biofuel. The use of microalgae as a feedstock source for bioethanol production requires high yields of both biomass and carbohydrates. With mixotrophic cultures, wastewater can be used to culture algae. The aim of the study was to increase the carbohydrate content in the microalgae Spirulina with the additions of residues from the ultra and nanofiltration of whey protein. The nutrient deficit in the Zarrouk medium diluted to 20% and the addition of 2.5% of both residue types led to high carbohydrate productivity (60 mg L(-1) d(-1)). With these culture conditions, the increase in carbohydrate production in Spirulina indicated that the conditions were appropriate for use with microalgae as a feedstock in the production of bioethanol. PMID:26967336

  4. Application of information theory to a three-body coarse-grained representation of proteins in the PDB: insights into the structural and evolutionary roles of residues in protein structure.

    PubMed

    Thompson, Jared J; Tabatabaei Ghomi, Hamed; Lill, Markus A

    2014-12-01

    Knowledge-based methods for analyzing protein structures, such as statistical potentials, primarily consider the distances between pairs of bodies (atoms or groups of atoms). Considerations of several bodies simultaneously are generally used to characterize bonded structural elements or those in close contact with each other, but historically do not consider atoms that are not in direct contact with each other. In this report, we introduce an information-theoretic method for detecting and quantifying distance-dependent through-space multibody relationships between the sidechains of three residues. The technique introduced is capable of producing convergent and consistent results when applied to a sufficiently large database of randomly chosen, experimentally solved protein structures. The results of our study can be shown to reproduce established physico-chemical properties of residues as well as more recently discovered properties and interactions. These results offer insight into the numerous roles that residues play in protein structure, as well as relationships between residue function, protein structure, and evolution. The techniques and insights presented in this work should be useful in the future development of novel knowledge-based tools for the evaluation of protein structure.

  5. On the use of capillary electrophoresis for the determination of inorganic anions and cations, and carbohydrates in residues collected after a simulated suicide bombing attack.

    PubMed

    Sarazin, Cédric; Delaunay, Nathalie; Costanza, Christine; Eudes, Véronique; Gareil, Pierre

    2013-01-15

    In order to train scientist field investigators after terrorist attacks, the laboratory of the Prefecture de Police of Paris simulated a suicide bombing attack in a bus. After collection of the residues, analyses were carried out to determine the composition of the original explosive charge. This article focuses on the combined use, for the first time, of three new capillary electrophoresis methods for the determination of inorganic anions and cations, and carbohydrates in two representative extracts. Capillary electrophoresis appears as an effective tool to identify and quantify the compounds in real extracts and is fully complementary to chromatographic methods. PMID:23200391

  6. Occurrence of alpha-D-galactosyl residues in the thyroglobulins from several species. Localization in the saccharide chains of the complex carbohydrate units.

    PubMed

    Spiro, R G; Bhoyroo, V D

    1984-08-10

    Treatment of thyroglobulins from several mammalian sources (calf, sheep, pig, dog, rat, rabbit, guinea pig, and man) with alpha-galactosidase demonstrated a species-dependent occurrence of terminal alpha-D-galactosyl residues which ranged from 11 mol/mol of protein (23% of total galactose) in calf to a complete absence in man. The presence of the alpha-D-galactosyl groups resulted in a partial binding of the thyroglobulins (greater than 70% in calf and sheep) to Bandeiraea simplicifolia I-agarose, and this lectin-thyroglobulin interaction could be quantitated by a solid-phase assay utilizing 125I-labeled B. simplicifolia I. Sequential glycosidase digestions of calf thyroglobulin glycopeptides containing the complex carbohydrate unit (unit B) and characterization of oligosaccharide obtained by partial acid hydrolysis indicated that the alpha-D-galactosyl residues are located on oligosaccharide branches with an alpha-D-Gal-(1----3)-beta-D-Gal-(1----4)-D-GlcNAc sequence. While mild acid treatment of calf thyroglobulin glycopeptides yielded a disaccharide, alpha-D-Gal-(1----3)-D-Gal, and a trisaccharide, alpha-D-Gal-(1----3)-beta-D-Gal-(1----4)-D-GlcNAc, which could be resolved by B. simplicifolia I-agarose or thin-layer chromatography, similar hydrolysis of the human unit B-containing glycopeptides did not produce such components. A study of various glycopeptides indicated that the alpha-D-galactosyl residues are unevenly distributed among the multiple complex carbohydrate units of calf thyroglobulin and are preferentially located in units with a relatively low sialic acid content. During affinity chromatography on B. simplicifolia I-agarose, glycopeptides with multiple alpha-D-galactosyl groups bound more firmly to the lectin than those which contained only a single residue. In contrast to the alpha-D-galactosyl residues, beta-linked galactose of calf thyroglobulin was primarily bound in penultimate locations being susceptible to enzymatic release only after prior

  7. PDB@: an offline toolkit for exploration and analysis of PDB files.

    PubMed

    Mani, Udayakumar; Ravisankar, Sadhana; Ramakrishnan, Sai Mukund

    2013-12-01

    Protein Data Bank (PDB) is a freely accessible archive of the 3-D structural data of biological molecules. Structure based studies offers a unique vantage point in inferring the properties of a protein molecule from structural data. This is too big a task to be done manually. Moreover, there is no single tool, software or server that comprehensively analyses all structure-based properties. The objective of the present work is to develop an offline computational toolkit, PDB@ containing in-built algorithms that help categorizing the structural properties of a protein molecule. The user has the facility to view and edit the PDB file to his need. Some features of the present work are unique in itself and others are an improvement over existing tools. Also, the representation of protein properties in both graphical and textual formats helps in predicting all the necessary details of a protein molecule on a single platform.

  8. Counting carbohydrates

    MedlinePlus

    Carb counting; Carbohydrate-controlled diet; Diabetic diet; Diabetes-counting carbohydrates ... Many foods contain carbohydrates (carbs), including: Fruit and fruit juice Cereal, bread, pasta, and rice Milk and milk products, soy milk Beans, legumes, ...

  9. A series of PDB related databases for everyday needs.

    PubMed

    Joosten, Robbie P; te Beek, Tim A H; Krieger, Elmar; Hekkelman, Maarten L; Hooft, Rob W W; Schneider, Reinhard; Sander, Chris; Vriend, Gert

    2011-01-01

    The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB. Each database holds one entry, if possible, for each PDB entry. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials from the other systems. PDB_REDO holds re-refined, and often improved, copies of all structures solved by X-ray. WHY_NOT summarizes why certain files could not be produced. All these systems are updated weekly. The data sets can be used for the analysis of properties of protein structures in areas ranging from structural genomics, to cancer biology and protein design.

  10. The PDB is a covering set of small protein structures.

    PubMed

    Kihara, Daisuke; Skolnick, Jeffrey

    2003-12-01

    Structure comparisons of all representative proteins have been done. Employing the relative root mean square deviation (RMSD) from native enables the assessment of the statistical significance of structure alignments of different lengths in terms of a Z-score. Two conclusions emerge: first, proteins with their native fold can be distinguished by their Z-score. Second and somewhat surprising, all small proteins up to 100 residues in length have significant structure alignments to other proteins in a different secondary structure and fold class; i.e. 24.0% of them have 60% coverage by a template protein with a RMSD below 3.5A and 6.0% have 70% coverage. If the restriction that we align proteins only having different secondary structure types is removed, then in a representative benchmark set of proteins of 200 residues or smaller, 93% can be aligned to a single template structure (with average sequence identity of 9.8%), with a RMSD less than 4A, and 79% average coverage. In this sense, the current Protein Data Bank (PDB) is almost a covering set of small protein structures. The length of the aligned region (relative to the whole protein length) does not differ among the top hit proteins, indicating that protein structure space is highly dense. For larger proteins, non-related proteins can cover a significant portion of the structure. Moreover, these top hit proteins are aligned to different parts of the target protein, so that almost the entire molecule can be covered when combined. The number of proteins required to cover a target protein is very small, e.g. the top ten hit proteins can give 90% coverage below a RMSD of 3.5A for proteins up to 320 residues long. These results give a new view of the nature of protein structure space, and its implications for protein structure prediction are discussed.

  11. Representation of viruses in the remediated PDB archive

    SciTech Connect

    Lawson, Catherine L. Dutta, Shuchismita; Westbrook, John D.; Henrick, Kim; Berman, Helen M.

    2008-08-01

    A new data model for PDB entries of viruses and other biological assemblies with regular noncrystallographic symmetry is described. A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive.

  12. Ultrasensitive Capillary Electrophoretic Analysis of Potentially Immunogenic Carbohydrate Residues in Biologics: Galactose-α-1,3-Galactose Containing Oligosaccharides

    PubMed Central

    Szabo, Zoltan; Guttman, Andras; Bones, Jonathan; Shand, Randi L.; Meh, David; Karger, Barry L.

    2012-01-01

    With the recent growth of the global monoclonal antibody market, ultrasensitive techniques are required for rapid analysis of possible immunogenic residues, such as galactose-α-1,3-galactose (α-1,3-Gal) on therapeutic proteins expressed in murine or CHO cell lines. We report a capillary electrophoretic approach in conjunction with exoglycosidase digestion for structural elucidation of N-linked IgG glycans containing the above immunogenic epitope. The method uses commercially available reagents and instrumentation, thus making the described methodology readily available for implementation and validation within the biotechnology industry. The method was first evaluated using polyclonal mouse IgG N-glycans which are known to contain α-1,3-Gal containing epitopes. High reproducibility in migration time enabled determination of GU values for five α-1,3-Gal containing structures. The method was successfully applied to the analysis of a NCI reference standard monoclonal antibody and two development phase monoclonal antibodies. The limit of detection and limit of quantitation were 1 and 2 µg of intact protein IgG starting material, respectively, further indicating the high sensitivity of the described method. PMID:22571495

  13. Carbohydrate binding properties of banana (Musa acuminata) lectin I. Novel recognition of internal alpha1,3-linked glucosyl residues.

    PubMed

    Mo, H; Winter, H C; Van Damme, E J; Peumans, W J; Misaki, A; Goldstein, I J

    2001-05-01

    Examination of lectins of banana (Musa acuminata) and the closely related plantain (Musa spp.) by the techniques of quantitative precipitation, hapten inhibition of precipitation, and isothermal titration calorimetry showed that they are mannose/glucose binding proteins with a preference for the alpha-anomeric form of these sugars. Both generate precipitin curves with branched chain alpha-mannans (yeast mannans) and alpha-glucans (glycogens, dextrans, and starches), but not with linear alpha-glucans containing only alpha1,4- and alpha1,6-glucosidic bonds (isolichenan and pullulan). The novel observation was made that banana and plantain lectins recognize internal alpha1,3-linked glucosyl residues, which occur in the linear polysaccharides elsinan and nigeran. Concanavalin A and lectins from pea and lentil, also mannose/glucose binding lectins, did not precipitate with any of these linear alpha-glucans. This is, the authors believe, the first report of the recognition of internal alpha1,3-glucosidic bonds by a plant lectin. It is possible that these lectins are present in the pulp of their respective fruit, complexed with starch.

  14. Using ATR-FT/IR to detect carbohydrate-related molecular structure features of carinata meal and their in situ residues of ruminal fermentation in comparison with canola meal

    NASA Astrophysics Data System (ADS)

    Xin, Hangshu; Yu, Peiqiang

    2013-10-01

    .05) during 48 h ruminal degradation in both carinata meal and canola meal. Although carinata meal differed from canola meal in some carbohydrate spectral parameters, multivariate results from agglomerative hierarchical cluster analysis and principal component analysis showed that both original and in situ residues of two meals were not fully distinguished from each other within carbohydrate spectral regions. It was concluded that carbohydrate structural conformation could be detected in carinata meal by using ATR-FT/IR techniques and further study is needed to explore more information on molecular spectral features of other functional group such as protein structure profile and their association with potential nutrient supply and availability of carinata meal in animals.

  15. Carbohydrate markers of organism purity and growth environment

    SciTech Connect

    Wunschel, David S.; Fox, Alvin

    2012-01-01

    Recent experience with Bacillus spore characterization has demonstrated that carbohydrate content can provide potentially vital bioforensic information. Like other metabolites, the carbohydrate profiles of samples reflect variations in cellular structures as well as presence of residual carbohydrates from the medium found as trace components. The presence and characteristics of residual carbohydrates, such as agar, represent strong indicators of culturing method. The methods to detect residual carbohydrates can be extended to other compounds used in processing and preservation of microbes in a dry form.

  16. The PDB_REDO server for macromolecular structure model optimization.

    PubMed

    Joosten, Robbie P; Long, Fei; Murshudov, Garib N; Perrakis, Anastassis

    2014-07-01

    The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011 ▶), Structure, 19, 1395-1412]. The PDB_REDO procedure aims for 'constructive validation', aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallo-graphers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB. PMID:25075342

  17. The PDB_REDO server for macromolecular structure model optimization

    PubMed Central

    Joosten, Robbie P.; Long, Fei; Murshudov, Garib N.; Perrakis, Anastassis

    2014-01-01

    The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011 ▶), Structure, 19, 1395–1412]. The PDB_REDO procedure aims for ‘constructive validation’, aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallo­graphers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB. PMID:25075342

  18. Carbohydrate Analysis

    NASA Astrophysics Data System (ADS)

    Bemiller, James N.

    Carbohydrates are important in foods as a major source of energy, to impart crucial textural properties, and as dietary fiber which influences physiological processes. Digestible carbohydrates, which are converted into monosaccharides, which are absorbed, provide metabolic energy. Worldwide, carbohydrates account for more than 70% of the caloric value of the human diet. It is recommended that all persons should limit calories from fat (the other significant source) to not more than 30% and that most of the carbohydrate calories should come from starch. Nondigestible polysaccharides (all those other than starch) comprise the major portion of dietary fiber (Sect. 10.5). Carbohydrates also contribute other attributes, including bulk, body, viscosity, stability to emulsions and foams, water-holding capacity, freeze-thaw stability, browning, flavors, aromas, and a range of desirable textures (from crispness to smooth, soft gels). They also provide satiety. Basic carbohydrate structures, chemistry, and terminology can be found in references (1, 2).

  19. BDB: databank of PDB files with consistent B-factors.

    PubMed

    Touw, Wouter G; Vriend, Gert

    2014-11-01

    Protein structures available from the PDB contain for each atom the coordinates, the occupancy and the B-factor that indicates the mobility of the atom. The values that should represent B-factors can relate to atomic motions in different ways. We present here a databank in which all B-factors have been converted to the one, homogeneous representation that is most useful for protein engineering applications. The Databank of PDB files with consistent B-factors (BDB) is freely available through http://www.cmbi.umcn.nl/bdb/.

  20. Carbohydrate Loading.

    ERIC Educational Resources Information Center

    Csernus, Marilyn

    Carbohydrate loading is a frequently used technique to improve performance by altering an athlete's diet. The objective is to increase glycogen stored in muscles for use in prolonged strenuous exercise. For two to three days, the athlete consumes a diet that is low in carbohydrates and high in fat and protein while continuing to exercise and…

  1. Selective production of hemicellulose-derived carbohydrates from wheat straw using dilute HCl or FeCl3 solutions under mild conditions. X-ray and thermo-gravimetric analysis of the solid residues.

    PubMed

    Marcotullio, G; Krisanti, E; Giuntoli, J; de Jong, W

    2011-05-01

    The present work explores the combined production of hemicellulose-derived carbohydrates and an upgraded solid residue from wheat straw using a dilute-acid pretreatment at mild temperature. Dilute aqueous HCl solutions were studied at temperatures of 100 and 120°C, and they were compared to dilute FeCl(3) under the same conditions. Comparable yields of soluble sugars and acetic acid were obtained, affording an almost complete removal of pentoses when using 200 mM aqueous solutions at 120°C. The solid residues of pretreatment were characterized showing a preserved crystallinity of the cellulose, and a almost complete removal of ash forming matter other than Si. Results showed upgraded characteristic of the residues for thermal conversion applications compared to the untreated wheat straw.

  2. [Carbohydrates in clinical nutrition].

    PubMed

    Lysikov, Iu A

    2013-01-01

    The article presents data on role of carbohydrate in clinical nutrition. The review described carbohydrate metabolism, hormonal regulation of carbohydrate, carbohydrate energy source role, carbohydrate requirements in critical study.

  3. ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements

    PubMed Central

    Vignesh, Dhandapani; Daniel, Paul; Raja, Natarajan; Balasubramanian, Ponnusamy; Arul, Loganathan

    2010-01-01

    Detailed structural analysis of protein necessitates investigation at primary, secondary and tertiary levels, respectively. Insight into protein secondary structures pave way for understanding the type of secondary structural elements involved (α-helices, β-strands etc.), the amino acid sequence that encode the secondary structural elements, number of residues, length and, percentage composition of the respective elements in the protein. Here we present a standalone tool entitled “ExSer” which facilitate an automated extraction of the amino acid sequence that encode for the secondary structural regions of a protein from the protein data bank (PDB) file. Availability ExSer is freely downloadable from http://code.google.com/p/tool-exser/ PMID:20975886

  4. Healthy carbohydrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Functional foods include dietary fiber consisting of health-promoting carbohydrates. We have produced novel prebiotics from orange peel and observed that they extend the shelf life of probiotic bacteria in synbiotics. Some pectic-oligosaccharides and xyloglucan-oligosaccharides also have anti-adhesi...

  5. Luffa acutangula agglutinin: Primary structure determination and identification of a tryptophan residue involved in its carbohydrate-binding activity using mass spectrometry.

    PubMed

    Kumar, Gnanesh; Mishra, Padmanabh; Anantharam, Vellareddy; Surolia, Avadhesha

    2015-12-01

    A lectin from phloem exudates of Luffa acutangula (ridge gourd) was purified on chitin affinity chromatography and characterized for its amino acid sequence and to study the role of tryptophan in its activity. The purified lectin was subjected to various proteolytic digestions, and the resulting peptides were analyzed by liquid chromatography coupled electrospray ionization ion trap mass spectrometer. The peptide precursor ions were fragmented by collision-induced dissociation or electron transfer dissociation experiments, and a manual interpretation of MS/MS was performed to deduce amino acid sequence. This gave rise to almost complete sequence coverage of the lectin which showed high-sequence similarity with deduced sequences of phloem lectins present in the database. Chemical modification of lysine, tyrosine, histidine, arginine, aspartic acid, and glutamic acid residues did not inhibit the hemagglutinating activity. However, the modification of tryptophan residues using N-bromosuccinimide showed the loss of hemagglutinating activity. Additionally, the mapping of tryptophan residues was performed to determine the extent and number of residues modified, which revealed that six residues per molecule were oxidized suggesting their accessibility. The retention of the lectin activity was seen when the modifications were performed in the presence of chitooligosaccharides due to protection of a tryptophan residue (W102) in the protein. These studies taken together have led to the identification of a particular tryptophan residue (W102) in the activity of the lectin. PMID:26597132

  6. Learning about Carbohydrates

    MedlinePlus

    ... Here's Help White House Lunch Recipes Learning About Carbohydrates KidsHealth > For Kids > Learning About Carbohydrates Print A ... of energy for the body. Two Types of Carbohydrates There are two major types of carbohydrates (or ...

  7. Carbohydrate intake.

    PubMed

    Leturque, Armelle; Brot-Laroche, Edith; Le Gall, Maude

    2012-01-01

    Carbohydrates represent more than 50% of the energy sources present in most human diets. Sugar intake is regulated by metabolic, neuronal, and hedonic factors, and gene polymorphisms are involved in determining sugar preference. Nutrigenomic adaptations to carbohydrate availability have been evidenced in metabolic diseases, in the persistence of lactose digestion, and in amylase gene copy number. Furthermore, dietary oligosaccharides, fermentable by gut flora, can modulate the microbiotal diversity to the benefit of the host. Genetic diseases linked to mutations in the disaccharidase genes (sucrase-isomaltase, lactase) and in sugar transporter genes (sodium/glucose cotransporter 1, glucose transporters 1 and 2) severely impact carbohydrate intake. These diseases are revealed upon exposure to food containing the offending sugar, and withdrawal of this sugar from the diet prevents disease symptoms, failure to thrive, and premature death. Tailoring the sugar composition of diets to optimize wellness and to prevent the chronic occurrence of metabolic diseases is a future goal that may yet be realized through continued development of nutrigenetics and nutrigenomics approaches. PMID:22656375

  8. Effects of Synchronization of Carbohydrate and Protein Supply in Total Mixed Ration with Korean Rice Wine Residue on Ruminal Fermentation, Nitrogen Metabolism and Microbial Protein Synthesis in Holstein Steers

    PubMed Central

    Piao, Min Yu; Kim, Hyun J.; Seo, J. K.; Park, T. S.; Yoon, J. S.; Kim, K. H.; Ha, Jong K.

    2012-01-01

    Three Holstein steers in the growing phase, each with a ruminal cannula, were used to test the hypothesis that the synchronization of the hourly rate of carbohydrate and nitrogen (N) released in the rumen would increase the amount of retained nitrogen for growth and thus improve the efficiency of microbial protein synthesis (EMPS). In Experiment 1, in situ degradability coefficients of carbohydrate and N in feeds including Korean rice wine residue (RWR) were determined. In Experiment 2, three total mixed ration (TMR) diets having different rates of carbohydrate and N release in the rumen were formulated using the in situ degradability of the feeds. All diets were made to contain similar contents of crude protein (CP) and neutral detergent fiber (NDF) but varied in their hourly pattern of nutrient release. The synchrony index of the three TMRs was 0.51 (LS), 0.77 (MS) and 0.95 (HS), respectively. The diets were fed at a restricted level (2% of the animal’s body weight) in a 3×3 Latin-square design. Synchronizing the hourly supply of energy and N in the rumen did not significantly alter the digestibility of dry matter, organic matter, crude protein, NDF or acid detergent fiber (ADF) (p>0.05). The ruminal NH3-N content of the LS group at three hours after feeding was significantly higher (p<0.05) than that of the other groups; however, the mean values of ruminal NH3-N, pH and VFA concentration among the three groups were not significantly different (p>0.05). In addition, the purine derivative (PD) excretion in urine and microbial-N production (MN) among the three groups were not significantly different (p>0.05). In conclusion, synchronizing dietary energy and N supply to the rumen did not have a major effect on nutrient digestion or microbial protein synthesis (MPS) in Holstein steers. PMID:25049518

  9. Reading PDB: perception of molecules from 3D atomic coordinates.

    PubMed

    Urbaczek, Sascha; Kolodzik, Adrian; Groth, Inken; Heuser, Stefan; Rarey, Matthias

    2013-01-28

    The analysis of small molecule crystal structures is a common way to gather valuable information for drug development. The necessary structural data is usually provided in specific file formats containing only element identities and three-dimensional atomic coordinates as reliable chemical information. Consequently, the automated perception of molecular structures from atomic coordinates has become a standard task in cheminformatics. The molecules generated by such methods must be both chemically valid and reasonable to provide a reliable basis for subsequent calculations. This can be a difficult task since the provided coordinates may deviate from ideal molecular geometries due to experimental uncertainties or low resolution. Additionally, the quality of the input data often differs significantly thus making it difficult to distinguish between actual structural features and mere geometric distortions. We present a method for the generation of molecular structures from atomic coordinates based on the recently published NAOMI model. By making use of this consistent chemical description, our method is able to generate reliable results even with input data of low quality. Molecules from 363 Protein Data Bank (PDB) entries could be perceived with a success rate of 98%, a result which could not be achieved with previously described methods. The robustness of our approach has been assessed by processing all small molecules from the PDB and comparing them to reference structures. The complete data set can be processed in less than 3 min, thus showing that our approach is suitable for large scale applications.

  10. Disorders of Carbohydrate Metabolism

    MedlinePlus

    ... Metabolic Disorders Disorders of Carbohydrate Metabolism Disorders of Amino Acid Metabolism Disorders of Lipid Metabolism Carbohydrates are sugars. ... Metabolic Disorders Disorders of Carbohydrate Metabolism Disorders of Amino Acid Metabolism Disorders of Lipid Metabolism NOTE: This is ...

  11. [Carbohydrates and fiber].

    PubMed

    Lajolo, F M; de Menezes, E W; Filisetti-Cozzi, T M

    1988-09-01

    Dietary carbohydrates comprise two fractions that may be classified as digestible, and which are useful as energy sources (simple and complex carbohydrates) and fiber, which is presumed to be of no use to the human body. There are insufficient epidemiologic data on the metabolic effects of simple carbohydrates and it is not advisable to make quantitative recommendations of intake. It is questionable to recommend in developing countries that a fixed proportion of dietary energy be derived from simple sugars, due to the high prevalence of deficient energy intake, cultural habits, and regional differences in food intake and physical activity. In relation to recommendations of complex carbohydrates, it should be considered that their absorption is influenced by many factors inherent to the individual and to the foods. Fiber is defined as a series of different substances derived from tissue structures, cellular residues and undigested chemical substances that may be partially utilized after intestinal bacteria have acted on them. There is not a clear definition of the chemical composition of fiber, but it consists mainly of polysaccharides (such as cellulose, hemicellulose and pectins), lignin and end products of the interactions of various food components. The effects of fiber, such as control of food intake, regulation of gastrointestinal transit, post-prandial blood concentrations of cholesterol, glucose and insulin, flatulence and alterations in nutrient bioavailability are due to various physical properties inherent to its chemical components. Impairment of nutrient absorption may be harmful, mainly among populations whose food intake is lower than their energy needs, and with a high fiber content. This may be particularly important in pregnant women, growing children and the elderly, and should be considered when making nutrient recommendations. A precise knowledge of fiber is also important to calculate the real energy value of foods, mainly for two reasons: 1

  12. PDB ligand conformational energies calculated quantum-mechanically.

    PubMed

    Sitzmann, Markus; Weidlich, Iwona E; Filippov, Igor V; Liao, Chenzhong; Peach, Megan L; Ihlenfeldt, Wolf-Dietrich; Karki, Rajeshri G; Borodina, Yulia V; Cachau, Raul E; Nicklaus, Marc C

    2012-03-26

    We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a "high-quality" subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G(d) basis set and a single-point energy calculation at B3LYP/6-311++G(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most "conservative" choice of all the possible conformational energies-the energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformer-significant energy values were found. The range of 0 to ~25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of "outliers" of yet higher energies were seen only at resolutions above 1.3 Å. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R(free)-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient

  13. Patient management in the ICU: the PDB System.

    PubMed Central

    Salasidis, R.; Padjen, A. L.; Fleiszer, D.

    1991-01-01

    The Intensive Care Unit is the area in patient care where the amount of patient data from a variety of sources is particularly large. The problem for clinicians lies in the ability to gather, and use these data in the decision making process. A well designed computer based patient data management system, incorporating a variety of data analysis tools, would have a dramatic impact in patient care in an environment such as this. The PDB System has been in continuous use at the Montreal General Hospital's Surgical and Trauma Intensive Care Unit since Jan. 88. Its initial implementation in two beds in our SICU has allowed the complete replacement of the conventional patient paper record. It is used by all ICU staff, including nurses, physicians, and ward clerks for the recording/viewing of all patient vital data, laboratory data, medications, and optionally chart notes. In addition, medical staff has the option to use the entered data to perform a variety of data analysis procedures. PMID:1807781

  14. hpvPDB: An Online Proteome Reserve for Human Papillomavirus.

    PubMed

    Kumar, Satish; Jena, Lingaraja; Daf, Sangeeta; Mohod, Kanchan; Goyal, Peyush; Varma, Ashok K

    2013-12-01

    Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB) domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design.

  15. hpvPDB: An Online Proteome Reserve for Human Papillomavirus

    PubMed Central

    Jena, Lingaraja; Daf, Sangeeta; Mohod, Kanchan; Goyal, Peyush; Varma, Ashok K.

    2013-01-01

    Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB) domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design. PMID:24465243

  16. Carbohydrates and Diabetes

    MedlinePlus

    ... How Can I Help a Friend Who Cuts? Carbohydrates and Diabetes KidsHealth > For Teens > Carbohydrates and Diabetes Print A A A Text Size ... that you should keep track of how many carbohydrates (carbs) you eat. But what exactly are carbohydrates ...

  17. soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts.

    PubMed

    Lesburg, Charles A; Duca, José S

    2008-07-01

    soaPDB is a web application that allows generation and organization of saved PDB searches, and offers automatic email alerts. This tool is used from a web interface to store PDB searches and results in a backend relational database. Written using the Ruby on Rails open-source web framework, soaPDB is easy to deploy, maintain and customize. soaPDB is freely available upon request for local installation and is also available at http://soapdb.dyndns.org:3000. PMID:18487276

  18. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

    PubMed

    Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes; Battle, Gary M; Berrisford, John M; Conroy, Matthew J; Dana, Jose M; Gore, Swanand P; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter M S; Lagerstedt, Ingvar; Mir, Saqib; Fernandez Montecelo, Manuel A; Mukhopadhyay, Abhik; Oldfield, Thomas J; Patwardhan, Ardan; Sanz-García, Eduardo; Sen, Sanchayita; Slowley, Robert A; Wainwright, Michael E; Deshpande, Mandar S; Iudin, Andrii; Sahni, Gaurav; Salavert Torres, Jose; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David R; Clark, Alice R; Smart, Oliver S; Korir, Paul K; Kleywegt, Gerard J

    2016-01-01

    The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data.

  19. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

    PubMed Central

    Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes; Battle, Gary M.; Berrisford, John M.; Conroy, Matthew J.; Dana, Jose M.; Gore, Swanand P.; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter M. S.; Lagerstedt, Ingvar; Mir, Saqib; Fernandez Montecelo, Manuel A.; Mukhopadhyay, Abhik; Oldfield, Thomas J.; Patwardhan, Ardan; Sanz-García, Eduardo; Sen, Sanchayita; Slowley, Robert A.; Wainwright, Michael E.; Deshpande, Mandar S.; Iudin, Andrii; Sahni, Gaurav; Salavert Torres, Jose; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David R.; Clark, Alice R.; Smart, Oliver S.; Korir, Paul K.; Kleywegt, Gerard J.

    2016-01-01

    The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the ‘best structures’ for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data. PMID:26476444

  20. Biological Macromolecular Structures Data from the RCSB Protein Data Bank (RCSB PDB)

    DOE Data Explorer

    The Research Collaboratory for Structural Bioinformatics (RCSB) is a non-profit consortium that works to improve understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules. The RCSB PDB is one of three sites serving as deposition, data processing, and distribution sites of the Protein Data Bank Archive. Each site provides its own view of the primary data, thus providing a variety of tools and resources for the global community. RCSB is also the official keeper for the PDB archive, with sole access authority to the PDB archive directory structure and contents. The RCSB PDB Information Portal for Biological Macromolecular Structures offers online tools for search and retrieval, for visualizing structures, for depositing, validating, or downloading data, news and highlights, a discussion forum, and links to other areas of related research. The PDB archive is a repository of atomic coordinates and other information describing proteins and other important biological macromolecules. Structural biologists use methods such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy to determine the location of each atom relative to each other in the molecule. They then deposit this information, which is then annotated and publicly released into the archive by the wwPDB. Results can be viewed as 3-D images or models.

  1. Complex carbohydrates (image)

    MedlinePlus

    ... later. Complex carbohydrate foods provide vitamins, minerals, and fiber that are important to the health of an ... which do not have the vitamins, minerals, and fiber found in complex and natural carbohydrates. Refined sugars ...

  2. Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria.

    PubMed Central

    Postma, P W; Lengeler, J W; Jacobson, G R

    1993-01-01

    Numerous gram-negative and gram-positive bacteria take up carbohydrates through the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS). This system transports and phosphorylates carbohydrates at the expense of PEP and is the subject of this review. The PTS consists of two general proteins, enzyme I and HPr, and a number of carbohydrate-specific enzymes, the enzymes II. PTS proteins are phosphoproteins in which the phospho group is attached to either a histidine residue or, in a number of cases, a cysteine residue. After phosphorylation of enzyme I by PEP, the phospho group is transferred to HPr. The enzymes II are required for the transport of the carbohydrates across the membrane and the transfer of the phospho group from phospho-HPr to the carbohydrates. Biochemical, structural, and molecular genetic studies have shown that the various enzymes II have the same basic structure. Each enzyme II consists of domains for specific functions, e.g., binding of the carbohydrate or phosphorylation. Each enzyme II complex can consist of one to four different polypeptides. The enzymes II can be placed into at least four classes on the basis of sequence similarity. The genetics of the PTS is complex, and the expression of PTS proteins is intricately regulated because of the central roles of these proteins in nutrient acquisition. In addition to classical induction-repression mechanisms involving repressor and activator proteins, other types of regulation, such as antitermination, have been observed in some PTSs. Apart from their role in carbohydrate transport, PTS proteins are involved in chemotaxis toward PTS carbohydrates. Furthermore, the IIAGlc protein, part of the glucose-specific PTS, is a central regulatory protein which in its nonphosphorylated form can bind to and inhibit several non-PTS uptake systems and thus prevent entry of inducers. In its phosphorylated form, P-IIAGlc is involved in the activation of adenylate cyclase and thus in the

  3. Carbohydrates in Supramolecular Chemistry.

    PubMed

    Delbianco, Martina; Bharate, Priya; Varela-Aramburu, Silvia; Seeberger, Peter H

    2016-02-24

    Carbohydrates are involved in a variety of biological processes. The ability of sugars to form a large number of hydrogen bonds has made them important components for supramolecular chemistry. We discuss recent advances in the use of carbohydrates in supramolecular chemistry and reveal that carbohydrates are useful building blocks for the stabilization of complex architectures. Systems are presented according to the scaffold that supports the glyco-conjugate: organic macrocycles, dendrimers, nanomaterials, and polymers are considered. Glyco-conjugates can form host-guest complexes, and can self-assemble by using carbohydrate-carbohydrate interactions and other weak interactions such as π-π interactions. Finally, complex supramolecular architectures based on carbohydrate-protein interactions are discussed.

  4. PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools

    PubMed Central

    Malik, Adeel; Firoz, Ahmad; Jha, Vivekanand; Ahmad, Shandar

    2010-01-01

    Understanding of the three-dimensional structures of proteins that interact with carbohydrates covalently (glycoproteins) as well as noncovalently (protein-carbohydrate complexes) is essential to many biological processes and plays a significant role in normal and disease-associated functions. It is important to have a central repository of knowledge available about these protein-carbohydrate complexes as well as preprocessed data of predicted structures. This can be significantly enhanced by tools de novo which can predict carbohydrate-binding sites for proteins in the absence of structure of experimentally known binding site. PROCARB is an open-access database comprising three independently working components, namely, (i) Core PROCARB module, consisting of three-dimensional structures of protein-carbohydrate complexes taken from Protein Data Bank (PDB), (ii) Homology Models module, consisting of manually developed three-dimensional models of N-linked and O-linked glycoproteins of unknown three-dimensional structure, and (iii) CBS-Pred prediction module, consisting of web servers to predict carbohydrate-binding sites using single sequence or server-generated PSSM. Several precomputed structural and functional properties of complexes are also included in the database for quick analysis. In particular, information about function, secondary structure, solvent accessibility, hydrogen bonds and literature reference, and so forth, is included. In addition, each protein in the database is mapped to Uniprot, Pfam, PDB, and so forth. PMID:20671979

  5. Web servers and services for electrostatics calculations with APBS and PDB2PQR

    SciTech Connect

    Unni, Samir; Huang, Yong; Hanson, Robert M.; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred; Nielsen, Jens E.; Baker, Nathan A.

    2011-04-02

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/.

  6. Radioiodinated branched carbohydrates

    DOEpatents

    Goodman, Mark M.; Knapp, Jr., Furn F.

    1989-01-01

    A radioiodinated branched carbohydrate for tissue imaging. Iodine-123 is stabilized in the compound by attaching it to a vinyl functional group that is on the carbohydrate. The compound exhibits good uptake and retention and is promising in the development of radiopharmaceuticals for brain, heart and tumor imaging.

  7. Comparison of temporal trends in VOCs as measured with PDB samplers and low-flow sampling methods

    USGS Publications Warehouse

    Harte, P.T.

    2002-01-01

    Analysis of temporal trends in tetrachloroethylene (PCE) concentration determined by two sample techniques showed that passive diffusion bag (pdb) samplers adequately sample the large variation in PCE concentrations at the site. The slopes of the temporal trends in concentrations were comparable between the two techniques, and the pdb sample concentration generally reflected the instantaneous concentration sampled by the low-flow technique. Thus, the pdb samplers provided an appropriate sampling technique for PCE at these wells. One or two wells did not make the case for widespread application of pdb samples at all sites. However, application of pdb samples in some circumstances was appropriate for evaluating temporal and spatial variations in VOC concentrations, thus, should be considered as a useful tool in hydrogeology.

  8. Carbohydrates as allergens.

    PubMed

    Commins, Scott P

    2015-01-01

    Complex carbohydrates are effective inducers of Th2 responses, and carbohydrate antigens can stimulate the production of glycan-specific antibodies. In instances where the antigen exposure occurs through the skin, the resulting antibody production can contain IgE class antibody. The glycan-stimulated IgE may be non-specific but may also be antigen specific. This review focuses on the production of cross-reactive carbohydrate determinants, the recently identified IgE antibody response to a mammalian oligosaccharide epitope, galactose-alpha-1,3-galactose (alpha-gal), as well as discusses practical implications of carbohydrates in allergy. In addition, the biological effects of carbohydrate antigens are reviewed in setting of receptors and host recognition.

  9. Dietary carbohydrates for diabetics.

    PubMed

    Rivellese, Angela A; Giacco, Rosalba; Costabile, Giuseppina

    2012-12-01

    The literature on the impact of dietary carbohydrates in the regulation of blood glucose levels and other metabolic abnormalities in diabetic patients over the last 3 years is reviewed. We try to differentiate the metabolic effects due to the amount of carbohydrates from those due to their different types. The review comprises a part dealing with the effects of diets having low or high carbohydrate content on body weight reduction, and a part in which the amount and the quality of carbohydrates are discussed in relation to isoenergetic diets. Overall, the data accumulated in the period considered seem to confirm that the decrease in energy intake is more important than the qualitative composition of the diet to reduce body weight, but that both the amount and the quality of carbohydrates are important in modulating blood glucose levels and other cardiovascular risk factors in both the fasting and the postprandial phases in diabetic individuals. PMID:22847773

  10. Pd/B4C/Y multilayer coatings for extreme ultraviolet applications near 10  nm wavelength.

    PubMed

    Windt, David L; Gullikson, Eric M

    2015-06-20

    A new extreme ultraviolet (EUV) multilayer coating has been developed comprising Pd and Y layers with thin B4C barrier layers at each interface, for normal incidence applications near 10 nm wavelength. Periodic, nonperiodic, and dual-stack coatings have been investigated and compared with similar structures comprising either Mo/Y or Pd/B4C bilayers. We find that Pd/B4C/Y multilayers provide higher reflectance than either Mo/Y or Pd/B4C, with much lower film stress than Pd/B4C. We have also investigated the performance of periodic multilayers comprising repetitions of Pd/Y, Ru/Y, or Ru/B4C/Y, as well as Pd/B4C multilayers deposited using reactive sputtering with an Ar:N2 gas mixture in order to reduce stress: these material combinations were all found to provide poor EUV performance. The temporal stability of a periodic Pd/B4C/Y multilayer stored in air was investigated over a period of 16 months, and a slight reduction in peak reflectance was observed. Periodic Pd/B4C/Y multilayers were also found to be thermally stable up to 100°C; at higher temperatures (200°C and 300°C) we observe a slight reduction in peak reflectance and a slight increase in multilayer period. High-resolution transmission electron microscopy and selected area diffraction of an as-deposited Pd/B4C/Y film indicates a fully amorphous structure, with interfaces that are both smoother and more abrupt than those observed in a comparable Pd/B4C multilayer in which the Pd layers are polycrystalline. The new Pd/B4C/Y multilayers are suitable for normal-incidence imaging and spectroscopy applications, including solar physics, plasma physics, high-brightness EUV light sources, and others. PMID:26193039

  11. Computerized molecular modeling of carbohydrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Computerized molecular modleing continues to increase in capability and applicability to carbohydrates. This chapter covers nomenclature and conformational aspects of carbohydrates, perhaps of greater use to carbohydrate-inexperienced computational chemists. Its comments on various methods and studi...

  12. Carbohydrates and Diabetes (For Parents)

    MedlinePlus

    ... Story" 5 Things to Know About Zika & Pregnancy Carbohydrates and Diabetes KidsHealth > For Parents > Carbohydrates and Diabetes ... many kids with diabetes take to stay healthy. Carbohydrates and Blood Sugar The two main forms of ...

  13. Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins

    PubMed Central

    Hsing, Michael; Cherkasov, Artem

    2008-01-01

    Background Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable indels in protein sequences may be indicative of protein essentiality and their role in protein interaction networks. Examples of utilization of indels for structure-based drug design have also been recently demonstrated. Nonetheless many structural and functional characteristics of indels remain less researched or unknown. Description We have created a web-based resource, Indel PDB, representing a structural database of insertions/deletions identified from the sequence alignments of highly similar proteins found in the Protein Data Bank (PDB). Indel PDB utilized large amounts of available structural information to characterize 1-, 2- and 3-dimensional features of indel sites. Indel PDB contains 117,266 non-redundant indel sites extracted from 11,294 indel-containing proteins. Unlike loop databases, Indel PDB features more indel sequences with secondary structures including alpha-helices and beta-sheets in addition to loops. The insertion fragments have been characterized by their sequences, lengths, locations, secondary structure composition, solvent accessibility, protein domain association and three dimensional structures. Conclusion By utilizing the data available in Indel PDB, we have studied and presented here several sequence and structural features of indels. We anticipate that Indel PDB will not only enable future functional studies of indels, but will also assist protein modeling efforts and identification of indel-directed drug binding sites. PMID:18578882

  14. Carbohydrate Counting and Diabetes

    MedlinePlus

    ... both energy and nutrients, such as vitamins and minerals, and fiber. Fiber can help you prevent constipation, ... meet the body’s needs for energy, vitamins and minerals, and fiber. Experts suggest that carbohydrate intake for ...

  15. Carbohydrate Dehydration Demonstrations.

    ERIC Educational Resources Information Center

    Dolson, David A.; And Others

    1995-01-01

    Discusses the impact of various factors on the "charring reaction" of a carbohydrate with concentrated sulfuric acid including the type of sugar, the degree of fineness of the sugar crystals, and the amount of water added. (JRH)

  16. Carbohydrates and Depression.

    ERIC Educational Resources Information Center

    Wurtman, Richard J.; Wurtman, Judith J.

    1989-01-01

    Describes the symptoms, such as appetite change and mood fluctuation, basic mechanisms, and some treatments of Seasonal Affective Disorder (SAD), Carbohydrate-Craving Obesity (CCO) and Premenstrual Syndrome (PMS). Provides several tables and diagrams, and three reading references. (YP)

  17. Carbohydrate Metabolism Disorders

    MedlinePlus

    Metabolism is the process your body uses to make energy from the food you eat. Food is ... disorder, something goes wrong with this process. Carbohydrate metabolism disorders are a group of metabolic disorders. Normally ...

  18. Carbohydrate Dehydration Demonstrations

    NASA Astrophysics Data System (ADS)

    Dolson, David A.; Battino, Rubin; Letcher, Trevor M.; Pegel, K. H.; Revaprasadu, N.

    1995-10-01

    The "charring reaction" of a carbohydrate with concentrated H2SO4 is a demonstration of the dehydrating power of H2SO4. In this paper several sugars and supermarket carbohydrates are systematically studied with respect to size of particles, addition of water, and amount of H2SO4 added. The results are tabulated as to the amount of time to blackening and to the attainment of a particular volume of the charred material. Detailed safety precautions are included.

  19. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

    PubMed

    Adams, Paul D; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A; Berman, Helen M; Bhat, Talapady N; Blaney, Jeff M; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K; Case, David A; Clark, Kirk L; Darden, Tom; Emsley, Paul; Feher, Victoria A; Feng, Zukang; Groom, Colin R; Harris, Seth F; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E; Markley, John L; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T; Padyana, Anil K; Peishoff, Catherine E; Pieniazek, Susan; Read, Randy J; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna C; Warren, Gregory L; Westbrook, John D; Williams, Pamela; Yang, Huanwang; Young, Jasmine

    2016-04-01

    Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. PMID:27050687

  20. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

    PubMed

    Adams, Paul D; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A; Berman, Helen M; Bhat, Talapady N; Blaney, Jeff M; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K; Case, David A; Clark, Kirk L; Darden, Tom; Emsley, Paul; Feher, Victoria A; Feng, Zukang; Groom, Colin R; Harris, Seth F; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E; Markley, John L; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T; Padyana, Anil K; Peishoff, Catherine E; Pieniazek, Susan; Read, Randy J; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna C; Warren, Gregory L; Westbrook, John D; Williams, Pamela; Yang, Huanwang; Young, Jasmine

    2016-04-01

    Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.

  1. PhyreStorm: A Web Server for Fast Structural Searches Against the PDB.

    PubMed

    Mezulis, Stefans; Sternberg, Michael J E; Kelley, Lawrence A

    2016-02-22

    The identification of structurally similar proteins can provide a range of biological insights, and accordingly, the alignment of a query protein to a database of experimentally determined protein structures is a technique commonly used in the fields of structural and evolutionary biology. The PhyreStorm Web server has been designed to provide comprehensive, up-to-date and rapid structural comparisons against the Protein Data Bank (PDB) combined with a rich and intuitive user interface. It is intended that this facility will enable biologists inexpert in bioinformatics access to a powerful tool for exploring protein structure relationships beyond what can be achieved by sequence analysis alone. By partitioning the PDB into similar structures, PhyreStorm is able to quickly discard the majority of structures that cannot possibly align well to a query protein, reducing the number of alignments required by an order of magnitude. PhyreStorm is capable of finding 93±2% of all highly similar (TM-score>0.7) structures in the PDB for each query structure, usually in less than 60s. PhyreStorm is available at http://www.sbg.bio.ic.ac.uk/phyrestorm/. PMID:26517951

  2. Diarrhea caused by carbohydrate malabsorption.

    PubMed

    Hammer, Heinz F; Hammer, Johann

    2012-09-01

    This article will focus on the role of the colon in the pathogenesis of diarrhea in carbohydrate malabsorption or physiologically incomplete absorption of carbohydrates, and on the most common manifestation of carbohydrate malabsorption, lactose malabsorption. In addition, incomplete fructose absorption, the role of carbohydrate malabsorption in other malabsorptive diseases, and congenital defects that lead to malabsorption will be covered. The article concludes with a section on diagnostic tools to evaluate carbohydrate malabsorption.

  3. Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences.

    PubMed

    Dutta, Shuchismita; Zardecki, Christine; Goodsell, David S; Berman, Helen M

    2010-10-01

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) supports scientific research and education worldwide by providing an essential resource of information on biomolecular structures. In addition to serving as a deposition, data-processing and distribution center for PDB data, the RCSB PDB offers resources and online materials that different audiences can use to customize their structural biology instruction. These include resources for general audiences that present macromolecular structure in the context of a biological theme, method-based materials for researchers who take a more traditional approach to the presentation of structural science, and materials that mix theme-based and method-based approaches for educators and students. Through these efforts the RCSB PDB aims to enable optimal use of structural data by researchers, educators and students designing and understanding experiments in biology, chemistry and medicine, and by general users making informed decisions about their life and health.

  4. Carbohydrates, pollinators, and cycads.

    PubMed

    Marler, Thomas E; Lindström, Anders J

    2015-01-01

    Cycad biology, ecology, and horticulture decisions are not supported by adequate research, and experiments in cycad physiology in particular have been deficient. Our recent report on free sugar content in a range of cycad taxa and tissues sets the stage for developing continued carbohydrate research. Growth and development of cycad pollen, mediation of the herbivory traits of specialist pollinators, and support of expensive strobilus behavioral traits are areas of cycad pollination biology that would benefit from a greater understanding of the role of carbohydrate relations. PMID:26479502

  5. Carbohydrates, pollinators, and cycads

    PubMed Central

    Marler, Thomas E; Lindström, Anders J

    2015-01-01

    Cycad biology, ecology, and horticulture decisions are not supported by adequate research, and experiments in cycad physiology in particular have been deficient. Our recent report on free sugar content in a range of cycad taxa and tissues sets the stage for developing continued carbohydrate research. Growth and development of cycad pollen, mediation of the herbivory traits of specialist pollinators, and support of expensive strobilus behavioral traits are areas of cycad pollination biology that would benefit from a greater understanding of the role of carbohydrate relations. PMID:26479502

  6. Carbohydrates, pollinators, and cycads.

    PubMed

    Marler, Thomas E; Lindström, Anders J

    2015-01-01

    Cycad biology, ecology, and horticulture decisions are not supported by adequate research, and experiments in cycad physiology in particular have been deficient. Our recent report on free sugar content in a range of cycad taxa and tissues sets the stage for developing continued carbohydrate research. Growth and development of cycad pollen, mediation of the herbivory traits of specialist pollinators, and support of expensive strobilus behavioral traits are areas of cycad pollination biology that would benefit from a greater understanding of the role of carbohydrate relations.

  7. Understanding carbohydrate-carbohydrate interactions by means of glyconanotechnology.

    PubMed

    de la Fuente, Jesus M; Penadés, Soledad

    2004-01-01

    Carbohydrate-carbohydrate interaction is a reliable and versatile mechanism for cell adhesion and recognition. Glycosphingolipid (GSL) clusters at the cell membrane are mainly involved in this interaction. To investigate carbohydrate-carbohydrate interaction an integrated strategy (Glyconanotechnology) was developed. This strategy includes polyvalent tools (gold glyconanoparticles) mimicking GSL clustering at the cell membrane as well as analytical techniques such as AFM, TEM, and SPR to evaluate the interactions. The results obtained by means of this strategy and current status are presented.

  8. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB-REDO strategies

    SciTech Connect

    Rimsa, Vadim; Eadsforth, Thomas C.; Joosten, Robbie P.; Hunter, William N.

    2014-02-01

    The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase. A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB-REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn{sup 2+}-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn{sup 2+}, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate.

  9. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies

    PubMed Central

    Rimsa, Vadim; Eadsforth, Thomas C.; Joosten, Robbie P.; Hunter, William N.

    2014-01-01

    A potential cytosolic metallocarboxypeptidase from Burk­holderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB_REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn2+-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn2+, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate. PMID:24531462

  10. Specific Carbohydrate Diet: Does It Work?

    MedlinePlus

    ... Specific Carbohydrate Diet (SCD) Go Back The Specific Carbohydrate Diet (SCD) Email Print + Share There is no ... diet that has received attention is the Specific Carbohydrate Diet. This diet limits poorly digestible carbohydrates to ...

  11. RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank

    PubMed Central

    Quinn, Gregory B.; Bi, Chunxiao; Christie, Cole H.; Pang, Kyle; Prlić, Andreas; Nakane, Takanori; Zardecki, Christine; Voigt, Maria; Berman, Helen M.; Rose, Peter W.

    2015-01-01

    Summary: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB’s integrated MyPDB service. Availability and implementation: RCSB PDB Mobile is freely available from the Apple App Store and Google Play (http://www.rcsb.org). Contact: pwrose@ucsd.edu PMID:25183487

  12. Carbohydrate force fields

    PubMed Central

    Foley, B. Lachele; Tessier, Matthew B.; Woods, Robert J.

    2014-01-01

    Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion. PMID:25530813

  13. Carbohydrate post-glycosylational modifications

    PubMed Central

    Yu, Hai; Chen, Xi

    2008-01-01

    Carbohydrate modification is a common phenomenon in nature. Many carbohydrate modifications such as some epimerization, O-acetylation, O-sulfation, O-methylation, N-deacetylation, and N-sulfation, take place after the formation of oligosaccharide or polysaccharide backbones. These modifications can be categorized as carbohydrate post-glycosylational modifications (PGMs). Carbohydrate PGMs further extend the complexity of the structures and the synthesis of carbohydrates and glycoconjugates. They also increase the capacity of the biological information that can be controlled by finely tuning the structures of carbohydrates. Developing efficient methods to obtain structurally defined naturally occurring oligosaccharides, polysaccharides, and glycoconjugates with carbohydrate PGMs is essential for understanding the biological significance of carbohydrate PGMs. Combine with high-throughput screening methods, synthetic carbohydrates with PGMs are invaluable probes in structure-activity relationship studies. We illustrate here several classes of carbohydrates with PGMs and their applications. Recent progress in chemical, enzymatic, and chemoenzymatic syntheses of these carbohydrates and their derivatives are also presented. PMID:17340000

  14. Understanding carbohydrate-carbohydrate interactions by means of glyconanotechnology.

    PubMed

    de la Fuente, Jesus M; Penadés, Soledad

    2004-01-01

    Carbohydrate-carbohydrate interaction is a reliable and versatile mechanism for cell adhesion and recognition. Glycosphingolipid (GSL) clusters at the cell membrane are mainly involved in this interaction. To investigate carbohydrate-carbohydrate interaction an integrated strategy (Glyconanotechnology) was developed. This strategy includes polyvalent tools (gold glyconanoparticles) mimicking GSL clustering at the cell membrane as well as analytical techniques such as AFM, TEM, and SPR to evaluate the interactions. The results obtained by means of this strategy and current status are presented. PMID:15483380

  15. Nearest-cell: a fast and easy tool for locating crystal matches in the PDB

    SciTech Connect

    Ramraj, V.; Evans, G.; Diprose, J. M.; Esnouf, R. M.

    2012-12-01

    A fast and easy tool to locate unit-cell matches in the PDB is described. When embarking upon X-ray diffraction data collection from a potentially novel macromolecular crystal form, it can be useful to ascertain whether the measured data reflect a crystal form that is already recorded in the Protein Data Bank and, if so, whether it is part of a large family of related structures. Providing such information to crystallographers conveniently and quickly, as soon as the first images have been recorded and the unit cell characterized at an X-ray beamline, has the potential to save time and effort as well as pointing to possible search models for molecular replacement. Given an input unit cell, and optionally a space group, Nearest-cell rapidly scans the Protein Data Bank and retrieves near-matches.

  16. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.

    PubMed

    Sali, Andrej; Berman, Helen M; Schwede, Torsten; Trewhella, Jill; Kleywegt, Gerard; Burley, Stephen K; Markley, John; Nakamura, Haruki; Adams, Paul; Bonvin, Alexandre M J J; Chiu, Wah; Peraro, Matteo Dal; Di Maio, Frank; Ferrin, Thomas E; Grünewald, Kay; Gutmanas, Aleksandras; Henderson, Richard; Hummer, Gerhard; Iwasaki, Kenji; Johnson, Graham; Lawson, Catherine L; Meiler, Jens; Marti-Renom, Marc A; Montelione, Gaetano T; Nilges, Michael; Nussinov, Ruth; Patwardhan, Ardan; Rappsilber, Juri; Read, Randy J; Saibil, Helen; Schröder, Gunnar F; Schwieters, Charles D; Seidel, Claus A M; Svergun, Dmitri; Topf, Maya; Ulrich, Eldon L; Velankar, Sameer; Westbrook, John D

    2015-07-01

    Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, on October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models? PMID:26095030

  17. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

    PubMed Central

    Sali, Andrej; Berman, Helen M.; Schwede, Torsten; Trewhella, Jill; Kleywegt, Gerard; Burley, Stephen K.; Markley, John; Nakamura, Haruki; Adams, Paul; Bonvin, Alexandre M.J.J.; Chiu, Wah; Dal Peraro, Matteo; Di Maio, Frank; Ferrin, Thomas E.; Grünewald, Kay; Gutmanas, Aleksandras; Henderson, Richard; Hummer, Gerhard; Iwasaki, Kenji; Johnson, Graham; Lawson, Catherine L.; Meiler, Jens; Marti-Renom, Marc A.; Montelione, Gaetano T.; Nilges, Michael; Nussinov, Ruth; Patwardhan, Ardan; Rappsilber, Juri; Read, Randy J.; Saibil, Helen; Schröder, Gunnar F.; Schwieters, Charles D.; Seidel, Claus A. M.; Svergun, Dmitri; Topf, Maya; Ulrich, Eldon L.; Velankar, Sameer; Westbrook, John D.

    2016-01-01

    Summary Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models? PMID:26095030

  18. Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.

    PubMed

    Névéol, Aurélie; Wilbur, W John; Lu, Zhiyong

    2012-01-01

    High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, <50% for PDB and GEO. Furthermore, we showed that text-mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/

  19. Impact of Dietary Carbohydrate and Protein Levels on Carbohydrate Metabolism

    ERIC Educational Resources Information Center

    Lasker, Denise Ann

    2009-01-01

    The goal of this dissertation was to investigate the impact of changing dietary carbohydrate (CARB) intakes within recommended dietary guidelines on metabolic outcomes specifically associated with glycemic regulations and carbohydrate metabolism. This research utilized both human and animal studies to examine changes in metabolism across a wide…

  20. Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins.

    PubMed

    Jo, Sunhwan; Song, Kevin C; Desaire, Heather; MacKerell, Alexander D; Im, Wonpil

    2011-11-15

    Understanding how glycosylation affects protein structure, dynamics, and function is an emerging and challenging problem in biology. As a first step toward glycan modeling in the context of structural glycobiology, we have developed Glycan Reader and integrated it into the CHARMM-GUI, http://www.charmm-gui.org/input/glycan. Glycan Reader greatly simplifies the reading of PDB structure files containing glycans through (i) detection of carbohydrate molecules, (ii) automatic annotation of carbohydrates based on their three-dimensional structures, (iii) recognition of glycosidic linkages between carbohydrates as well as N-/O-glycosidic linkages to proteins, and (iv) generation of inputs for the biomolecular simulation program CHARMM with the proper glycosidic linkage setup. In addition, Glycan Reader is linked to other functional modules in CHARMM-GUI, allowing users to easily generate carbohydrate or glycoprotein molecular simulation systems in solution or membrane environments and visualize the electrostatic potential on glycoprotein surfaces. These tools are useful for studying the impact of glycosylation on protein structure and dynamics.

  1. Stereochemical Control in Carbohydrate Chemistry

    ERIC Educational Resources Information Center

    Batchelor, Rhys; Northcote, Peter T.; Harvey, Joanne E.; Dangerfield, Emma M.; Stocker, Bridget L.

    2008-01-01

    Carbohydrates, in the form of glycoconjugates, have recently been shown to control a wide range of cellular processes. Accordingly, students interested in the study of organic chemistry and biomedical sciences should be exposed to carbohydrate chemistry. To this end, we have developed a sequence of experiments that leads the student from the…

  2. Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation*

    PubMed Central

    Payne, Christina M.; Bomble, Yannick J.; Taylor, Courtney B.; McCabe, Clare; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.

    2011-01-01

    Proteins employ aromatic residues for carbohydrate binding in a wide range of biological functions. Glycoside hydrolases, which are ubiquitous in nature, typically exhibit tunnels, clefts, or pockets lined with aromatic residues for processing carbohydrates. Mutation of these aromatic residues often results in significant activity differences on insoluble and soluble substrates. However, the thermodynamic basis and molecular level role of these aromatic residues remain unknown. Here, we calculate the relative ligand binding free energy by mutating tryptophans in the Trichoderma reesei family 6 cellulase (Cel6A) to alanine. Removal of aromatic residues near the catalytic site has little impact on the ligand binding free energy, suggesting that aromatic residues immediately upstream of the active site are not directly involved in binding, but play a role in the glucopyranose ring distortion necessary for catalysis. Removal of aromatic residues at the entrance and exit of the Cel6A tunnel, however, dramatically impacts the binding affinity, suggesting that these residues play a role in chain acquisition and product stabilization, respectively. The roles suggested from differences in binding affinity are confirmed by molecular dynamics and normal mode analysis. Surprisingly, our results illustrate that aromatic-carbohydrate interactions vary dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, these results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for biomass utilization. Generally, these results suggest that nature employs aromatic-carbohydrate interactions with a wide range of binding affinities for diverse functions. PMID:21965672

  3. Abuse potential of carbohydrates for overweight carbohydrate cravers

    PubMed Central

    Spring, Bonnie; Schneider, Kristin; Smith, Malaina; Kendzor, Darla; Appelhans, Bradley; Hedeker, Donald; Pagoto, Sherry

    2010-01-01

    Rationale The long-rejected construct of food addiction is undergoing re-examination. Objectives . To evaluate whether a novel carbohydrate food shows abuse potential for rigorously defined carbohydrate cravers, as evidenced by selective self-administration and mood enhancement during double-blind discrimination testing. Methods Discrete trials choice testing was performed with 61 overweight (BMI m=27.64, SD=2.59) women (ages 18–45; 19.70% African American) whose diet records showed >4 weekly afternoon/evening emotional eating episodes confined to snacks with carbohydrate:protein ≥ 6:1. After being induced into a sad mood, participants were exposed, double-blind and in counterbalanced order, to taste-matched carbohydrate and protein beverages. They were asked to choose and self-administer the drink that made them feel better. Results Women overwhelmingly chose the carbohydrate beverage, even though blinded. Mixed-effects regression modeling, controlling for beverage order, revealed greater liking and greater reduction in dysphoria following the carbohydrate beverage compared to the protein beverage, but no differential effect on vigor. Conclusion For women who crave them, carbohydrates appear to display abuse potential, plausibly contributing to overconsumption and overweight. PMID:18273603

  4. Oral carbohydrate loading with 18% carbohydrate beverage alleviates insulin resistance.

    PubMed

    Tamura, Takahiko; Yatabe, Tomoaki; Kitagawa, Hiroyuki; Yamashita, Koichi; Hanazaki, Kazuhiro; Yokoyama, Masataka

    2013-01-01

    Preoperative 12.6% oral carbohydrate loading is an element of the Enhanced Recovery After Surgery (ERAS) protocol aimed at alleviating postoperative insulin resistance; however, in Japan, beverages with 18% carbohydrate content are generally used for preoperative carbohydrate loading. We investigated the effect of 18% carbohydrate loading on alleviating insulin resistance. Six healthy volunteers participated in this crossover-randomized study and were segregated into 2 groups: volunteers in the carbohydrate-loading group (group A) who fasted from after 9 pm and ingested 375 mL of a beverage containing 18% carbohydrate (ArginaidWaterTM; Nestle, Tokyo, Japan) between 9 pm and 12 pm, and 250 mL of the same liquid at 6:30 am. Volunteers in control group (group B) drank only water. At 8:30 am, a hyperinsulinemic normoglycemic clamp was initiated. Glucose infusion rate (GIR) and levels of ketone bodies and cytokines (IL-1β, IL-6, and TNF-α) before clamping were evaluated. p<0.05 was considered statistically significant. Levels of blood glucose, insulin, and cytokines at the start of the clamp were similar in both the groups. The GIR in group A was significantly higher than that in group B (11.5±2.4 vs 6.2±2.2 mg/kg/min, p=0.005), while blood ketone body levels were significantly lower in group A (22±4 vs 124±119 μmol/L, p=0.04). Preoperative 18% carbohydrate loading could prevent the decrease in insulin sensitivity and suppress catabolism in healthy volunteers. Thus, carbohydrate loading with a beverage with 18% carbohydrate content might contribute to improvements in perioperative management. PMID:23353610

  5. RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

    PubMed Central

    Antczak, Maciej; Zok, Tomasz; Popenda, Mariusz; Lukasiak, Piotr; Adamiak, Ryszard W.; Blazewicz, Jacek; Szachniuk, Marta

    2014-01-01

    In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee—a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/. PMID:24771339

  6. Decarbonylation and dehydrogenation of carbohydrates

    DOEpatents

    Andrews, Mark A.; Klaeren, Stephen A.

    1991-01-01

    Carbohydrates, especially aldose or ketose sugars, including those whose carbonyl group is masked by hemi-acetal or hemi-ketal formation, are decarbonylated by heating the feed carbohydrate together with a transition metal complex in a suitable solvent. Also, primary alcohols, including sugar alditols are simultaneously dehydrogenated and decarbonylated by heating a mixture of rhodium and ruthenium complexes and the alcohol and optionally a hydrogen acceptor in an acceptable solvent. Such defarbonylation and/or dehydrogenation of sugars provides a convenient procedure for the synthesis of certain carbohydrates and may provide a means for the conversion of biomass into useful products.

  7. Quantifying the Role of Water in Protein–Carbohydrate Interactions

    PubMed Central

    Tschampel, Sarah M.; Woods, Robert J.

