D-Galacturonic acid as a highly reactive compound in nonenzymatic browning. 1. Formation of browning active degradation products.

PubMed

Bornik, Maria-Anna; Kroh, Lothar W

2013-04-10

Thermal treatment of an aqueous solution of D-galacturonic acid at pH 3, 5, and 8 led to rapid browning of the solution and to the formation of carbocyclic compounds such as reductic acid (2,3-dihydroxy-2-cyclopenten-1-one), DHCP (4,5-dihydroxy-2-cyclopenten-1-one), and furan-2-carbaldehyde, as degradation products in weak acidic solution. Studies on their formation revealed 2-ketoglutaraldehyde as their common key intermediate. Norfuraneol (4-hydroxy-5-methyl-3-(2H)-furanone) is a typical alkaline degradation product and formed after isomerization. Further model studies revealed reductic acid as an important and more browning active compound than furan-2-carbaldehyde, which led to a red color of the model solution. This red-brown color is also characteristic of thermally treated uronic acid solutions.

Combined enzymatic and colorimetric method for determining the uronic acid and methylester content of pectin: Application to tomato products.

PubMed

Anthon, Gordon E; Barrett, Diane M

2008-09-01

A simple procedure for determining the galacturonic acid and methanol contents of soluble and insoluble pectins, relying on enzymatic pectin hydrolysis and colorimetric quantification, is described. Pectin samples are incubated with a commercial pectinase preparation, Viscozyme, then the galacturonic acid content of the hydrolyzed pectin is quantified colorimetrically using a modification of the Cu reduction procedure originally described by Avigad and Milner. This modification, substituting the commonly used Folin-Ciocalteau reagent for the arsenic containing Nelson reagent, gives a response that is linear, sensitive, and selective for uronic acids over neutral sugars. This method also avoids the use of concentrated acids needed for the commonly used m-phenylphenol method. Methanol, released by the action of the pectin methylesterase found in the Viscozyme, is quantified using alcohol oxidase and Purpald. This combined enzymatic and colorimetric procedure correctly determined the galacturonic acid and methanol content of purified, soluble citrus pectin. Application of the procedure to water insoluble pectins was evaluated with water insoluble material from apples and oranges. In both cases good agreement was obtained between this method and commonly used methods based on chemical pectin hydrolysis. Good agreement between these procedures was also found in the analysis of both soluble and insoluble pectins from several tomato products. Copyright © 2008 Elsevier Ltd. All rights reserved.

Characterization of an acidic polysaccharide isolated from the leaves of Corchorus olitorius (Moroheiya).

PubMed

Ohtani, K; Okai, K; Yamashita, U; Yuasa, I; Misaki, A

1995-03-01

An acidic polysaccharide was isolated from the water-soluble mucilage extracted from dried leaves of Corchorus olitorius, known as Moroheiya in Japan (3.0 g per 100 g). This polysaccharide showed a single peak in a Sepharose CL-6B column, and the specific rotation in H2O at 25 degrees C was +250 degrees. The polysaccharide was rich in uronic acid (65%), and consisted of rhamnose, glucose, galacturonic acid, and glucuronic acid in a molar ratio of 1.0:0.2:0.2:0.9:1.7, in addition to 3.7% of the acetyl group. A methylation analysis, Smith degradation study and fragmentation analysis suggested that this polysaccharide mainly consisted of O-4 substituted galacturonic acid and glucuronic acid, and O-2 substituted rhamnose residues, and that most of the (1-->4)-linked uronic acid residues were substituted at the O-3 position with glucuronic acid residues. This polysaccharide showed proliferative activity toward the murine splenocyte.

Polymerization on the rocks: negatively-charged alpha-amino acids

NASA Technical Reports Server (NTRS)

Hill, A. R. Jr; Bohler, C.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1998-01-01

Oligomers of the negatively-charged amino acids, glutamic acid, aspartic acid, and O-phospho-L-serine are adsorbed by hydroxylapatite and illite with affinities that increase with oligomer length. In the case of oligo-glutamic acids adsorbed on hydroxylapatite, addition of an extra residue results in an approximately four-fold increase in the strength of adsorption. Oligomers much longer than the 7-mer are retained tenaciously by the mineral. Repeated incubation of short oligo-glutamic acids adsorbed on hydroxylapatite or illite with activated monomer leads to the accumulation of oligomers at least 45 units long. The corresponding reactions of aspartic acid and O-phospho-L-serine on hydroxylapatite are less effective in generating long oligomers, while illite fails to accumulate substantial amounts of long oligomers of aspartic acid or of O-phospho-L-serine.

The transcriptional activator GaaR of Aspergillus niger is required for release and utilization of d- galacturonic acid from pectin

DOE PAGES

Alazi, Ebru; Niu, Jing; Kowalczyk, Joanna E.; ...

2016-05-13

We identified the d-galacturonic acid (GA)-responsive transcriptional activator GaaR of the saprotrophic fungus, Aspergillus niger, which was found to be essential for growth on GA and polygalacturonic acid (PGA). Growth of the ΔgaaR strain was reduced on complex pectins. Genome-wide expression analysis showed that GaaR is required for the expression of genes necessary to release GA from PGA and more complex pectins, to transport GA into the cell, and to induce the GA catabolic pathway. Residual growth of ΔgaaR on complex pectins is likely due to the expression of pectinases acting on rhamnogalacturonan and subsequent metabolism of the monosaccharides othermore » than GA.« less

Coccolithophores put a CAP on calcification and carbon

NASA Astrophysics Data System (ADS)

Rickaby, R. E. M.; Lee, R. B. Y.; Mavridou, D. A. I.; Papadakos, G.; McClelland, H. L. O.; Anderson, C. J.

2014-12-01

Unlike the majority of biomineralization, mediated via proteins, the coccolithophores employ acidic polysaccharides (CAPs) as the template for the multitude of intricate calcium carbonate liths which are precipitated inside their cells and expelled to form an external spherical armour. Massive accumulations of these calcium carbonate coccoliths (we estimate a flux of ~ 6x1025 liths/year) form sediments on the deep seafloor, a dominant sink of carbon from the atmosphere over geological timescales, and a buffer for seawater chemistry. This acidic, coccolith-associated polysaccharide (CAP) plays a dual role, likely determined by the calcifying vesicle chemistry, promoting and limiting precipitation. We have developed and demonstrated novel techniques for the extraction and characterisation of these biomineral-mediating molecules, encapsulated and preserved within liths from sediments as old as the Mesozoic. Modern cultures of extant coccolithophores show that the composition of CAP is distinctive for different species, and even strains of e.g. Emiliania huxleyi, suggestive that interactions with galacturonic acid residues are key to dictating the architecture of the liths. Furthermore, it appears that the galacturonic acid content reflects an adaptive response of the CAP to the chemistry within the coccolith vesicle where calcification is induced; in particular the size of the internal carbon pool and inferred saturation state. Extraction of CAPs from the Coccolithale fraction of sediments suggests that the galacturonic acid content of these relatively large and inefficient carbon concentrators evolves in response to declining CO2 availability and thus may provide a novel means for reconstructing paleo pCO2.

Occurrence of lipid A variants with 27-hydroxyoctacosanoic acid in lipopolysaccharides from members of the family Rhizobiaceae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhat, U.R.; Carlson, R.W.; Mayer, H.

1991-04-01

Lipopolysaccharides (LPSs) isolated from several strains of Rhizobium, Bradyrhizobium, Agrobacterium, and Azorhizobium were screened for the presence of 27-hydroxyoctacosanoic acid. The LPSs from all strains, with the exception of Azorhizobium caulinodans, contained various amounts of this long-chain hydroxy fatty acid in the lipid A fractions. Analysis of the lipid A sugars revealed three types of backbones: those containing glucosamine (as found in Rhizobium meliloti and Thizobium fredii), those containing glucosamine and galacturonic acid (as found in Rhizobium leguminosarum bv. phaseoli, trifolii, and viciae), and those containing clucosamine and galacturonic acid (as found in Rhizobium leguminosarum bv. phaseoli, trifolii, and viciae),more » and those containing 2,3-diamino-2,3-dideoxyglucose either alone or in combination with glucosamine (as found in Bradyrhizobium japonicum and Bradyrhizobium sp. (Lupinus) strain DSM 30140). The distribution of 27-hydroxyoctacosamoic acid as well as analysis of lipid A backbone sugars revealed the taxonomic relatedness of various strains of the Rhizobiaceae.« less

Lack of galactose or galacturonic acid in Bradyrhizobium japonicum USDA 110 exopolysaccharide leads to different symbiotic responses in soybean.

PubMed

Quelas, Juan Ignacio; Mongiardini, Elías J; Casabuono, Adriana; López-García, Silvina L; Althabegoiti, M Julia; Covelli, Julieta M; Pérez-Giménez, Julieta; Couto, Alicia; Lodeiro, Aníbal R

2010-12-01

Exopolysaccharide (EPS) and lipopolysaccharide (LPS) from Bradyrhizobium japonicum are important for infection and nodulation of soybean (Glycine max), although their roles are not completely understood. To better understand this, we constructed mutants in B. japonicum USDA 110 impaired in galactose or galacturonic acid incorporation into the EPS without affecting the LPS. The derivative LP 3010 had a deletion of lspL-ugdH and produced EPS without galacturonic acid whereas LP 3013, with an insertion in exoB, produced EPS without galactose. In addition, the strain LP 3017, with both mutations, had EPS devoid of both galactosides. The missing galactosides were not replaced by other sugars. The defects in EPS had different consequences. LP 3010 formed biofilms and nodulated but was defective in competitiveness for nodulation; and, inside nodules, the peribacteroid membranes tended to fuse, leading to the merging of symbiosomes. Meanwhile, LP 3013 and LP 3017 were unable to form biofilms and produced empty pseudonodules but exoB suppressor mutants were obtained when LP 3013 plant inoculation was supplemented with wild-type EPS. Similar phenotypes were observed with all these mutants in G. soja. Therefore, the lack of each galactoside in the EPS has a different functional effect on the B. japonicum-soybean symbiosis.

Extraction of pectins and hemicelluloses from cell walls of suspension culture cells of cotton by endopolygalacturonase treatment

DOE Office of Scientific and Technical Information (OSTI.GOV)

An, Jinhua; Maness, N.O.; Mort, A.J.

1989-04-01

Walls of cotton suspension cultures were treated with a highly purified endopolygalacturonase coded for by a gene from Erwinia carotovora expressed in E. coli. About 80 percent of the walls galacturonic acid was solubilized and could be fractionated by ion exchange chromatography into three classes: (1) tri- and tetra-galacturonides from digestion of homogalacturonans, (2) high molecular weight fragments rich in galacturonic acid, rhamnose and other neutral sugars indicative of rhamnogalacturonan I, and (3) a well defined low molecular weight polymer resembling rhamnogalacturonan II. Treatment of the insoluble wall residue with alkali allowed extraction of the remainder of the wall galacturonicmore » acid as high molecular weight polymers resembling rhamnogalacturonan I but in association with what is probably xyloglucan. The purified polymers will be compared to those obtained by others from different species, especially those of sycamore.« less

Microwave-assisted extraction of pectin from cocoa peel

NASA Astrophysics Data System (ADS)

Sarah, M.; Hanum, F.; Rizky, M.; Hisham, M. F.

2018-02-01

Pectin is a polymer of d-galacturonate acids linked by β-1,4 glycosidic bond. This study isolates pectin from cocoa peel (Theobroma cacao) using citric acid as solvent by microwave-assisted extraction method. Cocoa peels (moisture content of 10%) with citric acid solution (pH of 1.5) irradiated by microwave energy at various microwave power (180, 300, 450 and 600 W) for 10, 15, 20, 25 and 30 minutes respectively. Pectin obtained from this study was collected and filtrated by adding 96% ethanol to precipitate the pectin. The best results obtained from extraction process using microwave power of 180 Watt for 30 minutes. This combination of power and time yielded 42.3% pectin with moisture content, ash content, weight equivalent, methoxyl content and galacturonate levels were 8.08%, 5%, 833.33 mg, 6.51% and 58,08%, respectively. The result finding suggested that microwave-assisted extraction method has a great potency on the commercial pectin production.

Structural studies on HCN oligomers. [catalysts for prebiotic processes

NASA Technical Reports Server (NTRS)

Ferris, J. P.; Edelson, E. H.; Auyeung, J. M.; Joshi, P. C.

1981-01-01

NMR spectral studies on the HCN oligomers suggest the presence of carboxamide and urea groupings. The release of CO2, H2O, HCN, CH3CN, HCONH2 and pyridine on pyrolysis is consistent with the presence of these groupings as well as carboxylic acid groups. No basic primary amine groupings could be detected with fluorescamine. Hydrazinolysis of the HCN oligomers releases 10% of the amino acids normally released by acid hydrolysis. The oligomers give a positive biuret test but this is not due to the presence of peptide bonds. There is no conclusive evidence for the presence of peptide bonds in the HCN oligomers. No diglycine was detected on partial hydrolysis of the HCN oligomers at pH 8.5 suggesting that HCN oligomers were not a source of prebiotic peptides.

Diamines Containing Pendent Phenylethynyl Groups

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Smith, Joseph G., Jr. (Inventor); Hergenrother, Paul M. (Inventor)

1997-01-01

Controlled molecular weight imide oligomers and co-oligomers containing pendent phenylethynyl groups (PEPIs) and endcapped with nonreactive or phenylethynyl groups have been prepared by the cyclodehydration of the precursor amide acid oligomers or co-oligomers containing pendent phenylethynyl groups and endcapped with nonreactive or phenylethynyl groups. The amine terminated amide acid oligomers or co-oligomers are prepared from the reaction of dianhydride(s) with an excess of diamine(s) and diamine containing pendent phenylethynyl groups and subsequently endcapped with a phenylethynyl phthalic anhydride or monofunctional anhydride. The anhydride terminated amide acid oligomers and co-oligomers are prepared from the reaction of diamine(s) and diamine containing pendent phenylethynyl group(s) with an excess of dianhydride(s) and subsequently endcapped with a phenylethynyl amine or monofunctional amine. The polymerizations are carried out in polar aprotic solvents such as and N,N-dimethylacetamide under nitrogen at room temperature. The amide acid oligomers or co-oligomers are subsequently cyclodehydrated either thermally or chemically to the corresponding imide oligomers. The polymers and copolymers prepared from these materials exhibit a unique and unexpected combination of properties that includes higher glass transition temperatures after curing and higher retention of neat resin, adhesive and carbon fiber reinforced mechanical properties at temperatures up to 204 C under wet conditions without sacrificing melt flow behavior and processability as compared to similar materials. These materials are useful as adhesives, coatings, films, moldings, and composite matrices.

Degradation of a Sodium Acrylate Oligomer by an Arthrobacter sp

PubMed Central

Hayashi, Takaya; Mukouyama, Masaharu; Sakano, Kouichi; Tani, Yoshiki

1993-01-01

Arthrobacter sp. strain NO-18 was first isolated from soil as a bacterium which could degrade the sodium acrylate oligomer and utilize it as the sole source of carbon. When 0.2% (wt/wt) oligomer was added to the culture medium, the acrylate oligomer was found to be degraded by 70 to 80% in 2 weeks, using gel permeation chromatography. To determine the maximum molecular weight for biodegradation, the degradation test was done with the hexamer, heptamer, and octamer, which were separated from the oligomer mixture by fractional gel permeation chromatography. The hexamer and heptamer were consumed to the extents of 58 and 36%, respectively, in 2 weeks, but the octamer was not degraded. Oligomers with three different terminal groups were synthesized to examine the effect of the different terminal groups on biodegradation, but few differences were found. Arthrobacter sp. NO-18 assimilated acrylic acid, propionic acid, glutaric acid, 2-methylglutaric acid, and 1,3,5-pentanetricarboxylic acid. Degradation of the acrylic unit structure by this strain is discussed. PMID:8517751

Separation and determination of secoisolariciresinol diglucoside oligomers and their hydrolysates in the flaxseed extract by high-performance liquid chromatography.

PubMed

Li, Xin; Yuan, Jian-Ping; Xu, Shi-Ping; Wang, Jiang-Hai; Liu, Xin

2008-03-28

Flaxseed contains the largest amount of lignan secoisolariciresinol diglucoside (SDG) oligomers and is the richest dietary source of SDG. SDG oligomers in the flaxseed extract are often hydrolyzed to break the ester linkages for the release of SDG and the glycosidic bonds for the release of secoisolariciresinol (SECO). The hydrolysates of SDG oligomers are complicated because of the production of esters in an alcohol-containing medium. In this study, a new gradient reversed-phase high-performance liquid chromatography (HPLC) method has been developed to be suitable for the separation and determination of: (1) SDG oligomers extracted from the defatted flaxseed powder by a 70% aqueous methanol solution; (2) SDG oligomers and their alkaline hydrolysates, including SDG, p-coumaric acid glucoside and its methyl ester, ferulic acid glucoside and its methyl ester in an alkaline hydrolytic solution; and (3) the succedent acid hydrolysates, including secoisolariciresinol monoglucoside (SMG), SECO, anhydrosecoisolariciresinol (anhydro-SECO), p-coumaric acid and its methyl ester, ferulic acid and its methyl ester, 5-hydroxymethyl-2-furfural (HMF) and its degradation product in an acid hydrolytic solution. The content of SDG oligomers in a defatted flaxseed powder was found to be 38.5 mg/g on a dry matter basis, corresponding to a SDG content of 15.4 mg/g, which was determined after alkaline hydrolysis. Furthermore, this study presented a major reaction pathway for the hydrolysis of SDG oligomers.

DNA sequence similarity recognition by hybridization to short oligomers

DOEpatents

Milosavljevic, Aleksandar

1999-01-01

Methods are disclosed for the comparison of nucleic acid sequences. Data is generated by hybridizing sets of oligomers with target nucleic acids. The data thus generated is manipulated simultaneously with respect to both (i) matching between oligomers and (ii) matching between oligomers and putative reference sequences available in databases. Using data compression methods to manipulate this mutual information, sequences for the target can be constructed.

Mechanisms leading to oligomers and SOA through aqueous photooxidation: insights from OH radical oxidation of acetic acid and methylglyoxal

NASA Astrophysics Data System (ADS)

Tan, Y.; Lim, Y. B.; Altieri, K. E.; Seitzinger, S. P.; Turpin, B. J.

2012-01-01

Previous experiments have demonstrated that the aqueous OH radical oxidation of methylglyoxal produces low volatility products including pyruvate, oxalate and oligomers. These products are found predominantly in the particle phase in the atmosphere, suggesting that methylglyoxal is a precursor of secondary organic aerosol (SOA). Acetic acid plays a central role in the aqueous oxidation of methylglyoxal and it is a ubiquitous product of gas phase photochemistry, making it a potential "aqueous" SOA precursor in its own right. However, the fate of acetic acid upon aqueous-phase oxidation is not well understood. In this research, acetic acid (20 μM-10 mM) was oxidized by OH radicals, and pyruvic acid and methylglyoxal experimental samples were analyzed using new analytical methods, in order to better understand the formation of SOA from acetic acid and methylglyoxal. Glyoxylic, glycolic, and oxalic acids formed from acetic acid and OH radicals. In contrast to the aqueous OH radical oxidation of methylglyoxal, the aqueous OH radical oxidation of acetic acid did not produce succinic acid and oligomers. This suggests that the methylgloxal-derived oligomers do not form through the acid catalyzed esterification pathway proposed previously. Using results from these experiments, radical mechanisms responsible for oligomer formation from methylglyoxal oxidation in clouds and wet aerosols are proposed. The importance of acetic acid/acetate as an SOA precursor is also discussed. We hypothesize that this and similar chemistry is central to the daytime formation of oligomers in wet aerosols.

Optimization of pectin extraction from banana peels with citric acid by using response surface methodology.

PubMed

Oliveira, Túlio Ítalo S; Rosa, Morsyleide F; Cavalcante, Fabio Lima; Pereira, Paulo Henrique F; Moates, Graham K; Wellner, Nikolaus; Mazzetto, Selma E; Waldron, Keith W; Azeredo, Henriette M C

2016-05-01

A central composite design was used to determine effects of pH (2.0-4.5), extraction temperature (70-90 °C) and time (120-240 min) on the yield, degree of methoxylation (DM) and galacturonic acid content (GA) of pectins extracted from banana peels with citric acid. Changes in composition during the main steps of pectin extraction were followed by Fourier transform infrared (FTIR) spectroscopy. FTIR was also used to determine DM and GA of pectins. Harsh temperature and pH conditions enhanced the extraction yield, but decreased DM. GA presented a maximum value at 83 °C, 190 min, and pH 2.7. The yield of galacturonic acid (YGA), which took into account both the extraction yield and the pectin purity, was improved by higher temperature and lower pH values. The optimum extraction conditions, defined as those resulting in a maximum YGA while keeping DM at a minimum of 51%, were: 87 °C, 160 min, pH 2.0. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of the A structure

NASA Technical Reports Server (NTRS)

Kozlov, I. A.; Politis, P. K.; Van Aerschot, A.; Busson, R.; Herdewijn, P.; Orgel, L. E.; Bada, J. L. (Principal Investigator); Dolan, M. (Principal Investigator)

1999-01-01

Hexitol nucleic acid (HNA) is an analogue of DNA containing the standard nucleoside bases, but with a phosphorylated 1,5-anhydrohexitol backbone. HNA oligomers form duplexes having the nucleic acid A structure with complementary DNA or RNA oligomers. The HNA decacytidylate oligomer is an efficient template for the oligomerization of the 5'-phosphoroimidazolides of guanosine or deoxyguanosine. Comparison of the oligomerization efficiencies on HNA, RNA, and DNA decacytidylate templates under various conditions suggests strongly that only nucleic acid double helices with the A structure support efficient template-directed synthesis when 5'-phosphoroimidazolides of nucleosides are used as substrates.

Microbial Community-Level Physiological Profiles (CLPP) and herbicide mineralization potential in groundwater affected by agricultural land use

NASA Astrophysics Data System (ADS)

Janniche, Gry Sander; Spliid, Henrik; Albrechtsen, Hans-Jørgen

2012-10-01

Diffuse groundwater pollution from agricultural land use may impact the microbial groundwater community, which was investigated as Community-Level Physiological Profiles (CLPP) using EcoPlate™. Water was sampled from seven piezometers and a spring in a small agricultural catchment with diffuse herbicide and nitrate pollution. Based on the Shannon-Wiener and Simpson's diversity indices the diversity in the microbial communities was high. The response from the EcoPlates™ showed which substrates support groundwater bacteria, and all 31 carbon sources were utilized by organisms from at least one water sample. However, only nine carbon sources were utilized by all water samples: D-Mannitol, N-acetyl-D-glucosamine, putrescine, D-galacturonic acid, itaconic acid, 4-hydroxy benzoic acid, tween 40, tween 80, and L-asparagine. In all water samples the microorganisms preferred D-mannitol, D-galacturonic acid, tween 40, and 4-hydroxy benzoic acid as substrates, whereas none preferred 2-hydroxy benzoic acid, α-D-lactose, D,L-α-glycerol phosphate, α-ketobutyric acid, L-threonine and glycyl-L-glutamic acid. Principal Component Analysis of the CLPP's clustered the most agriculturally affected groundwater samples, indicating that the agricultural land use affects the groundwater microbial communities. Furthermore, the ability to mineralize atrazine and isoproturon, which have been used in the catchment, was also associated with this cluster.

Polymerization on the rocks: theoretical introduction

NASA Technical Reports Server (NTRS)

Orgel, L. E.; Bada, J. L. (Principal Investigator)

1998-01-01

It is difficult if not impossible to synthesize long polymers of amino acids, nucleotides, etc., in homogeneous aqueous solution. We suggest that long polymers were synthesized on the surface of minerals in a prebiotic process analogous to solid-phase synthesis. Provided that the affinity of a mineral for an oligomer increases with the length of the oligomer, adsorption must become essentially irreversible for sufficiently long oligomers. Irreversibly adsorbed oligomers may be elongated indefinitely by repeated cycles in which the mineral with its adsorbed oligomers is first incubated with activated monomers and then washed free of deactivated monomer and side-products. We discuss in some detail the formation of oligomers of negatively-charged amino acids such as glutamic acid on anion-exchange minerals such as hydroxylapatite or illite. We show that the average length of adsorbed oligomers at steady state, n, depends on the balance between the rate of chain elongation and the rate of hydrolysis, and we derive a very approximate formula for n.

Synthesis, physico-chemical properties and complexing abilities of new amphiphilic ligands from D-galacturonic acid.

PubMed

Allam, Anas; Behr, Jean-Bernard; Dupont, Laurent; Nardello-Rataj, Véronique; Plantier-Royon, Richard

2010-04-19

This paper describes a convenient and efficient synthesis of new complexing surfactants from d-galacturonic acid and n-octanol as renewable raw materials in a two-step sequence. In the first step, simultaneous O-glycosidation-esterification under Fischer conditions was achieved. The anomeric ratio of the products was studied based on the main experimental parameters and the activation mode (thermal or microwave). In the second step, aminolysis of the n-octyl ester was achieved with various functionalized primary amines under standard thermal or microwave activation. The physico-chemical properties of these new amphiphilic ligands were measured and these compounds were found to exhibit interesting surface properties. Complexing abilities of one uronamide ligand functionalized with a pyridine moiety toward Cu(II) ions was investigated in solution by EPR titrations. A solid compound was also synthesized and characterized, its relative structure was deduced from spectroscopic data. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Characterisation of pectins extracted from banana peels (Musa AAA) under different conditions using an experimental design.

PubMed

Happi Emaga, Thomas; Ronkart, Sébastien N; Robert, Christelle; Wathelet, Bernard; Paquot, Michel

2008-05-15

An experimental design was used to study the influence of pH (1.5 and 2.0), temperature (80 and 90°C) and time (1 and 4h) on extraction of pectin from banana peels (Musa AAA). Yield of extracted pectins, their composition (neutral sugars, galacturonic acid, and degree of esterification) and some macromolecular characteristics (average molecular weight, intrinsic viscosity) were determined. It was found that extraction pH was the most important parameter influencing yield and pectin chemical composition. Lower pH values negatively affected the galacturonic acid content of pectin, but increased the pectin yield. The values of degree of methylation decreased significantly with increasing temperature and time of extraction. The average molecular weight ranged widely from 87 to 248kDa and was mainly influenced by pH and extraction time. Copyright © 2007 Elsevier Ltd. All rights reserved.

Structural characterization of anti-complementary polysaccharides from the leaves of Artemisia princeps.

PubMed

Yamada, H; Otsuka, Y; Omura, S

1986-08-01

Structural characterizations of the anti-complementary acidic heteroglycans, AAF IIb-2 and IIb-3, obtained from the leaves of Artemisia princeps pamp have been studied. AAF IIb-2 consists of rhamnose, xylose, arabinose, galactose, glucose and uronic acids (glucuronic acid and galacturonic acid) in the molar ratio of 7.6:7.6:13.0:10.9:3.0:57.9, and AAF IIb-3 consists of the same sugars in the ratio of 3.9:2.6:24.7:19.7:2.6:46.5. Methylation analysis including carboxyl-reduction and also selective enzymolysis using EXO-alpha- L-arabinofuranosidase suggested that AAF IIb-3 has a main chain consisting of (1-->4)-linked galacturonic acid and (1-->2)-linked rhamnose mostly substituted at the O-4 position. AAF IIb-3 also contained arabino-3,6-galactan moiety and most of the arabinose was present as an alpha- L-furanosyl residue in the non-reducing terminals and highly branched side chains which mostly attached to the O-3 position of (1-->6)-linked galactopyranosyl residue. The basic structure of AAF IIb-2 is similar to that of AAF IIb-3, but IIb-3 has a higher arabinogalactan content than IIb-2.

Imide Oligomers Endcapped with Phenylethynl Phthalic Anhydrides and Polymers Therefrom

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

1998-01-01

Controlled molecular weight phenylethynyl terminated imide oligomers (PETIs) have been prepared by the cyclodehydration of precursor phenylethynyl terminated amic acid oligomers. Amino terminated amic acid oligomers are prepared from the reaction of dianhydride(s) with an excess of diamine(s) and subsequently endcapped with phenylethynyl phthalic anhydride(s) (PEPA). The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N.N-dimethylacetamide under nitrogen at room temperature. The amic acid oligomers are subsequently cyclodehydrated either thermally or cheznicauy to the corresponding imide oligomers. Direct preparation of PETIs from the reaction of dianhydxide(s) with an excess of diamine(s) and endcapped with phenylethynyl phthalic anhydride(s) has been performed in m-cresol. Phenylethynyl phthalic anhydrides are synthesized by the palladium catalyzed reaction of phenylacetylene with bromo substituted phthalic anhydrides in triethylamine. These new materials exhibit excellent properties and are potentially useful as adhesives, coatings, films, moldings and composite matrices.

Imide oligomers endcapped with phenylethynyl phthalic anhydrides and polymers therefrom

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Smith, Jr., Joseph G. (Inventor)

1996-01-01

Controlled molecular weight phenylethynyl terminated imide oligomers (PETIs) have been prepared by the cyclodehydration of precursor phenylethynyl terminated amic acid oligomers. Amino terminated amic acid oligomers are prepared from the reaction of dianhydride(s) with an excess of diamine(s) and subsequently endcapped with phenylethynyl phthalic anhydride(s) (PEPA). The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide under nitrogen at room temperature. The amic acid oligomers are subsequently cyclodehydrated either thermally or chemically to the corresponding imide oligomers. Direct preparation of PETIs from the reaction of dianhydride(s) with an excess of diamine(s) and endcapped with phenylethynyl phthalic anhydride(s) has been performed in m-cresol. Phenylethynyl phthalic anhydrides are synthesized by the palladium catalyzed reaction of phenylacetylene with bromo substituted phthalic anhydrides in triethylamine. These new materials exhibit excellent properties and are potentially useful as adhesives, coatings, films, moldings and composite matrices.

Automated UV-C mutagenesis of Kluyveromyces marxianus NRRL Y-1109 and selection for microaerophilic growth and ethanol production at elevated temperature on biomass sugars.

PubMed

Hughes, Stephen R; Bang, Sookie S; Cox, Elby J; Schoepke, Andrew; Ochwat, Kate; Pinkelman, Rebecca; Nelson, Danielle; Qureshi, Nasib; Gibbons, William R; Kurtzman, Cletus P; Bischoff, Kenneth M; Liu, Siqing; Cote, Gregory L; Rich, Joseph O; Jones, Marjorie A; Cedeño, David; Doran-Peterson, Joy; Riaño-Herrera, Nestor M; Rodríguez-Valencia, Nelson; López-Núñez, Juan C

2013-08-01

The yeast Kluyveromyces marxianus is a potential microbial catalyst for fuel ethanol production from a wide range of biomass substrates. To improve its growth and ethanol yield at elevated temperature under microaerophilic conditions, K. marxianus NRRL Y-1109 was irradiated with UV-C using automated protocols on a robotic platform for picking and spreading irradiated cultures and for processing the resulting plates. The plates were incubated under anaerobic conditions on xylose or glucose for 5 mo at 46 °C. Two K. marxianus mutant strains (designated 7-1 and 8-1) survived and were isolated from the glucose plates. Both mutant strains, but not wild type, grew aerobically on glucose at 47 °C. All strains grew anaerobically at 46 °C on glucose, galactose, galacturonic acid, and pectin; however, only 7-1 grew anaerobically on xylose at 46 °C. Saccharomyces cerevisiae NRRL Y-2403 did not grow at 46 °C on any of these substrates. With glucose as a carbon source, ethanol yield after 3 d at 46 °C was higher for 8-1 than for wild type (0.51 and 0.43 g ethanol/g glucose, respectively). With galacturonic acid as a carbon source, the ethanol yield after 7 d at 46 °C was higher for 7-1 than for wild type (0.48 and 0.34 g ethanol/g galacturonic acid, respectively). These mutant strains have potential application in fuel ethanol production at elevated temperature from sugar constituents of starch, sucrose, pectin, and cellulosic biomass.

Hydrolysis kinetics of secoisolariciresinol diglucoside oligomers from flaxseed.

PubMed

Yuan, Jian-Ping; Li, Xin; Xu, Shi-Ping; Wang, Jiang-Hai; Liu, Xin

2008-11-12

Flaxseed is the richest dietary source of the lignan secoisolariciresinol diglucoside (SDG) and contains the largest amount of SDG oligomers, which are often hydrolyzed to break the ester linkages for the release of SDG and the glycosidic bonds for the release of secoisolariciresinol (SECO). The alkaline hydrolysis reaction kinetics of SDG oligomers from flaxseed and the acid hydrolysis process of SDG and other glucosides were investigated. For the kinetic modeling, a pseudo-first-order reaction was assumed. The results showed that the alkaline hydrolysis of SDG oligomers followed first-order reaction kinetics under mild alkaline hydrolytic conditions and that the concentration of sodium hydroxide had a strong influence on the activation energy of the alkaline hydrolysis of SDG oligomers. The results also indicated that the main acid hydrolysates of SDG included secoisolariciresinol monoglucoside (SMG), SECO, and anhydrosecoisolariciresinol (anhydro-SECO) and that the extent and the main hydrolysates of the acid hydrolysis reaction depended on the acid concentration, hydrolysis temperature, and time. In addition, the production and change of p-coumaric acid glucoside, ferulic acid glucoside and their methyl esters and p-coumaric acid, ferulic acid, and their methyl esters during the process of hydrolysis was also investigated.

HCN - A plausible source of purines, pyrimidines and amino acids on the primitive earth

NASA Technical Reports Server (NTRS)

Ferris, J.-P.; Joshi, P. C.; Edelson, E. H.; Lawless, J. G.

1978-01-01

Dilute (0.1 M) solutions of HCN condense to oligomers at pH 9.2, and hydrolysis of these oligomers yields 4,5-dihydroxypyrimidine, orotic acid, 5-hydroxyuracil, adenine, 4-aminoimidazole-5-carboxamide, and amino acids. It is suggested that the three main classes of nitrogen-containing biomolecules - purines, pyrimidines, and amino acids may have originated from HCN on the primitive earth. It is also suggested that the presence of orotic acid and 4-aminoimidazole-5-carboxamide might indicate that contemporary biosynthetic pathways for nucleotides evolved from the compounds released on hydrolysis of HCN oligomers.