    2006-01-01

    Water-mediated interactions play a key role in carbohydrate–lectin binding, where the interactions involve a conserved water that is separated from the bulk solvent and present a bridge between the side chains of the protein and the carbohydrate ligand. To apply quantum mechanical methods to examine the role of conserved waters, we present an analysis in which the relevant carbohydrate atoms are modeled by methanol, and in which the protein is replaced by a limited number of amino acid side chains. Clusters containing a conserved water and a representative amino acid fragment were also examined to determine the influence of amino acid side chains on interaction energies. To quantify the differential binding energies of methanol versus water, quantum mechanical calculations were performed at the B3LYP/6-311++G(3df,3pd)//B3LYP/6-31+G(d) level in which either a methanol molecule was bound to the conserved water (liganded state) or in which a water molecule replaces the methanol (unliganded state). Not surprisingly, the binding of a water to clusters containing charged amino acid side chains was more favorable by 1.55 to 7.23 kcal/mol than that for the binding of a water to the corresponding pure water clusters. In contrast, the binding energy of water to clusters containing polar-uncharged amino acid side chains ranged from 4.35 kcal/mol less favorable to 4.72 kcal/mol more favorable than for binding to the analogous pure water clusters. The overall trend for the binding of methanol versus water, in any of the clusters, favored methanol by an average value of 1.05 kcal/mol. To extend these studies to a complex between a protein (Concanavalin A) and its carbohydrate ligand, a cluster was examined that contained the side chains of three key amino acids, namely asparagine, aspartate, and arginine, as well as a key water molecule, arranged as in the X-ray diffraction structure of Con A. Again, using methanol as a model for the endogenous carbohydrate ligand, energies of

  8. Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.

    PubMed

    Lagerstedt, Ingvar; Moore, William J; Patwardhan, Ardan; Sanz-García, Eduardo; Best, Christoph; Swedlow, Jason R; Kleywegt, Gerard J

    2013-11-01

    The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed.

  9. Carbohydrate Recognition Properties of Human Ficolins

    PubMed Central

    Gout, Evelyne; Garlatti, Virginie; Smith, David F.; Lacroix, Monique; Dumestre-Pérard, Chantal; Lunardi, Thomas; Martin, Lydie; Cesbron, Jean-Yves; Arlaud, Gérard J.; Gaboriaud, Christine; Thielens, Nicole M.

    2010-01-01

    Ficolins are oligomeric innate immune recognition proteins consisting of a collagen-like region and a fibrinogen-like recognition domain that bind to pathogen- and apoptotic cell-associated molecular patterns. To investigate their carbohydrate binding specificities, serum-derived L-ficolin and recombinant H- and M-ficolins were fluorescently labeled, and their carbohydrate binding ability was analyzed by glycan array screening. L-ficolin preferentially recognized disulfated N-acetyllactosamine and tri- and tetrasaccharides containing terminal galactose or N-acetylglucosamine. Binding was sensitive to the position and orientation of the bond between N-acetyllactosamine and the adjacent carbohydrate. No significant binding of H-ficolin to any of the 377 glycans probed could be detected, providing further evidence for its poor lectin activity. M-ficolin bound preferentially to 9-O-acetylated 2-6-linked sialic acid derivatives and to various glycans containing sialic acid engaged in a 2-3 linkage. To further investigate the structural basis of sialic acid recognition by M-ficolin, point mutants were produced in which three residues of the fibrinogen domain were replaced by their counterparts in L-ficolin. Mutations G221F and A256V inhibited binding to the 9-O-acetylated sialic acid derivatives, whereas Y271F abolished interaction with all sialic acid-containing glycans. The crystal structure of the Y271F mutant fibrinogen domain was solved, showing that the mutation does not alter the structure of the ligand binding pocket. These analyses reveal novel ficolin ligands such as sulfated N-acetyllactosamine (L-ficolin) and gangliosides (M-ficolin) and provide precise insights into the sialic acid binding specificity of M-ficolin, emphasizing the essential role of Tyr271 in this respect. PMID:20032467

  10. Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

    SciTech Connect

    Joosten, Robbie P.; Womack, Thomas; Vriend, Gert; Bricogne, Gérard

    2009-02-01

    An evaluation of validation and real-space intervention possibilities for improving existing automated (re-)refinement methods. The deposition of X-ray data along with the customary structural models defining PDB entries makes it possible to apply large-scale re-refinement protocols to these entries, thus giving users the benefit of improvements in X-ray methods that have occurred since the structure was deposited. Automated gradient refinement is an effective method to achieve this goal, but real-space intervention is most often required in order to adequately address problems detected by structure-validation software. In order to improve the existing protocol, automated re-refinement was combined with structure validation and difference-density peak analysis to produce a catalogue of problems in PDB entries that are amenable to automatic correction. It is shown that re-refinement can be effective in producing improvements, which are often associated with the systematic use of the TLS parameterization of B factors, even for relatively new and high-resolution PDB entries, while the accompanying manual or semi-manual map analysis and fitting steps show good prospects for eventual automation. It is proposed that the potential for simultaneous improvements in methods and in re-refinement results be further encouraged by broadening the scope of depositions to include refinement metadata and ultimately primary rather than reduced X-ray data.

  11. Cell-surface carbohydrates of Entamoeba invadens.

    PubMed

    Ribeiro, S; Soares, R M; Alviano, C S; Da Silva, E F; De Souza, W; Angluster, J

    1997-01-01

    Cell-surface carbohydrates of Entamoeba invadens trophozoites were analyzed using (a) a panel of highly purified lectins specific for molecules containing N-acetylglucosamine or sialic acid, N-acetylgalactosamine, galactose, mannose-like residues, and fucose; (b) Escherichia coli K-12 with mannose-sensitive fimbria; (c) enzymatic digestion; and (d) scanning electron microscopy. The presence of galactose (D-Gal) and N-acetylgalactosamine (D-GalNAc) was detected in the amoeba. Previous trypsinization induced the appearance of Glycine max (SBA, specific for D-GalNAc residues)-binding sites, whereas such treatment completely abolished the ability of Ricinus communis (RCAI) and Axinalla polypoides (APP, specific for D-Gal) lectins and partially abolished that of Euonymus europaeus (EEL, specific for D-Gal) lectins to agglutinate the trophozoites. The agglutinating activity of E. coli K-12 adheans with the amoeba was markedly increased after trypsin digestion, indicating that mannose units become exposed after enzyme treatment. These findings were essentially confirmed by scanning electron microscopy. After neuraminidase treatment the parasites became strongly agglutinated with SBA and Arachis hypogaea (PNA, specific for D-Gal) and the cell interaction with Wisteria floribunda (WFH, specific for D-GalNAc) was markedly increased. These results suggest that in E. invadens trophozoites, sialic acid residues are linked to D-Gal and D-GalNAc. PMID:9342747

  12. Carbohydrate drugs: current status and development prospect.

    PubMed

    Zhang, Yan; Wang, Fengshan

    2015-04-01

    In recent years, there has been a great effort devoted to the investigation of the roles of carbohydrates in various essential biological processes and the development of carbohydrates to therapeutic drugs. This review summarizes the carbohydrate drugs which have been recorded in several pharmacopoeias, marketed, and under development. A prospect of the future development of carbohydrate drugs is discussed as well.

  13. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

    DOE PAGES

    Adams, Paul  D.; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A.; Berman, Helen  M.; Bhat, Talapady  N.; Blaney, Jeff  M.; Bolton, Evan; Bricogne, Gerard; Brown, David; et al

    2016-04-05

    Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ~75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery/design, and the goodness-of-fit of ligand models to electron density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide Protein Data Bank/Cambridge Crystallographicmore » Data Centre/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the Protein Data Bank? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.« less

  14. Cancer Vaccines and Carbohydrate Epitopes

    PubMed Central

    Heimburg-Molinaro, Jamie; Lum, Michelle; Vijay, Geraldine; Jain, Miten; Almogren, Adel; Rittenhouse-Olson, Kate

    2011-01-01

    Tumor-associated carbohydrate antigens (TACA) result from the aberrant glycosylation that is seen with transformation to a tumor cell. The carbohydrate antigens that have been found to be tumor-associated include the mucin related Tn, Sialyl Tn, and Thomsen-Friedenreich antigens, the blood group Lewis related LewisY, Sialyl LewisX and Sialyl LewisA, and LewisX, (also known as stage-specific embryonic antigen-1, SSEA-1), the glycosphingolipids Globo H and stage-specific embryonic antigen-3 (SSEA-3), the sialic acid containing glycosphingolipids, the gangliosides GD2, GD3, GM2, fucosyl GM1, and Neu5GcGM3, and polysialic acid. Recent developments have furthered our understanding of the T-independent type II response that is seen in response to carbohydrate antigens. The selection of a vaccine target antigen is based on not only the presence of the antigen in a variety of tumor tissues but also on the role this antigen plays in tumor growth and metastasis. These roles for TACAs are being elucidated. Newly acquired knowledge in understanding the T-independent immune response and in understanding the key roles that carbohydrates play in metastasis are being applied in attempts to develop an effective vaccine response to TACAs. The role of each of the above mentioned carbohydrate antigens in cancer growth and metastasis and vaccine attempts using these antigens will be described. PMID:21964054

  15. Biologically-Inspired Peptide Reagents for Enhancing IMS-MS Analysis of Carbohydrates

    NASA Astrophysics Data System (ADS)

    Bohrer, Brian C.; Clemmer, David E.

    2011-09-01

    The binding properties of a peptidoglycan recognition protein are translated via combinatorial chemistry into short peptides. Non-adjacent histidine, tyrosine, and arginine residues in the protein's binding cleft that associate specifically with the glycan moiety of a peptidoglycan substrate are incorporated into linear sequences creating a library of 27 candidate tripeptide reagents (three possible residues permutated across three positions). Upon electrospraying the peptide library and carbohydrate mixtures, some noncovalent complexes are observed. The binding efficiencies of the peptides vary according to their amino acid composition as well as the disaccharide linkage and carbohydrate ring-type. In addition to providing a charge-carrier for the carbohydrate, peptide reagents can also be used to differentiate carbohydrate isomers by ion mobility spectrometry. The utility of these peptide reagents as a means of enhancing ion mobility analysis of carbohydrates is illustrated by examining four glucose-containing disaccharide isomers, including a pair that is not resolved by ion mobility alone. The specificity and stoichiometry of the peptide-carbohydrate complexes are also investigated. Trihistidine demonstrates both suitable binding efficiency and successful resolution of disaccharides isomers, suggesting it may be a useful reagent in IMS analyses of carbohydrates.

  16. Identification of reducing and nonreducing neutral carbohydrates by laser-enhanced in-source decay (LEISD) MALDI MS.

    PubMed

    Yang, Hongmei; Li, Zong-Jun; Wan, Debin; Lian, Wenhui; Liu, Shuying

    2013-05-01

    In this work, laser-enhanced in-source decay (LEISD) technique of matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR-MS) was used to distinguish reducing and nonreducing carbohydrates. Interestingly, easier cleavage of (1 → 2)-linked glycosidic bonds for nonreducing carbohydrates containing D-fructofuranosyl units was observed in MALDI-FT-ICR-MS, which was in agreement with the result of theoretical calculation by the software package Gaussian 09. Importantly, no cross-ring cleavage of fructofuranosyl residues was detected in the LEISD spectra of nonreducing carbohydrates. LEISD method therefore offers an attractive alternative for fast and efficient differentiation of reducing and nonreducing carbohydrates, and the positions of nonreducing monosaccharide residues in a carbohydrate chain could be easily speculated.

  17. New carbohydrate-based materials

    SciTech Connect

    Callstrom, M.R.

    1992-07-01

    We have prepared a series of new carbohydrate-based materials based on the use of carbohydrates as a template for the introduction of functionality to polymeric materials with complete regio- and stereochemical control. The synthesis of these new materials by the use of chemical and enzymatic methods allows for the rational design of new materials based on the properties of the monomeric subunit. These materials have potential applications that range from their use in enhanced oil recovery to biodegradable plastics to biological applications including targeted drug delivery and enzyme stabilization.

  18. CHARACTERIZATION OF THE CARBOHYDRATE COMPONENTS OF Taenia solium ONCOSPHERE PROTEINS AND THEIR ROLE IN THE ANTIGENICITY

    PubMed Central

    Arana, Yanina; Verastegui, Manuela; Tuero, Iskra; Grandjean, Louis; Garcia, Hector H.; Gilman, Robert H.

    2015-01-01

    This study examines the carbohydrate composition of Taenia solium whole oncosphere antigens (WOAs), in order to improve the understanding of the antigenicity of the T. solium. Better knowledge of oncosphere antigens is crucial to accurately diagnose previous exposure to T. solium eggs and thus predict the development of neurocysticercosis. A set of seven lectins conjugates with wide carbohydrate specificity were used on parasite fixations and somatic extracts. Lectin fluorescence revealed that D-mannose, D-glucose, D-galactose and N-acetyl-D-galactosamine residues were the most abundant constituents of carbohydrate chains on the surface of T. solium oncosphere. Lectin blotting showed that post-translational modification with N-glycosylation was abundant while little evidence of O-linked carbohydrates was observed. Chemical oxidation and enzymatic deglycosylation in situ were performed to investigate the immunoreactivity of the carbohydrate moieties. Linearizing or removing the carbohydrate moieties from the protein backbones did not diminish the immunoreactivity of these antigens, suggesting that a substantial part of the host immune response against T. solium oncosphere is directed against the peptide epitopes on the parasite antigens. Finally, using carbohydrate probes, we demonstrated for the first time that the presence of several lectins on the surface of the oncosphere was specific to carbohydrates found in intestinal mucus, suggesting a possible role in initial attachment of the parasite to host cells. PMID:23982308

  19. Characterization of the carbohydrate components of Taenia solium oncosphere proteins and their role in the antigenicity.

    PubMed

    Arana, Yanina; Verastegui, Manuela; Tuero, Iskra; Grandjean, Louis; Garcia, Hector H; Gilman, Robert H

    2013-10-01

    This study examines the carbohydrate composition of Taenia solium whole oncosphere antigens (WOAs), in order to improve the understanding of the antigenicity of the T. solium. Better knowledge of oncosphere antigens is crucial to accurately diagnose previous exposure to T. solium eggs and thus predict the development of neurocysticercosis. A set of seven lectins conjugates with wide carbohydrate specificity were used on parasite fixations and somatic extracts. Lectin fluorescence revealed that D-mannose, D-glucose, D-galactose and N-acetyl-D-galactosamine residues were the most abundant constituents of carbohydrate chains on the surface of T. solium oncosphere. Lectin blotting showed that posttranslational modification with N-glycosylation was abundant while little evidence of O-linked carbohydrates was observed. Chemical oxidation and enzymatic deglycosylation in situ were performed to investigate the immunoreactivity of the carbohydrate moieties. Linearizing or removing the carbohydrate moieties from the protein backbones did not diminish the immunoreactivity of these antigens, suggesting that a substantial part of the host immune response against T. solium oncosphere is directed against the peptide epitopes on the parasite antigens. Finally, using carbohydrate probes, we demonstrated for the first time that the presence of several lectins on the surface of the oncosphere was specific to carbohydrates found in intestinal mucus, suggesting a possible role in initial attachment of the parasite to host cells.

  20. GenomewidePDB 2.0: A Newly Upgraded Versatile Proteogenomic Database for the Chromosome-Centric Human Proteome Project.

    PubMed

    Jeong, Seul-Ki; Hancock, William S; Paik, Young-Ki

    2015-09-01

    Since the launch of the Chromosome-centric Human Proteome Project (C-HPP) in 2012, the number of "missing" proteins has fallen to 2932, down from ∼5932 since the number was first counted in 2011. We compared the characteristics of missing proteins with those of already annotated proteins with respect to transcriptional expression pattern and the time periods in which newly identified proteins were annotated. We learned that missing proteins commonly exhibit lower levels of transcriptional expression and less tissue-specific expression compared with already annotated proteins. This makes it more difficult to identify missing proteins as time goes on. One of the C-HPP goals is to identify alternative spliced product of proteins (ASPs), which are usually difficult to find by shot-gun proteomic methods due to their sequence similarities with the representative proteins. To resolve this problem, it may be necessary to use a targeted proteomics approach (e.g., selected and multiple reaction monitoring [S/MRM] assays) and an innovative bioinformatics platform that enables the selection of target peptides for rarely expressed missing proteins or ASPs. Given that the success of efforts to identify missing proteins may rely on more informative public databases, it was necessary to upgrade the available integrative databases. To this end, we attempted to improve the features and utility of GenomewidePDB by integrating transcriptomic information (e.g., alternatively spliced transcripts), annotated peptide information, and an advanced search interface that can find proteins of interest when applying a targeted proteomics strategy. This upgraded version of the database, GenomewidePDB 2.0, may not only expedite identification of the remaining missing proteins but also enhance the exchange of information among the proteome community. GenomewidePDB 2.0 is available publicly at http://genomewidepdb.proteomix.org/.

  1. Carbohydrates - Multiple Languages: MedlinePlus

    MedlinePlus

    ... Supplements Videos & Tools You Are Here: Home → Multiple Languages → All Health Topics → Carbohydrates URL of this page: https://medlineplus.gov/languages/carbohydrates.html Other topics A-Z A B ...

  2. Carbohydrate-based immune adjuvants

    PubMed Central

    Petrovsky, Nikolai; Cooper, Peter D

    2011-01-01

    The role for adjuvants in human vaccines has been a matter of vigorous scientific debate, with the field hindered by the fact that for over 80 years, aluminum salts were the only adjuvants approved for human use. To this day, alum-based adjuvants, alone or combined with additional immune activators, remain the only adjuvants approved for use in the USA. This situation has not been helped by the fact that the mechanism of action of most adjuvants has been poorly understood. A relative lack of resources and funding for adjuvant development has only helped to maintain alum’s relative monopoly. To seriously challenge alum’s supremacy a new adjuvant has many major hurdles to overcome, not least being alum’s simplicity, tolerability, safety record and minimal cost. Carbohydrate structures play critical roles in immune system function and carbohydrates also have the virtue of a strong safety and tolerability record. A number of carbohydrate compounds from plant, bacterial, yeast and synthetic sources have emerged as promising vaccine adjuvant candidates. Carbohydrates are readily biodegradable and therefore unlikely to cause problems of long-term tissue deposits seen with alum adjuvants. Above all, the Holy Grail of human adjuvant development is to identify a compound that combines potent vaccine enhancement with maximum tolerability and safety. This has proved to be a tough challenge for many adjuvant contenders. Nevertheless, carbohydrate-based compounds have many favorable properties that could place them in a unique position to challenge alum’s monopoly over human vaccine usage. PMID:21506649

  3. Biophysical characterization of laforin-carbohydrate interaction.

    PubMed

    Dias, David M; Furtado, Joana; Wasielewski, Emeric; Cruz, Rui; Costello, Bernard; Cole, Lindsay; Faria, Tiago Q; Baaske, Philipp; Brito, Rui M M; Ciulli, Alessio; Simões, Isaura; Macedo-Ribeiro, Sandra; Faro, Carlos; Geraldes, Carlos F G C; Castanheira, Pedro

    2016-02-01

    Laforin is a human dual-specificity phosphatase (DSP) involved in glycogen metabolism regulation containing a carbohydrate-binding module (CBM). Mutations in the gene coding for laforin are responsible for the development of Lafora disease, a progressive fatal myoclonus epilepsy with early onset, characterized by the intracellular deposition of abnormally branched, hyperphosphorylated insoluble glycogen-like polymers, called Lafora bodies. Despite the known importance of the CBM domain of laforin in the regulation of glycogen metabolism, the molecular mechanism of laforin-glycogen interaction is still poorly understood. Recently, the structure of laforin with bound maltohexaose was determined and despite the importance of such breakthrough, some molecular interaction details remained missing. We herein report a thorough biophysical characterization of laforin-carbohydrate interaction using soluble glycans. We demonstrated an increased preference of laforin for the interaction with glycans with higher order of polymerization and confirmed the importance of tryptophan residues for glycan interaction. Moreover, and in line with what has been described for other CBMs and lectins, our results confirmed that laforin-glycan interactions occur with a favourable enthalpic contribution counter-balanced by an unfavourable entropic contribution. The analysis of laforin-glycan interaction through the glycan side by saturation transfer difference (STD)-NMR has shown that the CBM-binding site can accommodate between 5 and 6 sugar units, which is in line with the recently obtained crystal structure of laforin. Overall, the work in the present study complements the structural characterization of laforin and sheds light on the molecular mechanism of laforin-glycan interaction, which is a pivotal requisite to understand the physiological and pathological roles of laforin.

  4. Accuracy of Carbohydrate Counting in Adults.

    PubMed

    Meade, Lisa T; Rushton, Wanda E

    2016-07-01

    In Brief This study investigates carbohydrate counting accuracy in patients using insulin through a multiple daily injection regimen or continuous subcutaneous insulin infusion. The average accuracy test score for all patients was 59%. The carbohydrate test in this study can be used to emphasize the importance of carbohydrate counting to patients and to provide ongoing education. PMID:27621531

  5. Carbohydrates as enantioinduction components in stereoselective catalysis

    PubMed Central

    Henderson, Alexander S.

    2016-01-01

    Carbohydrate derivatives are readily available chiral molecules, yet they are infrequently employed as enantioinduction components in stereoselective catalysis. In this review, synthetic approaches to carbohydrate-based ligands and catalysts are outlined, along with example applications in enantioselective catalysis. A wide range of carbohydrate-based functionality is covered, and key trends and future opportunities are identified. PMID:27064817

  6. Photo-Generation of Carbohydrate Microarrays

    NASA Astrophysics Data System (ADS)

    Carroll, Gregory T.; Wang, Denong; Turro, Nicholas J.; Koberstein, Jeffrey T.

    The unparalleled structural diversity of carbohydrates among biological molecules has been recognized for decades. Recent studies have highlighted carbohydrate signaling roles in many important biological processes, such as fertilization, embryonic development, cell differentiation and cellȁ4cell communication, blood coagulation, inflammation, chemotaxis, as well as host recognition and immune responses to microbial pathogens. In this chapter, we summarize recent progress in the establishment of carbohydrate-based microarrays and the application of these technologies in exploring the biological information content in carbohydrates. A newly established photochemical platform of carbohydrate microarrays serves as a model for a focused discussion.

  7. Carbohydrate Nanoparticles for Brain Delivery.

    PubMed

    Lalatsa, A; Barbu, E

    2016-01-01

    Many brain tumors and neurological diseases can greatly benefit from the use of emerging nanotechnologies based on targeted nanomedicines that are able to noninvasively transport highly potent and specific pharmaceuticals across the blood-brain barrier. Carbohydrates have received considerable interest as materials for drug carriers due to their natural origin and inherent biodegradability and biocompatibility, as well as due to their hydrophilic character and ease of chemical modification combined with low cost and the possibility for large-scale manufacturing. This chapter provides an overview of the latest research involving the use of carbohydrate-based nanoparticles for drug delivery to the central nervous system. After reviewing the challenges posed by delivering drugs into the brain, the current state-of-the-art approaches for delivery of actives across the blood-brain barrier, including invasive and noninvasive strategies, are presented. A particular focus has been placed on chitosan polymers as they are among the most promising carbohydrate nanocarriers for the preparation and testing of chitosan-based nanomedicines that led, in preclinical proof-of-concept studies, to enhanced brain drug levels and increased pharmacodynamics responses after intravenous, nasal, and oral administration. While chitosan nanoparticles are to date among the most studied and most promising carriers, approaches based on other polysaccharides such as dextran, pullulan, and cellulose warrant further research in the attempt to advance the existing technologies for overcoming the blood-brain barrier. PMID:27678176

  8. Peptide mimotopes of Mycobacterium tuberculosis carbohydrate immunodeterminants

    PubMed Central

    2004-01-01

    Cell-surface saccharides of Mycobacterium tuberculosis appear to be crucial factors in tuberculosis pathogenicity and could be useful antigens in tuberculosis immunodiagnosis. In the present study, we report the successful antigenic and immunogenic mimicry of mannose-containing cell-wall compounds of M. tuberculosis by dodecamer peptides identified by phage-display technology. Using a rabbit antiserum raised against M. tuberculosis cell-surface saccharides as a target for biopanning, peptides with three different consensus sequences were identified. Phage-displayed and chemically synthesized peptides bound to the anticarbohydrate antiserum. Rabbit antibodies elicited against the peptide QEPLMGTVPIRAGGGS recognize the mannosylated M. tuberculosis cell-wall antigens arabinomannan and lipoarabinomannan, and the glycosylated recombinant protein alanine/proline-rich antigen. Furthermore, antibodies were also able to react with mannan from Saccharomyces cerevisiae, but not with phosphatidylinositol dimannosides or arabinogalactan from mycobacteria. These results suggest that the immunogenic peptide mimics oligomannosidic epitopes. Interestingly, this report provides evidence that, in contrast with previously known carbohydrate mimotopes, no aromatic residues are necessary in a peptide sequence for mimicking unusual glycoconjugates synthesized by mycobacteria. The possible usefulness of the identified peptide mimotopes as surrogate reagents for immunodiagnosis and for the study of functional roles of the native non-peptide epitopes is discussed. PMID:15560754

  9. Peptide mimotopes of Mycobacterium tuberculosis carbohydrate immunodeterminants.

    PubMed

    Gevorkian, Goar; Segura, Erika; Acero, Gonzalo; Palma, José P; Espitia, Clara; Manoutcharian, Karen; López-Marín, Luz M

    2005-04-15

    Cell-surface saccharides of Mycobacterium tuberculosis appear to be crucial factors in tuberculosis pathogenicity and could be useful antigens in tuberculosis immunodiagnosis. In the present study, we report the successful antigenic and immunogenic mimicry of mannose-containing cell-wall compounds of M. tuberculosis by dodecamer peptides identified by phage-display technology. Using a rabbit antiserum raised against M. tuberculosis cell-surface saccharides as a target for biopanning, peptides with three different consensus sequences were identified. Phage-displayed and chemically synthesized peptides bound to the anticarbohydrate antiserum. Rabbit antibodies elicited against the peptide QEPLMGTVPIRAGGGS recognize the mannosylated M. tuberculosis cell-wall antigens arabinomannan and lipoarabinomannan, and the glycosylated recombinant protein alanine/proline-rich antigen. Furthermore, antibodies were also able to react with mannan from Saccharomyces cerevisiae, but not with phosphatidylinositol dimannosides or arabinogalactan from mycobacteria. These results suggest that the immunogenic peptide mimics oligomannosidic epitopes. Interestingly, this report provides evidence that, in contrast with previously known carbohydrate mimotopes, no aromatic residues are necessary in a peptide sequence for mimicking unusual glycoconjugates synthesized by mycobacteria. The possible usefulness of the identified peptide mimotopes as surrogate reagents for immunodiagnosis and for the study of functional roles of the native non-peptide epitopes is discussed.

  10. A systematic study of chemogenomics of carbohydrates.

    PubMed

    Gu, Jiangyong; Luo, Fang; Chen, Lirong; Yuan, Gu; Xu, Xiaojie

    2014-03-01

    Chemogenomics focuses on the interactions between biologically active molecules and protein targets for drug discovery. Carbohydrates are the most abundant compounds in natural products. Compared with other drugs, the carbohydrate drugs show weaker side effects. Searching for multi-target carbohydrate drugs can be regarded as a solution to improve therapeutic efficacy and safety. In this work, we collected 60 344 carbohydrates from the Universal Natural Products Database (UNPD) and explored the chemical space of carbohydrates by principal component analysis. We found that there is a large quantity of potential lead compounds among carbohydrates. Then we explored the potential of carbohydrates in drug discovery by using a network-based multi-target computational approach. All carbohydrates were docked to 2389 target proteins. The most potential carbohydrates for drug discovery and their indications were predicted based on a docking score-weighted prediction model. We also explored the interactions between carbohydrates and target proteins to find the pathological networks, potential drug candidates and new indications.

  11. Carbohydrates

    MedlinePlus

    ... in fiber: Canned and dried beans, such as kidney beans, black beans, pinto beans, black-eyed peas, split ... crackers Beans and legumes, such as black beans, kidney beans, and garbanzo beans Vegetables, such as broccoli, Brussels ...

  12. Carbohydrates

    MedlinePlus

    ... Look for terms such as: Corn sweetener Corn syrup High-fructose corn syrup Dextrose Fructose Glucose Lactose Maltose Sucrose Honey Sugar Brown sugar Invert sugar Molasses Malt syrup Syrup You also should limit the amount of ...

  13. Carbohydrates

    MedlinePlus

    ... syrup If you are thinking about using a sugar substitute, you may wonder if they are safe. The ... with nutrients, such as fruits and vegetables. Some sugar substitutes you can buy include: Aspartame (say: ASS-per- ...

  14. A Systematic Analysis of the Structures of Heterologously Expressed Proteins and Those from Their Native Hosts in the RCSB PDB Archive

    PubMed Central

    Zhou, Ren-Bin; Lu, Hui-Meng; Liu, Jie; Shi, Jian-Yu; Zhu, Jing; Lu, Qin-Qin; Yin, Da-Chuan

    2016-01-01

    Recombinant expression of proteins has become an indispensable tool in modern day research. The large yields of recombinantly expressed proteins accelerate the structural and functional characterization of proteins. Nevertheless, there are literature reported that the recombinant proteins show some differences in structure and function as compared with the native ones. Now there have been more than 100,000 structures (from both recombinant and native sources) publicly available in the Protein Data Bank (PDB) archive, which makes it possible to investigate if there exist any proteins in the RCSB PDB archive that have identical sequence but have some difference in structures. In this paper, we present the results of a systematic comparative study of the 3D structures of identical naturally purified versus recombinantly expressed proteins. The structural data and sequence information of the proteins were mined from the RCSB PDB archive. The combinatorial extension (CE), FATCAT-flexible and TM-Align methods were employed to align the protein structures. The root-mean-square distance (RMSD), TM-score, P-value, Z-score, secondary structural elements and hydrogen bonds were used to assess the structure similarity. A thorough analysis of the PDB archive generated five-hundred-seventeen pairs of native and recombinant proteins that have identical sequence. There were no pairs of proteins that had the same sequence and significantly different structural fold, which support the hypothesis that expression in a heterologous host usually could fold correctly into their native forms. PMID:27517583

  15. A Systematic Analysis of the Structures of Heterologously Expressed Proteins and Those from Their Native Hosts in the RCSB PDB Archive.

    PubMed

    Zhou, Ren-Bin; Lu, Hui-Meng; Liu, Jie; Shi, Jian-Yu; Zhu, Jing; Lu, Qin-Qin; Yin, Da-Chuan

    2016-01-01

    Recombinant expression of proteins has become an indispensable tool in modern day research. The large yields of recombinantly expressed proteins accelerate the structural and functional characterization of proteins. Nevertheless, there are literature reported that the recombinant proteins show some differences in structure and function as compared with the native ones. Now there have been more than 100,000 structures (from both recombinant and native sources) publicly available in the Protein Data Bank (PDB) archive, which makes it possible to investigate if there exist any proteins in the RCSB PDB archive that have identical sequence but have some difference in structures. In this paper, we present the results of a systematic comparative study of the 3D structures of identical naturally purified versus recombinantly expressed proteins. The structural data and sequence information of the proteins were mined from the RCSB PDB archive. The combinatorial extension (CE), FATCAT-flexible and TM-Align methods were employed to align the protein structures. The root-mean-square distance (RMSD), TM-score, P-value, Z-score, secondary structural elements and hydrogen bonds were used to assess the structure similarity. A thorough analysis of the PDB archive generated five-hundred-seventeen pairs of native and recombinant proteins that have identical sequence. There were no pairs of proteins that had the same sequence and significantly different structural fold, which support the hypothesis that expression in a heterologous host usually could fold correctly into their native forms.

  16. Preoperative Oral Carbohydrate Loading in Pancreaticoduodenectomy

    PubMed Central

    Son, Kum-Hee; Kim, So-Young; Cho, Yeong-Ah; Han, Sung-Sik; Park, Sang-Jae

    2016-01-01

    Overnight fasting before elective surgery has been the routine to reduce the risk of pulmonary aspiration. Recently, several international guidelines for preoperative fasting recommend to intake carbohydrate-containing fluids up to 2 to 3 hours before the induction of anesthesia to improve postoperative recovery. Based on the recommendations, we developed a "preoperative carbohydrate diet" provided for the preoperative patients. The purpose of this case report is to share our experience of applying preoperative carbohydrate loading prior to surgery. PMID:27482525

  17. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

    SciTech Connect

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-10-01

    Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

  18. Carbohydrate metabolism in Spirochaeta stenostrepta.

    PubMed

    Hespell, R B; Canale-Parola, E

    1970-07-01

    The pathways of carbohydrate metabolism in Spirochaeta stenostrepta, a free-living, strictly anaerobic spirochete, were studied. The organism fermented glucose to ethyl alcohol, acetate, lactate, CO(2), and H(2). Assays of enzymatic activities in cell extracts, and determinations of radioactivity distribution in products formed from (14)C-labeled glucose indicated that S. stenostrepta degraded glucose via the Embden-Meyerhof pathway. The spirochete utilized a clostridial-type clastic reaction to metabolize pyruvate to acetyl-coenzyme A, CO(2), and H(2), without production of formate. Acetyl-coenzyme A was converted to ethyl alcohol by nicotinamide adenine dinucleotide-dependent acetaldehyde and alcohol dehydrogenase activities. Phosphotransacetylase and acetate kinase catalyzed the formation of acetate from acetyl-coenzyme A. Hydrogenase and lactate dehydrogenase activities were detected in cell extracts. A rubredoxin was isolated from cell extracts of S. stenostrepta. Preparations of this rubredoxin stimulated acetyl phosphate formation from pyruvate by diethylaminoethyl cellulose-treated extracts of S. stenostrepta, an indication that rubredoxin may participate in pyruvate cleavage by this spirochete. Nutritional studies showed that S. stenostrepta fermented a variety of carbohydrates, but did not ferment amino acids or other organic acids. An unidentified growth factor present in yeast extract was required by the organism. Exogenous supplements of biotin, riboflavin, and vitamin B(12) were either stimulatory or required for growth. PMID:5423371

  19. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data.

    PubMed

    Terwilliger, Thomas C; Bricogne, Gerard

    2014-10-01

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

  20. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

    PubMed Central

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-01-01

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering. PMID:25286839

  1. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

    DOE PAGES

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-09-30

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when itmore » was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.« less

  2. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

    SciTech Connect

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-09-30

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

  3. Structural characterization of carbohydrate attached to the glycoprotein cellulase enzymes of Trichoderma reesei QM 9414

    SciTech Connect

    de Chasteigner du Mee, C.P.R.

    1984-01-01

    Cellobiohydrolases I(D) and II were purified by ion exchange chromatography from an extracellular culture filtrate of Tricoderma reesei QM 9414. Neutral sugar composition of each was determined by gas-liquid chromatographic analysis of the peracetylated alditol and aldononitrile acetate derivatives of sugars released by either reductive US -elimination or acid hydrolysis. The alkaline borohydride-released carbohydrate was analyzed by high-pressure liquid chromatography (HPLC). The HPLC data demonstrated that each molecule of cellobiohydrolase I(D) contained 5.9% carbohydrate and that cellobiohydrolase II contained 18.9% carbohydrate. The purified oligosaccharides were shown by methylation analysis to contain (1-2) and (1-6) glycosidic linkages and the position of the 6-substituted residues was confirmed by acetolysis. The sequence and anomeric nature of the sugar residues in each oligosaccharide was determined by sequential glycosidase digestion, and all the residues were found to be -linked. Proton decoupled TC-NMR analysis suggested that for cellobiohydrolase I(D), each oligosaccharide was attached to a threonyl residue on the polypeptide and for cellobiohydrolase II, each oligosaccharide was attached to threonyl and seryl residues on the polypeptides. Coupled TC-NMR and H-NMR data to define the structures of the oligosaccharides attached to the enzyme were determined and are reported. Thus, work with the cellobiohydrolases and the endoglucanases indicated that the predominant cellulase enzymes secreted by T. reesei QM 9414 are each glycosylated with similar oligosaccharides.

  4. Advances in Food Composition Tables of Japan--Amino Acid, Fatty Acid and Available Carbohydrate Tables.

    PubMed

    Yasui, Takeshi

    2015-01-01

    The new revised version of the Standard Tables of Food Composition in Japan (STFCJ 2015) will be published in 2015. The aim of the present paper is to share information on issues we have encountered during the revision. New analytical data on amino acid composition will be provided for approximately 230 foods, fatty acid composition for approximately 140 foods, and available carbohydrate (starch, glucose, fructose, sucrose, maltose, and lactose) composition for approximately 340 foods. These data will be published separately as three supplements to the STFCJ 2015: amino acid tables, fatty acid tables, and available carbohydrate tables. Available carbohydrate tables will also provide polyol (sorbitol and mannitol) and organic acid (acetic acid, lactic acid, citric acid, etc.) data. In the supplements, amino acid content will be adjusted for protein content calculated as reference nitrogen multiplied by a nitrogen to protein conversion factor, and fatty acid content adjusted for extractable lipid content, as in previous revisions. Available carbohydrate content, however, will be adjusted for water content. Values of protein content calculated as the sum of amino acid residues , lipid content expressed as triacylglycerol equivalents of fatty acids , and available carbohydrate content will appear in the main tables of the STFCJ 2015. Protein, fat and available carbohydrate contents were significantly decreased when the preferred analytical methods of FAO were applied instead of the acceptable methods. Online publication of Japanese and English versions of these tables, reference materials, and a retrievable food composition database is planned. PMID:26598876

  5. Vacuum ultraviolet photoionization of carbohydrates and nucleotides.

    PubMed

    Shin, Joong-Won; Bernstein, Elliot R

    2014-01-28

    Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5(')-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C-C and C-O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results. PMID:25669546

  6. Vacuum ultraviolet photoionization of carbohydrates and nucleotides

    SciTech Connect

    Shin, Joong-Won; Bernstein, Elliot R.

    2014-01-28

    Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5{sup ′}-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C–C and C–O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.

  7. Vacuum ultraviolet photoionization of carbohydrates and nucleotides.

    PubMed

    Shin, Joong-Won; Bernstein, Elliot R

    2014-01-28

    Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5(')-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C-C and C-O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.

  8. Vacuum ultraviolet photoionization of carbohydrates and nucleotides

    NASA Astrophysics Data System (ADS)

    Shin, Joong-Won; Bernstein, Elliot R.

    2014-01-01

    Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5'-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C-C and C-O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.

  9. Determining a carbohydrate profile for Hansenula polymorpha

    NASA Technical Reports Server (NTRS)

    Petersen, G. R.

    1985-01-01

    The determination of the levels of carbohydrates in the yeast Hansenula polymorpha required the development of new analytical procedures. Existing fractionation and analytical methods were adapted to deal with the problems involved with the lysis of whole cells. Using these new procedures, the complete carbohydrate profiles of H. polymorpha and selected mutant strains were determined and shown to correlate favourably with previously published results.

  10. Industrial applications of marine carbohydrates.

    PubMed

    Sudha, Prasad N; Aisverya, S; Nithya, R; Vijayalakshmi, K

    2014-01-01

    Biomaterials have been used increasingly in various fields, such as drug delivery, imaging, and tissue engineering. The main reason justifying the widespread use of biomaterials relies on its valuable and low-cost source of new drugs. Current research goals are focused on identifying more potent and specific compounds with antitumor, immunomodulatory, antihyperlipidemic, anticoagulant, and antiviral activities. The increasing knowledge of structural analysis and chemical modifications enables the use of these marine carbohydrates in a newer way for the human welfare. This chapter focuses on the recent developments related to industrial and biomedical applications using chitin, chitosan, alginate, agar, and carrageenan derivatives and reports the main advances published over the last 10-15 years.

  11. A functional carbohydrate chip platform for analysis of carbohydrate-protein interaction

    NASA Astrophysics Data System (ADS)

    Seo, Jeong Hyun; Kim, Chang Sup; Hwang, Byeong Hee; Cha, Hyung Joon

    2010-05-01

    A carbohydrate chip based on glass or other transparent surfaces has been suggested as a potential tool for high-throughput analysis of carbohydrate-protein interactions. Here we proposed a facile, efficient, and cost-effective method whereby diverse carbohydrate types are modified in a single step and directly immobilized onto a glass surface, with retention of functional orientation. We modified various types of carbohydrates by reductive amination, in which reducing sugar groups were coupled with 4-(2-aminoethyl)aniline, which has di-amine groups at both ends. The modified carbohydrates were covalently attached to an amino-reactive NHS-activated glass surface by formation of stable amide bonds. This proposed method was applied for efficient construction of a carbohydrate microarray to analyze carbohydrate-protein interactions. The carbohydrate chip prepared using our method can be successfully used in diverse biomimetic studies of carbohydrates, including carbohydrate-biomolecule interactions, and carbohydrate sensor chip or microarray development for diagnosis and screening.

  12. ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.

    PubMed

    Sehnal, David; Svobodová Vařeková, Radka; Pravda, Lukáš; Ionescu, Crina-Maria; Geidl, Stanislav; Horský, Vladimír; Jaiswal, Deepti; Wimmerová, Michaela; Koča, Jaroslav

    2015-01-01

    Following the discovery of serious errors in the structure of biomacromolecules, structure validation has become a key topic of research, especially for ligands and non-standard residues. ValidatorDB (freely available at http://ncbr.muni.cz/ValidatorDB) offers a new step in this direction, in the form of a database of validation results for all ligands and non-standard residues from the Protein Data Bank (all molecules with seven or more heavy atoms). Model molecules from the wwPDB Chemical Component Dictionary are used as reference during validation. ValidatorDB covers the main aspects of validation of annotation, and additionally introduces several useful validation analyses. The most significant is the classification of chirality errors, allowing the user to distinguish between serious issues and minor inconsistencies. Other such analyses are able to report, for example, completely erroneous ligands, alternate conformations or complete identity with the model molecules. All results are systematically classified into categories, and statistical evaluations are performed. In addition to detailed validation reports for each molecule, ValidatorDB provides summaries of the validation results for the entire PDB, for sets of molecules sharing the same annotation (three-letter code) or the same PDB entry, and for user-defined selections of annotations or PDB entries. PMID:25392418

  13. Detailed insights from microarray and crystallographic studies into carbohydrate recognition by microneme protein 1 (MIC1) of Toxoplasma gondii

    PubMed Central

    Garnett, James A; Liu, Yan; Leon, Ester; Allman, Sarah A; Friedrich, Nikolas; Saouros, Savvas; Curry, Stephen; Soldati-Favre, Dominique; Davis, Benjamin G; Feizi, Ten; Matthews, Stephen

    2009-01-01

    The intracellular protozoan Toxoplasma gondii is among the most widespread parasites. The broad host cell range of the parasite can be explained by carbohydrate microarray screening analyses that have demonstrated the ability of the T. gondii adhesive protein, TgMIC1, to bind to a wide spectrum of sialyl oligosaccharide ligands. Here, we investigate by further microarray analyses in a dose-response format the differential binding of TgMIC1 to 2-3- and 2-6-linked sialyl carbohydrates. Interestingly, two novel synthetic fluorinated analogs of 3′SiaLacNAc1–4 and 3′SiaLacNAc1–3 were identified as highly potent ligands. To understand the structural basis of the carbohydrate binding specificity of TgMIC1, we have determined the crystal structures of TgMIC1 micronemal adhesive repeat (MAR)-region (TgMIC1-MARR) in complex with five sialyl-N-acetyllactosamine analogs. These crystal structures have revealed a specific, water-mediated hydrogen bond network that accounts for the preferential binding of TgMIC1-MARR to arrayed 2-3-linked sialyl oligosaccharides and the high potency of the fluorinated analogs. Furthermore, we provide strong evidence for the first observation of a C—F···H—O hydrogen bond within a lectin-carbohydrate complex. Finally, detailed comparison with other oligosaccharide-protein complexes in the Protein Data Bank (PDB) reveals a new family of sialic-acid binding sites from lectins in parasites, bacteria, and viruses. PMID:19593815

  14. NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB

    PubMed Central

    Doreleijers, Jurgen F.; Vranken, Wim F.; Schulte, Christopher; Markley, John L.; Ulrich, Eldon L.; Vriend, Gert; Vuister, Geerten W.

    2012-01-01

    For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists are available, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. The accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculation using the available experimental data and present-day software. Such efforts, however, generally fail on half of all NMR ensembles due to the syntactic and semantic heterogeneity of the underlying data and the wide variety of formats used for their deposition. We have combined the remediated restraint information from our NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank and the Common Interface for NMR structure Generation (CING) structure validation reports into the weekly updated NRG-CING database (http://nmr.cmbi.ru.nl/NRG-CING). Eleven programs have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available experimental NMR data. The longitudinal validation of these data in a publicly available relational database yields a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The remediated NMR experimental data sets and validation reports are freely available online. PMID:22139937

  15. Isolation of carbohydrate-metabolizing, extremely halophilic bacteria.

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Hochstein, L. I.

    1972-01-01

    Four previously unrecognized strains of extremely halophilic bacteria that utilize carbohydrates have been isolated. Gas production proved an unreliable index of carbohydrate metabolism; therefore, carbohydrate utilization was measured by determining acid formation and sugar disappearance during growth. By these procedures, carbohydrate utilization was readily detected. The results suggest that carbohydrate dissimilation by extremely halophilic bacteria may be more common than previously thought and that the apparent rarity of carbohydrate-metabolizing halophiles may be an artifact of the isolation procedures used.

  16. Carbohydrate Polymers for Nonviral Nucleic Acid Delivery

    PubMed Central

    Sizovs, Antons; McLendon, Patrick M.; Srinivasachari, Sathya

    2014-01-01

    Carbohydrates have been investigated and developed as delivery vehicles for shuttling nucleic acids into cells. In this review, we present the state of the art in carbohydrate-based polymeric vehicles for nucleic acid delivery, with the focus on the recent successes in preclinical models, both in vitro and in vivo. Polymeric scaffolds based on the natural polysaccharides chitosan, hyaluronan, pullulan, dextran, and schizophyllan each have unique properties and potential for modification, and these results are discussed with the focus on facile synthetic routes and favorable performance in biological systems. Many of these carbohydrates have been used to develop alternative types of biomaterials for nucleic acid delivery to typical polyplexes, and these novel materials are discussed. Also presented are polymeric vehicles that incorporate copolymerized carbohydrates into polymer backbones based on polyethylenimine and polylysine and their effect on transfection and biocompatibility. Unique scaffolds, such as clusters and polymers based on cyclodextrin (CD), are also discussed, with the focus on recent successes in vivo and in the clinic. These results are presented with the emphasis on the role of carbohydrate and charge on transfection. Use of carbohydrates as molecular recognition ligands for cell-type specific delivery is also briefly reviewed. We contend that carbohydrates have contributed significantly to progress in the field of non-viral DNA delivery, and these new discoveries are impactful for developing new vehicles and materials for treatment of human disease. PMID:21504102

  17. Characterizing carbohydrate-protein interactions by NMR

    PubMed Central

    Bewley, Carole A.; Shahzad-ul-Hussan, Syed

    2013-01-01

    Interactions between proteins and soluble carbohydrates and/or surface displayed glycans are central to countless recognition, attachment and signaling events in biology. The physical chemical features associated with these binding events vary considerably, depending on the biological system of interest. For example, carbohydrate-protein interactions can be stoichiometric or multivalent, the protein receptors can be monomeric or oligomeric, and the specificity of recognition can be highly stringent or rather promiscuous. Equilibrium dissociation constants for carbohydrate binding are known to vary from micromolar to millimolar, with weak interactions being far more prevalent; and individual carbohydrate binding sites can be truly symmetrical or merely homologous, and hence, the affinities of individual sites within a single protein can vary, as can the order of binding. Several factors, including the weak affinities with which glycans bind their protein receptors, the dynamic nature of the glycans themselves, and the non-equivalent interactions among oligomeric carbohydrate receptors, have made NMR an especially powerful tool for studying and defining carbohydrate-protein interactions. Here we describe those NMR approaches that have proven to be the most robust in characterizing these systems, and explain what type of information can (or cannot) be obtained from each. Our goal is to provide to the reader the information necessary for selecting the correct experiment or sets of experiments to characterize their carbohydrate-protein interaction of interest. PMID:23784792

  18. Carbohydrate functionalized carbon nanotubes and their applications.

    PubMed

    Gorityala, Bala Kishan; Ma, Jimei; Wang, Xin; Chen, Peng; Liu, Xue-Wei

    2010-08-01

    Carbon nanotubes (CNTs) have attracted tremendous attention in biomedical applications due to their molecular size and unique properties. This tutorial review summarizes the strategies to functionalize CNTs with bioactive carbohydrates, which improve their solubility, biocompatibility and biofunctionalities while preserving their desired properties. In addition, studies on the usage of carbohydrate functionalized CNTs to detect bacteria, to bind to specific lectins, to deliver glycomimetic drug molecules into cells and to probe cellular activities as biosensors are reviewed. Improvement in biocompatibility and introduction of bio-functionalities by integration of carbohydrate with CNTs are paving the way to glyconanotechnology and may provide new tools for glycobiological studies. PMID:20585681

  19. Reductive opening of carbohydrate phenylsulfonylethylidene (PSE) acetals.

    PubMed

    Chéry, Florence; Cabianca, Elena; Tatibouët, Arnaud; De Lucchi, Ottorino; Lindhorst, Thisbe K; Rollin, Patrick

    2015-11-19

    The phenylsulfonylethylidene (PSE) acetal is a relatively new protecting group in carbohydrate chemistry. However, carbohydrate-derived phenylsulfonylethylidene (PSE) acetals show a different behavior in reductive desulfonylation than simple symmetrical acetals. Here we have investigated various SET-type reaction conditions in order to open PSE acetals regioselectively and to produce chiral ω-hydroxyethenyl ethers. Whereas sodium amalgam leads to a mixture of regioisomeric vinyl ethers besides the ethylidene acetal, samarium iodide is suited for regioselective ring opening. This is shown with seven different carbohydrate PSE acetals, both of the 1,3-dioxane and the 1,3-dioxolane type. PMID:26469209

  20. Complex carbohydrates: the science and the label.

    PubMed

    1995-07-01

    This conference resulted in a foundation upon which consensus will be built in the future. Further, it provided a forum for the articulation of the critical need for carbohydrates in human nutrition. We have come a long way in the past 25 years in the food and nutrition sciences and this conference well illustrated that point. At the White House Conference on Nutrition in 1969, macronutrients were never even mentioned as being necessary to nutrition; only micronutrients were emphasized. In 1977 the term complex carbohydrate was used without definition in the Dietary Goals for the United States. This conference encapsulated the tremendous strides that have been made concerning the chemical, nutritional, biologic, and physiologic importance of carbohydrates in health and disease. It is fascinating to review the recommendations concerning complex carbohydrate from 1977 on. Recommendations were made by the Senate Select Committee in 1977; the Dietary Guidelines of 1980, 1985, and 1990; the Surgeon General's report of 1979 and 1988; the 10th edition of Recommended Dietary Allowances; the 1989 National Academy of Sciences Diet and Health: Implications for Reducing Chronic Disease Risk; the 1991 FDA proposal for labeling; and the 1992 Food Guide Pyramid. Indeed, as Dr. Joanne Slavin pointed out, "there is a wide range of consensus that increased complex carbohydrate is consistent with good health," and certainly as Dr. Gary Henderson said, "the term complex carbohydrate has equity with consumers." With this level of apparent clarity it is difficult at first to identify a problem for the food label. After all, if consumer health would benefit, why not simply do it? However, a problem does exist in that carbohydrates may be classified chemically in groups that are difficult to analyze and to define as to their physiologic function in the body. Indeed, complex carbohydrates defined by chain length may have molecular structures less complex than those of smaller units and may

  1. Utilization of carbohydrates by radiation processing

    NASA Astrophysics Data System (ADS)

    Kume, T.; Nagasawa, N.; Yoshii, F.

    2002-03-01

    Upgrading and utilization of carbohydrates such as chitosan, sodium alginate, carrageenan, cellulose, pectin have been investigated for recycling these bio-resources and reducing the environmental pollution. These carbohydrates were easily degraded by irradiation and various kinds of biological activities such as anti-microbial activity, promotion of plant growth, suppression of heavy metal stress, phytoalexins induction, etc. were induced. On the other hand, some carbohydrate derivatives, carboxymethylcellulose and carboxymethylstarch, could be crosslinked under certain radiation condition and produce the biodegradable hydrogel for medical and agricultural use.

  2. Carbohydrate functionalized carbon nanotubes and their applications.

    PubMed

    Gorityala, Bala Kishan; Ma, Jimei; Wang, Xin; Chen, Peng; Liu, Xue-Wei

    2010-08-01

    Carbon nanotubes (CNTs) have attracted tremendous attention in biomedical applications due to their molecular size and unique properties. This tutorial review summarizes the strategies to functionalize CNTs with bioactive carbohydrates, which improve their solubility, biocompatibility and biofunctionalities while preserving their desired properties. In addition, studies on the usage of carbohydrate functionalized CNTs to detect bacteria, to bind to specific lectins, to deliver glycomimetic drug molecules into cells and to probe cellular activities as biosensors are reviewed. Improvement in biocompatibility and introduction of bio-functionalities by integration of carbohydrate with CNTs are paving the way to glyconanotechnology and may provide new tools for glycobiological studies.

  3. A development of chimeric VEGFR2 TK inhibitor based on two ligand conformers from PDB: 1Y6A complex--medicinal chemistry consequences of a TKs analysis.

    PubMed

    Lintnerová, Lucia; García-Caballero, Melissa; Gregáň, Fridrich; Melicherčík, Milan; Quesada, Ana R; Dobiaš, Juraj; Lác, Ján; Sališová, Marta; Boháč, Andrej

    2014-01-24

    VEGFR2 is an important mediator of angiogenesis and influences fate of some cancer stem cells. Here we analysed all 34 structures of VEGFR2 TK available from PDB database. From them a complex PDB: 1Y6A has an exceptional AAZ ligand bound to TK in form of two conformers (U- and S-shaped). This observation inspired us to develop three chimeric bispyridyl VEGFR2 inhibitors by combining structural features of both AAZ conformers and/or their relative ligand AAX (PDB: 1Y6B). Our most interesting inhibitor 22SYM has an enzymatic VEGFR2 TK activity (IC50: 15.1 nM) comparable or better to the active compounds from clinical drugs Nexavar and Sutent. 22SYM inhibits growth, migration and tube formation of endothelial cells (EC) and selectively induces EC apoptosis. 22SYM also inhibits in vivo angiogenesis in Zebrafish embryo assay. Additionally to the above results, we proved here that tyrosine kinases in an inactive form possessing Type I inhibitors can adopt both a closed or an opened conformation of kinase A-loop independently on their DFG-out arrangement. We proposed here that an activity of certain Type I inhibitors (e.g. 22SYM-like) in complex with DFG-out TK can be negatively influenced by collisions with a dynamically moving TK A-loop.

  4. Carbohydrate feeding and exercise: effect of beverage carbohydrate content.

    PubMed

    Murray, R; Seifert, J G; Eddy, D E; Paul, G L; Halaby, G A

    1989-01-01

    The purpose of this study was to determine the effect of ingesting fluids of varying carbohydrate content upon sensory response, physiologic function, and exercise performance during 1.25 h of intermittent cycling in a warm environment (Tdb = 33.4 degrees C). Twelve subjects (7 male, 5 female) completed four separate exercise sessions; each session consisted of three 20 min bouts of cycling at 65% VO2max, with each bout followed by 5 min rest. A timed cycling task (1200 pedal revolutions) completed each exercise session. Immediately prior to the first 20 min cycling bout and during each rest period, subjects consumed 2.5 ml.kg BW-1 of water placebo (WP), or solutions of 6%, 8%, or 10% sucrose with electrolytes (20 mmol.l-1 Na+, 3.2 mmol.l-1 K+). Beverages were administered in double blind, counterbalanced order. Mean (+/- SE) times for the 1200 cycling task differed significantly: WP = 13.62 +/- 0.33 min, *6% = 13.03 +/- 0.24 min, 8% = 13.30 +/- 0.25 min, 10% = 13.57 +/- 0.22 min (* = different from WP and 10%, P less than 0.05). Compared to WP, ingestion of the CHO beverages resulted in higher plasma glucose and insulin concentrations, and higher RER values during the final 20 min of exercise (P less than 0.05). Markers of physiologic function and sensory perception changed similarly throughout exercise; no differences were observed among subjects in response to beverage treatments for changes in plasma concentrations of lactate, sodium, potassium, for changes in plasma volume, plasma osmolality, rectal temperature, heart rate, oxygen uptake, rating of perceived exertion, or for indices of gastrointestinal distress, perceived thirst, and overall beverage acceptance.(ABSTRACT TRUNCATED AT 250 WORDS)

  5. Biochemical suitability of crop residues for cellulosic ethanol: disincentives to nitrogen fertilization in corn agriculture.

    PubMed

    Gallagher, Morgan E; Hockaday, William C; Masiello, Caroline A; Snapp, Sieglinde; McSwiney, Claire P; Baldock, Jeffrey A

    2011-03-01

    Concerns about energy security and climate change have increased biofuel demand, particularly ethanol produced from cellulosic feedstocks (e.g., food crop residues). A central challenge to cropping for cellulosic ethanol is the potential environmental damage from increased fertilizer use. Previous analyses have assumed that cropping for carbohydrate in residue will require the same amount of fertilizer as cropping for grain. Using (13)C nuclear magnetic resonance, we show that increases in biomass in response to fertilization are not uniform across biochemical classes (carbohydrate, protein, lipid, lignin) or tissues (leaf and stem, grain, reproductive support). Although corn grain responds vigorously and nonlinearly, corn residue shows only modest increases in carbohydrate yields in response to high levels of fertilization (25% increase with 202 kg N ha(-1)). Lignin yields in the residue increased almost twice as much as carbohydrate yields in response to nitrogen, implying that residue feedstock quality declines as more fertilizer is applied. Fertilization also increases the decomposability of corn residue, implying that soil carbon sequestration becomes less efficient with increased fertilizer. Our results suggest that even when corn is grown for grain, benefits of fertilization decline rapidly after the ecosystem's N demands are met. Heavy application of fertilizer yields minimal grain benefits and almost no benefits in residue carbohydrates, while degrading the cellulosic ethanol feedstock quality and soil carbon sequestration capacity. PMID:21348531

  6. Carbohydrate moieties can induce mediator release: a detailed characterization of two major timothy grass pollen allergens.

    PubMed

    Wicklein, Daniel; Lindner, Buko; Moll, Hermann; Kolarich, Daniel; Altmann, Friedrich; Becker, Wolf-Meinhard; Petersen, Arnd

    2004-05-01

    Specific IgE binding to carbohydrate moieties of glycosylated allergens has been known for years, but the importance of these structures for the elicitation of allergic reactions is still a matter of debate. Because of their conserved carbohydrate structures, especially N-glycans have always been prime candidates for IgE cross-reactivity between allergens from unrelated species. The aim of our study was to determine whether carbohydrate structures on glycoproteins can by themselves elucidate allergic reactions. We characterized in detail the carbohydrate moieties of the major allergens Phl p 1 and Phl p 13 of timothy grass pollen (Phleum pratense L.) by performing tryptic digests followed by HPLC, N-terminal sequencing, sugar analysis, MALDI-TOF- and ESI-ICRFT-MS. Phl p 1 contains one N-glycan with one of the two glycoforms MMXF3 and M0XF3 and a single furanosidic arabinose, which is bound to a hydroxyproline residue in direct vicinity to the N-glycan. This O-glycosylation is probably due to an arabinosylation consensus sequence found in the N-terminal part of Phl p 1 and other group 1 allergens, but displayed no IgE-reactivity. Thus, Phl p 1 is monovalent with respect to its IgE-binding carbohydrate epitopes and showed no mediator release. In contrast, the carbohydrate moiety of Phl p 13, which carries four of the same N-glycans (like Phl p 1), can cross-link IgE-receptors via carbohydrate chains and elicits IL-4 release from basophils.

  7. Rapid Analysis of Listeria monocytogenes Cell Wall Teichoic Acid Carbohydrates by ESI-MS/MS

    PubMed Central

    Eugster, Marcel R.; Loessner, Martin J.

    2011-01-01

    We report the application of electrospray ionization (ESI) mass spectrometry for compositional characterization of wall teichoic acids (WTA), a major component of Gram-positive bacterial cell walls. Tandem mass spectrometry (ESI-MS/MS) of purified and chemically hydrolyzed monomeric WTA components provided sufficient information to identify WTA monomers and their specific carbohydrate constituents. A lithium matrix was used for ionization of uncharged WTA monomers, and successfully applied to analyze the WTA molecules of four Listeria strains differing in carbohydrate substitution on a conserved polyribitol-phosphate backbone structure. Carbohydrate residues such as N-acetylglucosamine or rhamnose linked to the WTA could directly be identified by ESI-MS/MS, circumventing the need for quantitative analysis by gas chromatography. The presence of a terminal N-acetylglucosamine residue tethered to the ribitol was confirmed using fluorescently labeled wheat-germ agglutinin. In conclusion, the mass spectrometry method described here will greatly facilitate compositional analysis and characterization of teichoic acids and similar macromolecules from diverse bacterial species, and represents a significant advance in the identification of serovar-specific carbohydrates and sugar molecules on bacteria. PMID:21738682

  8. Workshop to establish databases of carbohydrate spectra

    SciTech Connect

    1995-12-31

    The workshop was organized to formulate guidelines for establishing spectral databases of complex carbohydrates. The databases will enable the scientific community to avoid the great waste of research effort and funds that frequently occurs when carbohydrate chemists are forced to duplicate the structural characterization of previously characterized complex carbohydrates. Chemists waste their effort on repetitive characterizations because in the absence of spectral databases they are unaware they are analyzing a known molecule until they have completely determined its structure. Chemists will be able to avoid much of this wasted effort when the collections of mass and of nuclear magnetic resonance (NMR) spectra initiated at the workshop are subsequently developed into searchable databases. Then scientists only need query the databases with the spectrum or with information defining the spectrum of an unidentified carbohydrate to find out if it has been previously characterized.

  9. Ectoine and 5-hydroxyectoine accumulation in the halophile Virgibacillus halodenitrificans PDB-F2 in response to salt stress.

    PubMed

    Tao, Ping; Li, Hui; Yu, Yunjiang; Gu, Jidong; Liu, Yongdi

    2016-08-01

    The moderately halophilic bacterium Virgibacillus halodenitrificans PDB-F2 copes with salinity by synthesizing or taking up compatible solutes. The main compatible solutes in this strain were ectoine and hydroxyectoine, as determined by (1)H nuclear magnetic resonance spectroscopy ((1)H-NMR). A high-performance liquid chromatography (HPLC) analysis showed that ectoine was the major solute that was synthesized in response to elevated salinity, while hydroxyectoine was a minor solute. However, the hydroxyectoine/ectoine ratio increased from 0.04 at 3 % NaCl to 0.45 at 15 % NaCl in the late exponential growth phase. A cluster of ectoine biosynthesis genes was identified, including three genes in the order of ectA, ectB, and ectC. The hydroxyectoine biosynthesis gene ectD was not part of the ectABC gene cluster. Reverse transcription-quantitative polymerase chain reactions (RT-qPCR) showed that the expression of the ect genes was salinity dependent. The expression of ectABC reached a maximum at 12 % NaCl, while ectD expression increased up to 15 % NaCl. Ectoine and hydroxyectoine production was growth phase dependent. The hydroxyectoine/ectoine ratio increased from 0.018 in the early exponential phase to 0.11 in the stationary phase at 5 % NaCl. Hydroxyectoine biosynthesis started much later than ectoine biosynthesis after osmotic shock, and the temporal expression of the ect genes differed under these conditions, with the ectABC genes being expressed first, followed by ectD gene. Increased culture salinity triggered ectoine or hydroxyectoine uptake when they were added to the medium. Hydroxyectoine was accumulated preferentially when both ectoine and hydroxyectoine were provided exogenously.

  10. Ectoine and 5-hydroxyectoine accumulation in the halophile Virgibacillus halodenitrificans PDB-F2 in response to salt stress.