Size-Dependent Affinity of Glycine and Its Short Oligomers to Pyrite Surface: A Model for Prebiotic Accumulation of Amino Acid Oligomers on a Mineral Surface

PubMed Central

Afrin, Rehana; Ganbaatar, Narangerel; Aono, Masashi; Cleaves, H. James; Yano, Taka-aki; Hara, Masahiko

2018-01-01

The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been proposed as an important step in many origins of life scenarios. To investigate such notions, we used AFM-based force measurements to probe possible non-covalent interactions between pyrite and amino acids, starting from the simplest amino acid, Gly. Although Gly itself interacted with the pyrite surface only weakly, progressively larger unbinding forces and binding frequencies were obtained using oligomers from di-Gly to penta-Gly. In addition to an expected increase of the configurational entropy and size-dependent van der Waals force, the increasing number of polar peptide bonds, among others, may be responsible for this observation. The effect of chain length was also investigated by performing similar experiments using l-lysine vs. poly-l-lysine (PLL), and l-glutamic acid vs. poly-l-glutamic acid. The results suggest that longer oligomers/polymers of amino acids can be preferentially adsorbed on pyrite surfaces. PMID:29370126

Phenylethynyl Phthalic Anhydride

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

1997-01-01

Controlled molecular weight PhenylEthynyl Terminated Imide oligomers (PETIs) have been prepared by the cyclodehydration of precursor phenylethynyl terminated amic acid oligomers. Amino terminated amic acid oligomers are prepared from the reaction of dianhydride(s) with an excess of diamine(s) and subsequently endcapped with PhenylEthynyl Phthalic Anhydride(s) (PEPA). The polymerizations are carried out in polar aprotic solvents such as N-methyl-2pyrrolidinone or N N-dimethylacetamide under nitrogen at room temperature. The amic acid oligomers are subsequently cyclodehydrated either thermally or chemically to the corresponding imide oligomers. Direct preparation of PETIs from the reaction of dianhydride(s) with an excess of diamine(s) and endcapped with phenylethynyl phthalic anhydride(s) has been performed in m-cresol. Phenylethynyl phthalic anhydrides are synthesized by the palladium catalyzed reaction of phenylacetylene with bromo substituted phthalic anhydrides in triethylamine. These new materials exhibit excellent properties and are potentially useful as adhesives, coatings, films, moldings and composite matrices.

Purification, crystallization and preliminary X-ray diffraction analysis of a novel keto-deoxy-d-galactarate (KDG) dehydratase from Agrobacterium tumefaciens

PubMed Central

Taberman, Helena; Andberg, Martina; Parkkinen, Tarja; Richard, Peter; Hakulinen, Nina; Koivula, Anu; Rouvinen, Juha

2014-01-01

d-Galacturonic acid is the main component of pectin. It could be used to produce affordable renewable fuels, chemicals and materials through biotechnical conversion. Keto-deoxy-d-galactarate (KDG) dehydratase is an enzyme in the oxidative pathway of d-galacturonic acid in Agrobacterium tumefaciens (At). It converts 3-deoxy-2-keto-l-threo-hexarate to α-ketoglutaric semialdehyde. At KDG dehydratase was crystallized by the hanging-drop vapour-diffusion method. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 169.1, b = 117.8, c = 74.3 Å, β = 112.4° and an asymmetric unit of four monomers. X-ray diffraction data were collected to 1.9 Å resolution using synchrotron radiation. The three-dimensional structure of At KDG dehydratase will provide valuable information on the function of the enzyme and will allow it to be engineered for biorefinery-based applications. PMID:24419616

Extraction, characterization and gelling behavior enhancement of pectins from the cladodes of Opuntia ficus indica.

PubMed

Lefsih, Khalef; Delattre, Cédric; Pierre, Guillaume; Michaud, Philippe; Aminabhavi, Tejraj M; Dahmoune, Farid; Madani, Khodir

2016-01-01

Total Pectins Fraction (TPF) was extracted at room temperature from dried cladodes of Opuntia ficus indica. TPF is constituted of three pectic fractions WSP, CSP and ASP, which are made up of 66.6%, 44.3% and 81.1% (w/w) of galacturonic acid, respectively. The antioxidant ability of TPF increased with the concentration increasing. It scavenged hydroxyl radical by 90% and chelated 90% of ferrous ions at 5 g/L. FTIR study was carried out. Strong characteristic absorption peaks at 1,618 cm(-1) assigned to the vibration of COO(-) group of galacturonic acid. In the fingerprint region, we noticed three well-defined peaks at 1054, 1085, and 1,154 cm(-1) characteristic of pectic polysaccharides. TPF are non-gelling pectins. The co-crosslinking of TPF with carrageenan was carried out and the gelling behavior was successfully improved. Thermo-sensitive hydrogel was obtained with 82% of TPF and 18% of carrageenan (w/w). Copyright © 2015 Elsevier B.V. All rights reserved.

Quinoa (Chenopodium quinoa W.) and amaranth (Amaranthus caudatus L.) provide dietary fibres high in pectic substances and xyloglucans.

PubMed

Lamothe, Lisa M; Srichuwong, Sathaporn; Reuhs, Bradley L; Hamaker, Bruce R

2015-01-15

Dietary fibre of quinoa and amaranth was analysed for its insoluble and soluble fibre content, composition, and structure. Total dietary fibre content was 10% for quinoa and 11% for amaranth. For both pseudocereals, 78% of its dietary fibre was insoluble. Insoluble fibre (IDF) from quinoa and amaranth was mainly composed of galacturonic acid, arabinose, galactose, xylose and glucose. Linkage analysis indicated that IDF was composed of homogalacturonans and rhamnogalacturonan-I with arabinan side-chains (∼55-60%), as well as highly branched xyloglucans (∼30%) and cellulose. For both pseudocereals, 22% of total dietary fibre was soluble; a higher proportion than that found in wheat and maize (∼15%). The soluble fibre (SDF) was composed of glucose, galacturonic acid and arabinose; for amaranth, xylose was also a major constituent. Xyloglucans made up ∼40-60% of the SDF and arabinose-rich pectic polysaccharides represented ∼34-55%. Copyright © 2014. Published by Elsevier Ltd.

Mechanisms leading to oligomers and SOA through aqueous photooxidation: insights from OH radical oxidation of acetic acid

NASA Astrophysics Data System (ADS)

Tan, Y.; Lim, Y. B.; Altieri, K. E.; Seitzinger, S. P.; Turpin, B. J.

2011-06-01

Previous experiments have demonstrated that the aqueous OH radical oxidation of methylglyoxal produces low volatility products including oxalate and oligomers. These products are found predominantly in the particle phase in the atmosphere, suggesting that methylglyoxal is a precursor of secondary organic aerosol (SOA). Acetic acid is an important intermediate in aqueous methylglyoxal oxidation and a ubiquitous product of gas phase photochemistry, making it a potential "aqueous" SOA precursor in its own right. Altieri et al. (2008) proposed that acetic acid was the precursor of oligoesters observed in methylglyoxal oxidation. However, the fate of acetic acid upon aqueous-phase oxidation is not well understood. In this research, acetic acid at concentrations relevant to atmospheric waters (20 μM-10 mM) was oxidized by OH radical. Products were analyzed by ion chromatography (IC), electrospray ionization mass spectrometry (ESI-MS), and IC-ESI-MS. The formation of glyoxylic, glycolic, and oxalic acids were observed. In contrast to methylglyoxal oxidation, succinic acid and oligomers were not detected. Using results from these and methylglyoxal + OH radical experiments, radical mechanisms responsible for oligomer formation from methylglyoxal oxidation in clouds and wet aerosols are proposed. The importance of acetic acid/acetate as an SOA precursor is also discussed. We hypothesize that this and similar chemistry is central to the daytime formation of oligomers in wet aerosols.

Chemical evolution. XXI - The amino acids released on hydrolysis of HCN oligomers

NASA Technical Reports Server (NTRS)

Ferris, J. P.; Wos, J. D.; Nooner, D. W.; Oro, J.

1974-01-01

Major amino acids released by hydrolysis of acidic and basic HCN oligomers are identified by chromatography as Gly, Asp, and diaminosuccinic acid. Smaller amounts of Ala, Ile and alpha-aminoisobutyric acid are also detected. The amino acids released did not change appreciably when the hydrolysis medium was changed from neutral to acidic or basic. The presence of both meso and d, l-diaminosuccinic acids was established by paper chromatography and on an amino acid analyzer.

Phenylethynyl terminated imide oligomers

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Bryant, Robert G. (Inventor); Jensen, Brian J. (Inventor); Havens, Stephen J. (Inventor)

1994-01-01

Four phenylethynyl amine compounds - 3 and 4-aminophenoxy-4'-phenylethynylbenzophenone, and 3 and 4-amino-4'-phenylethynylbenzophenone - were readily prepared and were used to endcap imide oligomers. Phenylethynyl-terminated amide acid oligomers and phenylethynyl-terminated imide oligomers with various molecular weights and compositions were prepared and characterized. These oligomers were cured at 300 to 400 C to provide crosslinked polyimides with excellent solvent resistance, high strength and modulus, and good high temperature properties. Adhesive panels, composites, films, and moldings from these phenylethynyl terminated imide oligomers gave excellent mechanical performance.

Phenylethynyl terminated imide oligomers

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Bryant, Robert G. (Inventor); Jensen, Brian J. (Inventor); Havens, Stephen J. (Inventor)

1995-01-01

Four phenylethynyl amine compounds - 3 and 4-aminophenoxy-4'-phenylethynylbenzophenone, and 3 and 4-amino-4'-phenylethynylbenzophenone - were readily prepared and were used to endcap imide oligomers. Phenylethynyl-terminated amide acid oligomers and phenylethynyl-terminated imide oligomers with various molecular weights and compositions were prepared and characterized. These oligomers were cured at 300 to 400 C to provide crosslinked polyimides with excellent solvent resistance, high strength and modulus, and good high temperature properties. Adhesive panels, composites, films, and moldings from these phenylethynyl terminated imide oligomers gave excellent mechanical performance.

Effects of microwave power and irradiation time on pectin extraction from watermelon rinds (Citrullus lanatus) with acetic acid using microwave assisted extraction method

NASA Astrophysics Data System (ADS)

Sari, A. M.; Ishartani, D.; Dewanty, P. S.

2018-01-01

The aims of this research are to study the effect of microwave power (119.7 W, 199.5 W and 279.3 W) and irradiation time (6, 9 and 12 min) on pectin extraction by using Microwave Assisted Extraction (MAE) with acetic acid and to do a preliminary characterization of pectin from watermelon rinds. A randomized factorial design with two factors was used to determine the effect of microwave power and processing time on the yield, equivalent weight, degree of methoxylation (DM), galacturonic acid content (GA) and the degree of esterification (DE) of extracted pectin. The results showed that extracted pectin from watermelon rinds using MAE method have yield ranged from 3.925% to 5.766%, with equivalent weight ranged from 1249.702 to 2007.756. Extracted pectin have a DM value ranged from 3.89% to 10.81%. Galacturonic acid content that meets with IPPA standard resulted from extraction condition of 279.3-watt microwave power for 9 min and 12 min. The degree of esterification (DE) value ranged from 56.86% to 85.76%, and this value exhibited a relatively high methoxyl pectin (>50%). The best pectin properties was obtained at a microwave power of 279.3 watts for 12 min.

Expression and characterization of hyperthermostable exo-polygalacturonase RmGH28 from Rhodothermus marinus

USDA-ARS?s Scientific Manuscript database

The gene RmGH28 from the organism Rhodothermus marinus putatively encoding a glycosyl hydrolase family 28 polygalacturonase was expressed in E. coli, and the enzyme purified and biochemically characterized. The gene was found to encode an exo- polygalacturonase, with galacturonic acid monomer and th...

Comparative Toxicity of Halogenated Hydrocarbons: Molecular Aspects

DTIC Science & Technology

1993-07-13

peroxisome proliferators, namely perfluorooctanoic acid ( PFOA ), perfluorodecanoic acid ( PFDA ) and the tri-and tetra-oligomers of chlorotrifluooethylene...ACID ( PFOA ), PERFLUORO - DECANOIC ACID ( PFDA ) AND THE TRI-AND TETRA-OLIGOMERS OF CHLORO -TR.tLUORO ETHYLENE (CTFE) HAVE BEEN INVESTIGATED IN THE RAT AND...AVAILABILITY STATEMENT 12b. DISTRIBUTION CODE NO LIMITATION NOT KNOWN 13. ABSTRACT (Maximum 200 words) THE COMPARATIVE HEPATOTOXICITIES OF PERFLUOROOCTANOIC

A simple procedure for preparing chitin oligomers through acetone precipitation after hydrolysis in concentrated hydrochloric acid.

PubMed

Kazami, Nao; Sakaguchi, Masayoshi; Mizutani, Daisuke; Masuda, Tatsuhiko; Wakita, Satoshi; Oyama, Fumitaka; Kawakita, Masao; Sugahara, Yasusato

2015-11-05

Chitin oligomers are of interest because of their numerous biologically relevant properties. To prepare chitin oligomers containing 4-6 GlcNAc units [(GlcNAc)4-6], α- and β-chitin were hydrolyzed with concentrated hydrochloric acid at 40 °C. The reactant was mixed with acetone to recover the acetone-insoluble material, and (GlcNAc)4-6 was efficiently recovered after subsequent water extraction. Composition analysis using gel permeation chromatography and MALDI-TOF mass spectrometry indicated that (GlcNAc)4-6 could be isolated from the acetone-insoluble material with recoveries of approximately 17% and 21% from the starting α-chitin and β-chitin, respectively. The acetone precipitation method is highly useful for recovering chitin oligomers from the acid hydrolysate of chitin. The changes in the molecular size and higher-order structure of chitin during the course of hydrolysis were also analyzed, and a model that explains the process of oligomer accumulation is proposed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sequence-specific unusual (1-->2)-type helical turns in alpha/beta-hybrid peptides.

PubMed

Prabhakaran, Panchami; Kale, Sangram S; Puranik, Vedavati G; Rajamohanan, P R; Chetina, Olga; Howard, Judith A K; Hofmann, Hans-Jörg; Sanjayan, Gangadhar J

2008-12-31

This article describes novel conformationally ordered alpha/beta-hybrid peptides consisting of repeating l-proline-anthranilic acid building blocks. These oligomers adopt a compact, right-handed helical architecture determined by the intrinsic conformational preferences of the individual amino acid residues. The striking feature of these oligomers is their ability to display an unusual periodic pseudo beta-turn network of nine-membered hydrogen-bonded rings formed in the forward direction of the sequence by 1-->2 amino acid interactions both in solid-state and in solution. Conformational investigations of several of these oligomers by single-crystal X-ray diffraction, solution-state NMR, and ab initio MO theory suggest that the characteristic steric and dihedral angle restraints exerted by proline are essential for stabilizing the unusual pseudo beta-turn network found in these oligomers. Replacing proline by the conformationally flexible analogue alanine (Ala) or by the conformationally more constrained alpha-amino isobutyric acid (Aib) had an adverse effect on the stabilization of this structural architecture. These findings increase the potential to design novel secondary structure elements profiting from the steric and dihedral angle constraints of the amino acid constituents and help to augment the conformational space available for synthetic oligomer design with diverse backbone structures.

Aβ42-oligomer Interacting Peptide (AIP) neutralizes toxic amyloid-β42 species and protects synaptic structure and function

NASA Astrophysics Data System (ADS)

Barucker, Christian; Bittner, Heiko J.; Chang, Philip K.-Y.; Cameron, Scott; Hancock, Mark A.; Liebsch, Filip; Hossain, Shireen; Harmeier, Anja; Shaw, Hunter; Charron, François M.; Gensler, Manuel; Dembny, Paul; Zhuang, Wei; Schmitz, Dietmar; Rabe, Jürgen P.; Rao, Yong; Lurz, Rudi; Hildebrand, Peter W.; McKinney, R. Anne; Multhaup, Gerhard

2015-10-01

The amyloid-β42 (Aβ42) peptide is believed to be the main culprit in the pathogenesis of Alzheimer disease (AD), impairing synaptic function and initiating neuronal degeneration. Soluble Aβ42 oligomers are highly toxic and contribute to progressive neuronal dysfunction, loss of synaptic spine density, and affect long-term potentiation (LTP). We have characterized a short, L-amino acid Aβ-oligomer Interacting Peptide (AIP) that targets a relatively well-defined population of low-n Aβ42 oligomers, rather than simply inhibiting the aggregation of Aβ monomers into oligomers. Our data show that AIP diminishes the loss of Aβ42-induced synaptic spine density and rescues LTP in organotypic hippocampal slice cultures. Notably, the AIP enantiomer (comprised of D-amino acids) attenuated the rough-eye phenotype in a transgenic Aβ42 fly model and significantly improved the function of photoreceptors of these flies in electroretinography tests. Overall, our results indicate that specifically “trapping” low-n oligomers provides a novel strategy for toxic Aβ42-oligomer recognition and removal.

Genome-Wide Identification and Expression Analysis of the UGlcAE Gene Family in Tomato.

PubMed

Ding, Xing; Li, Jinhua; Pan, Yu; Zhang, Yue; Ni, Lei; Wang, Yaling; Zhang, Xingguo

2018-05-27

The UGlcAE has the capability of interconverting UDP-d-galacturonic acid and UDP-d-glucuronic acid, and UDP-d-galacturonic acid is an activated precursor for the synthesis of pectins in plants. In this study, we identified nine UGlcAE protein-encoding genes in tomato. The nine UGlcAE genes that were distributed on eight chromosomes in tomato, and the corresponding proteins contained one or two trans-membrane domains. The phylogenetic analysis showed that SlUGlcAE genes could be divided into seven groups, designated UGlcAE1 to UGlcAE6 , of which the UGlcAE2 were classified into two groups. Expression profile analysis revealed that the SlUGlcAE genes display diverse expression patterns in various tomato tissues. Selective pressure analysis indicated that all of the amino acid sites of SlUGlcAE proteins are undergoing purifying selection. Fifteen stress-, hormone-, and development-related elements were identified in the upstream regions (0.5 kb) of these SlUGlcAE genes. Furthermore, we investigated the expression patterns of SlUGlcAE genes in response to three hormones (indole-3-acetic acid (IAA), gibberellin (GA), and salicylic acid (SA)). We detected firmness, pectin contents, and expression levels of UGlcAE family genes during the development of tomato fruit. Here, we systematically summarize the general characteristics of the SlUGlcAE genes in tomato, which could provide a basis for further function studies of tomato UGlcAE genes.

Phenylethynyl amine

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Bryant, Robert G. (Inventor); Jensen, Brian J. (Inventor); Havens, Stephen J. (Inventor)

1997-01-01

Four phenylethynyl amine compounds--3 and 4-aminophenoxy-4'-phenylethynylbenzophenone, and 3 and 4-amino-4'-phenylethynylbenzophenone--were readily prepared and were used to endcap imide oligomers. Phenylethynyl-terminated amide acid oligomers and phenylethynyl-terminated imide oligomers with various molecular weights and compositions were prepared and characterized. These oligomers were cured at 300.degree. C. to 400.degree. C. to provide crosslinked polyimides with excellent solvent resistance, high strength and modulus and good high temperature properties. Adhesive panels, composites, films and moldings from these phenylethynyl terminated imide oligomers gave excellent mechanical performance.

Divergent synthetic approach to 6”-modified α-GalCer analogues

PubMed Central

Pauwels, Nora; Aspeslagh, Sandrine; Vanhoenacker, Gerd; Sandra, Koen; Yu, Esther D.; Zajonc, Dirk M.; Elewaut, Dirk; Linclau, Bruno; Van Calenbergh, Serge

2011-01-01

A synthetic approach is presented for the synthesis of galacturonic acid and d-fucosyl modified KRN7000. The approach allows for late-stage functionalisation of both the sugar 6”-OH and the sphingosine amino groups, which enables convenient synthesis of promising 6”-modified KRN7000 analogues. PMID:22042483

Nanostructural Characterization of Modified Homogalacturonan with Pectin Methylesterase from Jelly Fig (Ficus awkeotsang Makino) Achenes and Modeling of Enzyme Mode of Action

USDA-ARS?s Scientific Manuscript database

1. Justification: Pectin is a major hydrocolloid used in various food, cosmetics, and medicine pharmaceutical products. The relative amount of unmethylesterified galacturonic acid (GalA)residues and their distribution are key determinants of pectin functionality. Pectin methylesterase (PME) modifies...

Pectin from Opuntia ficus indica: Optimization of microwave-assisted extraction and preliminary characterization.

PubMed

Lefsih, Khalef; Giacomazza, Daniela; Dahmoune, Farid; Mangione, Maria Rosalia; Bulone, Donatella; San Biagio, Pier Luigi; Passantino, Rosa; Costa, Maria Assunta; Guarrasi, Valeria; Madani, Khodir

2017-04-15

Optimization of microwave-assisted extraction (MAE) of water-soluble pectin (WSP) from Opuntia ficus indica cladodes was performed using Response Surface Methodology. The effect of extraction time (X 1 ), microwave power (X 2 ), pH (X 3 ) and solid-to-liquid ratio (X 4 ) on the extraction yield was examined. The optimum conditions of MAE were as follows: X 1 =2.15min; X 2 =517W; X 3 =2.26 and X 4 =2g/30.6mL. The maximum obtained yield of pectin extraction was 12.57%. Total carbohydrate content of WSP is about 95.5% including 34.4% of Galacturonic acid. Pectin-related proteins represent only the 0.66% of WSP mass. HPSEC and light scattering analyses reveal that WSP is mostly constituted of high molecular pectin and FTIR measurements show that the microwave treatment does not alter the chemical structure of WSP, in which Galacturonic acid content and yield are 34.4% and 4.33%, respectively. Overall, application of MAE can give rise to high quality pectin. Copyright © 2016 Elsevier Ltd. All rights reserved.

Purification, characterization and in vitro anticoagulant activity of polysaccharides from Gentiana scabra Bunge roots.

PubMed

Cai, Weirong; Xu, Huiling; Xie, Liangliang; Sun, Jian; Sun, Taotao; Wu, Xiaoyan; Fu, Qinbao

2016-04-20

Three water-soluble polysaccharide fractions (GSP-1, GSP-2 and GSP-3) were obtained from Gentiana scabra Bunge roots by DEAE-Sepharose CL-6B and Sepharose CL-6B column chromatography. Their chemical characterizations were determined by high performance gel permeation chromatography (HPGPC), high performance anion exchange chromatography coupled with pulsed amperometric detection (HPAEC-PAD) and Fourier transform infrared (FT-IR) spectrometer. Moreover, their in vitro anticoagulant activities were evaluated by activated partial thromboplastin time (APTT), thrombin time (TT) and prothrombin time (PT) assays. GSP-1 and GSP-2 were composed of rhamnose, arabinose, galactose, glucose and galacturonic acid, while GSP-3 consisted of rhamnose, arabinose, galactose and galacturonic acid with a weight-average molecular weight of 5.8×10(4)Da. In comparison with the control group (saline), GSP, GSP-1, GSP-2 and GSP-3 could prolong APTT and TT, but not PT. Overall, GSP-3 exhibited potent anticoagulant activity and would be expected to be a potential source of anticoagulant. Copyright © 2015 Elsevier Ltd. All rights reserved.

Purification, characterization and immunomodulatory activity of polysaccharides from stem lettuce.

PubMed

Nie, Chenzhipeng; Zhu, Peilei; Ma, Shuping; Wang, Mingchun; Hu, Youdong

2018-05-15

Stem lettuce has a long history of cultivation in China and possesses high nutritional and medicinal value. In our previous studies, extraction optimization, characterization, and bioactivities of stem lettuce polysaccharides (SLP) were investigated. In this study, SLP were further separated into two purified polysaccharides, SLP-1 and SLP-2, by anion exchange chromatography followed by size exclusion chromatography. SLP-1, with a molecular weight of 90 KDa, was mainly composed of galacturonic acid, galactose and arabinose in a molar ratio of 17.6:41.7:33.9. SLP-2, with a molecular weight of 44 KDa, was mainly composed of mannose, galacturonic acid, galactose and arabinose in a molar ratio of 11.5:69.5:9.3:8.2. In addition, both purified polysaccharides contain sulphate radicals, have triple helical structures and can promote macrophage proliferation without cytotoxicity. SLP-2 was better able to stimulate phagocytic and nitric oxide production than SLP-1. The results suggest that polysaccharides from stem lettuce could be explored as immunomodulatory agents in the field of pharmaceuticals and functional foods. Copyright © 2018 Elsevier Ltd. All rights reserved.

Chemical evolution. XXIX - Pyrimidines from hydrogen cyanide

NASA Technical Reports Server (NTRS)

Ferris, J. P.; Joshi, P. C.; Lawless, J. G.

1978-01-01

Compounds obtained by hydrolysis of HCN oligomers formed by allowing pH 9.2, 0.1 M cyanide to stand at room temperature for 4 to 12 months were analyzed. Hydrolysis of HCN oligomers yielded 4,5-dihydroxypyrimidine and 5-hydroxyuracil; orotic acid was detected after hydrolysis at pH 8.5. A unified pathway from diaminofumaronitrile to the pyrimidines observed is suggested. As purines, pyrimidines and amino acids are released by hydrolysis of HCN oligomers in either acidic or mildly basic aqueous solutions, they could have been formed on the primitive earth in spite of fluctuations in pH. 4,5-dihydroxypyrimidines appear to be likely candidates for incorporation into primitive nucleic acids, as they should undergo Watson-Crick hydrogen bonding with adenine.

Factors Affecting the Initial Adhesion and Retention of the Plant Pathogen Xylella fastidiosa in the Foregut of an Insect Vector

PubMed Central

Almeida, Rodrigo P. P.

2014-01-01

Vector transmission of bacterial plant pathogens involves three steps: pathogen acquisition from an infected host, retention within the vector, and inoculation of cells into susceptible tissue of an uninfected plant. In this study, a combination of plant and artificial diet systems were used to determine the importance of several genes on the initial adhesion and retention of the bacterium Xylella fastidiosa to an efficient insect vector. Mutant strains included fimbrial (fimA and pilB) and afimbrial (hxfA and hxfB) adhesins and three loci involved in regulatory systems (rpfF, rpfC, and cgsA). Transmission assays with variable retention time indicated that HxfA and HxfB were primarily important for early adhesion to vectors, while FimA was necessary for both adhesion and retention. The long pilus protein PilB was not deficient in initial adhesion but may be important for retention. Genes upregulated under the control of rpfF are important for both initial adhesion and retention, as transmission rates of this mutant strain were initially low and decreased over time, while disruption of rpfC and cgsA yielded trends similar to that shown by the wild-type control. Because induction of an X. fastidiosa transmissible state requires pectin, a series of experiments were used to test the roles of a polygalacturonase (pglA) and the pectin and galacturonic acid carbohydrates on the transmission of X. fastidiosa. Results show that galacturonic acid, or PglA activity breaking pectin into its major subunit (galacturonic acid), is required for X. fastidiosa vector transmission using an artificial diet system. This study shows that early adhesion and retention of X. fastidiosa are mediated by different factors. It also illustrates that the interpretation of results of vector transmission experiments, in the context of vector-pathogen interaction studies, is highly dependent on experimental design. PMID:24185853

Factors affecting the initial adhesion and retention of the plant pathogen Xylella fastidiosa in the foregut of an insect vector.

PubMed

Killiny, Nabil; Almeida, Rodrigo P P

2014-01-01

Vector transmission of bacterial plant pathogens involves three steps: pathogen acquisition from an infected host, retention within the vector, and inoculation of cells into susceptible tissue of an uninfected plant. In this study, a combination of plant and artificial diet systems were used to determine the importance of several genes on the initial adhesion and retention of the bacterium Xylella fastidiosa to an efficient insect vector. Mutant strains included fimbrial (fimA and pilB) and afimbrial (hxfA and hxfB) adhesins and three loci involved in regulatory systems (rpfF, rpfC, and cgsA). Transmission assays with variable retention time indicated that HxfA and HxfB were primarily important for early adhesion to vectors, while FimA was necessary for both adhesion and retention. The long pilus protein PilB was not deficient in initial adhesion but may be important for retention. Genes upregulated under the control of rpfF are important for both initial adhesion and retention, as transmission rates of this mutant strain were initially low and decreased over time, while disruption of rpfC and cgsA yielded trends similar to that shown by the wild-type control. Because induction of an X. fastidiosa transmissible state requires pectin, a series of experiments were used to test the roles of a polygalacturonase (pglA) and the pectin and galacturonic acid carbohydrates on the transmission of X. fastidiosa. Results show that galacturonic acid, or PglA activity breaking pectin into its major subunit (galacturonic acid), is required for X. fastidiosa vector transmission using an artificial diet system. This study shows that early adhesion and retention of X. fastidiosa are mediated by different factors. It also illustrates that the interpretation of results of vector transmission experiments, in the context of vector-pathogen interaction studies, is highly dependent on experimental design.

Neuroprotective Effects of Ferruginol, Jatrophone, and Junicedric Acid Against Amyloid-β Injury in Hippocampal Neurons.

PubMed

Zolezzi, Juan M; Lindsay, Carolina B; Serrano, Felipe G; Ureta, Roxana C; Theoduloz, Cristina; Schmeda-Hirschmann, Guillermo; Inestrosa, Nibaldo C

2018-01-01

Soluble amyloid-β (Aβ) oligomers have been recognized as early neurotoxic intermediates with a key role in the synaptic dysfunction observed in Alzheimer's disease (AD). Aβ oligomers block hippocampal long-term potentiation (LTP) and impair rodent spatial memory. Additionally, the presence of Aβ oligomers is associated with imbalanced intracellular calcium levels and apoptosis in neurons. In this context, we evaluated the effects of three diterpenes (ferruginol, jatrophone, and junicedric acid) that are found in medicinal plants and have several forms of biological activity. The intracellular calcium levels in hippocampal neurons increased in the presence of ferruginol, jatrophone, and junicedric acid, a result that was consistent with the observed increase in CA1 synaptic transmission in mouse hippocampal slices. Additionally, assays using Aβ peptide demonstrated that diterpenes, particularly ferruginol, restore LTP and reduce apoptosis. Recovery of the Aβ oligomer-induced loss of the synaptic proteins PSD-95, synapsin, VGlut, and NMDA receptor subunit 2A was observed in mouse hippocampal slices treated with junicedric acid. This cascade of events may be associated with the regulation of kinases, e.g., protein kinase C (PKC) and calcium/calmodulin-dependent protein kinase II (CaMKII), in addition to the activation of the canonical Wnt signaling pathway and could thus provide protection against Aβ oligomers, which trigger synaptic dysfunction. Our results suggest a potential neuroprotective role for diterpenes against the Aβ oligomers-induced neurodegenerative alterations, which make them interesting molecules to be further studied in the context of AD.

Yield and quality of pectins extractable from the peels of thai mango cultivars depending on fruit ripeness.

PubMed

Sirisakulwat, Suparat; Nagel, Andreas; Sruamsiri, Pittaya; Carle, Reinhold; Neidhart, Sybille

2008-11-26

Pectins, recovered from the peels of four mango ( Mangifera indica L.) cultivars by mimicking industrial techniques, were evaluated in terms of yield, composition, macromolecular properties, and technofunctional quality. Freeze-dried peels of mature-green fruits, after major mesocarp softening, and at full ripeness were extracted using hot acid. The pectins were precipitated in propan-2-ol and their crude yields quantified as alcohol-insoluble substance. Like apple pomace, the dried peels provided hardly acetylated (DAc < 6.3%) rapid-set to ultrarapid-set high-methoxyl pectins at starch-adjusted yields of 11-21 g/100 g. However, despite similar high molecular weight fractions and galacturonic acid/rhamnose ratios, their average molecular weight was markedly reduced by a characteristic, almost monodisperse fraction of 16000-19000. Expanded galactans, indicated by galactose/rhamnose ratios of 15-24 mol/mol, probably represented arabinogalactan side-chain fragments withstanding hot-acid extraction at pH 1.5 and 2.0, as implied by arabinose/galactose ratios of 8-15 and 33-56 mol/100 mol, respectively. Limited galacturonic acid contents made the mango peel pectins less valuable than commercial apple pectins with regard to gelling capacity and thickening properties. Whereas starch and matrix glycan fragments almost completely degraded during ripening, depolymerization of pectins and galactans was insignificant. Technofunctional properties, modulated by extraction at different pH values, were ascribed to structural differences influencing macromolecular entanglements.

Acidification of apple and orange hosts by Penicillium digitatum and Penicillium expansum.

PubMed

Vilanova, L; Viñas, I; Torres, R; Usall, J; Buron-Moles, G; Teixidó, N

2014-05-16

New information about virulence mechanisms of Penicillium digitatum and Penicillium expansum could be an important avenue to control fungal diseases. In this study, the ability of P. digitatum and P. expansum to enhance their virulence by locally modulating the pH of oranges and apples was evaluated. For each host, pH changes with a compatible pathogen and a non-host pathogen were recorded, and the levels of different organic acids were evaluated to establish possible relationships with host pH modifications. Moreover, fruits were harvested at three maturity stages to determine whether fruit maturity could affect the pathogens' virulence. The pH of oranges and apples decreased when the compatible pathogens (P. digitatum and P. expansum, respectively) decayed the fruit. The main organic acid detected in P. digitatum-decayed oranges was galacturonic acid produced as a consequence of host maceration in the rot development process. However, the obtained results showed that this acid was not responsible for the pH decrease in decayed orange tissue. The mixture of malic and citric acids could at least contribute to the acidification of P. digitatum-decayed oranges. The pH decrease in P. expansum decayed apples is related to the accumulation of gluconic and fumaric acids. The pH of oranges and apples was not affected when the non-host pathogen was not able to macerate the tissues. However, different organic acid contents were detected in comparison to healthy tissues. The main organic acids detected in P. expansum-oranges were oxalic and gluconic and in P. digitatum-apples were citric, gluconic and galacturonic. Further research is needed to identify the pathogenicity factors of both fungi because the contribution of organic acids has profound implications. Copyright © 2014 Elsevier B.V. All rights reserved.

Edible films from pectin: Physical-mechanical and antimicrobial properties - A Review

USDA-ARS?s Scientific Manuscript database

Pectin is one of the main components of the plant cell wall and chemically, pectin is constituted by poly a1–4-galacturonic acids. According to its degree of esterification with methanol, pectin can be classified as high methoxyl pectin or low methoxyl pectin. In food industry, pectin is listed as g...

Preparation of Stable Amyloid-β Oligomers Without Perturbative Methods.

PubMed

Kotler, Samuel A; Ramamoorthy, Ayyalusamy

2018-01-01

Soluble amyloid-β (Aβ) oligomers have become a focal point in the study of Alzheimer's disease due to their ability to elicit cytotoxicity. A number of recent studies have concentrated on the structural characterization of soluble Aβ oligomers to gain insight into their mechanism of toxicity. Consequently, providing reproducible protocols for the preparation of such oligomers is of utmost importance. The method presented in this chapter details a protocol for preparing an Aβ oligomer, with a primarily disordered secondary structure, without the need for chemical modification or amino acid substitution. Due to the stability of these disordered Aβ oligomers and the reproducibility with which they form, they are amenable for biophysical and high-resolution structural characterization.