    PubMed

    Tao, Ping; Li, Hui; Yu, Yunjiang; Gu, Jidong; Liu, Yongdi

    2016-08-01

    The moderately halophilic bacterium Virgibacillus halodenitrificans PDB-F2 copes with salinity by synthesizing or taking up compatible solutes. The main compatible solutes in this strain were ectoine and hydroxyectoine, as determined by (1)H nuclear magnetic resonance spectroscopy ((1)H-NMR). A high-performance liquid chromatography (HPLC) analysis showed that ectoine was the major solute that was synthesized in response to elevated salinity, while hydroxyectoine was a minor solute. However, the hydroxyectoine/ectoine ratio increased from 0.04 at 3 % NaCl to 0.45 at 15 % NaCl in the late exponential growth phase. A cluster of ectoine biosynthesis genes was identified, including three genes in the order of ectA, ectB, and ectC. The hydroxyectoine biosynthesis gene ectD was not part of the ectABC gene cluster. Reverse transcription-quantitative polymerase chain reactions (RT-qPCR) showed that the expression of the ect genes was salinity dependent. The expression of ectABC reached a maximum at 12 % NaCl, while ectD expression increased up to 15 % NaCl. Ectoine and hydroxyectoine production was growth phase dependent. The hydroxyectoine/ectoine ratio increased from 0.018 in the early exponential phase to 0.11 in the stationary phase at 5 % NaCl. Hydroxyectoine biosynthesis started much later than ectoine biosynthesis after osmotic shock, and the temporal expression of the ect genes differed under these conditions, with the ectABC genes being expressed first, followed by ectD gene. Increased culture salinity triggered ectoine or hydroxyectoine uptake when they were added to the medium. Hydroxyectoine was accumulated preferentially when both ectoine and hydroxyectoine were provided exogenously. PMID:27106915

  11. Carbohydrate protease conjugates: Stabilized proteases for peptide synthesis

    SciTech Connect

    Wartchow, C.A.; Wang, Peng; Bednarski, M.D.; Callstrom, M.R. |

    1995-12-31

    The synthesis of oligopeptides using stable carbohydrate protease conjugates (CPCs) was examined in acetonitrile solvent systems. CPC[{alpha}-chymotrypsin] was used for the preparation of peptides containing histidine, phenylalanine, tryptophan in the P{sub 1} position in 60-93% yield. The CPC[{alpha}-chymotrypsin]-catalyzed synthesis of octamer Z-Gly-Gly-Phe-Gly-Gly-Phe-Gly-Gly-OEt from Z-Gly-Gly-Phe-Gly-Gly-Phe-OMe was achieved in 71% yield demonstrating that synthesis peptides containing both hydrophylic and hydrophobic amino acids. The P{sub 2} specificity of papain for aromatic residues was utilized for the 2 + 3 coupling of Z-Tyr-Gly-OMe to H{sub 2}N-Gly-Phe-Leu-OH to generate the leucine enkephalin derivative in 79% yield. Although papain is nonspecific for the hydrolysis of N-benzyloxycarbonyl amino acid methyl esters in aqueous solution, the rates of synthesis for these derivitives with nucleophile leucine tert-butyl ester differed by nearly 2 orders of magnitude. CPC[thermolysin] was used to prepare the aspartame precursor Z-Asp-Phe-OMe in 90% yield. The increased stability of CPCs prepared from periodate-modified poly(2-methacryl- amido-2-deoxy-D-glucose), poly(2-methacrylamido-2-deoxy-D-galactose), and poly(5-methacryl-amido-5-deoxy-D-ribose), carbohydrate materials designed to increase the aldehyde concentration in aqueous solution, suggests that the stability of CPCs is directly related to the aldehyde concentration of the carbohydrate material. Periodate oxidation of poly(2-methacrylamido-2-deoxy-D-glucose) followed by covalent attachment to {alpha}-chymotrypsin gave a CPC with catalytic activity in potassium phosphate buffer at 90{degrees}C for 2 h. 1 fig., 1 tab., 40 refs.

  12. Cell-Wall Carbohydrates of the Endosperm of the Seed of Gleditsia triacanthos1

    PubMed Central

    Manzi, Adriana E.; Ancibor, Elena; Cerezo, Alberto S.

    1990-01-01

    The endosperm of the seed of Gleditsia triacanthos L. contains 18.55% of its dry weight as nonreserve, cell-wall carbohydrates. Of this carbohydrate material, comprising mainly mannose, galactose, and glucose, 76.1% was of low-molecular weight or highly hydrophilic. Mannose, galactose, and glucose were also the major sugar components of the polysaccharides extracted with alkali (23.1% of the cell-wall), while the same sugars, with minor amounts of arabinose, form the residues. Methylation analysis of the polysaccharides and the borate-sodium hydroxide residue indicate that the cell walls are built up on a network of galactomannans, with high Man/Gal ratios, reinforced with minor amounts of cellulose. Images Figure 2 Figure 2 PMID:16667408

  13. Carbohydrate Nutrition and Team Sport Performance.

    PubMed

    Williams, Clyde; Rollo, Ian

    2015-11-01

    The common pattern of play in 'team sports' is 'stop and go', i.e. where players perform repeated bouts of brief high-intensity exercise punctuated by lower intensity activity. Sprints are generally 2-4 s long and recovery between sprints is of variable length. Energy production during brief sprints is derived from the degradation of intra-muscular phosphocreatine and glycogen (anaerobic metabolism). Prolonged periods of multiple sprints drain muscle glycogen stores, leading to a decrease in power output and a reduction in general work rate during training and competition. The impact of dietary carbohydrate interventions on team sport performance have been typically assessed using intermittent variable-speed shuttle running over a distance of 20 m. This method has evolved to include specific work to rest ratios and skills specific to team sports such as soccer, rugby and basketball. Increasing liver and muscle carbohydrate stores before sports helps delay the onset of fatigue during prolonged intermittent variable-speed running. Carbohydrate intake during exercise, typically ingested as carbohydrate-electrolyte solutions, is also associated with improved performance. The mechanisms responsible are likely to be the availability of carbohydrate as a substrate for central and peripheral functions. Variable-speed running in hot environments is limited by the degree of hyperthermia before muscle glycogen availability becomes a significant contributor to the onset of fatigue. Finally, ingesting carbohydrate immediately after training and competition will rapidly recover liver and muscle glycogen stores.

  14. Carbohydrate Nutrition and Team Sport Performance.

    PubMed

    Williams, Clyde; Rollo, Ian

    2015-11-01

    The common pattern of play in 'team sports' is 'stop and go', i.e. where players perform repeated bouts of brief high-intensity exercise punctuated by lower intensity activity. Sprints are generally 2-4 s long and recovery between sprints is of variable length. Energy production during brief sprints is derived from the degradation of intra-muscular phosphocreatine and glycogen (anaerobic metabolism). Prolonged periods of multiple sprints drain muscle glycogen stores, leading to a decrease in power output and a reduction in general work rate during training and competition. The impact of dietary carbohydrate interventions on team sport performance have been typically assessed using intermittent variable-speed shuttle running over a distance of 20 m. This method has evolved to include specific work to rest ratios and skills specific to team sports such as soccer, rugby and basketball. Increasing liver and muscle carbohydrate stores before sports helps delay the onset of fatigue during prolonged intermittent variable-speed running. Carbohydrate intake during exercise, typically ingested as carbohydrate-electrolyte solutions, is also associated with improved performance. The mechanisms responsible are likely to be the availability of carbohydrate as a substrate for central and peripheral functions. Variable-speed running in hot environments is limited by the degree of hyperthermia before muscle glycogen availability becomes a significant contributor to the onset of fatigue. Finally, ingesting carbohydrate immediately after training and competition will rapidly recover liver and muscle glycogen stores. PMID:26553494

  15. Dietary Carbohydrates and Childhood Functional Abdominal Pain.

    PubMed

    Chumpitazi, Bruno P; Shulman, Robert J

    2016-01-01

    Childhood functional gastrointestinal disorders (FGIDs) affect a large number of children throughout the world. Carbohydrates (which provide the majority of calories consumed in the Western diet) have been implicated both as culprits for the etiology of symptoms and as potential therapeutic agents (e.g., fiber) in childhood FGIDs. In this review, we detail how carbohydrate malabsorption may cause gastrointestinal symptoms (e.g., bloating) via the physiologic effects of both increased osmotic activity and increased gas production from bacterial fermentation. Several factors may play a role, including: (1) the amount of carbohydrate ingested; (2) whether ingestion is accompanied by a meal or other food; (3) the rate of gastric emptying (how quickly the meal enters the small intestine); (4) small intestinal transit time (the time it takes for a meal to enter the large intestine after first entering the small intestine); (5) whether the meal contains bacteria with enzymes capable of breaking down the carbohydrate; (6) colonic bacterial adaptation to one's diet, and (7) host factors such as the presence or absence of visceral hypersensitivity. By detailing controlled and uncontrolled trials, we describe how there is a general lack of strong evidence supporting restriction of individual carbohydrates (e.g., lactose, fructose) for childhood FGIDs. We review emerging evidence suggesting that a more comprehensive restriction of fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) may be effective. Finally, we review how soluble fiber (a complex carbohydrate) supplementation via randomized controlled intervention trials in childhood functional gastrointestinal disorders has demonstrated efficacy. PMID:27355647

  16. Chemical labeling of carbohydrates by oxidation and sodium borohydride reduction.

    PubMed

    Fukuda, M

    2001-05-01

    This unit describes a collection of methods for chemical labeling of carbohydrates (free oligosaccharides or oligosaccharides conjugated to proteins, peptides, or lipids) by oxidation followed by reduction or by direct reduction. Oligosaccharides can be labeled with either radioisotopes or nonradioactive fluorescent molecules. These labelings allow one to follow the oligosaccharides during chromatography and in cells if labeled by fluorescent molecules. Selective oxidation with mild periodate followed by reduction with tritiated sodium borohydride results in selective radiolabeling of sialic acid residues on oligosaccharides or glycoproteins. Alternatively, treatment of samples with galactose oxidase results in oxidation of galactose or N-acetylgalactosamine residues at nonreducing termini, rendering these residues susceptible to labeling with NaB[3H]4. Oxidized glycoconjugates can also be labeled using the fluorescent probe lucifer yellow CH. Free oligosaccharides can be labeled by reduction with NaB[3H]4. An additional protocol describes the release and simultaneous labeling of O-glycan oligosaccharides by alkaline beta-elimination in the presence of NaB[3H]4.

  17. Carbohydrate drinks and cycling performance.

    PubMed

    Bacharach, D W; von Duvillard, S P; Rundell, K W; Meng, J; Cring, M R; Szmedra, L; Castle, J M

    1994-06-01

    We compared the effects of similarly tasting orange flavored drinks containing 0% (P), 6.4% (E1), and 10% (E2) carbohydrate (CHO) using 12 well-trained cyclists (VO2max = 5.0 l/min-1) on metabolic responses to exercise (EX) and a sprint type performance ride (PR). Each subject completed 3 separate 2 h EX bouts at 65% VO2max followed by a PR identified as the time in sec to complete 500 revolutions at a constant belt resistance of 29.4 N (ANOVA*). The CHO feedings or placebo of 3 ml/kg body weight were given double blind and counter-balanced at 0 min and every 20 min thereafter during EX. Blood samples were drawn and core temperature (Tr) was recorded at 0, 30, 60, 90, and 120 min of EX and 1 min post PR. Blood samples were analyzed for glucose (G) and lactate [LA-]. Blood G at 0 min were similar; however, at 120 min, G was 3.96 mM for P*, 4.57 mM for E1, and 4.77 mM for E2. Blood [LA-] remained similar throughout EX averaging (P, 2.6 mM; E1, 2.9 mM; E2, 2.5 mM). Tr at 120 min was also similar (P, 38.5 degrees C; E1, 38.6 degrees C; E2, 38.3 degrees C). Mean PR times for P(264.4 s)**, E1 (255.3 s)*, E2 (252.4 s)* indicate consumption of a CHO drink during EX improves PR. Furthermore, a 10% CHO drink improves PR more than a 6.4% CHO drink.

  18. Carbohydrate ligands for endothelial - Leukocyte adhesion molecule 1

    SciTech Connect

    Tiemeyer, M.; Swiedler, S.J.; Ishihara, Masayuki; Moreland, M.; Schweingruber, H.; Hirtzer, P.; Brandley, B.K. )

    1991-02-15

    The acute inflammatory response requires that circulating leukocytes bind to and penetrate the vascular wall to access the site of injury. Several receptors have been implicated in this interaction, including a family of putative carbohydrate-binding proteins. The authors report here the identification of an endogenous carbohydrate ligand for one of these receptors, endothelial-leukocyte adhesion molecule 1 (ELAM-1). Radiolabeled COS cells transfected with a plasmid containing the cDNA for ELAM-1 were used as probes to screen glycolipids extracted from human leukocytes. COS cells transfected with this plasmid adhered to a subset of sialylated glycolipids resolved on TLC plates or adsorbed on polyvinyl chloride microtiter wells. Adhesion to these glycolipids required calcium but was not inhibited by heparin, chondroitin sulfate, keratan sulfate, or yeast phosphomannan. Monosaccharide composition, linkage analysis, and fast atom bombardment mass spectrometry of the glycolipids indicate that the ligands for ELAM-1 are terminally sialylated lactosylceramides with a variable number of N-acetyllactosamine repeats and at least one fucosylated N-acetylglucosamine residue.

  19. Glycoprotein labeling with click chemistry (GLCC) and carbohydrate detection.

    PubMed

    Wu, Zhengliang L; Huang, Xinyi; Burton, Andrew J; Swift, Karl A D

    2015-08-14

    Molecular labeling and detection techniques are essential to research in life science. Here, a method for glycoprotein labeling/carbohydrate detection through glycan replacement, termed glycoprotein labeling with click chemistry (GLCC), is described. In this method, a glycoprotein is first treated with specific glycosidases to remove certain sugar residues, a procedure that creates acceptor sites for a specific glycosyltransferase. A 'clickable' monosaccharide is then installed onto these sites by the glycosyltransferase. This modified glycoprotein is then conjugated to a reporter molecule using a click chemistry reaction. For glycoproteins that already contain vacant glycosylation sites, deglycosylation is not needed before the labeling step. As a demonstration, labeling on fetal bovine fetuin, mouse immunoglobulin IgG and bacterial expressed human TNFα and TNFβ are shown. Compared to traditional ways of protein labeling, labeling at glycosylation sites with GLCC is considerably more specific and less likely to have adverse effects, and, when utilized as a method for carbohydrate detection, this method is also highly specific and sensitive.

  20. Characterizing the glycocalyx of poultry spermatozoa; semen cryopreservation methods alter the carbohydrate component of rooster sperm membrane glycoconjugates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The carbohydrate-rich zone on the sperm surface is essential for inmunoprotection in the female tract and early gamete interactions. We recently have shown the glycocalyx of chicken sperm to be extensively sialylated and contain residues of mannose, glucose, galactose, fucose, N-acetyl-galactosamine...

  1. Thermodynamic, kinetic, and electron microscopy studies of concanavalin A and Dioclea grandiflora lectin cross-linked with synthetic divalent carbohydrates.

    PubMed

    Dam, Tarun K; Oscarson, Stefan; Roy, René; Das, Sanjoy K; Pagé, Daniel; Macaluso, Frank; Brewer, C Fred

    2005-03-11

    The jack bean lectin concanavalin A (ConA) and the Dioclea grandiflora lectin (DGL) are highly homologous Man/Glc-specific members of the Diocleinae subtribe. Both lectins bind, cross-link, and precipitate with carbohydrates possessing multiple terminal nonreducing Man residues. The present study investigates the binding and cross-linking interactions of ConA and DGL with a series of synthetic divalent carbohydrates that possess spacer groups with increasing flexibility and length between terminal alpha-mannopyranoside residues. Isothermal titration microcalorimetry was used to determine the thermodynamics of binding of the two lectins to the divalent analogs, and kinetic light scattering and electron microscopy studies were used to characterize the cross-linking interactions of the lectins with the carbohydrates. The results demonstrated that divalent analogs with flexible spacer groups between the two terminal Man residues possess higher affinities for the two lectins as compared with those with inflexible spacer groups. Furthermore, despite their high degree of homology, ConA and DGL exhibit differences in their kinetics of cross-linking and precipitation with the divalent analogs. Electron microscopy shows the loss of organized cross-linked lattices of the two lectins with analogs possessing increased distance between the terminal Man residues. The loss of lattice patterns with the analogs is distinct for each lectin. These results have important implications for the interactions of lectins with multivalent carbohydrate receptors in biological systems.

  2. Temporal changes in the carbohydrates expressed on BG01 human embryonic stem cells during differentiation as embryoid bodies.

    PubMed

    Wearne, Kimberly A; Winter, Harry C; Goldstein, Irwin J

    2008-02-01

    Cell surface carbohydrates present on BG01 human embryonic stem cells after 28 days of differentiation were examined using two classes of carbohydrate binding proteins: lectins and antibodies specific for carbohydrate epitopes. Specificity of lectin staining was verified using carbohydrate ligands to block lectin interaction, glycohydrolases to cleave specific sugar residues that are receptors for these proteins, and periodate oxidation to destroy susceptible sugar residues. Specific antibodies were used to identify various tissue types and germ layers present in the 12- and 28-day differentiating embryoid bodies. Results from 12 and 28-day differentiated embryoid bodies were compared to determine changes over time. A slight increase in the sialylation of alpha-GalNAc was seen between 12 and 28 days of differentiation due to the presence of sialyl Tn and/or other sialylated alpha-GalNAc residues. Increases were also observed in GalNAc, the T antigen (Gal beta1,3 GalNAc), and difucosylated LacNAc residues during this time interval. Additionally, some distinct differences in the pattern of lectin staining between 12 and 28 days were observed. Not unexpectedly, the presence of most differentiated cell-types increased during this time period with the exception of neural progenitors, which decreased. Undifferentiated cells, which were prevalent in the 12-day EBs, were undetectable after 28 days. We conclude that several changes in glycosylation occurred during the differentiation of embryonic stem cells, and that these changes may play a role in embryonic development.

  3. Monitoring processivity and length control of a carbohydrate polymerase

    PubMed Central

    Levengood, Matthew R.; Splain, Rebecca A.; Kiessling, Laura L.

    2011-01-01

    Carbohydrate polymerases are abundant in nature. Although they play vital physiological roles, the molecular mechanisms that they use for the controlled assembly of polymers are largely unknown. One fundamental issue is whether an enzyme utilizes a processive or distributive mechanism for chain elongation. The shortage of mechanistic information on polysaccharide-generating glycosyltransferases became apparent when we sought to carry out investigations of GlfT2, a glycosyltransferase essential for cell wall biosynthesis in Mycobacterium tuberculosis. GlfT2 catalyzes the formation of the cell wall galactan, which is a linear polysaccharide consisting of 20-40 repeating D-galactofuranose (Galf) residues. Recombinant GlfT2 can act on synthetic acceptors to produce polymers with lengths similar to those of endogenous galactan, indicating that GlfT2 has an intrinsic ability to control polymer length. To address whether GlfT2 utilizes a processive or distributive mechanism, we developed a mass spectrometry assay. Our approach, which relies on acceptors labeled with stable isotopes, provides direct evidence that GlfT2 is a processive polymerase that maintains contact with the glycan substrate through successive monomer additions. Given this finding, we probed further the catalytic mechanism of GlfT2 to address the basis of an observed kinetic lag phase. These studies suggest that GlfT2 possesses subsites for Galf residue binding and that substrates that can fill these subsites undergo efficient processive polymerization. The presence of these subsites and the kinetic lag phase are common features of processive enzymes. We anticipate that the strategies described herein can be applied to mechanistic studies of other carbohydrate polymerization reactions. PMID:21739979

  4. Linkage of carbohydrate to hydroxyamino acids in mucopolysaccharides and mucoproteins

    PubMed Central

    Adams, J. B.

    1965-01-01

    1. Glycosidic linkage of carbohydrate to the primary hydroxyl groups of threonine and serine has been established in human blood-group A and Lea substances, bovine submaxillary-gland mucin and human pseudomyxomatous mucin. 2. Treatment of these substances in 0·09n-lithium hydroxide at 100° for 1hr. led to β-elimination at these glycosidic linkages with the resultant formation of α-oxobutyric acid and glycine from threonine linkages, and pyruvic acid from serine linkages. Though most of the threonine was destroyed in every case, about one-third to one-half of the serine residues resisted alkaline cleavage. Such results, indicative of the presence of unbound serine residues, allow, in submaxillary mucin, for a close correlation between the remaining serine, threonine, glutamic acid and aspartic acid and the available sialyl-(2→6)-N-acetylgalactosamine prosthetic groups. 3. The stoichiometry of the β-eliminations has been demonstrated for pseudomyxomatous mucin. The α-oxo acids were separated and determined as their quinoxalinol derivatives by thin-layer chromatography on silica gel. Reaction at the threonine centres favoured α-oxobutyric acid formation (70%, via the intermediary dehydropeptide) over the alternative pathway to glycine (30%). 4. 100% of the hexosamine was destroyed in submaxillary-gland mucin, 85% in pseudomyxomatous mucin and about 60% in the blood-group substances. In the latter cases, the glucosamine/galactosamine ratio was increased from about 4:1 to 8–10:1, suggesting a preferential destruction of galactosamine. Evidence was obtained, however, for a further destruction of hexosamine, in addition to that which could be theoretically attached to peptide at possible known binding sites. 5. The major part of the alkali-resistant hexosamine in the blood-group substances was non-diffusible and was accompanied by the constituent carbohydrates in similar molar proportions to the native materials. ImagesFig. 1. PMID:16749136

  5. Carbohydrate Level and Growth of Tomato Plants

    PubMed Central

    Gent, Martin P. N.

    1984-01-01

    To what extent can the influence of environment on greenhouse tomato plants (Lycopersicon esculentum L.) be explained by a linear response of the growth rate to carbohydrate level? To answer this question, young tomato plants were transplanted in January and March and grown for one-month periods under natural light either with or without CO2 enrichment to 1000 microliters per liter and either under a constant minimum temperature of 15°C or a minimum temperature that fluctuated between 20°C for 12 hours including the photoperiod and 10°C for the remaining 12 hours. The carbohydrate levels were measured for plants under all growth conditions at several times in the diurnal cycle. At the average irradiance in January, 2.3 megajoules per square meter per day, plants under CO2 enrichment grew 15% faster and had, on average, total nonstructural carbohydrate levels 27 milligrams per gram greater and soluble carbohydrates 3 milligrams per gram greater at all hours of the day than did plants grown under ambient CO2. Plants grown under fluctuating diurnal temperature grew slightly faster and had total nonstructural carbohydrate levels on average 8 milligrams per gram greater than plants grown under a more constant temperature. At the average irradiance in March-April, 4.3 megajoules per square meter per day, growth and carbohydrate level increased with CO2 enrichment under the control temperature regime but not under fluctuating temperatures. Plants in all growth regimens grew faster than in January. Over all plantings and growth regimens, relative growth rates were more highly correlated to total nonstructural carbohydrate levels than they were to irradiance, CO2, or temperature. PMID:16663908

  6. Low-carbohydrate diets and performance.

    PubMed

    Cook, Chad M; Haub, Mark D

    2007-07-01

    Athletes are continually searching for means to optimize their performance. Within the past 20 years, athletes and scientists have reported or observed that consuming a carbohydrate-restricted diet may improve performance. The original theories explaining the purported benefits centered on the fact that fat oxidation increases, thereby "sparing" muscle glycogen. More recent concepts that explain the plausibility of the ergogenicity of low-carbohydrate, or high-fat, diets on exercise performance pertain to an effect similar to altitude training. We and others have observed that although fat oxidation may be increased, the ability to maintain high-intensity exercise (above the lactate threshold) seems to be compromised or at least indifferent when compared with consumption of more carbohydrate. That said, clinical studies clearly demonstrate that ad libitum low-carbohydrate diets elicit greater decreases in body weight and fat than energy-equivalent low-fat diets, especially over a short duration. Thus, although low-carbohydrate and high-fat diets appear detrimental or indifferent relative to performance, they may be a faster means to achieve a more competitive body composition.

  7. Carbohydrates and T cells: a sweet twosome.

    PubMed

    Avci, Fikri Y; Li, Xiangming; Tsuji, Moriya; Kasper, Dennis L

    2013-04-01

    Carbohydrates as T cell-activating antigens have been generating significant interest. For many years, carbohydrates were thought of as T-independent antigens, however, more recent research had demonstrated that mono- or oligosaccharides glycosidically linked to peptides can be recognized by T cells. T cell recognition of these glycopeptides depends on the structure of both peptide and glycan portions of the antigen. Subsequently, it was discovered that natural killer T cells recognized glycolipids when presented by the antigen presenting molecule CD1d. A transformative insight into glycan-recognition by T cells occurred when zwitterionic polysaccharides were discovered to bind to and be presented by MHCII to CD4+ T cells. Based on this latter observation, the role that carbohydrate epitopes generated from glycoconjugate vaccines had in activating helper T cells was explored and it was found that these epitopes are presented to specific carbohydrate recognizing T cells through a unique mechanism. Here we review the key interactions between carbohydrate antigens and the adaptive immune system at the molecular, cellular and systems levels exploring the significant biological implications in health and disease.

  8. Potential effect of ultrasound on carbohydrates.

    PubMed

    Bera, Smritilekha; Mondal, Dhananjoy; Martin, Jacob T; Singh, Man

    2015-06-17

    The use of ultrasound has emerged as one of the most useful alternative energy sources for the synthesis of carbohydrate-derived biologically and pharmaceutically potential compounds. Spectacular advances have been made in the field of sonication-assisted organic reactions, which are known for producing superior yields, enhanced reactivity of the reactant, improved stereoselectivity, and shortened reaction times. Orthogonal protection-deprotection reactions and/or modification and manipulation of functional groups in carbohydrates are common synthetic steps in carbohydrate chemistry. These reaction steps can be driven by the ultrasonic energy generated by acoustic cavitation via the formation and subsequent collapse of ultrasound-induced bubbles. The ultrasound-assisted synthesis of differently functionalised monosaccharides is useful in a wide variety of applications of carbohydrate chemistry such as the glycosylation of oligosaccharides, one pot domino reactions, thioglycoside syntheses, azidoglycoside syntheses, 1,3-dipolar cycloaddition reactions, and syntheses of natural products. This review article covers ultrasound-mediated reactions on carbohydrates that have been described in the literature since 2000.

  9. Screening method of carbohydrate-binding proteins in biological sources by capillary affinity electrophoresis and its application to determination of Tulipa gesneriana agglutinin in tulip bulbs.

    PubMed

    Nakajima, Kazuki; Kinoshita, Mitsuhiro; Oda, Yasuo; Masuko, Takashi; Kaku, Hanae; Shibuya, Naoto; Kakehi, Kazuaki

    2004-09-01

    We developed capillary affinity electrophoresis (CAE) to analyze the molecular interaction between carbohydrate chains and proteins in solution state. A mixture of oligosaccharides derived from a glycoprotein was labeled with 8-aminopyrene-1,3,6-trisulfonate (APTS), and used as glycan library without isolation. Interaction of a carbohydrate-binding protein with each oligosaccharide in the mixture could be simultaneously observed, and relative affinities of oligosaccharides toward the protein were accurately determined. In this study, we applied CAE to detect the presence of lectins in some plants (Japanese elderberry bark and tulip bulb). In the crude extract of the elderberry bark, binding activity toward sialo-carbohydrate chains could be easily detected. We also examined the presence of lectins in the crude extract of tulip bulbs and determined the detailed carbohydrate-binding specificity of Tulipa gesneriana agglutinin (TGA), one of the lectins from tulip bulbs. Kinetic studies demonstrated that TGA showed novel carbohydrate-binding specificity and preferentially recognized triantennary oligosaccharides with Gal residues at nonreducing termini and a Fuc residue linked through alpha(1-6) linkage at chitobiose portion of the reducing termini but not tetraantennary carbohydrates. The results described here indicate that CAE will be a valuable method for both screening of lectins in natural sources and determination of their detailed carbohydrate-binding specificities.

  10. LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria.

    PubMed

    González-Díaz, Humberto; Munteanu, Cristian R; Postelnicu, Lucian; Prado-Prado, Francisco; Gestal, Marcos; Pazos, Alejandro

    2012-03-01

    Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense.

  11. Investigation of Carbohydrate Recognition via Computer Simulation

    SciTech Connect

    Johnson, Quentin R.; Lindsay, Richard J.; Petridis, Loukas; Shen, Tongye

    2015-04-28

    Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. Here, we focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We review the current state of this technique and its successful applications for studying protein-sugar interactions in recent years.

  12. Investigation of Carbohydrate Recognition via Computer Simulation.

    PubMed

    Johnson, Quentin R; Lindsay, Richard J; Petridis, Loukas; Shen, Tongye

    2015-01-01

    Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Recently, interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. We focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We review the current state of this technique and its successful applications for studying protein-sugar interactions in recent years. PMID:25927900

  13. Nutraceutical and pharmacological implications of marine carbohydrates.

    PubMed

    Pallela, Ramjee

    2014-01-01

    Current day's research has been focusing much on the potential pharmacological or nutraceutical agents of selective health benefits with less toxicity. As a consequence of increased demand of nutritional supplements of great medicinal values, development of therapeutic agents from natural sources, in particular, marine environment are being considered much important. A diverse array of marine natural products containing medicinally useful nutritional substances, i.e., marine nutraceuticals have been focused to the benefit of mankind. Carbohydrates, by being constituted in considerable amount of many marine organisms display several nutraceutical and pharmaceutical behavior to defend from various diseases. Moreover, the carbohydrates from algae as well as from shellfish wastes, like chitosan and its derivatives, showed tremendous applications in biology and biomedicine. In the current chapter, several of marine carbohydrates from various marine flora and fauna have been covered with their applications and prospects in the development of nutraceuticals and pharmaceuticals. PMID:25300547

  14. Investigation of Carbohydrate Recognition via Computer Simulation

    DOE PAGES

    Johnson, Quentin R.; Lindsay, Richard J.; Petridis, Loukas; Shen, Tongye

    2015-04-28

    Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. Here, we focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We reviewmore » the current state of this technique and its successful applications for studying protein-sugar interactions in recent years.« less

  15. Investigation of Carbohydrate Recognition via Computer Simulation.

    PubMed

    Johnson, Quentin R; Lindsay, Richard J; Petridis, Loukas; Shen, Tongye

    2015-04-28

    Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Recently, interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. We focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We review the current state of this technique and its successful applications for studying protein-sugar interactions in recent years.

  16. Heterogeneously-Catalyzed Conversion of Carbohydrates

    NASA Astrophysics Data System (ADS)

    Vigier, Karine De Oliveira; Jérôme, François

    Polyfunctionality of carbohydrates and their low solubility in conventional organic solvents make rather complex their conversion to higher value added chemicals. Therefore, innovative processes are now strongly needed in order to increase the selectivity of these reactions. Here, we report an overview of the different heterogeneously-catalyzed processes described in the literature. In particular, hydrolysis, dehydration, oxidation, esterification, and etherification of carbohydrates are presented. We shall discuss the main structural parameters that need to be controlled and that permit the conversion of carbohydrates to bioproducts with good selectivity. The conversion of monosaccharides and disaccharides over solid catalysts, as well as recent advances in the heterogeneously-catalyzed conversion of cellulose, will be presented.

  17. Boronic acids for fluorescence imaging of carbohydrates.

    PubMed

    Sun, Xiaolong; Zhai, Wenlei; Fossey, John S; James, Tony D

    2016-02-28

    "Fluorescence imaging" is a particularly exciting and rapidly developing area of research; the annual number of publications in the area has increased ten-fold over the last decade. The rapid increase of interest in fluorescence imaging will necessitate the development of an increasing number of molecular receptors and binding agents in order to meet the demand in this rapidly expanding area. Carbohydrate biomarkers are particularly important targets for fluorescence imaging given their pivotal role in numerous important biological events, including the development and progression of many diseases. Therefore, the development of new fluorescent receptors and binding agents for carbohydrates is and will be increasing in demand. This review highlights the development of fluorescence imaging agents based on boronic acids a particularly promising class of receptors given their strong and selective binding with carbohydrates in aqueous media.

  18. Nutraceutical and pharmacological implications of marine carbohydrates.

    PubMed

    Pallela, Ramjee

    2014-01-01

    Current day's research has been focusing much on the potential pharmacological or nutraceutical agents of selective health benefits with less toxicity. As a consequence of increased demand of nutritional supplements of great medicinal values, development of therapeutic agents from natural sources, in particular, marine environment are being considered much important. A diverse array of marine natural products containing medicinally useful nutritional substances, i.e., marine nutraceuticals have been focused to the benefit of mankind. Carbohydrates, by being constituted in considerable amount of many marine organisms display several nutraceutical and pharmaceutical behavior to defend from various diseases. Moreover, the carbohydrates from algae as well as from shellfish wastes, like chitosan and its derivatives, showed tremendous applications in biology and biomedicine. In the current chapter, several of marine carbohydrates from various marine flora and fauna have been covered with their applications and prospects in the development of nutraceuticals and pharmaceuticals.

  19. Computer Simulations Reveal Multiple Functions for Aromatic Residues in Cellulase Enzymes (Fact Sheet)

    SciTech Connect

    Not Available

    2012-07-01

    NREL researchers use high-performance computing to demonstrate fundamental roles of aromatic residues in cellulase enzyme tunnels. National Renewable Energy Laboratory (NREL) computer simulations of a key industrial enzyme, the Trichoderma reesei Family 6 cellulase (Cel6A), predict that aromatic residues near the enzyme's active site and at the entrance and exit tunnel perform different functions in substrate binding and catalysis, depending on their location in the enzyme. These results suggest that nature employs aromatic-carbohydrate interactions with a wide variety of binding affinities for diverse functions. Outcomes also suggest that protein engineering strategies in which mutations are made around the binding sites may require tailoring specific to the enzyme family. Cellulase enzymes ubiquitously exhibit tunnels or clefts lined with aromatic residues for processing carbohydrate polymers to monomers, but the molecular-level role of these aromatic residues remains unknown. In silico mutation of the aromatic residues near the catalytic site of Cel6A has little impact on the binding affinity, but simulation suggests that these residues play a major role in the glucopyranose ring distortion necessary for cleaving glycosidic bonds to produce fermentable sugars. Removal of aromatic residues at the entrance and exit of the cellulase tunnel, however, dramatically impacts the binding affinity. This suggests that these residues play a role in acquiring cellulose chains from the cellulose crystal and stabilizing the reaction product, respectively. These results illustrate that the role of aromatic-carbohydrate interactions varies dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, the results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for

  20. A study of the influence of charged residues on β-hairpin formation by nuclear magnetic resonance and molecular dynamics.

    PubMed

    Makowska, Joanna; Zmudzińska, Wioletta; Uber, Dorota; Chmurzyński, Lech

    2014-12-01

    Chain reversals are often nucleation sites in protein folding. The β-hairpins of FBP28 WW domain and IgG are stable and have been proved to initiate the folding and are, therefore, suitable for studying the influence of charged residues on β-hairpin conformation. In this paper, we carried out NMR examination of the conformations in solution of two fragments from the FPB28 protein (PDB code: 1E0L) (N-terminal part) namely KTADGKT-NH2 (1E0L 12-18, D7) and YKTADGKTY-NH2 (1E0L 11-19, D9), one from the B3 domain of the protein G (PDB code: 1IGD), namely DDATKT-NH2 (1IGD 51-56) (Dag1), and three variants of Dag1 peptide: DVATKT-NH2 (Dag2), OVATKT-NH2 (Dag3) and KVATKT-NH2 (Dag4), respectively, in which the original charged residue were replaced with non-polar residues or modified charged residues. It was found that both the D7 and D9 peptides form a large fraction bent conformations. However, no hydrophobic contacts between the terminal Tyr residues of D9 occur, which suggests that the presence of a pair of like-charged residues stabilizes chain reversal. Conversely, only the Dag1 and Dag2 peptides exhibit some chain reversal; replacing the second aspartic-acid residue with a valine and the first one with a basic residue results in a nearly extended conformation. These results suggest that basic residues farther away in sequence can result in stabilization of chain reversal owing to screening of the non-polar core. Conversely, smaller distance in sequence prohibits this screening, while the presence oppositely-charged residues can stabilize a turn because of salt-bridge formation.

  1. A study of the influence of charged residues on β-hairpin formation by nuclear magnetic resonance and molecular dynamics.

    PubMed

    Makowska, Joanna; Zmudzińska, Wioletta; Uber, Dorota; Chmurzyński, Lech

    2014-12-01

    Chain reversals are often nucleation sites in protein folding. The β-hairpins of FBP28 WW domain and IgG are stable and have been proved to initiate the folding and are, therefore, suitable for studying the influence of charged residues on β-hairpin conformation. In this paper, we carried out NMR examination of the conformations in solution of two fragments from the FPB28 protein (PDB code: 1E0L) (N-terminal part) namely KTADGKT-NH2 (1E0L 12-18, D7) and YKTADGKTY-NH2 (1E0L 11-19, D9), one from the B3 domain of the protein G (PDB code: 1IGD), namely DDATKT-NH2 (1IGD 51-56) (Dag1), and three variants of Dag1 peptide: DVATKT-NH2 (Dag2), OVATKT-NH2 (Dag3) and KVATKT-NH2 (Dag4), respectively, in which the original charged residue were replaced with non-polar residues or modified charged residues. It was found that both the D7 and D9 peptides form a large fraction bent conformations. However, no hydrophobic contacts between the terminal Tyr residues of D9 occur, which suggests that the presence of a pair of like-charged residues stabilizes chain reversal. Conversely, only the Dag1 and Dag2 peptides exhibit some chain reversal; replacing the second aspartic-acid residue with a valine and the first one with a basic residue results in a nearly extended conformation. These results suggest that basic residues farther away in sequence can result in stabilization of chain reversal owing to screening of the non-polar core. Conversely, smaller distance in sequence prohibits this screening, while the presence oppositely-charged residues can stabilize a turn because of salt-bridge formation. PMID:25316116

  2. Oxygen solubility and permeability of carbohydrates.

    PubMed

    Whitcombe, Michael J; Parker, Roger; Ring, Stephen G

    2005-06-13

    The saturated oxygen concentration in a series of aqueous solutions of sorbitol (up to 35% w/w) and maltitol (up to 50% w/w) was measured using colorimetric reagent vials based on Rhodazine D. The results indicate that the solubility of oxygen in low-water carbohydrates is considerably lower than its solubility in pure water. It was concluded that the low-oxygen solubility is a major factor contributing to the barrier properties of low-water content carbohydrates used in the encapsulation of flavours, lipids, peptides and other oxidisable species.

  3. Synthesis of chiral dopants based on carbohydrates.

    PubMed

    Tsuruta, Toru; Koyama, Tetsuo; Yasutake, Mikio; Hatano, Ken; Matsuoka, Koji

    2014-07-01

    Chiral dopants based on carbohydrates for nematic liquid crystals were synthesized from D-glucose, and their helical twisting power (HTP) values were evaluated. The chiral dopants induced helices in the host nematic liquid crystals. An acetyl derivative having an ether-type glycosidic linkage between carbohydrate and a mesogenic moiety showed the highest HTP value of 10.4 μm(-1), while an acetyl derivative having an anomeric ester-type linkage did not show any HTP. It was surprising that this molecule had no HTP despite the presence of chirality in the molecule. A relationship between HTP and specific rotation was not observed in this study.

  4. Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase.

    PubMed

    Ohlin, Mats; von Schantz, Laura; Schrader, Tobias E; Ostermann, Andreas; Logan, Derek T; Fisher, S Zoë

    2015-08-01

    Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that bind specific types of carbohydrates. Ultra high-resolution X-ray crystallographic studies of CBMs have helped to decipher the basis for specificity in carbohydrate-protein interactions. However, additional studies are needed to better understand which structural determinants confer which carbohydrate-binding properties. To address these issues, neutron crystallographic studies were initiated on one experimentally engineered CBM derived from a xylanase, X-2 L110F, a protein that is able to bind several different plant carbohydrates such as xylan, β-glucan and xyloglucan. This protein evolved from a CBM present in xylanase Xyn10A of Rhodothermus marinus. The protein was complexed with a branched xyloglucan heptasaccharide. Large single crystals of hydrogenous protein (∼1.6 mm(3)) were grown at room temperature and subjected to H/D exchange. Both neutron and X-ray diffraction data sets were collected to 1.6 Å resolution. Joint neutron and X-ray refinement using phenix.refine showed significant density for residues involved in carbohydrate binding and revealed the details of a hydrogen-bonded water network around the binding site. This is the first report of a neutron structure of a CBM and will add to the understanding of protein-carbohydrate binding interactions.

  5. Minimally refined biomass fuel. [carbohydrate-water-alcohol mixture

    SciTech Connect

    Pearson, R.K.; Hirschfeld, T.B.

    1981-03-26

    A minimally refined fluid composition, suitable as a fuel mixture and derived from biomass material, is comprised of one or more water-soluble carbohydrates such as sucrose, one or more alcohols having less than four carbons, and water. The carbohydrate provides the fuel source; water-solubilizes the carbohydrate; and the alcohol aids in the combustion of the carbohydrate and reduces the viscosity of the carbohydrate/water solution. Because less energy is required to obtain the carbohydrate from the raw biomass than alcohol, an overall energy savings is realized compared to fuels employing alcohol as the primary fuel.

  6. Carbohydrate mouth rinse and caffeine improves high-intensity interval running capacity when carbohydrate restricted.

    PubMed

    Kasper, Andreas M; Cocking, Scott; Cockayne, Molly; Barnard, Marcus; Tench, Jake; Parker, Liam; McAndrew, John; Langan-Evans, Carl; Close, Graeme L; Morton, James P

    2016-08-01

    We tested the hypothesis that carbohydrate mouth rinsing, alone or in combination with caffeine, augments high-intensity interval (HIT) running capacity undertaken in a carbohydrate-restricted state. Carbohydrate restriction was achieved by performing high-intensity running to volitional exhaustion in the evening prior to the main experimental trials and further refraining from carbohydrate intake in the post-exercise and overnight period. On the subsequent morning, eight males performed 45-min steady-state (SS) exercise (65% [Formula: see text]) followed by HIT running to exhaustion (1-min at 80% [Formula: see text]interspersed with 1-min walking at 6 km/h). Subjects completed 3 trials consisting of placebo capsules (administered immediately prior to SS and immediately before HIT) and placebo mouth rinse at 4-min intervals during HIT (PLACEBO), placebo capsules but 10% carbohydrate mouth rinse (CMR) at corresponding time-points or finally, caffeine capsules (200 mg per dose) plus 10% carbohydrate mouth rinse (CAFF + CMR) at corresponding time-points. Heart rate, capillary glucose, lactate, glycerol and NEFA were not different at exhaustion during HIT (P > 0.05). However, HIT capacity was different (P < 0.05) between all pair-wise comparisons such that CAFF + CMR (65 ± 26 min) was superior to CMR (52 ± 23 min) and PLACEBO (36 ± 22 min). We conclude that carbohydrate mouth rinsing and caffeine ingestion improves exercise capacity undertaken in carbohydrate-restricted states. Such nutritional strategies may be advantageous for those athletes who deliberately incorporate elements of training in carbohydrate-restricted states (i.e. the train-low paradigm) into their overall training programme in an attempt to strategically enhance mitochondrial adaptations of skeletal muscle. PMID:26035740

  7. Carbohydrate mouth rinse and caffeine improves high-intensity interval running capacity when carbohydrate restricted.

    PubMed

    Kasper, Andreas M; Cocking, Scott; Cockayne, Molly; Barnard, Marcus; Tench, Jake; Parker, Liam; McAndrew, John; Langan-Evans, Carl; Close, Graeme L; Morton, James P

    2016-08-01

    We tested the hypothesis that carbohydrate mouth rinsing, alone or in combination with caffeine, augments high-intensity interval (HIT) running capacity undertaken in a carbohydrate-restricted state. Carbohydrate restriction was achieved by performing high-intensity running to volitional exhaustion in the evening prior to the main experimental trials and further refraining from carbohydrate intake in the post-exercise and overnight period. On the subsequent morning, eight males performed 45-min steady-state (SS) exercise (65% [Formula: see text]) followed by HIT running to exhaustion (1-min at 80% [Formula: see text]interspersed with 1-min walking at 6 km/h). Subjects completed 3 trials consisting of placebo capsules (administered immediately prior to SS and immediately before HIT) and placebo mouth rinse at 4-min intervals during HIT (PLACEBO), placebo capsules but 10% carbohydrate mouth rinse (CMR) at corresponding time-points or finally, caffeine capsules (200 mg per dose) plus 10% carbohydrate mouth rinse (CAFF + CMR) at corresponding time-points. Heart rate, capillary glucose, lactate, glycerol and NEFA were not different at exhaustion during HIT (P > 0.05). However, HIT capacity was different (P < 0.05) between all pair-wise comparisons such that CAFF + CMR (65 ± 26 min) was superior to CMR (52 ± 23 min) and PLACEBO (36 ± 22 min). We conclude that carbohydrate mouth rinsing and caffeine ingestion improves exercise capacity undertaken in carbohydrate-restricted states. Such nutritional strategies may be advantageous for those athletes who deliberately incorporate elements of training in carbohydrate-restricted states (i.e. the train-low paradigm) into their overall training programme in an attempt to strategically enhance mitochondrial adaptations of skeletal muscle.

  8. The mean hydration of carbohydrates as studied by normalized two-dimensional radial pair distributions.

    PubMed

    Andersson, C; Engelsen, S B

    1999-04-01

    The hydration of carbohydrates plays a key role in many biological processes. Molecular dynamics simulations provide an effective tool for investigating the hydration of complex solutes such as carbohydrates. In this article we devise an algorithm for the calculation of two-dimensional radial pair distributions describing the probability of finding a water molecule in a site defined by two reference atoms. The normalized 2D radial pair distribution is proposed as an effective tool for investigating and comparing localized or ordered water sites around flexible molecules such as carbohydrates when analyzing molecular dynamics simulations and the utility of 2D radial pair distributions is demonstrated using sucrose as an example. In this relatively simple structure, 2D radial pair distributions were able to characterize and quantify the importance of two unique interresidue hydration sites in which a water molecule is forming a bridge between the glycopyranosyl and fructofuranosyl residues. The approach is proposed to be a valuable tool for comparing and understanding the hydration of flexible biomolecules such as carbohydrates. PMID:10680115

  9. Effects of carbohydrate, protein and lipid content of organic waste on hydrogen production and fermentation products.

    PubMed

    Alibardi, Luca; Cossu, Raffaello

    2016-01-01

    Organic waste from municipalities, food waste and agro-industrial residues are ideal feedstocks for use in biological conversion processes in biorefinery chains, representing biodegradable materials containing a series of substances belonging to the three main groups of the organic matter: carbohydrates, proteins and lipids. Biological hydrogen production by dark fermentation may assume a central role in the biorefinery concept, representing an up-front treatment for organic waste capable of hydrolysing complex organics and producing biohydrogen. This research study was aimed at evaluating the effects of carbohydrate, protein and lipid content of organic waste on hydrogen yields, volatile fatty acid production and carbon-fate. Biogas and hydrogen productions were linearly correlated to carbohydrate content of substrates while proteins and lipids failed to produce significant contributions. Chemical composition also produced effects on the final products of dark fermentation. Acetic and butyric acids were the main fermentation products, with their ratio proving to correlate with carbohydrate and protein content. The results obtained in this research study enhance the understanding of data variability on hydrogen yields from organic waste. Detailed information on waste composition and chemical characterisation are essential to clearly identify the potential performances of the dark fermentation process.

  10. Effects of carbohydrate, protein and lipid content of organic waste on hydrogen production and fermentation products.

    PubMed

    Alibardi, Luca; Cossu, Raffaello

    2016-01-01

    Organic waste from municipalities, food waste and agro-industrial residues are ideal feedstocks for use in biological conversion processes in biorefinery chains, representing biodegradable materials containing a series of substances belonging to the three main groups of the organic matter: carbohydrates, proteins and lipids. Biological hydrogen production by dark fermentation may assume a central role in the biorefinery concept, representing an up-front treatment for organic waste capable of hydrolysing complex organics and producing biohydrogen. This research study was aimed at evaluating the effects of carbohydrate, protein and lipid content of organic waste on hydrogen yields, volatile fatty acid production and carbon-fate. Biogas and hydrogen productions were linearly correlated to carbohydrate content of substrates while proteins and lipids failed to produce significant contributions. Chemical composition also produced effects on the final products of dark fermentation. Acetic and butyric acids were the main fermentation products, with their ratio proving to correlate with carbohydrate and protein content. The results obtained in this research study enhance the understanding of data variability on hydrogen yields from organic waste. Detailed information on waste composition and chemical characterisation are essential to clearly identify the potential performances of the dark fermentation process. PMID:26254676

  11. Kiwifruit, carbohydrate availability, and the glycemic response.

    PubMed

    Monro, John A

    2013-01-01

    An appreciable proportion, about 10%, of the dry weight of kiwifruit consists of primary cell walls. About 80% of dry matter is available carbohydrate consisting of glucose, fructose, and sucrose, and about 10% is digestible protein. The cell wall component, being nonstarch polysaccharide, is undigested in the stomach and small intestine, so the component increases in relative concentration in the gut lumen where its physicochemical properties may be important in modulating carbohydrate digestion and absorption. Released from the constraint of fruit structure, the dietary fiber swells to four times its original volume during in vitro digestion. When the digested remnants are allowed to settle into a packed but uncompressed state, as in the gut, they reduce the rate of glucose diffusion by about 40% and profoundly reduce digesta mixing, especially in the presence of a low background of soluble viscous polysaccharide. An in vitro estimation of the glycemic index (GI) of carbohydrate in kiwifruit, and in vivo estimates show the carbohydrate to be of low GI. On a whole fruit basis because of the high water content of kiwifruit, a 100g kiwifruit would be equivalent to about 5g (1 teaspoon) of glucose in its effect on blood glucose; thus, kiwifruit have low glycemic impact and are suitable for those with diabetes.

  12. General Properties, Occurrence, and Preparation of Carbohydrates

    NASA Astrophysics Data System (ADS)

    Robyt, John F.

    D-Glucose and its derivatives and analogues, N-acetyl-D-glucosamine, N-acetyl-D-muramic acid, D-glucopyranosyl uronic acid, and D-glucitol represent 99.9% of the carbohydrates on the earth. D-Glucose is found in the free state in human blood and in the combined state in disaccharides, sucrose, lactose, and α,α-trehalose, in cyclic dextrins, and in polysaccharides, starch, glycogen, cellulose, dextrans; N-acetyl-D-glucosamine and an analogue N-acetyl-D-muramic acid are found in bacterial cell wall polysaccharide, murein, along with teichoic acids made up of poly-glycerol or -ribitol phosphodiesters. Other carbohydrates, D-mannose, D-mannuronic acid, D-galactose, N-acetyl-D-galactosamine, D-galacturonic acid, D-iduronic acid, L-guluronic acid, L-rhamnose, L-fucose, D-xylose, and N-acetyl-D-neuraminic acid are found in glycoproteins, hemicelluloses, glycosaminoglycans, and polysaccharides of plant exudates, bacterial capsules, alginates, and heparin. D-Ribofuranose-5-phosphate is found in many coenzymes and is the backbone of RNAs (ribonucleic acid), and 2-deoxy-D-ribofuranose-5-phosphate is the backbone of DNA (deoxyribonucleic acid). D-Fructofuranose is found in sucrose, inulin, and levan. The general properties and occurrence of these carbohydrates and general methods of isolation and preparation of carbohydrates are presented.

  13. Carbohydrate Metabolism During Ascospore Development in Yeast

    PubMed Central

    Kane, Sherwin M.; Roth, Robert

    1974-01-01

    Carbohydrate metabolism, under sporulation conditions, was compared in sporulating and non-sporulating diploids of Saccharomyces cerevisiae. Total carbohydrate was fractionated into trehalose, glycogen, mannan, and an alkali-insoluble fraction composed of glucan and insoluble glycogen. The behavior of three fractions was essentially the same in both sporulating and non-sporulating strains; trehalose, mannan, and the insoluble fraction were all synthesized to about the same extent regardless of a strain's ability to undergo meiosis or sporulation. In contrast, aspects of soluble glycogen metabolism depended on sporulation. Although glycogen synthesis took place in both sporulating and non-sporulating strains, only sporulating strains exhibited a period of glycogen degradation, which coincided with the final maturation of ascospores. We also determined the carbohydrate composition of spores isolated from mature asci. Spores contained all components present in vegetative cells, but in different proportions. In cells, the most abundant carbohydrate was mannan, followed by glycogen, then trehalose, and finally the alkali-insoluble fraction; in spores, trehalose was most abundant, followed by the alkali-insoluble fraction, glycogen, and mannan in that order. PMID:4595206

  14. Separation and quantification of microalgal carbohydrates.

    PubMed

    Templeton, David W; Quinn, Matthew; Van Wychen, Stefanie; Hyman, Deborah; Laurens, Lieve M L

    2012-12-28

    Structural carbohydrates can constitute a large fraction of the dry weight of algal biomass and thus accurate identification and quantification is important for summative mass closure. Two limitations to the accurate characterization of microalgal carbohydrates are the lack of a robust analytical procedure to hydrolyze polymeric carbohydrates to their respective monomers and the subsequent identification and quantification of those monosaccharides. We address the second limitation, chromatographic separation of monosaccharides, here by identifying optimum conditions for the resolution of a synthetic mixture of 13 microalgae-specific monosaccharides, comprised of 8 neutral, 2 amino sugars, 2 uronic acids and 1 alditol (myo-inositol as an internal standard). The synthetic 13-carbohydrate mix showed incomplete resolution across 11 traditional high performance liquid chromatography (HPLC) methods, but showed improved resolution and accurate quantification using anion exchange chromatography (HPAEC) as well as alditol acetate derivatization followed by gas chromatography (for the neutral- and amino-sugars only). We demonstrate the application of monosaccharide quantification using optimized chromatography conditions after sulfuric acid analytical hydrolysis for three model algae strains and compare the quantification and complexity of monosaccharides in analytical hydrolysates relative to a typical terrestrial feedstock, sugarcane bagasse.

  15. Indicators of normal carbohydrate digestion in children

    Technology Transfer Automated Retrieval System (TEKTRAN)

    More research is needed to determine the nutritional and clinical significance of the intermediate values of low but not deficient duodenal disaccharidase activities, but the Dahlqvist-method biopsy assay of activity serves as a gnomon of carbohydrate digestion, in the sense that Anaximander used a ...

  16. FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDB.

    PubMed

    Wernersson, Rasmus; Rapacki, Kristoffer; Staerfeldt, Hans-Henrik; Sackett, Peter Wad; Mølgaard, Anne

    2006-07-01

    FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB) for structures of homologous proteins. The results are displayed both as an annotated sequence alignment, where the user-provided annotations as well as the sequence conservation between the query and the target sequence are displayed, and also as a publication-quality image of the 3D protein structure with the selected features and sequence conservation enhanced. The results are also returned in a readily parsable text format as well as a PyMol (http://pymol.sourceforge.net/) script file, which allows the user to easily modify the protein structure image to suit a specific purpose. FeatureMap3D can also be used without sequence annotation, to evaluate the quality of the alignment of the input sequences to the most homologous structures in the PDB, through the sequence conservation colored 3D structure visualization tool. FeatureMap3D is available at: http://www.cbs.dtu.dk/services/FeatureMap3D/. PMID:16845115

  17. Force fields and scoring functions for carbohydrate simulation.

    PubMed

    Xiong, Xiuming; Chen, Zhaoqiang; Cossins, Benjamin P; Xu, Zhijian; Shao, Qiang; Ding, Kai; Zhu, Weiliang; Shi, Jiye

    2015-01-12

    Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design.

  18. High Carbohydrate-Fiber Nutrition for Running and Health.

    ERIC Educational Resources Information Center

    Battinelli, Thomas

    1983-01-01

    The roles of carbohydrates, fats, proteins, and fiber in producing energy for health and exercise are discussed. Long-distance runners should have a high intake of complex carbohydrates and fiber. (PP)

  19. Exercise and Regulation of Carbohydrate Metabolism.

    PubMed

    Mul, Joram D; Stanford, Kristin I; Hirshman, Michael F; Goodyear, Laurie J

    2015-01-01

    Carbohydrates are the preferred substrate for contracting skeletal muscles during high-intensity exercise and are also readily utilized during moderate intensity exercise. This use of carbohydrates during physical activity likely played an important role during the survival of early Homo sapiens, and genes and traits regulating physical activity, carbohydrate metabolism, and energy storage have undoubtedly been selected throughout evolution. In contrast to the life of early H. sapiens, modern lifestyles are predominantly sedentary. As a result, intake of excessive amounts of carbohydrates due to the easy and continuous accessibility to modern high-energy food and drinks has not only become unnecessary but also led to metabolic diseases in the face of physical inactivity. A resulting metabolic disease is type 2 diabetes, a complex endocrine disorder characterized by abnormally high concentrations of circulating glucose. This disease now affects millions of people worldwide. Exercise has beneficial effects to help control impaired glucose homeostasis with metabolic disease, and is a well-established tool to prevent and combat type 2 diabetes. This chapter focuses on the effects of exercise on carbohydrate metabolism in skeletal muscle and systemic glucose homeostasis. We will also focus on the molecular mechanisms that mediate the effects of exercise to increase glucose uptake in skeletal muscle. It is now well established that there are different proximal signaling pathways that mediate the effects of exercise and insulin on glucose uptake, and these distinct mechanisms are consistent with the ability of exercise to increase glucose uptake in the face of insulin resistance in people with type 2 diabetes. Ongoing research in this area is aimed at defining the precise mechanism by which exercise increases glucose uptake and insulin sensitivity and the types of exercise necessary for these important health benefits.

  20. Exercise and Regulation of Carbohydrate Metabolism

    PubMed Central

    Mul, Joram D.; Stanford, Kristin I.; Hirshman, Michael F.; Goodyear, Laurie J.

    2016-01-01

    Carbohydrates are the preferred substrate for contracting skeletal muscles during high-intensity exercise and are also readily utilized during moderate intensity exercise. This use of carbohydrates during physical activity likely played an important role during the survival of early Homo sapiens, and genes and traits regulating physical activity, carbohydrate metabolism, and energy storage have undoubtedly been selected throughout evolution. In contrast to the life of early H. sapiens, modern lifestyles are predominantly sedentary. As a result, intake of excessive amounts of carbohydrates due to the easy and continuous accessibility to modern high-energy food and drinks has not only become unnecessary but also led to metabolic diseases in the face of physical inactivity. A resulting metabolic disease is type 2 diabetes, a complex endocrine disorder characterized by abnormally high concentrations of circulating glucose. This disease now affects millions of people worldwide. Exercise has beneficial effects to help control impaired glucose homeostasis with metabolic disease, and is a well-established tool to prevent and combat type 2 diabetes. This chapter focuses on the effects of exercise on carbohydrate metabolism in skeletal muscle and systemic glucose homeostasis. We will also focus on the molecular mechanisms that mediate the effects of exercise to increase glucose uptake in skeletal muscle. It is now well established that there are different proximal signaling pathways that mediate the effects of exercise and insulin on glucose uptake, and these distinct mechanisms are consistent with the ability of exercise to increase glucose uptake in the face of insulin resistance in people with type 2 diabetes. Ongoing research in this area is aimed at defining the precise mechanism by which exercise increases glucose uptake and insulin sensitivity and the types of exercise necessary for these important health benefits. PMID:26477909

  1. Energy and carbohydrate for training and recovery.

    PubMed

    Burke, Louise M; Loucks, Anne B; Broad, Nick

    2006-07-01

    Soccer players should achieve an energy intake that provides sufficient carbohydrate to fuel the training and competition programme, supplies all nutrient requirements, and allows manipulation of energy or nutrient balance to achieve changes in lean body mass, body fat or growth. Although the traditional culture of soccer has focused on carbohydrate intake for immediate match preparation, top players should adapt their carbohydrate intake on a daily basis to ensure adequate fuel for training and recovery between matches. For players with a mobile playing style, there is sound evidence that dietary programmes that restore and even super-compensate muscle glycogen levels can enhance activity patterns during matches. This will presumably also benefit intensive training, such as twice daily practices. As well as achieving a total intake of carbohydrate commensurate with fuel needs, the everyday diet should promote strategic intake of carbohydrate and protein before and after key training sessions to optimize the adaptations and enhance recovery. The achievement of the ideal physique for soccer is a long-term goal that should be undertaken over successive years, and particularly during the off-season and pre-season. An increase in lean body mass or a decrease in body fat is the product of a targeted training and eating programme. Consultation with a sports nutrition expert can assist soccer players to manipulate energy and nutrient intake to meet such goals. Players should be warned against the accidental or deliberate mismatch of energy intake and energy expenditure, such that energy availability (intake minus the cost of exercise) falls below 125 kJ (30 kcal) per kilogram of fat-free mass per day. Such low energy availability causes disturbances to hormonal, metabolic, and immune function. PMID:16766497

  2. Pyrrolic tripodal receptors for carbohydrates. Role of functional groups and binding geometry on carbohydrate recognition.

    PubMed

    Cacciarini, Martina; Nativi, Cristina; Norcini, Martina; Staderini, Samuele; Francesconi, Oscar; Roelens, Stefano

    2011-02-21

    The contribution from several H-bonding groups and the impact of geometric requirements on the binding ability of benzene-based tripodal receptors toward carbohydrates have been investigated by measuring the affinity of a set of structures toward octyl β-D-glucopyranoside, selected as a representative monosaccharide. The results reported in the present study demonstrate that a judicious choice of correct geometry and appropriate functional groups is critical to achieve the complementary hydrogen bonding interactions required for an effective carbohydrate recognition.

  3. Cancer vaccine with mimotopes of tumor-associated carbohydrate antigens.

    PubMed

    Kozbor, Danuta

    2010-03-01

    The GD2 ganglioside, displayed by five carbohydrate Neu5Acalpha2-8Neu5Acalpha2-3(GalNAcbeta1-4)Galbeta1-4Glcbeta residues attached to a ceramide chain that anchors the ganglioside in the cell membrane, is expressed on neuroectodermally derived tumors. GD2 has been used as a target for passive and active immunotherapy in patients with malignant melanoma and neuroblastoma. We have generated 47-LDA mimotope of GD2 by screening a phage display peptide library with anti-GD2 mAb 14G2a and reported that vaccination with the 47-LDA mimotope elicited GD2 cross-reactive IgG antibody responses as well as MHC class I-restricted CD8(+) T cells to syngeneic neuroblastoma tumor cells. The cytotoxic activity of the vaccine-induced CTLs was independent of GD2 expression, suggesting recognition of a novel tumor-associated antigen cross-reacting with 47-LDA. Immunoblotting studies using 14G2a mAb demonstrated that this antibody cross-reacts with a 105 kDa glycoprotein expressed by GD2(+) and GD2(-) neuroblastoma and melanoma cells. Functional studies of tumor cells grown in three-dimensional (3D) collagen cultures with 14G2a mAb showed decreases in matrix metalloproteinase-2 activation, a process regulated by 105 kDa activated leukocyte cell adhesion molecules (ALCAM/CD166). The CD166 glycoprotein was shown to be recognized by 14G2a antibody, and inhibition of CD166 expression by RNA interference ablated the cell sensitivity to lysis by 47-LDA-induced CD8(+) T cells in vitro and in vivo. These results suggest that the vaccine-induced CTLs recognize a 47-LDA cross-reactive epitope expressed by CD166 and reveal a novel mechanism of induction of potent tumor-specific cellular responses by mimotopes of tumor-associated carbohydrate antigens.

  4. Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module

    PubMed Central

    Yao, Chaoxiang; Junaid, Muhammad; Lu, Zhenghui; Zhang, Houjin; Ma, Yanhe

    2015-01-01

    Cellulases are the key enzymes used in the biofuel industry. A typical cellulase contains a catalytic domain connected to a carbohydrate-binding module (CBM) through a flexible linker. Here we report the structure of an atypical trimodular cellulase which harbors a catalytic domain, a CBM46 domain and a rigid CBM_X domain between them. The catalytic domain shows the features of GH5 family, while the CBM46 domain has a sandwich-like structure. The catalytic domain and the CBM46 domain form an extended substrate binding cleft, within which several tryptophan residues are well exposed. Mutagenesis assays indicate that these residues are essential for the enzymatic activities. Gel affinity electrophoresis shows that these tryptophan residues are involved in the polysaccharide substrate binding. Also, electrostatic potential analysis indicates that almost the entire solvent accessible surface of CelB is negatively charged, which is consistent with the halophilic nature of this enzyme. PMID:26562160

  5. Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module.

    PubMed

    Zhang, Huaidong; Zhang, Guimin; Yao, Chaoxiang; Junaid, Muhammad; Lu, Zhenghui; Zhang, Houjin; Ma, Yanhe

    2015-01-01

    Cellulases are the key enzymes used in the biofuel industry. A typical cellulase contains a catalytic domain connected to a carbohydrate-binding module (CBM) through a flexible linker. Here we report the structure of an atypical trimodular cellulase which harbors a catalytic domain, a CBM46 domain and a rigid CBM_X domain between them. The catalytic domain shows the features of GH5 family, while the CBM46 domain has a sandwich-like structure. The catalytic domain and the CBM46 domain form an extended substrate binding cleft, within which several tryptophan residues are well exposed. Mutagenesis assays indicate that these residues are essential for the enzymatic activities. Gel affinity electrophoresis shows that these tryptophan residues are involved in the polysaccharide substrate binding. Also, electrostatic potential analysis indicates that almost the entire solvent accessible surface of CelB is negatively charged, which is consistent with the halophilic nature of this enzyme.

  6. Influence of Grape Maturity on Complex Carbohydrate Composition of Red Sparkling Wines.

    PubMed

    Martínez-Lapuente, Leticia; Apolinar-Valiente, Rafael; Guadalupe, Zenaida; Ayestarán, Belén; Pérez-Magariño, Silvia; Williams, Pascale; Doco, Thierry

    2016-06-22

    This paper studied how grape maturity affected complex carbohydrate composition during red sparkling wine making and wine aging. Grape ripening stage (premature and mature grapes) showed a significant impact on the content, composition, and evolution of polysaccharides and oligosaccharides of sparkling wines. Polysaccharides rich in arabinose and galactose, mannoproteins, rhamnogalacturonans II, and oligosaccharides in base wines increased with maturity. For both maturity stages, polysaccharides rich in arabinose and galactose, and the glucuronic acid glycosyl residue of the oligosaccharides were the major carbohydrates detected in all vinification stages. The total glycosyl content of oligosaccharides decreased during the whole period of aging on yeast lees. The reduction of polysaccharides rich in arabinose and galactose and rhamnogalacturonans type II during the aging was more pronounced in mature samples. To our knowledge, this is the first report of the polysaccharide and oligosaccharide composition of red sparkling wines.

  7. Influence of Grape Maturity on Complex Carbohydrate Composition of Red Sparkling Wines.

    PubMed

    Martínez-Lapuente, Leticia; Apolinar-Valiente, Rafael; Guadalupe, Zenaida; Ayestarán, Belén; Pérez-Magariño, Silvia; Williams, Pascale; Doco, Thierry

    2016-06-22

    This paper studied how grape maturity affected complex carbohydrate composition during red sparkling wine making and wine aging. Grape ripening stage (premature and mature grapes) showed a significant impact on the content, composition, and evolution of polysaccharides and oligosaccharides of sparkling wines. Polysaccharides rich in arabinose and galactose, mannoproteins, rhamnogalacturonans II, and oligosaccharides in base wines increased with maturity. For both maturity stages, polysaccharides rich in arabinose and galactose, and the glucuronic acid glycosyl residue of the oligosaccharides were the major carbohydrates detected in all vinification stages. The total glycosyl content of oligosaccharides decreased during the whole period of aging on yeast lees. The reduction of polysaccharides rich in arabinose and galactose and rhamnogalacturonans type II during the aging was more pronounced in mature samples. To our knowledge, this is the first report of the polysaccharide and oligosaccharide composition of red sparkling wines. PMID:27226011

  8. Carbohydrate-based Cu(I) stabilizing ligands and their use in the synthesis of carbohydrate-ferrocene conjugates.

    PubMed

    Schmidt, Magnus S; Leitner, Kim; Welter, Moritz; Wurmthaler, Lena A; Ringwald, Markus

    2014-03-31

    A series of carbohydrate-ferrocene conjugates have been synthesized by copper(I)-catalyzed cycloaddition of carbohydrate-azides and ethynylferrocene (CuAAC). Newly carbohydrate-based tris-triazoles have been used as Cu(I) stabilizing ligands and showed at least comparable, in some cases even better results compared to the use of tris-(benzyltriazolylmethyl)amine (TBTA).

  9. Organotin-catalyzed highly regioselective thiocarbonylation of nonprotected carbohydrates and synthesis of deoxy carbohydrates in a minimum number of steps.

    PubMed

    Muramatsu, Wataru; Tanigawa, Satoko; Takemoto, Yuki; Yoshimatsu, Hirofumi; Onomura, Osamu

    2012-04-16

    Nonprotected carbohydrates: The catalytic regioselective thiocarbonylation of carbohydrates by using organotin dichloride under mild conditions was demonstrated. The reaction afforded various deoxy saccharides in high yields and excellent regioselectivity in a minimum number of steps. The regioselectivity of the thiocarbonylation is attributed to the intrinsic character of the carbohydrates based on the stereorelationship of their hydroxy groups (see scheme).

  10. Solubility of carbohydrates in heavy water.

    PubMed

    Cardoso, Marcus V C; Carvalho, Larissa V C; Sabadini, Edvaldo

    2012-05-15

    The solubility of several mono-(glucose and xylose), di-(sucrose and maltose), tri-(raffinose) and cyclic (α-cyclodextrin) saccharides in H(2)O and in D(2)O were measured over a range of temperatures. The solution enthalpies for the different carbohydrates in the two solvents were determined using the vant' Hoff equation and the values in D(2)O are presented here for the first time. Our findings indicate that the replacement of H(2)O by D(2)O remarkably decreases the solubilities of the less soluble carbohydrates, such as maltose, raffinose and α-cyclodextrin. On the other hand, the more soluble saccharides, glucose, xylose, and sucrose, are practically insensitive to the H/D replacement in water. PMID:22480785

  11. Carbohydrate Engineered Cells for Regenerative Medicine

    PubMed Central

    Du, Jian; Yarema, Kevin J.

    2010-01-01

    Carbohydrates are integral components of the stem cell niche on several levels; proteoglycans are a major constituent of the extracellular matrix (ECM) surrounding a cell, glycosoaminoglycans (GAGs) help link cells to the ECM and the neighboring cells, and small but informationally-rich oligosaccharides provide a “sugar code” that identifies each cell and provides it with unique functions. This article samples roles that glycans play in development and then describes how metabolic glycoengineering – a technique where monosaccharide analogs are introduced into the metabolic pathways of a cell and are biosynthetically incorporated into the glycocalyx – is overcoming many of the long-standing barriers to manipulating carbohydrates in living cells and tissues and is becoming an intriguing new tool for tissue engineering and regenerative medicine. PMID:20117158

  12. Pre-operative nutrition and carbohydrate loading.

    PubMed

    Kratzing, Caroline

    2011-08-01

    An optimal nutritional state is an important consideration in providing successful operative outcomes. Unfortunately, many aspects of surgery are not constructive to providing this. In addition, the metabolic and immune response to injury induces a catabolic state and insulin resistance, a known risk factor of post-operative complications. Aggressive insulin therapy post-operatively has been shown to reduce morbidity and mortality but similar results can be achieved when insulin resistance is lessened by the use of pre-operative carbohydrate loading. Consuming carbohydrate-containing drinks up to 2 h before surgery has been found to be an effective way to attenuate insulin resistance, minimise protein losses, reduce hospital stays and improve patient comfort without adversely affecting gastric emptying. Enhanced recovery programmes have employed carbohydrate loading as one of several strategies aimed at reducing post-operative stress and improving the recovery process. Studies examining the benefits of these programmes have demonstrated significantly shorter post-operative hospital stays, faster return to normal functions and lower occurrences of surgical complications. As a consequence of the favourable evidence they are now being implemented in many surgical units. Further benefit to post-operative recovery may be found with the use of immune-enhancing diets, i.e. supplementation with n-3 fatty acids, arginine, glutamine and/or nucleotides. These have the potential to boost the immune system, improve wound healing and reduce inflammatory markers. Research exploring the benefits of immunonutrition and solidifying the use of carbohydrate loading is ongoing; however, there is strong evidence to link good pre-operative nutrition and improved surgical outcomes.

  13. Crystallisation and crystal forms of carbohydrate derivatives

    NASA Astrophysics Data System (ADS)

    Lennon, Lorna

    This thesis is focused on the synthesis and solid state analysis of carbohydrate derivatives, including many novel compounds. Although the synthetic chemistry surrounding carbohydrates is well established in the literature, the crystal chemistry of carbohydrates is less well studied. Therefore this research aims to improve understanding of the solid state properties of carbohydrate derivatives through gaining more information on their supramolecular bonding. Chapter One focuses on an introduction to the solid state of organic compounds, with a background to crystallisation, including issues that can arise during crystal growth. Chapter Two is based on glucopyranuronate derivatives which are understudied in terms of their solid state forms. This chapter reports on the formation of novel glucuronamides and utilising the functionality of the amide bond for crystallisation. TEMPO oxidation was completed to form glucopyranuronates by oxidation of the primary alcohol groups of glucosides to the carboxylic acid derivatives, to increase functionality for enhanced crystal growth. Chapter Three reports on the synthesis of glucopyranoside derivatives by O-glycosylation reactions and displays crystal structures, including a number of previously unsolved acetate protected and deprotected crystal structures. More complex glycoside derivatives were also researched in an aim to study the resultant supramolecular motifs. Chapter Four contains the synthesis of aryl cellobioside derivatives including the novel crystal structures that were solved for the acetate protected and deprotected compounds. Research was carried out to determine if 1-deoxycellodextrins could act as putative isostructures for cellulose. Our research displays the presence of isostructural references with 1-deoxycellotriose shown to be similar to cellulose III11, 1-deoxycellotetraose correlates with cellulose IV11 and 1-deoxycellopentose shows isostructurality similar to that of cellulose II. Chapter Five contains

  14. Direct synthesis of methyl phosphoramidates in carbohydrates.

    PubMed

    Dhurandhare, Vijay M; Mishra, Girija Prasad; Lam, Sarah; Wang, Cheng-Chung

    2015-09-28

    A direct installation of a methyl phosphoramidate group by using methyl benzylphosphoramidochloridate into carbohydrates and amino acid is described. This one-step synthesis is efficient for both primary and secondary alcohols and exhibited excellent regioselectivity and functional group compatibility. Formation of a single diastereomer is observed in certain cases. The N-benzyl protecting group on methyl phosphoramidates is easily removed under mild conditions.

  15. [Recent advance in carbohydrate-based cancer vaccines].

    PubMed

    Huo, Chang-Xin; Ye, Xin-Shan

    2012-03-01

    The abnormal glycans expressing on the surface of tumor cells are good targets to develop carbohydrate-based anti-cancer vaccines. However, one of the major problems is that carbohydrate antigens possess weak immunogenicity. This review summarizes the recent efforts to overcome this problem: glycoconjugates produced by coupling the carbohydrate antigens and proper carrier proteins improve their immunogenicity, many glycoconjugates have entered clinical trials; the vaccines become chemically well-defined when coupling the carbohydrate antigens with a T-cell peptide epitope and an immunostimulant to form fully synthetic multi-component glycoconjugate vaccines; the modification of carbohydrate antigens in combination with the technology of metabolic oligosaccharide engineering of tumor cells induces a strong immune response; and the fact that the antibodies elicited against the unnatural carbohydrate antigens can recognize the native carbohydrate antigens on tumor cells provides a new promising strategy for the development of anti-cancer vaccines.

  16. Harvesting carbohydrate-rich Arthrospira platensis by spontaneous settling.

    PubMed

    Depraetere, Orily; Pierre, Guillaume; Deschoenmaeker, Frédéric; Badri, Hanène; Foubert, Imogen; Leys, Natalie; Markou, Giorgos; Wattiez, Ruddy; Michaud, Philippe; Muylaert, Koenraad

    2015-03-01

    The filamentous cyanobacterium Arthrospira platensis is an attractive feedstock for carbohydrate-based biofuels because it accumulated up to 74% of carbohydrates when nitrogen stressed. Nitrogen stressed A. platensis also settled spontaneously, and this occurred simultaneously with carbohydrates accumulation, suggesting a link between both phenomena. The increased settling velocity was neither due to production of extracellular carbohydrates, nor due to degradation of gas vacuoles, but was caused by an increase in the specific density of the filaments as a result of accumulation of carbohydrates under the form of glycogen. Settling velocities of carbohydrate-rich A. platensis reached 0.64mh(-1), which allowed the biomass to be harvested using a lamella separator. The biomass could be concentrated at least 15 times, allowing removal of 94% of the water using gravity settling, thus offering a potential application as a low-cost and high-throughput method for primary dewatering of carbohydrate-rich A. platensis.

  17. Harvesting carbohydrate-rich Arthrospira platensis by spontaneous settling.

    PubMed

    Depraetere, Orily; Pierre, Guillaume; Deschoenmaeker, Frédéric; Badri, Hanène; Foubert, Imogen; Leys, Natalie; Markou, Giorgos; Wattiez, Ruddy; Michaud, Philippe; Muylaert, Koenraad

    2015-03-01

    The filamentous cyanobacterium Arthrospira platensis is an attractive feedstock for carbohydrate-based biofuels because it accumulated up to 74% of carbohydrates when nitrogen stressed. Nitrogen stressed A. platensis also settled spontaneously, and this occurred simultaneously with carbohydrates accumulation, suggesting a link between both phenomena. The increased settling velocity was neither due to production of extracellular carbohydrates, nor due to degradation of gas vacuoles, but was caused by an increase in the specific density of the filaments as a result of accumulation of carbohydrates under the form of glycogen. Settling velocities of carbohydrate-rich A. platensis reached 0.64mh(-1), which allowed the biomass to be harvested using a lamella separator. The biomass could be concentrated at least 15 times, allowing removal of 94% of the water using gravity settling, thus offering a potential application as a low-cost and high-throughput method for primary dewatering of carbohydrate-rich A. platensis. PMID:25585253

  18. Hearing Loss, Dizziness, and Carbohydrate Metabolism

    PubMed Central

    Albernaz, Pedro L. Mangabeira

    2015-01-01

    Introduction  Metabolic activity of the inner ear is very intense, and makes it sensitive to changes in the body homeostasis. This study involves a group of patients with inner ear disorders related to carbohydrate metabolism disturbances, including hearing loss, tinnitus, dizziness, and episodes of vertigo. Objectives  To describe the symptoms of metabolic inner ear disorders and the examinations required to establish diagnoses. These symptoms are often the first to allow for an early diagnosis of metabolic disorders and diabetes. Methods  Retrospective study of 376 patients with inner ear symptoms suggestive of disturbances of carbohydrate metabolism. The authors present patientś clinical symptoms and clinical evaluations, with emphasis on the glucose and insulin essays. Results  Authors based their conclusions on otolaryngological findings, diagnostic procedures and treatment principles. They found that auditory and vestibular symptoms usually occur prior to other manifestations of metabolic changes, leading to an early diagnosis of hyperinsulinemia, intestinal sugar malabsorption or diabetes. Previously undiagnosed diabetes mellitus type II was found in 39 patients. Conclusions  The identification of carbohydrate metabolism disturbances is important not only to minimize the patients' clinical symptoms, but also to help maintain their general health. PMID:27413410

  19. Glycosylated Conductive Polymer: A Multimodal Biointerface for Studying Carbohydrate-Protein Interactions.

    PubMed

    Zeng, Xiangqun; Qu, Ke; Rehman, Abdul

    2016-09-20

    polymerization but also enable the simultaneous analysis of the binding events with orthogonal electrical, optical, or mass sensing label-free readouts. We established this approach using polyaniline and polythiophene as examples. Two general methods were demonstrated for glycosylated polymer fabrications (i.e., electropolymerization of monomer bearing α-mannoside residues or click chemistry based mannose conjugation to electrochemically preformed quinone fused polymer with potential to introduce different carbohydrate moieties and construct glycan arrays in a similar manner). Their conjugated π system extending over a large number of recurrent monomer units renders them sensitive optoelectronic materials. The carbohydrate-protein interactions on the side chain could disrupt the electrostatic, H-bonding, steric, or van der Waals interactions within or between polymers, leading to a change of conductivity or optical absorption of the conductive polymers. This will allow concurrent interrogation of these interactions with adjoining biological processes and mechanisms in multimodal fashion. Furthermore, the functionalized glycosylated conductive polymers can be designed and synthesized with controlled oxidation states, desired ionic dopants, and the imperative density and orientation of the sugar ligands that enable the assessment of differential receptor binding profiles of carbohydrate-protein interactions with much more detailed information and high accuracy. Finally, the glycosylated biosensing interfaces were successfully validated for their applications in Gram-negative bacterial detection, antibiotic resistance studies, and antimicrobial susceptibility assays, all based on inferring carbohydrate-protein interactions directly on cell surfaces, thus illustrating their potential uses in infectious disease research, clinical diagnostics, and environmental monitoring of harmful pathogens.

  20. Glycosylated Conductive Polymer: A Multimodal Biointerface for Studying Carbohydrate-Protein Interactions.

    PubMed

    Zeng, Xiangqun; Qu, Ke; Rehman, Abdul

    2016-09-20

    polymerization but also enable the simultaneous analysis of the binding events with orthogonal electrical, optical, or mass sensing label-free readouts. We established this approach using polyaniline and polythiophene as examples. Two general methods were demonstrated for glycosylated polymer fabrications (i.e., electropolymerization of monomer bearing α-mannoside residues or click chemistry based mannose conjugation to electrochemically preformed quinone fused polymer with potential to introduce different carbohydrate moieties and construct glycan arrays in a similar manner). Their conjugated π system extending over a large number of recurrent monomer units renders them sensitive optoelectronic materials. The carbohydrate-protein interactions on the side chain could disrupt the electrostatic, H-bonding, steric, or van der Waals interactions within or between polymers, leading to a change of conductivity or optical absorption of the conductive polymers. This will allow concurrent interrogation of these interactions with adjoining biological processes and mechanisms in multimodal fashion. Furthermore, the functionalized glycosylated conductive polymers can be designed and synthesized with controlled oxidation states, desired ionic dopants, and the imperative density and orientation of the sugar ligands that enable the assessment of differential receptor binding profiles of carbohydrate-protein interactions with much more detailed information and high accuracy. Finally, the glycosylated biosensing interfaces were successfully validated for their applications in Gram-negative bacterial detection, antibiotic resistance studies, and antimicrobial susceptibility assays, all based on inferring carbohydrate-protein interactions directly on cell surfaces, thus illustrating their potential uses in infectious disease research, clinical diagnostics, and environmental monitoring of harmful pathogens. PMID:27524389

  1. Renewable Hydrogen Carrier Carbohydrate: Constructing the Carbon-Neutral Carbohydrate Economy

    SciTech Connect

    Zhang, Y.-H. Percival; Mielenz, Jonathan R

    2011-01-01

    Abstract The hydrogen economy presents an appealing energy future but its implementation must solve numerous problems ranging from low-cost sustainable production, high-density storage, costly infrastructure, to eliminating safety concern. The use of renewable carbohydrate as a high-density hydrogen carrier and energy source for hydrogen production is possible due to emerging cell-free synthetic biology technology called cell-free synthetic pathway biotransformation (SyPaB). Assembly of numerous enzymes and co-enzymes in vitro can create complicated set of biological reactions or pathways that microorganisms cannot complete, for example, C6H10O5 (aq) + 7 H2O (l) 12 H2 (g) + 6 CO2 (g) (PLoS One 2007, 2:e456). Thanks to 100% selectivity of enzymes, modest reaction conditions, and high-purity of generated hydrogen, carbohydrate is a promising hydrogen carrier for end users. Gravimetric density of carbohydrate is 14.8 H2 mass% if water can be recycled from PEM fuel cells or 8.33% H2 mass% without water recycling. Renewable carbohydrate can be isolated from plant biomass or would be produced from a combination of solar electricity/hydrogen and carbon dioxide fixation mediated by high-efficiency artificial photosynthesis mediated by SyPaB. The construction of this carbon-neutral carbohydrate economy would address numerous sustainability challenges, such as electricity and hydrogen storage, CO2 fixation and long-term storage, water conservation, transportation fuel production, plus feed and food production.

  2. The long underestimated carbonyl function of carbohydrates – an organocatalyzed shot into carbohydrate chemistry.

    PubMed

    Mahrwald, R

    2015-09-21

    The aggressive and strong development of organocatalysis provides several protocols for the convenient utilization of the carbonyl function of unprotected carbohydrates in C-C-bond formation processes. These amine-catalyzed mechanisms enable multiple cascade-protocols for the synthesis of a wide range of carbohydrate-derived compound classes. Several, only slightly different protocols, have been developed for the application of 1,3-dicarbonyl compounds in the stereoselective chain-elongation of unprotected carbohydrates and the synthesis of highly functionalized C-glycosides of defined configuration. In addition, C-glycosides can also be accessed by amine-catalyzed reactions with methyl ketones. By a one-pot cascade reaction of isocyanides with unprotected aldoses and amino acids access to defined configured glycopeptide mimetics is achieved. Depending on the reaction conditions different origins to control the installation of configuration during the bond-formation process were observed.

  3. Characterizing the Glycocalyx of Poultry Spermatozoa: II. Low Temperature Storage of Turkey Semen and Sperm Mobility Phenotype Impact the Carbohydrate Component of Membrane Glycoconjugates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The turkey sperm glycocalyx is known to contain residues of sialic acid, alpha-mannose/alpha-glucose, alpha- and beta-galactose, alpha-fucose, alpha- and beta-N-acetyl-galactosamine, monomers and dimers of N-acetyl-glucosamine and N-acetyl-lactosamine. Potential changes in these carbohydrates during...

  4. Effects of electrolytes in carbohydrate beverages on gastric emptying and secretion.

    PubMed

    Rehrer, N J; Beckers, E J; Brouns, F; Saris, W H; Ten Hoor, F

    1993-01-01

    Two experiments were done at rest to examine gastric residue and secretion volume and electrolyte composition after ingestion of beverages of varying composition. In the first experiment the effects of two different sport drinks, one isotonic (7% carbohydrate, primarily sucrose) (I) and one hypertonic (18% carbohydrate, primarily maltodextrin) (H), and a control beverage (0.08 g.l-1 aspartame in water) (C) on titratable acid, pH, osmolality, gastric emptying and secretion volume, and Na+, K+, and Cl- content were measured. In a second experiment five solutions were tested all containing 150 g.l-1 maltodextrin, with 28 meq.l-1 Na+ (low Na), 140 meq.l-1 Na+(high Na), 28 meq.l-1 K+(K), or 140 meq.l-1 Na+ and 28 meq.l-1 K+(high NaK). Beverages H and C, and distilled water (W) were also tested. Samples were taken via a nasogastric tube. A dye dilution technique for serial sampling was employed to determine beverage and secretion volumes. After receiving a bolus of 8 ml.kg-1 body weight, samples of gastric residue were taken at 0, 10, 20, 30, 40, 60, and 80 min. Gastric secretion of Na+, K+, and Cl- was fairly constant despite large differences in beverage composition. Changes in gastric residue pH, titratable acid, osmolality, and electrolyte composition reflected the increasing proportion of the residue that was from gastric secretions. The effects of varying concentrations of Na+ and K+ (in a 150 g.l-1 maltodextrin solution) on gastric emptying were not significant. The high carbohydrate concentration and/or the large volume ingested may have overridden any effect of sodium or potassium. No differences were observed between W and C. Secretion was decreased in these two solutions versus all the others. Although nonsignificant, there was a trend for greater secretion in H versus the other carbohydrate containing solutions in experiment 2. This may be a result of the higher pH maintained after ingestion of this beverage.

  5. Interleukin-2 carbohydrate recognition modulates CTLL-2 cell proliferation.

    PubMed

    Fukushima, K; Yamashita, K

    2001-03-01

    Interleukin-2 (IL-2) specifically recognizes high-mannose type glycans with five or six mannosyl residues. To determine whether the carbohydrate recognition activity of IL-2 contributes to its physiological activity, the inhibitory effects of high-mannose type glycans on IL-2-dependent CTLL-2 cell proliferation were investigated. Man(5)GlcNAc(2)Asn added to CTLL-2 cell cultures inhibited not only phosphorylation of tyrosine kinases but also IL-2-dependent cell proliferation. We found that a complex of IL-2, IL-2 receptor alpha, beta, gamma subunits, and tyrosine kinases was formed in rhIL-2-stimulated CTLL-2 cells. Among the components of this complex, only the IL-2 receptor alpha subunit was stained with Galanthus nivalis agglutinin which specifically recognizes high-mannose type glycans. This staining was diminished after digestion of the glycans with endo-beta-N-acetylglucosaminidase H or D, suggesting that at least a N-glycan containing Man(5)GlcNAc(2) is linked to the extracellular portion of the IL-2 receptor alpha subunit. Our findings indicate that IL-2 binds the IL-2 receptor alpha subunit through Man(5)GlcNAc(2) and a specific peptide sequence on the surface of CTLL-2 cells. When IL-2 binds to the IL-2Ralpha subunit, this may trigger formation of the high affinity complex of IL-2-IL-2Ralpha, -beta, and -gamma subunits, leading to cellular signaling.

  6. Radiofluorinated carbohydrates for positron emission tomography.

    PubMed

    Mun, Jiyoung

    2013-01-01

    2-Deoxy-2-[(18)F]fluoro-D-glucose (2-(18)FDG) has represented radiofluorinated carbohydrates as the most successful tracer for positron emission tomography (PET). 2-(18)FDG uptake depends on glucose metabolism, which is related to a disease progression. 2-(18)FDG has been widely used in oncology, neurology, cardiology, infectious diseases, and inflammation, to complement anatomical modalities such as CT and MRI. Followed by the success of 2-(18)FDG, various radiofluorinated carbohydrates have been evaluated as PET tracers, which include analogs of D-ribose, D-mannose, D-galactose, D-talose, D-fructose, D-allose, lactose, L-fucose, N-acetylneuraminic acid, and L-ascorbic acid. Among those radiofluorinated carbohydrates, several have implied potential for further development. 2-Deoxy-2-[(18)F]fluoro-D-galactose has been developed to assess liver function and diagnose hepatic carcinoma. 6-Deoxy-6-[(18)F]fluoro-D-fructose showed promising characteristics for diagnosis of breast cancer. Three radiofluorinated analogs of lactose have been designed as the substrates of the overexpressed hepatocarcinoma-intestine-pancreas/pancreatitis-associated protein in peritumoral pancreatic tissue for early diagnosis of pancreatic cancer. The metabolism of 6-[(18)F]fluoro-L-fucose suggested that it is a bioactive analog of L-fucose in the synthesis of glycoconjugate macromolecules. 6-Deoxy-6-[(18)F]fluoro-L-ascorbic acid was evaluated to assess antioxidant function of L-ascorbic acid in rodent models of transient global ischemia and glutathione deficiency.

  7. Light period regulation of carbohydrate partitioning

    NASA Technical Reports Server (NTRS)

    Janes, Harry W.

    1994-01-01

    We have shown that the photosynthetic period is important in regulating carbon partitioning. Even when the same amount of carbon is fixed over a 24h period considerably more is translocated out of the leaf under the longer photosynthetic period. This is extremely important when parts of the plant other than the leaves are to be sold. It is also important to notice the amount of carbon respired in the short photosynthetic period. The light period effect on carbohydrate fixation, dark respiration, and translocation is shown in this report.

  8. Carbohydrates/nucleosides/RNA-DNA-ligand interactions

    SciTech Connect

    Kaptein, R.; McConnell, B.; Serianni, A.S.; Silks, L.A. III

    1994-12-01

    Carbohydrate and nucleotide structural determination using modern spectroscopic techniques is dependent on our ability to label oligonucleotides and oligosaccharides with stable isotopes. Uniform Carbon 13 and Nitrogen 15 labeling of oligonucleotides is important to present-day efforts, which are focused on determining the structure of relatively small oligosaccharides and oligonucleotides, which form the elements of larger structures. Because of the relatively recent interest in three-dimensional structure, the development of techniques used to label them has lagged behind parallel techniques used to label peptides and proteins. Therefore, this group`s discussion focused primarily on problems faced today in obtaining oligonucleotides labeled uniformly with carbon 13 and nitrogen 15.

  9. Multimodal CARS microscopy of structured carbohydrate biopolymers

    PubMed Central

    Slepkov, Aaron D.; Ridsdale, Andrew; Pegoraro, Adrian F.; Moffatt, Douglas J.; Stolow, Albert

    2010-01-01

    We demonstrate the utility of multimodal coherent anti-Stokes Raman scattering (CARS) microscopy for the study of structured condensed carbohydrate systems. Simultaneous second-harmonic generation (SHG) and spectrally-scanned CARS microscopy was used to elucidate structure, alignment, and density in cellulose cotton fibers and in starch grains undergoing rapid heat-moisture swelling. Our results suggest that CARS response of the O-H stretch region (3000 cm−1–3400 cm−1), together with the commonly-measured C-H stretch (2750 cm−1–2970 cm−1) and SHG provide potentially important structural information and contrast in these materials. PMID:21258555

  10. Carbohydrate nanotechnology: hierarchical assembly using nature's other information carrying biopolymers.

    PubMed

    Han, Xu; Zheng, Yeting; Munro, Catherine J; Ji, Yiwen; Braunschweig, Adam B

    2015-08-01

    Despite their central role in directing some of the most complex biological processes, carbohydrates--nature's other information carrying biopolymer--have been largely ignored as building blocks for synthetic hierarchical assemblies. The non-stoichiometric binding and astronomical diversity characteristic of carbohydrates could lead to tantalizingly complex assembly algorithms, but these attributes simultaneously increase the difficulty of preparing carbohydrate assemblies and anticipating their behavior. Convergences in biotechnology, nanotechnology, polymer chemistry, surface science, and supramolecular chemistry have led to many recent important breakthroughs in glycan microarrays and synthetic carbohydrate receptors, where the idiosyncrasies of carbohydrate structure and binding are increasingly considered. We hope to inspire more researchers to consider carbohydrate structure, diversity, and binding as attractive tools for constructing synthetic hierarchical assemblies.

  11. A carbohydrate-anion recognition system in aprotic solvents.

    PubMed

    Ren, Bo; Dong, Hai; Ramström, Olof

    2014-05-01

    A carbohydrate-anion recognition system in nonpolar solvents is reported, in which complexes form at the B-faces of β-D-pyranosides with H1-, H3-, and H5-cis patterns similar to carbohydrate-π interactions. The complexation effect was evaluated for a range of carbohydrate structures; it resulted in either 1:1 carbohydrate-anion complexes, or 1:2 complex formation depending on the protection pattern of the carbohydrate. The interaction was also evaluated with different anions and solvents. In both cases it resulted in significant binding differences. The results indicate that complexation originates from van der Waals interactions or weak CH⋅⋅⋅A(-) hydrogen bonds between the binding partners and is related to electron-withdrawing groups of the carbohydrates as well as increased hydrogen-bond-accepting capability of the anions. PMID:24616327

  12. The structure of the carbohydrate backbone of the lipopolysaccharide of Pectinatus frisingensis strain VTT E-79104.

    PubMed

    Vinogradov, Evgeny; Li, Jianjun; Sadovskaya, Irina; Jabbouri, Said; Helander, Ilkka M

    2004-06-22

    The structure of the carbohydrate backbone of the lipopolysaccharide from Pectinatus frisingensis strain VTT E-79104 was analyzed using chemical degradations, NMR spectroscopy, mass spectrometry, and chemical methods. The LPS contains two major structural variants, differing in the presence or absence of an octasaccharide fragment. The largest structure of the carbohydrate backbone of the LPS, that could be deduced from experimental results, consists of 20 monosaccharides arranged in a nonrepetitive sequence: [carbohydrate structure: see text] where R is H or 4-O-Me-alpha-L-Fuc-(1-2)-4-O-Me-beta-Hep-(1-3)-alpha-GlcNAc-(1-2)-beta-Man-(1-3)-beta-ManNAc-(1-4)-alpha-Gal-(1-4)-beta-Hep-(1-3)-beta-GalNAc-(1- where Hep is a residue of D-glycero-D-galacto-heptose; all monosaccharides have the D-configuration except for 4-O-Me-L-Fuc and L-Ara4N. This structure is architecturally similar to the oligosaccharide system reported previously in P. frisingensis VTT E-82164 LPS, but differs from the latter in composition and also in the size of the outer region.

  13. Identification of a novel family of carbohydrate-binding modules with broad ligand specificity

    PubMed Central

    Duan, Cheng-Jie; Feng, Yu-Liang; Cao, Qi-Long; Huang, Ming-Yue; Feng, Jia-Xun

    2016-01-01

    Most enzymes that act on carbohydrates include non-catalytic carbohydrate-binding modules (CBMs) that recognize and target carbohydrates. CBMs bring their appended catalytic modules into close proximity with the target substrate and increase the hydrolytic rate of enzymes acting on insoluble substrates. We previously identified a novel CBM (CBMC5614-1) at the C-terminus of endoglucanase C5614-1 from an uncultured microorganism present in buffalo rumen. In the present study, that the functional region of CBMC5614-1 involved in ligand binding was localized to 134 amino acids. Two representative homologs of CBMC5614-1, sharing the same ligand binding profile, targeted a range of β-linked polysaccharides that adopt very different conformations. Targeted substrates included soluble and insoluble cellulose, β-1,3/1,4-mixed linked glucans, xylan, and mannan. Mutagenesis revealed that three conserved aromatic residues (Trp-380, Tyr-411, and Trp-423) play an important role in ligand recognition and targeting. These results suggest that CBMC5614-1 and its homologs form a novel CBM family (CBM72) with a broad ligand-binding specificity. CBM72 members can provide new insight into CBM-ligand interactions and may have potential in protein engineering and biocatalysis. PMID:26765840

  14. Effects of carbohydrates on the oNPG converting activity of β-galactosidases.

    PubMed

    Warmerdam, Anja; Wang, Jue; Boom, Remko M; Janssen, Anja E M

    2013-07-01

    The effects of high concentrations of carbohydrates on the o-nitrophenyl β-d-galactopyranoside (oNPG) converting activity of β-galactosidase from Bacillus circulans are studied to get a better understanding of the enzyme behavior in concentrated and complicated systems in which enzymatic synthesis of galacto-oligosaccharides is usually performed. The components that were tested were glucose, galactose, lactose, sucrose, trehalose, raffinose, Vivinal GOS, dextran-6000, dextran-70,000, and sarcosine. Small carbohydrates act as acceptors in the reaction. This speeds up the limiting step, which is binding of the galactose residue with the acceptor and release of the product. Simultaneously, both inert and reacting additives seem to cause some molecular crowding, which results in a higher enzyme affinity for the substrate. The effect of molecular crowding on the enzyme activity is small compared to the effect of carbohydrates acting in the reactions as acceptors. The effects of reactants on β-galactosidases from B. circulans, A. oryzae, and K. lactis are compared.

  15. Composition of the carbohydrate granules of the cyanobacterium, Cyanothece sp. strain ATCC 51142

    NASA Technical Reports Server (NTRS)

    Schneegurt, M. A.; Sherman, D. M.; Sherman, L. A.; Mitchell, C. A. (Principal Investigator)

    1997-01-01

    Cyanothece sp. strain ATCC 51142 is an aerobic, unicellular, diazotrophic cyanobacterium that temporally separates O2-sensitive N2 fixation from oxygenic photosynthesis. The energy and reducing power needed for N2 fixation appears to be generated by an active respiratory apparatus that utilizes the contents of large interthylakoidal carbohydrate granules. We report here on the carbohydrate and protein composition of the granules of Cyanothece sp. strain ATCC 51142. The carbohydrate component is a glucose homopolymer with branches every nine residues and is chemically identical to glycogen. Granule-associated protein fractions showed temporal changes in the number of proteins and their abundance during the metabolic oscillations observed under diazotrophic conditions. There also were temporal changes in the protein pattern of the granule-depleted supernatant fractions from diazotrophic cultures. None of the granule-associated proteins crossreacted with antisera directed against several glycogen-metabolizing enzymes or nitrogenase, although these proteins were tentatively identified in supernatant fractions. It is suggested that the granule-associated proteins are structural proteins required to maintain a complex granule architecture.

  16. Evolutionary bases of carbohydrate recognition and substrate discrimination in the ROK protein family.

    PubMed

    Conejo, Maria S; Thompson, Steven M; Miller, Brian G

    2010-06-01

    The ROK (repressor, open reading frame, kinase) protein family (Pfam 00480) is a large collection of bacterial polypeptides that includes sugar kinases, carbohydrate responsive transcriptional repressors, and many functionally uncharacterized gene products. ROK family sugar kinases phosphorylate a range of structurally distinct hexoses including the key carbon source D: -glucose, various glucose epimers, and several acetylated hexosamines. The primary sequence elements responsible for carbohydrate recognition within different functional categories of ROK polypeptides are largely unknown due to a limited structural characterization of this protein family. In order to identify the structural bases for substrate discrimination in individual ROK proteins, and to better understand the evolutionary processes that led to the divergent evolution of function in this family, we constructed an inclusive alignment of 227 representative ROK polypeptides. Phylogenetic analyses and ancestral sequence reconstructions of the resulting tree reveal a discrete collection of active site residues that dictate substrate specificity. The results also suggest a series of mutational events within the carbohydrate-binding sites of ROK proteins that facilitated the expansion of substrate specificity within this family. This study provides new insight into the evolutionary relationship of ROK glucokinases and non-ROK glucokinases (Pfam 02685), revealing the primary sequence elements shared between these two protein families, which diverged from a common ancestor in ancient times. PMID:20512568

  17. Carbohydrate-carbohydrate interaction prominence in 3D supramolecular self-assembly.

    PubMed

    Fuss, Martina; Luna, Mónica; Alcántara, David; de la Fuente, Jesús M; Enríquez-Navas, Pedro M; Angulo, Jesús; Penadés, Soledad; Briones, Fernando

    2008-09-18

    Self-association in water of biologically significant carbohydrate molecules is a controversial topic due to the strong solvation of these molecules in this solvent and the difficulty to experimentally detect these very weak intermolecular forces by biophysical techniques. Herein we report the tremendous ability of amphiphilic carbohydrate molecules to form complex three-dimensional architectures. We have experimentally observed the 3D self-assembly into multilayers of disaccharide neoglycolipid dimers on graphite by means of noncontact AFM and we have also theoretically modeled the interaction between two dimers in order to learn about the structure and composition of these layers. A simple bilayer structure as observed for many amphiphilic lipids was discarded by the experiments. Instead, based on the good agreement between experiments and calculations, we propose that multilayer formation takes place through the assembly of building blocks consisting of two dimers each. The fundamental key in the formation of this supramolecular structure is the complementarity between the van der Waals surfaces of the amphiphilic carbohydrate molecules, a result which differs from the most common idea that H-bonding interactions are prominent in carbohydrate-mediated interactions.

  18. Carbohydrate Analysis: Can We Control the Ripening of Bananas?

    NASA Astrophysics Data System (ADS)

    Deal, S. Todd; Farmer, Catherine E.; Cerpovicz, Paul F.

    2002-04-01

    We have developed an experiment for nutritional/introductory biochemistry courses that focuses on carbohydrate analysis--specifically, the carbohydrates found in bananas and the change in carbohydrate composition as the banana ripens. Pairs of students analyze the starch and reducing sugar content of green, ripe, and overripe bananas. Using the techniques and knowledge gained from these analyses, they then investigate the influence of various storage methods on the ripening process. While this experiment was developed for an introductory-level biochemistry lab, it can easily be adapted for use in other laboratory programs that seek to teach the fundamentals of carbohydrate analysis.

  19. Carbohydrate Recognition by Boronolectins, Small Molecules, and Lectins

    PubMed Central

    Jin, Shan; Cheng, Yunfeng; Reid, Suazette; Li, Minyong; Wang, Binghe

    2009-01-01

    Carbohydrates are known to mediate a large number of biological and pathological events. Small and macromolecules capable of carbohydrate recognition have great potentials as research tools, diagnostics, vectors for targeted delivery of therapeutic and imaging agents, and therapeutic agents. However, this potential is far from being realized. One key issue is the difficulty in the development of “binders” capable of specific recognition of carbohydrates of biological relevance. This review discusses systematically the general approaches that are available in developing carbohydrate sensors and “binders/receptors,” and their applications. The focus is on discoveries during the last five years. PMID:19291708

  20. The least-cost low-carbohydrate diet is expensive.

    PubMed

    Raffensperger, John F

    2008-01-01

    This article describes the use of operations research methods to study the minimum possible cost of a low-carbohydrate diet. The study compares this cost to the minimum cost of a diet with no limitation on carbohydrate. The rationale for this study is the popularity of the low-carbohydrate diets and their perceived high cost. The method used was an operations research approach to find a set of least cost diets, varying the required carbohydrate. This method was chosen to avoid potential concerns with real diets that may be nutritionally deficient or could be had for a lower cost. The major finding is that the cheapest possible low-carbohydrate diet costs about triple the cost of the cheapest diet with no constraint on carbohydrate. Furthermore, the minimum cost of a diet low in both carbohydrate and fat is 5 to 10 times the cost of the cheapest diet, depending on the relative amounts of these nutrients. As carbohydrate and fat are constrained, cost increases dramatically and nonlinearly. The study identifies which nutrients had the greatest effect on cost for a low-carbohydrate and low-fat diet.

  1. Crystal structure of the lectin from Dioclea grandiflora complexed with core trimannoside of asparagine-linked carbohydrates.

    PubMed

    Rozwarski, D A; Swami, B M; Brewer, C F; Sacchettini, J C

    1998-12-01

    The seed lectin from Dioclea grandiflora (DGL) has recently been shown to possess high affinity for 3, 6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose, the core trimannoside of asparagine-linked carbohydrates, but lower affinity for biantennary complex carbohydrates. In the previous paper, the thermodynamics of DGL binding to deoxy analogs of the core trimannoside and to a biantennary complex carbohydrate were determined by isothermal titration microcalorimetry. The data suggest that DGL recognizes specific hydroxyl groups of the trimannoside similar to that of the jack bean lectin concanavalin A (ConA) (Gupta, D. Dam, T. K., Oscarson, S., and Brewer, C. F. (1997) J. Biol. Chem. 272, 6388-6392). However, the thermodynamics of DGL binding to certain deoxy analogs and to the complex carbohydrate are different from that of ConA. In the present paper, the x-ray crystal structure of DGL complexed to the core trimannoside was determined to a resolution of 2.6 A. The overall structure of the DGL complex is similar to the structure of the ConA-trimannoside complex (Naismith, J. H., and Field, R. A. (1996) J. Biol. Chem. 271, 972-976). The location and conformation of the bound trimannoside as well as its hydrogen-bonding interactions in both complexes are nearly identical. However, differences exist in the location of two loops outside of the respective binding sites containing residues 114-125 and 222-227. The latter residues affect the location of a network of hydrogen-bonded water molecules that interact with the trisaccharide. Differences in the arrangement of ordered water molecules in the binding site and/or protein conformational differences outside of the binding site may account for the differences in the thermodynamics of binding of the two lectins to deoxy analogs of the trimannoside. Molecular modeling studies suggest how DGL discriminates against binding the biantennary complex carbohydrate relative to ConA.

  2. Cancer vaccine with mimotopes of tumor-associated carbohydrate antigens

    PubMed Central

    Kozbor, Danuta

    2009-01-01

    The GD2 ganglioside, displayed by five carbohydrate Neu5Acα2-8Neu5Acα2-3(GalNAcβ1-4)Galβ1-4Glcβ residues attached to a ceramide chain that anchors the ganglioside in the cell membrane, is expressed on neuroectodermally derived tumors. GD2 has been used as a target for passive and active immunotherapy in patients with malignant melanoma and neuroblastoma. We have generated 47-LDA mimotope of GD2 by screening a phage display peptide library with anti-GD2 mAb 14G2a and reported that vaccination with the 47-LDA mimotope elicited GD2 cross-reactive IgG antibody responses as well as MHC class I-restricted CD8+ T cells to syngeneic neuroblastoma tumor cells. The cytotoxic activity of the vaccine-induced CTLs was independent of GD2 expression, suggesting recognition of a novel tumor-associated antigen cross-reacting with 47-LDA. Immunoblotting studies using 14G2a mAb demonstrated that this antibody cross-reacts with a 105 kDa glycoprotein expressed by GD2+ and GD2− neuroblastoma and melanoma cells. Functional studies of tumor cells grown in three-dimensional (3D) collagen cultures with 14G2a mAb showed decreases in matrix metalloproteinase-2 activation, a process regulated by 105 kDa activated leukocyte cell adhesion molecules (ALCAM/CD166). The CD166 glycoprotein was shown to be recognized by 14G2a antibody, and inhibition of CD166 expression by RNA interference ablated the cell sensitivity to lysis by 47-LDA-induced CD8+ T cells in vitro and in vivo. These results suggest that the vaccine-induced CTLs recognize a 47-LDA cross-reactive epitope expressed by CD166 and reveal a novel mechanism of induction of potent tumor-specific cellular responses by mimotopes of tumor-associated carbohydrate antigens. PMID:19763891

  3. Cancer vaccine with mimotopes of tumor-associated carbohydrate antigens.

    PubMed

    Kozbor, Danuta

    2010-03-01

    The GD2 ganglioside, displayed by five carbohydrate Neu5Acalpha2-8Neu5Acalpha2-3(GalNAcbeta1-4)Galbeta1-4Glcbeta residues attached to a ceramide chain that anchors the ganglioside in the cell membrane, is expressed on neuroectodermally derived tumors. GD2 has been used as a target for passive and active immunotherapy in patients with malignant melanoma and neuroblastoma. We have generated 47-LDA mimotope of GD2 by screening a phage display peptide library with anti-GD2 mAb 14G2a and reported that vaccination with the 47-LDA mimotope elicited GD2 cross-reactive IgG antibody responses as well as MHC class I-restricted CD8(+) T cells to syngeneic neuroblastoma tumor cells. The cytotoxic activity of the vaccine-induced CTLs was independent of GD2 expression, suggesting recognition of a novel tumor-associated antigen cross-reacting with 47-LDA. Immunoblotting studies using 14G2a mAb demonstrated that this antibody cross-reacts with a 105 kDa glycoprotein expressed by GD2(+) and GD2(-) neuroblastoma and melanoma cells. Functional studies of tumor cells grown in three-dimensional (3D) collagen cultures with 14G2a mAb showed decreases in matrix metalloproteinase-2 activation, a process regulated by 105 kDa activated leukocyte cell adhesion molecules (ALCAM/CD166). The CD166 glycoprotein was shown to be recognized by 14G2a antibody, and inhibition of CD166 expression by RNA interference ablated the cell sensitivity to lysis by 47-LDA-induced CD8(+) T cells in vitro and in vivo. These results suggest that the vaccine-induced CTLs recognize a 47-LDA cross-reactive epitope expressed by CD166 and reveal a novel mechanism of induction of potent tumor-specific cellular responses by mimotopes of tumor-associated carbohydrate antigens. PMID:19763891

  4. Impact of dietary polyphenols on carbohydrate metabolism.

    PubMed

    Hanhineva, Kati; Törrönen, Riitta; Bondia-Pons, Isabel; Pekkinen, Jenna; Kolehmainen, Marjukka; Mykkänen, Hannu; Poutanen, Kaisa

    2010-03-31

    Polyphenols, including flavonoids, phenolic acids, proanthocyanidins and resveratrol, are a large and heterogeneous group of phytochemicals in plant-based foods, such as tea, coffee, wine, cocoa, cereal grains, soy, fruits and berries. Growing evidence indicates that various dietary polyphenols may influence carbohydrate metabolism at many levels. In animal models and a limited number of human studies carried out so far, polyphenols and foods or beverages rich in polyphenols have attenuated postprandial glycemic responses and fasting hyperglycemia, and improved acute insulin secretion and insulin sensitivity. The possible mechanisms include inhibition of carbohydrate digestion and glucose absorption in the intestine, stimulation of insulin secretion from the pancreatic beta-cells, modulation of glucose release from the liver, activation of insulin receptors and glucose uptake in the insulin-sensitive tissues, and modulation of intracellular signalling pathways and gene expression. The positive effects of polyphenols on glucose homeostasis observed in a large number of in vitro and animal models are supported by epidemiological evidence on polyphenol-rich diets. To confirm the implications of polyphenol consumption for prevention of insulin resistance, metabolic syndrome and eventually type 2 diabetes, human trials with well-defined diets, controlled study designs and clinically relevant end-points together with holistic approaches e.g., systems biology profiling technologies are needed.

  5. Relationship between carbohydrate sweeteners and oral diseases.

    PubMed

    Makinen, K K; Isokangas, P

    1988-01-01

    Dental caries and periodontal disease are wide-spread oral illnesses whose etiology is intimately associated with the consumption of carbohydrate sweeteners. Since dental caries is multifactorial in nature, it is reasonable to assume that there is no single method, usable in the foreseeable future, which would lead to its eradication. Consequently, any new caries preventive measures must function coherently with those currently in use, so that the concerted action of all methods would lead to the best cariostatic effect. Strict restriction of sucrose intake without suggestion of alternatives is not realistic. This fact has given rise to attempts to replace sucrose, especially in products consumed between meals, with sweeteners that are less cariogenic. Human clinical trials and several animal experiments have shown promising clinical results obtained by replacing sucrose with certain sugar alcohols (polyols). Among the sugar alcohols, the best results so far have been obtained with xylitol, which is chemically a pentitol containing five carbon atoms. Chewing gums containing xylitol have been shown to be strong instruments against caries in caries-active age-groups and in high-risk subjects. More research is needed to assess the ability of mixtures of xylitol with sorbitol, palatinit, maltitol, other sugar alcohols, and intense sweeteners to prevent oral plaque diseases. Although thorough clinical trials on the relationship between carbohydrate sweeteners and periodontal diseases have not been performed, the available data indicate that dietary polyols may have a restricted dampening effect on periodontal and gingival inflammations. PMID:3041451

  6. Impact of Dietary Polyphenols on Carbohydrate Metabolism

    PubMed Central

    Hanhineva, Kati; Törrönen, Riitta; Bondia-Pons, Isabel; Pekkinen, Jenna; Kolehmainen, Marjukka; Mykkänen, Hannu; Poutanen, Kaisa

    2010-01-01

    Polyphenols, including flavonoids, phenolic acids, proanthocyanidins and resveratrol, are a large and heterogeneous group of phytochemicals in plant-based foods, such as tea, coffee, wine, cocoa, cereal grains, soy, fruits and berries. Growing evidence indicates that various dietary polyphenols may influence carbohydrate metabolism at many levels. In animal models and a limited number of human studies carried out so far, polyphenols and foods or beverages rich in polyphenols have attenuated postprandial glycemic responses and fasting hyperglycemia, and improved acute insulin secretion and insulin sensitivity. The possible mechanisms include inhibition of carbohydrate digestion and glucose absorption in the intestine, stimulation of insulin secretion from the pancreatic β–cells, modulation of glucose release from the liver, activation of insulin receptors and glucose uptake in the insulin-sensitive tissues, and modulation of intracellular signalling pathways and gene expression. The positive effects of polyphenols on glucose homeostasis observed in a large number of in vitro and animal models are supported by epidemiological evidence on polyphenol-rich diets. To confirm the implications of polyphenol consumption for prevention of insulin resistance, metabolic syndrome and eventually type 2 diabetes, human trials with well-defined diets, controlled study designs and clinically relevant end-points together with holistic approaches e.g., systems biology profiling technologies are needed. PMID:20480025

  7. Acute Effects of Carbohydrate Supplementation on Intermittent Sports Performance.

    PubMed

    Baker, Lindsay B; Rollo, Ian; Stein, Kimberly W; Jeukendrup, Asker E

    2015-07-01

    Intermittent sports (e.g., team sports) are diverse in their rules and regulations but similar in the pattern of play; that is, intermittent high-intensity movements and the execution of sport-specific skills over a prolonged period of time (~1-2 h). Performance during intermittent sports is dependent upon a combination of anaerobic and aerobic energy systems, both of which rely on muscle glycogen and/or blood glucose as an important substrate for energy production. The aims of this paper are to review: (1) potential biological mechanisms by which carbohydrate may impact intermittent sport performance; (2) the acute effects of carbohydrate ingestion on intermittent sport performance, including intermittent high-intensity exercise capacity, sprinting, jumping, skill, change of direction speed, and cognition; and (3) what recommendations can be derived for carbohydrate intake before/during exercise in intermittent sports based on the available evidence. The most researched intermittent sport is soccer but some sport-specific studies have also been conducted in other sports (e.g., rugby, field hockey, basketball, American football, and racquet sports). Carbohydrate ingestion before/during exercise has been shown in most studies to enhance intermittent high-intensity exercise capacity. However, studies have shown mixed results with regards to the acute effects of carbohydrate intake on sprinting, jumping, skill, change of direction speed, and cognition. In most of these studies the amount of carbohydrate consumed was ~30-60 g/h in the form of a 6%-7% carbohydrate solution comprised of sucrose, glucose, and/or maltodextrin. The magnitude of the impact that carbohydrate ingestion has on intermittent sport performance is likely dependent on the carbohydrate status of the individual; that is, carbohydrate ingestion has the greatest impact on performance under circumstances eliciting fatigue and/or hypoglycemia. Accordingly, carbohydrate ingestion before and during a game

  8. Effects of disturbance regime on carbohydrate reserves in meadow plants.

    PubMed

    Janeček, Štěpán; Bartušková, Alena; Bartoš, Michael; Altman, Jan; de Bello, Francesco; Doležal, Jiří; Latzel, Vít; Lanta, Vojtěch; Lepš, Jan; Klimešová, Jitka

    2015-10-27

    Carbohydrate storage enables plants to tolerate both seasonally unfavourable conditions and recover from disturbance. Although short-term changes in storage levels due to disturbance are fairly well known, less is known about long-term changes in storage levels, especially in response to cessation of repeated disturbance. Additionally, whereas it is presumably the total amount (pool) of storage carbohydrate reserves that is of importance, typically carbohydrate concentrations are measured instead, as a proxy. We assessed changes in carbohydrate concentrations and pools in storage organs and changes in above- versus belowground biomass in response to mowing cessation in nine herbs from two meadows (dry and wet) at the (June) peak of vegetation development and the (October) growing season end 1 and 3 years after the change in the disturbance regime. We tested three hypotheses: (1) storage will increase with abandonment of mowing only in the first year after disturbance cessation, but not further increase subsequently, as high storage would hinder competitive ability; (2) storage will increase towards the end of the season in both disturbed and undisturbed plants; and (3) changes in carbohydrate concentrations are accurate predictors of changes in pools. Although species-specific changes in carbohydrate reserves occurred in the wet meadow, more general trends appeared in the dry meadow. There, plants accumulated higher carbohydrate reserves at the end of the season, especially in unmown plots. However, the reserves for plants in both disturbance regimes were the same at the growing season peak (June) in both examined years. The increase in storage of carbohydrates on unmown plots in October was manifested by increases of both storage organ biomass and carbohydrate concentration, whereas in mown plots, it was due only to increased carbohydrate concentration. Although concentrations and pools represent different aspects of plant carbohydrate economy, concentrations will

  9. Acute Effects of Carbohydrate Supplementation on Intermittent Sports Performance.

    PubMed

    Baker, Lindsay B; Rollo, Ian; Stein, Kimberly W; Jeukendrup, Asker E

    2015-07-14

    Intermittent sports (e.g., team sports) are diverse in their rules and regulations but similar in the pattern of play; that is, intermittent high-intensity movements and the execution of sport-specific skills over a prolonged period of time (~1-2 h). Performance during intermittent sports is dependent upon a combination of anaerobic and aerobic energy systems, both of which rely on muscle glycogen and/or blood glucose as an important substrate for energy production. The aims of this paper are to review: (1) potential biological mechanisms by which carbohydrate may impact intermittent sport performance; (2) the acute effects of carbohydrate ingestion on intermittent sport performance, including intermittent high-intensity exercise capacity, sprinting, jumping, skill, change of direction speed, and cognition; and (3) what recommendations can be derived for carbohydrate intake before/during exercise in intermittent sports based on the available evidence. The most researched intermittent sport is soccer but some sport-specific studies have also been conducted in other sports (e.g., rugby, field hockey, basketball, American football, and racquet sports). Carbohydrate ingestion before/during exercise has been shown in most studies to enhance intermittent high-intensity exercise capacity. However, studies have shown mixed results with regards to the acute effects of carbohydrate intake on sprinting, jumping, skill, change of direction speed, and cognition. In most of these studies the amount of carbohydrate consumed was ~30-60 g/h in the form of a 6%-7% carbohydrate solution comprised of sucrose, glucose, and/or maltodextrin. The magnitude of the impact that carbohydrate ingestion has on intermittent sport performance is likely dependent on the carbohydrate status of the individual; that is, carbohydrate ingestion has the greatest impact on performance under circumstances eliciting fatigue and/or hypoglycemia. Accordingly, carbohydrate ingestion before and during a game

  10. Acute Effects of Carbohydrate Supplementation on Intermittent Sports Performance

    PubMed Central

    Baker, Lindsay B.; Rollo, Ian; Stein, Kimberly W.; Jeukendrup, Asker E.

    2015-01-01

    Intermittent sports (e.g., team sports) are diverse in their rules and regulations but similar in the pattern of play; that is, intermittent high-intensity movements and the execution of sport-specific skills over a prolonged period of time (~1–2 h). Performance during intermittent sports is dependent upon a combination of anaerobic and aerobic energy systems, both of which rely on muscle glycogen and/or blood glucose as an important substrate for energy production. The aims of this paper are to review: (1) potential biological mechanisms by which carbohydrate may impact intermittent sport performance; (2) the acute effects of carbohydrate ingestion on intermittent sport performance, including intermittent high-intensity exercise capacity, sprinting, jumping, skill, change of direction speed, and cognition; and (3) what recommendations can be derived for carbohydrate intake before/during exercise in intermittent sports based on the available evidence. The most researched intermittent sport is soccer but some sport-specific studies have also been conducted in other sports (e.g., rugby, field hockey, basketball, American football, and racquet sports). Carbohydrate ingestion before/during exercise has been shown in most studies to enhance intermittent high-intensity exercise capacity. However, studies have shown mixed results with regards to the acute effects of carbohydrate intake on sprinting, jumping, skill, change of direction speed, and cognition. In most of these studies the amount of carbohydrate consumed was ~30–60 g/h in the form of a 6%–7% carbohydrate solution comprised of sucrose, glucose, and/or maltodextrin. The magnitude of the impact that carbohydrate ingestion has on intermittent sport performance is likely dependent on the carbohydrate status of the individual; that is, carbohydrate ingestion has the greatest impact on performance under circumstances eliciting fatigue and/or hypoglycemia. Accordingly, carbohydrate ingestion before and during a

  11. Effects of disturbance regime on carbohydrate reserves in meadow plants

    PubMed Central

    Janeček, Štěpán; Bartušková, Alena; Bartoš, Michael; Altman, Jan; de Bello, Francesco; Doležal, Jiří; Latzel, Vít; Lanta, Vojtěch; Lepš, Jan; Klimešová, Jitka

    2015-01-01

    Carbohydrate storage enables plants to tolerate both seasonally unfavourable conditions and recover from disturbance. Although short-term changes in storage levels due to disturbance are fairly well known, less is known about long-term changes in storage levels, especially in response to cessation of repeated disturbance. Additionally, whereas it is presumably the total amount (pool) of storage carbohydrate reserves that is of importance, typically carbohydrate concentrations are measured instead, as a proxy. We assessed changes in carbohydrate concentrations and pools in storage organs and changes in above- versus belowground biomass in response to mowing cessation in nine herbs from two meadows (dry and wet) at the (June) peak of vegetation development and the (October) growing season end 1 and 3 years after the change in the disturbance regime. We tested three hypotheses: (1) storage will increase with abandonment of mowing only in the first year after disturbance cessation, but not further increase subsequently, as high storage would hinder competitive ability; (2) storage will increase towards the end of the season in both disturbed and undisturbed plants; and (3) changes in carbohydrate concentrations are accurate predictors of changes in pools. Although species-specific changes in carbohydrate reserves occurred in the wet meadow, more general trends appeared in the dry meadow. There, plants accumulated higher carbohydrate reserves at the end of the season, especially in unmown plots. However, the reserves for plants in both disturbance regimes were the same at the growing season peak (June) in both examined years. The increase in storage of carbohydrates on unmown plots in October was manifested by increases of both storage organ biomass and carbohydrate concentration, whereas in mown plots, it was due only to increased carbohydrate concentration. Although concentrations and pools represent different aspects of plant carbohydrate economy, concentrations will

  12. Easy Identification of Residues Involved on Structural Differences Between Nonphosphorylated and Phosphorylated CDK2Cyclin A Complexes Using Two-Dimensional Networks.

    PubMed

    Riadi, Gonzalo; Caballero, Julio

    2014-02-01

    The structures of proteins in Protein Data Bank (PDB) contain a lot of information that can be revealed through the use of tools to facilitate their organization and analysis. The increase in available structural data of nonphosphorylated and phosphorylated CDK2cyclin A (npCDK2cycA and pCDK2cycA) complexes has enabled a more realistic description of the fine structural details of the interface residues of these proteins. This work reports the application of two-dimensional network representations (TDNRs) to the structures deposited in PDB to distinguish the differences in the surface between both complexes due to phosphorylation. As a result, a detailed map of the hydrogen bonds (HBs) and hydrophobic interactions between the T-loop residues of CDK2 and the residues of cycA that are different among nonphosphorylated and phosphorylated complexes were described. In addition, we found some interesting subtle differences in the CDK2cycA interface between nonphosphorylated and phosphorylated complexes due to residues that are not located at the T-loop of CDK2. We noted that some HB interactions in CDK2cycA complex are reinforced when the CDK2 is phosphorylated. PMID:27485571

  13. The use of carbohydrates during exercise as an ergogenic aid.

    PubMed

    Cermak, Naomi M; van Loon, Luc J C

    2013-11-01

    Carbohydrate and fat are the two primary fuel sources oxidized by skeletal muscle tissue during prolonged (endurance-type) exercise. The relative contribution of these fuel sources largely depends on the exercise intensity and duration, with a greater contribution from carbohydrate as exercise intensity is increased. Consequently, endurance performance and endurance capacity are largely dictated by endogenous carbohydrate availability. As such, improving carbohydrate availability during prolonged exercise through carbohydrate ingestion has dominated the field of sports nutrition research. As a result, it has been well-established that carbohydrate ingestion during prolonged (>2 h) moderate-to-high intensity exercise can significantly improve endurance performance. Although the precise mechanism(s) responsible for the ergogenic effects are still unclear, they are likely related to the sparing of skeletal muscle glycogen, prevention of liver glycogen depletion and subsequent development of hypoglycemia, and/or allowing high rates of carbohydrate oxidation. Currently, for prolonged exercise lasting 2-3 h, athletes are advised to ingest carbohydrates at a rate of 60 g·h⁻¹ (~1.0-1.1 g·min⁻¹) to allow for maximal exogenous glucose oxidation rates. However, well-trained endurance athletes competing longer than 2.5 h can metabolize carbohydrate up to 90 g·h⁻¹ (~1.5-1.8 g·min⁻¹) provided that multiple transportable carbohydrates are ingested (e.g. 1.2 g·min⁻¹ glucose plus 0.6 g·min⁻¹ of fructose). Surprisingly, small amounts of carbohydrate ingestion during exercise may also enhance the performance of shorter (45-60 min), more intense (>75 % peak oxygen uptake; VO(₂peak)) exercise bouts, despite the fact that endogenous carbohydrate stores are unlikely to be limiting. The mechanism(s) responsible for such ergogenic properties of carbohydrate ingestion during short, more intense exercise bouts has been suggested to reside in the central nervous

  14. Distribution of structural carbohydrates in corn plants as influenced by corn residue management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As part of the Sun Grant Regional Partnership corn stover project, continuous corn (Zea mays L.) field studies incorporating stover removal management practices (0 and 100% removal) were established in both Alabama and South Carolina. Plots in both states were representative of major soil types in t...

  15. Comparing Low-Fat and Low-Carbohydrate Diets

    MedlinePlus

    ... of Internal Medicine Summaries for Patients Comparing Low-Fat and Low-Carbohydrate Diets The full report is titled “Effects of Low-Carbohydrate and Low-Fat Diets. A Randomized Trial.” It is in the ...

  16. Preoperative gastric emptying. Effects of anxiety and oral carbohydrate administration.

    PubMed Central

    Nygren, J; Thorell, A; Jacobsson, H; Larsson, S; Schnell, P O; Hylén, L; Ljungqvist, O

    1995-01-01

    BACKGROUND: Overnight fasting is routine before elective surgery. This may not be the optimal way to prepare for surgical stress, however, because intravenous carbohydrate supplementation instead of fasting has recently been shown to reduce postoperative insulin resistance. In the current study, gastric emptying of a carbohydrate-rich drink was investigated before elective surgery and in a control situation. METHODS: Twelve patients scheduled for elective surgery were randomly given 400 mL of either a carbohydrate-rich drink (285 mOsm/kg, 12.0% carbohydrates, n = 6) or water 4 hours before being anesthetized. Gastric emptying was measured (gamma camera, 99Tcm). Each patient repeated the protocol postoperatively as a control. All values were presented as the mean +/- SEM by means of a nonparametric statistical evaluation. RESULTS: Despite the increased anxiety experienced by patients before surgery (p < 0.005), gastric emptying did not differ between the experimental and control situations. Initially, water emptied more rapidly than carbohydrate. However, after 90 minutes, the stomach was emptied regardless of the solution administered (3.2 +/- 1.1% [mean +/- SEM] remaining in the stomach in the carbohydrate group versus 2.3 +/- 1.2% remaining in the stomach in the water group). CONCLUSIONS: Preoperative anxiety does not prolong gastric emptying. The stomach had been emptied 90 minutes after ingestion of both the carbohydrate-rick drink and water, thereby indicating the possibility of allowing an intake of iso-osmolar carbohydrate-rich fluids before surgery. PMID:8526579

  17. Genetic Analyses of Soluble Carbohydrate Concentrations in Onion Bulbs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fructans are the primary soluble carbohydrate in onion (Allium cepa L.) bulbs and show significant correlations with dry weights and pungency. In this research, we estimated the genetic effects and interactions between two chromosome regions associated with higher amounts of soluble carbohydrates i...