Oligomerization of L-gamma-carboxyglutamic acid

NASA Technical Reports Server (NTRS)

Hill, A. R. Jr; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1999-01-01

Unlike glutamic acid, L-gamma-carboxyglutamic acid does not oligomerize efficiently when treated with carbonyldiimidazole in aqueous solution. However, divalent ions such as Mg2+ catalyze the reaction, and lead to the formation of oligomers in good yield. In the presence of hydroxylapatite, L-gamma-carboxyglutamic acid oligomerizes efficiently in a reaction that proceeds in the absence of divalent ions but is further catalyzed when they are present. After 'feeding' 50 times with activated amino acid in the presence of the Mg2+ ion, oligomers longer than the 20-mer could be detected. The effect of hydroxylapatite on peptide elongation is very sensitive to the nature of the activated amino acid and the acceptor peptide. Glutamic acid oligomerizes more efficiently than L-gamma-carboxyglutamic acid on hydroxylapatite and adds more efficiently to decaglutamic acid in solution. One might, therefore, expect that glutamic acid would add more efficiently than L-gamma-carboxyglutamic acid to decaglutamic acid on hydroxylapatite. The contrary is true--the addition of L-gamma-carboxyglutamic acid is substantially more efficient. This suggests that oligomerization on the surface of hydroxylapatite depends on the detailed match between the structure of the surface of the mineral and the structure of the oligomer.

Analysis of linear and cyclic oligomers in polyamide-6 without sample preparation by liquid chromatography using the sandwich injection method. II. Methods of detection and quantification and overall long-term performance.

PubMed

Mengerink, Y; Peters, R; Kerkhoff, M; Hellenbrand, J; Omloo, H; Andrien, J; Vestjens, M; van der Wal, S

2000-05-05

By separating the first six linear and cyclic oligomers of polyamide-6 on a reversed-phase high-performance liquid chromatographic system after sandwich injection, quantitative determination of these oligomers becomes feasible. Low-wavelength UV detection of the different oligomers and selective post-column reaction detection of the linear oligomers with o-phthalic dicarboxaldehyde (OPA) and 3-mercaptopropionic acid (3-MPA) are discussed. A general methodology for quantification of oligomers in polymers was developed. It is demonstrated that the empirically determined group-equivalent absorption coefficients and quench factors are a convenient way of quantifying linear and cyclic oligomers of nylon-6. The overall long-term performance of the method was studied by monitoring a reference sample and the calibration factors of the linear and cyclic oligomers.

Novel and economic acid-base indicator based on (p-toluidine) oligomer: Synthesis; characterization and solvatochromism applications

NASA Astrophysics Data System (ADS)

Zoromba, M. Sh.

2017-12-01

A new (p-toluidine) oligomer (PTO) was facile synthesized and economically routed via chemical oxidative polymerization by potassium dichromate as an initiator in an acidic aqueous medium at room temperature. The characterization of (p-toluidine) oligomer (PTO) has been described by various techniques including Fourier transform infra-red (FTIR), UV-Visible measurements, Mass spectra, H NMR, and thermal gravimetric analysis (TGA). Solvatochromism of PTO was studied in different polaritiy solvents such as acetic acid, acetone, dimethyl formamide, ethanol, isopropanol, chloroform, p-xylene, dichloromethane and carbon teterachloride. The absorption bands were bathochromically shifted with increased polarity of the solvent (positive solvatochromism). PTO shows three isosbestic points at 333, 388 and 472 nm in a binary mixture of acetone and chloroform. The deprotonation constants of PTO were found to be 3.1 and 5.8, based on spectrophotometric calculations. PTO was successfully used as an acid-base indicator; the acid solution color sharply turned from pink (acidic medium) to yellow (basic medium) at the end point.

Pectic oligosaccharides from agricultural by-products: production, characterization and health benefits.

PubMed

Babbar, Neha; Dejonghe, Winnie; Gatti, Monica; Sforza, Stefano; Elst, Kathy

2016-08-01

Pectin containing agricultural by-products are potential sources of a new class of prebiotics known as pectic oligosaccharides (POS). In general, pectin is made up of homogalacturonan (HG, α-1,4-linked galacturonic acid monomers) and rhamnogalacturonan (RG, alternate galacturonic acid and rhamnose backbone with neutral side chains). Controlled hydrolysis of pectin containing agricultural by-products like sugar beet, apple, olive and citrus by chemical, enzymatic and hydrothermal can be used to produce oligo-galacturonides (GalpOS), galacto-oligosaccharides (GalOS), rhamnogalacturonan-oligosaccharides (RGOS), etc. However, extensive research is needed to establish the role of POS, both as a prebiotic as well as therapeutic agent. This review comprehensively covers different facets of POS, including the nature and chemistry of pectin and POS, potential agricultural residual sources of pectin, pre-treatment methods for facilitating selective extraction of pectin, identification and characterization of POS, health benefits and important applications of POS in food and feed. This review has been compiled to establish a platform for future research in the purification and characterization of POS and for in vivo and in vitro studies of important POS, so that they could be commercially exploited.

Pectin Biosynthesis Is Critical for Cell Wall Integrity and Immunity in Arabidopsis thaliana

PubMed Central

Bethke, Gerit; Thao, Amanda; Xiong, Guangyan; Hatsugai, Noriyuki; Katagiri, Fumiaki; Pauly, Markus

2016-01-01

Plant cell walls are important barriers against microbial pathogens. Cell walls of Arabidopsis thaliana leaves contain three major types of polysaccharides: cellulose, various hemicelluloses, and pectins. UDP-d-galacturonic acid, the key building block of pectins, is produced from the precursor UDP-d-glucuronic acid by the action of glucuronate 4-epimerases (GAEs). Pseudomonas syringae pv maculicola ES4326 (Pma ES4326) repressed expression of GAE1 and GAE6 in Arabidopsis, and immunity to Pma ES4326 was compromised in gae6 and gae1 gae6 mutant plants. These plants had brittle leaves and cell walls of leaves had less galacturonic acid. Resistance to specific Botrytis cinerea isolates was also compromised in gae1 gae6 double mutant plants. Although oligogalacturonide (OG)-induced immune signaling was unaltered in gae1 gae6 mutant plants, immune signaling induced by a commercial pectinase, macerozyme, was reduced. Macerozyme treatment or infection with B. cinerea released less soluble uronic acid, likely reflecting fewer OGs, from gae1 gae6 cell walls than from wild-type Col-0. Although both OGs and macerozyme-induced immunity to B. cinerea in Col-0, only OGs also induced immunity in gae1 gae6. Pectin is thus an important contributor to plant immunity, and this is due at least in part to the induction of immune responses by soluble pectin, likely OGs, that are released during plant-pathogen interactions. PMID:26813622

Nitrogen Containing Organic Compounds and Oligomers in Secondary Organic Aerosol Formed by Photooxidation of Isoprene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Tran B.; Laskin, Julia; Laskin, Alexander

2011-07-06

Electrospray ionization high-resolution mass spectrometry (ESI HR-MS) was used to probe molecular structures of oligomers in secondary organic aerosol (SOA) generated in laboratory experiments on isoprene photooxidation at low- and high-NOx conditions. Up to 80-90% of the observed products are oligomers and up to 33% are nitrogen-containing organic compounds (NOC). We observe oligomers with up to 8 monomer units in length. Tandem mass spectrometry (MSn) confirms NOC compounds are organic nitrates and elucidates plausible chemical building blocks contributing to oligomer formation. Most organic nitrates are comprised of methylglyceric acid units. Other important multifunctional C2-C5 monomer units are identified including methylglyoxal,more » hydroxyacetone, hydroxyacetic acid, glycolaldehyde, and 2-methyltetrols. The majority of the NOC oligomers contain only one nitrate moiety resulting in a low average N:C ratio of 0.019. Average O:C ratios of the detected SOA compounds are 0.54 under the low-NOx conditions and 0.83 under the high-NOx conditions. Our results underscore the importance of isoprene photooxidation as a source of NOC in organic particulate matter.« less

Secretory Expression and Characterization of an Acidic Endo-Polygalacturonase Gene from Aspergillus niger SC323 in Saccharomyces cerevisiae.

PubMed

Zhou, Huoxiang; Li, Xi; Guo, Mingyue; Xu, Qingrui; Cao, Yu; Qiao, Dairong; Cao, Yi; Xu, Hui

2015-07-01

The endo-polygalacturonase gene (endo-pgaA) was cloned from DNA of Aspergillus niger SC323 using the cDNA synthesized by overlapping PCR, and successfully expressed in Saccharomyces cerevisiae EBY100 through fusing the α-factor signal peptide of yeast. The full-length cDNA consists of 1,113 bp and encodes a protein of 370 amino acids with a calculated molecular mass of 38.8 kDa. After induction by galactose for 48 h, the activity of recombinant endo-PgaA in the culture supernatant can reach up to 1,448.48 U/mg. The recombinant protein was purified to homogeneity by ammonium sulfate precipitation and gel filtration column chromatography and subsequently characterized. The optimal pH and temperature of the purified recombinant enzyme were 5.0 and 50°C, respectively. The Michaelis-Menten constant (Km) and maximal velocity (Vmax) of the enzyme for pectin were 88.54 μmol/ml and 175.44 μmol/mg/min, respectively. The enzyme activity was enhanced by Ca(2+), Cu(2+), and Na(+), and strongly inhibited by Pb(2+) and Mn(2+). The pectin hydrolysates were mainly galacturonic acid and other oligo-galacturonates. Therefore, these characteristics suggest that the recombinant endo-PgaA may be of potential use in the food and feed industries.

Preparation of Chito-Oligomers by Hydrolysis of Chitosan in the Presence of Zeolite as Adsorbent

PubMed Central

Ibrahim, Khalid A.; El-Eswed, Bassam I.; Abu-Sbeih, Khaleel A.; Arafat, Tawfeeq A.; Al Omari, Mahmoud M. H.; Darras, Fouad H.; Badwan, Adnan A.

2016-01-01

An increasing interest has recently been shown to use chitin/chitosan oligomers (chito-oligomers) in medicine and food fields because they are not only water-soluble, nontoxic, and biocompatible materials, but they also exhibit numerous biological properties, including antibacterial, antifungal, and antitumor activities, as well as immuno-enhancing effects on animals. Conventional depolymerization methods of chitosan to chito-oligomers are either chemical by acid-hydrolysis under harsh conditions or by enzymatic degradation. In this work, hydrolysis of chitosan to chito-oligomers has been achieved by applying adsorption-separation technique using diluted HCl in the presence of different types of zeolite as adsorbents. The chito-oligomers were retrieved from adsorbents and characterized by differential scanning calorimetry (DSC), liquid chromatography/mass spectroscopy (LC/MS), and ninhydrin test. PMID:27455287

Electrophoretic studies of polygalacturonate oligomers and their interactions with metal ions.

PubMed

Wiedmer, S K; Cassely, A; Hong, M; Novotny, M V; Riekkola, M L

2000-09-01

Polygalacturonic acid, a linear homopolysaccharide, was investigated by capillary electrophoresis (CE) using linear polyacrylamide-coated capillaries and laser-induced fluorescence (LIF) detection. A successful separation of its fluorescently labeled oligomers was achieved through sieving in polyacrylamide entangled matrices. The reaction conditions for the derivatization of polygalacturonic acid were optimized. In studying the interactions between polygalacturonic acid and various metal ions, the end-label, free-solution electrophoretic (ELFSE) technique, developed earlier in our laboratory (Sudor, J., Novotny, M. V., Anal. Chem. 1995, 67, 4205-4209) was found preferable to the sieving method. ELFSE is fast and convenient in that no polymer solutions are needed for the separation. The investigation showed that for the moderately large oligomers, the strongest binding occurred with calcium and cadmium ions, while the smallest interaction was observed with magnesium ions.

Studies of Biosilicification; The Role of Proteins, Carbohydrates and Model Compounds in Structure Control

DTIC Science & Technology

2005-12-31

No. carbons Pore volume data. Resolution of complex monosaccharide mixtures from plant cell wall isolates by high pH anion exchange chromatography. To...interwoven polysaccharide chains embedded in a gel matrix of galacturonic acid rich polysaccharides connected by calcium bridges. This network also...picomolar levels). Also, it allows the determination of intact monosaccharides without pre or post column derivatisation, decreasing the time of

The isolation and the characterization of two polysaccharides from the branch bark of mulberry (Morus alba L.).

PubMed

Qiu, Fan; He, Tian-Zhen; Zhang, Yu-Qing

2016-07-01

Two water-soluble polysaccharides termed MBBP-1 and MBBP-2 were isolated from the branches of the mulberry tree (Morus alba L.) using hot water extraction and purified on Anion-exchange DEAE52-cellulose and Sephadex G-100 column. MBBP-1 was shown to be composed of rhamnose, xylose, arabinose, mannose, glucose and galactose in the molar ratio of 4.53:2.49:4.38:4.67:17.85:5.88. MBBP-2 was composed of rhamnose, xylose, arabinose, mannose, glucose, galactose and galacturonic acid in the molar ratio of 26.85:13.8:3.14:4.4:6.1:3.19:4.9. Their structural characteristics were further investigated by FI-IR spectroscopy, Smith degradation, methylation analysis and NMR spectroscopy. Based on the data obtained, MBBP-1 had a backbone mainly consisting of (1 → 3)-linked glucose. MBBP-2 had a backbone mainly consisting of (1 → 3)-linked rhamnose and (1 → 2, 4)-linked xylose. Antioxidant assays indicated that antioxidant activities of MBBP-2 were significantly stronger than those of MBBP-1, and this was likely in relation to the different content of 8.2 % galacturonic acid in MBBP-2.

The beta-1,4-endogalactanase A gene from Aspergillus niger is specifically induced on arabinose and galacturonic acid and plays an important role in the degradation of pectic hairy regions.

PubMed

De Vries, Ronald P; Parenicová, Lucie; Hinz, Sandra W A; Kester, Harry C M; Beldman, Gerrit; Benen, Jacques A E; Visser, Jaap

2002-10-01

The Aspergillus nigerbeta-1,4-endogalactanase encoding gene (galA) was cloned and characterized. The expression of galA in A. niger was only detected in the presence of sugar beet pectin, d-galacturonic acid and l-arabinose, suggesting that galA is coregulated with both the pectinolytic genes as well as the arabinanolytic genes. The corresponding enzyme, endogalactanase A (GALA), contains both active site residues identified previously for the Pseudomonas fluorescensbeta-1,4-endogalactanase. The galA gene was overexpressed to facilitate purification of GALA. The enzyme has a molecular mass of 48.5 kDa and a pH optimum between 4 and 4.5. Incubations of arabinogalactans of potato, onion and soy with GALA resulted initially in the release of d-galactotriose and d-galactotetraose, whereas prolonged incubation resulted in d-galactose and d-galactobiose, predominantly. MALDI-TOF analysis revealed the release of l-arabinose substituted d-galacto-oligosaccharides from soy arabinogalactan. This is the first report of the ability of a beta-1,4-endogalactanase to release substituted d-galacto-oligosaccharides. GALA was not active towards d-galacto-oligosaccharides that were substituted with d-glucose at the reducing end.

Detection of human antibodies binding with smooth and rough LPSs from Proteus mirabilis O3 strains S1959, R110, R45.

PubMed

Gleńska-Olender, J; Durlik, K; Konieczna, I; Kowalska, P; Gawęda, J; Kaca, W

2017-11-01

Bacteria of the genus Proteus of the family Enterobacteriaceae are facultative human pathogens responsible mainly for urinary tract and wound infections, bacteremia and the development of rheumatoid arthritis (RA). We have analyzed and compared by ELISA the titer of antibodies in plasmas of healthy individuals and in sera of rheumatoid arthritis patients recognizing a potential host cross-reactive epitope (lysine-galacturonic acid epitopes) present in Proteus lipopolysaccharide (LPS). In our experiments LPSs isolated from two mutants of smooth Proteus mirabilis 1959 (O3), i.e. strains R110 and R45, were used. R110 (Ra type mutant) is lacking the O-specific polysaccharide, but possesses a complete core oligosaccharide, while R45 (Re type) has a reduced core oligosaccharide and contains two 3-deoxy-D-manno-oct-2-ulosonic acid residues and one of 4-amino-4-deoxy-L-arabinopyranose residues. Titer of P. mirabilis S1959 LPS-specific-antibodies increased with the age of blood donors. RA and blood donors' sera contained antibodies against S and Ra and Re type of P. mirabilis O3 LPSs. Antibodies recognizing lysine-galacturonic acid epitopes of O3 LPS were detected by ELISA in some plasmas of healthy individuals and sera of rheumatoid arthritis patients. RA patients antibodies reacting with P. mirabilis S1959 S and R LPSs may indicate a potential role of anti-LPS antibodies in molecular mimicry in RA diseases.

A novel highly charged exopolysaccharide produced by two strains of Stenotrophomonas maltophilia recovered from patients with cystic fibrosis.

PubMed

Cescutti, Paola; Cuzzi, Bruno; Liut, Gianfranco; Segonds, Christine; Di Bonaventura, Giovanni; Rizzo, Roberto

2011-09-27

Stenotrophomonas maltophilia is a non-fermenting Gram-negative microorganism capable of causing chronic pulmonary infection in cystic fibrosis patients and its ability to form biofilms on polystyrene and glass surfaces, as well as on cystic fibrosis-derived bronchial epithelial IB3-I cells was recently demonstrated. The latter evidence might explain the power of S. maltophilia to produce persistent lung infections, despite intensive antibiotic treatment. In addition to being important components of the extracellular biofilm matrix, polysaccharides are involved in virulence, as they contribute to bacterial survival in a hostile environment. With the aim of contributing to the elucidation of S. maltophilia virulence factors, the exopolysaccharides produced by two mucoid clinical isolates of S. maltophilia obtained from two cystic fibrosis patients were completely characterised, mainly by means of ESI-MS and NMR spectroscopy. The results showed that, although the two isolates were recovered from two different patients living in different countries (Italy and France), the exopolysaccharides produced have an identical primary structure, with the following repeating unit: The exopolysaccharide is highly negatively charged for the presence of three uronic acids on four residues in the repeating unit. Moreover, an ether-linked d-lactate substituent is located on C-3 and one O-acetyl group on C-4 of the galacturonic acid side chain. Another O-acetyl group substitutes C-2 of the galacturonic acid in the backbone, making this primary structure unique. Copyright © 2011 Elsevier Ltd. All rights reserved.

Preparation, characterization and bioactivities of Athelia rolfsii exopolysaccharide-zinc complex (AEPS-zinc).

PubMed

Dong, Jinman; Li, Hongmei; Min, Weihong

2018-07-01

A new Athelia rolfsii exopolysaccharides (AEPS) were purified by Sephacryl S-300 and S-200. The physicochemical characteristics of AEPS fractions were assayed by HPGPC and GC methods. The structures of AEPS and AEPS‑zinc complex were characterized by SEM, FTIR and NMR. Moreover, the bioactivities of complex were also evaluated by experiments in vitro and in vivo. AEPSI consisted of glucose, galacturonic acid, talose, galactose, mannose and xylose, the relative contents of them were 24.74, 19.60, 33.65, 8.77, 7.97 and 5.28%, respectively. AEPSII consisted of glucose, inositol, galacturonic acid, ribitol, gluconic acid, talose and xylose, whose relative contents were 36.06, 21.21, 12.78, 11.07, 6.58, 5.45 and 6.82%, respectively. The Mw and Mn of AEPSI were 6.1324×10 4 and 1.4218×10 4 Da, those of AEPSII were 517 and 248Da. SEM observations showed that microstructures of AEPS and AEPS‑zinc complex were obviously different both in size and shape. FTIR and NMR analysis indicated that AEPS might chelate with zinc ion through hydroxy and carboxy group. In vitro experiments showed that AEPS‑zinc complex had a good bioavailability, in vivo experiments showed that it had good effect on improving zinc deficiency and antioxidant activities, which suggested that it could be used as zinc supplementation with high antioxidant activities. Copyright © 2018 Elsevier B.V. All rights reserved.

Structural Characterization of Monomers and Oligomers of D-Amino Acid-Containing Peptides Using T-Wave Ion Mobility Mass Spectrometry

NASA Astrophysics Data System (ADS)

Pang, Xueqin; Jia, Chenxi; Chen, Zhengwei; Li, Lingjun

2017-01-01

The D-residues are crucial to biological function of D-amino acid containing peptides (DAACPs). Previous ion mobility mass spectrometry (IM-MS) studies revealing oligomerization patterns of amyloid cascade demonstrated conversion from native soluble unstructured assembly to fibril ß-sheet oligomers, which has been implicated in amyloid diseases, such as Alzheimer's disease and type 2 diabetes. Although neuropeptides are typically present at very low concentrations in circulation, their local concentrations could be much higher in large dense core vesicles, forming dimers or oligomers. We studied the oligomerization of protonated and metal-adducted achatin I and dermorphin peptide isomers with IM-MS. Our results suggested that dimerization, oligomerization, and metal adduction augment the structural differences between D/L peptide isomers compared to protonated monomers. Dimers and oligomers enhanced the structural differences between D/L peptide isomers in both aqueous and organic solvent system. Furthermore, some oligomer forms were only observed for either D- or L-isomers, indicating the importance of chiral center in oligomerization process. The oligomerization patterns of D/L isomers appear to be similar. Potassium adducts were detected to enlarge the structural differences between D/L isomers.

Porous Cross-Linked Polyimide Networks

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B. (Inventor); Guo, Haiquan (Inventor)

2015-01-01

Porous cross-linked polyimide networks are provided. The networks comprise an anhydride end-capped polyamic acid oligomer. The oligomer (i) comprises a repeating unit of a dianhydride and a diamine and terminal anhydride groups, (ii) has an average degree of polymerization of 10 to 50, (iii) has been cross-linked via a cross-linking agent, comprising three or more amine groups, at a balanced stoichiometry of the amine groups to the terminal anhydride groups, and (iv) has been chemically imidized to yield the porous cross-linked polyimide network. Also provided are porous cross-linked polyimide aerogels comprising a cross-linked and imidized anhydride end-capped polyamic acid oligomer, wherein the oligomer comprises a repeating unit of a dianhydride and a diamine, and the aerogel has a density of 0.10 to 0.333 g/cm.sup.3 and a Young's modulus of 1.7 to 102 MPa. Also provided are thin films comprising aerogels, and methods of making porous cross-linked polyimide networks.

Stereocomplexes Formed From Select Oligomers of Polymer d-lactic Acid (PDLA) and l-lactate May Inhibit Growth of Cancer Cells and Help Diagnose Aggressive Cancers-Applications of the Warburg Effect.

PubMed

Goldberg, Joel S

2011-02-15

It is proposed that select oligomers of polymer d-lactic acid (PDLA) will form a stereocomplex with l-lactate in vivo, producing lactate deficiency in tumor cells. Those cancer cells that utilize transport of lactate to maintain electrical neutrality may cease to multiply or die because of lactate trapping, and those cancer cells that benefit from utilization of extracellular lactate may be impaired. Intracellular trapping of lactate produces a different physiology than inhibition of LDH because the cell loses the option of shuttling pyruvate to an alternative pathway to produce an anion. Conjugated with stains or fluorescent probes, PDLA oligomers may be an agent for the diagnosis of tissue lactate and possibly cell differentiation in biopsy specimens. Preliminary experimental evidence is presented confirming that PDLA in high concentrations is cytotoxic and that l-lactate forms a presumed stereocomplex with PDLA. Future work should be directed at isolation of biologically active oligomers of PDLA.

Regeneration of cello-oligomers via selective depolymerization of cellulose fibers derived from printed paper wastes.

PubMed

Voon, Lee Ken; Pang, Suh Cem; Chin, Suk Fun

2016-05-20

Cellulose extracted from printed paper wastes were selectively depolymerized under controlled conditions into cello-oligomers of controllable chain lengths via dissolution in an ionic liquid, 1-allyl-3-methylimidazolium chloride (AMIMCl), and in the presence of an acid catalyst, Amberlyst 15DRY. The depolymerization process was optimized against reaction temperature, concentration of acid catalyst, and reaction time. Despite rapid initial depolymerization process, the rate of cellulose depolymerization slowed down gradually upon prolonged reaction time, with 75.0 wt% yield of regenerated cello-oligomers (mean Viscosimetric Degree of Polymerization value of 81) obtained after 40 min. The depolymerization of cellulose fibers at 80 °C appeared to proceed via a second-order kinetic reaction with respect to the catalyst concentration of 0.23 mmol H3O(+). As such, the cellulose depolymerization process could afford some degree of control on the degree of polymerization or chain lengths of cello-oligomers formed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Association Thermodynamics and Conformational Stability of β-Sheet Amyloid β(17-42) Oligomers: Effects of E22Q (Dutch) Mutation and Charge Neutralization

PubMed Central

Blinov, Nikolay; Dorosh, Lyudmyla; Wishart, David; Kovalenko, Andriy

2010-01-01

Amyloid fibrils are associated with many neurodegenerative diseases. It was found that amyloidogenic oligomers, not mature fibrils, are neurotoxic agents related to these diseases. Molecular mechanisms of infectivity, pathways of aggregation, and molecular structure of these oligomers remain elusive. Here, we use all-atom molecular dynamics, molecular mechanics combined with solvation analysis by statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D-RISM-KH) in a new MM-3D-RISM-KH method to study conformational stability, and association thermodynamics of small wild-type Aβ17–42 oligomers with different protonation states of Glu22, as well the E22Q (Dutch) mutants. The association free energy of small β-sheet oligomers shows near-linear trend with the dimers being thermodynamically more stable relative to the larger constructs. The linear (within statistical uncertainty) dependence of the association free energy on complex size is a consequence of the unilateral stacking of monomers in the β-sheet oligomers. The charge reduction of the wild-type Aβ17–42 oligomers upon protonation of the solvent-exposed Glu22 at acidic conditions results in lowering the association free energy compared to the wild-type oligomers at neutral pH and the E22Q mutants. The neutralization of the peptides because of the E22Q mutation only marginally affects the association free energy, with the reduction of the direct electrostatic interactions mostly compensated by the unfavorable electrostatic solvation effects. For the wild-type oligomers at acidic conditions such compensation is not complete, and the electrostatic interactions, along with the gas-phase nonpolar energetic and the overall entropic effects, contribute to the lowering of the association free energy. The differences in the association thermodynamics between the wild-type Aβ17–42 oligomers at neutral pH and the Dutch mutants, on the one hand, and the Aβ17–42 oligomers with protonated Glu22, on the other, may be explained by destabilization of the inter- and intrapeptide salt bridges between Asp23 and Lys28. Peculiarities in the conformational stability and the association thermodynamics for the different models of the Aβ17–42 oligomers are rationalized based on the analysis of the local physical interactions and the microscopic solvation structure. PMID:20338850

Overall and specific migration from multilayer high barrier food contact materials - kinetic study of cyclic polyester oligomers migration.

PubMed

Úbeda, Sara; Aznar, Margarita; Vera, Paula; Nerín, Cristina; Henríquez, Luis; Taborda, Laura; Restrepo, Claudia

2017-10-01

Most multilayer high barrier materials used in food packaging have a polyurethane adhesive layer in their structures. In order to assess the safety of these materials, it is important to determine the compounds intentionally added to the adhesives (IAS) as well as those non-intentionally added substances (NIAS). During the manufacture of polyurethane adhesives, some by-products can be formed, such as cyclic polyester oligomers coming from the reaction between dicarboxylic acids and glycols. Since these compounds are not listed in the Regulation 10/2011/EU, they should not be found in migration above 0.01 mg/kg of simulant. In this study two flexible multilayer packaging materials were used and migration was evaluated in simulant A (ethanol 10% v/v), simulant B (acetic acid 3% w/v) and simulant ethanol 95% v/v during 10 days at 60ºC. Identification and quantification of non-volatile compounds was carried out by UPLC-MS-QTOF. Most of migrants were oligomers such as cyclic polyesters and caprolactam oligomers. Overall migration and specific migration of adipic acid-diethylene glycol and phthalic acid-diethylene glycol were monitored over time and analysed by UPLC-MS-TQ. In most cases, ethanol 95% v/v was the simulant with the highest concentration values. Overall migration kinetics followed a similar pattern than specific migration kinetics.

Chemical evolution. XXII - The hydantoins released on hydrolysis of HCN oligomers

NASA Technical Reports Server (NTRS)

Ferris, J. P.; Wos, J. D.; Lobo, A. P.

1974-01-01

The isolation of three hydantoins from HCN oligomers is described. One of these hydantoins, 5-carboxymethylidine hydantoin (5-CMH), rearranges to pyrimidine orotic acid in basic solution. The isolation of 5-CMH suggests the possibility that pyrimidines were formed directly from HCN on the primitive earth.

Detection of aniline oligomers on polyaniline-gold interface using resonance Raman scattering.

PubMed

Trchová, Miroslava; Morávková, Zuzana; Dybal, Jiří; Stejskal, Jaroslav

2014-01-22

In situ deposited conducting polyaniline films prepared by the oxidation of aniline with ammonium peroxydisulfate in aqueous media of various acidities on gold and silicon supports were characterized by Raman spectroscopy. Enhanced Raman bands were found in the spectra of polyaniline films produced in the solutions of weak acids or in water on gold surface. These bands were weak for the films prepared in solutions of a strong acid on a gold support. The same bands are present in the Raman spectra of the reaction intermediates deposited during aniline oxidation in water or aqueous solutions of weak or strong acids on silicon removed from the reaction mixture at the beginning of the reaction. Such films are formed by aniline oligomers adsorbed on the surface. They were detected on the polyaniline-gold interface using resonance Raman scattering on the final films deposited on gold. The surface resonance Raman spectroscopy of the monolayer of oligomers found in the bulk polyaniline film makes this method advantageous in surface science, with many applications in electrochemistry, catalysis, and biophysical, polymer, or analytical chemistry.

A Combined Photochemical and Multicomponent Reaction Approach to Precision Oligomers.

PubMed

Konrad, Waldemar; Bloesser, Fabian R; Wetzel, Katharina S; Boukis, Andreas C; Meier, Michael A R; Barner-Kowollik, Christopher

2018-03-07

We introduce the convergent synthesis of linear monodisperse sequence-defined oligomers through a unique approach, combining the Passerini three-component reaction (P-3CR) and a Diels-Alder (DA) reaction based on photocaged dienes. A set of oligomers is prepared resting on a Passerini linker unit carrying an isocyano group for chain extension by P-3CR and a maleimide moiety for photoenol conjugation enabling a modular approach for chain growth. Monodisperse oligomers are accessible in a stepwise fashion by switching between both reaction types. Employing sebacic acid as a core unit allows the synthesis of a library of symmetric sequence-defined oligomers. The oligomers consist of alternating P-3CR and photoblocks with molecular weights up to 3532.16 g mol -1 , demonstrating the successful switching from P-3CR to photoenol conjugation. In-depth characterization was carried out including size-exclusion chromatography (SEC), high-resolution electrospray ionization mass spectrometry (ESI-MS) and NMR spectroscopy, evidencing the monodisperse nature of the precision oligomers. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The effect of polar end of long-chain fluorocarbon oligomers in promoting the superamphiphobic property over multi-scale rough Al alloy surfaces

NASA Astrophysics Data System (ADS)

Saifaldeen, Zubayda S.; Khedir, Khedir R.; Camci, Merve T.; Ucar, Ahmet; Suzer, Sefik; Karabacak, Tansel

2016-08-01

Rough structures with re-entrant property and their subsequent surface energy reduction with long-chain fluorocarbon oligomers are both critical in developing superamphiphobic (SAP, i.e. both super hydrophobic and superoleophobic) surfaces. However, morphology of the low-surface energy layer on a rough re-entrant substrate can strongly depend on the fluorocarbon oligomers used. In this study, the effect of polar end of different kinds of long-chain fluorocarbon oligomers in promoting a self-assembled monolayer with close packed molecules and robust adhesion on multi-scale rough Al alloy surfaces was investigated. Hierarchical Al alloy surfaces with microgrooves and nanograss structures were developed by a simple combination of one-directional mechanical sanding and post treatment in boiling de-ionized water (DIW). Three types of long-chain fluorocarbon oligomers of 1H, 1H, 2H, 2H-perfluorodecyltriethoxysilane (PFDTS), 1H, 1H, 2H, 2H-perfluorodecyltrichlorosilane (PFDCS), and perfluorooctanoic acid (PFOA) were chemically vaporized onto these rough Al alloy surfaces. The PFDCS exhibited the lowest surface free energy of less than 10 mN/m. The contact angle and sliding angle measurements for water, ethylene glycol, and peanut oil verified the SAP property of hierarchical rough Al alloy surfaces treated with alkylsilane oligomers (PFDTS, PFDCS). However, the hierarchical surfaces treated with fluorocarbon oligomer with polar acidic tail (PFOA) showed highly amphiphobic properties but could not reach the threshold for SAP. Chemical stability of the hierarchical Al alloy surfaces treated with the fluorocarbon oligomers was tested under the harsh conditions of ultra-sonication in acetone and annealing at high temperature after different treatment times. Contact angle measurements revealed the robustness of the alkylsilane oligomers and deterioration of the PFOA coating particularly for low surface tension liquids. The robust adhesion and close-packing of the alkylsilane molecules as well as their vertical orientation with exposure of more CF3 groups instead of CF2 groups due to the polar silane-based tail are believed to be the main reasons behind their improved chemical stability. The selection of fluorocarbon oligomer with proper polar tail which can promote a self-assembled monolayer with close-packed molecules could make it possible for utilizing shorter fluorocarbon oligomers, which is environmentally favorable, to develop high surface energy materials with SAP properties.

Study of Nanocomposites of Amino Acids and Organic Polyethers by Means of Mass Spectrometry and Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Zobnina, V. G.; Kosevich, M. V.; Chagovets, V. V.; Boryak, O. A.

A problem of elucidation of structure of nanomaterials based on combination of proteins and polyether polymers is addressed on the monomeric level of single amino acids and oligomers of PEG-400 and OEG-5 polyethers. Efficiency of application of combined approach involving experimental electrospray mass spectrometry and computer modeling by molecular dynamics simulation is demonstrated. It is shown that oligomers of polyethers form stable complexes with amino acids valine, proline, histidine, glutamic, and aspartic acids. Molecular dynamics simulation has shown that stabilization of amino acid-polyether complexes is achieved due to winding of the polymeric chain around charged groups of amino acids. Structural motives revealed for complexes of single amino acids with polyethers can be realized in structures of protein-polyether nanoparticles currently designed for drug delivery.

Template-directed synthesis of oligoguanylic acids - Metal ion catalysis

NASA Technical Reports Server (NTRS)

Bridson, P. K.; Fakhrai, H.; Lohrmann, R.; Orgel, L. E.; Van Roode, M.