  18. Effect of mouth-rinsing carbohydrate solutions on endurance performance.

    PubMed

    Rollo, Ian; Williams, Clyde

    2011-06-01

    Ingesting carbohydrate-electrolyte solutions during exercise has been reported to benefit self-paced time-trial performance. The mechanism responsible for this ergogenic effect is unclear. For example, during short duration (≤1 hour), intense (>70% maximal oxygen consumption) exercise, euglycaemia is rarely challenged and adequate muscle glycogen remains at the cessation of exercise. The absence of a clear metabolic explanation has led authors to speculate that ingesting carbohydrate solutions during exercise may have a 'non-metabolic' or 'central effect' on endurance performance. This hypothesis has been explored by studies investigating the performance responses of subjects when carbohydrate solutions are mouth rinsed during exercise. The solution is expectorated before ingestion, thus removing the provision of carbohydrate to the peripheral circulation. Studies using this method have reported that simply having carbohydrate in the mouth is associated with improvements in endurance performance. However, the performance response appears to be dependent upon the pre-exercise nutritional status of the subject. Furthermore, the ability to identify a central effect of a carbohydrate mouth rinse maybe affected by the protocol used to assess its impact on performance. Studies using functional MRI and transcranial stimulation have provided evidence that carbohydrate in the mouth stimulates reward centres in the brain and increases corticomotor excitability, respectively. However, further research is needed to determine whether the central effects of mouth-rinsing carbohydrates, which have been seen at rest and during fatiguing exercise, are responsible for improved endurance performance.

  19. Carbohydrate-responsive gene expression in adipose tissue of rats

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although obesity is often associated with high fat diets, it can develop from a variety of meal patterns. Excessive intake of simple carbohydrates is one consistent eating behavior leading to obesity. However, the impact of over-consumption of diets with high carbohydrate-to-fat ratios (C/F) on body...

  20. Identification of carbohydrate anomers using ion mobility-mass spectrometry.

    PubMed

    Hofmann, J; Hahm, H S; Seeberger, P H; Pagel, K

    2015-10-01

    Carbohydrates are ubiquitous biological polymers that are important in a broad range of biological processes. However, owing to their branched structures and the presence of stereogenic centres at each glycosidic linkage between monomers, carbohydrates are harder to characterize than are peptides and oligonucleotides. Methods such as nuclear magnetic resonance spectroscopy can be used to characterize glycosidic linkages, but this technique requires milligram amounts of material and cannot detect small amounts of coexisting isomers. Mass spectrometry, on the other hand, can provide information on carbohydrate composition and connectivity for even small amounts of sample, but it cannot be used to distinguish between stereoisomers. Here, we demonstrate that ion mobility-mass spectrometry--a method that separates molecules according to their mass, charge, size, and shape--can unambiguously identify carbohydrate linkage-isomers and stereoisomers. We analysed six synthetic carbohydrate isomers that differ in composition, connectivity, or configuration. Our data show that coexisting carbohydrate isomers can be identified, and relative concentrations of the minor isomer as low as 0.1 per cent can be detected. In addition, the analysis is rapid, and requires no derivatization and only small amounts of sample. These results indicate that ion mobility-mass spectrometry is an effective tool for the analysis of complex carbohydrates. This method could have an impact on the field of carbohydrate synthesis similar to that of the advent of high-performance liquid chromatography on the field of peptide assembly in the late 1970s.

  1. [Carbohydrate component of immunoglobulin G in cattle suffering from leukosis].

    PubMed

    Meged', E F; Korotkoruchko, V P; Radionov, N T

    1982-01-01

    No essential differences are found in the composition and total amount of carbohydrates in the studied preparations of the immunoglobulin G subfraction in cattle suffering from leucosis and of the immunoglobulin G subfraction, identical in evolution, in healthy animals. It is shown that the main mass of carbohydrates is connected with Fc-fragment and heavy chains of the protein under study. PMID:7135515

  2. Why use DFT methods in the study of carbohydrates?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The recent advances in density functional theory (DFT) and computer technology allow us to study systems with more than 100 atoms routinely. This makes it feasible to study large carbohydrate molecules via quantum mechanical methods, whereas in the past, studies of carbohydrates were restricted to ...

  3. [3 + 2] cycloaddition on carbohydrate templates: stereoselective synthesis of pyrrolidines.

    PubMed

    Cai, Shuting; Gorityala, Bala Kishan; Ma, Jimei; Leow, Min Li; Liu, Xue-Wei

    2011-03-01

    Pyrrolidine derivatives were prepared in high diastereoselectivities and good yields via a [3 + 2] cycloaddition of a tert-butyldimethylsilyl protected carbohydrate-based allene with a diverse range of imines. The subsequent removal of the carbohydrate auxiliary afforded a variety of pyrrolidines with excellent enantioselectivities (up to 99% ee). Selective reduction of the pyrrolidines further demonstrated the potential of this strategy.

  4. Chemical Changes in Carbohydrates Produced by Thermal Processing.

    ERIC Educational Resources Information Center

    Hoseney, R. Carl

    1984-01-01

    Discusses chemical changes that occur in the carbohydrates found in food products when these products are subjected to thermal processing. Topics considered include browning reactions, starch found in food systems, hydrolysis of carbohydrates, extrusion cooking, processing of cookies and candies, and alterations in gums. (JN)

  5. Identification of carbohydrate anomers using ion mobility-mass spectrometry

    NASA Astrophysics Data System (ADS)

    Hofmann, J.; Hahm, H. S.; Seeberger, P. H.; Pagel, K.

    2015-10-01

    Carbohydrates are ubiquitous biological polymers that are important in a broad range of biological processes. However, owing to their branched structures and the presence of stereogenic centres at each glycosidic linkage between monomers, carbohydrates are harder to characterize than are peptides and oligonucleotides. Methods such as nuclear magnetic resonance spectroscopy can be used to characterize glycosidic linkages, but this technique requires milligram amounts of material and cannot detect small amounts of coexisting isomers. Mass spectrometry, on the other hand, can provide information on carbohydrate composition and connectivity for even small amounts of sample, but it cannot be used to distinguish between stereoisomers. Here, we demonstrate that ion mobility-mass spectrometry--a method that separates molecules according to their mass, charge, size, and shape--can unambiguously identify carbohydrate linkage-isomers and stereoisomers. We analysed six synthetic carbohydrate isomers that differ in composition, connectivity, or configuration. Our data show that coexisting carbohydrate isomers can be identified, and relative concentrations of the minor isomer as low as 0.1 per cent can be detected. In addition, the analysis is rapid, and requires no derivatization and only small amounts of sample. These results indicate that ion mobility-mass spectrometry is an effective tool for the analysis of complex carbohydrates. This method could have an impact on the field of carbohydrate synthesis similar to that of the advent of high-performance liquid chromatography on the field of peptide assembly in the late 1970s.

  6. Intestinal adaptations of rainbow trout to changes in dietary carbohydrate.

    PubMed

    Buddington, R K; Hilton, J W

    1987-10-01

    Although omnivores are able to alter the structure and functions of their digestive system in response to changes in dietary carbohydrate content, it is unclear whether carnivores are capable of such adaptive flexibility. Hence we recorded growth rates, intestinal morphometrics and histology, and nutrient uptake rates and concentrations of disaccharidases in the intestines of a carnivorous fish, the rainbow trout, fed different levels and types of carbohydrate. The trout is unable to adaptively regulate digestive system structure and function to increase glucose availability in response to increasing levels of dietary carbohydrates, even to easily digestible forms such as glucose. Paradoxically, a reduction in the concentrations of enzymes associated with carbohydrate digestion in response to elevated levels of easily digested carbohydrates suggests that carnivores may actually try to repress carbohydrate digestion when glucose is available in high quantities. Thus the lower levels of carbohydrate in the diet of trout throughout their evolution has resulted in a reduced ability to phenotypically regulate the digestion of carbohydrates.

  7. Genome of Bifidobacteria and Carbohydrate Metabolism

    PubMed Central

    2015-01-01

    In recent years, the knowledge about bifidobacteria has considerably evolved thanks to recent progress in molecular biology. The analysis of the whole genome sequences of 48 taxa of bifidobacteria offers new perspectives for their classification, especially to set up limit between two species. Indeed, several species are presenting a high homology and should be reclassified. On the other hand, some subspecies are presenting a low homology and should therefore be reclassified into different species. In addition, a better knowledge of the genome of bifidobacteria allows a better understanding of the mechanisms involved in complex carbohydrate metabolism. The genome of some species of bifidobacteria from human but also from animal origin demonstrates high presence in genes involved in the metabolism of complex oligosaccharides. Those species should be further tested to confirm their potential to metabolize complex oligosaccharides in vitro and in vivo. PMID:26761794

  8. [Carbohydrate absorption and malabsorption (author's transl)].

    PubMed

    Caspary, W F

    1977-06-01

    Starch is digested intraluminally by alpha-amylase to maltose, maltotriose, and alpha-limit dextrins. These products, as well as the disaccharides sucrose and lactose, undergo enzymatic hydrolysis to monosaccharides at the brush border surface. The monosaccharides enter the absorbing cell by specific transport mechanisms ("carriers"). Primary carbohydrate (CH) intolerance is characterized by the congenital or acquired absence of individual brush border enzymes or of monosaccharide "carriers" without morphologic abnormalities of the intestinal villus: lactose, sucrose and trehalose intolerance and glucose-galactose malabsorption (brush border diseases). Secondary CH intolerance arises when surface digestion and absorption are reduced due to structural changes of the intestinal mucosa: e.g., decrease or absence of villi with sprue and reduction of the absorbing surface with intestinal resection. Watery diarrhea is the lead symptom. Many drugs delay or interfere with CH absorption. This action may be viewed either as an unwanted side effect or as a welcome therapeutic principle.

  9. Arabinogalactan proteins: focus on carbohydrate active enzymes

    PubMed Central

    Knoch, Eva; Dilokpimol, Adiphol; Geshi, Naomi

    2014-01-01

    Arabinogalactan proteins (AGPs) are a highly diverse class of cell surface proteoglycans that are commonly found in most plant species. AGPs play important roles in many cellular processes during plant development, such as reproduction, cell proliferation, pattern formation and growth, and in plant-microbe interaction. However, little is known about the molecular mechanisms of their function. Numerous studies using monoclonal antibodies that recognize different AGP glycan epitopes have shown the appearance of a slightly altered AGP glycan in a specific stage of development in plant cells. Therefore, it is anticipated that the biosynthesis and degradation of AGP glycan is tightly regulated during development. Until recently, however, little was known about the enzymes involved in the metabolism of AGP glycans. In this review, we summarize recent discoveries of carbohydrate active enzymes (CAZy; http://www.cazy.org/) involved in the biosynthesis and degradation of AGP glycans, and we discuss the biological role of these enzymes in plant development. PMID:24966860

  10. Carbohydrate based materials for gamma radiation shielding

    NASA Astrophysics Data System (ADS)

    Tabbakh, F.; Babaee, V.; Naghsh-Nezhad, Z.

    2015-05-01

    Due to the limitation in using lead as a shielding material for its toxic properties and limitation in abundance, price or non-flexibility of other commonly used materials, finding new shielding materials and compounds is strongly required. In this conceptual study carbohydrate based compounds were considered as new shielding materials. The simulation of radiation attenuation is performed using MCNP and Geant4 with a good agreement in the results. It is found that, the thickness of 2 mm of the proposed compound may reduce up to 5% and 50% of 1 MeV and 35 keV gamma-rays respectively in comparison with 15% and 100% for the same thickness of lead.

  11. A method for (13)C-labeling of metabolic carbohydrates within French bean leaves (Phaseolus vulgaris L.) for decomposition studies in soils.

    PubMed

    Girardin, Cyril; Rasse, Daniel P; Biron, Philippe; Ghashghaie, Jaleh; Chenu, Claire

    2009-06-01

    The molecular composition of plant residues is suspected to largely govern the fate of their constitutive carbon (C) in soils. Labile compounds, such as metabolic carbohydrates, are affected differently from recalcitrant and structural compounds by soil-C stabilisation mechanisms. Producing (13)C-enriched plant residues with specifically labeled fractions would help us to investigate the fate in soils of the constitutive C of these compounds. The objective of the present research was to test (13)C pulse chase labeling as a method for specifically enriching the metabolic carbohydrate components of plant residues, i.e. soluble sugars and starch. Bean plants were exposed to a (13)CO(2)-enriched atmosphere for 0.5, 1, 2, 3 and 21 h. The major soluble sugars were then determined on water-soluble extracts, and starch on HCl-hydrolysable extracts. The results show a quick differential labeling between water-soluble and water-insoluble compounds. For both groups, (13)C-labeling increased linearly with time. The difference in delta(13)C signature between water-soluble and insoluble fractions was 7 per thousand after 0.5 h and 70 per thousand after 21 h. However, this clear isotopic contrast masked a substantial labeling variability within each fraction. By contrast, metabolic carbohydrates on the one hand (i.e. soluble sugars + starch) and other fractions (essentially cell wall components) on the other hand displayed quite homogeneous signatures within fractions, and a significant difference in labeling between fractions: delta(13)C = 414 +/- 3.7 per thousand and 56 +/- 5.5 per thousand, respectively. Thus, the technique generates labeled plant residues displaying contrasting (13)C-isotopic signatures between metabolic carbohydrates and other compounds, with homogenous signatures within each group. Metabolic carbohydrates being labile compounds, our findings suggest that the technique is particularly appropriate for investigating the effect of compound lability on the long

  12. Carbohydrate supplementation improves stroke performance in tennis.

    PubMed

    Vergauwen, L; Brouns, F; Hespel, P

    1998-08-01

    The effect of carbohydrate supplementation on stroke quality during prolonged simulated tennis match-play was investigated. Well-trained tennis palyers reported to the test center three times. At each occasion they performed a pretest, consisting of the leuven Tennis Performance Test (LTPT) and a shuttle run (SHR), which they repeated (posttest) after a 2-h strenuous training session. Throughout the test session, they received in a double blind random order either a placebo drink (P), a carbohydrate solution (0.7 gxkg(-1) BWxh(-1); CHO), or CHO plus a dose of caffeine (5 mg per kg BW). Stroke quality was evaluated during the LTPT by means of measurements of error rate, ball velocity, precision of ball placement, and a velocity-precision (VP) and a velocity-precision-error (VPE) index. Pretest scores were similar during P and CHO. During P, compared with the pretest, stroke quality during the posttest deteriorated (P < 0.05) both for the first service and strokes during defensive rallies and for SHR performance. However, compared with P, the increase in error rate and number of nonreached balls indefensive rallies was smaller (P < 0.05) during CHO. Similarily, CHO attenuated (P < 0.05) the increase in error rate and the decrease in both the VP (P < 0.1) and VPE (P < 0.05) indices for the first service upon fatigue. Furthermore, CHO improved posttest SHR performance. Stroke quality and SHR time were similar during CHO alone and during combined CHO plus caffeine administration, both for the pretest and for the pretest and for the posttest. It is concluded that CHO supplementation improves stroke quality during the final stages of prolonged tennis play. The data prove that CHO intake may facilitate the maintenance of physical quality during long-lasting intermittent exercise to fatigue. PMID:9710871

  13. Formation of insoluble, nonhydrolyzable, sulfur-rich macromolecules via incorporation of inorganic sulfur species into algal carbohydrates

    NASA Astrophysics Data System (ADS)

    Kok, Marika D.; Schouten, Stefan; Sinninghe Damsté, Jaap S.

    2000-08-01

    The process of sulfur incorporation into organic matter was simulated in the laboratory by sulfurization of cell material of the prymnesiophyte alga Phaeocystis in sea water with inorganic polysulfides at 50°C. Flash pyrolysis of the residue, obtained after extraction and several hydrolysis steps, yielded mainly C 1-C 4 alkylbenzenes and C 1-C 4 alkylphenols and, in contrast to control and blank experiments, relatively high amounts of C 0-C 4 alkylthiophenes. The distribution of the thiophenes is very similar to that in pyrolysates of type II-S kerogens. The formation of high-molecular-weight sulfur-rich macromolecules co-occurs with a marked drop in the content of hydrolyzable carbohydrates. This indicates that sulfurization results in the preservation of algal carbohydrate carbon in a macromolecular structure composed of (poly)sulfidic cross-linked carbohydrate skeletons, which upon pyrolysis yields alkylthiophenes. Sulfurization of glucose under similar conditions resulted in the formation of a nonhydrolyzable, solid material, which yielded high amounts of organic sulfur compounds upon pyrolysis, mainly short-chain alkylthiophenes, although with a different distribution than that in the pyrolysate of the sulfurized algal material. The carbon numbers of these organic sulfur compounds extend beyond six, indicating that the length of the carbon skeleton of the pyrolysis products is not limited by the length of the carbon skeleton of the substrate. These results suggest that the sulfurization of carbohydrates may be an important pathway in the preservation of organic matter in euxinic depositional environments.

  14. Defined presentation of carbohydrates on a duplex DNA scaffold.

    PubMed

    Schlegel, Mark K; Hütter, Julia; Eriksson, Magdalena; Lepenies, Bernd; Seeberger, Peter H

    2011-12-16

    A new method for the spatially defined alignment of carbohydrates on a duplex DNA scaffold is presented. The use of an N-hydroxysuccinimide (NHS)-ester phosphoramidite along with carbohydrates containing an alkylamine linker allows for on-column labeling during solid-phase oligonucleotide synthesis. This modification method during solid-phase synthesis only requires the use of minimal amounts of complex carbohydrates. The covalently attached carbohydrates are presented in the major groove of the B-form duplex DNA as potential substrates for murine type II C-type lectin receptors mMGL1 and mMGL2. CD spectroscopy and thermal melting revealed only minimal disturbance of the overall helical structure. Surface plasmon resonance and cellular uptake studies with bone-marrow-derived dendritic cells were used to assess the capability of these carbohydrate-modified duplexes to bind to mMGL receptors.

  15. Relationship of carbohydrate molecular spectroscopic features in combined feeds to carbohydrate utilization and availability in ruminants

    NASA Astrophysics Data System (ADS)

    Zhang, Xuewei; Yu, Peiqiang

    To date, there is no study on the relationship between carbohydrate (CHO) molecular structures and nutrient availability of combined feeds in ruminants. The objective of this study was to use molecular spectroscopy to reveal the relationship between CHO molecular spectral profiles (in terms of functional groups (biomolecular, biopolymer) spectral peak area and height intensity) and CHO chemical profiles, CHO subfractions, energy values, and CHO rumen degradation kinetics of combined feeds of hulless barley with pure wheat dried distillers grains with solubles (DDGS) at five different combination ratios (hulless barley to pure wheat DDGS: 100:0, 75:25, 50:50, 25:75, 0:100). The molecular spectroscopic parameters assessed included: lignin biopolymer molecular spectra profile (peak area and height, region and baseline: ca. 1539-1504 cm-1); structural carbohydrate (STCHO, peaks area region and baseline: ca. 1485-1186 cm-1) mainly associated with hemi- and cellulosic compounds; cellulosic materials peak area (centered at ca. 1240 cm-1 with region and baseline: ca. 1272-1186 cm-1); total carbohydrate (CHO, peaks area region and baseline: ca. 1186-946 cm-1). The results showed that the functional groups (biomolecular, biopolymer) in the combined feeds are sensitive to the changes of carbohydrate chemical and nutrient profiles. The changes of the CHO molecular spectroscopic features in the combined feeds were highly correlated with CHO chemical profiles, CHO subfractions, in situ CHO rumen degradation kinetics and fermentable organic matter supply. Further study is needed to investigate possibility of using CHO molecular spectral features as a predictor to estimate nutrient availability in combined feeds for animals and quantify their relationship.

  16. Blood Triglycerides Levels and Dietary Carbohydrate Indices in Healthy Koreans

    PubMed Central

    Kang, Ji Yeon

    2016-01-01

    Objectives: Previous studies have obtained conflicting findings regarding possible associations between indices measuring carbohydrate intake and dyslipidemia, which is an established risk factor of coronary heart disease. In the present study, we examined cross-sectional associations between carbohydrate indices, including the dietary glycemic index (GI), glycemic load (GL), total amount of carbohydrates, and the percentage of energy from carbohydrates, and a range of blood lipid parameters. Methods: This study included 1530 participants (554 men and 976 women) from 246 families within the Healthy Twin Study. We analyzed the associations using a generalized linear mixed model to control for familial relationships. Results: Levels of the Apo B were inversely associated with dietary GI, GL, and the amount of carbohydrate intake for men, but these relationships were not significant when fat-adjusted values of the carbohydrate indices were used. Triglyceride levels were positively associated with dietary GI and GL in women, and this pattern was more notable in overweight participants (body mass index [BMI] ≥25 kg/m2). However, total, low-density lipoprotein and high-density lipoprotein cholesterol levels were not significantly related with carbohydrate intake overall. Conclusions: Of the blood lipid parameters we investigated, only triglyceride levels were positively related with dietary carbohydrate indices among women participants in the Healthy Twin Study, with an interactive role observed for BMI. However, these associations were not observed in men, suggesting that the association between blood lipid levels and carbohydrate intake depends on the type of lipid, specific carbohydrate indices, gender, and BMI. PMID:27255074

  17. Comparative analysis of carbohydrate active enzymes in Clostridium termitidis CT1112 reveals complex carbohydrate degradation ability.

    PubMed

    Munir, Riffat I; Schellenberg, John; Henrissat, Bernard; Verbeke, Tobin J; Sparling, Richard; Levin, David B

    2014-01-01

    Clostridium termitidis strain CT1112 is an anaerobic, gram positive, mesophilic, cellulolytic bacillus isolated from the gut of the wood-feeding termite, Nasutitermes lujae. It produces biofuels such as hydrogen and ethanol from cellulose, cellobiose, xylan, xylose, glucose, and other sugars, and therefore could be used for biofuel production from biomass through consolidated bioprocessing. The first step in the production of biofuel from biomass by microorganisms is the hydrolysis of complex carbohydrates present in biomass. This is achieved through the presence of a repertoire of secreted or complexed carbohydrate active enzymes (CAZymes), sometimes organized in an extracellular organelle called cellulosome. To assess the ability and understand the mechanism of polysaccharide hydrolysis in C. termitidis, the recently sequenced strain CT1112 of C. termitidis was analyzed for both CAZymes and cellulosomal components, and compared to other cellulolytic bacteria. A total of 355 CAZyme sequences were identified in C. termitidis, significantly higher than other Clostridial species. Of these, high numbers of glycoside hydrolases (199) and carbohydrate binding modules (95) were identified. The presence of a variety of CAZymes involved with polysaccharide utilization/degradation ability suggests hydrolysis potential for a wide range of polysaccharides. In addition, dockerin-bearing enzymes, cohesion domains and a cellulosomal gene cluster were identified, indicating the presence of potential cellulosome assembly.

  18. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

    NASA Astrophysics Data System (ADS)

    Lipska, Agnieszka G.; Seidman, Steven R.; Sieradzan, Adam K.; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A.

    2016-05-01

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models.

  19. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.

    PubMed

    Lipska, Agnieszka G; Seidman, Steven R; Sieradzan, Adam K; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A

    2016-05-14

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models. PMID:27179474

  20. [Performance enhancement by carbohydrate intake during sport: effects of carbohydrates during and after high-intensity exercise].

    PubMed

    Beelen, Milou; Cermak, Naomi M; van Loon, Luc J C

    2015-01-01

    Endogenous carbohydrate availability does not provide sufficient energy for prolonged moderate to high-intensity exercise. Carbohydrate ingestion during high-intensity exercise can therefore enhance performance.- For exercise lasting 1 to 2.5 hours, athletes are advised to ingest 30-60 g of carbohydrates per hour.- Well-trained endurance athletes competing for longer than 2.5 hours at high intensity can metabolise up to 90 g of carbohydrates per hour, provided that a mixture of glucose and fructose is ingested.- Athletes participating in intermittent or team sports are advised to follow the same strategies but the timing of carbohydrate intake depends on the type of sport.- If top performance is required again within 24 hours after strenuous exercise, the advice is to supplement endogenous carbohydrate supplies quickly within the first few hours post-exercise by ingesting large amounts of carbohydrate (1.2 g/kg/h) or a lower amount of carbohydrate (0.8 g/kg/h) with a small amount of protein (0.2-0.4 g/kg/h).

  1. Carbohydrate Content in the GDM Diet: Two Views: View 1: Nutrition Therapy in Gestational Diabetes: The Case for Complex Carbohydrates.

    PubMed

    Hernandez, Teri L

    2016-05-01

    IN BRIEF Restriction of dietary carbohydrate has been the cornerstone for treatment of gestational diabetes mellitus (GDM). However, there is evidence that a balanced liberalization of complex carbohydrate as part of an overall eating plan in GDM meets treatment goals and may mitigate maternal adipose tissue insulin resistance, both of which may promote optimal metabolic outcomes for mother and offspring.

  2. Pesticide residues in eagles

    USGS Publications Warehouse

    Reichel, W.L.; Cromartie, E.; Lamont, T.G.; Mulhern, B.M.; Prouty, R.M.

    1969-01-01

    Bald and golden eagles found sick or dead in 18 States and Canada during 1964-1965 were analyzed for pesticide residues. Residues in bald eagles were considerably higher than in golden eagles. Residues of DDE, DDD, and dieldrin were detected in all samples of bald eagle carcasses; other compounds found, less frequently were heptachlor epoxide, endrin, and DCBP, a metabolite of DDT. DDE was detected in all samples of golden eagle carcasses; DDD, DDT, dieldrin, and heptachlor epoxide were detected less frequently.

  3. A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations.

    PubMed

    Flores, David I; Sotelo-Mundo, Rogerio R; Brizuela, Carlos A

    2014-01-01

    The automatic identification of catalytic residues still remains an important challenge in structural bioinformatics. Sequence-based methods are good alternatives when the query shares a high percentage of identity with a well-annotated enzyme. However, when the homology is not apparent, which occurs with many structures from the structural genome initiative, structural information should be exploited. A local structural comparison is preferred to a global structural comparison when predicting functional residues. CMASA is a recently proposed method for predicting catalytic residues based on a local structure comparison. The method achieves high accuracy and a high value for the Matthews correlation coefficient. However, point substitutions or a lack of relevant data strongly affect the performance of the method. In the present study, we propose a simple extension to the CMASA method to overcome this difficulty. Extensive computational experiments are shown as proof of concept instances, as well as for a few real cases. The results show that the extension performs well when the catalytic site contains mutated residues or when some residues are missing. The proposed modification could correctly predict the catalytic residues of a mutant thymidylate synthase, 1EVF. It also successfully predicted the catalytic residues for 3HRC despite the lack of information for a relevant side chain atom in the PDB file. PMID:25268770

  4. A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations.

    PubMed

    Flores, David I; Sotelo-Mundo, Rogerio R; Brizuela, Carlos A

    2014-01-01

    The automatic identification of catalytic residues still remains an important challenge in structural bioinformatics. Sequence-based methods are good alternatives when the query shares a high percentage of identity with a well-annotated enzyme. However, when the homology is not apparent, which occurs with many structures from the structural genome initiative, structural information should be exploited. A local structural comparison is preferred to a global structural comparison when predicting functional residues. CMASA is a recently proposed method for predicting catalytic residues based on a local structure comparison. The method achieves high accuracy and a high value for the Matthews correlation coefficient. However, point substitutions or a lack of relevant data strongly affect the performance of the method. In the present study, we propose a simple extension to the CMASA method to overcome this difficulty. Extensive computational experiments are shown as proof of concept instances, as well as for a few real cases. The results show that the extension performs well when the catalytic site contains mutated residues or when some residues are missing. The proposed modification could correctly predict the catalytic residues of a mutant thymidylate synthase, 1EVF. It also successfully predicted the catalytic residues for 3HRC despite the lack of information for a relevant side chain atom in the PDB file.

  5. A Simple Extension to the CMASA Method for the Prediction of Catalytic Residues in the Presence of Single Point Mutations

    PubMed Central

    Flores, David I.; Sotelo-Mundo, Rogerio R.; Brizuela, Carlos A.

    2014-01-01

    The automatic identification of catalytic residues still remains an important challenge in structural bioinformatics. Sequence-based methods are good alternatives when the query shares a high percentage of identity with a well-annotated enzyme. However, when the homology is not apparent, which occurs with many structures from the structural genome initiative, structural information should be exploited. A local structural comparison is preferred to a global structural comparison when predicting functional residues. CMASA is a recently proposed method for predicting catalytic residues based on a local structure comparison. The method achieves high accuracy and a high value for the Matthews correlation coefficient. However, point substitutions or a lack of relevant data strongly affect the performance of the method. In the present study, we propose a simple extension to the CMASA method to overcome this difficulty. Extensive computational experiments are shown as proof of concept instances, as well as for a few real cases. The results show that the extension performs well when the catalytic site contains mutated residues or when some residues are missing. The proposed modification could correctly predict the catalytic residues of a mutant thymidylate synthase, 1EVF. It also successfully predicted the catalytic residues for 3HRC despite the lack of information for a relevant side chain atom in the PDB file. PMID:25268770

  6. Health Effects of Low-Carbohydrate Diets: Where Should New Research Go?

    PubMed Central

    Wylie-Rosett, Judith; Aebersold, Karin; Conlon, Beth; Isasi, Carmen R.; Ostrovsky, Natania W.

    2013-01-01

    There has been considerable debate about the metabolic effects of restricting carbohydrate intake in weight and diabetes management. However, the American Diabetes Association has noted that weight and metabolic improvements can be achieved with low carbohydrate, low fat (implicitly higher carbohydrate), or a Mediterranean style diet (usually an intermediate level of carbohydrate). Our paper addresses variability in the definition for low or restricted carbohydrate, the effects of carbohydrate restriction on diabetes-related health outcomes, strategies for restricting carbohydrate intake, and potential genetic variability in response to dietary carbohydrate restriction. Issues for future research are also addressed. PMID:23266565

  7. Carbohydrate binding specificity of the B-cell maturation mitogen from Artocarpus integrifolia seeds.

    PubMed

    Misquith, S; Rani, P G; Surolia, A

    1994-12-01

    Artocarpin, a mannose-specific lectin, is a homotetrameric protein (M(r) 65,000) devoid of covalently attached carbohydrates and consists of four isolectins with pI in the range 5-6.5. Investigations of its carbohydrate binding specificity reveal that among monosaccharides, mannose is preferred over glucose. Among mannooligosaccharides, mannotriose (Man alpha 1-3[Man alpha 1-6]Man) and mannopentaose are the strongest ligands followed by Man alpha 1-3Man. Extension of these ligands by GlcNAc at the reducing ends of mannooligosaccharides tested remarkably improves their inhibitory potencies, while substitution of both the alpha 1-3 and alpha 1-6 mannosyl residues of mannotriose and the core pentasaccharide of N-linked glycans (Man alpha 1-3[Man alpha 1-6]Man beta 1-4GlcNAc beta 1-4GlcNAc) by GlcNAc or N-acetyllactosamine in beta 1-2 linkage diminishes their inhibitory potencies. Sialylated oligosaccharides are non-inhibitory. Moreover, the substitution of either alpha 1-3 or alpha 1-6 linked mannosyl residues of M5Gn or both by mannose in alpha 1-2 linkage leads to a considerable reduction of their inhibitory power. Addition of a xylose residue in beta 1-2 linkage to the core pentasaccharide improves the inhibitory activity. Considering the fact that artocarpin has the strongest affinity for the xylose containing hepasaccharide from horseradish peroxidase, which differs significantly from all the mannose/glucose-specific lectins, it should prove a useful tool for the isolation and characterization of glycoproteins displaying such structure.

  8. Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity.

    PubMed

    Warda, Alicja K; Siezen, Roland J; Boekhorst, Jos; Wells-Bennik, Marjon H J; de Jong, Anne; Kuipers, Oscar P; Nierop Groot, Masja N; Abee, Tjakko

    2016-01-01

    We characterised carbohydrate utilisation of 20 newly sequenced Bacillus cereus strains isolated from food products and food processing environments and two laboratory strains, B. cereus ATCC 10987 and B. cereus ATCC 14579. Subsequently, genome sequences of these strains were analysed together with 11 additional B. cereus reference genomes to provide an overview of the different types of carbohydrate transporters and utilization systems found in B. cereus strains. The combined application of API tests, defined growth media experiments and comparative genomics enabled us to link the carbohydrate utilisation capacity of 22 B. cereus strains with their genome content and in some cases to the panC phylogenetic grouping. A core set of carbohydrates including glucose, fructose, maltose, trehalose, N-acetyl-glucosamine, and ribose could be used by all strains, whereas utilisation of other carbohydrates like xylose, galactose, and lactose, and typical host-derived carbohydrates such as fucose, mannose, N-acetyl-galactosamine and inositol is limited to a subset of strains. Finally, the roles of selected carbohydrate transporters and utilisation systems in specific niches such as soil, foods and the human host are discussed.

  9. Assessing Bacterial Interactions Using Carbohydrate-Based Microarrays

    PubMed Central

    Flannery, Andrea; Gerlach, Jared Q.; Joshi, Lokesh; Kilcoyne, Michelle

    2015-01-01

    Carbohydrates play a crucial role in host-microorganism interactions and many host glycoconjugates are receptors or co-receptors for microbial binding. Host glycosylation varies with species and location in the body, and this contributes to species specificity and tropism of commensal and pathogenic bacteria. Additionally, bacterial glycosylation is often the first bacterial molecular species encountered and responded to by the host system. Accordingly, characterising and identifying the exact structures involved in these critical interactions is an important priority in deciphering microbial pathogenesis. Carbohydrate-based microarray platforms have been an underused tool for screening bacterial interactions with specific carbohydrate structures, but they are growing in popularity in recent years. In this review, we discuss carbohydrate-based microarrays that have been profiled with whole bacteria, recombinantly expressed adhesins or serum antibodies. Three main types of carbohydrate-based microarray platform are considered; (i) conventional carbohydrate or glycan microarrays; (ii) whole mucin microarrays; and (iii) microarrays constructed from bacterial polysaccharides or their components. Determining the nature of the interactions between bacteria and host can help clarify the molecular mechanisms of carbohydrate-mediated interactions in microbial pathogenesis, infectious disease and host immune response and may lead to new strategies to boost therapeutic treatments. PMID:27600247

  10. Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity.

    PubMed

    Warda, Alicja K; Siezen, Roland J; Boekhorst, Jos; Wells-Bennik, Marjon H J; de Jong, Anne; Kuipers, Oscar P; Nierop Groot, Masja N; Abee, Tjakko

    2016-01-01

    We characterised carbohydrate utilisation of 20 newly sequenced Bacillus cereus strains isolated from food products and food processing environments and two laboratory strains, B. cereus ATCC 10987 and B. cereus ATCC 14579. Subsequently, genome sequences of these strains were analysed together with 11 additional B. cereus reference genomes to provide an overview of the different types of carbohydrate transporters and utilization systems found in B. cereus strains. The combined application of API tests, defined growth media experiments and comparative genomics enabled us to link the carbohydrate utilisation capacity of 22 B. cereus strains with their genome content and in some cases to the panC phylogenetic grouping. A core set of carbohydrates including glucose, fructose, maltose, trehalose, N-acetyl-glucosamine, and ribose could be used by all strains, whereas utilisation of other carbohydrates like xylose, galactose, and lactose, and typical host-derived carbohydrates such as fucose, mannose, N-acetyl-galactosamine and inositol is limited to a subset of strains. Finally, the roles of selected carbohydrate transporters and utilisation systems in specific niches such as soil, foods and the human host are discussed. PMID:27272929

  11. Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity

    PubMed Central

    Warda, Alicja K.; Siezen, Roland J.; Boekhorst, Jos; Wells-Bennik, Marjon H. J.; de Jong, Anne; Kuipers, Oscar P.; Nierop Groot, Masja N.; Abee, Tjakko

    2016-01-01

    We characterised carbohydrate utilisation of 20 newly sequenced Bacillus cereus strains isolated from food products and food processing environments and two laboratory strains, B. cereus ATCC 10987 and B. cereus ATCC 14579. Subsequently, genome sequences of these strains were analysed together with 11 additional B. cereus reference genomes to provide an overview of the different types of carbohydrate transporters and utilization systems found in B. cereus strains. The combined application of API tests, defined growth media experiments and comparative genomics enabled us to link the carbohydrate utilisation capacity of 22 B. cereus strains with their genome content and in some cases to the panC phylogenetic grouping. A core set of carbohydrates including glucose, fructose, maltose, trehalose, N-acetyl-glucosamine, and ribose could be used by all strains, whereas utilisation of other carbohydrates like xylose, galactose, and lactose, and typical host-derived carbohydrates such as fucose, mannose, N-acetyl-galactosamine and inositol is limited to a subset of strains. Finally, the roles of selected carbohydrate transporters and utilisation systems in specific niches such as soil, foods and the human host are discussed. PMID:27272929

  12. Degradation properties of protein and carbohydrate during sludge anaerobic digestion.

    PubMed

    Yang, Guang; Zhang, Panyue; Zhang, Guangming; Wang, Yuanyuan; Yang, Anqi

    2015-09-01

    Degradation of protein and carbohydrate is vital for sludge anaerobic digestion performance. However, few studies focused on degradation properties of protein and carbohydrate. This study investigated detailed degradation properties of sludge protein and carbohydrate in order to gain insight into organics removal during anaerobic digestion. Results showed that carbohydrate was more efficiently degraded than protein and was degraded prior to protein. The final removal efficiencies of carbohydrate and protein were 49.7% and 32.2%, respectively. The first 3 days were a lag phase for protein degradation since rapid carbohydrate degradation in this phase led to repression of protease formation. Kinetics results showed that, after initial lag phase, protein degradation followed the first-order kinetic with rate constants of 0.0197 and 0.0018 d(-1) during later rapid degradation phase and slow degradation phase, respectively. Carbohydrate degradation also followed the first-order kinetics with a rate constant of 0.007 d(-1) after initial quick degradation phase.

  13. Assessing Bacterial Interactions Using Carbohydrate-Based Microarrays

    PubMed Central

    Flannery, Andrea; Gerlach, Jared Q.; Joshi, Lokesh; Kilcoyne, Michelle

    2015-01-01

    Carbohydrates play a crucial role in host-microorganism interactions and many host glycoconjugates are receptors or co-receptors for microbial binding. Host glycosylation varies with species and location in the body, and this contributes to species specificity and tropism of commensal and pathogenic bacteria. Additionally, bacterial glycosylation is often the first bacterial molecular species encountered and responded to by the host system. Accordingly, characterising and identifying the exact structures involved in these critical interactions is an important priority in deciphering microbial pathogenesis. Carbohydrate-based microarray platforms have been an underused tool for screening bacterial interactions with specific carbohydrate structures, but they are growing in popularity in recent years. In this review, we discuss carbohydrate-based microarrays that have been profiled with whole bacteria, recombinantly expressed adhesins or serum antibodies. Three main types of carbohydrate-based microarray platform are considered; (i) conventional carbohydrate or glycan microarrays; (ii) whole mucin microarrays; and (iii) microarrays constructed from bacterial polysaccharides or their components. Determining the nature of the interactions between bacteria and host can help clarify the molecular mechanisms of carbohydrate-mediated interactions in microbial pathogenesis, infectious disease and host immune response and may lead to new strategies to boost therapeutic treatments.

  14. Sugar for my honey: carbohydrate partitioning in ectomycorrhizal symbiosis.

    PubMed

    Nehls, Uwe; Grunze, Nina; Willmann, Martin; Reich, Marlis; Küster, Helge

    2007-01-01

    Simple, readily utilizable carbohydrates, necessary for growth and maintenance of large numbers of microbes are rare in forest soils. Among other types of mutualistic interactions, the formation of ectomycorrhizas, a symbiosis between tree roots and certain soil fungi, is a way to overcome nutrient and carbohydrate limitations typical for many forest ecosystems. Ectomycorrhiza formation is typical for trees in boreal and temperate forests of the northern hemisphere and alpine regions world-wide. The main function of this symbiosis is the exchange of fungus-derived nutrients for plant-derived carbohydrates, enabling the colonization of mineral nutrient-poor environments. In ectomycorrhizal symbiosis up to 1/3 of plant photoassimilates could be transferred toward the fungal partner. The creation of such a strong sink is directly related to the efficiency of fungal hexose uptake at the plant/fungus interface, a modulated fungal carbohydrate metabolism in the ectomycorrhiza, and the export of carbohydrates towards soil growing hyphae. However, not only the fungus but also the plant partner increase its expression of hexose importer genes at the plant/fungus interface. This increase in hexose uptake capacity of plant roots in combination with an increase in photosynthesis may explain how the plant deals with the growing fungal carbohydrate demand in symbiosis and how it can restrict this loss of carbohydrates under certain conditions to avoid fungal parasitism. PMID:17078984

  15. Biological butanol production from microalgae-based biodiesel residues by Clostridium acetobutylicum.

    PubMed

    Cheng, Hai-Hsuan; Whang, Liang-Ming; Chan, Kun-Chi; Chung, Man-Chien; Wu, Shu-Hsien; Liu, Cheng-Pin; Tien, Shih-Yuan; Chen, Shan-Yuan; Chang, Jo-Shu; Lee, Wen-Jhy

    2015-05-01

    This study conducted batch experiments to evaluate the potential of butanol production from microalgae biodiesel residues by Clostridium acetobutylicum. The results indicated that with 90 g/L of glucose as the sole substrate the highest butanol yield of 0.2 g/g-glucose was found, but the addition of butyrate significantly enhanced the butanol yield. The highest butanol yield of 0.4 g/g-glucose was found with 60 g/L of glucose and 18 g/L of butyrate. Using microalgae biodiesel residues as substrate, C. acetobutylicum produced 3.86 g/L of butanol and achieved butanol yield of 0.13 g/g-carbohydrate via ABE fermentation, but the results indicated that approximately one third of carbohydrate was not utilized by C. acetobutylicum. Biological butanol production from microalgae biodiesel residues can be possible, but further research on fermentation strategies are required to improve production yield.

  16. [Computation techniques in the conformational analysis of carbohydrates].

    PubMed

    Gebst, A G; Grachev, A A; Shashkov, A S; Nifant'ev, N E

    2007-01-01

    A growing number of modern studies of carbohydrates is devoted to spatial mechanisms of their participation in the cell recognition processes and directed design of inhibitors of these processes. Any progress in this field is impossible without the development of theoretical conformational analysis of carbohydrates. In this review, we generalize literature data on the potentialities of using of different molecular-mechanic force fields, the methods of quantum mechanics, and molecular dynamics to study the conformation of glycoside bond. A possibility of analyzing the reactivity of carbohydrates with the computation techniques is also discussed in brief.

  17. [Soil carbohydrates: their determination methods and indication functions].

    PubMed

    Zhang, Wei; Xie, Hongtu; He, Hongbo; Zheng, Lichen; Wang, Ge

    2006-08-01

    Soil carbohydrates are the important component of soil organic matter, and play an important role in soil aggregation formation. Their hydrolysis methods involve sulfur acid (H2SO4), hydrochloric acid (HCl), and trifluoroacetic acid (TFA) hydrolysis, and their determination methods include colorimetry, gas-liquid chromatography (GLC) , high performance liquid chromatography (HPLC), and high performance anion-exchange chromatography with pulsed amperometric detection (HPAE-PAD). This paper summarized the methods of carbohydrates' hydrolysis, purification and detection, with focus on the derived methods of GLC, and briefly introduced the indication functions of carbohydrates in soil organic matter turnover.

  18. Elucidating the exact role of engineered CRABPII residues for the formation of a retinal protonated Schiff base

    SciTech Connect

    Vasileiou, Chrysoula; Wang, Wenjing; Jia, Xiaofei; Lee, Kin Sing Stephen; Watson, Camille T.; Geiger, James H.; Borhan, Babak

    2010-03-04

    Cellular Retinoic Acid Binding Protein II (CRABPII) has been reengineered to specifically bind and react with all-trans-retinal to form a protonated Schiff base. Each step of this process has been dissected and four residues (Lys132, Tyr134, Arg111, and Glu121) within the CRABPII binding site have been identified as crucial for imine formation and/or protonation. The precise role of each residue has been examined through site directed mutagenesis and crystallographic studies. The crystal structure of the R132K:L121E-CRABPII (PDB-3I17) double mutant suggests a direct interaction between engineered Glu121 and the native Arg111, which is critical for both Schiff base formation and protonation.

  19. Saturated fat, carbohydrates and cardiovascular disease.

    PubMed

    Kuipers, R S; de Graaf, D J; Luxwolda, M F; Muskiet, M H A; Dijck-Brouwer, D A J; Muskiet, F A J

    2011-09-01

    The dietary intake of saturated fatty acids (SAFA) is associated with a modest increase in serum total cholesterol, but not with cardiovascular disease (CVD). Replacing dietary SAFA with carbohydrates (CHO), notably those with a high glycaemic index, is associated with an increase in CVD risk in observational cohorts, while replacing SAFA with polyunsaturated fatty acids (PUFA) is associated with reduced CVD risk. However, replacing a combination of SAFA and trans-fatty acids with n-6 PUFA (notably linoleic acid) in controlled trials showed no indication of benefit and a signal toward increased coronary heart disease risk, suggesting that n-3 PUFA may be responsible for the protective association between total PUFA and CVD. High CHO intakes stimulate hepatic SAFA synthesis and conservation of dietary SAFA . Hepatic de novo lipogenesis from CHO is also stimulated during eucaloric dietary substitution of SAFA by CHO with high glycaemic index in normo-insulinaemic subjects and during hypocaloric high-CHO/low-fat diets in subjects with the metabolic syndrome. The accumulation of SAFA stimulates chronic systemic low-grade inflammation through its mimicking of bacterial lipopolysaccharides and÷or the induction of other pro-inflammatory stimuli. The resulting systemic low-grade inflammation promotes insulin resistance, reallocation of energy-rich substrates and atherogenic dyslipidaemia that concertedly give rise to increased CVD risk. We conclude that avoidance of SAFA accumulation by reducing the intake of CHO with high glycaemic index is more effective in the prevention of CVD than reducing SAFA intake per se.

  20. Carbohydrate degrading polypeptide and uses thereof

    DOEpatents

    Sagt, Cornelis Maria Jacobus; Schooneveld-Bergmans, Margot Elisabeth Francoise; Roubos, Johannes Andries; Los, Alrik Pieter

    2015-10-20

    The invention relates to a polypeptide having carbohydrate material degrading activity which comprises the amino acid sequence set out in SEQ ID NO: 2 or an amino acid sequence encoded by the nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 4, or a variant polypeptide or variant polynucleotide thereof, wherein the variant polypeptide has at least 96% sequence identity with the sequence set out in SEQ ID NO: 2 or the variant polynucleotide encodes a polypeptide that has at least 96% sequence identity with the sequence set out in SEQ ID NO: 2. The invention features the full length coding sequence of the novel gene as well as the amino acid sequence of the full-length functional protein and functional equivalents of the gene or the amino acid sequence. The invention also relates to methods for using the polypeptide in industrial processes. Also included in the invention are cells transformed with a polynucleotide according to the invention suitable for producing these proteins.

  1. Carbohydrate Dependence During Prolonged, Intense Endurance Exercise.

    PubMed

    Hawley, John A; Leckey, Jill J

    2015-11-01

    A major goal of training to improve the performance of prolonged, continuous, endurance events lasting up to 3 h is to promote a range of physiological and metabolic adaptations that permit an athlete to work at both higher absolute and relative power outputs/speeds and delay the onset of fatigue (i.e., a decline in exercise intensity). To meet these goals, competitive endurance athletes undertake a prodigious volume of training, with a large proportion performed at intensities that are close to or faster than race pace and highly dependent on carbohydrate (CHO)-based fuels to sustain rates of muscle energy production [i.e., match rates of adenosine triphosphate (ATP) hydrolysis with rates of resynthesis]. Consequently, to sustain muscle energy reserves and meet the daily demands of training sessions, competitive athletes freely select CHO-rich diets. Despite renewed interest in high-fat, low-CHO diets for endurance sport, fat-rich diets do not improve training capacity or performance, but directly impair rates of muscle glycogenolysis and energy flux, limiting high-intensity ATP production. When highly trained athletes compete in endurance events lasting up to 3 h, CHO-, not fat-based fuels are the predominant fuel for the working muscles and CHO, not fat, availability becomes rate limiting for performance. PMID:26553495

  2. Role of carbohydrates in thyrotropin binding sites.

    PubMed

    Pekonen, F

    1980-07-01

    The role of carbohydrates in thyrotropin binding was studied by glycosidase treatment of human thyroid membranes. Removal of over 75% of membrane sialic acid resulted in a 50% increase of TSH binding, measured in 10 mM Tris-HCl, 50 mM NaCl, 0.1% bSA, pH 7.4, 37 degrees C (buffer A). This augmentation was due to an increase in binding to high affinity sites (Ka 1 X 10(10)M-1). The binding was highly specific and was not significantly inhibited by gangliosides. In contrast, low affinity binding of TSH was unchanged either in buffer A or in 10 mM Tris-acetate, 0.1% bSA pH 6.0, 4 degrees C (buffer B) and was inhibited by gangliosides. Treatment of membranes with beta-galactosidase, beta-N-acetylglucosaminidase and alpha-L-fucosidase had little effect on TSH binding. The data suggests that membrane-associated sialic acid inhibits TSH binding to high affinity receptors and that gangliosides are not involved in tthis TSH-receptor interaction.

  3. The Dependence of Carbohydrate-Aromatic Interaction Strengths on the Structure of the Carbohydrate.

    PubMed

    Hsu, Che-Hsiung; Park, Sangho; Mortenson, David E; Foley, B Lachele; Wang, Xiaocong; Woods, Robert J; Case, David A; Powers, Evan T; Wong, Chi-Huey; Dyson, H Jane; Kelly, Jeffery W

    2016-06-22

    Interactions between proteins and carbohydrates are ubiquitous in biology. Therefore, understanding the factors that determine their affinity and selectivity are correspondingly important. Herein, we have determined the relative strengths of intramolecular interactions between a series of monosaccharides and an aromatic ring close to the glycosylation site in an N-glycoprotein host. We employed the enhanced aromatic sequon, a structural motif found in the reverse turns of some N-glycoproteins, to facilitate face-to-face monosaccharide-aromatic interactions. A protein host was used because the dependence of the folding energetics on the identity of the monosaccharide can be accurately measured to assess the strength of the carbohydrate-aromatic interaction. Our data demonstrate that the carbohydrate-aromatic interaction strengths are moderately affected by changes in the stereochemistry and identity of the substituents on the pyranose rings of the sugars. Galactose seems to make the weakest and allose the strongest sugar-aromatic interactions, with glucose, N-acetylglucosamine (GlcNAc) and mannose in between. The NMR solution structures of several of the monosaccharide-containing N-glycoproteins were solved to further understand the origins of the similarities and differences between the monosaccharide-aromatic interaction energies. Peracetylation of the monosaccharides substantially increases the strength of the sugar-aromatic interaction in the context of our N-glycoprotein host. Finally, we discuss our results in light of recent literature regarding the contribution of electrostatics to CH-π interactions and speculate on what our observations imply about the absolute conservation of GlcNAc as the monosaccharide through which N-linked glycans are attached to glycoproteins in eukaryotes. PMID:27249581

  4. Production of vanillin from waste residue of rice bran oil by Aspergillus niger and Pycnoporus cinnabarinus.

    PubMed

    Zheng, Lirong; Zheng, Pu; Sun, Zhihao; Bai, Yanbing; Wang, Jun; Guo, Xinfu

    2007-03-01

    A new technology of transforming ferulic acid, which was from waste residue of rice bran oil, into vanillin was developed by a combination of fungal strains Aspergillus niger CGMCC0774 and Pycnoporus cinnabarinus CGMCC1115. Various concentrations of ferulic acid were compared, and the highest yield reached 2.2 g l(-1) of vanillic acid by A. niger CGMCC0774 in a 25 l fermenter when concentration of ferulic acid was 4 g l(-1). The filtrate of A. niger CGMCC0774 culture was concentrated and vanillic acid in the filtrate was bio-converted into vanillin by P. cinnabarinus CGMCC1115. The yield of vanillin reached 2.8 g l(-1) when 5 g l(-1) of glucose and 25 g of HZ802 resin were supplemented in the bioconversion medium. The 13C isotope analysis indicated that delta13C(PDB) of vanillin prepared was much different from chemically synthesized vanillin. PMID:16782330

  5. The skinny on high-protein, low-carbohydrate diets.

    PubMed

    Cunningham, Wendy; Hyson, Dianne

    2006-01-01

    Short-term studies of high-protein, low-carbohydrate diets have shown weight loss and improvements in plasma lipid profiles. Studies of greater than 6 months' duration, however, have failed to show continued benefit of high-protein, low-carbohydrate diets on weight loss and cardiovascular risk factors compared with conventional diets. Without concurrent weight loss and caloric restriction, these diets offer no additional benefit to lipids or body weight over other weight-loss regimens. In fact, high-protein, low-carbohydrate diets may add additional risk to individuals with cardiovascular disease due to their high fat and cholesterol content combined with decreased intake of fruits, vegetables, whole grains, and other nutrients related to cardiovascular risk. In addition, high-protein, low-carbohydrate diets have been implicated in other risks, including impaired renal, bone, and gastrointestinal health.

  6. Multicomponent cascade reactions of unprotected carbohydrates and amino acids.

    PubMed

    Voigt, Benjamin; Linke, Michael; Mahrwald, Rainer

    2015-06-01

    Herein an operationally simple multicomponent reaction of unprotected carbohydrates with amino acids and isonitriles is presented. By the extension of this Ugi-type reaction to an unprotected disaccharide a novel glycopeptide structure was accessible.

  7. Porphyrin binding to jacalin is facilitated by the inherent plasticity of the carbohydrate-binding site: novel mode of lectin-ligand interaction.

    PubMed

    Goel, M; Anuradha, P; Kaur, K J; Maiya, B G; Swamy, M J; Salunke, D M

    2004-02-01

    The crystal structure of the complex of meso-tetrasulfonatophenylporphyrin (H(2)TPPS) with jack fruit (Artocarpus integriflora) agglutinin (jacalin) has been determined at 1.8 A resolution. A porphyrin pair is sandwiched between two symmetry-related jacalin monomers in the crystal, leading to a cross-linking network of protein molecules. Apart from the stacking interactions, H(2)TPPS also forms hydrogen bonds, some involving water bridges, with jacalin at the carbohydrate-binding site. The residues that are involved in rendering galactopyranoside specificity to jacalin undergo conformational adjustments in order to accommodate the H(2)TPPS molecule. The water molecules at the carbohydrate-binding site of jacalin cement the jacalin-porphyrin interactions, optimizing their complementarity. Interactions of porphyrin with jacalin are relatively weak compared with those observed between galactopyranoside and jacalin, perhaps because the former largely involves water-mediated hydrogen bonds. While H(2)TPPS binds to jacalin at the carbohydrate-binding site as in the case of ConA, its mode of interaction with jacalin is very different. H(2)TPPS does not enter the carbohydrate-binding cavity of jacalin. Instead, it sits over the binding site. While the porphyrin binding is mediated by replicating the hydrogen-bonding network of mannopyranoside through the sulfonate atoms in the case of ConA, the plasticity associated with the carbohydrate-binding site accommodates the pluripotent porphyrin molecule in the case of jacalin through an entirely different set of interactions.

  8. The role of carbohydrates in infection strategies of enteric pathogens.

    PubMed

    Kato, Kentaro; Ishiwa, Akiko

    2015-03-01

    Enteric pathogens cause considerable public health concerns worldwide including tropical regions. Here, we review the roles of carbohydrates in the infection strategies of various enteric pathogens including viruses, bacteria and protozoa, which infect the epithelial lining of the human and animal intestine. At host cell entry, enteric viruses, including norovirus, recognize mainly histo-blood group antigens. At the initial step of bacterial infections, carbohydrates also function as receptors for attachment. Here, we describe the function of carbohydrates in infection by Salmonella enterica and several bacterial species that produce a variety of fimbrial adhesions. During invasion by enteropathogenic protozoa, apicomplexan parasites utilize sialic acids or sulfated glycans. Carbohydrates serve as receptors for infection by these microbes; however, their usage of carbohydrates varies depending on the microbe. On the surface of the mucosal tissues of the gastrointestinal tract, various carbohydrate moieties are present and play a crucial role in infection, representing the site of infection or route of access for most microbes. During the infection and/or invasion process of the microbes, carbohydrates function as receptors for various microbes, but they can also function as a barrier to infection. One approach to develop effective prophylactic and therapeutic antimicrobial agents is to modify the drug structure. Another approach is to modify the mode of inhibition of infection depending on the individual pathogen by using and mimicking the interactions with carbohydrates. In addition, similarities in mode of infection may also be utilized. Our findings will be useful in the development of new drugs for the treatment of enteric pathogens. PMID:25859152

  9. A review of low-carbohydrate ketogenic diets.

    PubMed

    Westman, Eric C; Mavropoulos, John; Yancy, William S; Volek, Jeff S

    2003-11-01

    In response to the emerging epidemic of obesity in the United States, a renewal of interest in alternative diets has occurred, especially in diets that limit carbohydrate intake. Recent research has demonstrated that low-carbohydrate ketogenic diets can lead to weight loss and favorable changes in serum triglycerides and high-density lipoprotein cholesterol. This review summarizes the physiology and recent clinical studies regarding this type of diet.

  10. Functional relationship between oxytocin and appetite for carbohydrates versus saccharin.

    PubMed

    Herisson, Florence M; Brooks, Lydia L; Waas, Joseph R; Levine, Allen S; Olszewski, Pawel K

    2014-08-20

    Centrally acting oxytocin (OT) inhibits feeding. Recent evidence suggests a link between OT and control of carbohydrate and saccharin intake, but it is unclear whether OT affects appetite for only carbohydrates, especially sweet ones, or sweet tastants irrespective of their carbohydrate content. Therefore, a blood-brain barrier penetrant OT receptor antagonist, L-368,899, was administered in mice and intake of liquid diets containing carbohydrates sucrose, glucose, fructose, polycose, or cornstarch (CS) or the noncarbohydrate, noncaloric sweetener saccharin was studied in episodic intake paradigms: one in which only one tastant was available and the other in which a choice between a carbohydrate (sucrose, glucose, or fructose) and saccharin was provided. We also used real-time PCR to examine hypothalamic Ot mRNA levels in mice provided short-term access to sucrose, CS, or saccharin. In the no-choice paradigm, L-368,899 increased the intake of all carbohydrates, whereas its effect on saccharin consumption showed only a trend. A 10 times lower dose (0.3 mg/kg) stimulated intake of sucrose than other carbohydrates. In the choice test, a very low 0.1 mg/kg dose of L-368,899 doubled the proportion of sucrose consumption relative to saccharin, but did not affect fructose or glucose preference. Ot gene expression increased after sucrose and CS, but not saccharin exposure compared with the controls; however, a higher level of significance was detected in the sucrose group. We conclude that OT inhibits appetite for carbohydrates. Sucrose consumption considerably enhances Ot gene expression and is particularly sensitive to OT receptor blockade, suggesting a special functional relationship between OT and sugar intake.

  11. Hydrocracking of carbohydrates making glycerol, glycols and other polyols

    DOEpatents

    Andrews, Mark A.; Klaeren, Stephen A.

    1991-01-01

    A homogeneous process for hydrocracking of carbohydrates in the presence of soluble transition metal hydrogenation catalyst with the production of lower polyhydric alcohols. A carbohydrate is contacted with hydrogen in the presence of a soluble transition metal catalyst and a strong base at a temperature of from about 25.degree. C. to about 200.degree. C. and a pressure of from about 15 to about 3000 psi.

  12. Recent Development in Carbohydrate Based Anti-cancer Vaccines

    PubMed Central

    Yin, Zhaojun; Huang, Xuefei

    2012-01-01

    The development of carbohydrate based anti-cancer vaccines is of high current interests. Herein, the latest development in this exciting field is reviewed. After a general introduction about tumor associated carbohydrate antigens and immune responses, the review is focused on the various strategies that have been developed to enhance the immunogenecity of these antigens. The results from animal studies and clinical trials are presented. PMID:22468019

  13. Lanthanide-chelating carbohydrate conjugates are useful tools to characterize carbohydrate conformation in solution and sensitive sensors to detect carbohydrate-protein interactions.

    PubMed

    Canales, Ángeles; Mallagaray, Álvaro; Berbís, M Álvaro; Navarro-Vázquez, Armando; Domínguez, Gema; Cañada, F Javier; André, Sabine; Gabius, Hans-Joachim; Pérez-Castells, Javier; Jiménez-Barbero, Jesús

    2014-06-01

    The increasing interest in the functional versatility of glycan epitopes in cellular glycoconjugates calls for developing sensitive methods to define carbohydrate conformation in solution and to characterize protein-carbohydrate interactions. Measurements of pseudocontact shifts in the presence of a paramagnetic cation can provide such information. In this work, the energetically privileged conformation of a disaccharide (lactose as test case) was experimentally inferred by using a synthetic carbohydrate conjugate bearing a lanthanide binding tag. In addition, the binding of lactose to a biomedically relevant receptor (the human adhesion/growth-regulatory lectin galectin-3) and its consequences in structural terms were defined, using Dy(3+), Tb(3+), and Tm(3+). The described approach, complementing the previously tested protein tagging as a way to exploit paramagnetism, enables to detect binding, even weak interactions, and to characterize in detail topological aspects useful for physiological ligands and mimetics in drug design.

  14. SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures

    PubMed Central

    Biro, Jan C; Fördös, Gergely

    2005-01-01

    Background The interacting residues of protein and nucleic acid sequences are close to each other – they are co-located. Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB) contain all information about these co-locations; however it is not an easy task to penetrate this complex information. We developed a JAVA tool, called SeqX for this purpose. Results SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. The user a. selects a structure from PDB; b. chooses an atom that is commonly present in every residues of the nucleic acid and/or protein structure(s) c. defines a distance from these atoms (3–15 Å). The SeqX tool detects every residue that is located within the defined distances from the defined "backbone" atom(s); provides a DotPlot-like visualization (Residues Contact Map), and calculates the frequency of every possible residue pairs (Residue Contact Table) in the observed structure. It is possible to exclude +/- 1 to 10 neighbor residues in the same polymeric chain from detection, which greatly improves the specificity of detections (up to 60% when tested on dsDNA). Results obtained on protein structures showed highly significant correlations with results obtained from literature (p < 0.0001, n = 210, four different subsets). The co-location frequency of physico-chemically compatible amino acids is significantly higher than is calculated and expected in random protein sequences (p < 0.0001, n = 80). Conclusion The tool is simple and easy to use and provides a quick and reliable visualization and analyses of residue co-locations in protein and nucleic acid structures. Availability and requirements SeqX, Java J2SE Runtime Environment 5.0 (available from [see Additional file 1] ) and at least a 1 GHz processor and with a minimum 256 Mb RAM. Source codes are available from the authors. PMID:16011796

  15. Determination of free and total carbohydrate profile in soluble coffee.

    PubMed

    Prodolliet, J; Bruelhart, M; Lador, F; Martinez, C; Obert, L; Blanc, M B; Parchet, J M

    1995-01-01

    A liquid chromatographic (LC) method was evaluated for the determination of free and total carbohydrates in soluble coffee. Samples are solubilized in water for free carbohydrates or hydrolyzed with 1.00N hydrochloric acid for total carbohydrates. An aliquot of the sample solution is analyzed on a pellicular anion-exchange polystyrene-divinylbenzene column using pure water as the mobile phase. Carbohydrates are quantitated by a pulsed amperometric detector. All major carbohydrates found in soluble coffee are determined in a single run. The technique allowed the detection of fraudulent addition of coffee husks or parchments as well as cereals or caramelized sugar for the 63 commercial products analyzed. High levels of free mannitol, free fructose, free glucose, sucrose, total glucose, and total xylose are a good indication of adulteration. Data were compared with those obtained from separate enzymatic determinations and from a different LC procedure. A close agreement among the methods was observed. However, the original method was superior in precision and was the only procedure that enabled the quantitation of all major carbohydrates. The technique is, therefore, a very powerful tool for routine analysis and for purity assessment of soluble coffee.