1981-01-01

The effects of Zn(2+), Pb(2+) and other metal ions on the efficiency and stereo-selectivity of the template-directed oligomerization of guanosine 5'-phosphorimidazolide are investigated. Reactions were run in the presence of a polyC template in a 2,6-lutidine buffer, and products analyzed by high-performance liquid chromatography on an RPC-5 column. The presence of the Pb(2+) ion is found to lead to the formation of 2'-5' linked oligomers up to the 40-mer, while Zn(2+) favors the formation of predominantly 3'-5' linked oligomers up to the 35-mer. When amounts of uracil, cytidine or adenosine 5'-phosphorimidazole equal to those of the guanosine derivative are included in the reaction mixture, the incorrect base is incorporated into the oligomer about 10% of the time with a Pb(2+) catalyst, but less than 0.5% of the time with Zn(2+). The Sn(2+), Sb(3+) and Bi(3+) ions are also found to promote the formation of 2'-5' oligomers, although not as effectively as Pb(2+), while no metal ions other than Zn(2+) promote the formation of the 3'-5' oligomers. The results may be important for the understanding of the evolution of nucleic acid replication in the absence of enzymes.

Characterisation of a haemagglutinin from Hokkaido red bean (Phaseolus vulgaris cv. Hokkaido red bean).

PubMed

Wong, Jack H; Wan, Chung T; Ng, Tzi B

2010-01-15

A haemagglutinin was purified from Japanese Hokkaido red beans (Phaseolus vulgaris cv. Hokkaido red bean) with a procedure that included three chromatographic media. Haemagglutinating activity was adsorbed on DEAE cellulose, Affi-gel blue gel and Mono S. The pure haemagglutinin was a homodimer and each subunit was around 30 kDa in molecular mass. The haemagglutinating activity of this agglutinin could not be inhibited by a variety of simple sugars at 200 mmol L(-1) concentration including alpha-L-fucose, D(+)-galactose, D(+)-glucose, D(+)-glucosamine, D(-)galactosamine, galacturonic acid, (+)-lactose, D(+)-melibose, L(-)-mannose, D(+)-mannose, D-mannosamine, D(+)-raffinose, L-rhamnose, (+)-xylose and galacturonic acid. The haemagglutinating activity was fully retained at pH 4-11 and at 0-80 degrees C, but was completely lost at extreme pH values (0-2 and 13-14) and at very high temperatures (90 degrees C and 100 degrees C). The haemagglutinin exhibited a weak mitogenic activity toward mouse splenocytes, a stronger anti-proliferative activity than Con A toward HepG2 (human hepatoma) cells and inhibited >80% of HIV-1 reverse transcriptase inhibitory activity at 3.3 micromol L(-1). It was devoid of anti-fungal activity. Hokkaido red bean haemagglutinin possesses a potent anti-proliferative effect on HepG2 cells. Copyright (c) 2009 Society of Chemical Industry.

Pectin-rich biomass as feedstock for fuel ethanol production.

PubMed

Edwards, Meredith C; Doran-Peterson, Joy

2012-08-01

The USA has proposed that 30 % of liquid transportation fuel be produced from renewable resources by 2030 (Perlack and Stokes 2011). It will be impossible to reach this goal using corn kernel-based ethanol alone. Pectin-rich biomass, an under-utilized waste product of the sugar and juice industry, can augment US ethanol supplies by capitalizing on this already established feedstock. Currently, pectin-rich biomass is sold (at low value) as animal feed. This review focuses on the three most studied types of pectin-rich biomass: sugar beet pulp, citrus waste and apple pomace. Fermentations of these materials have been conducted with a variety of ethanologens, including yeasts and bacteria. Escherichia coli can ferment a wide range of sugars including galacturonic acid, the primary component of pectin. However, the mixed acid metabolism of E. coli can produce unwanted side products. Saccharomyces cerevisiae cannot naturally ferment galacturonic acid nor pentose sugars but has a homoethanol pathway. Erwinia chrysanthemi is capable of degrading many of the cell wall components of pectin-rich materials, including pectin. Klebsiella oxytoca can metabolize a diverse array of sugars including cellobiose, one degradation product of cellulose. However, both E. chrysanthemi and K. oxytoca produce side products during fermentation, similar to E. coli. Using pectin-rich residues from industrial processes is beneficial because the material is already collected and partially pretreated to facilitate enzymatic deconstruction of the plant cell walls. Using biomass already produced for other purposes is an attractive practice because fewer greenhouse gases (GHG) will be anticipated from land-use changes.

DEVELOPMENT OF SEPARATION SYSTEMS FOR POLYNUCLEAR AROMATIC HYDROCARBON ENVIRONMENTAL CONTAMINANTS USING MICELLAR ELECTROKINETIC CHROMATOGRAPHY WITH MOLECULAR MICELLES AND FREE ZONE ELECTROPHORESIS

EPA Science Inventory

Of four systems available from the literature, based on cyclodextrins, dioctylsulfosuccinate, bile salts, and molecular micelles consisting of oligomers of undecylenic acid, the most successful separation system in our hands is based on the molecular micelles, oligomers of sodiu...

Stereocomplexes Formed From Select Oligomers of Polymer d-lactic Acid (PDLA) and l-lactate May Inhibit Growth of Cancer Cells and Help Diagnose Aggressive Cancers—Applications of the Warburg Effect

PubMed Central

Goldberg, Joel S.

2011-01-01

It is proposed that select oligomers of polymer d-lactic acid (PDLA) will form a stereocomplex with l-lactate in vivo, producing lactate deficiency in tumor cells. Those cancer cells that utilize transport of lactate to maintain electrical neutrality may cease to multiply or die because of lactate trapping, and those cancer cells that benefit from utilization of extracellular lactate may be impaired. Intracellular trapping of lactate produces a different physiology than inhibition of LDH because the cell loses the option of shuttling pyruvate to an alternative pathway to produce an anion. Conjugated with stains or fluorescent probes, PDLA oligomers may be an agent for the diagnosis of tissue lactate and possibly cell differentiation in biopsy specimens. Preliminary experimental evidence is presented confirming that PDLA in high concentrations is cytotoxic and that l-lactate forms a presumed stereocomplex with PDLA. Future work should be directed at isolation of biologically active oligomers of PDLA. PMID:21487535

Characterization of a uronate dehydrogenase from Thermobispora bispora for production of glucaric acid from hemicellulose substrate.

PubMed

Li, Yaxian; Xue, Yemin; Cao, Zhigang; Zhou, Tao; Alnadari, Fawze

2018-06-23

A thermostable uronate dehydrogenase Tb-UDH from Thermobispora bispora was over-expressed in Escherichia coli using the T7 polymerase expression system. The Tb-UDH was purified by metal affinity chromatography, and gave a single band on SDS-PAGE. The maximum activity on glucuronic acid was found at 60 °C and pH 7.0. The purified enzyme retained over 58% of its activity after holding a pH ranging from 7.0 to 7.5 for 1 h at 60 °C. The K m and V max values of the purified Tb-UDH for Glucuronic acid (GluUA) were 0.165 mM and 117.7 U mg -1 , respectively, those for galacturonic acid (GalUA) were 0.115 mM and 104.2 U mg -1 , respectively, and those for NAD + were 0.120 mM and 133.3 U mg -1 , respectively; the turnover number (k cat ) with GluUA as a substrate was higher than that with GalUA; however, the Michaelis constant (K m ) for GalUA was lower than that for GluUA. After 60 min of incubation at 50 °C, Tb-UDH exhibited a conversion ratio for glucuronic acid to the glucaric acid of 84% on chemical reagent and 81.3% on hydrolysates from breech xylans formed by xylanase and α-glucuronidase. This work shows that biocatalytic routes have great potential for the conversion of hemicellulose substrate into value-added products derived from renewable biomass. TOC GRAPHIC: (A) The structure of the xylan is described and the site of action of the xylan degrading enzyme is indicated. (B) The effect of substrate concentration on recombinant Tb-UDH activity when galacturonic acid was used as substrate. (C) SDS-PAGE analysis of E. coli BL21 (DE3) harboring pET-20b(+) and pET-20b-Tb-UDH. (D) Oxidative conversion of glucuronic acid from a beechwood xylan to glucaric acid.

Applications of pectinases in the commercial sector: a review.

PubMed

Kashyap, D R; Vohra, P K; Chopra, S; Tewari, R

2001-05-01

Pectinases are one of the upcoming enzymes of fruit and textile industries. These enzymes break down complex polysaccharides of plant tissues into simpler molecules like galacturonic acids. The role of acidic pectinases in bringing down the cloudiness and bitterness of fruit juices is well established. Recently, there has been a good number of reports on the application of alkaline pectinases in the textile industry for the retting and degumming of fiber crops, production of good quality paper, fermentation of coffee and tea, oil extractions and treatment of pectic waste water. This review discusses various types of pectinases and their applications in the commercial sector.

Nitroxyl-mediated oxidation of lignin and polycarboxylated products

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stahl, Shannon S.; Rafiee, Mohammad

Methods of selectively modifying lignin, polycarboxylated products thereof, and methods of deriving aromatic compounds therefrom. The methods comprise electrochemically oxidizing lignin using stable nitroxyl radicals to selectively oxidize primary hydroxyls on .beta.-O-4 phenylpropanoid units to corresponding carboxylic acids while leaving the secondary hydroxyls unchanged. The oxidation results in polycarboxylated lignin in the form of a polymeric .beta.-hydroxy acid. The polymeric .beta.-hydroxy acid has a high loading of carboxylic acid and can be isolated in acid form, deprotonated, and/or converted to a salt. The .beta.-hydroxy acid, anion, or salt can also be subjected to acidolysis to generate various aromatic monomers ormore » oligomers. The initial oxidation of lignin to the polycarboxylated form renders the lignin more susceptible to acidolysis and thereby enhances the yield of aromatic monomers and oligomers obtained through acidolysis.« less

Abiotic ligation of DNA oligomers templated by their liquid crystal ordering

NASA Astrophysics Data System (ADS)

Fraccia, Tommaso P.; Smith, Gregory P.; Zanchetta, Giuliano; Paraboschi, Elvezia; Yi, Yougwooo; Walba, David M.; Dieci, Giorgio; Clark, Noel A.; Bellini, Tommaso

2015-03-01

It has been observed that concentrated solutions of short DNA oligomers develop liquid crystal ordering as the result of a hierarchically structured supramolecular self-assembly. In mixtures of oligomers with various degree of complementarity, liquid crystal microdomains are formed via the selective aggregation of those oligomers that have a sufficient degree of duplexing and propensity for physical polymerization. Here we show that such domains act as fluid and permeable microreactors in which the order-stabilized molecular contacts between duplex terminals serve as physical templates for their chemical ligation. In the presence of abiotic condensing agents, liquid crystal ordering markedly enhances ligation efficacy, thereby enhancing its own phase stability. The coupling between order-templated ligation and selectivity provided by supramolecular ordering enables an autocatalytic cycle favouring the growth of DNA chains, up to biologically relevant lengths, from few-base long oligomers. This finding suggests a novel scenario for the abiotic origin of nucleic acids.

Method to produce water-soluble sugars from biomass using solvents containing lactones

DOEpatents

Dumesic, James A.; Luterbacher, Jeremy S.

2015-06-02

A process to produce an aqueous solution of carbohydrates that contains C6-sugar-containing oligomers, C6 sugar monomers, C5-sugar-containing oligomers, C5 sugar monomers, or any combination thereof is presented. The process includes the steps of reacting biomass or a biomass-derived reactant with a solvent system including a lactone and water, and an acid catalyst. The reaction yields a product mixture containing water-soluble C6-sugar-containing oligomers, C6-sugar monomers, C5-sugar-containing oligomers, C5-sugar monomers, or any combination thereof. A solute is added to the product mixture to cause partitioning of the product mixture into an aqueous layer containing the carbohydrates and a substantially immiscible organic layer containing the lactone.

Method to produce water-soluble sugars from biomass using solvents containing lactones

DOEpatents

Dumesic, James A.; Luterbacher, Jeremy S.

2017-08-08

A process to produce an aqueous solution of carbohydrates that contains C6-sugar-containing oligomers, C6 sugar monomers, C5-sugar-containing oligomers, C5 sugar monomers, or any combination thereof is presented. The process includes the steps of reacting biomass or a biomass-derived reactant with a solvent system including a lactone and water, and an acid catalyst. The reaction yields a product mixture containing water-soluble C6-sugar-containing oligomers, C6-sugar monomers, C5-sugar-containing oligomers, C5-sugar monomers, or any combination thereof. A solute is added to the product mixture to cause partitioning of the product mixture into an aqueous layer containing the carbohydrates and a substantially immiscible organic layer containing the lactone.

Isolation, purification and some structural features of the mucilaginous exudate from Musa paradisiaca.

PubMed

Mondal, S K; Ray, B; Thakur, S; Ghosal, P K

2001-03-01

The water-soluble polysaccharides isolated from the vascular gel of Musa paradisiaca, were fractionated via anion exchange chromatography into four fractions. Fractionated polymers contained arabinose, xylose and galacturonic acid as major sugars, together with traces of galactose, rhamnose, mannose and glucose residues. Methylation analysis revealed the presence of a highly branched arabinoxylan with a significant amount of terminal arabinopyranosyl units and an arabinogalactan type I pectin. Periodate oxidation studies supported the results of methylation analysis.

{sup 252}Cf-plasma desorption mass spectra of bacterial oligosaccharides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elkin, Y.N.; Komandrova, N.A.; Tomshich, S.V.

1994-07-20

The possibility has been investigated of using the MSBKh instrument ({sup 252}Cf plasma desorption mass spectrometer) for studying the oligosaccharides of the O-specific chains of bacterial lipopolysaccharides. Experimental results on the ionization of galacturonic acid and of neutral and bacterial oligosaccharides containing NHR and COOH groups have been obtained and are discussed. The instrument has been used for estimating the compositions of fractions in the separation of degradation products of O-specific polysaccharide chains and establishing their structures.

The pectic disaccharides lepidimoic acid and β-d-xylopyranosyl-(1→3)-d-galacturonic acid occur in cress-seed exudate but lack allelochemical activity

PubMed Central

Iqbal, Amjad; Miller, Janice G.; Murray, Lorna; Sadler, Ian H.; Fry, Stephen C.

2016-01-01

Background and aims Cress-seed (Lepidium sativum) exudate exerts an allelochemical effect, promoting excessive hypocotyl elongation and inhibiting root growth in neighbouring Amaranthus caudatus seedlings. We investigated acidic disaccharides present in cress-seed exudate, testing the proposal that the allelochemical is an oligosaccharin—lepidimoic acid (LMA; 4-deoxy-β-l-threo-hex-4-enopyranuronosyl-(1→2)-l-rhamnose). Methods Cress-seed exudate was variously treated [heating, ethanolic precipitation, solvent partitioning, high-voltage paper electrophoresis and gel-permeation chromatography (GPC)], and the products were bioassayed for effects on dark-grown Amaranthus seedlings. Two acidic disaccharides, including LMA, were isolated and characterized by electrophoresis, thin-layer chromatography (TLC) and nuclear magnetic resonance (NMR) spectroscopy, and then bioassayed. Key Results Cress-seed exudate contained low-Mr, hydrophilic, heat-stable material that strongly promoted Amaranthus hypocotyl elongation and inhibited root growth, but that separated from LMA on electrophoresis and GPC. Cress-seed exudate contained ∼250 µm LMA, whose TLC and electrophoretic mobilities, susceptibility to mild acid hydrolysis and NMR spectra are reported. A second acidic disaccharide, present at ∼120 µm, was similarly characterized, and shown to be β-d-xylopyranosyl-(1→3)-d-galacturonic acid (Xyl→GalA), a repeat unit of xylogalacturonan. Purified LMA and Xyl→GalA when applied at 360 and 740 µm, respectively, only slightly promoted Amaranthus hypocotyl growth, but equally promoted root growth and thus had no effect on the hypocotyl:root ratio, unlike total cress-seed exudate. Conclusions LMA is present in cress seeds, probably formed by rhamnogalacturonan lyase action on rhamnogalacturonan-I during seed development. Our results contradict the hypothesis that LMA is a cress allelochemical that appreciably perturbs the growth of potentially competing seedlings. Since LMA and Xyl→GalA slightly promoted both hypocotyl and root elongation, their effect could be nutritional. We conclude that rhamnogalacturonan-I and xylogalacturonan (pectin domains) are not sources of oligosaccharins with allelochemical activity, and the biological roles (if any) of the disaccharides derived from them are unknown. The main allelochemical principle in cress-seed exudate remains to be identified. PMID:26957370

A method for the 32P labeling of peptides or peptide nucleic acid oligomers

NASA Technical Reports Server (NTRS)

Kozlov, I. A.; Nielsen, P. E.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1998-01-01

A novel approach to the radioactive labeling of peptides and PNA oligomers is described. It is based on the conjugation of a deoxynucleoside 3'-phosphate with the terminal amine of the substrate, followed by phosphorylation of the 5'-hydroxyl group of the nucleotide using T4 polynucleotide kinase and [gamma-32P]ATP.

β-Amyloid Oligomers Induce Phosphorylation of Tau and Inactivation of Insulin Receptor Substrate via c-Jun N-Terminal Kinase Signaling: Suppression by Omega-3 Fatty Acids and Curcumin

PubMed Central

Ma, Qiu-Lan; Yang, Fusheng; Rosario, Emily R.; Ubeda, Oliver J.; Beech, Walter; Gant, Dana J.; Chen, Ping Ping; Hudspeth, Beverly; Chen, Cory; Zhao, Yongle; Vinters, Harry V.; Frautschy, Sally A.

2009-01-01

Both insulin resistance (type II diabetes) and β-amyloid (Aβ) oligomers are implicated in Alzheimer's disease (AD). Here, we investigate the role of Aβ oligomer-induced c-Jun N-terminal kinase (JNK) activation leading to phosphorylation and degradation of the adaptor protein insulin receptor substrate-1 (IRS-1). IRS-1 couples insulin and other trophic factor receptors to downstream kinases and neuroprotective signaling. Increased phospho-IRS-1 is found in AD brain and insulin-resistant tissues from diabetics. Here, we report Aβ oligomers significantly increased active JNK and phosphorylation of IRS-1 (Ser616) and tau (Ser422) in cultured hippocampal neurons, whereas JNK inhibition blocked these responses. The omega-3 fatty acid docosahexaenoic acid (DHA) similarly inhibited JNK and the phosphorylation of IRS-1 and tau in cultured hippocampal neurons. Feeding 3xTg-AD transgenic mice a diet high in saturated and omega-6 fat increased active JNK and phosphorylated IRS-1 and tau. Treatment of the 3xTg-AD mice on high-fat diet with fish oil or curcumin or a combination of both for 4 months reduced phosphorylated JNK, IRS-1, and tau and prevented the degradation of total IRS-1. This was accompanied by improvement in Y-maze performance. Mice fed with fish oil and curcumin for 1 month had more significant effects on Y-maze, and the combination showed more significant inhibition of JNK, IRS-1, and tau phosphorylation. These data indicate JNK mediates Aβ oligomer inactivation of IRS-1 and phospho-tau pathology and that dietary treatment with fish oil/DHA, curcumin, or a combination of both has the potential to improve insulin/trophic signaling and cognitive deficits in AD. PMID:19605645

Inhibiting nucleation of amyloid structure in a huntingtin fragment by targeting α-helix rich oligomeric intermediates

PubMed Central

Mishra, Rakesh; Jayaraman, Murali; Roland, Bartholomew P.; Landrum, Elizabeth; Fullam, Timothy; Kodali, Ravindra; Thakur, Ashwani K.; Arduini, Irene; Wetzel, Ronald

2011-01-01

Although oligomeric intermediates are transiently formed in almost all known amyloid assembly reactions, their mechanistic roles are poorly understood. Recently we demonstrated a critical role for the 17 amino acid N-terminal segment (httNT) of huntingtin (htt) in oligomer-mediated amyloid assembly of htt N-terminal fragments. In this mechanism, the httNT segment forms the α-helix rich core of the oligomers, leaving most or all of each polyglutamine (polyQ) segment disordered and solvent-exposed. Nucleation of amyloid structure occurs within this local high concentration of disordered polyQ. Here we demonstrate the kinetic importance of httNT self-assembly by describing inhibitory httNT-containing peptides that appear to work by targeting nucleation within the oligomer fraction. These molecules inhibit amyloid nucleation by forming mixed oligomers with the httNT domains of polyQ-containing htt N-terminal fragments. In one class of inhibitor, nucleation is passively suppressed due to the reduced local concentration of polyQ within the mixed oligomer. In the other class, nucleation is actively suppressed by a proline-rich polyQ segment covalently attached to httNT. Studies with D-amino acid and scrambled sequence versions of httNT suggest that inhibition activity is strongly linked to the propensity of inhibitory peptides to make amphipathic α-helices. HttNT derivatives with C-terminal cell penetrating peptide segments, also exhibit excellent inhibitory activity. The httNT-based peptides described here, especially those with protease-resistant D-amino acids and/or with cell penetrating sequences, may prove useful as lead therapeutics for inhibiting nucleation of amyloid formation in Huntington’s disease. PMID:22178478

A quantification method for heat-decomposable methylglyoxal oligomers and its application on 1,3,5-trimethylbenzene SOA

NASA Astrophysics Data System (ADS)

Rodigast, Maria; Mutzel, Anke; Herrmann, Hartmut

2017-03-01

Methylglyoxal forms oligomeric compounds in the atmospheric aqueous particle phase, which could establish a significant contribution to the formation of aqueous secondary organic aerosol (aqSOA). Thus far, no suitable method for the quantification of methylglyoxal oligomers is available despite the great effort spent for structure elucidation. In the present study a simplified method was developed to quantify heat-decomposable methylglyoxal oligomers as a sum parameter. The method is based on the thermal decomposition of oligomers into methylglyoxal monomers. Formed methylglyoxal monomers were detected using PFBHA (o-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine hydrochloride) derivatisation and gas chromatography-mass spectrometry (GC/MS) analysis. The method development was focused on the heating time (varied between 15 and 48 h), pH during the heating process (pH = 1-7), and heating temperature (50, 100 °C). The optimised values of these method parameters are presented. The developed method was applied to quantify heat-decomposable methylglyoxal oligomers formed during the OH-radical oxidation of 1,3,5-trimethylbenzene (TMB) in the Leipzig aerosol chamber (LEipziger AerosolKammer, LEAK). Oligomer formation was investigated as a function of seed particle acidity and relative humidity. A fraction of heat-decomposable methylglyoxal oligomers of up to 8 % in the produced organic particle mass was found, highlighting the importance of those oligomers formed solely by methylglyoxal for SOA formation. Overall, the present study provides a new and suitable method for quantification of heat-decomposable methylglyoxal oligomers in the aqueous particle phase.

Solid-Phase Synthesis of Diverse Peptide Tertiary Amides By Reductive Amination

PubMed Central

Pels, Kevin; Kodadek, Thomas

2015-01-01

The synthesis of libraries of conformationally-constrained peptide-like oligomers is an important goal in combinatorial chemistry. In this regard an attractive building block is the N-alkylated peptide, also known as peptide tertiary amide (PTA). PTAs are strongly biased conformationally due to allylic 1,3 strain interactions. We report here an improved synthesis of these species on solid supports through the use of reductive amination chemistry using amino acid-terminated, bead-displayed oligomers and diverse aldehydes. The utility of this chemistry is demonstrated by the synthesis of a library of 10,000 mixed peptoid-PTA oligomers. PMID:25695359

Solid-phase synthesis of diverse peptide tertiary amides by reductive amination.

PubMed

Pels, Kevin; Kodadek, Thomas

2015-03-09

The synthesis of libraries of conformationally constrained peptide-like oligomers is an important goal in combinatorial chemistry. In this regard an attractive building block is the N-alkylated peptide, also known as a peptide tertiary amide (PTA). PTAs are conformationally constrained because of allylic 1,3 strain interactions. We report here an improved synthesis of these species on solid supports through the use of reductive amination chemistry using amino acid-terminated, bead-displayed oligomers and diverse aldehydes. The utility of this chemistry is demonstrated by the synthesis of a library of 10,000 mixed peptoid-PTA oligomers.

Iron-induced oligomerization of human FXN81-210 and bacterial CyaY frataxin and the effect of iron chelators

PubMed Central

Ahlgren, Eva-Christina; Fekry, Mostafa; Wiemann, Mathias; Söderberg, Christopher A.; Bernfur, Katja; Gakh, Olex; Rasmussen, Morten; Højrup, Peter; Emanuelsson, Cecilia; Isaya, Grazia

2017-01-01

Patients suffering from the progressive neurodegenerative disease Friedreich’s ataxia have reduced expression levels of the protein frataxin. Three major isoforms of human frataxin have been identified, FXN42-210, FXN56-210 and FXN81-210, of which FXN81-210 is considered to be the mature form. Both long forms, FXN42-210 and FXN56-210, have been shown to spontaneously form oligomeric particles stabilized by the extended N-terminal sequence. The short variant FXN81-210, on other hand, has only been observed in the monomeric state. However, a highly homologous E. coli frataxin CyaY, which also lacks an N-terminal extension, has been shown to oligomerize in the presence of iron. To explore the mechanisms of stabilization of short variant frataxin oligomers we compare here the effect of iron on the oligomerization of CyaY and FXN81-210. Using dynamic light scattering, small-angle X-ray scattering, electron microscopy (EM) and cross linking mass spectrometry (MS), we show that at aerobic conditions in the presence of iron both FXN81-210 and CyaY form oligomers. However, while CyaY oligomers are stable over time, FXN81-210 oligomers are unstable and dissociate into monomers after about 24 h. EM and MS studies suggest that within the oligomers FXN81-210 and CyaY monomers are packed in a head-to-tail fashion in ring-shaped structures with potential iron-binding sites located at the interface between monomers. The higher stability of CyaY oligomers can be explained by a higher number of acidic residues at the interface between monomers, which may result in a more stable iron binding. We also show that CyaY oligomers may be dissociated by ferric iron chelators deferiprone and DFO, as well as by the ferrous iron chelator BIPY. Surprisingly, deferiprone and DFO stimulate FXN81-210 oligomerization, while BIPY does not show any effect on oligomerization in this case. The results suggest that FXN81-210 oligomerization is primarily driven by ferric iron, while both ferric and ferrous iron participate in CyaY oligomer stabilization. Analysis of the amino acid sequences of bacterial and eukaryotic frataxins suggests that variations in the position of the acidic residues in helix 1, β-strand 1 and the loop between them may control the mode of frataxin oligomerization. PMID:29200434

Purification, Biochemical Characterization, and Amino Acid Sequence of a Novel Type of Lectin from Aplysia dactylomela Eggs with Antibacterial/Antibiofilm Potential.

PubMed

Carneiro, Rômulo Farias; Torres, Renato Cézar Farias; Chaves, Renata Pinheiro; de Vasconcelos, Mayron Alves; de Sousa, Bruno Lopes; Goveia, André Castelo Rodrigues; Arruda, Francisco Vassiliepe; Matos, Maria Nágila Carneiro; Matthews-Cascon, Helena; Freire, Valder Nogueira; Teixeira, Edson Holanda; Nagano, Celso Shiniti; Sampaio, Alexandre Holanda

2017-02-01

A new lectin from Aplysia dactylomela eggs (ADEL) was isolated by affinity chromatography on HCl-activated Sepharose™ media. Hemagglutination caused by ADEL was inhibited by several galactosides, mainly galacturonic acid (Ka = 6.05 × 10 6  M -1 ). The primary structure of ADEL consists of 217 residues, including 11 half-cystines involved in five intrachain and one interchain disulfide bond, resulting in a molecular mass of 57,228 ± 2 Da, as determined by matrix-assisted laser desorption/ionization time of flight mass spectrometry. ADEL showed high similarity with lectins isolated from Aplysia eggs, but not with other known lectins, indicating that these lectins could be grouped into a new family of animal lectins. Three glycosylation sites were found in its polypeptide backbone. Data from peptide-N-glycosidase F digestion and MS suggest that all oligosaccharides attached to ADEL are high in mannose. The secondary structure of ADEL is predominantly β-sheet, and its tertiary structure is sensitive to the presence of ligands, as observed by CD. A 3D structure model of ADEL was created and shows two domains connected by a short loop. Domain A is composed of a flat three-stranded and a curved five-stranded β-sheet, while domain B presents a flat three-stranded and a curved four-stranded β-sheet. Molecular docking revealed favorable binding energies for interactions between lectin and galacturonic acid, lactose, galactosamine, and galactose. Moreover, ADEL was able to agglutinate and inhibit biofilm formation of Staphylococcus aureus, suggesting that this lectin may be a potential alternative to conventional use of antimicrobial agents in the treatment of infections caused by Staphylococcal biofilms.

Nitrogen-Containing, Light-Absorbing Oligomers Produced in Aerosol Particles Exposed to Methylglyoxal, Photolysis, and Cloud Cycling.

PubMed

De Haan, David O; Tapavicza, Enrico; Riva, Matthieu; Cui, Tianqu; Surratt, Jason D; Smith, Adam C; Jordan, Mary-Caitlin; Nilakantan, Shiva; Almodovar, Marisol; Stewart, Tiffany N; de Loera, Alexia; De Haan, Audrey C; Cazaunau, Mathieu; Gratien, Aline; Pangui, Edouard; Doussin, Jean-François

2018-04-03

Aqueous methylglyoxal chemistry has often been implicated as an important source of oligomers in atmospheric aerosol. Here we report on chemical analysis of brown carbon aerosol particles collected from cloud cycling/photolysis chamber experiments, where gaseous methylglyoxal and methylamine interacted with glycine, ammonium, or methylammonium sulfate seed particles. Eighteen N-containing oligomers were identified in the particulate phase by liquid chromatography/diode array detection/electrospray ionization high-resolution quadrupole time-of-flight mass spectrometry. Chemical formulas were determined and, for 6 major oligomer products, MS 2 fragmentation spectra were used to propose tentative structures and mechanisms. Electronic absorption spectra were calculated for six tentative product structures by an ab initio second order algebraic-diagrammatic-construction/density functional theory approach. For five structures, matching calculated and measured absorption spectra suggest that they are dominant light-absorbing species at their chromatographic retention times. Detected oligomers incorporated methylglyoxal and amines, as expected, but also pyruvic acid, hydroxyacetone, and significant quantities of acetaldehyde. The finding that ∼80% (by mass) of detected oligomers contained acetaldehyde, a methylglyoxal photolysis product, suggests that daytime methylglyoxal oligomer formation is dominated by radical addition mechanisms involving CH 3 CO*. These mechanisms are evidently responsible for enhanced browning observed during photolytic cloud events.

Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30.

PubMed

Lee, Hasup; Baek, Minkyung; Lee, Gyu Rie; Park, Sangwoo; Seok, Chaok

2017-03-01

Many proteins function as homo- or hetero-oligomers; therefore, attempts to understand and regulate protein functions require knowledge of protein oligomer structures. The number of available experimental protein structures is increasing, and oligomer structures can be predicted using the experimental structures of related proteins as templates. However, template-based models may have errors due to sequence differences between the target and template proteins, which can lead to functional differences. Such structural differences may be predicted by loop modeling of local regions or refinement of the overall structure. In CAPRI (Critical Assessment of PRotein Interactions) round 30, we used recently developed features of the GALAXY protein modeling package, including template-based structure prediction, loop modeling, model refinement, and protein-protein docking to predict protein complex structures from amino acid sequences. Out of the 25 CAPRI targets, medium and acceptable quality models were obtained for 14 and 1 target(s), respectively, for which proper oligomer or monomer templates could be detected. Symmetric interface loop modeling on oligomer model structures successfully improved model quality, while loop modeling on monomer model structures failed. Overall refinement of the predicted oligomer structures consistently improved the model quality, in particular in interface contacts. Proteins 2017; 85:399-407. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Strain-specific Fibril Propagation by an Aβ Dodecamer

NASA Astrophysics Data System (ADS)

Dean, Dexter N.; Das, Pradipta K.; Rana, Pratip; Burg, Franklin; Levites, Yona; Morgan, Sarah E.; Ghosh, Preetam; Rangachari, Vijayaraghavan

2017-01-01

Low molecular weight oligomers of amyloid-β (Aβ) have emerged as the primary toxic agents in the etiology of Alzheimer disease (AD). Polymorphism observed within the aggregation end products of fibrils are known to arise due to microstructural differences among the oligomers. Diversity in aggregate morphology correlates with the differences in AD, cementing the idea that conformational strains of oligomers could be significant in phenotypic outcomes. Therefore, it is imperative to determine the ability of strains to faithfully propagate their structure. Here we report fibril propagation of an Aβ42 dodecamer called large fatty acid-derived oligomers (LFAOs). The LFAO oligomeric strain selectively induces acute cerebral amyloid angiopathy (CAA) in neonatally-injected transgenic CRND8 mice. Propagation in-vitro occurs as a three-step process involving the association of LFAO units. LFAO-seeded fibrils possess distinct morphology made of repeating LFAO units that could be regenerated upon sonication. Overall, these data bring forth an important mechanistic perspective into strain-specific propagation of oligomers that has remained elusive thus far.

Role of the reaction of stabilized Criegee intermediates with peroxy radicals in particle formation and growth in air.

PubMed

Zhao, Yue; Wingen, Lisa M; Perraud, Véronique; Greaves, John; Finlayson-Pitts, Barbara J

2015-05-21

Ozonolysis of alkenes is an important source of secondary organic aerosol (SOA) in the atmosphere. However, the mechanisms by which stabilized Criegee intermediates (SCI) react to form and grow the particles, and in particular the contributions from oligomers, are not well understood. In this study, ozonolysis of trans-3-hexene (C6H12), as a proxy for small alkenes, was investigated with an emphasis on the mechanisms of particle formation and growth. Ozonolysis experiments were carried out both in static Teflon chambers (18-20 min reaction times) and in a glass flow reactor (24 s reaction time) in the absence and presence of OH or SCI scavengers, and under different relative humidity (RH) conditions. The chemical composition of polydisperse and size-selected SOA particles was probed using different mass spectrometric techniques and infrared spectroscopy. Oligomers having SCI as the chain unit are found to be the dominant components of such SOA particles. The formation mechanism for these oligomers suggested by our results follows the sequential addition of SCI to organic peroxy (RO2) radicals, in agreement with previous studies by Moortgat and coworkers. Smaller particles are shown to have a relatively greater contribution from longer oligomers. Higher O/C ratios are observed in smaller particles and are similar to those of oligomers resulting from RO2 + nSCI, supporting a significant role for longer oligomers in particle nucleation and early growth. Under atmospherically relevant RH of 30-80%, water vapor suppresses oligomer formation through scavenging SCI, but also enhances particle nucleation. Under humid conditions, or in the presence of formic or hydrochloric acid as SCI scavengers, peroxyhemiacetals are formed by the acid-catalyzed particle phase reaction between oligomers from RO2 + nSCI and a trans-3-hexene derived carbonyl product. In contrast to the ozonolysis of trans-3-hexene, oligomerization involving RO2 + nSCI does not appear to be prevalent in the ozonolysis of α-cedrene (C15H24), indicating different particle formation mechanisms for small and large complex alkenes that need to be taken into account in atmospheric models.

Determination of oligomers in virgin and recycled polyethylene terephthalate (PET) samples by UPLC-MS-QTOF.

PubMed

Ubeda, Sara; Aznar, Margarita; Nerín, Cristina

2018-03-01

An oligomer is a molecule that consists of a few monomer units. It can be formed during polymer manufacturing and also due to polymer degradation processes or even during use conditions. Since oligomers are not included in chemical databases, their identification is a complex process. In this work, the oligomers present in 20 different PET pellet samples have been determined. Two different sample treatment procedures, solvent extraction and total dissolution, were applied in order to select the most efficient one. The analyses were carried out by UPLC-MS-QTOF. The use of high resolution mass spectrometry allowed the structural elucidation of these compounds and their correct identification. The main oligomers identified were cyclic as well as lineal from the first, second, and third series. All of them were composed of terephthalic acid (TPA), diethylene glycol (DEG), and ethylene glycol (EG). Quantitative values were very different in both procedures. In total dissolution of PET samples, the concentration of oligomers was always, at least, 10 times higher than in solvent extraction; some of the compounds were only detected when total dissolution was used. Results showed that the oligomers with the highest concentration values were dimers and trimers, cyclic, as well as lineal, from the first and second series. The oligomer with the maximum concentration value was TPA 2 -EG-DEG that was found in all the samples in a concentration range from 2493 to 19,290 ng/g PET. No differences between virgin and recycled PET were found. Migration experiments were performed in two PET bottles, and results showed the transference of most of these oligomers to a fat food simulant (ethanol 95%). Graphical abstract Graphical abstract of the two procedures developd and optimized for identifying oligomers in PET pellets and in migration form PET bottles.

Dietary DHA supplementation in an APP/PS1 transgenic rat model of AD reduces behavioral and Aβ pathology and modulates Aβ oligomerization.

PubMed

Teng, Edmond; Taylor, Karen; Bilousova, Tina; Weiland, David; Pham, Thaidan; Zuo, Xiaohong; Yang, Fusheng; Chen, Ping-Ping; Glabe, Charles G; Takacs, Alison; Hoffman, Dennis R; Frautschy, Sally A; Cole, Gregory M

2015-10-01

Increased dietary consumption of docosahexaenoic acid (DHA) is associated with decreased risk for Alzheimer's disease (AD). These effects have been postulated to arise from DHA's pleiotropic effects on AD pathophysiology, including its effects on β-amyloid (Aβ) production, aggregation, and toxicity. While in vitro studies suggest that DHA may inhibit and reverse the formation of toxic Aβ oligomers, it remains uncertain whether these mechanisms operate in vivo at the physiological concentrations of DHA attainable through dietary supplementation. We sought to clarify the effects of dietary DHA supplementation on Aβ indices in a transgenic APP/PS1 rat model of AD. Animals maintained on a DHA-supplemented diet exhibited reductions in hippocampal Aβ plaque density and modest improvements on behavioral testing relative to those maintained on a DHA-depleted diet. However, DHA supplementation also increased overall soluble Aβ oligomer levels in the hippocampus. Further quantification of specific conformational populations of Aβ oligomers indicated that DHA supplementation increased fibrillar (i.e. putatively less toxic) Aβ oligomers and decreased prefibrillar (i.e. putatively more toxic) Aβ oligomers. These results provide in vivo evidence suggesting that DHA can modulate Aβ aggregation by stabilizing soluble fibrillar Aβ oligomers and thus reduce the formation of both Aβ plaques and prefibrillar Aβ oligomers. However, since fibrillar Aβ oligomers still retain inherent neurotoxicity, DHA may need to be combined with other interventions that can additionally reduce fibrillar Aβ oligomer levels for more effective prevention of AD in clinical settings. Published by Elsevier Inc.

Assessing the Impact of Backbone Length and Capping Agent on the Conformational Preferences of a Model Peptide: Conformation Specific IR and UV Spectroscopy of 2-AMINOISOBUTYRIC Acid

NASA Astrophysics Data System (ADS)

Gord, Joseph R.; Hewett, Daniel M.; Kubasik, Matthew A.; Zwier, Timothy S.

2015-06-01

2-Aminoisobutyric acid (Aib) is an achiral, α-amino acid having two equivalent methyl groups attached to C_α. Extended Aib oligomers are known to have a strong preference for the adoption of a 310-helical structure in the condensed phase. Here, we have taken a simplifying step and focused on the intrinsic folding propensities of Aib by looking at a series of capped Aib oligomers in the gas phase, free from the influence of solvent molecules and cooled in a supersonic expansion. Resonant two-photon ionization and IR-UV holeburning have been used to record single-conformation UV spectra using the Z-cap as the UV chromophore. Resonant ion-dip infrared (RIDIR) spectroscopy provides single-conformation IR spectra in the OH stretch and NH stretch regions. Data have been collected on a set of Z-(Aib)n-X oligomers with n = 1, 2, 4, 6 and X = -OH and -OMethyl. The impacts of these capping groups and differences in backbone length have been found to dramatically influence the conformational space accessed by the molecules studied here. Oligomers of n=4 have sufficient backbone length for a full turn of the 310-helix to be formed. Early interpretation of the data collected shows clear spectroscopic markers signaling the onset of 310-helix formation as well as evidence of structures incorporating C7 and C14 hydrogen bonded rings. Toniolo, C.; Bonora, G. M.; Barone, V.; Bavoso, A.; Benedetti, E.; Di Blasio, B.; Grimaldi, P.; Lelj, F.; Pavone, V.; Pedone, C., Conformation of Pleionomers of α-Aminoisobutyric Acid. Macromolecules 1985, 18, 895-902.

Esters of oligo-(glycerol carbonate-glycerol): New biobased oligomeric surfactants.

PubMed

Holmiere, Sébastien; Valentin, Romain; Maréchal, Philippe; Mouloungui, Zéphirin

2017-02-01

Glycerol carbonate is one of the most potentially multifunction glycerol-derived compounds. Glycerol is an important by-product of the oleochemical industry. The oligomerization of glycerol carbonate, assisted by the glycerol, results in the production of polyhydroxylated oligomers rich in linear carbonate groups. The polar moieties of these oligomers (M w <1000Da) were supplied by glycerol and glycerol carbonate rather than ethylene oxide as in most commercial surfactants. The insertion of linear carbonate groups into the glycerol-based skeleton rendered the oligomers amphiphilic, resulting in a decrease in air/water surface tension to 57mN/m. We improved the physical and chemical properties of the oligomers, by altering the type of acylation reaction and the nature of the acyl donor. The polar head is constituted of homo-oligomers and hetero-oligomers. Homo-oligomers are oligoglycerol and/or oligocarbonate, hetero-oligomers are oligo(glycerol-glycerol carbonate). Coprah oligoesters had the best surfactant properties (CMC<1mg/mL, π cmc <30mN/m), outperforming molecules of fossil origin, such as ethylene glycol monododecyl ether, glycol ethers and fatty acid esters of sorbitan polyethoxylates. The self-assembling properties of oligocarbonate esters were highlighted by their ability to stabilize inverse and multiple emulsions. The oligo-(glycerol carbonate-glycerol ether) with relatively low molecular weights showed properties of relatively high-molecular weight molecules, and constitute a viable "green" alternative to ethoxylated surfactants. Copyright © 2016 Elsevier Inc. All rights reserved.

Chemical analysis of a polysaccharide of unripe (green) tomato (Lycopersicon esculentum).

PubMed

Chandra, Krishnendu; Ghosh, Kaushik; Ojha, Arnab K; Islam, Syed S

2009-11-02

A polysaccharide (PS-I) isolated from the aqueous extract of the unripe (green) tomatoes (Lycopersicon esculentum) consists of D-galactose, D-methyl galacturonate, D-arabinose, L-arabinose, and L-rhamnose. Structural investigation of the polysaccharide was carried out using total acid hydrolysis, methylation analysis, periodate oxidation study, and NMR studies ((1)H, (13)C, DQF-COSY, TOCSY, NOESY, ROESY, HMQC, and HMBC). On the basis of above-mentioned experiments the structure of the repeating unit of the polysaccharide (PS-I) was established as: [structure: see text].

Theoretical study on the cage-like nanostructures formed by amino acids and their potential applications as drug carriers

NASA Astrophysics Data System (ADS)

Weng, Pei Pei; Fan, Jian Fen; Lin, Hui Fang; Zhao, Xin; Si, Xia Lan

2017-12-01

The cage-like octamer, decamer and dodecamer constructed from aspartic acid monomers have been studied to explore their potential applications as drug carriers using the density functional theory. The calculation results indicate that these stable cage-like oligomers are mainly connected by the -C=O…HOOC- and -HN…HOOC- H-bonds and still keep stability and good drum-shaped topologies after the incorporation of 5-fluorouracil, paraldehyde and C24, respectively. The self-assembled cage-like oligomers may be applied to the preparation of new biological materials and the design of drug delivery systems.

Semisynthesis and Structure-Activity Studies of Uncarinic Acid C Isolated from Uncaria rhynchophylla as a Specific Inhibitor of the Nucleation Phase in Amyloid β42 Aggregation.

PubMed

Yoshioka, Takuya; Murakami, Kazuma; Ido, Kyohei; Hanaki, Mizuho; Yamaguchi, Kanoko; Midorikawa, Satohiro; Taniwaki, Shinji; Gunji, Hiroki; Irie, Kazuhiro

2016-10-28

Oligomers of the 42-mer amyloid-β protein (Aβ42), rather than fibrils, cause synaptic dysfunction in the pathology of Alzheimer's disease (AD). The nucleation phase in a nucleation-dependent aggregation model of Aβ42 is related to the formation of oligomers. Uncaria rhynchophylla is one component of "Yokukansan", a Kampo medicine, which is widely used for treating AD symptoms. Previously, an extract of U. rhynchophylla was found to reduce the aggregation of Aβ42, but its active principles have yet to be identified. In the present work, uncarinic acid C (3) was identified as an inhibitor of Aβ42 aggregation that is present in U. rhynchophylla. Moreover, compound 3 acted as a specific inhibitor of the nucleation phase of Aβ42 aggregation. Compound 3 was synthesized from saponin A (10), an abundant byproduct of rutin purified from Uncaria elliptica. Comprehensive structure-activity studies on 3 suggest that both a C-27 ferulate and a C-28 carboxylic acid group are required for its inhibitory activity. These findings may aid the development of oligomer-specific inhibitors for AD therapy.

Surveying the Hydrogen Bonding Landscape of AN Achiral, α-AMINO Acid: Conformation Specific IR and UV Spectroscopy of 2-AMINOISOBUTYRIC Acid

NASA Astrophysics Data System (ADS)

Gord, Joseph R.; Hewett, Daniel M.; Kubasik, Matthew A.; Zwier, Timothy S.

2014-06-01

2-Aminoisobutyric acid (Aib) is an achiral, α-amino acid having two equivalent methyl groups attached to Cα. Extended Aib oligomers are known to preferentially adopt a 310-helical structure in the condensed phase. Here, we take a simplifying step and focus on the intrinsic folding propensities of Aib by looking at a single, capped Aib structure and then extending to longer oligomers in the gas phase, free from the influence of solvent molecules and cooled in a supersonic expansion. Resonant two-photon ionization and IR-UV holeburning will be used to record single-conformation UV spectra using the Z-cap as UV chromophore. Resonant ion-dip infrared (RIDIR) spectroscopy provides single-conformation IR spectra in the OH stretch, NH stretch, amide I and amide II regions. Two conformational isomers have been identified for the smallest unit in the study, Z-Aib-OH, and four conformational isomers were seen for Z-Aib-Aib-OH, with widely-varying IR spectral patterns. In addition to investigating the conformational dependence on oligomer length, this work also studies the steric and electrostatic impact of different capping groups, R-X where X = -OH, -OMethyl, and -OtButyl. These caps are considered here for the case of Z-Aib-Aib-X. Extension to larger Z-(Aib)n-X oligomers will shed light on the extent to which the solution phase preference for 310-helix formation is retained in the gas phase, and when its onset first appears. When possible 13C isotopomers will be used to assist with the assignments and modulate the coupling between amide I fundamentals. Toniolo, C.; Bonora, G. M.; Barone, V.; Bavoso, A.; Benedetti, E.; Di Blasio, B.; Grimaldi, P.; Lelj, F.; Pavone, V.; Padone, C., Conformation of Pleionomers of α-Aminoisobutyric Acid. Macromolecules 1985, 18, 895-902.

Characterization of biomolecular nanoconjugates by high-throughput delivery and spectroscopic difference

PubMed Central

DeLong, Robert K; Risor, Azure; Kanomata, Masaaki; Laymon, Amanda; Jones, Brooke; Zimmerman, Scott D; Williams, Joseph; Witkowski, Colette; Warner, Mathew; Ruff, Michael; Garrad, Richard; Fallon, John K; Hickey, Anthony J; Sedaghat-Herati, Reza

2013-01-01

Aims Nanoparticle conjugates have the potential for delivering siRNA, splice-shifting oligomers or nucleic acid vaccines, and can be applicable to anticancer therapeutics. This article compares tripartite conjugates with gold nanoparticles or synthetic methoxypoly(ethylene glycol)-block-polyamidoamine dendrimers. Materials & methods Interactions with model liposomes of a 1:1 molar ratio of tripalmitin:cholesterol or phospholipid:cholesterol were investigated by high-throughput absorbance, as well as fluorescence difference and cellular luminescence assays. Results Spectral differences and dynamic light-scattering spectroscopy shifts demonstrated the interaction of conjugates with liposomes. Biological activity was demonstrated by upregulation of gene expression via splice-shifting oligomers, delivery of anti-B-Raf siRNA in cultured human cancer cells or tuberculosis antigen 85B plasmid expression vector in a coculture model of antigen presentation. Conclusion The data suggests that gold nanoparticles and methoxypoly(ethylene glycol)-block-polyamidoamine dendrimer nanoconjugates may have potential for binding, stabilization and delivery of splice-shifting oligomers, siRNA and nucleic acid vaccines for preclinical trials. PMID:22943129

Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic β-Proline Oligomers: Length-Dependent Convergence to Organized Structures.

PubMed

Otani, Yuko; Watanabe, Satoshi; Ohwada, Tomohiko; Kitao, Akio

2017-01-12

In this study, the solution structures of the homooligomers of a conformationally constrained bicyclic proline-type β-amino acid were studied by means of molecular dynamics (MD) calculations in explicit methanol and water using the umbrella sampling method. The ratio of trans-amide and cis-amide was estimated by NMR and the rotational barrier of the amide of acetylated bicyclic amino acid monomer was estimated by two-dimensional (2D) exchange spectroscopy (EXSY) or line-shape analysis. A bias potential was introduced with respect to the amide torsion angle ω to enhance conformational exchange including isomerization of amide bonds by lowering the rotation energy barrier. After determination of reweighting parameters to best reproduce the experimental results of the monomer amide, the free energy profile around the amide torsion angle ω was obtained from the MD trajectory by reweighting of the biased probability density. The MD simulation results support the existence of invertomers of nitrogen-pyramidalized amide. Furthermore, extended structures with a high fraction of trans-amide conformation appear to be increasingly stabilized as the oligomer is elongated, both in methanol and in water. Our conformational analysis of natural and non-natural tertiary-amide-based peptide oligomers indicates that these oligomers preferentially adopt a limited number of conformations.

Formation of nitrogen-containing oligomers by methylglyoxal and amines in simulated evaporating cloud droplets.

PubMed

De Haan, David O; Hawkins, Lelia N; Kononenko, Julia A; Turley, Jacob J; Corrigan, Ashley L; Tolbert, Margaret A; Jimenez, Jose L

2011-02-01

Reactions of methylglyoxal with amino acids, methylamine, and ammonium sulfate can take place in aqueous aerosol and evaporating cloud droplets. These processes are simulated by drying droplets and bulk solutions of these compounds (at low millimolar and 1 M concentrations, respectively) and analyzing the residuals by scanning mobility particle sizing, nuclear magnetic resonance, aerosol mass spectrometry (AMS), and electrospray ionization MS. The results are consistent with imine (but not diimine) formation on a time scale of seconds, followed by the formation of nitrogen-containing oligomers, methylimidazole, and dimethylimidazole products on a time scale of minutes to hours. Measured elemental ratios are consistent with imidazoles and oligomers being major reaction products, while effective aerosol densities suggest extensive reactions take place within minutes. These reactions may be a source of the light-absorbing, nitrogen-containing oligomers observed in urban and biomass-burning aerosol particles.

Montmorillonite catalysis of RNA oligomer formation in aqueous solution. A model for the prebiotic formation of RNA

NASA Technical Reports Server (NTRS)

Ferris, J. P.; Ertem, G.

1993-01-01

Oligomers of adenylic acid of up to the 11-mer in length are formed by the reaction of the phosphorimidazolide of adenosine (ImpA) in pH 8 aqueous solution at room temperature in the presence of Na(+)-montmorillonite. These oligomers are joined by phosphodiester bonds in which the 3',5'-linkage predominates over the 2',5'-linkage by a 2:1 ratio. Reaction of a 9:1 mixture of ImpA, A5'ppA results in the formation of oligomers with a 3:1 ratio of 3',5'- to 2',5'-linked phosphodiester bonds. A high proportion of these oligomers contain the A5'ppA grouping. A5'ppA reacts much more rapidly with ImpA than does 5'-ADP (ppA) or 5'-ATP (pppA). The exchangeable cation associated with the montmorillonite effects the observed catalysis with Li+, Na+, NH4+, and Ca2+ being the more effective while Mg2+ and Al3+ are almost ineffective catalysts. 2',5'-Linked oligomers, up to the tetramer in length, are formed using UO2(2+)-montmorillonite. The structure analysis of individual oligomer fractions was performed by selective enzymatic and KOH hydrolytic studies followed by HPLC analysis of the reaction products. It is concluded from the composition of the oligomers that the rate of addition ImpA to a 3'-terminus containing a 2',5'-linkage is slower than the addition to a nucleoside joined by a 3',5'-linked phosphodiester bond. The potential importance of mineral catalysis of the formation of RNA and other oligomers on primitive Earth is discussed.

Poly(ester amide)s based on (L)-lactic acid oligomers and α-amino acids: influence of the α-amino acid side chain in the poly(ester amide)s properties.

PubMed

Fonseca, Ana C; Coelho, Jorge F J; Valente, Joana F A; Correia, Tiago R; Correia, Ilídio J; Gil, Maria H; Simões, Pedro N

2013-01-01

Novel biodegradable and low cytotoxic poly(ester amide)s (PEAs) based on α-amino acids and (L)-lactic acid (L-LA) oligomers were successfully synthesized by interfacial polymerization. The chemical structure of the new polymers was confirmed by spectroscopic analyses. Further characterization suggests that the α-amino acid plays a critical role on the final properties of the PEA. L-phenylalanine provides PEAs with higher glass transition temperature, whereas glycine enhances the crystallinity. The hydrolytic degradation in PBS (pH = 7.4) at 37 °C also depends on the α-amino acid, being faster for glycine-based PEAs. The cytotoxic profiles using fibroblast human cells indicate that the PEAs did not elicit an acute cytotoxic effect. The strategy presented in this work opens the possibility of synthesizing biodegradable PEAs with low citotoxicity by an easy and fast method. It is worth to mention also that the properties of these materials can be fine-tuned only by changing the α-amino acid.

Protein Self-Assembly and Protein-Induced DNA Morphologies

NASA Astrophysics Data System (ADS)

Mawhinney, Matthew T.

The ability of biomolecules to associate into various structural configurations has a substantial impact on human physiology. The synthesis of protein polypeptide chains using the information encoded by DNA is mediated through the use of regulatory proteins, known as transcription factors. Some transcription factors perform function by inducing local curvature in deoxyribonucleic acid (DNA) strands, the mechanisms of which are not entirely known. An important architectural protein, eleven zinc finger CTCF (11 ZF CTCF) is involved in genome organization and hypothesized to mediate DNA loop formation. Direct evidence for these CTCF-induced DNA loops has yet to be observed. In this thesis, the effect of 11 ZF CTCF on DNA morphology is examined using atomic force microscopy, a powerful technique for visualizing biomolecules with nanometer resolution. The presence of CTCF is revealed to induce a variety of morphologies deviating from the relaxed state of control DNA samples, including compact circular complexes, meshes, and networks. Images reveal quasi-circular DNA/CTCF complexes consistent with a single DNA molecule twice wrapped around the protein. The structures of DNA and proteins are highly important for operations in the cell. Structural irregularities may lead to a variety of issues, including more than twenty human pathologies resulting from aberrant protein misfolding into amyloid aggregates of elongated fibrils. Insulin deficiency and resistance characterizing type 2 diabetes often requires administration of insulin. Injectable and inhalable delivery methods have been documented to result in the deposition of amyloid fibrils. Oligomers, soluble multiprotein assemblies, are believed to play an important role in this process. Insulin aggregation under physiological conditions is not well understood and oligomers have not yet been fully characterized. In this thesis, in vitro insulin aggregation at acidic and neutral pH is explored using a variety of techniques, including kinetic thioflavin T fluorescence, circular dichroism spectroscopy, atomic force and electron microscopy imaging. The size distribution of insulin oligomers at different assembly stages is characterized through covalent cross-linking and gel electrophoresis. Results show that at the earliest assembly stage, oligomers comprise up to 40% and 70% of soluble insulin at acidic and neutral pH, respectively. While the highest oligomer order increases with insulin concentration at acidic pH, the opposite tendency is observed at neutral pH, with heptamers formed in 10 muM insulin. These findings suggest that oligomers may be on- and off- pathway assemblies for insulin at acidic and neutral pH, respectively. Agitation, required to induce insulin aggregation at neutral pH, increases fibril formation rate and fibrillar mass by an order of magnitude each. Insulin incubated under agitated conditions at neutral pH rapidly aggregates into large micrometer-sized aggregates, which provides insight into injection-site amyloidosis and toxic pulmonary aggregates induced by administration of extraneous insulin.

Two forms of Vibrio cholerae O1 El Tor hemolysin derived from identical precursor protein.

PubMed

Ikigai, H; Ono, T; Nakae, T; Otsuru, H; Shimamura, T

1999-01-08

Vibrio cholerae O1 grown in heart infusion broth produces two forms of El Tor hemolysin (ETH) monomers of 65 and 50 kDa. These monomers form several different sizes of mixed oligomers ranging from 180 to 280 kDa in the liposomal membranes. We found that the N-terminal amino acid sequences, NH2-Trp-Pro-Ala-Pro-Ala-Asn-Ser-Glu, of both the 65- and 50-kDa toxins were identical. We assumed, therefore, that the 65- and 50-kDa toxins were derivatives of the identical precursor protein and the 50-kDa protein was a truncated derivative of 65-kDa ETH. To substantiate this assumption, we treated the 260-kDa oligomer with trypsin and obtained a 190-kDa oligomer. This 190-kDa oligomer consisted of only the 50-kDa subunits. Both 260- and 190-kDa oligomers formed ion channels indistinguishable from each other in planar lipid bilayers. These results suggest that the essential part of the ETH in forming the membrane-damaging aggregate is a 50-kDa protein.

Separation of Uncharged Oligodeoxynucleotide Analogs by Anion-Exchange Chromatography at High pH

NASA Technical Reports Server (NTRS)

Schmidt, Jurgen G.; Nielsen, Peter E.; Orgel, Leslie

1996-01-01

Ion-exchange chromatography is a well-established method for the analysis and purification of phosphodiester-linked oligonucleotides. If elution is carried out under alkaline conditions, the secondary structure of G- and C-rich oligomers is disrupted. Furthermore, elution times become more sensitive to the G and T content of the oligomer, because G and T are deprotonated at pH 10. In recent work on peptide-nucleic acids (PNAs) we noted that mixtures of PNA oligomers G(sub 4), G(Sub 6), G(sub 8), and G(sub 10) are readily separated by elution at pH 12 on an RPC-5 column. Here we show that this separation method is more generally applicable.

Effect of Maillard Reacted Peptides on Human Salt Taste and the Amiloride-Insensitive Salt Taste Receptor (TRPV1t)

PubMed Central

Katsumata, Tadayoshi; Nakakuki, Hiroko; Tokunaga, Chikara; Fujii, Noboru; Egi, Makoto; Phan, Tam-Hao T.; Mummalaneni, Shobha; DeSimone, John A.

2008-01-01

Maillard reacted peptides (MRPs) were synthesized by conjugating a peptide fraction (1000–5000 Da) purified from soy protein hydrolyzate with galacturonic acid, glucosamine, xylose, fructose, or glucose. The effect of MRPs was investigated on human salt taste and on the chorda tympani (CT) taste nerve responses to NaCl in Sprague–Dawley rats, wild-type, and transient receptor potential vanilloid 1 (TRPV1) knockout mice. MRPs produced a biphasic effect on human salt taste perception and on the CT responses in rats and wild-type mice in the presence of NaCl + benzamil (Bz, a blocker of epithelial Na+ channels), enhancing the NaCl response at low concentrations and suppressing it at high concentrations. The effectiveness of MRPs as salt taste enhancers varied with the conjugated sugar moiety: galacturonic acid = glucosamine > xylose > fructose > glucose. The concentrations at which MRPs enhanced human salt taste were significantly lower than the concentrations of MRPs that produced increase in the NaCl CT response. Elevated temperature, resiniferatoxin, capsaicin, and ethanol produced additive effects on the NaCl CT responses in the presence of MRPs. Elevated temperature and ethanol also enhanced human salt taste perception. N-(3-methoxyphenyl)-4-chlorocinnamid (a blocker of TRPV1t) inhibited the Bz-insensitive NaCl CT responses in the absence and presence of MRPs. TRPV1 knockout mice demonstrated no Bz-insensitive NaCl CT response in the absence or presence of MRPs. The results suggest that MRPs modulate human salt taste and the NaCl + Bz CT responses by interacting with TRPV1t. PMID:18603652

Ultrasound-assisted extraction of polysaccharides from Artemisia selengensis Turcz and its antioxidant and anticancer activities.

PubMed

Wang, Juan; Lu, He Dong; Muḥammad, Umair; Han, Jin Zhi; Wei, Zhao Hui; Lu, Zhao Xin; Bie, Xiao Mei; Lu, Feng Xia

2016-02-01

Artemisia selengensis Turcz (AST) is a perennial herb with therapeutic and economic applications in China. The effects of ultrasound-assisted extraction (UAE) parameters upon extraction yield (EY%), antioxidant and antitumor activities of the polysaccharides extracts were studied by using a factorial design and response surface methodology. The optimal conditions determined were as: ultrasonic power 146 W, extraction time 14.5 min. and extraction temperature 60 °C. The average molecular weights of two homogeneous polysaccharides (APS1 and APS2) purified by DEAE cellulose-52 and Sephadex G-100 column chromatography were 125.4 and 184.1 kDa, respectively. Monosaccharide analysis showed that APS1 and APS2 were composed of five common monomers i.e., galactose, mannose, arabinose, xylose and rhamnose and one different monomer glucose and galacturonic acid respectively, with a most abundant part in molar % of APS1 and APS2 were glucose (83.01 %) and galacturonic acid (48.87 %) while least were xylose (0.80 %) and mannose (1.73 %) respectively. The antioxidant properties were determined by evaluating DPPH, hydroxyl radical scavenging activity and reducing power which indicated both APS1 and APS2 showed strong scavenging activities and anticancer activities on HT-29, BGC823 and antitumor activity on HepG-2. As UAE improved the polysaccharides yield than CSE, meanwhile, no significant difference of polysaccharides chemical compositions. Therefore, the present study suggests that the consumption of AST leaves may beneficial for the treatment of many diseases.

Centrifugal partition chromatography in a biorefinery context: Separation of monosaccharides from hydrolysed sugar beet pulp.

PubMed

Ward, David P; Cárdenas-Fernández, Max; Hewitson, Peter; Ignatova, Svetlana; Lye, Gary J

2015-09-11

A critical step in the bioprocessing of sustainable biomass feedstocks, such as sugar beet pulp (SBP), is the isolation of the component sugars from the hydrolysed polysaccharides. This facilitates their subsequent conversion into higher value chemicals and pharmaceutical intermediates. Separation methodologies such as centrifugal partition chromatography (CPC) offer an alternative to traditional resin-based chromatographic techniques for multicomponent sugar separations. Highly polar two-phase systems containing ethanol and aqueous ammonium sulphate are examined here for the separation of monosaccharides present in hydrolysed SBP pectin: l-rhamnose, l-arabinose, d-galactose and d-galacturonic acid. Dimethyl sulfoxide (DMSO) was selected as an effective phase system modifier improving monosaccharide separation. The best phase system identified was ethanol:DMSO:aqueous ammonium sulphate (300gL(-1)) (0.8:0.1:1.8, v:v:v) which enabled separation of the SBP monosaccharides by CPC (200mL column) in ascending mode (upper phase as mobile phase) with a mobile phase flow rate of 8mLmin(-1). A mixture containing all four monosaccharides (1.08g total sugars) in the proportions found in hydrolysed SBP was separated into three main fractions; a pure l-rhamnose fraction (>90%), a mixed l-arabinose/d-galactose fraction and a pure d-galacturonic acid fraction (>90%). The separation took less than 2h demonstrating that CPC is a promising technique for the separation of these sugars with potential for application within an integrated, whole crop biorefinery. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, David N.; Apel, William A.; Thompson, Vicki S.

A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extractsmore » are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.« less

Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

DOEpatents

Thompson, David N.; Apel, William A.; Thompson, Vicki S.; Ward, Thomas E.

2016-03-22

A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

DOEpatents

Thompson, David N; Apel, William A; Thompson, Vicki S; Ward, Thomas E

2013-07-23

A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

DOEpatents

Thompson, David N; Apel, William A; Thompson, Vicki S; Ward, Thomas E

2014-04-08

A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

Characterization of thermal and mechanical properties of opligo(glycerol-glutaric acid)s

USDA-ARS?s Scientific Manuscript database

Dibutyltin oxide was used to catalyze the synthesis of oligo(glycerol-glutaric acid)s in the absence and presence of solvent. Reaction times were either 10h or 24h for reactions performed in DMF and 24h for the neat reaction. The oligomers were obtained on average in 84% yield and were characteriz...

Reactive Additives for Phenylethynyl-Containing Resins

NASA Technical Reports Server (NTRS)

Connell, John W.; Smith, Joseph G., Jr.; Hergenrother, Paul M.; Rommel, Monica L.

2005-01-01

Phenylethynyl-containing reactive additive (PERA) compounds and mixtures have been found to be useful for improving the processability of oligomers, polymers, co-oligomers, and copolymers that contain phenylethynyl groups. The additives can be incorporated in different forms: A solution of an amide acid or an imide of a PERA can be added to a solution of phenylethynyl-containing oligomer, polymer, co-oligomer, or copolymer; or An imide powder of a PERA can be mixed with a dry powder of a phenylethynyl-containing oligomer, polymer, co-oligomer, or copolymer. The effect of a given PERA on the processability and other properties of the resin system depends on whether the PERA is used in the amide acid or an imide form. With proper formulation, the PERA reduces the melt viscosity of the resin and thereby reduces the processing pressures needed to form the adhesive bonds, consolidate filled or unfilled moldings, or fabricate fiber-reinforced composite laminates. During thermal cure, a PERA reacts with itself as well as with the phenylethynyl-containing host resin and thereby becomes chemically incorporated into the resin system. The effects of the PERA on mechanical properties, relative to those of the host resin, depend on the amount of PERA used. Typically, the incorporation of the PERA results in (1) increases in the glass-transition temperature (Tg), modulus of elasticity, and parameters that characterize behavior under compression, and (2) greater retention of the aforementioned mechanical properties at elevated temperatures without (3) significant reduction of toughness or damage tolerance. Of the formulations tested thus far, the ones found to yield the best overall results were those for which the host resin was the amide acid form of a phenylethynyl-terminated imide (PETI) co-oligomer having a molecular weight of 5,000 g/mole [hence, designated PETI-5] and a PERA denoted as PERA-1. PETI-5 was made from 3,3',4'4'-biphenyltetracarboxylic dianhydride, 3,4'-oxydianiline (3,4'-ODA), 1,3-bis(3-aminophenoxy) benzene (1,3-APB), and 4-phenylethynylphthalic anhydride (PEPA). PERA-1 was made from 3,5-diamino- 4.-phenylethynylbenzophenon and equimolar amounts of phthalic anhydride and PEPA. To make PERA-1 in the imide form, the aforementioned ingredients were processed by refluxing in glacial acetic acid. To make the amide form of PERA-1, the ingredients were reacted in N-methyl-2-pyrrolidinone (NMP) under nitrogen at a temperature of 23 C (see figure). On the basis of the processability and other properties, a blend comprising 20 weight percent of PERA-1 and 80 weight percent PETI-5 was selected for further evaluation. Relative to neat PETI-5, the blend exhibited an increase in Tg; improved processability; and comparable values of shear strength in adhesion to titanium panels, open-hole compressive properties, compression properties after impact, and resistance to microcracking.

Sequential extraction of flavonoids and pectin from yellow passion fruit rind using pressurized solvent or ultrasound.

PubMed

de Souza, Caroline G; Rodrigues, Tigressa Hs; E Silva, Lorena Ma; Ribeiro, Paulo Rv; de Brito, Edy S

2018-03-01

Passion fruit rind (PFR) represents 90% of the total fruit weight and is wasted during juice processing. Passion fruit rind is known to contain flavonoids and pectin. An alternative use for this fruit juice industrial residue is to obtain these compounds. This study aimed to verify the influence of pressurized solvent extraction (PSE) or ultrasound assisted extraction (UAE) of flavonoid and pectin in a sequential process. The PSE using ethanol at 60:40 (v/v) yielded a total polyphenol content of 4.67 g GAE kg -1 PFR, orientin-7-O-glucoside (1.57 g kg -1 PFR) and luteolin-6-C-glucoside (2.44 g kg -1 PFR). Pectin yield was 165 g kg -1 PFR, either in PSE or UAE. Pectin characterization indicates that the pectic structure has basically homogalacturonans and galacturonate followed by a galacturonic acid ester unit, with methylation degree of 70%. With this study it can be concluded that mixtures of alcohols with water favor the extraction of bioactive compounds of passion fruit peel. Both PSE and UAE were effective in sequentially extracting flavonoids and pectin. The preferred solvent is ethanol due to its lower toxicity. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Study of intermolecular contacts in proteins and oligomer interfaces and preliminary investigations into the design and production of nanomaterials from proteins

NASA Astrophysics Data System (ADS)

Iyer, Ganesh Hariharan

The first part of this research involved a study of the nature and extent of nonbonded interactions at crystal and oligomer interfaces. A survey was compiled of several characteristics of intersubunit contacts in 58 different oligomeric proteins, and of the intermolecular contacts in 223 protein crystal structures. Routines written in "S" language were utilized for the generation of the observed and expected contacts. The information in the Protein Data Bank (PDB) was extracted using the database management system, Protein Knowledge Base (PKB). Potentials of mean force for atom-atom contacts and residue-residue contacts were derived by comparison of the number of observed interactions with the number expected by mass action. Preference association matrices and log-linear analyses were applied to determine the different factors that could contribute to the overall interactions at the interfaces of oligomers and crystals. Surface patches at oligomer and crystal interfaces were also studied to further investigate the origin of the differences in their stabilities. Total number of atoms in contact and the secondary structure elements involved are similar in the two types of interfaces. Crystal contacts result from more numerous interactions by polar residues, compared with a tendency toward nonpolar amino acid prominent in oligomer interfaces. Contact potentials indicate that hydrophobic interactions at oligomer interfaces favor aromatic amino acids and methionine over aliphatic amino acids; and that crystal contacts form in such a way as to avoid inclusion of hydrophobic interactions. The second part involved the development of a new class of biomaterials from two-dimensional arrays of ordered proteins. Point mutations were planned to introduce cysteine residues at appropriate locations to enable cross-linking at the molecular interface within given crystallographic planes. Crystallization and subsequent cross-linking of the modified protein would lead to the formation of arrays on subsequent dissociation of the crystal. Novel protein architectures can be generated from these cross-linked nanostructures. Experiments with model protein, maltose-binding protein (MBP) were performed to develop purification, cross-linking and crystallization techniques. The long-term goal of this project is to apply the experience gained with MBP to the fabrication of nanomaterials from other, application-specific proteins for ultrafiltration and microelectronic devices.