  16. Validation of lignocellulosic biomass carbohydrates determination via acid hydrolysis.

    PubMed

    Zhou, Shengfei; Runge, Troy M

    2014-11-01

    This work studied the two-step acid hydrolysis for determining carbohydrates in lignocellulosic biomass. Estimation of sugar loss based on acid hydrolyzed sugar standards or analysis of sugar derivatives was investigated. Four model substrates (starch, holocellulose, filter paper and cotton) and three levels of acid/material ratios (7.8, 10.3 and 15.4, v/w) were studied to demonstrate the range of test artifacts. The method for carbohydrates estimation based on acid hydrolyzed sugar standards having the most satisfactory carbohydrate recovery and relative standard deviation. Raw material and the acid/material ratio both had significant effect on carbohydrate hydrolysis, suggesting the acid to have impacts beyond a catalyst in the hydrolysis. Following optimal procedures, we were able to reach a carbohydrate recovery of 96% with a relative standard deviation less than 3%. The carbohydrates recovery lower than 100% was likely due to the incomplete hydrolysis of substrates, which was supported by scanning electron microscope (SEM) images.

  17. Bacterial, plant, and fungal carbohydrate structure databases: daily usage.

    PubMed

    Toukach, Philip V; Egorova, Ksenia S

    2015-01-01

    Natural carbohydrates play important roles in living systems and therefore are used as diagnostic and therapeutic targets. The main goal of glycomics is systematization of carbohydrates and elucidation of their role in human health and disease. The amount of information on natural carbohydrates accumulates rapidly, but scientists still lack databases and computer-assisted tools needed for orientation in the glycomic information space. Therefore, freely available, regularly updated, and cross-linked databases are demanded. Bacterial Carbohydrate Structure Database (Bacterial CSDB) was developed for provision of structural, bibliographic, taxonomic, NMR spectroscopic, and other related information on bacterial and archaeal carbohydrate structures. Its main features are (1) coverage above 90%, (2) high data consistence (above 90% of error-free records), and (3) presence of manually verified bibliographic, NMR spectroscopic, and taxonomic annotations. Recently, CSDB has been expanded to cover carbohydrates of plant and fungal origin. The achievement of full coverage in the plant and fungal domains is expected in the future. CSDB is freely available on the Internet as a web service at http://csdb.glycoscience.ru. This chapter aims at showing how to use CSDB in your daily scientific practice. PMID:25753703

  18. Bacterial, plant, and fungal carbohydrate structure databases: daily usage.

    PubMed

    Toukach, Philip V; Egorova, Ksenia S

    2015-01-01

    Natural carbohydrates play important roles in living systems and therefore are used as diagnostic and therapeutic targets. The main goal of glycomics is systematization of carbohydrates and elucidation of their role in human health and disease. The amount of information on natural carbohydrates accumulates rapidly, but scientists still lack databases and computer-assisted tools needed for orientation in the glycomic information space. Therefore, freely available, regularly updated, and cross-linked databases are demanded. Bacterial Carbohydrate Structure Database (Bacterial CSDB) was developed for provision of structural, bibliographic, taxonomic, NMR spectroscopic, and other related information on bacterial and archaeal carbohydrate structures. Its main features are (1) coverage above 90%, (2) high data consistence (above 90% of error-free records), and (3) presence of manually verified bibliographic, NMR spectroscopic, and taxonomic annotations. Recently, CSDB has been expanded to cover carbohydrates of plant and fungal origin. The achievement of full coverage in the plant and fungal domains is expected in the future. CSDB is freely available on the Internet as a web service at http://csdb.glycoscience.ru. This chapter aims at showing how to use CSDB in your daily scientific practice.

  19. Microelectrode array biosensor for studying carbohydrate-mediated interactions

    PubMed Central

    Chamberlain, Jeffrey W.; Maurer, Karl; Cooper, John; Lyon, Wanda J.; Danley, David L.; Ratner, Daniel M.

    2013-01-01

    Carbohydrate-mediated host-pathogen interactions are essential to bacterial and viral pathogenesis, and represent an attractive target for the development of antiadhesives to prevent infection. We present a versatile microelectrode array-based platform to investigate carbohydrate-mediated protein and bacterial binding, with the objective of developing a generalizable method for screening inhibitors of host-microbe interactions. Microelectrode arrays are well suited for interrogating biological binding events, including proteins and whole-cells, and are amenable to electrochemical derivitization, facilitating rapid deposition of biomolecules. In this study, we achieve microelectrode functionalization with carbohydrates via controlled polymerization of pyrrole to individual microelectrodes, followed by physisorption of neoglycoconjugates to the polypyrrole-coated electrodes. Bioactivity of the immobilized carbohydrates was confirmed with carbohydrate-binding proteins (lectins) detected by both fluorescent and electrochemical means. The platform’s ability to analyze whole-cell binding was demonstrated using strains of Escherichia coli and Salmonella enterica, and the dose-dependent inhibition of S. enterica by a soluble carbohydrate antiadhesive. PMID:22405843

  20. Interactions of vanadates with carbohydrates in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Ribeiro, Ana C. F.; Valente, Artur J. M.; Lobo, Victor M. M.; Azevedo, Eduarda F. G.; Amado, Ana M.; da Costa, A. M. Amorim; Ramos, M. Luísa; Burrows, H. D.

    2004-10-01

    The interaction between the vanadate ion (VO 3-, i.e. vanadium (V)) and the carbohydrates sucrose, glucose and fructose has been studied in aqueous solutions (pH ≈6, 298.15 K) using measurements of diffusion coefficients, electrical conductivity, Raman and multinuclear NMR spectroscopy. With sucrose and glucose, indications of hydrolysis of the anion in the absence of the sugars came from a decrease in the diffusion coefficient with increasing concentration. Significant effects on the diffusion coefficients were observed in the presence of sucrose and glucose, suggesting interactions between the carbohydrates and vanadate ion. Support for this came from electrical conductivity measurements, where there were indications of formation of oligomeric species. These were found to depend on the carbohydrate used: confirmation of oligomer formation came from Raman spectroscopy, where it was possible to identify these species, and see their dependence on the particular carbohydrate used. Information on the interactions between the carbohydrates glucose or sucrose and vanadate came from 51V and 1H NMR spectroscopy, where the dominant species appeared to be a 2:2 complex with glucose, possessing trigonal bipyramidal centres, whereas with sucrose it is suggested that octahedral species are formed. Studies with fructose were complicated by competing oxidation of this carbohydrate and reduction of vanadium (V).

  1. Fat and Carbohydrate Preferences in Mice

    PubMed Central

    Sclafani, Anthony; Zukerman, Steven; Glendinning, John I.; Margolskee, Robert F.

    2008-01-01

    Trpm5 and α-gustducin are key to the transduction of tastes of sugars, amino acids and bitter compounds. This study investigated the role of these signaling proteins in the preference for fat, starch, and starch-derived polysaccharides (Polycose), using Trpm5 knockout (Trpm5 KO) and α-gustducin knockout (Gust KO) mice. In initial two-bottle tests (24 h/day), Trpm5 KO mice showed no preference for soybean oil emulsions (0.313 - 2.5%), Polycose solutions (0.5 - 4%) or starch suspensions (0.5 - 4%). Gust KO mice displayed an attenuated preference for Polycose, but their preference for soybean oil and starch was comparable to that of C57BL/6J wild-type mice (WT). Gust KO mice preferred starch to Polycose whereas WT mice had the opposite preference. Following extensive experience with soybean oil emulsions (Intralipid) and Polycose solutions, the Trpm5 KO mice developed preferences comparable to the WT mice, although their absolute intakes remained suppressed. Similarly, Gust KO mice developed a strong Polycose preference with experience but they continued to consume less than WT mice. These results implicate α-gustducin and Trpm5 as mediators of polysaccharide taste and Trpm5 in fat taste. The disruption in Polycose, but not starch preference, in Gust KO mice indicates that distinct sensory signaling pathways mediate the response to these carbohydrates,. The experience-induced rescue of fat and Polycose preferences in the KO mice likely reflects the action of a post-oral conditioning mechanism, which functions in the absence of α-gustducin and Trpm5. PMID:17652359

  2. Magnesium and disturbances in carbohydrate metabolism.

    PubMed

    Mooren, Frank C

    2015-09-01

    Magnesium is actively involved in a number of metabolic reactions as an important co-factor, with special emphasis on carbohydrate metabolism. After a brief overview of the regulation of intra- and extracellular magnesium, the present review first describes the regulatory role of magnesium in important metabolic pathways involved in energy metabolism and glycaemic control. Next the clinical significance of hypomagnesaemic conditions with regard to the management of glucose in prediabetic stages, such as insulin resistance/impaired glucose tolerance and in type 2 diabetes mellitus are characterized. Cross-sectional as well as longitudinal studies suggest that a reduced dietary magnesium intake serves as a risk factor for the incidence of both impaired glucose regulation and type 2 diabetes. Mechanisms that might be responsible for diabetes-associated hypomagnesaemia are discussed. Furthermore, the role of hypomagnesaemia in the development and progression of chronic diabetic complications are addressed. Finally, the available literature on the effects of magnesium supplementation on glycaemic control parameters during prediabetic conditions (preventive approach) as well as type 2 diabetes mellitus (therapeutic approach) are reviewed systematically. There is considerable evidence that chronic magnesium supplementation may delay the progression from impaired glucose regulation to type 2 diabetes; however, the effects of oral magnesium supplementation as an adjunct therapy for type 2 diabetes are quite heterogeneous with respect to the various measures of glycaemic control. The results of this review suggest a requirement for critical consideration of the pros and cons of magnesium replacement therapy, based on variables such as magnesium status, stage of disease and glycaemic control.

  3. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes.

    PubMed

    Cockburn, Darrell; Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

  4. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes

    PubMed Central

    Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

  5. Analysis of the carbohydrate-binding-module from Fragaria x ananassa α-L-arabinofuranosidase 1.

    PubMed

    Sin, I N; Perini, M A; Martínez, G A; Civello, P M

    2016-10-01

    α-L-arabinofuranosidases (EC 3.2.1.55) are enzymes involved in the catabolism of several cell-wall polysaccharides such as pectins and hemicelluloses, catalyzing the hydrolysis of terminal non-reducing α-L-arabinofuranosil residues. Bioinformatic analysis of the aminoacidic sequences of Fragaria x ananassa α-L-arabinofuranosidases predict a putative carbohydrate-binding-module of the family CBM_4_9, associated to a wide range of carbohydrate affinities. In this study, we report the characterization of the binding affinity profile to different cell wall polysaccharides of the putative CBM of α-L-arabinofuranosidase 1 from Fragaria x ananassa (CBM-FaARA1). The sequence encoding for the putative CBM was cloned and expressed in Escherichia coli, and the resultant recombinant protein was purified from inclusion bodies by a Nickel affinity chromatography under denaturing conditions. The refolded recombinant protein was then subjected to binding assays and affinity gel electrophoresis, which indicated its ability to bind cellulose and also high affinity for homogalacturonans.

  6. Analysis of the carbohydrate-binding-module from Fragaria x ananassa α-L-arabinofuranosidase 1.

    PubMed

    Sin, I N; Perini, M A; Martínez, G A; Civello, P M

    2016-10-01

    α-L-arabinofuranosidases (EC 3.2.1.55) are enzymes involved in the catabolism of several cell-wall polysaccharides such as pectins and hemicelluloses, catalyzing the hydrolysis of terminal non-reducing α-L-arabinofuranosil residues. Bioinformatic analysis of the aminoacidic sequences of Fragaria x ananassa α-L-arabinofuranosidases predict a putative carbohydrate-binding-module of the family CBM_4_9, associated to a wide range of carbohydrate affinities. In this study, we report the characterization of the binding affinity profile to different cell wall polysaccharides of the putative CBM of α-L-arabinofuranosidase 1 from Fragaria x ananassa (CBM-FaARA1). The sequence encoding for the putative CBM was cloned and expressed in Escherichia coli, and the resultant recombinant protein was purified from inclusion bodies by a Nickel affinity chromatography under denaturing conditions. The refolded recombinant protein was then subjected to binding assays and affinity gel electrophoresis, which indicated its ability to bind cellulose and also high affinity for homogalacturonans. PMID:27262101

  7. Kinetics and mechanism of thermal degradation of pentose- and hexose-based carbohydrate polymers.

    PubMed

    Akbar, Jamshed; Iqbal, Mohammad S; Massey, Shazma; Masih, Rashid

    2012-10-15

    This work aims at study of thermal degradation kinetics and mechanism of pentose- and hexose-based carbohydrate polymers isolated from Plantago ovata (PO), Salvia aegyptiaca (SA) and Ocimum basilicum (OB). The analysis was performed by isoconversional method. The materials exhibited mainly two-stage degradation. The weight loss at ambient-115°C characterized by low activation energy corresponds to loss of moisture. The kinetic triplets consisting of E, A and g(α) model of the materials were determined. The major degradation stage represents a loss of high boiling volatile components. This stage is exothermic in nature. Above 340°C complete degradation takes place leaving a residue of 10-15%. The master plots of g(α) function clearly differentiated the degradation mechanism of hexose-based OB and SA polymers and pentose-based PO polymer. The pentose-based carbohydrate polymer showed D(4) type and the hexose-based polymers showed A(4) type degradation mechanism.

  8. Related lectins from snowdrop and maize differ in their carbohydrate-binding specificity.

    PubMed

    Fouquaert, Elke; Smith, David F; Peumans, Willy J; Proost, Paul; Balzarini, Jan; Savvides, Savvas N; Damme, Els J M Van

    2009-03-01

    Searches in an EST database from maize revealed the expression of a protein related to the Galanthus nivalis (GNA) agglutinin, referred to as GNA(maize). Heterologous expression of GNA(maize) in Pichia pastoris allowed characterization of the first nucleocytoplasmic GNA homolog from plants. GNA(maize) is a tetrameric protein which shares 64% sequence similarity with GNA. Glycan microarray analyses revealed important differences in the specificity. Unlike GNA, which binds strongly to high-mannose N-glycans, the lectin from maize reacts almost exclusively with more complex glycans. Interestingly, GNA(maize) prefers complex glycans containing beta1-2 GlcNAc residues. The obvious difference in carbohydrate-binding properties is accompanied by a 100-fold reduced anti-HIV activity. Although the sequences of GNA and GNA(maize) are clearly related they show only 28% sequence identity. Our results indicate that gene divergence within the family of GNA-related lectins leads to changes in carbohydrate-binding specificity, as shown on N-glycan arrays.

  9. Nickel-Catalyzed Proton-Deuterium Exchange (HDX) Procedures for Glycosidic Linkage Analysis of Complex Carbohydrates.

    PubMed

    Price, Neil P J; Hartman, Trina M; Vermillion, Karl E

    2015-07-21

    The structural analysis of complex carbohydrates typically requires the assignment of three parameters: monosaccharide composition, the position of glycosidic linkages between monosaccharides, and the position and nature of noncarbohydrate substituents. The glycosidic linkage positions are often determined by permethylation analysis, but this can be complicated by high viscosity or poor solubility, resulting in under-methylation. This is a drawback because an under-methylated position may be misinterpreted as the erroneous site of a linkage or substituent. Here, we describe an alternative approach to linkage analysis that makes use of a nonreversible deuterium exchange of C-H protons on the carbohydrate backbone. The exchange reaction is conducted in deuterated water catalyzed by Raney nickel, and results in the selective exchange of C-H protons adjacent to free hydroxyl groups. Hence, the position of the residual C-H protons is indicative of the position of glycosidic linkages or other substituents and can be readily assigned by heteronuclear single quantum coherence-nuclear magnetic resonance (HSQC-NMR) or, following suitable derivatization, by gas chromatography-mass spectroscopy (GC/MS) analysis. Moreover, because the only changes to the parent sugar are proton/deuterium exchanges, the composition and linkage analysis can be determined in a single step.

  10. Kinetics and mechanism of thermal degradation of pentose- and hexose-based carbohydrate polymers.

    PubMed

    Akbar, Jamshed; Iqbal, Mohammad S; Massey, Shazma; Masih, Rashid

    2012-10-15

    This work aims at study of thermal degradation kinetics and mechanism of pentose- and hexose-based carbohydrate polymers isolated from Plantago ovata (PO), Salvia aegyptiaca (SA) and Ocimum basilicum (OB). The analysis was performed by isoconversional method. The materials exhibited mainly two-stage degradation. The weight loss at ambient-115°C characterized by low activation energy corresponds to loss of moisture. The kinetic triplets consisting of E, A and g(α) model of the materials were determined. The major degradation stage represents a loss of high boiling volatile components. This stage is exothermic in nature. Above 340°C complete degradation takes place leaving a residue of 10-15%. The master plots of g(α) function clearly differentiated the degradation mechanism of hexose-based OB and SA polymers and pentose-based PO polymer. The pentose-based carbohydrate polymer showed D(4) type and the hexose-based polymers showed A(4) type degradation mechanism. PMID:22939355

  11. Expedient synthesis of C-aryl carbohydrates by consecutive biocatalytic benzoin and aldol reactions.

    PubMed

    Hernández, Karel; Parella, Teodor; Joglar, Jesús; Bujons, Jordi; Pohl, Martina; Clapés, Pere

    2015-02-16

    The introduction of aromatic residues connected by a C-C bond into the non-reducing end of carbohydrates is highly significant for the development of innovative structures with improved binding affinity and selectivity (e.g., C-aril-sLex). In this work, an expedient asymmetric "de novo" synthetic route to new aryl carbohydrate derivatives based on two sequential stereoselectively biocatalytic carboligation reactions is presented. First, the benzoin reaction of aromatic aldehydes to dimethoxyacetaldehyde is conducted, catalyzed by benzaldehyde lyase from Pseudomonas fluorescens biovar I. Then, the α-hydroxyketones formed are reduced by using NaBH4 yielding the anti diol. After acetal hydrolysis, the aldol addition of dihydroxyacetone, hydroxyacetone, or glycolaldehyde catalyzed by the stereocomplementary D-fructose-6-phosphate aldolase and L-rhamnulose-1-phosphate aldolase is performed. Both aldolases accept unphosphorylated donor substrates, avoiding the need of handling the phosphate group that the dihydroxyacetone phosphate-dependent aldolases require. In this way, 6-C-aryl-L-sorbose, 6-C-aryl-L-fructose, 6-C-aryl-L-tagatose, and 5-C-aryl-L-xylose derivatives are prepared by using this methodology.

  12. Nickel-Catalyzed Proton-Deuterium Exchange (HDX) Procedures for Glycosidic Linkage Analysis of Complex Carbohydrates.

    PubMed

    Price, Neil P J; Hartman, Trina M; Vermillion, Karl E

    2015-07-21

    The structural analysis of complex carbohydrates typically requires the assignment of three parameters: monosaccharide composition, the position of glycosidic linkages between monosaccharides, and the position and nature of noncarbohydrate substituents. The glycosidic linkage positions are often determined by permethylation analysis, but this can be complicated by high viscosity or poor solubility, resulting in under-methylation. This is a drawback because an under-methylated position may be misinterpreted as the erroneous site of a linkage or substituent. Here, we describe an alternative approach to linkage analysis that makes use of a nonreversible deuterium exchange of C-H protons on the carbohydrate backbone. The exchange reaction is conducted in deuterated water catalyzed by Raney nickel, and results in the selective exchange of C-H protons adjacent to free hydroxyl groups. Hence, the position of the residual C-H protons is indicative of the position of glycosidic linkages or other substituents and can be readily assigned by heteronuclear single quantum coherence-nuclear magnetic resonance (HSQC-NMR) or, following suitable derivatization, by gas chromatography-mass spectroscopy (GC/MS) analysis. Moreover, because the only changes to the parent sugar are proton/deuterium exchanges, the composition and linkage analysis can be determined in a single step. PMID:26075577

  13. Alcohol production from agricultural and forestry residues

    SciTech Connect

    Opilla, R.; Dale, L.; Surles, T.

    1980-05-01

    A variety of carbohydrate sources can be used as raw material for the production of ethanol. Section 1 is a review of technologies available for the production of ethanol from whole corn. Particular emphasis is placed on the environmental aspects of the process, including land utilization and possible air and water pollutants. Suggestions are made for technological changes intended to improve the economics of the process as well as to reduce some of the pollution from by-product disposal. Ethanol may be derived from renewable cellulosic substances by either enzymatic or acid hydrolysis of cellulose to sugar, followed by conventional fermentation and distillation. Section 2 is a review of the use of two agricultural residues - corn stover (field stalks remaining after harvest) and straw from wheat crops - as a cellulosic feedstock. Two processes have been evaluated with regard to environmental impact - a two-stage acid process developed by G.T. Tsao of Purdue University and an enzymatic process based on the laboratory findings of C.R. Wilke of the University of California, Berkeley. Section 3 deals with the environmental residuals expected from the manufacture of methyl and ethyl alcohols from woody biomass. The methanol is produced in a gasification process, whereas ethanol is produced by hydrolysis and fermentation processes similar to those used to derive ethanol from cellulosic materials.

  14. Modified carbohydrate-chitosan compounds, methods of making the same and methods of using the same

    DOEpatents

    Venditti, Richard A; Pawlak, Joel J; Salam, Abdus; El-Tahlawy, Khaled Fathy

    2015-03-10

    Compositions of matter are provided that include chitosan and a modified carbohydrate. The modified carbohydrate includes a carbohydrate component and a cross linking agent. The modified carbohydrate has increased carboxyl content as compared to an unmodified counterpart carbohydrate. A carboxyl group of the modified carbohydrate is covalently bonded with an amino group of chitosan. The compositions of matter provided herein may include cross linked starch citrate-chitosan and cross linked hemicellulose citrate-chitosan, including foams thereof. These compositions yield excellent absorbency and metal chelation properties. Methods of making cross linked modified carbohydrate-chitosan compounds are also provided.

  15. Residue chemistry guidelines.

    PubMed

    Olinger, C L; Schmitt, R D; Zager, E

    1993-01-01

    Residue chemistry guidelines are designed to determine what the potential residues in food are and how much may be present as a result of pesticide application, so that a tolerance level may be established. Some requirements are established to assist in the enforcement of tolerances by the USDA, FDA, and the states. I realize I have given you a quick overview of the residue chemistry requirements. There are many documents which are available if you should require more information, such as the Subdivision O Residue Chemistry Guidelines, Standard Evaluation Procedures (which are used by reviewers when evaluating the studies), the Data Reporting Guidelines (which provide guidance on preparing final reports), and the Technical Guidance from Phase III of Reregistration. We have also released various papers on studies when additional guidance is required. Most of these documents are available from NTIS. I hope you will consider this information when auditing residue chemistry studies. As I see the efforts that you, the QA professionals, have made to educate yourselves on residue chemistry studies through programs such as this meeting, I have a little more confidence in answering the question "Do you trust them?" with a "Yes." Thank you.

  16. The center for plant and microbial complex carbohydrates at The University of Georgia Complex Carbohydrate Research Center (CCRC)

    SciTech Connect

    Albersheim, P.; Darvill, A.

    1990-06-01

    The Complex Carbohydrate research Center (CCRC) has about 90 faculty, staff, postdoctoral research associates, and graduate students. The center grant funds are used to support training of graduate students, collaborative carbohydrate research projects with other institutions, service, and equipment maintenance. The subjects extend from oligosaccharides that protect plants against viruses to oligosaccharides that induce explants to flower, from receptors for oligosaccharides that elicit phytoalexins to oligosaccharides that regulate cation transport across plasma membranes, from the structures of pectic and hemicellulosic polysaccharides to the ability of pathogenesis-related enzymes to release phytoalexin elicitors from fungal cell walls, from the cloning of carbohydrate-degrading enzymes to the cloning of glycanase inhibitors, from the identification of oligosaccharides that kill plant cells to the cloning of receptors that perceive those oligosaccharides that inhibit root formation and stimulate flower formation, from characterization of bacterial polysaccharides that have useful physical characteristics to characterization of complex carbohydrates involved in Rhizobium symbioses, and from developing analytical methods to purify and characterize carbohydrates to the development of computer methods to reduce the need to structurally characterize carbohydrates. The CCRC's progress in collaborative research, training, and service is summarized in the appendices accompanying this report.

  17. How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria†

    PubMed Central

    Deutscher, Josef; Francke, Christof; Postma, Pieter W.

    2006-01-01

    The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens. PMID:17158705

  18. Identification of a carbohydrate recognition domain in filamentous hemagglutinin from Bordetella pertussis.

    PubMed Central

    Prasad, S M; Yin, Y; Rodzinski, E; Tuomanen, E I; Masure, H R

    1993-01-01

    The adherence of Bordetella pertussis to ciliated cells and macrophages is critical to colonization and infection of the respiratory tract. Adherence to both types of cells involves the recognition of eukaryotic carbohydrates by the bacterial adhesin filamentous hemagglutinin (Fha). The carbohydrate recognition domain (CRD) of Fha is considered an important antigen for subcomponent vaccines to maximize the generation of antiadherence antibodies capable of protecting against colonization. For identification of the CRD of Fha, a bank of eight monoclonal antibodies (MAbs) that mapped to four contiguous regions were tested for their ability to block Fha binding to lactosylceramide or to block bacterial binding to ciliated cells. Only MAb 12.5A9, which maps to amino acid residues 1141 to 1279, blocked both Fha binding to lactosylceramide and bacterial binding to ciliated cells. An 18-kDa polypeptide corresponding to this region was expressed in Escherichia coli. Cell lysates containing this protein bound to lactosylceramide in a manner identical to that of native Fha. Mutant strains of B. pertussis that contained an in-frame deletion of the coding sequence for this region produced a truncated Fha that showed negligible cross-reactivity with MAb 12.5A9. In an adherence assay, these mutant strains failed to bind efficiently to either ciliated cells or macrophages. The numbers of adherent bacteria for these strains were reduced to the number obtained with a nonadherent strain. We conclude that the region defined by residues 1141 to 1279 of Fha constitutes a CRD critical for bacterial adherence and represents a potential candidate for a subcomponent vaccine. Images PMID:8514379

  19. Synthesis, characterization and fluorescent properties of water-soluble glycopolymer bearing curcumin pendant residues.

    PubMed

    Zhang, Haisong; Yu, Meng; Zhang, Hailei; Bai, Libin; Wu, Yonggang; Wang, Sujuan; Ba, Xinwu

    2016-08-01

    Curcumin is a potential natural anticancer drug with low oral bioavailability because of poor water solubility. The aqueous solubility of curcumin is enhanced by means of modification with the carbohydrate units. Polymerization of the curcumin-containing monomer with carbohydrate-containing monomer gives the water-soluble glycopolymer bearing curcumin pendant residues. The obtained copolymers (P1 and P2) having desirable water solubility were well-characterized by infrared spectroscopy (IR), nuclear magnetic resonance (NMR), gel permeation chromatography (GPC), UV-Vis absorption spectroscopy, and photoluminescence spectroscopy. The copolymer P2 with a molar ratio of 1:6 (curcumin/carbohydrate) calculated from the proton NMR results exhibits a similar anticancer activity compared to original curcumin, which may serve as a potential chemotherapeutic agent in the field of anticancer medicine. PMID:27098211

  20. Final Technical Report - Commercially Important Carbohydrate Diacids - Building Blocks from Renewable Carbohydrates

    SciTech Connect

    Kiely, Donald E.

    2009-01-07

    The primary objective of this project was to develop oxidation methods appropriate for the conversion of agriculturally derived simple sugars to their corresponding diacids (aldaric acids) for use as biobased chemical building blocks for new biodegradable polymers and other materials. Principal target diacids were D-glucaric, meso-xylaric, D-mannaric and L-arabinaric acid, each to be prepared by nitric acid oxidation of the naturally occurring precursor carbohydrates (monosaccharides) D-glucose, D-xylose, D-mannose and L-arabinose, respectively, all from hydrolysis of naturally abundant plant polysaccharides. These conversions were to be designed for scale up to a level suitable for transfer first to a pilot plant scale, and then to an industrial plant scale. The core of the project involved a comprehensive study of the title oxidation employing a computer controlled reactor. The plan of action involved defining experimental parameters to allow for control of the oxidations with considerable precision and reproducibility. The prototype oxidations were typically run using ca. 0.75 molar amounts of carbohydrate, with a goal of eventually doubling the reaction size when appropriate reaction parameters were established. During the course of the funding period for this grant, the fundamentals of reaction control were established for oxidation of D-glucose, a critical component of the project given the exothermic character of the reaction. The reactions were monitored using a reliable GC/MS protocol. The glucose to glucaric acid conversion represented the most important and potentially highest value conversion. During the grant period we were able to establish one workable system to carry out the glucose to glucaric acid conversion, but were not able to optimize the process or establish a protocol that was satisfactory for a scale up to a pilot plant scale. However, the work carried out showed the possibility that with appropriate innovation and continued effort, a

  1. Baroreflex sensitivity in acute hypoxia and carbohydrate loading.

    PubMed

    Klemenc, Matjaž; Golja, Petra

    2011-10-01

    Hypoxia decreases baroreflex sensitivity (BRS) and can be a sufficient cause for syncope in healthy individuals. Carbohydrate loading enhances efferent sympathetic activity, which affects cardiac contractility, heart rate and vascular resistance, the main determinants of blood pressure. Thus, in both normoxia and hypoxia, carbohydrate loading may be more than simply metabolically beneficial, as it may affect blood pressure regulation. We hypothesised that carbohydrate loading will, in both normoxia and hypoxia, alter the regulation of blood pressure, as reflected in a change in baroreflex sensitivity. Fourteen subjects participated in two experiments, composed of a 15-min normoxic period, after which the subjects ingested water or an equal amount of water with carbohydrates. A 30-min rest period was then followed by a 10-min second normoxic and a 30-min hypoxic period. Blood pressure and heart rate were monitored continuously during the experiment to determine BRS. Despite an increased sympathetic activation, reflected in increased heart rate (P < 0.001) BRS was lower (P < 0.01) after carbohydrate loading, as compared to the water experiment, in both normoxic [23.7 (12.4) versus 28.8 (13.8) ms/mmHg] and hypoxic [16.8 (11.0) versus 24.3 (12.3) ms/mmHg] phases of the present study. As BRS was decreased in acute hypoxic exposure, the results confirm that hypoxia interferes with blood pressure regulation. However, although oral carbohydrate loading induced sympathoexcitation, it did not improve blood pressure regulation in hypoxia, as evident from the BRS data. Baroreflex effects of other forms of carbohydrate loading, not causing postprandial blood shifts to digestive system, should therefore be investigated. PMID:21360202

  2. Characterization of carbohydrates in rainwater from the southeastern North Carolina.

    PubMed

    Mullaugh, Katherine M; Byrd, Jade N; Avery, G Brooks; Mead, Ralph N; Willey, Joan D; Kieber, Robert J

    2014-07-01

    Carbohydrates have been widely reported in atmospheric aerosols, but have not previously been quantified in rainwater. We have identified and quantified a series of 11 specific compounds including monosaccharides (glucose, fructose, arabinose, galactose and pinitol), disaccharides (sucrose and trehalose), sugar alcohols (arabitol, dulcitol and mannitol) and the anhydrosaccharide levoglucosan. Rainwater analyzed in this study includes 52 distinct precipitation events in Wilmington, NC between June 2011 and October 2012. Our analysis indicates carbohydrates typically contribute <1% of total dissolved organic carbon in rain, but can account for as much as 10-35% during periods of high pollen or local fires. Concentrations of individual carbohydrates reached as high as 5.8 μM, with glucose and sucrose typically being the predominant species. The distribution of carbohydrates exhibited a distinct seasonal pattern, with higher concentrations of most carbohydrates, especially sucrose, in spring and summer, driven primarily by increased biogenic inputs during the growing season. Concentrations of carbohydrates were an order of magnitude higher in storms of terrestrial origin compared to marine events, further supporting a terrestrial biogenic origin of most species. Sequential sampling of Hurricane Irene showed significant quantities of carbohydrates present at the end of the storm when air mass back trajectories traversed over land. The highest level of levoglucosan, a compound associated with biomass burning, was detected in rain with an air mass back trajectory that traveled over a region affected by wildfires. When compared to aerosol concentrations reported by others, the sugar concentrations in rain demonstrate wet deposition is an important removal mechanism of this water-soluble and bioavailable fraction of atmospheric particulate organic matter.

  3. The changing roles of dietary carbohydrates: from simple to complex.

    PubMed

    Griel, Amy E; Ruder, Elizabeth H; Kris-Etherton, Penny M

    2006-09-01

    The dietary recommendations made for carbohydrate intake by many organizations/agencies have changed over time. Early recommendations were based on the need to ensure dietary sufficiency and focused on meeting micronutrient intake requirements. Because carbohydrate-containing foods are a rich source of micronutrients, starches, grains, fruits, and vegetables became the foundation of dietary guidance, including the base of the US Department of Agriculture's Food Guide Pyramid. Dietary sufficiency recommendations were followed by recommendations to reduce cholesterol levels and the risk for cardiovascular disease; reduction in total fat (and hence saturated fat) predominated. Beginning in the 1970s, carbohydrates were recommended as the preferred substitute for fat by the American Heart Association and others to achieve the recommended successive reductions in total fat and low-density lipoprotein cholesterol (LDL-C). Additional research on fats and fatty acids found that monounsaturated fatty acids could serve as an alternative substitution for saturated fats, providing equivalent lowering of LDL-C without concomitant reductions in high-density lipoprotein cholesterol and increases in triglycerides witnessed when carbohydrates replace saturated fat. This research led to a sharper focus in the guidelines in the 1990s toward restricting saturated fat and liberalizing a range of intake of total fat. Higher-fat diets, still low in saturated fatty acids, became alternative strategies to lower-fat diets. As the population has become increasingly overweight and obese, the emergence of the metabolic syndrome and its associated disruptions in glucose and lipid metabolism has led to reconsiderations of the role of carbohydrate-containing foods in the American diet. Consequently, a review of the evidence for and against high-carbohydrate diets is important to put this controversy into perspective. The current dietary recommendations for carbohydrate intake are supported by the

  4. Baroreflex sensitivity in acute hypoxia and carbohydrate loading.

    PubMed

    Klemenc, Matjaž; Golja, Petra

    2011-10-01

    Hypoxia decreases baroreflex sensitivity (BRS) and can be a sufficient cause for syncope in healthy individuals. Carbohydrate loading enhances efferent sympathetic activity, which affects cardiac contractility, heart rate and vascular resistance, the main determinants of blood pressure. Thus, in both normoxia and hypoxia, carbohydrate loading may be more than simply metabolically beneficial, as it may affect blood pressure regulation. We hypothesised that carbohydrate loading will, in both normoxia and hypoxia, alter the regulation of blood pressure, as reflected in a change in baroreflex sensitivity. Fourteen subjects participated in two experiments, composed of a 15-min normoxic period, after which the subjects ingested water or an equal amount of water with carbohydrates. A 30-min rest period was then followed by a 10-min second normoxic and a 30-min hypoxic period. Blood pressure and heart rate were monitored continuously during the experiment to determine BRS. Despite an increased sympathetic activation, reflected in increased heart rate (P < 0.001) BRS was lower (P < 0.01) after carbohydrate loading, as compared to the water experiment, in both normoxic [23.7 (12.4) versus 28.8 (13.8) ms/mmHg] and hypoxic [16.8 (11.0) versus 24.3 (12.3) ms/mmHg] phases of the present study. As BRS was decreased in acute hypoxic exposure, the results confirm that hypoxia interferes with blood pressure regulation. However, although oral carbohydrate loading induced sympathoexcitation, it did not improve blood pressure regulation in hypoxia, as evident from the BRS data. Baroreflex effects of other forms of carbohydrate loading, not causing postprandial blood shifts to digestive system, should therefore be investigated.

  5. Characterization of carbohydrates in rainwater from the southeastern North Carolina.

    PubMed

    Mullaugh, Katherine M; Byrd, Jade N; Avery, G Brooks; Mead, Ralph N; Willey, Joan D; Kieber, Robert J

    2014-07-01

    Carbohydrates have been widely reported in atmospheric aerosols, but have not previously been quantified in rainwater. We have identified and quantified a series of 11 specific compounds including monosaccharides (glucose, fructose, arabinose, galactose and pinitol), disaccharides (sucrose and trehalose), sugar alcohols (arabitol, dulcitol and mannitol) and the anhydrosaccharide levoglucosan. Rainwater analyzed in this study includes 52 distinct precipitation events in Wilmington, NC between June 2011 and October 2012. Our analysis indicates carbohydrates typically contribute <1% of total dissolved organic carbon in rain, but can account for as much as 10-35% during periods of high pollen or local fires. Concentrations of individual carbohydrates reached as high as 5.8 μM, with glucose and sucrose typically being the predominant species. The distribution of carbohydrates exhibited a distinct seasonal pattern, with higher concentrations of most carbohydrates, especially sucrose, in spring and summer, driven primarily by increased biogenic inputs during the growing season. Concentrations of carbohydrates were an order of magnitude higher in storms of terrestrial origin compared to marine events, further supporting a terrestrial biogenic origin of most species. Sequential sampling of Hurricane Irene showed significant quantities of carbohydrates present at the end of the storm when air mass back trajectories traversed over land. The highest level of levoglucosan, a compound associated with biomass burning, was detected in rain with an air mass back trajectory that traveled over a region affected by wildfires. When compared to aerosol concentrations reported by others, the sugar concentrations in rain demonstrate wet deposition is an important removal mechanism of this water-soluble and bioavailable fraction of atmospheric particulate organic matter. PMID:24875870

  6. MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein–ligand fragment interaction, pathways and SNPs

    PubMed Central

    Tanramluk, Duangrudee; Narupiyakul, Lalita; Akavipat, Ruj; Gong, Sungsam; Charoensawan, Varodom

    2016-01-01

    Protein–ligand interaction analysis is an important step of drug design and protein engineering in order to predict the binding affinity and selectivity between ligands to the target proteins. To date, there are more than 100 000 structures available in the Protein Data Bank (PDB), of which ∼30% are protein–ligand (MW below 1000 Da) complexes. We have developed the integrative web server MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) with the aim of providing a user-friendly web interface to assist structural study and design of protein–ligand interactions. In brief, the server allows the users to input the chemical fragments and present all the unique molecular interactions to the target proteins with available three-dimensional structures in the PDB. The users can also link the ligands of interest to assess possible off-target proteins, human variants and pathway information using our all-in-one integrated tools. Taken together, we envisage that the server will facilitate and improve the study of protein–ligand interactions by allowing observation and comparison of ligand interactions with multiple proteins at the same time. (http://manoraa.org). PMID:27131358

  7. Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism*

    PubMed Central

    Gregg, Katie J.; Suits, Michael D. L.; Deng, Lehua; Vocadlo, David J.; Boraston, Alisdair B.

    2015-01-01

    O-Linked glycosylation is one of the most abundant post-translational modifications of proteins. Within the secretory pathway of higher eukaryotes, the core of these glycans is frequently an N-acetylgalactosamine residue that is α-linked to serine or threonine residues. Glycoside hydrolases in family 101 are presently the only known enzymes to be able to hydrolyze this glycosidic linkage. Here we determine the high-resolution structures of the catalytic domain comprising a fragment of GH101 from Streptococcus pneumoniae TIGR4, SpGH101, in the absence of carbohydrate, and in complex with reaction products, inhibitor, and substrate analogues. Upon substrate binding, a tryptophan lid (residues 724-WNW-726) closes on the substrate. The closing of this lid fully engages the substrate in the active site with Asp-764 positioned directly beneath C1 of the sugar residue bound within the −1 subsite, consistent with its proposed role as the catalytic nucleophile. In all of the bound forms of the enzyme, however, the proposed catalytic acid/base residue was found to be too distant from the glycosidic oxygen (>4.3 Å) to serve directly as a general catalytic acid/base residue and thereby facilitate cleavage of the glycosidic bond. These same complexes, however, revealed a structurally conserved water molecule positioned between the catalytic acid/base and the glycosidic oxygen. On the basis of these structural observations we propose a new variation of the retaining glycoside hydrolase mechanism wherein the intervening water molecule enables a Grotthuss proton shuttle between Glu-796 and the glycosidic oxygen, permitting this residue to serve as the general acid/base catalytic residue. PMID:26304114

  8. Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism.

    PubMed

    Gregg, Katie J; Suits, Michael D L; Deng, Lehua; Vocadlo, David J; Boraston, Alisdair B

    2015-10-16

    O-Linked glycosylation is one of the most abundant post-translational modifications of proteins. Within the secretory pathway of higher eukaryotes, the core of these glycans is frequently an N-acetylgalactosamine residue that is α-linked to serine or threonine residues. Glycoside hydrolases in family 101 are presently the only known enzymes to be able to hydrolyze this glycosidic linkage. Here we determine the high-resolution structures of the catalytic domain comprising a fragment of GH101 from Streptococcus pneumoniae TIGR4, SpGH101, in the absence of carbohydrate, and in complex with reaction products, inhibitor, and substrate analogues. Upon substrate binding, a tryptophan lid (residues 724-WNW-726) closes on the substrate. The closing of this lid fully engages the substrate in the active site with Asp-764 positioned directly beneath C1 of the sugar residue bound within the -1 subsite, consistent with its proposed role as the catalytic nucleophile. In all of the bound forms of the enzyme, however, the proposed catalytic acid/base residue was found to be too distant from the glycosidic oxygen (>4.3 Å) to serve directly as a general catalytic acid/base residue and thereby facilitate cleavage of the glycosidic bond. These same complexes, however, revealed a structurally conserved water molecule positioned between the catalytic acid/base and the glycosidic oxygen. On the basis of these structural observations we propose a new variation of the retaining glycoside hydrolase mechanism wherein the intervening water molecule enables a Grotthuss proton shuttle between Glu-796 and the glycosidic oxygen, permitting this residue to serve as the general acid/base catalytic residue.

  9. Chromatographic profiles of nonstructural carbohydrates contributing to the colorimetrically determined fructan, ethanol-soluble, and water-soluble carbohydrate contents of five grasses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nonstructural carbohydrates in forages are often analyzed by colorimetric assays of water and ethanol extracts. Water-soluble carbohydrates (WSC) include polysaccharides (starch and fructan) and mono- and disaccharides. Ethanol-soluble carbohydrates (ESC) consist only of mono-, di- and oligosaccha...

  10. Predicting water-soluble carbohydrates and ethanol-soluble carbohydrates in cool-season grasses with near-infrared reflectance spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grazing animals may require a high or low total nonstructural carbohydrate diet for optimal health and production. Understanding how nonstructural carbohydrates fluctuate in Kentucky pastures and being able to quantify and monitor nonstructural carbohydrates in a timely manner will greatly aid in m...

  11. Selectivity switch in the catalytic functionalization of nonprotected carbohydrates: selective synthesis in the presence of anomeric and structurally similar carbohydrates under mild conditions.

    PubMed

    Muramatsu, Wataru; Takemoto, Yuki

    2013-03-15

    A catalytic process for the chemo- and regioselective functionalization of nonprotected carbohydrates has been developed. This novel process allows selective thiocarbonylation, acylation, and sulfonylation of a particular hydroxy group in a particular carbohydrate in the simultaneous presence of structurally similar carbohydrates such as anomers. In addition, the chemoselectivity can be switched by regulating only the length of the alkyl chain in the organotin catalyst.

  12. Characterisation of the carbohydrate fraction of the temporary adhesive secreted by the tube feet of the sea star Asterias rubens.

    PubMed

    Hennebert, Elise; Wattiez, Ruddy; Flammang, Patrick

    2011-06-01

    In sea stars, adhesion takes place at the level of a multitude of small appendages, the tube feet. It involves the secretion of an adhesive material which, after tube foot detachment, remains on the substratum as a footprint. It was previously reported that the two main organic components of this material are proteins and carbohydrates. The carbohydrate moiety of the adhesive secretion of Asterias rubens was investigated using a set of 16 lectins which were used on sections through tube feet, on footprints, and on the proteins extracted from these footprints. After gel electrophoresis, these proteins separate into eight protein bands which were named sea star footprint proteins (Sfps). Eleven lectins label the tube foot epidermis at the level of the adhesive cells, four react with footprints, and eight with two of the extracted footprint proteins, which are therefore classified as glycoproteins. Sfp-290 appears to bear mostly N-linked oligosaccharides and Sfp-210 principally O-linked oligosaccharides. The outer chains of both glycoproteins enclose galactose, N-acetylgalactosamine, fucose, and sialic acid residues. Another part of the carbohydrate fraction of the footprints would be in the form of larger molecules, such as sialylated proteoglycans. These two types of glycoconjugates are presumably key components of the sea star temporary adhesive providing both cohesive and adhesive contributions through electrostatic interactions by the polar and hydrogen-bonding functional groups of their glycan chains.

  13. Quantifying the Responses of Mixed Rumen Microbes to Excess Carbohydrate

    PubMed Central

    Hackmann, Timothy J.; Diese, Leanne E.

    2013-01-01

    The aim of this study was to determine if a mixed microbial community from the bovine rumen would respond to excess carbohydrate by accumulating reserve carbohydrate, energy spilling (dissipating excess ATP energy as heat), or both. Mixed microbes from the rumen were washed with N-free buffer and dosed with glucose. Total heat production was measured by calorimetry. Energy spilling was calculated as heat production not accounted by (i) endogenous metabolism (heat production before dosing glucose) and (ii) synthesis of reserve carbohydrate (heat from synthesis itself and reactions yielding ATP for it). For cells dosed with 5 mM glucose, synthesis of reserve carbohydrate and endogenous metabolism accounted for nearly all heat production (93.7%); no spilling was detected (P = 0.226). For cells dosed with 20 mM glucose, energy spilling was not detected immediately after dosing, but it became significant (P < 0.05) by approximately 30 min after dosing with glucose. Energy spilling accounted for as much as 38.7% of heat production in one incubation. Nearly all energy (97.9%) and carbon (99.9%) in glucose were recovered in reserve carbohydrate, fermentation acids, CO2, CH4, and heat. This full recovery indicates that products were measured completely and that spilling was not a methodological artifact. These results should aid future research aiming to mechanistically account for variation in energetic efficiency of mixed microbial communities. PMID:23584777

  14. Digestion kinetics of carbohydrate fractions of citrus by-products

    PubMed Central

    Lashkari, Saman; Taghizadeh, Akbar

    2015-01-01

    The present experiment was carried out to determine the digestion kinetics of carbohydrate fractions of citrus by-products. Grapefruit pulp (GP), lemon pulp (LE), lime pulp (LI) and orange pulp (OP) were the test feed. Digestion kinetic of whole citrus by-products and neutral detergent fiber (NDF) fraction and acid detergent fiber (ADF) fractions of citrus by-products were measured using the in vitro gas production technique. Fermentation kinetics of the neutral detergent soluble carbohydrates (NDSC) fraction and hemicelluloses were calculated using a curve subtraction. The fermentation rate of whole was the highest for the LE (p < 0.05). For all citrus by-products lag time was longer for hemicellulose than other carbohydrate fractions. There was no significant difference among potential gas production (A) volumes of whole test feeds (p < 0.16). Dry matter (DM) digestibility contents of LE and LI were the highest (p < 0.02). The NDF digestibility was the highest (p < 0.05) in LI and GP, while the lowest (p < 0.03) values of ADF digestibility were observed in LI and LE. According to the results of the present study, carbohydrate fractions of citrus by-products have high potential for degradability. It could also be concluded that carbohydrate fractions of citrus by-products have remarkable difference in digestion kinetics and digestive behavior. PMID:25992250

  15. Carbohydrate digestion in Lutzomyia longipalpis' larvae (Diptera - Psychodidae).

    PubMed

    Vale, Vladimir F; Moreira, Bruno H; Moraes, Caroline S; Pereira, Marcos H; Genta, Fernando A; Gontijo, Nelder F

    2012-10-01

    Lutzomyia longipalpis is the principal species of phlebotomine incriminated as vector of Leishmania infantum, the etiological agent of visceral leishmaniasis in the Americas. Despite its importance as vector, almost nothing related to the larval biology, especially about its digestive system has been published. The objective of the present study was to obtain an overview of carbohydrate digestion by the larvae. Taking in account that phlebotomine larvae live in the soil rich in decaying materials and microorganisms we searched principally for enzymes capable to hydrolyze carbohydrates present in this kind of substrate. The principal carbohydrases encountered in the midgut were partially characterized. One of them is a α-amylase present in the anterior midgut. It is probably involved with the digestion of glycogen, the reserve carbohydrate of fungi. Two other especially active enzymes were present in the posterior midgut, a membrane bound α-glucosidase and a membrane bound trehalase. The first, complete the digestion of glycogen and the other probably acts in the digestion of trehalose, a carbohydrate usually encountered in microorganisms undergoing hydric stress. In a screening done with the use of p-nitrophenyl-derived substrates other less active enzymes were also observed in the midgut. A general view of carbohydrate digestion in L. longipalpis was presented. Our results indicate that soil microorganisms appear to be the main source of nutrients for the larvae.

  16. Pharmaceutical, cosmeceutical, and traditional applications of marine carbohydrates.

    PubMed

    Ahmed, Abdul Bakrudeen Ali; Adel, Mohaddeseh; Karimi, Pegah; Peidayesh, Mahvash

    2014-01-01

    Marine carbohydrates are most important organic molecules made by photosynthetic organisms. It is very essential for humankind: the role in being an energy source for the organism and they are considered as an important dissolve organic compound (DOC) in marine environment's sediments. Carbohydrates found in different marine environments in different concentrations. Polysaccharides of carbohydrates play an important role in various fields such as pharmaceutical, food production, cosmeceutical, and so on. Marine organisms are good resources of nutrients, and they are rich carbohydrate in sulfated polysaccharide. Seaweeds (marine microalgae) are used in different pharmaceutical industries, especially in pharmaceutical compound production. Seaweeds have a significant amount of sulfated polysaccharides, which are used in cosmeceutical industry, besides based on the biological applications. Since then, traditional people, cosmetics products, and pharmaceutical applications consider many types of seaweed as an important organism used in food process. Sulfated polysaccharides containing seaweed have potential uses in the blood coagulation system, antiviral activity, antioxidant activity, anticancer activity, immunomodulating activity, antilipidepic activity, etc. Some species of marine organisms are rich in polysaccharides such as sulfated galactans. Various polysaccharides such as agar and alginates, which are extracted from marine organisms, have several applications in food production and cosmeceutical industries. Due to their high health benefits, compound-derived extracts of marine polysaccharides have various applications and traditional people were using them since long time ago. In the future, much attention is supposed to be paid to unraveling the structural, compositional, and sequential properties of marine carbohydrate as well. PMID:25300548

  17. Carbohydrate-Mimetic Peptides for Pan Anti-Tumor Responses

    PubMed Central

    Kieber-Emmons, Thomas; Saha, Somdutta; Pashov, Anastas; Monzavi-Karbassi, Behjatolah; Murali, Ramachandran

    2014-01-01

    Molecular mimicry is fundamental to biology and transcends to many disciplines ranging from immune pathology to drug design. Structural characterization of molecular partners has provided insight into the origins and relative importance of complementarity in mimicry. Chemical complementarity is easy to understand; amino acid sequence similarity between peptides, for example, can lead to cross-reactivity triggering similar reactivity from their cognate receptors. However, conformational complementarity is difficult to decipher. Molecular mimicry of carbohydrates by peptides is often considered one of those. Extensive studies of innate and adaptive immune responses suggests the existence of carbohydrate mimicry, but the structural basis for this mimicry yields confounding details; peptides mimicking carbohydrates in some cases fail to exhibit both chemical and conformational mimicry. Deconvolution of these two types of complementarity in mimicry and its relationship to biological function can nevertheless lead to new therapeutics. Here, we discuss our experience examining the immunological aspects and implications of carbohydrate–peptide mimicry. Emphasis is placed on the rationale, the lessons learned from the methodologies to identify mimics, a perspective on the limitations of structural analysis, the biological consequences of mimicking tumor-associated carbohydrate antigens, and the notion of reverse engineering to develop carbohydrate-mimetic peptides in vaccine design strategies to induce responses to glycan antigens expressed on cancer cells. PMID:25071769

  18. Interaction of carbohydrates with alcohol dehydrogenase: Effect on enzyme activity.

    PubMed

    Jadhav, Swati B; Bankar, Sandip B; Granström, Tom; Ojamo, Heikki; Singhal, Rekha S; Survase, Shrikant A

    2015-09-01

    Alcohol dehydrogenase was covalently conjugated with three different oxidized carbohydrates i.e., glucose, starch and pectin. All the carbohydrates inhibited the enzyme. The inhibition was studied with respect to the inhibition rate constant, involvement of thiol groups in the binding, and structural changes in the enzyme. The enzyme activity decreased to half of its original activity at the concentration of 2 mg/mL of pectin, 4 mg/mL of glucose and 10 mg/mL of starch within 10 min at pH 7. This study showed oxidized pectin to be a potent inhibitor of alcohol dehydrogenase followed by glucose and starch. Along with the aldehyde-amino group interaction, thiol groups were also involved in the binding between alcohol dehydrogenase and carbohydrates. The structural changes occurring on binding of alcohol dehydrogenase with oxidized carbohydrates was also confirmed by fluorescence spectrophotometry. Oxidized carbohydrates could thus be used as potential inhibitors of alcohol dehydrogenase.

  19. Convenient syntheses and transformations of 2-C-malonyl carbohydrates.

    PubMed

    Yin, Jian; Sommermann, Thomas; Linker, Torsten

    2007-01-01

    2-C-malonyl carbohydrates were synthesized in only few steps and high yields by radical additions of malonates to glycals. For the first time, the undesired formation of nitrates was completely suppressed with anhydrous cerium ammonium nitrate (CAN) as oxidizing agent. A coherent explanation for the high stereoselectivities of the additions to gluco-configured glycals was provided by variation of the substituents in the 3-position. We established steric effects for the face selectivity, and electronic effects strongly influence the reactivity of the double bonds. The scope and limitation of transition-metal-mediated radical reactions in the synthesis of 2-C-branched carbohydrates was thoroughly investigated. Thus, unsaturated disaccharides and benzyl-protected glycals were used as substrates for the first time. Finally, the 2-C-malonyl carbohydrates were transformed into various products by decarboxylation, saponification and reduction, which afforded interesting precursors for C-disaccharides. In this paper we describe the syntheses of more than 40 new 2-C-analogues of carbohydrates, which were isolated in high yields in analytically pure form. Therefore, the transition-metal-mediated radical addition of malonates to glycals offers a simple and convenient entry to such important carbohydrate derivatives.

  20. Pharmaceutical, cosmeceutical, and traditional applications of marine carbohydrates.

    PubMed

    Ahmed, Abdul Bakrudeen Ali; Adel, Mohaddeseh; Karimi, Pegah; Peidayesh, Mahvash

    2014-01-01

    Marine carbohydrates are most important organic molecules made by photosynthetic organisms. It is very essential for humankind: the role in being an energy source for the organism and they are considered as an important dissolve organic compound (DOC) in marine environment's sediments. Carbohydrates found in different marine environments in different concentrations. Polysaccharides of carbohydrates play an important role in various fields such as pharmaceutical, food production, cosmeceutical, and so on. Marine organisms are good resources of nutrients, and they are rich carbohydrate in sulfated polysaccharide. Seaweeds (marine microalgae) are used in different pharmaceutical industries, especially in pharmaceutical compound production. Seaweeds have a significant amount of sulfated polysaccharides, which are used in cosmeceutical industry, besides based on the biological applications. Since then, traditional people, cosmetics products, and pharmaceutical applications consider many types of seaweed as an important organism used in food process. Sulfated polysaccharides containing seaweed have potential uses in the blood coagulation system, antiviral activity, antioxidant activity, anticancer activity, immunomodulating activity, antilipidepic activity, etc. Some species of marine organisms are rich in polysaccharides such as sulfated galactans. Various polysaccharides such as agar and alginates, which are extracted from marine organisms, have several applications in food production and cosmeceutical industries. Due to their high health benefits, compound-derived extracts of marine polysaccharides have various applications and traditional people were using them since long time ago. In the future, much attention is supposed to be paid to unraveling the structural, compositional, and sequential properties of marine carbohydrate as well.

  1. The statolith compartment in Chara rhizoids contains carbohydrate and protein

    NASA Technical Reports Server (NTRS)

    Wang-Cahill, F.; Kiss, J. Z.

    1995-01-01

    In contrast to higher plants, the alga Chara has rhizoids with single membrane-bound compartments that function as statoliths in gravity perception. Previous work has demonstrated that these statoliths contain barium sulfate crystals. In this study, we show that statoliths in Chara rhizoids react with a Coomassie Brilliant Blue cytochemical stain for proteins. While statoliths did not react with silver methenamine carbohydrate cytochemistry, the monoclonal antibody CCRC-M2, which is against a carbohydrate (sycamore-maple rhamnogalacturonan I), labeled the statolith compartment. These results demonstrate that in addition to barium sulfate, statoliths in Chara rhizoids have an organic matrix that consists of protein and carbohydrate moieties. Since the statoliths were silver methenamine negative, the carbohydrate in this compartment could be a 3-linked polysaccharide. CCRC-M2 also labeled Golgi cisternae, Golgi-associated vesicles, apical vesicles, and cell walls in the rhizoids. The specificity of CCRC-M2 immunolabeling was verified by several control experiments, including the demonstration that labeling was abolished when the antibody was preabsorbed with its antigen. Since in this and a previous study (John Z. Kiss and L. Andrew Staehelin, American Journal of Botany 80: 273-282, 1993) antibodies against higher plant carbohydrates crossreacted with cell walls of Chara in a specific manner, Characean algae may be a useful model system in biochemical and molecular studies of cell walls.

  2. Carbohydrate regulation in relation to colony growth in ants.

    PubMed

    Dussutour, A; Simpson, S J

    2008-07-01

    Ants and all social insects are faced with a nutritional challenge: the food entering the colony is brought by only a small number of its workers but is shared among all members of the colony. In this study, we investigated how ants maintain carbohydrates supply at both a collective and an individual level in response to changes in the concentration of available sucrose solution, colony demography and larval growth. We manipulated the concentration of sugar solutions available to ant colonies (dilute, medium and concentrated solutions) over extended periods and measured the capacity of colonies to maintain sugar supply through compensatory feeding. First, we demonstrated that ants regulated carbohydrate intake at a collective and individual level. Initially, ants consumed most and recruited fastest in response to more concentrated than to dilute sugar solutions, but over time this pattern reversed, such that the number of ants that fed and the volume ingested by each ant was a negative function of sugar concentration in the diet. Second, we found that ants became better at regulating their carbohydrate intake with the production of larvae in the nest. When the number of larvae was experimentally doubled, the ants regulated their consumption of carbohydrates more accurately than when the number of adult workers was doubled, suggesting that larvae play an important role in providing nutritional feedback to workers. Finally, we showed that ants defended a carbohydrate ;intake target' by allowing them to select among sugar solutions of different concentration.

  3. Digestion of carbohydrates and utilization of energy in sows fed diets with contrasting levels and physicochemical properties of dietary fiber.

    PubMed

    Serena, A; Jørgensen, H; Bach Knudsen, K E

    2008-09-01

    Three experimental diets were used to investigate the digestion of carbohydrates and utilization of energy in sows fed diets with different levels and physicochemical properties of dietary fiber (DF). The low-fiber diet (LF; DF, 16%; soluble DF, 4.8%) was based on wheat and barley. The high-fiber 1 diet (HF1; DF, 41%; soluble DF, 11%) was based on wheat and barley supplemented with the coproducts: sugar beet pulp, potato pulp, and pectin residue, and the high-fiber 2 diet (HF2; DF, 44%; soluble DF, 7.3%) was based on wheat and barley supplemented with approximately 1/3 of the coproducts used in diet HF1 and 2/3 of brewers spent grain, seed residue, and pea hull (1:1:1, respectively). The diets were studied in 2 series of experiments. In Exp. 1, the digestibility and ileal and fecal flow of nutrients were studied in 6 ileal-cannulated sows placed in metabolic cages designed as a repeated 3 x 3 Latin square design. In Exp. 2, energy metabolism was measured in respiration chambers using 6 sows in a repeated 3 x 3 Latin square design. The DF level influenced the ileal flow of most nutrients, in particular carbohydrates, which increased from 190 g/d when feeding the LF diet to 538 to 539 g/d when feeding the HF diets; this was also reflected in the digestibility of OM and carbohydrates (P < 0.05). The ranking of total excretion of fecal materials was HF2 > > HF1 > LF, which also was reflected in the digestibility of OM, protein, and carbohydrates. Feeding HF diets resulted in greater CH(4) production, which was related to the amount of carbohydrates (r = 0.79) and OM (r = 0.72) fermented in the large intestine, but with no difference in heat production (12.2 to 13.1 MJ/kg of DM). Retained energy (MJ/kg of DM) was decreased when feeding HF1 compared with LF and negative when feeding HF2. Feeding sows HF1 reduced the activity of animals (5.1 h/24 h) compared with LF (6.1 h/24 h; P = 0.045).

  4. Comparison of fungal carbohydrate esterases of family CE16 on artificial and natural substrates.

    PubMed

    Puchart, Vladimír; Agger, Jane W; Berrin, Jean-Guy; Várnai, Anikó; Westereng, Bjørge; Biely, Peter

    2016-09-10

    The enzymatic conversion of acetylated hardwood glucuronoxylan to functional food oligomers, biochemicals or fermentable monomers requires besides glycoside hydrolases enzymes liberating acetic acid esterifying position 2 and/or 3 in xylopyranosyl (Xylp) residues. The 3-O-acetyl group at internal Xylp residues substituted by MeGlcA is the only acetyl group of hardwood acetylglucuronoxylan and its fragments not attacked by acetylxylan esterases of carbohydrate esterase (CE) families 1, 4, 5 and 6 and by hemicellulolytic acetyl esterases classified in CE family 16. Monoacetylated aldotetraouronic acid 3″-Ac(3)MeGlcA(3)Xyl3, generated from the polysaccharide by GH10 endoxylanases, appears to be one of the most resistant fragments. The presence of the two substituents on the non-reducing-end Xylp residue prevents liberation of MeGlcA by α-glucuronidase of family GH67 and blocks the action of acetylxylan esterases. The Ac(3)MeGlcA(3)Xyl3 was isolated from an enzymatic hydrolysate of birchwood acetylglucuronoxylan and characterized by (1)H NMR spectroscopy as a mixture of two positional isomers, 3″-Ac(3)MeGlcA(3)Xyl3 and 4″-Ac(3)MeGlcA(3)Xyl3, the latter being the result of acetyl group migration. The mixture was used as a substrate for three members of CE16 family of fungal origin. Trichoderma reesei CE16 esterase, inactive on polymeric substrate, deacetylated both isomers. Podospora anserina and Aspergillus niger esterases, active on acetylglucuronoxylan, deesterified effectively only the 4″-isomer. The results indicate catalytic diversity among CE16 enzymes, but also their common and unifying catalytic ability to exo-deacetylate positions 3 and 4 on non-reducing-end Xylp residues, which is an important step in plant hemicellulose saccharification. PMID:27439201

  5. A peptide inhibitor of HIV-1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120

    PubMed Central

    Menendez, Alfredo; Calarese, Daniel A.; Stanfield, Robyn L.; Chow, Keith C.; Scanlan, Chris N.; Kunert, Renate; Katinger, Herman; Burton, Dennis R.; Wilson, Ian A.; Scott, Jamie K.

    2008-01-01

    MAb 2G12 neutralizes HIV-1 by binding with high affinity to a cluster of high-mannose oligosaccharides on the envelope glycoprotein, gp120. Screening of phage-displayed peptide libraries with 2G12 identified peptides that bind specifically, with Kds ranging from 0.4 to 200 μM. The crystal structure of a 21-mer peptide ligand in complex with 2G12 Fab was determined at 2.8 Å resolution. Comparison of this structure with previous structures of 2G12-carbohydrate complexes revealed striking differences in the mechanism of 2G12 binding to peptide vs. carbohydrate. The peptide occupies a site different from, but adjacent to, the primary carbohydrate-binding site on 2G12, and makes only slightly fewer contacts to the Fab than Man9GlcNAc2 (51 vs. 56, respectively). However, only two antibody contacts with the peptide are hydrogen bonds in contrast to six with Man9GlcNAc2, and only three of the antibody residues that interact with Man9GlcNAc2 also contact the peptide. Thus, this mechanism of peptide binding to 2G12 does not support structural mimicry of the native carbohydrate epitope on gp120, since it neither replicates the oligosaccharide footprint on the antibody nor most of the contact residues. Moreover, 2G12.1 peptide is not an immunogenic mimic of the 2G12 epitope, since antisera produced against it did not bind gp120.—Menendez, A., Calarese, D. A., Stanfield, R. L., Chow, K. C., Scanlan, C. N., Kunert, R., Katinger, H., Burton, D. R., Wilson, I. A., Scott, J. K. A peptide inhibitor of HIV-1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120. PMID:18198210

  6. Targeting a cluster of arginine residues of neuraminidase to avoid oseltamivir resistance in influenza A (H1N1): a theoretical study.