Pectic polysaccharide from the green fruits of Momordica charantia (Karela): structural characterization and study of immunoenhancing and antioxidant properties.

PubMed

Panda, Bibhash C; Mondal, Soumitra; Devi, K Sanjana P; Maiti, Tapas K; Khatua, Somanjana; Acharya, Krishnendu; Islam, Syed S

2015-01-12

A water soluble pectic polysaccharide (PS) isolated from the aqueous extract of the green fruits of Momordica charantia contains D-galactose and D-methyl galacturonate in a molar ratio of nearly 1:4. It showed splenocyte, thymocyte as well as macrophage activations. Moreover, it exhibited potent antioxidant activities. On the basis of total acid hydrolysis, methylation analysis, periodate oxidation, and 1D and 2D NMR studies, the structure of the repeating unit of the pectic polysaccharide was established as: [Formula: see text]. Copyright © 2014 Elsevier Ltd. All rights reserved.

Separation of 'Uncharged' Oligodeoxynucleotide Analogs by Anion-Exchange Chromatography at High pH

NASA Technical Reports Server (NTRS)

Schmidt, Jurgen G.; Orgel, Leslie E.; Nielsen, Peter E.

1996-01-01

Ion-exchange chromatography is a well-established method for the analysis and purification of phosphodiester-linked oligonucleotides. If elution is carried out under alkaline conditions, the secondary structure of G- and C-rich oligomers is disrupted. Furthermore, elution times become more sensitive to the G and T content of the oligomer, because G and T are deprotonated at pH 10. In recent work on peptide-nucleic acids (PNAs) we noted that mixtures of PNA oligomers G(sub 4), G(sub 6), G(sub 8), and G9(sub 10) are readily separated by elution at pH 12 on an RPC-5 column. Here we show that this separation method is more generally applicable.

Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

NASA Astrophysics Data System (ADS)

Wang, Bin; Lou, Zhichao; Zhang, Haiqian; Xu, Bingqian

2016-03-01

The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobic β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the conformations of oligomers observed from AFM images, the D and T units were more abundantly on mica surface at pH 4.5 because the ESP re-distribution of M units helped to stabilize these larger oligomers. The amino acid side chains involved in the binding interfaces were stabilized by hydrogen bonds and electrostatic interactions. The detailed analysis of the charged side chains at pH 4.5 indicated that the polarized ESPs induced the aggregations among M, D, and T to form larger oligomers. Therefore, the hydrogen bonds and electrostatic interactions worked together to form the stabilized prion oligomers.

Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Bin; Xu, Bingqian, E-mail: bxu@engr.uga.edu; Lou, Zhichao

2016-03-21

The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobicmore » β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the conformations of oligomers observed from AFM images, the D and T units were more abundantly on mica surface at pH 4.5 because the ESP re-distribution of M units helped to stabilize these larger oligomers. The amino acid side chains involved in the binding interfaces were stabilized by hydrogen bonds and electrostatic interactions. The detailed analysis of the charged side chains at pH 4.5 indicated that the polarized ESPs induced the aggregations among M, D, and T to form larger oligomers. Therefore, the hydrogen bonds and electrostatic interactions worked together to form the stabilized prion oligomers.« less

Two rhamnogalacturonide tetrasaccharides isolated from semi-retted flax fibers are signaling molecules in Rubus fruticosus L. cells.

PubMed Central

Dinand, E; Excoffier, G; Liénart, Y; Vignon, M R

1997-01-01

Water extraction of semi-retted flax (Linum usitatissimum L.) fiber bundles yielded a mixture of pectic oligosaccharides and two acidic rhamnogalacturonide tetrasaccharides that were separated by size-exclusion chromatography. One- and two-dimensional nuclear magnetic resonance studies and fast atom bombardment-mass spectrometry experiments indicated that the two tetrasaccharides have a common primary structure, i.e. alpha-D-delta GalpA(1-->2)-alpha-L- Rhap(1-->4)-alpha-D-GalpA-(1-->2)-L-alpha,beta-Rhap, with a rhamnopyranose as terminal reducing end, and a 4-deoxy-beta-L-threo-hex-4-enopyranosiduronic acid at the nonreducing end. However, the two tetrasaccharides differ by an acetyl group located at the O-3 position of the internal galacturonic acid residue. These two tetrasaccharides induce the activation of D-glycohydrolases of Rubus fructicosus L. cells or protoplasts within minutes. PMID:9342877

Maleic acid treatment of biologically detoxified corn stover liquor

USDA-ARS?s Scientific Manuscript database

Elimination of microbial and/or enzyme inhibitors from pretreated lignocellulose is critical for effective cellulose conversion and yeast fermentation of liquid hot-water (LHW) pretreated corn stover. In this study, xylan oligomers were hydrolyzed using either maleic acid or hemicellulases. Other so...

Ellagic acid promotes A{beta}42 fibrillization and inhibits A{beta}42-induced neurotoxicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Ying; Tsinghua University School of Medicine, Haidian District, Beijing 100084; Yang, Shi-gao

Smaller, soluble oligomers of {beta}-amyloid (A{beta}) play a critical role in the pathogenesis of Alzheimer's disease (AD). Selective inhibition of A{beta} oligomer formation provides an optimum target for AD therapy. Some polyphenols have potent anti-amyloidogenic activities and protect against A{beta} neurotoxicity. Here, we tested the effects of ellagic acid (EA), a polyphenolic compound, on A{beta}42 aggregation and neurotoxicity in vitro. EA promoted A{beta} fibril formation and significant oligomer loss, contrary to previous results that polyphenols inhibited A{beta} aggregation. The results of transmission electron microscopy (TEM) and Western blot displayed more fibrils in A{beta}42 samples co-incubated with EA in earlier phasesmore » of aggregation. Consistent with the hypothesis that plaque formation may represent a protective mechanism in which the body sequesters toxic A{beta} aggregates to render them harmless, our MTT results showed that EA could significantly reduce A{beta}42-induced neurotoxicity toward SH-SY5Y cells. Taken together, our results suggest that EA, an active ingredient in many fruits and nuts, may have therapeutic potential in AD.« less

Nanoscale Morphology, Dimensional Control and Electrical Properties of Oligoanilines

PubMed Central

Wang, Yue; Tran, Henry D.; Liao, Lei; Duan, Xiangfeng; Kaner, Richard B.

2010-01-01

While nanostructures of organic conductors have generated great interest in recent years, their nanoscale size and shape control remains a significant challenge. Here we report a general method for producing a variety of oligoaniline nanostructures with well-defined morphologies and dimensionalities. 1-D nanowires, 2-D nanoribbons, and 3-D rectangular nanoplates and nanoflowers of tetraaniline are produced by a solvent exchange process in which the dopant acid can be used to tune the oligomer morphology. The process appears to be a general route for producing nanostructures for a variety of other aniline oligomers such as the phenyl-capped tetramer. X-ray diffraction of the tetraniline nanostructures reveals that they possess different packing arrangements, which results in different nanoscale morphologies with different electrical properties for the structures. The conductivity of a single tetraaniline nanostructure is up to two orders of magnitude higher than the highest previously reported value and rivals that of pressed pellets of conventional polyaniline doped with acid. Furthermore, these oligomer nanostructures can be easily processed by a number of methods in order to create thin films composed of aligned nanostructures over a macroscopic area. PMID:20662516

Pseudopeptide foldamers: the homo-oligomers of pyroglutamic acid.

PubMed

Bernardi, Fernando; Garavelli, Marco; Scatizzi, Marco; Tomasini, Claudia; Trigari, Valerio; Crisma, Marco; Formaggio, Fernando; Peggion, Cristina; Toniolo, Claudio

2002-06-03

As a part of a program evaluating substituted gamma-lactams as conformationally constrained building blocks of pseudopeptide foldamers, we synthesized the homo-oligomers of L-pyroglutamic acid up to the tetramer level by solution methods. The preferred conformation of this pseudopeptide series in structure-supporting solvents was assessed by FT-IR absorption, 1H NMR and CD techniques. In addition, the crystal structure of the N alpha-protected dimer was established by X-ray diffraction. A high-level DFT computational modeling was performed based on the crystallographic parameters. In this analysis, we demonstrated that an alpha C-H...O=C intramolecular hydrogen bond is responsible for the stabilization of the s-trans L-pGlu-L-pGlu conformation by 1.4 kcal mol-1. This effect can be easily detected by 1H NMR spectroscopy, owing to the anomalous chemical shifts of the alpha CH protons present in all of the oligomers. In summary, we have developed a new polyimide-based, foldameric structure that, if appropriately functionalized, has promise as a rigid scaffold for novel functions and applications.

SAXS fingerprints of aldehyde dehydrogenase oligomers.

PubMed

Tanner, John J

2015-12-01

Enzymes of the aldehyde dehydrogenase (ALDH) superfamily catalyze the nicotinamide adenine dinucleotide-dependent oxidation of aldehydes to carboxylic acids. ALDHs are important in detoxification of aldehydes, amino acid metabolism, embryogenesis and development, neurotransmission, oxidative stress, and cancer. Mutations in genes encoding ALDHs cause metabolic disorders, including alcohol flush reaction (ALDH2), Sjögren-Larsson syndrome (ALDH3A2), hyperprolinemia type II (ALDH4A1), γ-hydroxybutyric aciduria (ALDH5A1), methylmalonic aciduria (ALDH6A1), pyridoxine dependent epilepsy (ALDH7A1), and hyperammonemia (ALDH18A1). We previously reported crystal structures and small-angle X-ray scattering (SAXS) analyses of ALDHs exhibiting dimeric, tetrameric, and hexameric oligomeric states (Luo et al., Biochemistry 54 (2015) 5513-5522; Luo et al., J. Mol. Biol. 425 (2013) 3106-3120). Herein I provide the SAXS curves, radii of gyration, and distance distribution functions for the three types of ALDH oligomer. The SAXS curves and associated analysis provide diagnostic fingerprints that allow rapid identification of the type of ALDH oligomer that is present in solution. The data sets provided here serve as a benchmark for characterizing oligomerization of ALDHs.

Matrix effect in matrix-assisted laser desorption/ionization mass spectra of derivatized oligomeric polyols.

PubMed

Borisov, Roman S; Polovkov, Nikolai Yu; Zhilyaev, Dmitry I; Zaikin, Vladimir G

2013-01-30

Herein we describe a strong matrix effect observed in the matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectra of silylated glycerol alkoxylates and manifested in the loss of the silyl groups in the presence of carboxyl-containing matrices. Commercially available glycerol alkoxylates containing three end OH groups as well as three matrices - 2,5-dihydroxybenzoic acid (DHB), 3-indoleacrylic acid (IAA) and 1,8,9-anthracenetriol (dithranol) - were chosen for the investigation. N,O-Bis(trimethylsilyl)trifluoroacetamide containing 1% trimethylchlorosilane, acetic anhydride and a formylation mixture (formic acid/acetyl chloride) were used for derivatization. Initial oligomers and derivatized products were analyzed by MALDI-ToF-mass spectrometry (MS) on an Autoflex II instrument, equipped with a nitrogen laser (λ 337 nm), in positive ion reflectron mode. Only [M + Na](+) ions were observed for underivatized polymers and for completely derivatized polymers in the presence of DHB and dithranol, respectively. In the case of IAA the mass spectra revealed sets of peaks for underivatized, and for partially and completely derivatized oligomers. No similar 'matrix effect' was observed in the case of acylated glycerol alkoxylates (acyl = formyl, acetyl): only peaks for completely derivatized oligomers were obtained in all matrices: DHB, IAA and dithranol. Using 1,9-nonandiol, we showed that the 'matrix effect' was due to trans-silylation of carboxyl-containing matrices (DHB and IAA) during co-crystallization of silylated oligomers and matrices. The obtained results show that matrix molecules can participate as reactive species in MALDI-ToF-MS experiments. The matrix should be carefully chosen when a derivatization approach is applied because the analysis of spectra of the completely derivatized products is particularly desirable in the quantitative determination of functional end-groups. Copyright © 2012 John Wiley & Sons, Ltd.

Toxic prefibrillar α-synuclein amyloid oligomers adopt a distinctive antiparallel β-sheet structure.

PubMed

Celej, María Soledad; Sarroukh, Rabia; Goormaghtigh, Erik; Fidelio, Gerardo D; Ruysschaert, Jean-Marie; Raussens, Vincent

2012-05-01

Parkinson's disease is an age-related movement disorder characterized by the presence in the mid-brain of amyloid deposits of the 140-amino-acid protein AS (α-synuclein). AS fibrillation follows a nucleation polymerization pathway involving diverse transient prefibrillar species varying in size and morphology. Similar to other neurodegenerative diseases, cytotoxicity is currently attributed to these prefibrillar species rather than to the insoluble aggregates. Nevertheless, the underlying molecular mechanisms responsible for cytotoxicity remain elusive and structural studies may contribute to the understanding of both the amyloid aggregation mechanism and oligomer-induced toxicity. It is already recognized that soluble oligomeric AS species adopt β-sheet structures that differ from those characterizing the fibrillar structure. In the present study we used ATR (attenuated total reflection)-FTIR (Fourier-transform infrared) spectroscopy, a technique especially sensitive to β-sheet structure, to get a deeper insight into the β-sheet organization within oligomers and fibrils. Careful spectral analysis revealed that AS oligomers adopt an antiparallel β-sheet structure, whereas fibrils adopt a parallel arrangement. The results are discussed in terms of regions of the protein involved in the early β-sheet interactions and the implications of such conformational arrangement for the pathogenicity associated with AS oligomers.

PETIs as High-Temperature Resin-Transfer-Molding Materials

NASA Technical Reports Server (NTRS)

Connell, John N.; Smith, Joseph G., Jr.; Hergenrother, Paul M.

2005-01-01

Compositions of, and processes for fabricating, high-temperature composite materials from phenylethynyl-terminated imide (PETI) oligomers by resin-transfer molding (RTM) and resin infusion have been developed. Composites having a combination of excellent mechanical properties and long-term high-temperature stability have been readily fabricated. These materials are particularly useful for the fabrication of high-temperature structures for jet-engine components, structural components on highspeed aircraft, spacecraft, and missiles. Phenylethynyl-terminated amide acid oligomers that are precursors of PETI oligomers are easily made through the reaction of a mixture of aromatic diamines with aromatic dianhydrides at high stoichiometric offsets and 4-phenylethynylphthalic anhydride (PEPA) as an end-capper in a polar solvent such as N-methylpyrrolidinone (NMP). These oligomers are subsequently cyclodehydrated -- for example, by heating the solution in the presence of toluene to remove the water by azeotropic distillation to form low-molecular-weight imide oligomers. More precisely, what is obtained is a mixture of PETI oligomeric species, spanning a range of molecular weights, that exhibits a stable melt viscosity of less than approximately 60 poise (and generally less than 10 poise) at a temperature below 300 deg C. After curing of the oligomers at a temperature of 371 deg C, the resulting polymer can have a glass-transition temperature (Tg) as high as 375 C, the exact value depending on the compositions.

Aqueous phase oligomerization of α,β-unsaturated carbonyls and acids investigated using ion mobility spectrometry coupled to mass spectrometry (IMS-MS)

NASA Astrophysics Data System (ADS)

Renard, Pascal; Tlili, Sabrine; Ravier, Sylvain; Quivet, Etienne; Monod, Anne

2016-04-01

One of the current essential issues to unravel our ability to forecast future climate change and air quality, implies a better understanding of natural processes leading to secondary organic aerosol (SOA) formation, and in particular the formation and fate of oligomers. The difficulty in characterizing macromolecules is to discern between large oxygenated molecules from series of oligomers containing repeated small monomers of diverse structures. In the present study, taking advantage from previously established radical vinyl oligomerization of methyl vinylketone (MVK) in the aqueous phase, where relatively simple oligomers containing up to 14 monomers were observed, we have investigated the same reactivity on several other unsaturated water soluble organic compounds (UWSOCs) and on a few mixtures of these precursor compounds. The technique used to characterize the formed oligomers was a traveling wave ion mobility spectrometry coupled to a hybrid quadrupole - time of flight mass spectrometer (IMS-MS) fitted with an electrospray source and ultra-high performance liquid chromatography (UPLC). The technique allows for an additional separation, especially for large ions, containing long carbon chains. We have shown the efficiency of the IMS-mass spectrometry technique to detect oligomers derived from MVK photooxidation in the aqueous phase. The results were then compared to other oligomers, derived from ten other individual biogenic UWSOCs. The technique allowed distinguishing between different oligomers arising from different precursors. It also clearly showed that compounds bearing a non-conjugated unsaturation did not provide oligomerization. Finally, it was shown that the IMS-mass spectrometry technique, applied to mixtures of unsaturated conjugated precursors, exhibited the ability of these precursors to co-oligomerize, i.e. forming only one complex oligomer system bearing monomers of different structures. The results are discussed in terms of atmospheric implications for the detection of oligomers in complex chamber and/or field samples.

Cloud forming potential of oligomers relevant to secondary organic aerosols

NASA Astrophysics Data System (ADS)

Xu, Wen; Guo, Song; Gomez-Hernandez, Mario; Zamora, Misti L.; Secrest, Jeremiah; Marrero-Ortiz, Wilmarie; Zhang, Annie L.; Collins, Don R.; Zhang, Renyi

2014-09-01

The hygroscopic growth factor (HGF) and cloud condensation nuclei (CCN) activity are measured for surrogates that mimic atmospherically relevant oligomers, including glyoxal trimer dihydrate, methyl glyoxal trimer dihydrate, sucrose, methyl glyoxal mixtures with sulfuric acid and glycolic acid, and 2,4-hexandienal mixtures with sulfuric acid and glycolic acid. For the single-component aerosols, the measured HGF ranges from 1.3 to 1.4 at a relative humidity of 90%, and the hygroscopicity parameter (κ) is in the range of 0.06 to 0.19 on the basis of the measured CCN activity and 0.13 to 0.22 on the basis of the measured HGF, compared to the calculated values of 0.08 to 0.16. Large differences exist in the κ values derived using the measured HGF and CCN data for the multi-component aerosols. Our results reveal that, in contrast to the oxidation process, oligomerization decreases particle hygroscopicity and CCN activity and provides guidance for analyzing the organic species in ambient aerosols.

Synthesis of Dicyclopentadiene Oligomer Over Nanoporous Al-MCM-41 Catalysts.

PubMed

Park, Eunseo; Kim, Jinhan; Yim, Jin-Heong; Han, Jeongsik; Kwon, Tae Soo; Park, Y K; Jeon, Jong-Ki

2016-05-01

One step reaction composed of DCPD oligomerization and DCPD oligomer isomerization was investigated over nanoporous Al-MCM-41 catalysts. The effects of aluminum grafting over MCM-41 on the catalyst characteristics were studied with respect to the synthesis of TCPD isomer. Physical and chemical properties of the catalysts were analyzed by N2 adsorption, temperature-programmed desorption of ammonia, and infrared spectroscopy of adsorbed pyridine. The overall number of acid sites as well as the number of Lewis acid sites increased with increasing of aluminum content over MCM-41. When utilizing MCM-41 and Al-MCM-41 as the catalyst, DCPD oligomerization reaction activity greatly increased compared to the thermal reaction. The highest TCPD isomer selectivity over the Al-MCM-41 catalyst with the highest aluminum content could be ascribed to the largest amount of acid sites. This study showed an increased level of TCPD isomer selectivity by an increasing level of Lewis acid sites through aluminum addition over MCM-41.

Helical Structure Determines Different Susceptibilities of dsDNA, dsRNA, and tsDNA to Counterion-Induced Condensation

PubMed Central

Kornyshev, Alexei A.; Leikin, Sergey

2013-01-01

Recent studies of counterion-induced condensation of nucleic acid helices into aggregates produced several puzzling observations. For instance, trivalent cobalt hexamine ions condensed double-stranded (ds) DNA oligomers but not their more highly charged dsRNA counterparts. Divalent alkaline earth metal ions condensed triple-stranded (ts) DNA oligomers but not dsDNA. Here we show that these counterintuitive experimental results can be rationalized within the electrostatic zipper model of interactions between molecules with helical charge motifs. We report statistical mechanical calculations that reveal dramatic and nontrivial interplay between the effects of helical structure and thermal fluctuations on electrostatic interaction between oligomeric nucleic acids. Combining predictions for oligomeric and much longer helices, we also interpret recent experimental studies of the role of counterion charge, structure, and chemistry. We argue that an electrostatic zipper attraction might be a major or even dominant force in nucleic acid condensation. PMID:23663846

Stabilization of anthocyanins in blackberry juice by glutathione fortification.

PubMed

Stebbins, Nathan B; Howard, Luke R; Prior, Ronald L; Brownmiller, Cindi; Mauromoustakos, Andy

2017-10-18

Blackberry anthocyanins provide attractive color and antioxidant activity. However, anthocyanins degrade during juice processing and storage, so maintaining high anthocyanin concentrations in berry juices may lead to greater antioxidant and health benefits for the consumer. This study evaluated potential additives to stabilize anthocyanins during blackberry juice storage. The anthocyanin stabilizing agents used were: glutathione, galacturonic acid, diethylenetriaminepentaacetic acid and tannic acid, which were added at a level of 500 mg L -1 . Juice anthocyanin, flavonol, and ellagitannin content and percent polymeric color were measured over five weeks of accelerated storage at 30 °C. Glutathione had the greatest protective effect on total anthocyanins and polymeric color. Therefore a second study was performed with glutathione in combination with lipoic and ascorbic acids in an effort to use antioxidant recycling to achieve a synergistic effect. However, the antioxidant recycling system had no protective effect relative to glutathione alone. Glutathione appears to be a promising blackberry juice additive to protect against anthocyanin degradation during storage.

Isolation and identification of oligomers from partial degradation of lime fruit cutin.

PubMed

Tian, Shiying; Fang, Xiuhua; Wang, Weimin; Yu, Bingwu; Cheng, Xiaofang; Qiu, Feng; Mort, Andrew J; Stark, Ruth E

2008-11-12

Complementary degradative treatments with low-temperature hydrofluoric acid and methanolic potassium hydroxide have been used to investigate the protective biopolymer cutin from Citrus aurantifolia (lime) fruits, augmenting prior enzymatic and chemical strategies to yield a more comprehensive view of its molecular architecture. Analysis of the resulting soluble oligomeric fragments with one- and two-dimensional NMR and MS methods identified a new dimer and three trimeric esters of primary alcohols based on 10,16-dihydroxyhexadecanoic acid and 10-oxo-16-hydroxyhexadecanoic acid units. Whereas only 10-oxo-16-hydroxyhexadecanoic acid units were found in the oligomers from hydrofluoric acid treatments, the dimer and trimer products isolated to date using diverse degradative methods included six of the seven possible stoichiometric ratios of monomer units. A novel glucoside-linked hydroxyfatty acid tetramer was also identified provisionally, suggesting that the cutin biopolymer can be bound covalently to the plant cell wall. Although the current findings suggest that the predominant molecular architecture of this protective polymer in lime fruits involves esters of primary and secondary alcohols based on long-chain hydroxyfatty acids, the possibility of additional cross-linking to enhance structural integrity is underscored by these and related findings of nonstandard cutin molecular architectures.

Effects of Pectin Molecular Weight Changes on the Structure, Dynamics, and Polysaccharide Interactions of Primary Cell Walls of Arabidopsis thaliana: Insights from Solid-State NMR.

PubMed

Phyo, Pyae; Wang, Tuo; Xiao, Chaowen; Anderson, Charles T; Hong, Mei

2017-09-11

Significant cellulose-pectin interactions in plant cell walls have been reported recently based on 2D 13 C solid-state NMR spectra of intact cell walls, but how these interactions affect cell growth has not been probed. Here, we characterize two Arabidopsis thaliana lines with altered expression of the POLYGALACTURONASE INVOLVED IN EXPANSION1 (PGX1) gene, which encodes a polygalacturonase that cleaves homogalacturonan (HG). PGX1 AT plants overexpress PGX1, have HG with lower molecular weight, and grow larger, whereas pgx1-2 knockout plants have HG with higher molecular weight and grow smaller. Quantitative 13 C solid-state NMR spectra show that PGX1 AT cell walls have lower galacturonic acid and xylose contents and higher HG methyl esterification than controls, whereas high molecular weight pgx1-2 walls have similar galacturonic acid content and methyl esterification as controls. 1 H-transferred 13 C INEPT spectra indicate that the interfibrillar HG backbones are more aggregated whereas the RG-I side chains are more dispersed in PGX1 AT cell walls than in pgx1-2 walls. In contrast, the pectins that are close to cellulose become more mobile and have weaker cross peaks with cellulose in PGX1 AT walls than in pgx1-2 walls. Together, these results show that polygalacturonase-mediated plant growth is accompanied by increased esterification and decreased cross-linking of HG, increased aggregation of interfibrillar HG, and weaker HG-cellulose interactions. These structural and dynamical differences give molecular insights into how pectins influence wall dynamics during cell growth.

Improved sample preparation and rapid UHPLC analysis of SO2 binding carbonyls in wine by derivatisation to 2,4-dinitrophenylhydrazine.

PubMed

Jackowetz, J N; Mira de Orduña, R

2013-08-15

Sulphur dioxide (SO2) is essential for the preservation of wines. The presence of SO2 binding compounds in musts and wines may limit sulphite efficacy leading to higher total SO2 additions, which may exceed SO2 limits permitted by law and pose health risks for sensitive individuals. An improved method for the quantification of significant wine SO2 binding compounds is presented that applies a novel sample treatment approach and rapid UHPLC separation. Glucose, galacturonic acid, alpha-ketoglutarate, pyruvate, acetoin and acetaldehyde were derivatised with 2,4-dinitrophenylhydrazine and separated using a solid core C18 phase by ultra high performance liquid chromatography. Addition of EDTA to samples prevented de novo acetaldehyde formation from ethanol oxidation. Optimised derivatisation duration enhanced reproducibility and allowed for glucose and galacturonic acid quantification. High glucose residues were found to interfere with the recovery of other SO2 binders, but practical SO2 concentrations and red wine pigments did not affect derivatisation efficiency. The calibration range, method accuracy, precision and limits of detection were found to be satisfactory for routine analysis of SO2 binders in wines. The current method represents a significant improvement in the comprehensive analysis of SO2 binding wine carbonyls. It allows for the quantification of major SO2 binders at practical analyte concentrations, and uses a simple sample treatment method that prevents treatment artifacts. Equipment utilisation could be reduced by rapid LC separation while maintaining analytical performance parameters. The improved method will be a valuable addition for the analysis of total SO2 binder pools in oenological samples. Published by Elsevier Ltd.

Regulation of L-ascorbic acid content in strawberry fruits

PubMed Central

Cruz-Rus, Eduardo; Amaya, Iraida; Sánchez-Sevilla, José F.; Botella, Miguel A.; Valpuesta, Victoriano

2011-01-01

Plants have several L-ascorbic acid (AsA) biosynthetic pathways, but the contribution of each one to the synthesis of AsA varyies between different species, organs, and developmental stages. Strawberry (Fragaria×ananassa) fruits are rich in AsA. The pathway that uses D-galacturonate as the initial substrate is functional in ripe fruits, but the contribution of other pathways to AsA biosynthesis has not been studied. The transcription of genes encoding biosynthetic enzymes such as D-galacturonate reductase (FaGalUR) and myo-inositol oxygenase (FaMIOX), and the AsA recycling enzyme monodehydroascorbate reductase (FaMDHAR) were positively correlated with the increase in AsA during fruit ripening. Fruit storage for 72 h in a cold room reduced the AsA content by 30%. Under an ozone atmosphere, this reduction was 15%. Ozone treatment increased the expression of the FaGalUR, FaMIOX, and L-galactose-1-phosphate phosphatase (FaGIPP) genes, and transcription of the L-galactono-1,4-lactone dehydrogenase (FaGLDH) and FAMDHAR genes was higher in the ozone-stored than in the air-stored fruits. Analysis of AsA content in a segregating population from two strawberry cultivars showed high variability, which did not correlate with the transcription of any of the genes studied. Study of GalUR protein in diverse cultivars of strawberry and different Fragaria species showed that a correlation between GalUR and AsA content was apparent in most cases, but it was not general. Three alleles were identified in strawberry, but any sequence effect on the AsA variability was eliminated by analysis of the allele-specific expression. Taken together, these results indicate that FaGalUR shares the control of AsA levels with other enzymes and regulatory elements in strawberry fruit. PMID:21561953

Chemistry and Properties of Imide Oligomers from Phenylethynyl-Containing Diamines

NASA Technical Reports Server (NTRS)

Smith, J. G., Jr.; Connell, J. W.

2000-01-01

As an extension of work on pendent phenylethynlyl-containing imide oligomer, three new diamines containing pendent phenylethynyl groups were prepared and characterized. These diamines were used to prepare pendent and pendent and terminal phenylethynyl imide oliogomers via the amide acid route in N-methyl-2-pyrrolidinone at a calculated number average molecular weight of 5000 g mol (exp -1). The pendent phenylethynyl groups were randomly distributed along the oliogomer backbone and provided a means of controlling the distance between reactive sites. The imide oligomers were characterized and thermally cured, and the cured polymers evaluated as thin films and compared with materials of similar composition prepared from 3,5-diamino-4'-phenylethynylbenzophenone. This work was performed as part of a continuing research effort to develop structural resins for potential aeronautical applications.

Hydrogenation and hydrodeoxygenation of biomass-derived oxygenates to liquid alkanes for transportation fuels.

PubMed

Sun, Shaohui; Yang, Ruishu; Wang, Xin; Yan, Shaokang

2018-04-01

An attractive approach for the production of transportation fuels from renewable biomass resources is to convert oxygenates into alkanes. In this paper, C 5 -C 20 alkanes formed via the hydrogenation and hydrodeoxygenation of the oligomers of furfuryl alcohol(FA) can be used as gasoline, diesel and jet fuel fraction. The first step of the process is the oligomers of FA convert into hydrogenated products over Raney Ni catalyst in a batch reactor. The second step of the process converts hydrogenated products to alkanes via hydrodeoxygenation over different bi-functional catalysts include hydrogenation and acidic deoxidization active sites. After this process, the oxygen content decreased from 22.1 wt% in the oligomers of FA to 0.58 wt% in the hydrodeoxygenation products.

A glycoproteomic approach reveals that the S-layer glycoprotein of Lactobacillus kefiri CIDCA 83111 is O- and N-glycosylated.

PubMed

Cavallero, Gustavo J; Malamud, Mariano; Casabuono, Adriana C; Serradell, M de Los Ángeles; Couto, Alicia S

2017-06-06

In Gram-positive bacteria, such as lactic acid bacteria, general glycosylation systems have not been documented so far. The aim of this work was to characterize in detail the glycosylation of the S-layer protein of Lactobacillus kefiri CIDCA 83111. A reductive β-elimination treatment followed by anion exchange high performance liquid chromatography analysis was useful to characterize the O-glycosidic structures. MALDI-TOF mass spectrometry analysis confirmed the presence of oligosaccharides bearing from 5 to 8 glucose units carrying galacturonic acid. Further nanoHPLC-ESI analysis of the glycopeptides showed two O-glycosylated peptides: the peptide sequence SSASSASSA already identified as a signature glycosylation motif in L. buchneri, substituted on average with eight glucose residues and decorated with galacturonic acid and another O-glycosylated site on peptide 471-476, with a Glc 5-8 GalA 2 structure. As ten characteristic sequons (Asn-X-Ser/Thr) are present in the S-layer amino acid sequence, we performed a PNGase F digestion to release N-linked oligosaccharides. Anion exchange chromatography analysis showed mainly short N-linked chains. NanoHPLC-ESI in the positive and negative ion modes were useful to determine two different peptides substituted with short N-glycan structures. To our knowledge, this is the first description of the structure of N-glycans in S-layer glycoproteins from Lactobacillus species. A detailed characterization of protein glycosylation is essential to establish the basis for understanding and investigating its biological role. It is known that S-layer proteins from kefir-isolated L. kefiri strains are involved in the interaction of bacterial cells with yeasts present in kefir grains and are also capable to antagonize the adverse effects of different enteric pathogens. Therefore, characterization of type and site of glycosidic chains in this protein may help to understand these important properties. Furthermore, this is the first description of N-glycosidic chains in S-layer glycoprotein from Lactobacillus spp. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of Extraction Conditions on the Saccharide (Neutral and Acidic) Composition of the Crude Pectic Extract from Various Agro-Industrial Residues.

PubMed

Babbar, Neha; Roy, Sandra Van; Wijnants, Marc; Dejonghe, Winnie; Caligiani, Augusta; Sforza, Stefano; Elst, Kathy

2016-01-13

The influence of different extraction methodologies was assessed on the composition of both neutral (arabinose, rhamnose, galactose) and acidic (galacturonic acid) pectic polysaccharides obtained from four agro-industrial residues, namely, berry pomace (BP), onion hulls (OH), pressed pumpkin (PP), and sugar beet pulp (SBP). For acidic pectic polysaccharides, the extraction efficiency was obtained as BP (nitric acid-assisted extraction, 2 h, 62.9%), PP (enzymatic-assisted extraction, 12 h, 75.0%), SBP (enzymatic-assisted extraction, 48 h, 89.8%; and nitric acid-assisted extraction, 4 h, 76.5%), and OH (sodium hexametaphosphate-assisted extraction, 0.5 h, 100%; and ammonium oxalate-assisted extraction, 0.5 h, 100%). For neutral pectic polysaccharides, the following results were achieved: BP (enzymatic-assisted extraction, 24 h, 85.9%), PP (nitric acid-assisted extraction, 6 h, 82.2%), and SBP (enzymatic assisted extraction, 48 h, 97.5%; and nitric acid-assisted extraction, 4 h, 83.2%). On the basis of the high recovery of pectic sugars, SBP and OH are interesting candidates for the further purification of pectin and production of pectin-derived products.

Imide Oligomers Containing Pendent and Terminal Phenylethynyl Groups-2

NASA Technical Reports Server (NTRS)

Connell, J. W.; Smith, J. G., Jr.; Hergenrother, P. M.

1998-01-01

As part of a program to develop high-performance/high-temperature structural resins for aeronautical applications, imide oligomers containing pendent and terminal phenylethynyl groups were prepared, characterized and the cured resins evaluated as composite matrices. The oligomers were prepared at a calculated number-average molecular weight of 5000 g/mol and contained 15-20 mol% pendent phenylethynyl groups. In previous work, an oligomer containing pendent and terminal phenylethynyl groups exhibited a high glass transition temperature (approximately 313 C), and laminates therefrom exhibited high compressive properties, but processability, fracture toughness, microcrack resistance and damage tolerance were less than desired. In an attempt to improve these deficiencies, modifications in the oligomeric backbone involving the incorporation of 1,3-bis(3-aminophenoxy)benzene were investigated as a means of improving processability and toughness without detracting from the high glass transition temperature and high compressive properties. The amide acid oligomeric solutions were prepared in N-methyl-2-pyrrolidinone and were subsequently processed into imide powder, thin films, adhesive tape and carbon fiber prepreg. Neat resin plaques were fabricated from imide powder by compression moulding. The maximum processing pressure was 1.4 MPa and the cure temperature ranged from 350 to 371 C for 1 h for the mouldings, adhesives, films and composites. The properties of the 1,3-bis(3-aniinophenoxy)benzene modified cured imide oligomers containing pendent and terminal phenylethynyl groups are compared with those of previously prepared oligomers containing pendent and terminal phenylethynyl groups of similar composition and molecular weight.

GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure.

PubMed

Baek, Minkyung; Park, Taeyong; Heo, Lim; Park, Chiwook; Seok, Chaok

2017-07-03

Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions and their regulation. Currently available web servers predict protein homo-oligomer structures either by template-based modeling using homo-oligomer templates selected from the protein structure database or by ab initio docking of monomer structures resolved by experiment or predicted by computation. The GalaxyHomomer server, freely accessible at http://galaxy.seoklab.org/homomer, carries out template-based modeling, ab initio docking or both depending on the availability of proper oligomer templates. It also incorporates recently developed model refinement methods that can consistently improve model quality. Moreover, the server provides additional options that can be chosen by the user depending on the availability of information on the monomer structure, oligomeric state and locations of unreliable/flexible loops or termini. The performance of the server was better than or comparable to that of other available methods when tested on benchmark sets and in a recent CASP performed in a blind fashion. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Crystal Structure of an Activated Variant of Small Heat Shock Protein Hsp16.5

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mchaourab, Hassane S.; Lin, Yi-Lun; Spiller, Benjamin W.

How does the sequence of a single small heat shock protein (sHSP) assemble into oligomers of different sizes? To gain insight into the underlying structural mechanism, we determined the crystal structure of an engineered variant of Methanocaldococcus jannaschii Hsp16.5 wherein a 14 amino acid peptide from human heat shock protein 27 (Hsp27) was inserted at the junction of the N-terminal region and the {alpha}-crystallin domain. In response to this insertion, the oligomer shell expands from 24 to 48 subunits while maintaining octahedral symmetry. Oligomer rearrangement does not alter the fold of the conserved {alpha}-crystallin domain nor does it disturb themore » interface holding the dimeric building block together. Rather, the flexible C-terminal tail of Hsp16.5 changes its orientation relative to the {alpha}-crystallin domain which enables alternative packing of dimers. This change in orientation preserves a peptide-in-groove interaction of the C-terminal tail with an adjacent {beta}-sandwich, thereby holding the assembly together. The interior of the expanded oligomer, where substrates presumably bind, retains its predominantly nonpolar character relative to the outside surface. New large windows in the outer shell provide increased access to these substrate-binding regions, thus accounting for the higher affinity of this variant to substrates. Oligomer polydispersity regulates sHSPs chaperone activity in vitro and has been implicated in their physiological roles. The structural mechanism of Hsp16.5 oligomer flexibility revealed here, which is likely to be highly conserved across the sHSP superfamily, explains the relationship between oligomer expansion observed in disease-linked mutants and changes in chaperone activity.« less

Crystal structure of an activated variant of small heat shock protein Hsp16.5.

PubMed

McHaourab, Hassane S; Lin, Yi-Lun; Spiller, Benjamin W

2012-06-26

How does the sequence of a single small heat shock protein (sHSP) assemble into oligomers of different sizes? To gain insight into the underlying structural mechanism, we determined the crystal structure of an engineered variant of Methanocaldococcus jannaschii Hsp16.5 wherein a 14 amino acid peptide from human heat shock protein 27 (Hsp27) was inserted at the junction of the N-terminal region and the α-crystallin domain. In response to this insertion, the oligomer shell expands from 24 to 48 subunits while maintaining octahedral symmetry. Oligomer rearrangement does not alter the fold of the conserved α-crystallin domain nor does it disturb the interface holding the dimeric building block together. Rather, the flexible C-terminal tail of Hsp16.5 changes its orientation relative to the α-crystallin domain which enables alternative packing of dimers. This change in orientation preserves a peptide-in-groove interaction of the C-terminal tail with an adjacent β-sandwich, thereby holding the assembly together. The interior of the expanded oligomer, where substrates presumably bind, retains its predominantly nonpolar character relative to the outside surface. New large windows in the outer shell provide increased access to these substrate-binding regions, thus accounting for the higher affinity of this variant to substrates. Oligomer polydispersity regulates sHSPs chaperone activity in vitro and has been implicated in their physiological roles. The structural mechanism of Hsp16.5 oligomer flexibility revealed here, which is likely to be highly conserved across the sHSP superfamily, explains the relationship between oligomer expansion observed in disease-linked mutants and changes in chaperone activity.

Distinct high molecular weight organic compound (HMW-OC) types in aerosol particles collected at a coastal urban site

NASA Astrophysics Data System (ADS)

Dall'Osto, M.; Healy, R. M.; Wenger, J. C.; O'Dowd, C.; Ovadnevaite, J.; Ceburnis, D.; Harrison, Roy M.; Beddows, D. C. S.

2017-12-01

Organic oligomers were discovered in laboratory-generated atmospheric aerosol over a decade ago. However, evidence for the presence of oligomers in ambient aerosols is scarce and mechanisms for their formation have yet to be fully elucidated. In this work, three unique aerosol particle types internally mixed with High molecular weight organic compounds (HMW-OC) species - likely oligomers - were detected in ambient air using single particle Aerosol Time-Of-Flight Mass Spectrometry (ATOFMS) in Cork (Ireland) during winter 2009. These particle types can be described as follows: (1) HMW-OCs rich in organic nitrogen - possibly containing nitrocatechols and nitroguaiacols - originating from primary emissions of biomass burning particles during evening times; (2) HMW-OCs internally mixed with nitric acid, occurring in stagnant conditions during night time; and (3) HMW-OCs internally mixed with sea salt, likely formed via photochemical reactions during day time. The study exemplifies the power of methodologies capable of monitoring the simultaneous formation of organic and inorganic particle-phase reaction products. Primary emissions and atmospheric aging of different types of HMW-OC contributes to aerosol with a range of acidity, hygroscopic and optical properties, which can have different impacts on climate and health.

Constitutive and inducible pectinolytic enzymes from Aspergillus flavipes FP-500 and their modulation by pH and carbon source

PubMed Central

Martínez-Trujillo, Aurora; Aranda, Juan S.; Gómez-Sánchez, Carlos; Trejo-Aguilar, Blanca; Aguilar-Osorio, Guillermo

2009-01-01

Growth and enzymes production by Aspergillus flavipes FP-500 were evaluated on pectin, polygalacturonic acid, galacturonic acid, arabinose, rhamnose, xylose, glycerol and glucose at different initial pH values. We found that the strain produced exopectinases, endopectinases and pectin lyases. Exopectinases and pectin lyase were found to be produced at basal levels as constitutive enzymes and their production was modulated by the available carbon source and pH of culture medium and stimulated by the presence of inducer in the culture medium. Endo-pectinase was basically inducible and was only produced when pectin was used as carbon source. Our results suggest that pectinases in A. flavipes FP-500 are produced in a concerted way. The first enzyme to be produced was exopectinase followed by Pectin Lyase and Endo-pectinase. PMID:24031315

Amplifying (Im)perfection: The Impact of Crystallinity in Discrete and Disperse Block Co-oligomers

PubMed Central

2017-01-01

Crystallinity is seldomly utilized as part of the microphase segregation process in ultralow-molecular-weight block copolymers. Here, we show the preparation of two types of discrete, semicrystalline block co-oligomers, comprising an amorphous oligodimethylsiloxane block and a crystalline oligo-l-lactic acid or oligomethylene block. The self-assembly of these discrete materials results in lamellar structures with unforeseen uniformity in the domain spacing. A systematic introduction of dispersity reveals the extreme sensitivity of the microphase segregation process toward chain length dispersity in the crystalline block. PMID:28994585

Amplifying (Im)perfection: The Impact of Crystallinity in Discrete and Disperse Block Co-oligomers.

PubMed

van Genabeek, Bas; Lamers, Brigitte A G; de Waal, Bas F M; van Son, Martin H C; Palmans, Anja R A; Meijer, E W

2017-10-25

Crystallinity is seldomly utilized as part of the microphase segregation process in ultralow-molecular-weight block copolymers. Here, we show the preparation of two types of discrete, semicrystalline block co-oligomers, comprising an amorphous oligodimethylsiloxane block and a crystalline oligo-l-lactic acid or oligomethylene block. The self-assembly of these discrete materials results in lamellar structures with unforeseen uniformity in the domain spacing. A systematic introduction of dispersity reveals the extreme sensitivity of the microphase segregation process toward chain length dispersity in the crystalline block.

A quantitative evaluation of the iron-sulfur world and its relevance to life's origins.

PubMed

Ross, David S

2008-04-01

The significance of Wächtershäuser's iron-sulfur world to the origin of life and the limits to its notional autocatalytic cycles are examined in kinetic simulations of the chain polymerization sequence: primitive materials-->amino acids-->oligomers. The simulations were run for the formation of all oligomers up to the 20-mer over a 1 Gy interval from the end of the period of heavy bombardment, during which period life emerged. Upper-limit rate constant estimates developed from the studies of Huber and Wächtershäuser were employed. The simulations showed that oligomer production consistent with life's start within that interval emerges only with an autocatalyst exhibiting a catalytic proficiency comparable to that of contemporary enzymes. The simulations, moreover, ignored likely thermodynamic and statistical burdens which, if included, would have led to the need for catalytic capacities well in excess of those in present-day enzymes. Prebiotic oligomers with such levels of activity are clearly not likely, and it is apparent that the iron-sulfur scheme could not have played a role in life's beginnings.

A quantitative evaluation of the iron-sulfur world and its relevance to life's origins

USGS Publications Warehouse

Ross, D.S.

2008-01-01

The significance of Wa??chtersha??user's iron-sulfur world to the origin of life and the limits to its notional autocatalytic cycles are examined in kinetic simulations of the chain polymerization sequence primitive materials ??? amino acids ??? oligomers The simulations were run for the formation of all oligomers up to the 20-mer over a 1 Gy interval from the end of the period of heavy bombardment, during which period life emerged. Upper-limit rate constant estimates developed from the studies of Huber and Wa??chtersha?? user were employed. The simulations showed that oligomer production consistent with life's start within that interval emerges only with an autocatalyst exhibiting a catalytic proficiency comparable to that of contemporary enzymes. The simulations, moreover, ignored likely thermodynamic and statistical burdens which, if included, would have led to the need for catalytic capacities well in excess of those in present-day enzymes. Prebiotic oligomers with such levels of activity are clearly not likely, and it is apparent that the iron-sulfur scheme could not have played a role in life's beginnings. ?? 2008 Mary Ann Liebert, Inc.

Oligomers, organosulfates, and nitroxy organosulfates identified in rainwater

NASA Astrophysics Data System (ADS)

Altieri, K. E.; Turpin, B. J.; Seitzinger, S. P.

2008-12-01

Wet deposition is an important removal mechanism for atmospheric organic matter, and a potentially important input for receiving ecosystems, yet less than 50 percent of rainwater organic matter is considered chemically characterized. Precipitation samples collected in New Jersey, USA, were analyzed by negative ion ultra-high resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). We document the presence of 552 unique compounds in the rainwater over a mass range of 50-500 Da, in four compound classes (i.e., CHO, CHOS, CHON, and CHONS). The presence of oligomers, organosulfates, nitroxy organosulfates, organic acids, and linear alkylbenzene sulfonates is reported. Some compounds detected have distinct primary sources; however, the composition of the bulk of this material suggests it is formed in the atmosphere and composed of known contributors to secondary organic aerosol. For example, eight oligomer series known to form through aqueous photooxidation of methylglyoxal and organosulfate compounds known to form from 4 precursors in smog chamber experiments were identified in the rainwater samples. The oligomers, organosulfates, and nitroxy organosulfates detected in the rainwater could all contribute to the HULIS fraction of atmospheric organic matter.

Multidimensional Self-Assembled Structures of Alkylated Cellulose Oligomers Synthesized via in Vitro Enzymatic Reactions.

PubMed

Yataka, Yusuke; Sawada, Toshiki; Serizawa, Takeshi

2016-10-04

The self-assembly of biomolecules into highly ordered nano-to-macroscale structures is essential in the construction of biological tissues and organs. A variety of biomolecular assemblies composed of nucleic acids, peptides, and lipids have been used as molecular building units for self-assembled materials. However, crystalline polysaccharides have rarely been utilized in self-assembled materials. In this study, we describe multidimensional self-assembled structures of alkylated cellulose oligomers synthesized via in vitro enzymatic reactions. We found that the alkyl chain length drastically affected the assembled morphologies and allomorphs of cellulose moieties. The modulation of the intermolecular interactions of cellulose oligomers by alkyl substituents was highly effective at controlling their assembly into multidimensional structures. This study proposes a new potential of crystalline oligosaccharides for structural components of molecular assemblies with controlled morphologies and crystal structures.

Catalysis of the Oligomerization of O-Phospho-Serine, Aspartic Acid, or Glutamic Acid by Cationic Micelles

NASA Technical Reports Server (NTRS)

Bohler, Christof; Hill, Aubrey R., Jr.; Orgel, Leslie E.

1996-01-01

Treatment of relatively concentrated aqueous solutions of 0-phospho-serine (50 mM), aspartic acid (100 mM) or glutamic acid (100 mM) with carbonyldiimidazole leads to the formation of an activated intermediate that oligomerizes efficiently. When the concentration of amino acid is reduced tenfold, few long oligomers can be detected. Positively-charged cetyltrimethyl ammonium bromide micelles concentrate the negatively-charged activated intermediates of the amino acids at their surfaces and catalyze efficient oligomerization even from dilute solutions.

Catalysis of the Oligomerization of O-Phospho-Serine, Aspartic Acid, or Glutamic Acid by Cationic Micelles

NASA Technical Reports Server (NTRS)

Boehler, Christof; Hill, Aubrey R., Jr.; Orgel, Leslie E.

1996-01-01

Treatment of relatively concentrated aqueous solutions of O-phospho-serine (50 mM), aspartic acid (100 mM) or glutamic acid (100 mM) with carbonyldiimidazole leads to the formation of an activated intermediate that oligomerizes efficiently. When the concentration of amino acid is reduced tenfold, few long oligomers can be detected. Positively-charged cetyltrimethyl ammonium bromide micelles concentrate the negatively-charged activated intermediates of the amino acids at their surfaces and catalyze efficient oligomerization even from dilute solutions.

Waterborne carboxyl-terminated hyperbranched oligomer polyester ligand: Synthesis, characterization and chelation with chromium(III)

NASA Astrophysics Data System (ADS)

Yao, Qi; Li, Chenying; Huang, Henghui; Chen, Hualin; Liu, Bailing

2017-09-01

A series of carboxyl-terminated hyperbranched oligomer polyester (HBP) with different degree of branching (DB) and number average molar mass (Mbarn) have been prepared. The molecular structure, degree of branching, molecular mass and its distribution of HBP were investigated by FTIR, 1H NMR, and GPC, respectively. And the coordination number, stability constant and degree of dissociation (α) between HBP and chromium(Ⅲ) were measured via continuous variation method (Job's plot). Experimental results show that the coordination capability between HBP and chromium(Ⅲ) affected by both DB and molecular mass, and the latter plays a decisive role. Moreover HBP outperforms low molecular weight of organic acids (citric acid, acetic acid) and linear polyacrylic acid with similar molecular mass. The coordination number and stability constants of HBP-3 (Mbarn = 1713 Da, Mbarw /Mbarn (PDI) = 1.11 and DB = 0.72) can reach 4 and 6.55e+008, which demonstrated it can be selected as a good ligand to coordination with chromium(Ⅲ). Therefore HBP can be used as chrome auxiliary in chrome tanning to improve the absorption of chromium.

Beta-Strand Interfaces of Non-Dimeric Protein Oligomers Are Characterized by Scattered Charged Residue Patterns

PubMed Central

Feverati, Giovanni; Achoch, Mounia; Zrimi, Jihad; Vuillon, Laurent; Lesieur, Claire

2012-01-01

Protein oligomers are formed either permanently, transiently or even by default. The protein chains are associated through intermolecular interactions constituting the protein interface. The protein interfaces of 40 soluble protein oligomers of stœchiometries above two are investigated using a quantitative and qualitative methodology, which analyzes the x-ray structures of the protein oligomers and considers their interfaces as interaction networks. The protein oligomers of the dataset share the same geometry of interface, made by the association of two individual β-strands (β-interfaces), but are otherwise unrelated. The results show that the β-interfaces are made of two interdigitated interaction networks. One of them involves interactions between main chain atoms (backbone network) while the other involves interactions between side chain and backbone atoms or between only side chain atoms (side chain network). Each one has its own characteristics which can be associated to a distinct role. The secondary structure of the β-interfaces is implemented through the backbone networks which are enriched with the hydrophobic amino acids favored in intramolecular β-sheets (MCWIV). The intermolecular specificity is provided by the side chain networks via positioning different types of charged residues at the extremities (arginine) and in the middle (glutamic acid and histidine) of the interface. Such charge distribution helps discriminating between sequences of intermolecular β-strands, of intramolecular β-strands and of β-strands forming β-amyloid fibers. This might open new venues for drug designs and predictive tool developments. Moreover, the β-strands of the cholera toxin B subunit interface, when produced individually as synthetic peptides, are capable of inhibiting the assembly of the toxin into pentamers. Thus, their sequences contain the features necessary for a β-interface formation. Such β-strands could be considered as ‘assemblons’, independent associating units, by homology to the foldons (independent folding unit). Such property would be extremely valuable in term of assembly inhibitory drug development. PMID:22496732

Shaking Alone Induces De Novo Conversion of Recombinant Prion Proteins to β-Sheet Rich Oligomers and Fibrils

PubMed Central

Ladner-Keay, Carol L.; Griffith, Bethany J.; Wishart, David S.

2014-01-01

The formation of β-sheet rich prion oligomers and fibrils from native prion protein (PrP) is thought to be a key step in the development of prion diseases. Many methods are available to convert recombinant prion protein into β-sheet rich fibrils using various chemical denaturants (urea, SDS, GdnHCl), high temperature, phospholipids, or mildly acidic conditions (pH 4). Many of these methods also require shaking or another form of agitation to complete the conversion process. We have identified that shaking alone causes the conversion of recombinant PrP to β-sheet rich oligomers and fibrils at near physiological pH (pH 5.5 to pH 6.2) and temperature. This conversion does not require any denaturant, detergent, or any other chemical cofactor. Interestingly, this conversion does not occur when the water-air interface is eliminated in the shaken sample. We have analyzed shaking-induced conversion using circular dichroism, resolution enhanced native acidic gel electrophoresis (RENAGE), electron microscopy, Fourier transform infrared spectroscopy, thioflavin T fluorescence and proteinase K resistance. Our results show that shaking causes the formation of β-sheet rich oligomers with a population distribution ranging from octamers to dodecamers and that further shaking causes a transition to β-sheet fibrils. In addition, we show that shaking-induced conversion occurs for a wide range of full-length and truncated constructs of mouse, hamster and cervid prion proteins. We propose that this method of conversion provides a robust, reproducible and easily accessible model for scrapie-like amyloid formation, allowing the generation of milligram quantities of physiologically stable β-sheet rich oligomers and fibrils. These results may also have interesting implications regarding our understanding of prion conversion and propagation both within the brain and via techniques such as protein misfolding cyclic amplification (PMCA) and quaking induced conversion (QuIC). PMID:24892647

Nucleoprotein from the unique human infecting Orthobunyavirus of Simbu serogroup (Oropouche virus) forms higher order oligomers in complex with nucleic acids in vitro.

PubMed

Murillo, Juliana Londoño; Cabral, Aline Diniz; Uehara, Mabel; da Silva, Viviam Moura; Dos Santos, Juliete Vitorino; Muniz, João Renato Carvalho; Estrozi, Leandro Farias; Fenel, Daphna; Garcia, Wanius; Sperança, Márcia Aparecida

2018-06-01

Oropouche virus (OROV) is the unique known human pathogen belonging to serogroup Simbu of Orthobunyavirus genus and Bunyaviridae family. OROV is transmitted by wild mosquitoes species to sloths, rodents, monkeys and birds in sylvatic environment, and by midges (Culicoides paraensis and Culex quinquefasciatus) to man causing explosive outbreaks in urban locations. OROV infection causes dengue fever-like symptoms and in few cases, can cause clinical symptoms of aseptic meningitis. OROV contains a tripartite negative RNA genome encapsidated by the viral nucleocapsid protein (NP), which is essential for viral genome encapsidation, transcription and replication. Here, we reported the first study on the structural properties of a recombinant NP from human pathogen Oropouche virus (OROV-rNP). OROV-rNP was successfully expressed in E. coli in soluble form and purified using affinity and size-exclusion chromatographies. Purified OROV-rNP was analyzed using a series of biophysical tools and molecular modeling. The results showed that OROV-rNP formed stable oligomers in solution coupled with endogenous E. coli nucleic acids (RNA) of different sizes. Finally, electron microscopy revealed a total of eleven OROV-rNP oligomer classes with tetramers (42%) and pentamers (43%) the two main populations and minor amounts of other bigger oligomeric states, such as hexamers, heptamers or octamers. The different RNA sizes and nucleotide composition may explain the diversity of oligomer classes observed. Besides, structural differences among bunyaviruses NP can be used to help in the development of tools for specific diagnosis and epidemiological studies of this group of viruses.

Physicochemical properties and antioxidant activities of polysaccharides from Gynura procumbens leaves by fractional precipitation.

PubMed

Li, Jing-En; Wang, Wen-Jun; Zheng, Guo-Dong; Li, Lin-Yan

2017-02-01

Four new polysaccharides (GPP-20, GPP-40, GPP-60 and GPP-80) were fractionated from Gynura procumbens leaves by 20%, 40%, 60% and 80% (v/v) ethanol, successively. Their physicochemical properties including the contents of neutral sugar, uronic acid and protein, as well as the monosaccharide composition were determined. In addition, the antioxidant activities of them were investigated via the reducing power assay and scavenging capacities of 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radicals and hydroxyl free radicals, respectively. The results indicated that apart from neutral sugar, they all contained uronic acids and proteins in their structures, which were further proved by the UV-vis and FT-IR spectra. Monosaccharide composition analysis implied that they all belonged to heteropolysaccharides consisted of arabinose, galactose, glucose, xylose and galacturonic acid with different types and ratios. What's more, GPP-20, GPP-40 and GPP-80 always exhibited better antioxidant activities than GPP-60 among these three antioxidant assays in vitro. Copyright © 2016 Elsevier B.V. All rights reserved.

Structural diversity of pectins isolated from the Styrian oil-pumpkin (Cucurbita pepo var. styriaca) fruit.

PubMed

Košťálová, Zuzana; Hromádková, Zdenka; Ebringerová, Anna

2013-03-01

To evaluate the seeded fruit biomass of the Styrian oil-pumpkin in view of its pectin component, a series of acidic polysaccharides were isolated by a six-step sequential extraction using hot water, EDTA, dilute HCl (twice) and dilute and stronger NaOH solutions. Chemical, physicochemical and spectroscopy analyses revealed that the first four fractions comprised partially methyl-esterified and acetylated pectins with varying proportions of rhamnogalacturonan regions ramified with galactose- and arabinose-containing side chains and showed considerable polymolecularity. The alkali-extracted polysaccharides contained lower amounts of pectins with homogalacturonan and arabinose-rich rhamnogalacturonan regions next to hemicelluloses prevailing in the last polysaccharide. Using (1)H-(13)C HSQC and HMBC spectroscopy, the resonances of free and methylesterified galacturonic acid residues in the purified acid-extracted pectin were unambiguously established and various diads formed by both residues identified. The results might serve as a basis for searching technological conditions to produce pectin from the oil-pumpkin fruit biomass. Copyright © 2012 Elsevier Ltd. All rights reserved.

In vitro fermentation of mulberry fruit polysaccharides by human fecal inocula and impact on microbiota.

PubMed

Chen, Chun; Huang, Qiang; Fu, Xiong; Liu, Rui Hai

2016-11-09

This study investigated the in vitro fermentation of polysaccharides from Morus alba L., the contribution of its carbohydrates to the fermentation, and the effect on the composition of gut microbiota. Over 48 h of fermentation, the pH value in the fecal culture decreased from 7.12 to 6.14, and the total short chain fatty acids (SCFA) and acetic, propionic, and butyric acids all significantly increased. After 48 h of fermentation, 45.36 ± 1.36% of the total carbohydrates in the polysaccharide, including 35.72 ± 1.51% of arabinose, 23.1 ± 1.19% of galactose, 41.43 ± 1.52% of glucose, 26.36 ± 1.93% of rhamnose and 65.57 ± 1.07% of galacturic acid, were consumed. The increase in acetic and butyric acids was primarily due to the fermentation of galactose and galacturonic acid in the polysaccharide, while the increase in propionic acid resulted mainly from the fermentation of arabinose and glucose. In addition, the polysaccharide could modulate the gut microbiota composition by increasing the Bacteroidetes population and decreasing the Firmicutes population. The results may facilitate the development of food products known as prebiotics, aimed at improving gastrointestinal health.

Redox proteomic profiling of neuroketal-adducted proteins in human brain: Regional vulnerability at middle age increases in the elderly.

PubMed

Domínguez, Mayelín; de Oliveira, Eliandre; Odena, María Antonia; Portero, Manuel; Pamplona, Reinald; Ferrer, Isidro

2016-06-01

Protein lipoxidation was assessed in the parietal cortex (PC), frontal cortex (FC), and cingulate gyrus (CG) in middle-aged and old-aged individuals with no clinical manifestations of cognitive impairment, in order to increase understanding of regional brain vulnerability to oxidative damage during aging. Twenty-five lipoxidized proteins were identified in all the three regions although with regional specificities, by using redox proteomics to detect target proteins of neuroketals (NKT) adduction. The number of cases with NKT-adducted proteins was higher in old-aged individuals but most oxidized proteins were already present in middle-aged individuals. Differences in vulnerability to oxidation were dependent on the sub-cellular localization, secondary structure, and external exposition of certain amino acids. Lipoxidized proteins included those involved in energy metabolism, cytoskeleton, proteostasis, neurotransmission and O2/CO2, and heme metabolism. Total NKT and soluble oligomer levels were estimated employing slot-blot, and these were compared between age groups. Oligomers increased with age in PC and FC; NKT significantly increased with age in FC, whereas total NKT and oligomer levels were not modified in CG, thus highlighting differences in brain regional vulnerability with age. Oligomers significantly correlated with NKT levels in the three cortical regions, suggesting that protein NKT adduction parallels soluble oligomer formation. Copyright © 2016 Elsevier Inc. All rights reserved.

Structural assemblies of the di- and oligomeric G-protein coupled receptor TGR5 in live cells: an MFIS-FRET and integrative modelling study

NASA Astrophysics Data System (ADS)

Greife, Annemarie; Felekyan, Suren; Ma, Qijun; Gertzen, Christoph G. W.; Spomer, Lina; Dimura, Mykola; Peulen, Thomas O.; Wöhler, Christina; Häussinger, Dieter; Gohlke, Holger; Keitel, Verena; Seidel, Claus A. M.

2016-11-01

TGR5 is the first identified bile acid-sensing G-protein coupled receptor, which has emerged as a potential therapeutic target for metabolic disorders. So far, structural and multimerization properties are largely unknown for TGR5. We used a combined strategy applying cellular biology, Multiparameter Image Fluorescence Spectroscopy (MFIS) for quantitative FRET analysis, and integrative modelling to obtain structural information about dimerization and higher-order oligomerization assemblies of TGR5 wildtype (wt) and Y111 variants fused to fluorescent proteins. Residue 111 is located in transmembrane helix 3 within the highly conserved ERY motif. Co-immunoprecipitation and MFIS-FRET measurements with gradually increasing acceptor to donor concentrations showed that TGR5 wt forms higher-order oligomers, a process disrupted in TGR5 Y111A variants. From the concentration dependence of the MFIS-FRET data we conclude that higher-order oligomers - likely with a tetramer organization - are formed from dimers, the smallest unit suggested for TGR5 Y111A variants. Higher-order oligomers likely have a linear arrangement with interaction sites involving transmembrane helix 1 and helix 8 as well as transmembrane helix 5. The latter interaction is suggested to be disrupted by the Y111A mutation. The proposed model of TGR5 oligomer assembly broadens our view of possible oligomer patterns and affinities of class A GPCRs.

Using optical profilometry to characterize cell membrane roughness influenced by amyloid-beta 42 aggregates and electric fields

NASA Astrophysics Data System (ADS)

Pan, Huei-Jyuan; Wang, Ruei-Lin; Xiao, Jian-Long; Chang, Yu-Jen; Cheng, Ji-Yen; Chen, Yun-Ru; Lee, Chau-Hwang

2014-01-01

The membrane roughness of Neuro-2a neroblastoma cells is measured by using noninterferometric wide-field optical profilometry. The cells are treated with the fibril and oligomer conformers of amyloid-beta (Aβ) 42, which is a peptide of 42 amino acids related to the development of Alzheimer's disease. We find that both the Aβ42 fibrils and Aβ42 oligomers reduced the cell membrane roughness, but the effect of Aβ42 oligomers was faster and stronger than that of the fibrils. We also apply direct-current electric field (dcEF) stimulations on the cells. A dcEF of 300 mV/mm can increase the membrane roughness under the treatment of Aβ42. These results suggest that Aβ42 can decrease the membrane compliance of live neuroblastoma cells, and dcEFs may counteract this effect.

Synthesis of long Prebiotic Oligomers on Mineral Surfaces

NASA Technical Reports Server (NTRS)

Ferris, James P.; Hill, Aubrey R., Jr.; Liu, Rihe; Orgel, Leslie E.

1996-01-01

Most theories of the origin of biological organization assume that polymers with lengths in the range of 30-60 monomers are needed to make a genetic system viable. But it has not proved possible to synthesize plausibly prebiotic polymers this long by condensation in aqueous solution, because hydrolysis competes with polymerization. The potential of mineral surfaces to facilitate prebiotic polymerization was pointed out long ago. Here we describe a system that models prebiotic polymerization by the oligomerization of activated monomers -both nucleotides and amino acids. We find that whereas the reactions in solution produce only short oligomers (the longest typically being a 10-mer), the presence of mineral surfaces (montmorillonite for nucleotides, illite and hydroxylapatite for amino adds) induces the formation of oligomers up to 55 monomers long. These are formed by successive "feedings" with the monomers; polymerization takes place on the mineral surfaces in a manner akin to solid-phase synthesis of biopolymers.

Examination of an aloe vera galacturonate polysaccharide capable of in situ gelation for the controlled release of protein therapeutics

NASA Astrophysics Data System (ADS)

McConaughy, Shawn David

A therapeutic delivery platform has been investigated with the ultimate goal of designing a sustained protein release matrix utilizing an in-situ gelling, acidic polysaccharide derived from the Aloe vera plant. The Aloe vera polysaccharide (AvP) has been examined in order to determine how chemical composition, structure, molecular weight and solution behavior affect gelation and protein/peptide delivery. Correlations are drawn between structural characteristics and solution behavior in order to determine the impact of polymer conformation and solvation on gel formation under conditions designed to simulate nasal applications. Steady state and dynamic rheology, classic and dynamic light scattering, zeta potential, pulse field gradient nuclear magnetic resonance and fluorescence spectroscopy have been employed to gain insight into the effects of galacturonic acid content, degree of methylation, entanglement and ionic strength on both solution behavior and the hydrogel state which ultimately governs protein/peptide release. This dissertation is divided into two sections. In the first section, a series of Aloe vera polysaccharides (AvP), from the pectin family have been structurally characterized indicating high galacturonic acid (GalA) content, low degree of methylester substitution (DM), low numbers of rhamnose residues and high molecular weight with respect to pectins extracted from traditional sources. The behavior of AvP was examined utilizing dilute solution, low-shear rheological techniques for specific molecular weight samples at selected conditions of ionic strength. From these dilute aqueous solution studies, the Mark-Houwink-Sakurada (MHS) constants (K and alpha), persistence length (Lp) and inherent chain stiffness (B parameter) were determined, indicating an expanded random coil in aqueous salt solutions. The critical concentration for transition from dilute to concentrated solution, C e, was determined by measuring both the zero shear viscosity and fluorescence emission of the probe molecule 1,8-anilino-1-naphthalene sulphonic acid (1,8-ANS) as a function of polymer concentration. Correlations are drawn between viscosity experiments and measurement of zeta potential. Increased degrees of intermolecular interactions are responsible for a shift of Ce to lower polymer concentrations with increasing ionic strength. Additionally, dynamic rheology data are presented highlighting the ability of AvP to form gels at low polymer and calcium ion concentrations, exemplifying the technological potential of this polysaccharide for in-situ drug delivery. In the second section, properties of Aloe vera galacturonate hydrogels formed via Ca2+ crosslinking have been studied in regard to key parameters influencing gel formation including molecular weight, ionic strength and molar ratio of Ca2+ to COO- functionality. Dynamic oscillatory rheology and pulsed field gradient NMR (PFG-NMR) studies have been conducted on hydrogels formed at specified Ca2+ concentrations in the presence and absence of Na+ and K+ ions, in order to assess the feasibility of in situ gelation for controlled delivery of therapeutics. Aqueous Ca2+ concentrations similar to those present in nasal and subcutaneous fluids induce the formation of elastic Aloe vera polysaccharide (AvP) hydrogel networks. By altering the ratio of Ca2+ to COO- functionality, networks may be tailored to provide elastic modulus (G') values between 20 and 20,000 Pa. The Aloe vera polysaccharide exhibits time dependent phase separation in the presence of monovalent electrolytes. Thus the relative rates of calcium induced gelation and phase separation become major considerations when designing a system for in situ delivery applications where both monovalent (Na+, K+) and divalent (Ca2+) ions are present. PFG-NMR and fluorescence microscopy confirm that distinctly different morphologies are present in gels formed in the presence and absence 0.15 M NaCl. Curve fitting of theoretical models to experimental release profiles of fluorescein labeled dextrans indicate diffusion rates are related to hydrogel morphology. These studies suggest that for efficient in situ release of therapeutic agents, polymer concentrations should be maintained above the critical entanglement concentration (Ce, 0.60 wt%) when [Ca2+]/[COO -] ratios are less than 1. Additionally, the monovalent electrolyte concentration in AvP solutions should not exceed 0.10 M prior to Ca 2+ crosslinking.