    PubMed

    Gema, L Ramírez-Salinas; Tolentino-Lopez, L E; Martínez-Ramos, F; Padilla-Martínez, I; García-Machorro, J; Correa-Basurto, J

    2015-01-01

    Following the influenza A (H1N1) pandemic in Mexico and around the world in 2009, the numbers of oseltamivir-resistant clinical cases have increased through a mechanism that remains unclear. In this work, we focus on studying the mutated NA structures ADA71175 (GenBank) and 3CKZ (PDB ID). Recently crystallized NA (PDB ID: 3NSS) was used as a wild-type structure and template to construct the three-dimensional (3D) structure of ADA71175. Then, the NA mutants and 3NSS natives as well as their refined monomer structures as determined through MD simulations (snapshots at 50 ns) were used as models to perform a docking study using a set of aryl-oseltamivir derivatives. These aryl-oseltamivir derivatives have better recognition properties than oseltamivir because of cation-π interactions with a cluster of Arg residues (118, 292, and 371) at the binding site. This cluster of Arg residues represents a potential binding site for aryl-oseltamivir derivatives that are potentially new NA inhibitors.

  7. DFT Solvation Studies of Carbohydrates: Solvation effects in alpha-linked carbohydrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the current paper we address the effect of solvation on the landscape of alpha-linked glucose residues. The solvent is introduced via the implicit solvation models COSMO and PCM. Geometry optimizations, at the B3LYP/6-311++G** level of theory with and without implicit solvation were carried out...

  8. Thermodynamics of binding of the core trimannoside of asparagine-linked carbohydrates and deoxy analogs to Dioclea grandiflora lectin.

    PubMed

    Dam, T K; Oscarson, S; Brewer, C F

    1998-12-01

    The Man/Glc-specific seed lectin from Dioclea grandiflora (DGL) is a member of the Diocleinae subtribe that includes the jack bean lectin concanavalin A (ConA). Both DGL and ConA bind with high affinity to the "core" trimannoside moiety, 3, 6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside, which is present in asparagine-linked carbohydrates. Recent hemagglutination inhibition studies suggest that DGL and ConA recognize similar epitopes of the trisaccharide but possess different binding specificities for complex carbohydrates (Gupta, D., Oscarson, S., Raju, T. S., Stanley, P., Toone, E. J., and Brewer, C. F. (1996) Eur. J. Biochem. 242, 320-326). In the present study, we have used isothermal titration microcalorimetry to determine the thermodynamics of binding of DGL to a complete set of monodeoxy analogs of the core trimannoside as well as a tetradeoxy analog. The thermodynamic data indicate that DGL recognizes the 2-, 3-, 4-, and 6-hydroxyl groups of the alpha(1,6) Man residue, the 3- and 4-hydroxyl group of the alpha(1, 3) Man residue, and the 2- and 4-hydroxyl groups of the central Man residue of the trimannoside. The thermodynamic data for the tetradeoxy analog lacking the 3- and 4-hydroxyl group of the alpha(1, 3) Man residue, and the 2- and 4-hydroxyl groups of the central Man residue of the trimannoside are consistent with the involvement of these hydroxyl groups in binding. While the overall pattern of data for DGL binding to the deoxy analogs is similar to that for ConA (Gupta, D., Dam, T. K., Oscarson, S., and Brewer, C. F. (1997) J. Biol. Chem. 272, 6388-6392), differences exist in the data for certain monodeoxy analogs binding to the two lectins. Differences are also observed in the thermodynamics of binding of DGL and ConA to a biantennary complex carbohydrate. In the following paper (Rozwarski, D. A., Swami, B. M., Brewer, C. F., and Sacchettini, J. C. (1998) J. Biol. Chem. 273, 32818-32825), the x-ray crystal structure of DGL complexed to the

  9. Effects of in ovo injection of carbohydrates on somatic characteristics and liver nutrient profiles of broiler embryos and hatchlings.

    PubMed

    Zhai, W; Bennett, L W; Gerard, P D; Pulikanti, R; Peebles, E D

    2011-12-01

    Effects of the in ovo injection of commercial diluent supplemented with dextrin or with dextrin in combination with various other carbohydrates on the somatic characteristics and liver nutrient profiles of Ross × Ross 708 broiler embryos and chicks were investigated. Results include information concerning the gluconeogenic energy status of the liver before and after hatch. Eggs containing live embryos were injected in the amnion on d 18 of incubation using an automated multiple-egg injector for the delivery of the following carbohydrates dissolved in 0.4 mL of commercial diluent: 1) 6.25% glucose and 18.75% dextrin; 2) 6.25% sucrose and 18.75% dextrin; 3) 6.25% maltose and 18.75% dextrin; and 4) 25% dextrin. Also, a noninjected control and a 0.4-mL diluent-injected control were included. Body weight relative to set egg weight on d 19 of incubation (E19) was increased by the injection of all carbohydrate solutions, and on the day of hatch was increased by the injection of diluent, sucrose and dextrin, and maltose and dextrin solutions. Hatchability of the fertilized eggs, residual yolk sac weight, and liver weight were not affected by any injection treatment; however, as compared with the 0.4 mL diluent-injected group, all of the supplementary carbohydrates, except for the glucose and dextrin combination group, increased liver glycogen and glucose concentrations on E19. Furthermore, all carbohydrates, except for the 25% dextrin treatment, decreased liver fat concentration on E19. From E19 to the day of hatch, liver glycogen concentrations dropped dramatically from an average of 3.2 to 0.6%. Despite treatment differences observed on E19 for liver glycogen, glucose, and fat concentrations, these differences were lost by the day of hatch. Nevertheless, liver glycogen and glucose concentrations were positively correlated on the day of hatch. In conclusion, the in ovo injection of various supplemental carbohydrates dissolved in 0.4 mL of commercial diluent altered the

  10. Fructose-maltodextrin ratio in a carbohydrate-electrolyte solution differentially affects exogenous carbohydrate oxidation rate, gut comfort, and performance.

    PubMed

    O'Brien, Wendy J; Rowlands, David S

    2011-01-01

    Solutions containing multiple carbohydrates utilizing different intestinal transporters (glucose and fructose) show enhanced absorption, oxidation, and performance compared with single-carbohydrate solutions, but the impact of the ratio of these carbohydrates on outcomes is unknown. In a randomized double-blind crossover, 10 cyclists rode 150 min at 50% peak power, then performed an incremental test to exhaustion, while ingesting artificially sweetened water or one of three carbohydrate-salt solutions comprising fructose and maltodextrin in the respective following concentrations: 4.5 and 9% (0.5-Ratio), 6 and 7.5% (0.8-Ratio), and 7.5 and 6% (1.25-Ratio). The carbohydrates were ingested at 1.8 g/min and naturally (13)C-enriched to permit evaluation of oxidation rate by mass spectrometry and indirect calorimetry. Mean exogenous carbohydrate oxidation rates were 1.04, 1.14, and 1.05 g/min (coefficient of variation 20%) in 0.5-, 0.8-, and 1.25-Ratios, respectively, representing likely small increases in 0.8-Ratio of 11% (90% confidence limits; ± 4%) and 10% (± 4%) relative to 0.5- and 1.25-Ratios, respectively. Comparisons of fat and total and endogenous carbohydrate oxidation rates between solutions were unclear. Relative to 0.5-Ratio, there were moderate improvements to peak power with 0.8- (3.6%; 99% confidence limits ± 3.5%) and 1.25-Ratio (3.0%; ± 3.7%) but unclear with water (0.4%; ± 4.4%). Increases in stomach fullness, abdominal cramping, and nausea were lowest with the 0.8- followed by the 1.25-Ratio solution. At high carbohydrate-ingestion rate, greater benefits to endurance performance may result from ingestion of 0.8- to 1.25-Ratio fructose-maltodextrin solutions. Small perceptible improvements in gut comfort favor the 0.8-Ratio and provide a clearer suggestion of mechanism than the relationship with exogenous carbohydrate oxidation.

  11. Microbial degradation of complex carbohydrates in the gut

    PubMed Central

    Flint, Harry J.; Scott, Karen P.; Duncan, Sylvia H.; Louis, Petra; Forano, Evelyne

    2012-01-01

    Bacteria that colonize the mammalian intestine collectively possess a far larger repertoire of degradative enzymes and metabolic capabilities than their hosts. Microbial fermentation of complex non-digestible dietary carbohydrates and host–derived glycans in the human intestine has important consequences for health. Certain dominant species, notably among the Bacteroidetes, are known to possess very large numbers of genes that encode carbohydrate active enzymes and can switch readily between different energy sources in the gut depending on availability. Nevertheless, more nutritionally specialized bacteria appear to play critical roles in the community by initiating the degradation of complex substrates such as plant cell walls, starch particles and mucin. Examples are emerging from the Firmicutes, Actinobacteria and Verrucomicrobium phyla, but more information is needed on these little studied groups. The impact of dietary carbohydrates, including prebiotics, on human health requires understanding of the complex relationship between diet composition, the gut microbiota and metabolic outputs. PMID:22572875

  12. Carbohydrate changes during growth and fruiting in Pleurotus ostreatus.

    PubMed

    Zhou, Shuai; Ma, Fuying; Zhang, Xiaoyu; Zhang, Jingsong

    2016-01-01

    The carbohydrate distribution in mushrooms is reported changing greatly in its different regions during growth and fruiting. In this study, the carbohydrate distribution in the compost and fruiting bodies of Pleurotus ostreatus was analysed. Sugar, polyol, polysaccharide, and chitin content during different growth phases and in different regions of the mushroom were determined. Results indicate that trehalose, mannitol, and glucose were first accumulated in the compost and then decreased during differentiation and growth of fruiting bodies. Meanwhile, trehalose, mannitol, and glucose also accumulated in the fruiting bodies and primarily distributed in the stipe, base, and pileus region, respectively. Polysaccharides mainly accumulated within the pileus and stipe regions, and chitin was mainly observed in the base region. These findings provide insights into carbohydrate function and utilisation during mushroom growth. PMID:27268245

  13. Platform Synthetic Lectins for Divalent Carbohydrate Recognition in Water

    PubMed Central

    Carter, Tom S.; Mooibroek, Tiddo J.; Stewart, Patrick F. N.; Crump, Matthew P.; Galan, M. Carmen

    2016-01-01

    Abstract Biomimetic carbohydrate receptors (“synthetic lectins”) have potential as agents for biological research and medicine. However, although effective strategies are available for “all‐equatorial” carbohydrates (glucose, etc.), the recognition of other types of saccharide under natural (aqueous) conditions is less well developed. Herein we report a new approach based on a pyrene platform with polar arches extending from aryl substituents. The receptors are compatible with axially substituted carbohydrates, and also feature two identical binding sites, thus mimicking the multivalency observed for natural lectins. A variant with negative charges forms 1:2 host/guest complexes with aminosugars, with K 1>3000 m −1 for axially substituted mannosamine, whereas a positively charged version binds the important α‐sialyl unit with K 1≈1300 m −1. PMID:27312071

  14. Carbohydrate mimetics and scaffolds: sweet spots in medicinal chemistry.

    PubMed

    Cipolla, Laura; La Ferla, Barbara; Airoldi, Cristina; Zona, Cristiano; Orsato, Alexandre; Shaikh, Nasrin; Russo, Laura; Nicotra, Francesco

    2010-04-01

    Several glycoprocessing enzymes and glycoreceptors have been recognized as important targets for therapeutic intervention. This concept has inspired the development of important classes of therapeutics, such as anti-influenza drugs inhibiting influenza virus neuraminidase, anti-inflammatory drugs targeting lectin-sialyl-Lewis X interaction and glycosidase inhibitors against HIV, Gaucher's disease, hepatitis and cancer. These therapeutics are mainly carbohydrate mimics in which proper modifications permit stronger interactions with the target protein, higher stability, better pharmacokinetic properties and easier synthesis. Furthermore, the conformational rigidity and polyfunctionality of carbohydrates stimulate their use as scaffolds for the generation of libraries by combinatorial decoration with different pharmacophores. This mini-review will present examples of how to exploit carbohydrates mimics and scaffolds in drug research. PMID:21426009

  15. Separation of carbohydrates using hydrophilic interaction liquid chromatography.

    PubMed

    Fu, Qing; Liang, Tu; Li, Zhenyu; Xu, Xiaoyong; Ke, Yanxiong; Jin, Yu; Liang, Xinmiao

    2013-09-20

    A strategy was developed to rapidly evaluate chromatographic properties of hydrophilic interaction chromatography (HILIC) columns for separating carbohydrates. Seven HILIC columns (Silica, Diol, TSK Amide-80, XAmide, Click Maltose, Click β-CD, and Click TE-Cys columns) were evaluated by using three monosaccharide and seven disaccharides as probes. The influence of column temperature on the peak shape and tautomerization of carbohydrates, as well as column selectivity were investigated. The influence of surface charge property on the retention was also studied by using glucose, glucuronic acid, and glucosamine, which indicated that buffer salt concentration and pH value in mobile phase was necessary to control the ionic interactions between ionic carbohydrates and HILIC columns. According to evaluation results, the XAmide column was selected as an example to establish experimental schemes for separation of complex mixtures of oligosaccharide.

  16. Effects of dietary carbohydrates on mutacin production and activity.

    PubMed

    Morency, H; Lavoie, M C

    1991-01-01

    Although mutacins (bacteriocins produced by Streptococcus mutans) were shown to be active in vivo, their ecological role in the oral cavity is still controversial. In the present paper, the effect of dietary carbohydrates, one of the ecological parameters which influences oral bacterial populations, on the activity and the production of mutacins from four S. mutans strains (C67-1, Ny257, Ny266 and T8) is described. Results obtained by the deferred antagonism test in solid media and by the mixed cultivation of the mutacinogenic strains with a sensitive indicator strain in liquid batch cultures, indicate that a minimal fermentable sugar concentration is needed for mutacin production. Among all the fermentable carbohydrates tested (fructose, glucose, lactose, mannitol and sucrose), none significantly affected the production and the activity of the four mutacinogenic strains used, in concentrations up to 5%. Although the results do not discount the possibility of mutacin inactivation in vivo, they indicate that they are not affected by dietary carbohydrates.

  17. Effect of Carbohydrate Ingestion on Sprint Performance Following Continuous Exercise

    NASA Astrophysics Data System (ADS)

    Siahkohian, M.; Farhadi, H.; Naghizadeh Baghi, A.; Valizadeh, A.

    The purpose of this study was to determine the effect of 5% carbohydrate ingestion on the sprint performance immediately following 90 min of running at 70-80% of maximal heart rate reserve. Thirty young active men were selected as subjects and allocated randomly to two carbohydrate (CHO, N = 15) and placebo (PL, N = 15) groups. Pre-test 200 m dash, 90 min running and post-test 200 m dash took place, respectively. Exercise heart rate monitored during 90 min running by a cardio frequency meter. Significant differences were found between the CHO and PL post-test 200 m dash records (p<0.05). Blood glucose was found to be significantly higher at the end of the 90 min running for the CHO group than for the PL group (p<0.01). The results suggest that carbohydrate ingestion during endurance exercise inhibits failing of Sprint performance of young active men.

  18. Preparation of water-soluble glycoconjugated poly(acrylamide) for NMR analyses of carbohydrate-carbohydrate interactions

    NASA Astrophysics Data System (ADS)

    Xuan, Trinh Anh; Trung, Phan Nghia; Dinh, Bui Long; Yamaguchi, Takumi; Kato, Koichi

    2014-05-01

    Oligosaccharide chains of glycoconjugates are important biopolymers not only as carriers of information in cell-cell interactions but also as markers of cellular differentiation, aging, and malignant alteration. Molecular interactions where carbohydrates are involved are usually considered as weak interactions, so the study and evaluation of these interactions is still in its infancy. The evidences and studies of carbohydrate-carbohydrate interactions (CCI) will be confirming the importance of this mechanism for specific cell adhesion and communication. Their development will go hand in hand with the development of new and more sensitive techniques to study weak interactions. Recently, synthetic glycopolymers with functions similar to those of such natural carbohydrates and with specific pendant saccharide moieties were used as a solution for enhancement CCI when forming polyvalent interactions. Carbohydrates are ubiquitous components of cell wall membranes and occur as glycolipids, glycoproteins, proteoglycans, and capsular polysaccharides. As such they can participate in forefront intramolecular and intracellular events. Apart from their recognized roles in the physicochemical properties of glycolipids and glycoproteins. In this study, we designed trisaccharide monomers for free radical polymerization. Subsequently, the trisaccharide unit for chemical conjugation was synthesized from galactosamine in good yield. For further NMR analyses of CCI, glycopolymers composed of these sugar derivatives will be provided.

  19. Microalgal carbohydrates: an overview of the factors influencing carbohydrates production, and of main bioconversion technologies for production of biofuels.

    PubMed

    Markou, Giorgos; Angelidaki, Irini; Georgakakis, Dimitris

    2012-11-01

    Microalgal biomass seems to be a promising feedstock for biofuel generation. Microalgae have relative high photosynthetic efficiencies, high growth rates, and some species can thrive in brackish water or seawater and wastewater from the food- and agro-industrial sector. Today, the main interest in research is the cultivation of microalgae for lipids production to generate biodiesel. However, there are several other biological or thermochemical conversion technologies, in which microalgal biomass could be used as substrate. However, the high protein content or the low carbohydrate content of the majority of the microalgal species might be a constraint for their possible use in these technologies. Moreover, in the majority of biomass conversion technologies, carbohydrates are the main substrate for production of biofuels. Nevertheless, microalgae biomass composition could be manipulated by several cultivation techniques, such as nutrient starvation or other stressed environmental conditions, which cause the microalgae to accumulate carbohydrates. This paper attempts to give a general overview of techniques that can be used for increasing the microalgal biomass carbohydrate content. In addition, biomass conversion technologies, related to the conversion of carbohydrates into biofuels are discussed.

  20. DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry.

    PubMed

    Chen, Yao Chi; Wright, Jon D; Lim, Carmay

    2012-07-01

    DR_bind is a web server that automatically predicts DNA-binding residues, given the respective protein structure based on (i) electrostatics, (ii) evolution and (iii) geometry. In contrast to machine-learning methods, DR_bind does not require a training data set or any parameters. It predicts DNA-binding residues by detecting a cluster of conserved, solvent-accessible residues that are electrostatically stabilized upon mutation to Asp(-)/Glu(-). The server requires as input the DNA-binding protein structure in PDB format and outputs a downloadable text file of the predicted DNA-binding residues, a 3D visualization of the predicted residues highlighted in the given protein structure, and a downloadable PyMol script for visualization of the results. Calibration on 83 and 55 non-redundant DNA-bound and DNA-free protein structures yielded a DNA-binding residue prediction accuracy/precision of 90/47% and 88/42%, respectively. Since DR_bind does not require any training using protein-DNA complex structures, it may predict DNA-binding residues in novel structures of DNA-binding proteins resulting from structural genomics projects with no conservation data. The DR_bind server is freely available with no login requirement at http://dnasite.limlab.ibms.sinica.edu.tw.

  1. Leguminous lectins as tools for studying the role of sugar residues in leukocyte recruitment.

    PubMed Central

    Alencar, N M; Teixeira, E H; Assreuy, A M; Cavada, B S; Flores, C A; Ribeiro, R A

    1999-01-01

    The natural physiological ligands for selectins are oligosaccharides found in glycoprotein or glycolipid molecules in cell membranes. In order to study the role of sugar residues in the in vivo lectin anti-inflammatory effect, we tested three leguminous lectins with different carbohydrate binding affinities in the peritonitis and paw oedema models induced by carrageenin in rats. L. sericeus lectin was more anti-inflammatory than D. virgata lectin, the effects being reversed by their specific binding sugars (N-acetylglucosamine and alpha-methylmannoside, respectively). However, V. macrocarpa, a galactose-specific lectin, was not anti-inflammatory. The proposed anti-inflammatory activity of lectins could be due to a blockage of neutrophil-selectin carbohydrate ligands. Thus, according to the present data, we suggest an important role for N-acetylglucosamine residue as the major ligand for selectins on rat neutrophil membranes. PMID:10704148

  2. Characterization of carbohydrate-protein matrices for nutrient delivery.

    PubMed

    Zhou, Yankun; Roos, Yrjö H

    2011-05-01

    Amorphous carbohydrates may show glass transition and crystallization as a result of thermal or water plasticization. Proteins often affect the state transitions of carbohydrates in carbohydrate-protein systems. Water sorption behavior and effects of water on glass transition and crystallization in freeze-dried lactose, trehalose, lactose-casein (3: 1), lactose-soy protein isolate (3:1), trehalose-casein (3:1), and trehalose-soy protein isolate (3:1) systems were studied. Water sorption was determined gravimetrically as a function of time, and Brunauer-Emmett-Teller (BET) and Guggenheim-Anderson-de Boer (GAB) models were fitted to the experimental data. Glass transition temperature (T(g)) and instant crystallization temperature (T(ic)) in anhydrous and water plasticized systems were measured using differential scanning calorimetry (DSC). The Gordon-Taylor equation was used to model water content dependence of the T(g) values. The critical water content and water activity (a(w)) at 24 °C were calculated and crystallization of lactose and trehalose in the systems was followed at and above 0.54 a(w). Carbohydrate-protein systems showed higher amounts of sorbed water and less rapid sugar crystallization than pure sugars. A greater sugar crystallization delay was found in carbohydrate-casein systems than in carbohydrate-soy protein isolate systems. The T(g) and T(ic) values decreased with increasing water content and a(w). However, higher T(ic) values for lactose-protein systems were found than for lactose at the same a(w). Trehalose showed lower T(ic) value than lactose at 0.44 a(w) but no instant crystallization was measured below 0.44 a(w). State diagrams for each system are useful in selecting processing parameters and storage conditions in nutrient delivery applications. PMID:22417357

  3. Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking.

    PubMed

    Nivedha, Anita K; Thieker, David F; Makeneni, Spandana; Hu, Huimin; Woods, Robert J

    2016-02-01

    Molecular docking programs are primarily designed to align rigid, drug-like fragments into the binding sites of macromolecules and frequently display poor performance when applied to flexible carbohydrate molecules. A critical source of flexibility within an oligosaccharide is the glycosidic linkages. Recently, Carbohydrate Intrinsic (CHI) energy functions were reported that attempt to quantify the glycosidic torsion angle preferences. In the present work, the CHI-energy functions have been incorporated into the AutoDock Vina (ADV) scoring function, subsequently termed Vina-Carb (VC). Two user-adjustable parameters have been introduced, namely, a CHI- energy weight term (chi_coeff) that affects the magnitude of the CHI-energy penalty and a CHI-cutoff term (chi_cutoff) that negates CHI-energy penalties below a specified value. A data set consisting of 101 protein-carbohydrate complexes and 29 apoprotein structures was used in the development and testing of VC, including antibodies, lectins, and carbohydrate binding modules. Accounting for the intramolecular energies of the glycosidic linkages in the oligosaccharides during docking led VC to produce acceptable structures within the top five ranked poses in 74% of the systems tested, compared to a success rate of 55% for ADV. An enzyme system was employed in order to illustrate the potential application of VC to proteins that may distort glycosidic linkages of carbohydrate ligands upon binding. VC represents a significant step toward accurately predicting the structures of protein-carbohydrate complexes. Furthermore, the described approach is conceptually applicable to any class of ligands that populate well-defined conformational states. PMID:26744922

  4. Binding of Sperm to the Zona Pellucida Mediated by Sperm Carbohydrate-Binding Proteins is not Species-Specific in Vitro between Pigs and Cattle.

    PubMed

    Takahashi, Kazuya; Kikuchi, Kazuhiro; Uchida, Yasuomi; Kanai-Kitayama, Saeko; Suzuki, Reiichiro; Sato, Reiko; Toma, Kazunori; Geshi, Masaya; Akagi, Satoshi; Nakano, Minoru; Yonezawa, Naoto

    2013-01-01

    Carbohydrates are candidates for the basis of species-selective interaction of gametes during mammalian fertilization. In this study, we sought to clarify the roles of sugar residues in the species-selective, sperm-oocyte interaction in pigs and cattle. Acrosome-intact porcine and bovine sperm exhibited their strongest binding affinities for β-Gal and α-Man residues, respectively. Porcine-sperm specificity changed from β-Gal to α-Man after the acrosome reaction, while bovine-sperm specificity did not. Binding of acrosome-intact and acrosome-reacted sperm decreased after trypsinization, indicating that the carbohydrate-binding components are proteins. While immature oocytes bound homologous sperm preferentially to heterologous sperm, oocytes matured in vitro bound similar numbers of homologous and heterologous sperm. Lectin staining revealed the aggregation of α-Man residues on the outer surface of the porcine zona during maturation. In both species, zona-free, mature oocytes bound homologous sperm preferentially to heterologous sperm. The lectin-staining patterns of the zona pellucida and zona-free oocytes coincided with the carbohydrate-binding specificities of acrosome-intact and acrosome-reacted sperm, respectively, supporting the involvement of carbohydrates in gamete recognition in pigs and cattle. These results also indicate that sperm-zona pellucida and sperm-oolemma bindings are not strictly species-specific in pigs and cattle, and further suggest that sperm penetration into the zona and/or fusion with oolemma may be species-specific between pigs and cattle.

  5. UK Food Standards Agency Workshop Report: carbohydrate and cardiovascular risk.

    PubMed

    Peacock, Emma; Stanley, John; Calder, Philip C; Jebb, Susan A; Thies, Frank; Seal, Chris J; Woodside, Jayne V; Sanders, Tom A B

    2010-06-01

    This report summarises a workshop convened by the UK Food Standards Agency (FSA) on 14 October 2008 to discuss current FSA-funded research on carbohydrates and cardiovascular health. The objective of this workshop was to discuss the results of recent research and to identify any areas which could inform future FSA research calls. This workshop highlighted that the FSA is currently funding some of the largest, well-powered intervention trials investigating the type of fat and carbohydrate, whole grains and fruit and vegetables, on various CVD risk factors. Results of these trials will make a substantive contribution to the evidence on diet and cardiovascular risk. PMID:20236556

  6. Synthesis of glycolipopeptidic building blocks for carbohydrate receptor discovery.

    PubMed

    Ziora, Zyta M; Wimmer, Norbert; New, Roger; Skwarczynski, Mariusz; Toth, Istvan

    2011-09-01

    A class of glycolipopeptides for use as building blocks for a new type of dynamic combinatorial library is reported. The members of the library consist of a variable carbohydrate moiety, coded amino acids, and lipoamino acids in order to convert them into amphiphiles. Glycolipopeptidic amphiphiles interact through non-covalent bonding when mixed together in aqueous phase and form micelles in dynamic close-packed fluid mosaic arrays. The head groups of amphiphiles are exposed on the micelle surface, providing entities which could be screened in biological assays to find the most potent combination of building blocks in order to identify new bioactive carbohydrate ligands. PMID:21641587

  7. Diagnosing and Treating Intolerance to Carbohydrates in Children

    PubMed Central

    Berni Canani, Roberto; Pezzella, Vincenza; Amoroso, Antonio; Cozzolino, Tommaso; Di Scala, Carmen; Passariello, Annalisa

    2016-01-01

    Intolerance to carbohydrates is relatively common in childhood, but still poorly recognized and managed. Over recent years it has come to the forefront because of progresses in our knowledge on the mechanisms and treatment of these conditions. Children with intolerance to carbohydrates often present with unexplained signs and symptoms. Here, we examine the most up-to-date research on these intolerances, discuss controversies relating to the diagnostic approach, including the role of molecular analysis, and provide new insights into modern management in the pediatric age, including the most recent evidence for correct dietary treatment. PMID:26978392

  8. Diagnosing and Treating Intolerance to Carbohydrates in Children.

    PubMed

    Berni Canani, Roberto; Pezzella, Vincenza; Amoroso, Antonio; Cozzolino, Tommaso; Di Scala, Carmen; Passariello, Annalisa

    2016-03-10

    Intolerance to carbohydrates is relatively common in childhood, but still poorly recognized and managed. Over recent years it has come to the forefront because of progresses in our knowledge on the mechanisms and treatment of these conditions. Children with intolerance to carbohydrates often present with unexplained signs and symptoms. Here, we examine the most up-to-date research on these intolerances, discuss controversies relating to the diagnostic approach, including the role of molecular analysis, and provide new insights into modern management in the pediatric age, including the most recent evidence for correct dietary treatment.

  9. Synthesis of carbohydrate-scaffolded thymine glycoconjugates to organize multivalency

    PubMed Central

    Ciuk, Anna K

    2015-01-01

    Summary Multivalency effects are essential in carbohydrate recognition processes as occurring on the cell surface. Thus many synthetic multivalent glycoconjugates have been developed as important tools for glycobiological research. We are expanding this collection of molecules by the introduction of carbohydrate-scaffolded divalent glycothymine derivatives that can be intramolecularily dimerized by [2 + 2] photocycloaddition. Thus, thymine functions as a control element that allows to restrict the conformational flexibility of the scaffolded sugar ligands and thus to “organize” multivalency. With this work we add a parameter to multivalency studies additional to valency. PMID:26124869

  10. Diagnosing and Treating Intolerance to Carbohydrates in Children.

    PubMed

    Berni Canani, Roberto; Pezzella, Vincenza; Amoroso, Antonio; Cozzolino, Tommaso; Di Scala, Carmen; Passariello, Annalisa

    2016-03-01

    Intolerance to carbohydrates is relatively common in childhood, but still poorly recognized and managed. Over recent years it has come to the forefront because of progresses in our knowledge on the mechanisms and treatment of these conditions. Children with intolerance to carbohydrates often present with unexplained signs and symptoms. Here, we examine the most up-to-date research on these intolerances, discuss controversies relating to the diagnostic approach, including the role of molecular analysis, and provide new insights into modern management in the pediatric age, including the most recent evidence for correct dietary treatment. PMID:26978392

  11. Interactions of polyphenols with carbohydrates, lipids and proteins.

    PubMed

    Jakobek, Lidija

    2015-05-15

    Polyphenols are secondary metabolites in plants, investigated intensively because of their potential positive effects on human health. Their bioavailability and mechanism of positive effects have been studied, in vitro and in vivo. Lately, a high number of studies takes into account the interactions of polyphenols with compounds present in foods, like carbohydrates, proteins or lipids, because these food constituents can have significant effects on the activity of phenolic compounds. This paper reviews the interactions between phenolic compounds and lipids, carbohydrates and proteins and their impact on polyphenol activity. PMID:25577120

  12. Interactions of polyphenols with carbohydrates, lipids and proteins.

    PubMed

    Jakobek, Lidija

    2015-05-15

    Polyphenols are secondary metabolites in plants, investigated intensively because of their potential positive effects on human health. Their bioavailability and mechanism of positive effects have been studied, in vitro and in vivo. Lately, a high number of studies takes into account the interactions of polyphenols with compounds present in foods, like carbohydrates, proteins or lipids, because these food constituents can have significant effects on the activity of phenolic compounds. This paper reviews the interactions between phenolic compounds and lipids, carbohydrates and proteins and their impact on polyphenol activity.

  13. Modelling OH⋯O hydrogen bonds in carbohydrates

    NASA Astrophysics Data System (ADS)

    Jeffrey, G. A.

    1990-09-01

    Hydrogen-bonding is particularly significant in the molecular modelling of the molecules of glycobiology because of the large number of OH⋯O functional groups for each carbohydrate monomer in these oligo- and macromolecules. This requires appropriate parameterization of the electrostatic interactions, which is considered to be the least well-developed component of molecular mechanics and dynamics formulations. Oligo- and polysaccharides are more difficult to model, in this respect, than oligo- and polypeptides and nucleotides because of the orientational freedom of the hydroxyl groups. The extension of present methods to carbohydrates is discussed.

  14. The primary structure and characterization of carbohydrate chains of the extracellular glycoprotein proteinase inhibitor from latex of Carica papaya.

    PubMed

    Odani, S; Yokokawa, Y; Takeda, H; Abe, S; Odani, S

    1996-10-01

    A secretory proteinase inhibitor was isolated from the latex of green fruits of papaya (Carica papaya). The protein exhibited stoichiometric inhibition of bovine trypsin and alpha-chymotrypsin by the same site or overlapping binding sites. The complete covalent structure consisting of 184 amino acids and two disulfide bonds was determined by protein analysis. During the structural analysis, a procedure was established to separate very hydrophilic peptides by reverse-phase HPLC. The result revealed that the latex protein belongs to an extensively diverse plant protein family that includes inhibitors of serine, cysteine and aspartic proteases, a taste-modifying protein, wound responsive proteins, storage proteins, amylase inhibitors and even an oxidoreductase. In this superfamily, the latex proteinase inhibitor is most similar to the curious protein, miraculin, which makes sour food taste sweet. Two carbohydrate chains, each probably composed of (mannose)5, (xylose)1, (fucose)0-2, and (N-acetylglucosamine)2 residues, were attached to asparagine 84 and 90. Mass-spectrometric and compositional analysis suggested that they may represent a new class of plant xylose-containing carbohydrate chains with five mannose residues.

  15. The primary structure and characterization of carbohydrate chains of the extracellular glycoprotein proteinase inhibitor from latex of Carica papaya.

    PubMed

    Odani, S; Yokokawa, Y; Takeda, H; Abe, S; Odani, S

    1996-10-01

    A secretory proteinase inhibitor was isolated from the latex of green fruits of papaya (Carica papaya). The protein exhibited stoichiometric inhibition of bovine trypsin and alpha-chymotrypsin by the same site or overlapping binding sites. The complete covalent structure consisting of 184 amino acids and two disulfide bonds was determined by protein analysis. During the structural analysis, a procedure was established to separate very hydrophilic peptides by reverse-phase HPLC. The result revealed that the latex protein belongs to an extensively diverse plant protein family that includes inhibitors of serine, cysteine and aspartic proteases, a taste-modifying protein, wound responsive proteins, storage proteins, amylase inhibitors and even an oxidoreductase. In this superfamily, the latex proteinase inhibitor is most similar to the curious protein, miraculin, which makes sour food taste sweet. Two carbohydrate chains, each probably composed of (mannose)5, (xylose)1, (fucose)0-2, and (N-acetylglucosamine)2 residues, were attached to asparagine 84 and 90. Mass-spectrometric and compositional analysis suggested that they may represent a new class of plant xylose-containing carbohydrate chains with five mannose residues. PMID:8898891

  16. Effects on sialic acid recognition of amino acid mutations in the carbohydrate-binding cleft of the rotavirus spike protein.

    PubMed

    Kraschnefski, Mark J; Bugarcic, Andrea; Fleming, Fiona E; Yu, Xing; von Itzstein, Mark; Coulson, Barbara S; Blanchard, Helen

    2009-03-01

    The rotavirus spike protein VP4 mediates attachment to host cells and subsequent membrane penetration. The VP8(*) domain of VP4 forms the spike tips and is proposed to recognize host-cell surface glycans. For sialidase-sensitive rotaviruses such as rhesus (RRV), this recognition involves terminal sialic acids. We show here that the RRV VP8(*)(64-224) protein competes with RRV infection of host cells, demonstrating its relevance to infection. In addition, we observe that the amino acids revealed by X-ray crystallography to be in direct contact with the bound sialic acid derivative methyl alpha-D-N-acetylneuraminide, and that are highly conserved amongst sialidase-sensitive rotaviruses, are residues that are also important in interactions with host-cell carbohydrates. Residues Arg101 and Ser190 of the RRV VP8(*) carbohydrate-binding site were mutated to assess their importance for binding to the sialic acid derivative and their competition with RRV infection of host cells. The crystallographic structure of the Arg(101)Ala mutant crystallized in the presence of the sialic acid derivative was determined at 295 K to a resolution of 1.9 A. Our multidisciplinary study using X-ray crystallography, saturation transfer difference nuclear magnetic resonance spectroscopy, isothermal titration calorimetry, and competitive virus infectivity assays to investigate RRV wild-type and mutant VP8(*) proteins has provided the first evidence that the carbohydrate-binding cavity in RRV VP8(*) is used for host-cell recognition, and this interaction is not only with the sialic acid portion but also with other parts of the glycan structure.

  17. Carbohydrate conjugation through microwave-assisted functionalization of single-walled carbon nanotubes using perfluorophenyl azides.

    PubMed

    Kong, Na; Shimpi, Manishkumar R; Ramström, Olof; Yan, Mingdi

    2015-03-20

    Carbohydrate-functionalized single-walled carbon nanotubes (SWNTs) were synthesized using microwave-assisted reaction of perfluorophenyl azide with the nanotubes. The results showed that microwave radiation provides a rapid and effective means to covalently attach carbohydrates to SWNTs, producing carbohydrate-SWNT conjugates for biorecognition. The carbohydrate-functionalized SWNTs were furthermore shown to interact specifically with cognate carbohydrate-specific proteins (lectins), resulting in predicted recognition patterns. The carbohydrate-presenting SWNTs constitute a new platform for sensitive protein- or cell recognition, which pave the way for glycoconjugated carbon nanomaterials in biorecognition applications.

  18. Supercritical fluid drying of carbohydrates: selection of suitable excipients and process conditions.

    PubMed

    Bouchard, Andréanne; Jovanović, Natasa; Hofland, Gerard W; Jiskoot, Wim; Mendes, Eduardo; Crommelin, Daan J A; Witkamp, Geert-Jan

    2008-03-01

    The processibility of 15 carbohydrates, more or less commonly used, was investigated as excipients in supercritical fluid drying. The focus was on the ability to produce amorphous powder, the stability of the powders towards crystallisation, and the residual water and ethanol content. The aqueous solutions were sprayed into a pressurised carbon dioxide-ethanol mixture flowing cocurrently through a coaxial two-fluid nozzle. The powder characteristics appeared to be influenced by the supersaturation level reached during the SCF-drying process and by the properties of the sugar species, such as water solubility and glass transition temperature, or the solution viscosities. The stability and the residual solvent content of a selected set of sugars and some mixtures were further analysed. The stability of amorphous powders was investigated at 4 degrees C, room temperature, 40 and 50 degrees C. Lactose, maltose, trehalose, raffinose, cyclodextrin, low-molecular-weight dextran and inulin could form free-flowing powders that remained amorphous during the 3-month stability study. Sucrose had to be mixed with other sugars to form a stable amorphous powder. Ethanol could be entrapped in supercritical fluid dried low-molecular-weight sugars, whereas polysaccharide powders were free of ethanol. Measures to prevent or overcome the presence of ethanol are discussed. PMID:17702554

  19. Characterization of the carbohydrate component of fraction I in the Neurospora crassa cell wall.

    PubMed Central

    Cardemil, L; Pincheira, G

    1979-01-01

    The carbohydrate portion of fraction I of the Neurospora crassa cell wall has been analyzed for sugar composition by gas-liquid chromatography and colorimetric methods. The analysis was performed comparatively in a wild-type strain (RL 3-8A) and three morphological mutants: scumbo (FGSC 49), peak-2a (a mutant known to be allelic to biscuit), and ragged (FGSC 296). Fraction I of all strains studied contains glucose, mannose, and galactose as the main sugars. Uronic acids and amino sugars are also present in small amounts. The glycosidic linkages binding the neutral sugars were analyzed by Lindberg's combined gas chromatography-mass spectrometry techniques for identification of the partially methylated alditol acitate sugar derivatives. The main polymeric portion of fraction I seems to be a linear glucan with the glucose residues linked by 1 leads to 3 and 1 leads to 4 bonds. A mannan portion with a branched configuration is also present, with galactose as the sugar residue which serves as branches in the molecule(s). The branched mannan portion appears to increase in amount in correlation with more drastic morphological changes of the mycelia. In this respect, the mutant ragged has the lowest mycelial growth rate and the largest amount of mannan. The importance of the polysaccharide structure of fraction I on the colonial morphology of the mycelia is discussed. Images PMID:155686

  20. Structural Insights into the Affinity of Cel7A Carbohydrate-binding Module for Lignin*

    PubMed Central

    Strobel, Kathryn L.; Pfeiffer, Katherine A.; Blanch, Harvey W.; Clark, Douglas S.

    2015-01-01

    The high cost of hydrolytic enzymes impedes the commercial production of lignocellulosic biofuels. High enzyme loadings are required in part due to their non-productive adsorption to lignin, a major component of biomass. Despite numerous studies documenting cellulase adsorption to lignin, few attempts have been made to engineer enzymes to reduce lignin binding. In this work, we used alanine-scanning mutagenesis to elucidate the structural basis for the lignin affinity of Trichoderma reesei Cel7A carbohydrate binding module (CBM). T. reesei Cel7A CBM mutants were produced with a Talaromyces emersonii Cel7A catalytic domain and screened for their binding to cellulose and lignin. Mutation of aromatic and polar residues on the planar face of the CBM greatly decreased binding to both cellulose and lignin, supporting the hypothesis that the cellulose-binding face is also responsible for lignin affinity. Cellulose and lignin affinity of the 31 mutants were highly correlated, although several mutants displayed selective reductions in lignin or cellulose affinity. Four mutants with increased cellulose selectivity (Q2A, H4A, V18A, and P30A) did not exhibit improved hydrolysis of cellulose in the presence of lignin. Further reduction in lignin affinity while maintaining a high level of cellulose affinity is thus necessary to generate an enzyme with improved hydrolysis capability. This work provides insights into the structural underpinnings of lignin affinity, identifies residues amenable to mutation without compromising cellulose affinity, and informs engineering strategies for family one CBMs. PMID:26209638

  1. Structural insights into the affinity of Cel7A carbohydrate-binding module for lignin.

    PubMed

    Strobel, Kathryn L; Pfeiffer, Katherine A; Blanch, Harvey W; Clark, Douglas S

    2015-09-11

    The high cost of hydrolytic enzymes impedes the commercial production of lignocellulosic biofuels. High enzyme loadings are required in part due to their non-productive adsorption to lignin, a major component of biomass. Despite numerous studies documenting cellulase adsorption to lignin, few attempts have been made to engineer enzymes to reduce lignin binding. In this work, we used alanine-scanning mutagenesis to elucidate the structural basis for the lignin affinity of Trichoderma reesei Cel7A carbohydrate binding module (CBM). T. reesei Cel7A CBM mutants were produced with a Talaromyces emersonii Cel7A catalytic domain and screened for their binding to cellulose and lignin. Mutation of aromatic and polar residues on the planar face of the CBM greatly decreased binding to both cellulose and lignin, supporting the hypothesis that the cellulose-binding face is also responsible for lignin affinity. Cellulose and lignin affinity of the 31 mutants were highly correlated, although several mutants displayed selective reductions in lignin or cellulose affinity. Four mutants with increased cellulose selectivity (Q2A, H4A, V18A, and P30A) did not exhibit improved hydrolysis of cellulose in the presence of lignin. Further reduction in lignin affinity while maintaining a high level of cellulose affinity is thus necessary to generate an enzyme with improved hydrolysis capability. This work provides insights into the structural underpinnings of lignin affinity, identifies residues amenable to mutation without compromising cellulose affinity, and informs engineering strategies for family one CBMs. PMID:26209638

  2. Structural insights into the affinity of Cel7A carbohydrate-binding module for lignin.

    PubMed

    Strobel, Kathryn L; Pfeiffer, Katherine A; Blanch, Harvey W; Clark, Douglas S

    2015-09-11

    The high cost of hydrolytic enzymes impedes the commercial production of lignocellulosic biofuels. High enzyme loadings are required in part due to their non-productive adsorption to lignin, a major component of biomass. Despite numerous studies documenting cellulase adsorption to lignin, few attempts have been made to engineer enzymes to reduce lignin binding. In this work, we used alanine-scanning mutagenesis to elucidate the structural basis for the lignin affinity of Trichoderma reesei Cel7A carbohydrate binding module (CBM). T. reesei Cel7A CBM mutants were produced with a Talaromyces emersonii Cel7A catalytic domain and screened for their binding to cellulose and lignin. Mutation of aromatic and polar residues on the planar face of the CBM greatly decreased binding to both cellulose and lignin, supporting the hypothesis that the cellulose-binding face is also responsible for lignin affinity. Cellulose and lignin affinity of the 31 mutants were highly correlated, although several mutants displayed selective reductions in lignin or cellulose affinity. Four mutants with increased cellulose selectivity (Q2A, H4A, V18A, and P30A) did not exhibit improved hydrolysis of cellulose in the presence of lignin. Further reduction in lignin affinity while maintaining a high level of cellulose affinity is thus necessary to generate an enzyme with improved hydrolysis capability. This work provides insights into the structural underpinnings of lignin affinity, identifies residues amenable to mutation without compromising cellulose affinity, and informs engineering strategies for family one CBMs.

  3. The factors affecting on estimation of carbohydrate content of meals in carbohydrate counting

    PubMed Central

    Kawamura, Tomoyuki; Takamura, Chihiro; Hirose, Masakazu; Hashimoto, Tomomi; Higashide, Takashi; Kashihara, Yoneo; Hashimura, Kayako; Shintaku, Haruo

    2015-01-01

    Abstract. The objective of this study was to identify factors affecting on errors in carbohydrate (CHO) content estimation during CHO counting. Thirty-seven type 1 diabetes patients and 22 of their parents and 28 physicians/dieticians were enrolled in this study. CHO counting was counted in “Carb”, with 1 Carb defined as 10 g of CHO. To evaluate the accuracy of CHO counting, 80 real-size photographs of cooked meals were presented to the subjects for Carb estimation. Carbs tended to be overestimated for foods containing relatively small amounts of Carbs. On the other hands, Carbs tended to be underestimated for foods with higher than 6 Carbs. Accurate estimation of the Carbs in food containing a large amount of rice was particularly difficult even in the subjects having the CHO counting experience. The Carb contents of high-calorie foods such as meats, fried foods, and desserts tended to be overestimated. This error was smaller in subjects having the CHO counting experience. In conclusion, misunderstanding of high-calorie dishes containing high amounts of CHO was observed in inexperienced subjects, indicating the efficacy of the current methodology of CHO counting. On the other hand it was difficult even for experienced subjects to assess the amount of seasoned rice, suggesting the need for a new methodology for accurate estimation. PMID:26568656

  4. The factors affecting on estimation of carbohydrate content of meals in carbohydrate counting.

    PubMed

    Kawamura, Tomoyuki; Takamura, Chihiro; Hirose, Masakazu; Hashimoto, Tomomi; Higashide, Takashi; Kashihara, Yoneo; Hashimura, Kayako; Shintaku, Haruo

    2015-10-01

    The objective of this study was to identify factors affecting on errors in carbohydrate (CHO) content estimation during CHO counting. Thirty-seven type 1 diabetes patients and 22 of their parents and 28 physicians/dieticians were enrolled in this study. CHO counting was counted in "Carb", with 1 Carb defined as 10 g of CHO. To evaluate the accuracy of CHO counting, 80 real-size photographs of cooked meals were presented to the subjects for Carb estimation. Carbs tended to be overestimated for foods containing relatively small amounts of Carbs. On the other hands, Carbs tended to be underestimated for foods with higher than 6 Carbs. Accurate estimation of the Carbs in food containing a large amount of rice was particularly difficult even in the subjects having the CHO counting experience. The Carb contents of high-calorie foods such as meats, fried foods, and desserts tended to be overestimated. This error was smaller in subjects having the CHO counting experience. In conclusion, misunderstanding of high-calorie dishes containing high amounts of CHO was observed in inexperienced subjects, indicating the efficacy of the current methodology of CHO counting. On the other hand it was difficult even for experienced subjects to assess the amount of seasoned rice, suggesting the need for a new methodology for accurate estimation. PMID:26568656

  5. Residual stresses in material processing

    SciTech Connect

    Kozaczek, K.J.; Watkins, T.R.; Hubbard, C.R.; Wang, Xun-Li; Spooner, S.

    1994-09-01

    Material manufacturing processes often introduce residual stresses into the product. The residual stresses affect the properties of the material and often are detrimental. Therefore, the distribution and magnitude of residual stresses in the final product are usually an important factor in manufacturing process optimization or component life prediction. The present paper briefly discusses the causes of residual stresses. It then adresses the direct, nondestructive methods of residual stress measurement by X-ray and neutron diffraction. Examples are presented to demonstrate the importance of residual stress measurement in machining and joining operations.

  6. Architectures of Multivalent Glycomimetics for Probing Carbohydrate-Lectin Interactions

    NASA Astrophysics Data System (ADS)

    Lahmann, Martina

    Well-defined multivalent glycoconjugates are valued tools in glycoscience and they are particularly valuable for the investigation of carbohydrate-lectin interactions. In addition to the relatively globularly shaped glycodendrimers many other designs have been realized. This chapter gives an overview on the common different architectures and their chemical synthesis by focussing on the achievements made since 2001.

  7. [Comparison between low-carbohydrate and mediterranean diet].

    PubMed

    Luisi, Maria Luisa Eliana; Gensini, Gian Franco

    2004-09-01

    Since seventies Robert Atkins promoted a low-carbohydrate, high-protein diet without calories counting. This dietetic approach, first described at the end of 1960 and periodically devised by different authors, is yet object of scientific discussion for its efficacy and safety. PMID:15478241

  8. Co-occurrence of carbohydrate malabsorption and primary epiploic appendagitis.

    PubMed

    Schnedl, Wolfgang J; Kalmar, Peter; Mangge, Harald; Krause, Robert; Wallner-Liebmann, Sandra J

    2015-09-21

    Unspecific abdominal complaints including bloating and irregular bowel movements may be caused by carbohydrate malabsorption syndromes, e.g., lactose and fructose malabsorption. These symptoms were investigated with hydrogen (H2) breath tests and correlated to carbohydrate malabsorption. During performing these H2-breath tests the patient presented with an acute, localized, non-migratory pain in the left lower abdominal quadrant. Primary epiploic appendagitis is a rare cause of abdominal acute or subacute complaints and diagnosis of primary epiploic appendagitis (PEA) is made when computed tomography reveals a characteristic lesion. We report on a patient with co-occurrence of lactose and fructose malabsorption, which was treated successfully with a diet free of culprit carbohydrates, with PEA recovering without medication or surgical treatment within few days. Since the abdominal unspecific symptoms had been present for months, they appeared not to be correlated to the acute localized abdominal pain, therefore we speculate on a random co-occurrence of combined carbohydrate malabsorption and PEA.

  9. Terrestrial carbohydrates support freshwater zooplankton during phytoplankton deficiency

    PubMed Central

    Taipale, Sami J.; Galloway, Aaron W. E.; Aalto, Sanni L.; Kahilainen, Kimmo K.; Strandberg, Ursula; Kankaala, Paula

    2016-01-01

    Freshwater food webs can be partly supported by terrestrial primary production, often deriving from plant litter of surrounding catchment vegetation. Although consisting mainly of poorly bioavailable lignin, with low protein and lipid content, the carbohydrates from fallen tree leaves and shoreline vegetation may be utilized by aquatic consumers. Here we show that during phytoplankton deficiency, zooplankton (Daphnia magna) can benefit from terrestrial particulate organic matter by using terrestrial-origin carbohydrates for energy and sparing essential fatty acids and amino acids for somatic growth and reproduction. Assimilated terrestrial-origin fatty acids from shoreline reed particles exceeded available diet, indicating that Daphnia may convert a part of their dietary carbohydrates to saturated fatty acids. This conversion was not observed with birch leaf diets, which had lower carbohydrate content. Subsequent analysis of 21 boreal and subarctic lakes showed that diet of herbivorous zooplankton is mainly based on high-quality phytoplankton rich in essential polyunsaturated fatty acids. The proportion of low-quality diets (bacteria and terrestrial particulate organic matter) was <28% of the assimilated carbon. Taken collectively, the incorporation of terrestrial carbon into zooplankton was not directly related to the concentration of terrestrial organic matter in experiments or lakes, but rather to the low availability of phytoplankton. PMID:27510848

  10. Locusts increase carbohydrate consumption to protect against a fungal biopesticide.

    PubMed

    Graham, Robert I; Deacutis, Juliane M; Pulpitel, Tamara; Ponton, Fleur; Simpson, Stephen J; Wilson, Kenneth

    2014-10-01

    There is growing evidence to suggest that hosts can alter their dietary intake to recoup the specific resources involved in mounting effective resistance against parasites and pathogens. We examined macronutrient ingestion and disease-resistance in the Australian plague locust (Chortoicetes terminifera), challenged with a fungal pathogen (Metarhizium acridum) under dietary regimes varying in their relative amounts of protein and digestible carbohydrate. Dietary protein influenced constitutive immune function to a greater extent than did carbohydrate, indicating higher protein costs of mounting an immune defence than carbohydrate or overall energy costs. However, it appears that increased immune function, as a result of greater protein ingestion, was not sufficient to protect locusts from fungal disease. We found that locusts restricted to diets high in protein (P) and low in carbohydrate (C) were more likely to die of a fungal infection than those restricted to diets with a low P:C ratio. We hypothesise that the fungus is more efficient at exploiting protein in the insect's haemolymph than the host is at producing immune effectors, tipping the balance in favour of the pathogen on high-protein diets. When allowed free-choice, survivors of a fungus-challenge chose a less-protein-rich diet than those succumbing to infection and those not challenged with fungus locusts. These results are contrary to previous studies on caterpillars in the genus Spodoptera challenged with bacterial and baculoviral pathogens, indicating that nutrient ingestion and pathogen resistance may be a complex interaction specific to different host species and disease agents.

  11. A carbohydrate-rich diet increases social immunity in ants.

    PubMed

    Kay, Adam D; Bruning, Abbie J; van Alst, Andy; Abrahamson, Tyler T; Hughes, W O H; Kaspari, Michael

    2014-03-01

    Increased potential for disease transmission among nest-mates means living in groups has inherent costs. This increased potential is predicted to select for disease resistance mechanisms that are enhanced by cooperative exchanges among group members, a phenomenon known as social immunity. One potential mediator of social immunity is diet nutritional balance because traits underlying immunity can require different nutritional mixtures. Here, we show how dietary protein-carbohydrate balance affects social immunity in ants. When challenged with a parasitic fungus Metarhizium anisopliae, workers reared on a high-carbohydrate diet survived approximately 2.8× longer in worker groups than in solitary conditions, whereas workers reared on an isocaloric, high-protein diet survived only approximately 1.3× longer in worker groups versus solitary conditions. Nutrition had little effect on social grooming, a potential mechanism for social immunity. However, experimentally blocking metapleural glands, which secrete antibiotics, completely eliminated effects of social grouping and nutrition on immunity, suggesting a causal role for secretion exchange. A carbohydrate-rich diet also reduced worker mortality rates when whole colonies were challenged with Metarhizium. These results provide a novel mechanism by which carbohydrate exploitation could contribute to the ecological dominance of ants and other social groups.

  12. Carbohydrate maldigestion induces necrotizing enterocolitis in preterm pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Necrotizing enterocolitis (NEC) remains the most severe gastrointestinal disorder in preterm infants. It is associated with the initiation of enteral nutrition and may be related to immature carbohydrate digestive capacity. We tested the hypothesis that a formula containing maltodextrin vs. lactose ...

  13. DFT solvation studies of carbohydrates: implicit and explicit solvation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Solvents play a role in carbohydrate structure. Therefore, it is important to include solvation effects in calculations to allow a more realistic comparison with experimental data. A possible way to include solvation effects is to use implicit solvation models such as COSMO and PCM. Another avenu...

  14. Effect of fat and carbohydrate consumption on endothelial function.

    PubMed

    Ong, P J; Dean, T S; Hayward, C S; Della Monica, P L; Sanders, T A; Collins, P

    Consumption of a meal high in monounsaturated fat was associated with acute impairment of endothelial function when compared with a carbohydrate-rich meal. Such a divergent response in endothelial function may be important in the modulation of vascular function in health and disease.

  15. Increase in carbohydrate utilization in high-altitude Andean mice.

    PubMed

    Schippers, Marie-Pierre; Ramirez, Oswaldo; Arana, Margarita; Pinedo-Bernal, Percy; McClelland, Grant B

    2012-12-18

    The low oxygen levels at high altitude are a potent and unavoidable physiological stressor to which highland mammals must adapt. One hypothesized adaptation to high altitude is an increased reliance on carbohydrates to support aerobic activities. Based on stoichiometries of combustion, ATP yield per mole of oxygen from carbohydrates is approximately 15% higher than from lipids (observed difference closer to 30%), and increased carbohydrate use represents an important oxygen-saving strategy that may be under high selective pressure. Although this hypothesis was first proposed nearly 30 years ago, the in vivo patterns of whole-body fuel use during exercise remain undefined for any highland mammal (including humans). Here we use a powerful multispecies approach to show that wild-caught high-altitude (4,000-4,500 m) native species of mice (Phyllotis andium and Phyllotis xanthopygus) from the Peruvian Andes use proportionately more carbohydrates and have higher oxidative capacities of cardiac muscles compared to closely related low-altitude (100-300 m) native counterparts (Phyllotis amicus and Phyllotis limatus). These results strongly infer that highland Phyllotis have evolved a metabolic strategy to economize oxygen when performing energy-demanding tasks at altitude. This study provides compelling evidence of adjustments in fuel use as an adaptation to high-altitude hypoxia in mammals. PMID:23219722

  16. Bibliography on carbohydrate synthesis. Selected works, 1861 - 1981

    NASA Technical Reports Server (NTRS)

    Dufour, P. A.

    1981-01-01

    International in scope, this bibliography cites 220 articles books, patents, and conference proceedings related to carbohydrate synthesis. The works are listed alphabetically by author in the following categories: (1) experimental and industrial chemistry; (2) space travel and feeding studies; (3) hardware; and (4) general reviews and progress.

  17. Brain serotonin content - Increase following ingestion of carbohydrate diet.

    NASA Technical Reports Server (NTRS)

    Fernstrom, J. D.; Wurtman, R. J.

    1971-01-01

    In the rat, the injection of insulin or the consumption of carbohydrate causes sequential increases in the concentrations of tryptophan in the plasma and the brain and of serotonin in the brain. Serotonin-containing neurons may thus participate in systems whereby the rat brain integrates information about the metabolic state in its relation to control of homeostasis and behavior.

  18. Science Study Aids 3: Carbohydrates - Nature's Energy Source.

    ERIC Educational Resources Information Center

    McConnell, Bill

    This publication is the third of a series of seven supplementary investigative materials for use in secondary science classes providing up-to-date research-related investigations. This unit is structured for grade levels 7 through 12. It is concerned with the role of carbohydrates as important nutrients for consumers. This guide will enable…

  19. Resistance of Brachystegia spiciformis to Carbohydrate and Phenological Manipulation

    NASA Astrophysics Data System (ADS)

    Richer, R. A.

    2006-12-01

    Despite the development of metabolic ecology, the role that carbohydrate stores play in regulating phenological events is unknown. Whole tree manipulation experiments in the common southern African tree species, Brachystegia spiciformis offer new insights into the physiological and environmental mechanisms controlling bud break. This experiment tested a novel hypothesis that decreasing Total Non-Structural Carbohydrates (TNC) in the stem could cue bud break in Brachystegia spiciformis. The experimental treatments included fertilization, canopy defoliation, shading and stem heating and were repeated over a two year period in the Kalahari sand savanna system of northwestern Zimbabwe. The treatments were designed to decrease stem carbohydrates and result in an earlier leaf flush. None of the treatments significantly decreased seasonal stem TNC. Likewise the heating, fertilization and defoliation treatments did not significantly affect the date of bud break from controls. However, shaded trees showed a significant delay in bud break. This delay in bud break could not be attributed to leaf level photosynthetic traits, stem water content, leaf pre-dawn water potential or delayed leaf fall. These results question widely accepted hypotheses about the mechanism controlling bud break in savanna ecosystems and may suggest a carbohydrate homeostatic mechanism.

  20. Terrestrial carbohydrates support freshwater zooplankton during phytoplankton deficiency.

    PubMed

    Taipale, Sami J; Galloway, Aaron W E; Aalto, Sanni L; Kahilainen, Kimmo K; Strandberg, Ursula; Kankaala, Paula

    2016-01-01

    Freshwater food webs can be partly supported by terrestrial primary production, often deriving from plant litter of surrounding catchment vegetation. Although consisting mainly of poorly bioavailable lignin, with low protein and lipid content, the carbohydrates from fallen tree leaves and shoreline vegetation may be utilized by aquatic consumers. Here we show that during phytoplankton deficiency, zooplankton (Daphnia magna) can benefit from terrestrial particulate organic matter by using terrestrial-origin carbohydrates for energy and sparing essential fatty acids and amino acids for somatic growth and reproduction. Assimilated terrestrial-origin fatty acids from shoreline reed particles exceeded available diet, indicating that Daphnia may convert a part of their dietary carbohydrates to saturated fatty acids. This conversion was not observed with birch leaf diets, which had lower carbohydrate content. Subsequent analysis of 21 boreal and subarctic lakes showed that diet of herbivorous zooplankton is mainly based on high-quality phytoplankton rich in essential polyunsaturated fatty acids. The proportion of low-quality diets (bacteria and terrestrial particulate organic matter) was <28% of the assimilated carbon. Taken collectively, the incorporation of terrestrial carbon into zooplankton was not directly related to the concentration of terrestrial organic matter in experiments or lakes, but rather to the low availability of phytoplankton. PMID:27510848

  1. Carbohydrate active enzymes revealed in Coptotermes formosanus transcriptome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A normalized cDNA library of Coptotermes formosanus was constructed using mixed RNA isolated from workers, soldiers, nymphs and alates of both sexes. Sequencing of this library generated 131,637 EST and 25,939 unigenes were assembled. Carbohydrate active enzymes (CAZymes) revealed in this library we...

  2. Force Fields for Carbohydrate-Divalent Cation Interactions.

    PubMed

    Chen, Hsieh; Cox, Jason R; Panagiotopoulos, Athanassios Z

    2016-06-16

    We report molecular dynamics simulations to study intermolecular interactions for carbohydrate-divalent cation complexes. We observed that common force fields from literature with standard Lorentz-Berthelot combining rules are unable to reproduce the experimental stability constants for model carbohydrate monomer (α-d-Allopyranose) and alkali earth metal cation (Mg(2+), Ca(2+), Sr(2+), or Ba(2+)) complexes. A modified combining rule with rescaled effective cross-interaction radius between cations and the hydroxyl oxygens on the carbohydrates was introduced to reproduce the experimental stability constants, which the preferential carbohydrate-cation complexing structures through the ax-eq-ax sequence of O-1, O-2, and O-3 on α-d-Allopyranose were also observed. The effective radius scaling factor obtained from (α-d-Allopyranose)-Ca(2+) complexes was directly transferrable to the similar six-membered ring (α-d-Ribopyranose)-Ca(2+) complexes; however, reparameterization for the scaling factor may be necessary for the five-membered ring (α-d-Ribofuranose)-Ca(2+) complexes. PMID:27210229

  3. 40 CFR 1065.705 - Residual and intermediate residual fuel.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... specifications for fuels meeting the definition of residual fuel in 40 CFR 80.2, including fuels marketed as... for Residual Fuel Characteristic Unit Category ISO-F- RMA 30 RMB 30 RMD 80 RME 180 RMF 180 RMG 380...

  4. 40 CFR 1065.705 - Residual and intermediate residual fuel.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... specifications for fuels meeting the definition of residual fuel in 40 CFR 80.2, including fuels marketed as... for Residual Fuel Characteristic Unit Category ISO-F- RMA 30 RMB 30 RMD 80 RME 180 RMF 180 RMG 380...

  5. SRC Residual fuel oils

    DOEpatents

    Tewari, Krishna C.; Foster, Edward P.

    1985-01-01

    Coal solids (SRC) and distillate oils are combined to afford single-phase blends of residual oils which have utility as fuel oils substitutes. The components are combined on the basis of their respective polarities, that is, on the basis of their heteroatom content, to assure complete solubilization of SRC. The resulting composition is a fuel oil blend which retains its stability and homogeneity over the long term.

  6. Physiological aspects of energy metabolism and gastrointestinal effects of carbohydrates.

    PubMed

    Elia, M; Cummings, J H

    2007-12-01

    The energy values of carbohydrates continue to be debated. This is because of the use of different energy systems, for example, combustible, digestible, metabolizable, and so on. Furthermore, ingested macronutrients may not be fully available to tissues, and the tissues themselves may not be able fully to oxidize substrates made available to them. Therefore, for certain carbohydrates, the discrepancies between combustible energy (cEI), digestible energy (DE), metabolizable energy (ME) and net metabolizable energy (NME) may be considerable. Three food energy systems are in use in food tables and for food labelling in different world regions based on selective interpretation of the digestive physiology and metabolism of food carbohydrates. This is clearly unsatisfactory and confusing to the consumer. While it has been suggested that an enormous amount of work would have to be undertaken to change the current ME system into an NME system, the additional changes may not be as great as anticipated. In experimental work, carbohydrate is high in the macronutrient hierarchy of satiation. However, studies of eating behaviour indicate that it does not unconditionally depend on the oxidation of one nutrient, and argue against the operation of a simple carbohydrate oxidation or storage model of feeding behaviour to the exclusion of other macronutrients. The site, rate and extent of carbohydrate digestion in, and absorption from the gut are key to understanding the many roles of carbohydrate, although the concept of digestibility has different meanings. Within the nutrition community, the characteristic patterns of digestion that occur in the small (upper) vs large (lower) bowel are known to impact in contrasting ways on metabolism, while in the discussion of the energy value of foods, digestibility is defined as the proportion of combustible energy that is absorbed over the entire length of the gastrointestinal tract. Carbohydrates that reach the large bowel are fermented to

  7. Water treatment residuals

    SciTech Connect

    Billings, C.H.

    1994-01-01

    Solutions to an environmental problem often create other environmental problems. That surely is the case in the water supply field. By providing new or expanded water treatment systems to comply with the maximum contaminant levels and treatment mandates of the Safe Drinking Water Act, water purveyors are generating large volumes of residuals that must be managed, ultimately disposed of, or recycled. Numerous federal, state, and local laws govern the management, transport, disposal, and recycling of wastes produced by water treatment systems. Because these laws can result in exorbitant waste disposal costs, restricting some projects entirely, water suppliers need to consider residual disposal early in the siting, selection, and design of treatment projects. To inform water suppliers about residual laws, AWWA commissioned a study published as a Water Industry Technical Action Fund report. In addition to identifying and describing applicable laws at the federal level and in six of the states, the study revealed a series of findings as to the consequences of those laws to water suppliers. This article is a brief overview of the findings of the report.

  8. Nickel-catalyzed proton-deuterium exchange (HDX) procedures for glycosidic linkage analysis of complex carbohydrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The structural analysis of complex carbohydrates typically requires the assignment of three parameters: monosaccharide composition, the position of glycosidic linkages between monosaccharides, and the position and nature of non-carbohydrate substituents. The glycosidic linkage positions are often de...

  9. Selecting and Effectively Using Sports Drinks, Carbohydrate Gels and Energy Bars

    MedlinePlus

    ... and Effectively Using Sports Drinks, Carbohydrate Gels and Energy Bars Depending upon the length of your workout ... can hinder performance. Sports drinks, carbohydrate gels and energy bars can help restore your body’s fluids and ...

  10. [Systematic evaluation of retention behavior of carbohydrates in hydrophilic interaction liquid chromatography].

    PubMed

    Fu, Qing; Wang, Jun; Liang, Tu; Xu, Xiaoyong; Jin, Yu

    2013-11-01

    A systematic evaluation of retention behavior of carbohydrates in hydrophilic interaction liquid chromatography (HILIC) was performed. The influences of mobile phase, stationary phase and buffer salt on the retention of carbohydrates were investigated. According to the results, the retention time of carbohydrates decreased as the proportion of acetonitrile in mobile phase decreased. Increased time of carbohydrates was observed as the concentration of buffer salt in mobile phase increased. The retention behavior of carbohydrates was also affected by organic solvent and HILIC stationary phase. Furthermore, an appropriate retention equation was used in HILIC mode. The retention equation lnk = a + blnC(B) + cC(B) could quantitatively describe the retention factors of carbohydrates of plant origin with good accuracy: the relative error of the predicted time to actual time was less than 0.3%. The evaluation results could provide guidance for carbohydrates to optimize the experimental conditions in HILIC method development especially for carbohydrate separation

  11. Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus.

    PubMed

    Khoroshkin, Matvei S; Leyn, Semen A; Van Sinderen, Douwe; Rodionov, Dmitry A

    2016-01-01

    Bifidobacteria, which represent common commensals of mammalian gut, are believed to have positive effects on human health. The influence of certain non-digestible carbohydrates (and their use as so-called prebiotics) on growth and metabolic activity of bifidobacteria is of increasing interest; however, mechanisms of transcriptional control of carbohydrate metabolism are poorly understood in these species. We used a comparative genomics approach to reconstruct carbohydrate utilization pathways and transcriptional regulons in 10 Bifidobacterium genomes. Analysis of regulatory gene regions revealed candidate DNA motifs and reconstructed regulons for 268 transcription factors from the LacI, ROK, DeoR, AraC, GntR, and TetR families that form 64 orthologous groups of regulators. Most of the reconstructed regulons are local and control specific catabolic pathways for host- and diet-derived glycans and monosaccharides. Mosaic distributions of many of these local regulators across Bifidobacterium species correlate with distribution of corresponding catabolic pathways. In contrast, the maltose, galactose, sucrose, and fructose regulons, as well as a novel global LacI-family regulator that is predicted to control the central carbohydrate metabolism and arabinose catabolism genes, are universally present in all 10 studied bifidobacteria. A novel group of TetR-family regulators presumably controls the glucoside and galactoside utilization pathways. Paralogs of the ribose repressor RbsR control the pyrimidine nucleoside utilization genes. Multiple paralogs of the maltose regulator MalR co-regulate large sets of genes involved in maltodextrin utilization. The inferred metabolic regulons provide new insights on diverse carbohydrate utilization networks in bifidobacteria that can be employed in metabolic modeling, phenotype prediction and the rational development of novel prebiotics.

  12. The effect of exercise on carbohydrate preference in female rats.

    PubMed

    Keeley, R J; Zelinski, E L; Fehr, L; McDonald, R J

    2014-02-01

    Exercise has a myriad of health benefits, including positive effects against heart disease, diabetes, and dementia. Cognitive performance improves following chronic exercise, both in animal models and humans. Studies have examined the effect of exercise on feeding, demonstrating a preference towards increased food consumption. Further, sex differences exist such that females tend to prefer carbohydrates over other macronutrients following exercise. However, no clear effect of exercise on macronutrient or carbohydrate selection has been described in animal or human studies. This research project sought to determine the effect of voluntary exercise on carbohydrate selection in female rats. Preference for a complex (starch) versus a simple (dextrose) carbohydrate was assessed using a discriminative preference to context paradigm in non-exercising and voluntarily exercising female rats. In addition, fasting blood glucose and performance in the Morris water task was examined in order to verify the effects of exercise on performance in this task. Female rats given access to running wheels preferred a context previously associated with starch, whereas females with no running wheel access preferred a context previously associated with dextrose. No changes in blood glucose were observed. However, cognitive differences in the Morris water task were observed such that voluntary exercise allowed rats to find a new location of a hidden platform following 4 days of training to an old platform location. These results suggest that voluntary exercise may decrease preservative behaviors in a spatial navigation task through the facilitation of plasticity mechanisms. This study is the first of its kind to demonstrate the influence of exercise on taste preference for complex and simple carbohydrates with this context conditioning paradigm. PMID:24406468

  13. Analysis of carbohydrates by anion exchange chromatography and mass spectrometry.

    PubMed

    Bruggink, Cees; Maurer, Rolf; Herrmann, Heiko; Cavalli, Silvano; Hoefler, Frank

    2005-08-26

    A versatile liquid chromatographic platform has been developed for analysing underivatized carbohydrates using high performance anion exchange chromatography (HPAEC) followed by an inert PEEK splitter that splits the effluent to the integrated pulsed amperometric detector (IPAD) and to an on-line single quadrupole mass spectrometer (MS). Common eluents for HPAEC such as sodium hydroxide and sodium acetate are beneficial for the amperometric detection but not compatible with electrospray ionisation (ESI). Therefore a membrane-desalting device was installed after the splitter and prior to the ESI interface converting sodium hydroxide into water and sodium acetate into acetic acid. To enhance the sensitivity for the MS detection, 0.5 mmol/l lithium chloride was added after the membrane desalter to form lithium adducts of the carbohydrates. To compare sensitivity of IPAD and MS detection glucose, fructose, and sucrose were used as analytes. A calibration with external standards from 2.5 to 1000 pmole was performed showing a linear range over three orders of magnitude. Minimum detection limits (MDL) with IPAD were determined at 5 pmole levels for glucose to be 0.12 pmole, fructose 0.22 pmole and sucrose 0.11 pmole. With MS detection in the selected ion mode (SIM) the lithium adducts of the carbohydrates were detected obtaining MDL's for glucose of 1.49 pmole, fructose 1.19 pmole, and sucrose 0.36 pmole showing that under these conditions IPAD is 3-10 times more sensitive for those carbohydrates. The applicability of the method was demonstrated analysing carbohydrates in real world samples such as chicory inulin where polyfructans up to a molecular mass of 7000 g/mol were detected as quadrupoly charged lithium adducts. Furthermore mono-, di-, tri-, and oligosaccharides were detected in chicory coffee, honey and beer samples. PMID:16106855

  14. Carbohydrate deficient transferrin: a marker for alcohol abuse.

    PubMed Central

    Kapur, A.; Wild, G.; Milford-Ward, A.; Triger, D. R.

    1989-01-01

    OBJECTIVE--To assess the value of serum carbohydrate deficient transferrin as detected by isoelectric focusing on agarose as an indicator of alcohol abuse. DESIGN--Coded analysis of serum samples taken from patients with carefully defined alcohol intake both with and without liver disease. Comparison of carbohydrate deficient transferrin with standard laboratory tests for alcohol abuse. SETTING--A teaching hospital unit with an interest in general medicine and liver disease. PATIENTS--22 "Self confessed" alcoholics admitting to a daily alcohol intake of at least 80 g for a minimum of three weeks; 15 of the 22 self confessed alcoholics admitted to hospital for alcohol withdrawal; 68 patients with alcoholic liver disease confirmed by biopsy attending outpatient clinics and claiming to be drinking less than 50 g alcohol daily; 47 patients with non-alcoholic liver disorders confirmed by biopsy; and 38 patients with disorders other than of the liver and no evidence of excessive alcohol consumption. INTERVENTION--Serial studies performed on the 15 patients undergoing alcohol withdrawal in hospital. MAIN OUTCOME measure--Determination of relative value of techniques for detecting alcohol abuse. RESULTS--Carbohydrate deficient transferrin was detected in 19 of the 22 (86%) self confessed alcohol abusers, none of the 47 patients with non-alcoholic liver disease, and one of the 38 (3%) controls. Withdrawal of alcohol led to the disappearance of carbohydrate deficient transferrin at a variable rate, though in some subjects it remained detectable for up to 15 days. Carbohydrate deficient transferrin was considerably superior to the currently available conventional markers for alcohol abuse. CONCLUSION--As the technique is fairly simple, sensitive, and inexpensive we suggest that it may be valuable in detecting alcohol abuse. Images FIG 1 PMID:2571374

  15. Recovery from cycling exercise: effects of carbohydrate and protein beverages.

    PubMed

    Goh, Qingnian; Boop, Christopher A; Luden, Nicholas D; Smith, Alexia G; Womack, Christopher J; Saunders, Michael J

    2012-07-01

    The effects of different carbohydrate-protein (CHO + Pro) beverages were compared during recovery from cycling exercise. Twelve male cyclists (VO(2peak): 65 ± 7 mL/kg/min) completed ~1 h of high-intensity intervals (EX1). Immediately and 120 min following EX1, subjects consumed one of three calorically-similar beverages (285-300 kcal) in a cross-over design: carbohydrate-only (CHO; 75 g per beverage), high-carbohydrate/low-protein (HCLP; 45 g CHO, 25 g Pro, 0.5 g fat), or low-carbohydrate/high-protein (LCHP; 8 g CHO, 55 g Pro, 4 g fat). After 4 h of recovery, subjects performed subsequent exercise (EX2; 20 min at 70% VO(2peak) + 20 km time-trial). Beverages were also consumed following EX2. Blood glucose levels (30 min after beverage ingestion) differed across all treatments (CHO > HCLP > LCHP; p < 0.05), and serum insulin was higher following CHO and HCLP ingestion versus LCHP. Peak quadriceps force, serum creatine kinase, muscle soreness, and fatigue/energy ratings measured pre- and post-exercise were not different between treatments. EX2 performance was not significantly different between CHO (48.5 ± 1.5 min), HCLP (48.8 ± 2.1 min) and LCHP (50.3 ± 2.7 min). Beverages containing similar caloric content but different proportions of carbohydrate/protein provided similar effects on muscle recovery and subsequent exercise performance in well-trained cyclists. PMID:22852050

  16. Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus

    PubMed Central

    Khoroshkin, Matvei S.; Leyn, Semen A.; Van Sinderen, Douwe; Rodionov, Dmitry A.

    2016-01-01

    Bifidobacteria, which represent common commensals of mammalian gut, are believed to have positive effects on human health. The influence of certain non-digestible carbohydrates (and their use as so-called prebiotics) on growth and metabolic activity of bifidobacteria is of increasing interest; however, mechanisms of transcriptional control of carbohydrate metabolism are poorly understood in these species. We used a comparative genomics approach to reconstruct carbohydrate utilization pathways and transcriptional regulons in 10 Bifidobacterium genomes. Analysis of regulatory gene regions revealed candidate DNA motifs and reconstructed regulons for 268 transcription factors from the LacI, ROK, DeoR, AraC, GntR, and TetR families that form 64 orthologous groups of regulators. Most of the reconstructed regulons are local and control specific catabolic pathways for host- and diet-derived glycans and monosaccharides. Mosaic distributions of many of these local regulators across Bifidobacterium species correlate with distribution of corresponding catabolic pathways. In contrast, the maltose, galactose, sucrose, and fructose regulons, as well as a novel global LacI-family regulator that is predicted to control the central carbohydrate metabolism and arabinose catabolism genes, are universally present in all 10 studied bifidobacteria. A novel group of TetR-family regulators presumably controls the glucoside and galactoside utilization pathways. Paralogs of the ribose repressor RbsR control the pyrimidine nucleoside utilization genes. Multiple paralogs of the maltose regulator MalR co-regulate large sets of genes involved in maltodextrin utilization. The inferred metabolic regulons provide new insights on diverse carbohydrate utilization networks in bifidobacteria that can be employed in metabolic modeling, phenotype prediction and the rational development of novel prebiotics. PMID:26903998

  17. Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima

    PubMed Central

    Rodionov, Dmitry A.; Rodionova, Irina A.; Li, Xiaoqing; Ravcheev, Dmitry A.; Tarasova, Yekaterina; Portnoy, Vasiliy A.; Zengler, Karsten; Osterman, Andrei L.

    2013-01-01

    Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies identified a large fraction of genes committed to carbohydrate degradation and utilization in the model bacterium Thermotoga maritima. Knowledge of these genes enabled comprehensive reconstruction of biochemical pathways comprising the carbohydrate utilization network. However, transcriptional factors (TFs) and regulatory mechanisms driving this network remained largely unknown. Here, we used an integrated approach based on comparative analysis of genomic and transcriptomic data for the reconstruction of the carbohydrate utilization regulatory networks in 11 Thermotogales genomes. We identified DNA-binding motifs and regulons for 19 orthologous TFs in the Thermotogales. The inferred regulatory network in T. maritima contains 181 genes encoding TFs, sugar catabolic enzymes and ABC-family transporters. In contrast to many previously described bacteria, a transcriptional regulation strategy of Thermotoga does not employ global regulatory factors. The reconstructed regulatory network in T. maritima was validated by gene expression profiling on a panel of mono- and disaccharides and by in vitro DNA-binding assays. The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons. Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima. In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales. PMID:23986752

  18. Carbohydrate digestibility predicts colon carcinogenesis in azoxymethane-treated rats.

    PubMed

    Jacobsen, Helene; Poulsen, Morten; Dragsted, Lars Ove; Ravn-Haren, Gitte; Meyer, Otto; Lindecrona, Rikke Hvid

    2006-01-01

    The purpose of this study was to compare the effect of carbohydrate structure and digestibility on azoxymethane (AOM)-induced colon carcinogenesis. Five groups of male Fischer 344 rats each comprising 30 animals were injected with AOM and fed a high-fat diet with 15% of various carbohydrates. The carbohydrate sources used were sucrose, cornstarch (a linear starch, reference group), potato starch (a branched starch), a short-chained oligofructose (Raftilose), and a long-chained inulin-type fructan (Raftiline). An interim sacrifice was performed after 9 wk to investigate markers of carbohydrate digestibility, including caecal fermentation (caecum weight and pH) and glucose and lipid metabolism [glucose, fructoseamine, HbA1c, triglycerides, and insulin-like growth factor (IGF) 1]. In addition potential early predictors of carcinogenicity [cell proliferation and aberrant crypt foci (ACF)] at 9 wk and their correlation to colon cancer risk after 32 wk were investigated. Tumor incidence was significantly reduced in animals fed oligofructose, and the number of tumors per animal was significantly reduced in animals fed inulin and oligofructose at 32 wk after AOM induction compared to the reference group fed sucrose. Increased caecum weight and decreased caecal pH were seen in groups fed oligofructose, inulin, and potato starch. Plasma triglyceride was decreased in rats fed oligofructose and inulin. Cell proliferation was increased in the proximal colon of rats fed sucrose, oligofructose, and inulin, and the number of cells per crypt decreased in rats fed oligofructose and inulin. The total number of ACF's was unaffected by treatment, and the size and multiplicity of ACF was unrelated to tumor development. It was concluded that less digestible carbohydrates with an early effect on caecum fermentation and plasma triglyceride decreased subsequent tumor incidence and multiplicity. This was unrelated to ACF, cell proliferation, and other markers of glucose and lipid metabolism.

  19. The effect of exercise on carbohydrate preference in female rats.

    PubMed

    Keeley, R J; Zelinski, E L; Fehr, L; McDonald, R J

    2014-02-01

    Exercise has a myriad of health benefits, including positive effects against heart disease, diabetes, and dementia. Cognitive performance improves following chronic exercise, both in animal models and humans. Studies have examined the effect of exercise on feeding, demonstrating a preference towards increased food consumption. Further, sex differences exist such that females tend to prefer carbohydrates over other macronutrients following exercise. However, no clear effect of exercise on macronutrient or carbohydrate selection has been described in animal or human studies. This research project sought to determine the effect of voluntary exercise on carbohydrate selection in female rats. Preference for a complex (starch) versus a simple (dextrose) carbohydrate was assessed using a discriminative preference to context paradigm in non-exercising and voluntarily exercising female rats. In addition, fasting blood glucose and performance in the Morris water task was examined in order to verify the effects of exercise on performance in this task. Female rats given access to running wheels preferred a context previously associated with starch, whereas females with no running wheel access preferred a context previously associated with dextrose. No changes in blood glucose were observed. However, cognitive differences in the Morris water task were observed such that voluntary exercise allowed rats to find a new location of a hidden platform following 4 days of training to an old platform location. These results suggest that voluntary exercise may decrease preservative behaviors in a spatial navigation task through the facilitation of plasticity mechanisms. This study is the first of its kind to demonstrate the influence of exercise on taste preference for complex and simple carbohydrates with this context conditioning paradigm.

  20. Understanding How Noncatalytic Carbohydrate Binding Modules Can Display Specificity for Xyloglucan*

    PubMed Central

    Luís, Ana S.; Venditto, Immacolata; Temple, Max J.; Rogowski, Artur; Baslé, Arnaud; Xue, Jie; Knox, J. Paul; Prates, José A.M.; Ferreira, Luís M. A.; Fontes, Carlos M. G. A.; Najmudin, Shabir; Gilbert, Harry J.

    2013-01-01

    Plant biomass is central to the carbon cycle and to environmentally sustainable industries exemplified by the biofuel sector. Plant cell wall degrading enzymes generally contain noncatalytic carbohydrate binding modules (CBMs) that fulfil a targeting function, which enhances catalysis. CBMs that bind β-glucan chains often display broad specificity recognizing β1,4-glucans (cellulose), β1,3-β1,4-mixed linked glucans and xyloglucan, a β1,4-glucan decorated with α1,6-xylose residues, by targeting structures common to the three polysaccharides. Thus, CBMs that recognize xyloglucan target the β1,4-glucan backbone and only accommodate the xylose decorations. Here we show that two closely related CBMs, CBM65A and CBM65B, derived from EcCel5A, a Eubacterium cellulosolvens endoglucanase, bind to a range of β-glucans but, uniquely, display significant preference for xyloglucan. The structures of the two CBMs reveal a β-sandwich fold. The ligand binding site comprises the β-sheet that forms the concave surface of the proteins. Binding to the backbone chains of β-glucans is mediated primarily by five aromatic residues that also make hydrophobic interactions with the xylose side chains of xyloglucan, conferring the distinctive specificity of the CBMs for the decorated polysaccharide. Significantly, and in contrast to other CBMs that recognize β-glucans, CBM65A utilizes different polar residues to bind cellulose and mixed linked glucans. Thus, Gln106 is central to cellulose recognition, but is not required for binding to mixed linked glucans. This report reveals the mechanism by which β-glucan-specific CBMs can distinguish between linear and mixed linked glucans, and show how these CBMs can exploit an extensive hydrophobic platform to target the side chains of decorated β-glucans. PMID:23229556

  1. Carbohydrate specificity of a lectin isolated from the fungus Sclerotium rolfsii.

    PubMed

    Wu, A M; Wu, J H; Tsai, M S; Hegde, G V; Inamdar, S R; Swamy, B M; Herp, A

    2001-09-14

    In order to investigate the functional roles of a phytopathogenic fungal lectin (SRL) isolated from the bodies of Sclerotium rolfsii, the binding properties of SRL were studied by enzyme linked lectinosorbent assay and by inhibition of SRL-glycan interaction. Among glycoproteins (gp) tested for binding, SRL reacted strongly with GalNAc alpha1-->4Ser/Thr (Tn) and/or Gal beta1-->3GalNAc alpha1-->(T(alpha)) containing gps: human T(alpha) and Tn glycophorin, asialo salivary gps, and asialofetuin, but its reactivity toward sialylated glycoproteins was reduced significantly. Of the sugar ligands tested for inhibition of SRL-asialofetuin binding, Thomsen-Friedenreich residue (T(alpha)) was the best, being 22.4 and 2.24 x 10(3) more active than GalNAc and Gal beta1--> residues, respectively. Other ligands tested were inactive. When the glycans used as inhibitors, T(alpha), and/or Tn containing gps, especially asialo PSM, asialo BSM, asialo OSM, active antifreeze gp, asialo glycophorin and Tn-glycophorin were very active, and 1.0 x 10(4) times more potent than GalNAc. From these results, it is clear that the combining site of SRL should be of a cavity type and recognizes only Tn and T(alpha) residues of glycans; it is suggested that T(alpha) and Tn glycotopes, which are present only in abnormal carbohydrate sequences of higher orders of mammal, are the most likely sites for phytopathogenic fungal attachment as an initial step of infection. The affinity of SRL for ligands can be ranked in decreasing order as follows: multivalent T(alpha) and Tn > monomeric T(alpha) and Tn > GalNAc > II (Gal beta1-->4GlcNAc), L (Gal beta1-->4Glc), and Gal. PMID:11589519

  2. Whey or Casein Hydrolysate with Carbohydrate for Metabolism and Performance in Cycling.

    PubMed

    Oosthuyse, T; Carstens, M; Millen, A M E

    2015-07-01

    The protein type most suitable for ingestion during endurance exercise is undefined. This study compared co-ingestion of either 15 g/h whey or casein hydrolysate with 63 g/h fructose: maltodextrin (0.8:1) on exogenous carbohydrate oxidation, exercise metabolism and performance. 2 h postprandial, 8 male cyclists ingested either: carbohydrate-only, carbohydrate-whey hydrolysate, carbohydrate-casein hydrolysate or placebo-water in a crossover, double-blind design during 2 h of exercise at 60%W max followed by a 16-km time trial. Data were evaluated by magnitude-based inferential statistics. Exogenous carbohydrate oxidation, measured from (13)CO2 breath enrichment, was not substantially influenced by co-ingestion of either protein hydrolysate. However, only co-ingestion of carbohydrate-casein hydrolysate substantially decreased (98% very likely decrease) total carbohydrate oxidation (mean±SD, 242±44; 258±47; 277±33 g for carbohydrate-casein, carbohydrate-whey and carbohydrate-only, respectively) and substantially increased (93% likely increase) total fat oxidation (92±14; 83±27; 73±19 g) compared with carbohydrate-only. Furthermore, only carbohydrate-casein hydrolysate ingestion resulted in a faster time trial (-3.6%; 90% CI: ±3.2%) compared with placebo-water (95% likely benefit). However, neither protein hydrolysate enhanced time trial performance when compared with carbohydrate-only. Under the conditions of this study, ingesting carbohydrate-casein, but not carbohydrate-whey hydrolysate, favourably alters metabolism during prolonged moderate-strenuous cycling without substantially altering cycling performance compared with carbohydrate-only.

  3. Cyanobacterial biomass as carbohydrate and nutrient feedstock for bioethanol production by yeast fermentation

    PubMed Central

    2014-01-01

    Background Microbial bioconversion of photosynthetic biomass is a promising approach to the generation of biofuels and other bioproducts. However, rapid, high-yield, and simple processes are essential for successful applications. Here, biomass from the rapidly growing photosynthetic marine cyanobacterium Synechococcus sp. PCC 7002 was fermented using yeast into bioethanol. Results The cyanobacterium accumulated a total carbohydrate content of about 60% of cell dry weight when cultivated under nitrate limitation. The cyanobacterial cells were harvested by centrifugation and subjected to enzymatic hydrolysis using lysozyme and two alpha-glucanases. This enzymatic hydrolysate was fermented into ethanol by Saccharomyces cerevisiae without further treatment. All enzyme treatments and fermentations were carried out in the residual growth medium of the cyanobacteria with the only modification being that pH was adjusted to the optimal value. The highest ethanol yield and concentration obtained was 0.27 g ethanol per g cell dry weight and 30 g ethanol L-1, respectively. About 90% of the glucose in the biomass was converted to ethanol. The cyanobacterial hydrolysate was rapidly fermented (up to 20 g ethanol L-1 day-1) even in the absence of any other nutrient additions to the fermentation medium. Conclusions Cyanobacterial biomass was hydrolyzed using a simple enzymatic treatment and fermented into ethanol more rapidly and to higher concentrations than previously reported for similar approaches using cyanobacteria or microalgae. Importantly, as well as fermentable carbohydrates, the cyanobacterial hydrolysate contained additional nutrients that promoted fermentation. This hydrolysate is therefore a promising substitute for the relatively expensive nutrient additives (such as yeast extract) commonly used for Saccharomyces fermentations. PMID:24739806

  4. Species differences in the carbohydrate binding preferences of surfactant protein D.

    PubMed

    Crouch, Erika C; Smith, Kelly; McDonald, Barbara; Briner, David; Linders, Bruce; McDonald, Joseph; Holmskov, Uffe; Head, James; Hartshorn, Kevan

    2006-07-01

    Interactions of surfactant protein D (SP-D) with micro-organisms and organic antigens involve binding to the trimeric neck plus carbohydrate recognition domain (neck+CRD). In these studies, we compared the ligand binding of homologous human, rat, and mouse trimeric neck+CRD fusion proteins, each with identical N-terminal tags remote from the ligand-binding surface. Although rat and mouse showed similar affinities for saccharide competitors, both differed markedly from the human protein. The human neck+CRD preferentially recognized N-acetyl-mannosamine, whereas the rat and mouse proteins showed greater affinity for myoinositol, maltose, and glucose. Although human neck+CRDs bound to maltosyl-agarose and fungal mannan, only rat and mouse neck+CRDs showed significant binding to maltosyl-Toyopearl beads, solid-phase maltosyl-albumin neo-glycoprotein, or the Phil82 strain of influenza A virus. Likewise, human SP-D dodecamers and trimeric subunits of full-length rat, but not full-length human SP-D trimers, bound to maltosyl-Toyopearl. Site-directed mutagenesis of the human neck+CRD demonstrated an important role of Asp324-Asp325 in the recognition of N-acetyl-mannosamine, and substitution of the corresponding murine sequence (Asn324-Asn325) conferred a capacity to interact with immobilized maltose. Thus, ligand recognition by human SP-D involves a complex interplay between saccharide presentation, the valency of trimeric subunits, and species-specific residues that flank the primary carbohydrate binding site.

  5. Probing the mechanism of ligand recognition in family 29 carbohydrate-binding modules.

    PubMed

    Flint, James; Bolam, David N; Nurizzo, Didier; Taylor, Edward J; Williamson, Michael P; Walters, Christopher; Davies, Gideon J; Gilbert, Harry J

    2005-06-24

    The recycling of photosynthetically fixed carbon, by the action of microbial plant cell wall hydrolases, is integral to one of the major geochemical cycles and is of considerable industrial importance. Non-catalytic carbohydrate-binding modules (CBMs) play a key role in this degradative process by targeting hydrolytic enzymes to their cognate substrate within the complex milieu of polysaccharides that comprise the plant cell wall. Family 29 CBMs have, thus far, only been found in an extracellular multienzyme plant cell wall-degrading complex from the anaerobic fungus Piromyces equi, where they exist as a CBM29-1:CBM29-2 tandem. Here we present both the structure of the CBM29-1 partner, at 1.5 A resolution, and examine the importance of hydrophobic stacking interactions as well as direct and solvent-mediated hydrogen bonds in the binding of CBM29-2 to different polysaccharides. CBM29 domains display unusual binding properties, exhibiting specificity for both beta-manno- and beta-gluco-configured ligands such as mannan, cellulose, and glucomannan. Mutagenesis reveals that "stacking" of tryptophan residues in the n and n+2 subsites plays a critical role in ligand binding, whereas the loss of tyrosine-mediated stacking in the n+4 subsite reduces, but does not abrogate, polysaccharide recognition. Direct hydrogen bonds to ligand, such as those provided by Arg-112 and Glu-78, play a pivotal role in the interaction with both mannan and cellulose, whereas removal of water-mediated interactions has comparatively little effect on carbohydrate binding. The interactions of CBM29-2 with the O2 of glucose or mannose contribute little to binding affinity, explaining why this CBM displays dual gluco/manno specificity. PMID:15784618

  6. Circular Permutation Provides an Evolutionary Link between Two Families of Calcium-dependent Carbohydrate Binding Modules*

    PubMed Central

    Montanier, Cedric; Flint, James E.; Bolam, David N.; Xie, Hefang; Liu, Ziyuan; Rogowski, Artur; Weiner, David P.; Ratnaparkhe, Supriya; Nurizzo, Didier; Roberts, Shirley M.; Turkenburg, Johan P.; Davies, Gideon J.; Gilbert, Harry J.

    2010-01-01

    The microbial deconstruction of the plant cell wall is a critical biological process, which also provides important substrates for environmentally sustainable industries. Enzymes that hydrolyze the plant cell wall generally contain non-catalytic carbohydrate binding modules (CBMs) that contribute to plant cell wall degradation. Here we report the biochemical properties and crystal structure of a family of CBMs (CBM60) that are located in xylanases. Uniquely, the proteins display broad ligand specificity, targeting xylans, galactans, and cellulose. Some of the CBM60s display enhanced affinity for their ligands through avidity effects mediated by protein dimerization. The crystal structure of vCBM60, displays a β-sandwich with the ligand binding site comprising a broad cleft formed by the loops connecting the two β-sheets. Ligand recognition at site 1 is, exclusively, through hydrophobic interactions, whereas binding at site 2 is conferred by polar interactions between a protein-bound calcium and the O2 and O3 of the sugar. The observation, that ligand recognition at site 2 requires only a β-linked sugar that contains equatorial hydroxyls at C2 and C3, explains the broad ligand specificity displayed by vCBM60. The ligand-binding apparatus of vCBM60 displays remarkable structural conservation with a family 36 CBM (CBM36); however, the residues that contribute to carbohydrate recognition are derived from different regions of the two proteins. Three-dimensional structure-based sequence alignments reveal that CBM36 and CBM60 are related by circular permutation. The biological and evolutionary significance of the mechanism of ligand recognition displayed by family 60 CBMs is discussed. PMID:20659893

  7. Nature of the Carbohydrate and Phosphate Associated with ColB2 and EDP208 Pilin

    PubMed Central

    Armstrong, G. D.; Frost, L. S.; Vogel, H. J.; Paranchych, W.

    1981-01-01

    Studies were carried out to elucidate the nature of phosphate and sugar linkages to F-like conjugative pili encoded by the ColB2Fdr (compatibility group FII) and EDP208 (compatibility group FV) plasmids. Both types of pili, when in the intact undissociated state, were found to contain approximately 3 mol of phosphate and 3 mol of sugar per mol of pilin. However, further purification of the two types of pilin by gel filtration chromatography in the presence of sodium dodecyl sulfate (SDS) removed all of the carbohydrate from EDP208 pilin and approximately 65% of the carbohydrate from ColB2 pilin. Approximately 0.8 to 1.0 mol of glucose per mol of protein remained associated with ColB2 pilin after SDS gel filtration chromatography, but it was not possible to determine whether this was covalently linked to the pilin, or tightly associated in an SDS-resistant manner. SDS-gel chromatography did not remove phosphate from either ColB2 or EDP208 pilins. 31P nuclear magnetic resonance studies indicated that the pilin-associated phosphate is involved in a phosphodiester linkage. Acetone precipitation or chloroform-methanol extraction of the purified pilin material reduced the phosphate associated with EDP208 pilin to less than 0.04 molecule per pilin monomer. ColB2 pilin, under the same conditions, retained approximately 0.5 phosphate per pilin monomer. The extracted phosphate-containing moieties were identified as phosphatidylglycerol and phosphatidylethanolamine by thin-layer chromatography. Since the 31P nuclear magnetic resonance spectra for both ColB2 and EDP208 were identical and no signal other than that of a phosphodiester was detected in the ColB2 spectrum, the phosphate remaining with the ColB2 pilin after chloroform-methanol extraction is most likely due to a tightly bound noncovalent residue. Images PMID:6110653

  8. Dietary glycemic index and carbohydrate in relation to early age-related macular degeneration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Little is known about the association between dietary carbohydrates and cataract in nondiabetic persons. The aim was to test whether recent dietary carbohydrate intakes or glycemic index (GI; a measure of carbohydrate intake quality) was associated with the presence of cortical or nuclear opacities....

  9. 21 CFR 172.866 - Synthetic glycerin produced by the hydrogenolysis of carbohydrates.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... of carbohydrates. 172.866 Section 172.866 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... produced by the hydrogenolysis of carbohydrates. Synthetic glycerin produced by the hydrogenolysis of carbohydrates may be safely used in food, subject to the provisions of this section: (a) It shall contain not...

  10. 21 CFR 172.866 - Synthetic glycerin produced by the hydrogenolysis of carbohydrates.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... of carbohydrates. 172.866 Section 172.866 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... produced by the hydrogenolysis of carbohydrates. Synthetic glycerin produced by the hydrogenolysis of carbohydrates may be safely used in food, subject to the provisions of this section: (a) It shall contain not...

  11. 21 CFR 172.866 - Synthetic glycerin produced by the hydrogenolysis of carbohydrates.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... of carbohydrates. 172.866 Section 172.866 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... produced by the hydrogenolysis of carbohydrates. Synthetic glycerin produced by the hydrogenolysis of carbohydrates may be safely used in food, subject to the provisions of this section: (a) It shall contain not...

  12. 21 CFR 172.866 - Synthetic glycerin produced by the hydrogenolysis of carbohydrates.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Synthetic glycerin produced by the hydrogenolysis of carbohydrates. 172.866 Section 172.866 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... carbohydrates. Synthetic glycerin produced by the hydrogenolysis of carbohydrates may be safely used in...

  13. Carbohydrate craving: A double-blind, placebo controlled test of the self-medication hypothesis

    PubMed Central

    Corsica, Joyce A.; Spring, Bonnie J.

    2008-01-01

    Carbohydrate craving, the overwhelming desire to consume carbohydrate-rich foods in an attempt to improve mood, remains a scientifically controversial construct. We tested whether carbohydrate preference and mood enhancement could be demonstrated in a double-blind, placebo-controlled self-administration trial. Overweight females who met strict operational criteria for carbohydrate craving participated in two three-day discrete choice trials over a two-week period. Participants reported their mood before and at several time points after undergoing a dysphoric mood induction and ingesting, under double-blind conditions, either a carbohydrate beverage or a taste-matched protein-rich nutrient balanced beverage. Every third testing day, participants were asked to self-administer the beverage preferred based on its previous mood effect. Results showed that, when rendered mildly dysphoric, carbohydrate cravers chose the carbohydrate beverage significantly more often than protein-rich beverage and reported that carbohydrate produced greater mood improvement. The carbohydrate beverage was perceived as being more palatable by the carbohydrate cravers, although not by independent taste testers who performed the pre-trial taste matching. Results support the existence of a carbohydrate craving syndrome in which carbohydrate ingestion medicates mildly dysphoric mood. PMID:18928908

  14. Effect of Carbohydrate Ingestion on Ratings of Perceived Exertion during a Marathon.

    ERIC Educational Resources Information Center

    Utter, Alan C.; Kang, Jie; Robertson, Robert J.; Nieman, David C.; Chaloupka, Edward C.; Suminski, Richard R.; Piccinni, Cristiana R.

    2002-01-01

    Investigated the effects of carbohydrate substrate availability on ratings of perceived exertion (RPE) and hormonal regulation during a competitive marathon. Data on marathon runners randomly assigned to receive carbohydrate or placebo indicated that those who ingested carbohydrate rather than placebo beverages were able to run at a higher…

  15. Carbohydrate-Loading: A Safe and Effective Method of Improving Endurance Performance.

    ERIC Educational Resources Information Center

    Beeker, Richard T.; Israel, Richard G.

    Carbohydrate-loading prior to distance events is a common practice among endurance athletes. The purposes of this paper are to review previous research and to clarify misconceptions which may exist concerning carbohydrate-loading. The most effective method of carbohydrate-loading involves a training run of sufficient intensity and duration to…

  16. Sports Nutrition for the Primary Care Physician: The Importance of Carbohydrate.

    ERIC Educational Resources Information Center

    Wheeler, Keith B.

    1989-01-01

    Discusses the relationship between nutrition and fatigue and how carbohydrates and timing of carbohydrate consumption can affect fatigued athletes. Nutrition plays a significant role in successful training and competition. Key concerns are the specific needs of athletes for carbohydrates before, during, and after exercise. (Author/SM)

  17. Effects of carbohydrate and caffeine ingestion on performance during a rugby union simulation protocol.

    PubMed

    Roberts, Simon P; Stokes, Keith A; Trewartha, Grant; Doyle, Jenny; Hogben, Patrick; Thompson, Dylan

    2010-06-01

    In this study, we investigated the effect of ingesting carbohydrate alone or with caffeine on performance of a rugby union-specific shuttle running protocol. On three occasions, at least one week apart in a counterbalanced trial order, eight male rugby union forwards ingested either placebo or carbohydrate (1.2 g x kg(-1) body mass x h(-1)) before and during a rugby union-specific protocol, with pre-exercise caffeine ingestion (4 mg x kg(-1)) before one of the carbohydrate trials (carbohydrate + caffeine). The intermittent exercise protocol included walking, jogging, and cruising at pre-determined intensities, simulated contact events, a sustained high-intensity test of speed and agility (Performance Test), and a 15-m sprint. Ratings of perceived exertion (RPE) were recorded every 5 min and a motor skills test was performed after each 21-min block. Performance Test times were not significantly different between trials but the likelihood of 2% improvements for carbohydrate + caffeine over placebo and carbohydrate were 98% and 44%, respectively. For carbohydrate + caffeine, 15-m sprints were faster than for placebo (P=0.05) and the motor skills test was performed faster in the carbohydrate + caffeine trial than the carbohydrate and placebo trials (P < 0.05), while RPE was lower in the carbohydrate + caffeine trial than the carbohydrate and placebo trials (P < 0.05). The results indicate a likely benefit to rugby performance following co-ingestion of carbohydrate and caffeine.

  18. Novel anti-carbohydrate autoantibodies in patients with inflammatory bowel disease: are they useful for clinical practice?

    PubMed

    Malickova, Karin; Lukas, Milan; Donoval, Robert; Sandova, Petra; Janatkova, Ivana

    2006-01-01

    The objective of this study was to test the diagnostic accuracy of novel anti-carbohydrate assays in patients with inflammatory bowel disease, namely in Crohn's disease. These carbohydrate assays are based on oligosaccharide chitobioside carbohydrate - anti-chitobioside carbohydrate antibodies (ACCA), laminaribioside carbohydrate anti-laminaribioside carbohydrate antibodies (ALCA), and mannobioside carbohydrate - anti-mannobioside carbohydrate antibodies (AMCA). We compared these assays with the anti-Saccharomyces cerevisiae antibodies (ASCA) assay. The results of this study suggest that ASCA are still the best serological marker for Crohn's disease. Further studies are required to explore the clinical utility of ACCA, ALCA and AMCA.

  19. Mutational analysis of the pumpkin (Cucurbita maxima) phloem exudate lectin, PP2 reveals Ser-104 is crucial for carbohydrate binding.

    PubMed

    Bobbili, Kishore Babu; Bandari, Shyam; Grobe, Kay; Swamy, Musti J

    2014-07-18

    The pumpkin phloem lectin (PP2) is an RNA-binding, defense-related, chitooligosaccharide-specific, homodimeric lectin of Mr 48 kDa expressed at high concentrations in the sieve elements and companion cells of pumpkin (Cucurbita maxima). In the present study, PP2 was expressed in the methylotrophic yeast Pichia pastoris with the Saccharomyces α-factor sequence to direct the recombinant protein into the secretory pathway as a prerequisite for unimpaired folding and posttranslational glycosylation of recombinant PP2. Previous computational modeling and ligand docking studies predicted a putative chitooligosaccharide-binding site on the PP2 surface, which was divided into three subsites, with two amino acid residues in each subsite identified as possible candidates for interaction with chitooligosaccharides (CHOs). In this work, mutational analysis and hemagglutination assays were employed to verify the role of the predicted residues in the carbohydrate binding activity of the protein. The results obtained revealed that mutation of Ser-104 to Ala (S104A) at subsite-2 resulted in about 90% loss of agglutination activity of the protein, indicating that Ser-104 is crucial for the binding of CHOs to PP2. Also, L100A (at subsite-1) and K200A (at subsite-3) independently decreased the lectin activity by about 40%, indicating that these two residues also contribute significantly to sugar binding by PP2. Together, these findings confirm that all the three subsites contribute to varying degrees toward PP2-carbohydrate interaction, and confirm the validity of the computational model, as proposed earlier.

  20. Widespread occurrence of the tfd-II genes in soil bacteria revealed by nucleotide sequence analysis of 2,4-dichlorophenoxyacetic acid degradative plasmids pDB1 and p712.

    PubMed

    Kim, Dong-Uk; Kim, Min-Sun; Lim, Jong-Sung; Ka, Jong-Ok

    2013-05-01

    Variovorax sp. strain DB1 and Pseudomonas pickettii strain 712 are 2,4-dicholorophenoxy-acetic acid (2,4-D)-degrading bacteria, which were isolated from agricultural soils in Republic of Korea and USA, respectively. Each strain harbors a 2,4-D degradative plasmid and is able to utilize 2,4-D as the sole source of carbon for its growth. The 2,4-D degradative plasmid pDB1 of strain DB1 consisted of a 65,269-bp circular molecule with a G+C content of 66.23% and had 68 ORFs. The 2,4-D degradative plasmid p712 of strain 712 was composed of a 62,798-bp circular molecule with a 62.11% G+C content and had 62 ORFs. The plasmids pDB1 and p712 share significantly homologous 2,4-D degradative genes with high similarity to the tfdR, tfdB-II, tfdC-II, tfdD-II, tfdE-II, tfdF-II, tfdK and tfdA genes of plasmid pJP4 of Alcaligenes eutrophus isolated from Australia. In a phylogenetic analysis with trfA, traL, and trbA genes, pDB1 belonged to IncP-1β with pJP4, while p712 belonged to IncP-1ε with pKJK5 and pEMT3. The results indicated that, in spite of the differences in their backbone regions, the 2,4-D catabolic genes of the two plasmids were closely related and also related to the well-known 2,4-D degradative plasmid pJP4 even though all were isolated from different geographic regions. Other similarities in the genetic organization and the presence of IS1071 suggested that these catabolic genes may be on a transposable element, leading to widespread occurrence in soil bacteria.

  1. Snow on the Seafloor? Methods to Detect Carbohydrates in Deep-sea Sediments Impacted by the Deepwater Horizon Oil Spill

    NASA Astrophysics Data System (ADS)

    Lincoln, S. A.; Freeman, K. H.

    2015-12-01

    A significant portion of the oil released from the Macondo well after the 2010 Deepwater Horizon (DwH) explosion reached the seafloor (1,2). The transfer of buoyant hydrocarbons from the sea surface and subsurface plumes to depths >1500 m, however, is not well understood. A prominent role for sinking marine snow--small, composite particles composed largely of extracellular polymeric substances exuded by algae and bacteria--has been proposed. Snow particles, rich in carbohydrates, may have sorbed and physically entrained oil from the water column as they sank. Several lines of evidence support this scenario: abundant snow was observed 3-4 weeks after the oil spill (3); oil and dispersants can induce marine snow formation (4); and flocculent material covering deep-sea corals near the DwH site contained biomarkers consistent with Macondo oil (5). To investigate whether the chemically complex marine oil snow leaves a direct sedimentary record, we analyzed carbohydrates at high resolution (2 mm intervals) in sediment cores collected at 4 sites in the northern Gulf of Mexico in 2013 using a modified phenol-sulfuric acid spectrophotometric method. We detected a sharp subsurface peak in carbohydrate concentrations near the Macondo well; we interpret this peak as post-DwH marine snow. Coeval carbohydrate, polycyclic aromatic hydrocarbon, and hopane profiles suggest a clear link between marine snow and Macondo oil components, as documented in a 3-year time-series at one site, and enable preliminary conclusions about the delivery and fate of marine snow components in sediments. We also characterized carbohydrates near the wellhead using fluorescent lectin-binding analyses developed for applications in cell biology. Particle morphologies include collapse structures suggestive of a water column origin. Finally, we explore the extent to which polysaccharide residues detected with selective lectins can be used to determine the provenance of marine snow (e.g., bacterial v. algal

  2. Identification of an E-selectin region critical for carbohydrate recognition and cell adhesion [published erratum appears in J Cell Biol 1993 Feb;120(4):1071

    PubMed Central

    1992-01-01

    E-selectin elicits cell adhesion by binding to the cell surface carbohydrate, sialyl Lewis X (sLe(x)). We evaluated the effects of mutations in the E-selectin lectin domain on the binding of a panel of anti-E-selectin mAbs and on the recognition of immobilized sLe(x) glycolipid. Functional residues were then superimposed onto a three- dimensional model of the E-selectin lectin domain. This analysis demonstrated that the epitopes recognized by blocking mAbs map to a patch near the antiparallel beta sheet derived from the NH2 and COOH termini of the lectin domain and two adjacent loops. Mutations that affect sLe(x) binding map to this same region. These results thus define a small region of the E-selectin lectin domain that is critical for carbohydrate recognition. PMID:1382077

  3. Selective preservation of carbohydrates in volcanic ash soils

    NASA Astrophysics Data System (ADS)

    Kaal, J.; Buurman, P.; Nierop, K. G. J.; Piccolo, A.

    2009-04-01

    Volcanic soils (Andosols) are formed in volcanic ash and depending on environmental and climatic factors they develop to two main forms, either allophanic Andosols (dominated by amorphous minerals) or non-allophanic Andosols (dominated by Al/Fe organic matter complexes). Andosols contain the largest amounts of organic carbon of all mineral soil orders. In recent studies using analytical pyrolysis techniques on the soil organic matter (SOM) of allophanic soils from the Azores Islands (Portugal) there was no indication of preservation of plant-derived organic matter by allophane or Al3+, but the presence of large amounts of (microbial) polysaccharides and chitin suggested that secondary organic matter products were stabilized. In the present study we used 13C NMR to further explore the organic matter of the Andosols of the Azores, and applied a molecular mixing model (MMM; ascribing characteristic resonances to the main biocomponent classes carbohydrate, protein, lipid, lignin and char) to the quantified NMR spectra to allow for a quantitative comparison with pyrolysis-GC/MS. The dominance of O-alkyl and di-O-alkyl C in the NMR spectra and carbohydrate contribution to the predictions made by the MMM (50 ± 8%) confirms that the majority of the SOM can still be recognised as carbohydrate. The accumulation of secondary/microbial carbohydrates (and, to a lesser extent, secondary proteinaceous matter and chitins) is thus a key characteristic of these Andosols. NMR-MMM and pyrolysis-GC/MS were in rough agreement. However, NMR does not recognise chitin (N-containing carbohydrate-like material) and chitin-associated protein, nor can it be used to estimate the degree of degradation of the carbohydrates. Therefore, NMR (as applied here) has a very limited capacity for characterisation of the SOM particularly in the Andosols studied. On the other hand, large peaks from carboxylic and amidic functional groups detected by NMR were not observed by pyrolysis-GC/MS. It is therefore

  4. A perspective on the primary and three-dimensional structures of carbohydrates.

    PubMed

    Widmalm, Göran

    2013-08-30

    Carbohydrates, in more biologically oriented areas referred to as glycans, constitute one of the four groups of biomolecules. The glycans, often present as glycoproteins or glycolipids, form highly complex structures. In mammals ten monosaccharides are utilized in building glycoconjugates in the form of oligo- (up to about a dozen monomers) and polysaccharides. Subsequent modifications and additions create a large number of different compounds. In bacteria, more than a hundred monosaccharides have been reported to be constituents of lipopolysaccharides, capsular polysaccharides, and exopolysaccharides. Thus, the number of polysaccharide structures possible to create is huge. NMR spectroscopy plays an essential part in elucidating the primary structure, that is, monosaccharide identity and ring size, anomeric configuration, linkage position, and sequence, of the sugar residues. The structural studies may also employ computational approaches for NMR chemical shift predictions (CASPER program). Once the components and sequence of sugar residues have been unraveled, the three-dimensional arrangement of the sugar residues relative to each other (conformation), their flexibility (transitions between and populations of conformational states), together with the dynamics (timescales) should be addressed. To shed light on these aspects we have utilized a combination of experimental liquid state NMR techniques together with molecular dynamics simulations. For the latter a molecular mechanics force field such as our CHARMM-based PARM22/SU01 has been used. The experimental NMR parameters acquired are typically (1)H,(1)H cross-relaxation rates (related to NOEs), (3)JCH and (3)JCCtrans-glycosidic coupling constants and (1)H,(13)C- and (1)H,(1)H-residual dipolar couplings. At a glycosidic linkage two torsion angles ϕ and ψ are defined and for 6-substituted residues also the ω torsion angle is required. Major conformers can be identified for which highly populated states are

  5. Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.

    PubMed

    Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H; Valafar, Homayoun

    2013-08-22

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work.

  6. Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.

    PubMed

    Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H; Valafar, Homayoun

    2013-01-01

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work. PMID:23973992

  7. Protein Structure Validation and Identification from Unassigned Residual Dipolar Coupling Data Using 2D-PDPA

    PubMed Central

    Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H.; Valafar, Homayoun

    2014-01-01

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work. PMID:23973992

  8. Selective biorecognition and preservation of cell function on carbohydrate-immobilized phosphorylcholine polymers.

    PubMed

    Iwasaki, Yasuhiko; Takami, Utae; Shinohara, Yurika; Kurita, Kimio; Akiyoshi, Kazunari

    2007-09-01

    To obtain synthetic materials capable of selectively recognizing proteins and cells, and preserving their functions, biomembrane mimetic polymers having a phospholipid polar group and carbohydrate side chains were designed. Poly[2-methacryloyloxyethyl phosphorylcholine (MPC)-co-n-butyl methacrylate (BMA)-co-2-lactobionamidoethyl methacrylate (LAMA)] (PMBL) was synthesized and coated on substrates by solvent evaporation. Selective binding of galactose-recognized lectin, RCA120, to a PMBL surface was investigated by measurement of surface plasmon resonance. The binding of RCA120 to the PMBL surface was confirmed by a remarkable change in resonance angle. The apparent affinity constant of RCA120 to PMBL3.0 (3.0 mol % LAMA unit in the feed) per LAMA unit was 2.77 x 10(5) M(-1). When a glucose-recognized lectin, concanavalin A, was in contact with PMBL, no change in the resonance angle was observed, and any nonspecific fouling of protein on PMBL was effectively reduced. Cells of the human hepatocellular liver carcinoma cell line (HepG2) having asialoglycoprotein receptors (ASGPRs) were seeded on polymer surfaces. On poly(BMA) (PBMA), many adherent cells were observed and were well-spread with monolayer adhesion, but cell adhesion was reduced on poly(MPC-co-BMA) (PMB). HepG2 adhesion was observed on PMBL because the cell has ASGPRs; the number of cells adhering to the PMBL polymer surfaces increased with an increase in the density of galactose residues on the surface. In contrast, adhesion of NIH-3T3 cells to PMBL was reduced in a manner similar to that on PMB because the NIH-3T3 cells did not have ASGPRs. Cell adhesion to the PMBL surface was well-regulated by ligand-receptor interactions. Furthermore, some of the cells adhering to the PMBL surface had a spheroid form, and similarly shaped spheroids were scattered on the surface. Although poly(BMA-co-LAMA) (PBL) has galactose residues, the adherent cells were spread in a manner similar to those on PBMA. The MPC units in

  9. The residual caries dilemma.

    PubMed

    Weerheijm, K L; Groen, H J

    1999-12-01

    Restorative dentistry is based on the assumption that bacterial infection of demineralized dentine should prompt operative intervention. One of the concepts of practical dentistry is to create a favourable environment for caries arrest with minimal operative intervention. The progress of remaining primary caries is key to any discussion of this concept. This discussion is important for the atraumatic restorative treatment (ART) approach, since the removal of all carious dentine is sometimes difficult using hand instruments only. In this paper the results of possible measures to guard against the effects of residual carious and its consequences are reviewed, in order to obtain an impression of the justification for (in)complete excavation of occlusal dentinal caries. Three types of measure are considered: isolating the caries process from the oral environment, excavating the carious dentine, and using a cariostatic filling material. Each of these measures contributes to the arrest of the caries process. However, none of these measures can arrest this process by itself. A combination of all three seems necessary. It is concluded that although residual caries does not seem to be the criterion for rerestoration, one has to strive for as complete caries removal as possible. If this cannot be fulfilled the sealing capacities of the filling material seem to be more important than its cariostatic properties. PMID:10600078

  10. Method for improving separation of carbohydrates from wood pulping and wood or biomass hydrolysis liquors

    DOEpatents

    Griffith, William Louis; Compere, Alicia Lucille; Leitten, Jr., Carl Frederick

    2010-04-20

    A method for separating carbohydrates from pulping liquors includes the steps of providing a wood pulping or wood or biomass hydrolysis pulping liquor having lignin therein, and mixing the liquor with an acid or a gas which forms an acid upon contact with water to initiate precipitation of carbohydrate to begin formation of a precipitate. During precipitation, at least one long chain carboxylated carbohydrate and at least one cationic polymer, such as a polyamine or polyimine are added, wherein the precipitate aggregates into larger precipitate structures. Carbohydrate gel precipitates are then selectively removed from the larger precipitate structures. The method process yields both a carbohydrate precipitate and a high purity lignin.

  11. Efficient O-Functionalization of Carbohydrates with Electrophilic Reagents.

    PubMed

    Tolnai, Gergely L; Nilsson, Ulf J; Olofsson, Berit

    2016-09-01

    Novel methodology for O-functionalization of carbohydrate derivatives has been established using bench-stable and easily prepared iodonium(III) reagents. Both electron-withdrawing and electron-donating aryl groups were introduced under ambient conditions and without precautions to exclude air or moisture. Furthermore, the approach was extended both to full arylation of cyclodextrin, and to trifluoroethylation of carbohydrate derivatives. This is the first general approach to introduce traditionally non-electrophilic groups into any of the OH groups around the sugar backbone. The methodology will be useful both in synthetic organic chemistry and biochemistry, as important functional groups can be incorporated under simple and robust reaction conditions in a fast and efficient manner. PMID:27528184

  12. Saccharification of bamboo carbohydrates for the production of ethanol

    SciTech Connect

    De Menezes, T.J.B.; Azzini, A.; Dos Santos, C.L.M.

    1983-04-01

    Bamboo carbohydrates were hydrolyzed with commercial amylases and a mixture of fungal culture broths containing cellulolytic and hemicellulolytic enzymes. The effects of cooking temperature and the size of fiber particles were also investigated. It was found that the higher the cooking temperature, the higher the rate of sugar formation and the lower the viscosity of the slurry. Additions of cellulose and hemicellulose digesting enzymes increased the sugar yield and decreased the viscosity of both the cooked and noncooked slurries. A smaller size of particle appeared to favor the average saccharification rate. Although glucose, xylose, and cellobiose were present in the hydrolysates, only 50% of the total carbohydrate was digested, and 78.9% of this was converted to reducing sugars. The alcohol efficiency for the fermentation of cooked and noncooked mashes by Saccharomyces was about 85%.

  13. High throughput screening of starch structures using carbohydrate microarrays.

    PubMed

    Tanackovic, Vanja; Rydahl, Maja Gro; Pedersen, Henriette Lodberg; Motawia, Mohammed Saddik; Shaik, Shahnoor Sultana; Mikkelsen, Maria Dalgaard; Krunic, Susanne Langgaard; Fangel, Jonatan Ulrik; Willats, William George Tycho; Blennow, Andreas

    2016-01-01

    In this study we introduce the starch-recognising carbohydrate binding module family 20 (CBM20) from Aspergillus niger for screening biological variations in starch molecular structure using high throughput carbohydrate microarray technology. Defined linear, branched and phosphorylated maltooligosaccharides, pure starch samples including a variety of different structures with variations in the amylopectin branching pattern, amylose content and phosphate content, enzymatically modified starches and glycogen were included. Using this technique, different important structures, including amylose content and branching degrees could be differentiated in a high throughput fashion. The screening method was validated using transgenic barley grain analysed during development and subjected to germination. Typically, extreme branching or linearity were detected less than normal starch structures. The method offers the potential for rapidly analysing resistant and slowly digested dietary starches. PMID:27468930

  14. High throughput screening of starch structures using carbohydrate microarrays

    PubMed Central

    Tanackovic, Vanja; Rydahl, Maja Gro; Pedersen, Henriette Lodberg; Motawia, Mohammed Saddik; Shaik, Shahnoor Sultana; Mikkelsen, Maria Dalgaard; Krunic, Susanne Langgaard; Fangel, Jonatan Ulrik; Willats, William George Tycho; Blennow, Andreas

    2016-01-01

    In this study we introduce the starch-recognising carbohydrate binding module family 20 (CBM20) from Aspergillus niger for screening biological variations in starch molecular structure using high throughput carbohydrate microarray technology. Defined linear, branched and phosphorylated maltooligosaccharides, pure starch samples including a variety of different structures with variations in the amylopectin branching pattern, amylose content and phosphate content, enzymatically modified starches and glycogen were included. Using this technique, different important structures, including amylose content and branching degrees could be differentiated in a high throughput fashion. The screening method was validated using transgenic barley grain analysed during development and subjected to germination. Typically, extreme branching or linearity were detected less than normal starch structures. The method offers the potential for rapidly analysing resistant and slowly digested dietary starches. PMID:27468930

  15. The Maillard reaction of bisoprolol fumarate with various reducing carbohydrates.

    PubMed

    Szalka, Mateusz; Lubczak, Jacek; Naróg, Dorota; Laskowski, Marek; Kaczmarski, Krzysztof

    2014-08-01

    HPLC analysis of drug products containing bisoprolol fumarate and lactose revealed the presence of N-formylbisoprolol, which is a final product of the Maillard reaction. Formulations containing secondary amines and reducing carbohydrates are prone to the condensation of amine and carbonyl functional groups and formation of glycosylamines in pharmaceutically relevant conditions. Further rearrangement occurs in the presence of a nucleophile and leads to the formation of 1-deoxy-1-amino-2-ketose also known as the Amadori Rearrangement Product (ARP). The influence of water content, carbohydrate, and lubricant types on the reaction rate was tested. The reaction progress was monitored by HPLC and UV-Vis spectrophotometry. The structures of intermediates were confirmed by the LC/MS(2) analysis. N-formylbisoprolol - the final reaction product - was synthesised and characterised by LC/MS(2), H(1) and C(13) NMR.

  16. Template free synthesis of natural carbohydrates functionalised fluorescent silver nanoclusters.

    PubMed

    Ebrahiminezhad, Alireza; Berenjian, Aydin; Ghasemi, Younes

    2016-06-01

    Template-assisted synthesis is one of the most recognised techniques for fabrication of silver nanoclusters (AgNCs). However, this process is time consuming, toxic and expensive. In this study, the authors report a completely novel approach for the green and facile synthesis of AgNCs using Matricaria chamomilla, without any additional template. Fluorescent and colloidally stable AgNCs with average particle size of 2.4 nm were successfully produced. They found that carbohydrates from Matricaria chamomilla act as an ideal template to generate fluorescent AgNCs. Moreover, oxygen-bearing functional groups were validated to be the active groups for anchoring and reducing of Ag(+) ions. The novel carbohydrate coating method makes the prepared nanoclusters completely hydrophilic and stable in aqueous matrices. PMID:27256890

  17. Alcohol induced changes of carbohydrate metabolism [author's transl].

    PubMed

    Ishii, H; Okuno, F; Joly, J G; Tsuchiya, M

    1978-10-01

    It is evident that ethanol by itself or one of its metabolites produces alterations in transport, metabolism and disposition of carbohydrates. Ethanol acts via changes in the redox state of co-factors; e.g. ethanol-induced hypoglycemia is due, partly, to the inhibition of hepatic gluconeogenesis by ethanol as a consequence of the increased NADH2/NAD ratio in patients whose glycogen stores are already depleted. On the other hand, hyperglycemia has also been described in patients with alcoholism. Although its mechanism is still obscure, abnormal hormonal secretion of insulin, catecholamines and glucocorticoids has been incriminated. Finally, structural changes of the liver and pancreas such as cirrhosis and pancreatitis produced by chronic alcohol consumption should also be considered as pathogenetic factors in a variety of clinical states involving deranged carbohydrate metabolism.

  18. Template free synthesis of natural carbohydrates functionalised fluorescent silver nanoclusters.

    PubMed

    Ebrahiminezhad, Alireza; Berenjian, Aydin; Ghasemi, Younes

    2016-06-01

    Template-assisted synthesis is one of the most recognised techniques for fabrication of silver nanoclusters (AgNCs). However, this process is time consuming, toxic and expensive. In this study, the authors report a completely novel approach for the green and facile synthesis of AgNCs using Matricaria chamomilla, without any additional template. Fluorescent and colloidally stable AgNCs with average particle size of 2.4 nm were successfully produced. They found that carbohydrates from Matricaria chamomilla act as an ideal template to generate fluorescent AgNCs. Moreover, oxygen-bearing functional groups were validated to be the active groups for anchoring and reducing of Ag(+) ions. The novel carbohydrate coating method makes the prepared nanoclusters completely hydrophilic and stable in aqueous matrices.

  19. Carbohydrates in diversity-oriented synthesis: challenges and opportunities.

    PubMed

    Lenci, E; Menchi, G; Trabocchi, A

    2016-01-21

    Over the last decade, Diversity-Oriented Synthesis (DOS) has become a new paradigm for developing large collections of structurally diverse small molecules as probes to investigate biological pathways, and to provide a larger array of the chemical space. Drug discovery and chemical biology are taking advantage of DOS approaches to exploit highly-diverse and complex molecular platforms, producing advances in both target and ligand discovery. In this view, carbohydrates are attractive building blocks for DOS libraries, due to their stereochemical diversity and high density of polar functional groups, thus offering many possibilities for chemical manipulation and scaffold decoration. This review will discuss research contributions and perspectives on the application of carbohydrate chemistry to explore the accessible chemical space through appendage, stereochemical and scaffold diversity.

  20. Orchestration of carbohydrate processing for crassulacean acid metabolism.

    PubMed

    Borland, Anne M; Guo, Hao-Bo; Yang, Xiaohan; Cushman, John C

    2016-06-01

    The production of phosphoenolpyruvate as a substrate for nocturnal CO2 uptake represents a significant sink for carbohydrate in CAM plants which has to be balanced with the provisioning of carbohydrate for growth and maintenance. In starch-storing CAM species, diversification in chloroplast metabolite transporters, and the deployment of both phosphorolytic and hydrolytic routes of starch degradation accommodate a division of labour in directing C-skeletons towards nocturnal carboxylation or production of sucrose for growth. In soluble-sugar storing CAM plants, the vacuole plays a central role in managing carbon homeostasis. The molecular identities of various types of vacuolar sugar transporters have only been identified for C3 species within the last 10 years. The recent availability of CAM genomes enables the identification of putative orthologues of vacuolar sugar transporters which represent strategic targets for orchestrating the diel provisioning of substrate for nocturnal carboxylation and growth. PMID:27101569