Structural analysis of an innate immunostimulant from broccoli, Brassica oleracea var. italica.

PubMed

Urai, Makoto; Kataoka, Keiko; Nishida, Satoshi; Sekimizu, Kazuhisa

2017-11-22

Vegetables are eaten as part of a healthy diet throughout the world, and some are also applied topically as a traditional medicine. We evaluated the innate immunostimulating activities of hot water extracts of various vegetables using the silkworm muscle contraction assay system, and found that broccoli, Brassica oleracea var. italica, contains a strong innate immunostimulant. We purified the innate immunostimulant from broccoli, and characterized the chemical structure by chemical analyses and NMR spectroscopy. The innate immunostimulant comprised galacturonic acid, galactose, glucose, arabinose, and rhamnose, and had a pectic-like polysaccharide structure. To determine the structural motif involved in the innate immunostimulating activity, we modified the structure by chemical and enzymatic treatment, and found that the activity was attenuated by pectinase digestion. These findings suggest that a pectic-like polysaccharide purified from broccoli has innate immune-stimulating activity, for which the polygalacturonic acid structure is necessary.

Tomato Fruit Cell Wall 1

PubMed Central

Koch, James L.; Nevins, Donald J.

1989-01-01

Cell wall isolation procedures were evaluated to determine their effect on the total pectin content and the degree of methylesterification of tomato (Lycopersicon esculentum L.) fruit cell walls. Water homogenates liberate substantial amounts of buffer soluble uronic acid, 5.2 milligrams uronic acid/100 milligrams wall. Solubilization appears to be a consequence of autohydrolysis mediated by polygalacturonase II, isoenzymes A and B, since the uronic acid release from the wall residue can be suppressed by homogenization in the presence of 50% ethanol followed by heating. The extent of methylesterification in heat-inactivated cell walls, 94 mole%, was significantly greater than with water homogenates, 56 mole%. The results suggest that autohydrolysis, mediated by cell wall-associated enzymes, accounts for the solubilization of tomato fruit pectin in vitro. Endogenous enzymes also account for a decrease in the methylesterification during the cell wall preparation. The heat-inactivated cell wall preparation was superior to the other methods studied since it reduces β-elimination during heating and inactivates constitutive enzymes that may modify pectin structure. This heat-inactivated cell wall preparation was used in subsequent enzymatic analysis of the pectin structure. Purified tomato fruit polygalacturonase and partially purified pectinmethylesterase were used to assess changes in constitutive substrates during tomato fruit ripening. Polygalacturonase treatment of heat-inactivated cell walls from mature green and breaker stages released 14% of the uronic acid. The extent of the release of polyuronides by polygalacturonase was fruit development stage dependent. At the turning stage, 21% of the pectin fraction was released, a value which increased to a maximum of 28% of the uronides at the red ripe stage. Pretreatment of the walls with purified tomato pectinesterase rendered walls from all ripening stages equally susceptible to polygalacturonase. Quantitatively, the release of uronides by polygalacturonase from all pectinesterase treated cell walls was equivalent to polygalacturonase treatment of walls at the ripe stage. Uronide polymers released by polygalacturonase contain galacturonic acid, rhamnose, galactose, arabinose, xylose, and glucose. As a function of development, an increase in the release of galacturonic acid and rhamnose was observed (40 and 6% of these polymers at the mature green stage to 54 and 15% at the red ripe stage, respectively). The amount of galactose and arabinose released by exogenous polygalacturonase decreased during development (41 and 11% from walls of mature green fruit to 11 and 6% at the red ripe stage, respectively). Minor amounts of glucose and xylose released from the wall by exogenous polygalacturonase (4-7%) remained constant throughout fruit development. PMID:16667142

Quantitative reconstruction of the nonvolatile sensometabolome of a red wine.

PubMed

Hufnagel, Jan Carlos; Hofmann, Thomas

2008-10-08

The first comprehensive quantitative determination of 82 putative taste-active metabolites and mineral salts, the ranking of these compounds in their sensory impact based on dose-over-threshold (DoT) factors, followed by the confirmation of their sensory relevance by taste reconstruction and omission experiments enabled the decoding of the nonvolatile sensometabolome of a red wine. For the first time, the bitterness of the red wine could be demonstrated to be induced by subthreshold concentrations of phenolic acid ethyl esters and flavan-3-ols. Whereas the velvety astringent onset was imparted by three flavon-3-ol glucosides and dihydroflavon-3-ol rhamnosides, the puckering astringent offset was caused by a polymeric fraction exhibiting molecular masses above >5 kDa and was found to be amplified by the organic acids. The perceived sourness was imparted by l-tartaric acid, d-galacturonic acid, acetic acid, succinic acid, l-malic acid, and l-lactic acid and was slightly suppressed by the chlorides of potassium, magnesium, and ammonium, respectively. In addition, d-fructose and glycerol as well as subthreshold concentrations of glucose, 1,2-propandiol, and myo-inositol were found to be responsible for the sweetness, whereas the mouthfulness and body of the red wine were induced only by glycerol, 1,2-propandiol, and myo-inositol.

SERS Detection of Amyloid Oligomers on Metallorganic-Decorated Plasmonic Beads.

PubMed

Guerrini, Luca; Arenal, Raul; Mannini, Benedetta; Chiti, Fabrizio; Pini, Roberto; Matteini, Paolo; Alvarez-Puebla, Ramon A

2015-05-13

Protein misfolded proteins are among the most toxic endogenous species of macromolecules. These chemical entities are responsible for neurodegenerative disorders such as Alzheimer's, Parkinson's, Creutzfeldt-Jakob's and different non-neurophatic amyloidosis. Notably, these oligomers show a combination of marked heterogeneity and low abundance in body fluids, which have prevented a reliable detection by immunological methods so far. Herein we exploit the selectivity of proteins to react with metallic ions and the sensitivity of surface-enhanced Raman spectroscopy (SERS) toward small electronic changes in coordination compounds to design and engineer a reliable optical sensor for protein misfolded oligomers. Our strategy relies on the functionalization of Au nanoparticle-decorated polystyrene beads with an effective metallorganic Raman chemoreceptor, composed by Al(3+) ions coordinated to 4-mercaptobenzoic acid (MBA) with high Raman cross-section, that selectively binds aberrant protein oligomers. The mechanical deformations of the MBA phenyl ring upon complexation with the oligomeric species are registered in its SERS spectrum and can be quantitatively correlated with the concentration of the target biomolecule. The SERS platform used here appears promising for future implementation of diagnostic tools of aberrant species associated with protein deposition diseases, including those with a strong social and economic impact, such as Alzheimer's and Parkinson's diseases.

High-order oligomers of intrinsically disordered brain proteins BASP1 and GAP-43 preserve the structural disorder.

PubMed

Forsova, Oksana S; Zakharov, Vladislav V

2016-04-01

Brain acid-soluble protein-1 (BASP1) and growth-associated protein-43 (GAP-43) are presynaptic membrane proteins participating in axon guidance, neuroregeneration and synaptic plasticity. They are presumed to sequester phosphatidylinositol-4,5-bisphosphate (PIP2 ) in lipid rafts. Previously we have shown that the proteins form heterogeneously sized oligomers in the presence of anionic phospholipids or SDS at submicellar concentration. BASP1 and GAP-43 are intrinsically disordered proteins (IDPs). In light of this, we investigated the structure of their oligomers. Using partial cross-linking of the oligomers with glutaraldehyde, the aggregation numbers of BASP1 and GAP-43 were estimated as 10-14 and 6-7 monomer subunits, respectively. The cross-linking pattern indicated that the subunits are circularly arranged. The circular dichroism (CD) spectra of the monomers were characteristic of coil-like IDPs showing unordered structure with a high population of polyproline-II conformation. The oligomerization was accompanied by a minor CD spectral change attributable to formation of a small amount of α-helix. The number of residues in the α-helical conformation was estimated as 13 in BASP1 and 18 in GAP-43. However, the overall structure of the oligomers remained disordered, indicating a high degree of 'fuzziness'. This was confirmed by measuring the hydrodynamic dimensions of the oligomers using polyacrylamide gradient gel electrophoresis and size-exclusion chromatography, and by assaying their sensitivity to proteolytic digestion. There is evidence that the observed α-helical folding occurs within the basic effector domains, which are presumably tethered together via anionic molecules of SDS or PIP2 . We conclude that BASP1 and GAP-43 oligomers preserve a mostly disordered structure, which may be of great importance for their function in PIP2 signaling pathway. © 2016 Federation of European Biochemical Societies.

PaeX, a Second Pectin Acetylesterase of Erwinia chrysanthemi 3937

PubMed Central

Shevchik, Vladimir E.; Hugouvieux-Cotte-Pattat, Nicole

2003-01-01

Erwinia chrysanthemi causes soft-rot diseases of various plants by enzymatic degradation of the pectin in plant cell walls. Pectin is a complex polysaccharide. The main chain is constituted of galacturonate residues, and some of them are modified by methyl and/or acetyl esterification. Esterases are necessary to remove these modifications and, thus, to facilitate the further degradation of the polysaccharidic chain. In addition to PaeY, the first pectin acetylesterase identified in the E. chrysanthemi strain 3937, we showed that this bacterium produces a second pectin acetylesterase encoded by the gene paeX. The paeX open reading frame encodes a 322-residue precursor protein of 34,940 Da, including a 21-amino-acid signal peptide. Analysis of paeX transcription, by using gene fusions, revealed that it is induced by pectic catabolic products and affected by catabolite repression. The expression of paeX is regulated by the repressor KdgR, which controls all the steps of pectin catabolism; by the repressor PecS, which controls most of the pectinase genes; and by catabolite regulatory protein, the global activator of sugar catabolism. The paeX gene is situated in a cluster of genes involved in the catabolism and transport of pectic oligomers. In induced conditions, the two contiguous genes kdgM, encoding an oligogalacturonate-specific porin, and paeX are both transcribed as an operon from a promoter proximal to kdgM, but transcription of paeX can also be uncoupled from that of kdgM in noninduced conditions. PaeX is homologous to the C-terminal domain of the Butyrivibrio fibriosolvens xylanase XynB and to a few bacterial esterases. PaeX contains the typical box (GxSxG) corresponding to the active site of the large family of serine hydrolases. Purified PaeX releases acetate from various synthetic substrates and from sugar beet pectin. The PaeX activity increased after previous depolymerization and demethylation of pectin, indicating that its preferred substrates are nonmethylated oligogalacturonides. PaeX is mostly found in the periplasmic space of E. chrysanthemi. These data suggest that PaeX is mainly involved in the deacetylation of esterified oligogalacturonides that enter the periplasm by the KdgM porin. PMID:12730169

PaeX, a second pectin acetylesterase of Erwinia chrysanthemi 3937.

PubMed

Shevchik, Vladimir E; Hugouvieux-Cotte-Pattat, Nicole

2003-05-01

Erwinia chrysanthemi causes soft-rot diseases of various plants by enzymatic degradation of the pectin in plant cell walls. Pectin is a complex polysaccharide. The main chain is constituted of galacturonate residues, and some of them are modified by methyl and/or acetyl esterification. Esterases are necessary to remove these modifications and, thus, to facilitate the further degradation of the polysaccharidic chain. In addition to PaeY, the first pectin acetylesterase identified in the E. chrysanthemi strain 3937, we showed that this bacterium produces a second pectin acetylesterase encoded by the gene paeX. The paeX open reading frame encodes a 322-residue precursor protein of 34,940 Da, including a 21-amino-acid signal peptide. Analysis of paeX transcription, by using gene fusions, revealed that it is induced by pectic catabolic products and affected by catabolite repression. The expression of paeX is regulated by the repressor KdgR, which controls all the steps of pectin catabolism; by the repressor PecS, which controls most of the pectinase genes; and by catabolite regulatory protein, the global activator of sugar catabolism. The paeX gene is situated in a cluster of genes involved in the catabolism and transport of pectic oligomers. In induced conditions, the two contiguous genes kdgM, encoding an oligogalacturonate-specific porin, and paeX are both transcribed as an operon from a promoter proximal to kdgM, but transcription of paeX can also be uncoupled from that of kdgM in noninduced conditions. PaeX is homologous to the C-terminal domain of the Butyrivibrio fibriosolvens xylanase XynB and to a few bacterial esterases. PaeX contains the typical box (GxSxG) corresponding to the active site of the large family of serine hydrolases. Purified PaeX releases acetate from various synthetic substrates and from sugar beet pectin. The PaeX activity increased after previous depolymerization and demethylation of pectin, indicating that its preferred substrates are nonmethylated oligogalacturonides. PaeX is mostly found in the periplasmic space of E. chrysanthemi. These data suggest that PaeX is mainly involved in the deacetylation of esterified oligogalacturonides that enter the periplasm by the KdgM porin.

Serum amyloid A forms stable oligomers that disrupt vesicles at lysosomal pH and contribute to the pathogenesis of reactive amyloidosis

PubMed Central

Gantz, Donald L.; Haupt, Christian; Gursky, Olga

2017-01-01

Serum amyloid A (SAA) is an acute-phase plasma protein that functions in innate immunity and lipid homeostasis. SAA is a protein precursor of reactive AA amyloidosis, the major complication of chronic inflammation and one of the most common human systemic amyloid diseases worldwide. Most circulating SAA is protected from proteolysis and misfolding by binding to plasma high-density lipoproteins. However, unbound soluble SAA is intrinsically disordered and is either rapidly degraded or forms amyloid in a lysosome-initiated process. Although acidic pH promotes amyloid fibril formation by this and many other proteins, the molecular underpinnings are unclear. We used an array of spectroscopic, biochemical, and structural methods to uncover that at pH 3.5–4.5, murine SAA1 forms stable soluble oligomers that are maximally folded at pH 4.3 with ∼35% α-helix and are unusually resistant to proteolysis. In solution, these oligomers neither readily convert into mature fibrils nor bind lipid surfaces via their amphipathic α-helices in a manner typical of apolipoproteins. Rather, these oligomers undergo an α-helix to β-sheet conversion catalyzed by lipid vesicles and disrupt these vesicles, suggesting a membranolytic potential. Our results provide an explanation for the lysosomal origin of AA amyloidosis. They suggest that high structural stability and resistance to proteolysis of SAA oligomers at pH 3.5–4.5 help them escape lysosomal degradation, promote SAA accumulation in lysosomes, and ultimately damage cellular membranes and liberate intracellular amyloid. We posit that these soluble prefibrillar oligomers provide a missing link in our understanding of the development of AA amyloidosis. PMID:28743750

Construction and characterization of the hetero-oligomer of the group II chaperonin from the hyperthermophilic archaeon, Thermococcus sp. strain KS-1.

PubMed

Sahlan, Muhamad; Kanzaki, Taro; Yohda, Masafumi

2009-05-01

The hyperthermophilic archaeon Thermococcus sp. strain KS-1 (T. KS-1) expresses two different chaperonin subunits, alpha and beta, for the folding of its proteins. The composition of the subunits in the hexadecameric double ring changes with temperature. The content of the beta subunit significantly increases according to the increase in temperature. The homo-oligomer of the beta subunit, Cpn beta, is more thermostable than that of the alpha subunit, Cpn alpha. Since Cpn alpha and Cpn beta also have different protein folding activities and interactions with prefoldin, the hetero-oligomer is thought to exhibit different characteristics according to the content of subunits. The hetero-oligomer of the T. KS-1 chaperonin has not been studied, however, because the alpha and beta subunits form hetero-oligomers of varying compositions when they are expressed simultaneously. In this study, we characterized the T. KS-1 chaperonin hetero-oligomer, Cpn alphabeta, containing both alpha and beta in the alternate order, which was constructed by the expression of alpha and beta subunits in a coordinated fashion and protease digestion. Cpn alphabeta protected citrate synthase from thermal aggregation, promoted the folding of acid-denatured GFP in an ATP-dependent manner, and exhibited an ATP-dependent conformational change. The yield of refolded GFP generated by Cpn alphabeta was almost equivalent to that generated by Cpn beta but lower than that generated by Cpn alpha. In contrast, Cpn alphabeta exhibited almost the same level of thermal stability as Cpn alpha, which was lower than that of Cpn beta. The affinity of Cpn alphabeta to prefoldin was found to be between those of Cpn alpha and Cpn beta, as expected.

Oligomerization of uridine phosphorimidazolides on montmorillonite: a model for the prebiotic synthesis of RNA on minerals

NASA Technical Reports Server (NTRS)

Ding, P. Z.; Kawamura, K.; Ferris, J. P.

1996-01-01

The 5'-phosphorimidazolide of uridine reacts on Na(+)-montmorillonite 22A in aqueous solution to give oligomers as long as 7 mers. The maximum chain length increases to 9 mers and the overall oligomer yield increases when 9:1 ImpU, A5' ppA mixtures react under the same conditions. The oligomer yield and maximum chain length decreases with the structure of the added pyrophosphate in the order A5' ppA > A5' ppU > U5' ppU. Structure analysis of individual oligomer fractions was performed by selective enzymatic hydrolyses followed by HPLC analysis of the products. The regioselectivity for 3',5'-bond formation is 80-90% in the 9:1 ImpU, A5' ppA reaction, a percentage comparable to that observed in the 9:1 ImpA, A5' ppA reaction. Oligomerization of ImpU is inhibited by addition of dA5' ppdA, and MeppA. No oligomers containing A5' ppU were products of the 9:1 ImpU,A5' ppA reaction, a finding consistent with the simple addition of the ImpU to the A5' ppA and not the rearrangement of an ImpU-A5' ppA adduct. Concentrations of lysine or arginine which were close to that of the ImpU did not inhibit oligomer formation. Treatment of Na(+)-montmorillonite with 1 M arginine yielded arginine-montmorillonite, an amino acid-mineral adduct which did not catalyze ImpU oligomerization. Neither the 4-9 mers formed in the 9:1 ImpU, A5' ppA reaction nor the 4-9 mers formed by the base hydrolysis of poly(U) served as templates for the formation of oligo(A)s.

Isolation of Erwinia chrysanthemi kduD mutants altered in pectin degradation.

PubMed Central

Condemine, G; Hugouvieux-Cotte-Pattat, N; Robert-Baudouy, J

1986-01-01

Mutants of Erwinia chrysanthemi impaired in pectin degradation were isolated by chemical and Mu d(Ap lac) insertion mutagenesis. A mutation in the kduD gene coding for 2-keto-3-deoxygluconate oxidoreductase prevented the growth of the bacteria on polygalacturonate as the sole carbon source. Analysis of the kduD::Mu d(Ap lac) insertions indicated that kduD is either an isolated gene or the last gene of a polycistronic operon. Some of the Mu d(Ap lac) insertions were kduD-lac fusions in which beta-galactosidase synthesis reflected kduD gene expression. In all these fusions, beta-galactosidase activity was shown to be sensitive to catabolite repression by glucose and to be inducible by polygalacturonate, galacturonate, and other intermediates of polygalacturonate catabolism. Galacturonate-mediated induction was prevented by a mutation which blocked its metabolism to 2-keto-3-deoxygluconate. 2-Keto-3-deoxygluconate appeared to be the true inducer of kduD expression resulting from galacturonate degradation. 5-Keto-4-deoxyuronate or 2,5-diketo-3-deoxygluconate were the true inducers, originating from polygalacturonate cleavage. These three intermediates also appeared to induce pectate lyases, oligogalacturonate lyase, and 5-keto-4-deoxyuronate isomerase synthesis. PMID:3949717

Ethanol production from eucalyptus wood hemicellulose hydrolysate by Pichia stipitis.

PubMed

Ferrari, M D; Neirotti, E; Albornoz, C; Saucedo, E

1992-10-05

Ethanol production was evaluated from eucalyptus wood hemicellulose acid hydrolysate using Pichia stipitis NRRL Y-7124. An initial lag phase characterized by flocculation and viability loss of the yeast inoculated was observed. Subsequently, cell regrowth occurred with sequential consumption of sugars and production of ethanol. Polyol formation was detected. Acetic acid present in the hydrolysate was an important inhibitor of the fermentation, reducing the rate and the yield. Its toxic effect was due essentially to its undissociated form. The fermentation was more effective at an oxygen transfer rate between 1.2 and 2.4 mmol/L h and an initial pH of 6.5. The hydrolysate used in the experiences had the following composition (expressed in grams per liter): xylose 30, arabinose 2.8, glucose 1.5, galactose 3.7, mannose 1.0, cellobiose 0.5, acetic acid 10, glucuronic acid 1.5, and galacturonic acid 1.0. The best values obtained were maximum ethanol concentration 12.6 g/L, fermentation time 75 h, fermentable sugar consumption 99% ethanol yield 0.35 g/g sugars consumed, and volumetric ethanol productivity 4 g/L day. ( (c) 1992 John Wiley & Sons, Inc.

Extraction and characterisation of pomace pectin from gold kiwifruit (Actinidia chinensis).

PubMed

Yuliarti, Oni; Goh, Kelvin K T; Matia-Merino, Lara; Mawson, John; Brennan, Charles

2015-11-15

Gold kiwifruit pomace extracted using citric acid, water and enzyme (Celluclast 1.5L) were studied in terms of pectin yield, protein, ash, non-starch polysaccharide, galacturonic acid (GalA), neutral sugar composition, molar mass (Mw), viscosity and degree of branching. Water-extracted pectin was considered closest to its native form. Enzyme extracted pectin showed the highest yield (∼ 4.5%w/w) as compared with the acid and water extraction methods (∼ 3.6-3.8%w/w). Pectin obtained from different extraction methods showed different degree of branching. The Mw and root mean square (RMS) radius varied with the extraction methods with values of 8.4 × 10(5) g/mol and 92 nm, 8.5 × 10(5)g/mol and 102 nm, 6.7 × 10(5) g/mol and 52 nm for acid, water and enzymatic extraction methods, respectively. Similar trend was observed for pectin viscosity, with water-extracted pectin giving a slightly higher viscosity followed by acid and enzyme-extracted pectin. This study showed that gold kiwifruit pomace pectin has potential application in food products. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nutrients, phytochemicals and antioxidant activities of 26 kidney bean cultivars.

PubMed

Kan, Lijiao; Nie, Shaoping; Hu, Jielun; Wang, Sunan; Cui, Steve W; Li, Yawen; Xu, Sifan; Wu, Yue; Wang, Junqiao; Bai, Zhouya; Xie, Mingyong

2017-10-01

Detailed characterization in nutrients and phytochemicals with antioxidant activities of 26 kidney beans was performed. The kidney beans contained high levels of dietary fiber (29.32-46.77%), resistant starch (9.16-18.09%) and protein (22.06-32.63%) but low levels of lipid (1.05-2.83%) and sugars (1.55-9.07%). The monosaccharide composition of soluble fiber was dominated by arabinose, galactose, mannose and galacturonic acid. The ratio of essential amino acid to the total amino acid was ranged from 0.29 to 0.36. The predominant fatty acid was polyunsaturated fatty acids, accounting for 47.54-67.26% of total fatty acids. The total tocopherol content was in the range of 12.83-68.35 μg/g, predominantly γ-tocopherol, followed by δ-tocopherol. In addition, certain levels of total phenolics and flavonoids with respective values of 0.25-3.79 mg gallic acid equivalent/g dry weight and 0.19-7.05 mg rutin equivalent/g dry weight resulted in significant antioxidant activities. And a good correlation was observed between TPC and FRAP values (R2 = 0.8030). The results indicated that kidney beans are excellent sources of health-promoting compounds. Copyright © 2016 Elsevier Ltd. All rights reserved.

Arachidonic acid mediates the formation of abundant alpha-helical multimers of alpha-synuclein

NASA Astrophysics Data System (ADS)

Iljina, Marija; Tosatto, Laura; Choi, Minee L.; Sang, Jason C.; Ye, Yu; Hughes, Craig D.; Bryant, Clare E.; Gandhi, Sonia; Klenerman, David

2016-09-01

The protein alpha-synuclein (αS) self-assembles into toxic beta-sheet aggregates in Parkinson’s disease, while it is proposed that αS forms soluble alpha-helical multimers in healthy neurons. Here, we have made αS multimers in vitro using arachidonic acid (ARA), one of the most abundant fatty acids in the brain, and characterized them by a combination of bulk experiments and single-molecule Fӧrster resonance energy transfer (sm-FRET) measurements. The data suggest that ARA-induced oligomers are alpha-helical, resistant to fibril formation, more prone to disaggregation, enzymatic digestion and degradation by the 26S proteasome, and lead to lower neuronal damage and reduced activation of microglia compared to the oligomers formed in the absence of ARA. These multimers can be formed at physiologically-relevant concentrations, and pathological mutants of αS form less multimers than wild-type αS. Our work provides strong biophysical evidence for the formation of alpha-helical multimers of αS in the presence of a biologically relevant fatty acid, which may have a protective role with respect to the generation of beta-sheet toxic structures during αS fibrillation.

Human proton coupled folic acid transporter is a monodisperse oligomer in the lauryl maltose neopentyl glycol solubilized state.

PubMed

Aduri, Nanda G; Ernst, Heidi A; Prabhala, Bala K; Bhatt, Shweta; Boesen, Thomas; Gajhede, Michael; Mirza, Osman

2018-01-08

The human proton coupled folic acid transporter PCFT is the major import route for dietary folates. Mutations in the gene encoding PCFT cause hereditary folic acid malabsorption, which manifests itself by compromised folate absorption from the intestine and also in impaired folate transport into the central nervous system. Since its recent discovery, PCFT has been the subject of numerous biochemical studies aiming at understanding its structure and mechanism. One major focus has been its oligomeric state, with some reports supporting oligomers and others a monomer. Here, we report the overexpression and purification of recombinant PCFT. Following detergent screening, n-Dodecyl β-D-maltoside (DDM) and lauryl maltose neopentyl glycol (LMNG) were chosen for further work as they exhibited the most optimal solubilization. We found that purified detergent solubilized PCFT was able to bind folic acid, thus indicating a functionally active protein. Size exclusion chromatography showed that PCFT in DDM was polydisperse; the LMNG preparation was clearly monodisperse but with shorter retention time than the major DDM peak. To assess the oligomeric state negative stain electron microscopy was performed which showed a particle with the size of a PCFT dimer. Copyright © 2017 Elsevier Inc. All rights reserved.

Plant immunity induced by COS-OGA elicitor is a cumulative process that involves salicylic acid.

PubMed

van Aubel, Géraldine; Cambier, Pierre; Dieu, Marc; Van Cutsem, Pierre

2016-06-01

Plant innate immunity offers considerable opportunities for plant protection but beside flagellin and chitin, not many molecules and their receptors have been extensively characterized and very few have successfully reached the field. COS-OGA, an elicitor that combines cationic chitosan oligomers (COS) with anionic pectin oligomers (OGA), efficiently protected tomato (Solanum lycopersicum) grown in greenhouse against powdery mildew (Leveillula taurica). Leaf proteomic analysis of plants sprayed with COS-OGA showed accumulation of Pathogenesis-Related proteins (PR), especially subtilisin-like proteases. qRT-PCR confirmed upregulation of PR-proteins and salicylic acid (SA)-related genes while expression of jasmonic acid/ethylene-associated genes was not modified. SA concentration and class III peroxidase activity were increased in leaves and appeared to be a cumulative process dependent on the number of sprayings with the elicitor. These results suggest a systemic acquired resistance (SAR) mechanism of action of the COS-OGA elicitor and highlight the importance of repeated applications to ensure efficient protection against disease. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

How to Tackle the Challenge of siRNA Delivery with Sequence-Defined Oligoamino Amides.

PubMed

Reinhard, Sören; Wagner, Ernst

2017-01-01

RNA interference (RNAi) as a mechanism of gene regulation provides exciting opportunities for medical applications. Synthetic small interfering RNA (siRNA) triggers the knockdown of complementary mRNA sequences in a catalytic fashion and has to be delivered into the cytosol of the targeted cells. The design of adequate carrier systems to overcome multiple extracellular and intracellular roadblocks within the delivery process has utmost importance. Cationic polymers form polyplexes through electrostatic interaction with negatively charged nucleic acids and present a promising class of carriers. Issues of polycations regarding toxicity, heterogeneity, and polydispersity can be overcome by solid-phase-assisted synthesis of sequence-defined cationic oligomers. These medium-sized highly versatile nucleic acid carriers display low cytotoxicity and can be modified and tailored in multiple ways to meet specific requirements of nucleic acid binding, polyplex size, shielding, targeting, and intracellular release of the cargo. In this way, sequence-defined cationic oligomers can mimic the dynamic and bioresponsive behavior of viruses. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theoretical study for volume changes associated with the helix-coil transition of peptides.

PubMed

Imai, T; Harano, Y; Kovalenko, A; Hirata, F

2001-12-01

We calculate the partial molar volumes and their changes associated with the coil(extended)-to-helix transition of two types of peptide, glycine-oligomer and glutamic acid-oligomer, in aqueous solutions by using the Kirkwood-Buff solution theory coupled with the three-dimensional reference interaction site model (3D-RISM) theory. The volume changes associated with the transition are small and positive. The volume is analyzed by decomposing it into five contributions following the procedure proposed by Chalikian and Breslauer: the ideal volume, the van der Waals volume, the void volume, the thermal volume, and the interaction volume. The ideal volumes and the van der Waals volumes do not change appreciably upon the transition. In the both cases of glycine-peptide and glutamic acid-peptide, the changes in the void volumes are positive, while those in the thermal volumes are negative, and tend to balance those in the void volumes. The change in the interaction volume of glycine-peptide does not significantly contribute, while that of glutamic acid-peptide makes a negative contribution. Copyright 2001 John Wiley & Sons, Inc. Biopolymers 59: 512-519, 2001

13-Helix folding of a β/γ-peptide manifold designed from a "minimal-constraint" blueprint.

PubMed

Grison, Claire M; Robin, Sylvie; Aitken, David J

2016-06-14

A bottom-up design rationale was adopted to devise β/γ-peptide foldamer manifolds which would adopt preferred 13-helix conformations, relying on minimal steric imposition brought by the constituent amino acid residues. In this way, a well-defined 13-helix conformer was revealed for short oligomers of trans-2-aminocyclobutanecarboxylic acid and γ(4)-amino acids in alternation, which gave good topological superposition upon an α-helix motif.

5'to 3' nucleic acid synthesis using 3'-photoremovable protecting group

DOEpatents

Pirrung, Michael C.; Shuey, Steven W.; Bradley, Jean-Claude

1999-01-01

The present invention relates, in general, to a method of synthesizing a nucleic acid, and, in particular, to a method of effecting 5' to 3' nucleic acid synthesis. The method can be used to prepare arrays of oligomers bound to a support via their 5' end. The invention also relates to a method of effecting mutation analysis using such arrays. The invention further relates to compounds and compositions suitable for use in such methods.

Controlled Release Formulations of Auxinic Herbicides

NASA Astrophysics Data System (ADS)

Kowalski, Witold J.; Siłowiecki, Andrzej.; Romanowska, Iwona; Glazek, Mariola; Bajor, Justyna; Cieciwa, Katarzyna; Rychter, Piotr

2013-04-01

Controlled release formulations are applied extensively for the release of active ingredients such as plant protection agents and fertilizers in response to growing concern for ecological problems associated with increased use of plant protection chemicals required for intensive agricultural practices [1]. We synthesized oligomeric mixtures of (R,S)-3-hydroxy butyric acid chemically bonded with 2,4-D, Dicamba and MCPA herbicides (HBA) respectively, and determined their molecular structure and molecular weight dispersion by the size exclusion chromatography, proton magnetic resonance spectrometry and electro-spray ionization mass spectrometry. Further we carried out bioassays of herbicidal effectiveness of the HBA herbicides vs. series of dicotyledonous weeds and crop injury tests [2, 3, 4]. Field bioassays were accomplished according to the EPPO standards [5]. Groups of representative weeds (the development stages in the BCCH scale: 10 - 30) were selected as targets. Statistical variabilities were assessed by the Fisher LSD test for plants treated with the studied herbicides in form of HBA oligomers, the reference herbicides in form of dimethyl ammonium salts (DMA), and untreated plants. No statistically significant differences in the crop injuries caused by the HBA vs. the DMA reference formulation were observed. The effectiveness of the HBA herbicides was lower through the initial period (ca. 2 weeks) relative to the DMA salts, but a significant increase in the effectiveness of the HBA systems followed during the remaining fraction of each assay. After 6 weeks all observed efficiencies approached 100%. The death of weeds treated with the HBA herbicides was delayed when compared with the DMA reference herbicides. The delayed uptake observed for the HBA oligomers relative to the DMA salts was due to controlled release phenomena. In case of the DMA salts the total amount of active ingredients was available at the target site. By contrast, the amount of an active ingredient in the HBA oligomers was chemically bound to the oligomer matrix and a controlled release followed in concert with the hydrolysis of ester bonds in the oligomer systems. Due to the high volatility and high water solubility of the DMA salts, significant amounts of active ingredients were predisposed to be dispersed in the environment. On the other hand, the HBA oligomers exhibit low volatility and low solubility in water, so they tend to exhibit lover migrating rates from the target site. The obtained plots suggested that in the case of the HBA oligomers the effectiveness were delayed in time when compared with the DMA salts. The integral effectiveness of the studied HBA oligomers was practically equivalent to the conventional DMA salts, but the release of the HBA herbicides was delayed in time vs. DMA salts. The mixtures of oligo (R,S)-3-hydroxybutyric acid containing chemically bonded 2,4-D, Dicamba and MCPA (HBA) were proposed as carriers of active ingredients that could be released to control the sensitive weeds. The synthesized HBA oligomers could be particularly useful in a number of practical applications, because they release the herbicide to plants at a controlled rate and in amounts required over a specified period of time, their degradation products are identical to metabolites formed in plant cells, the physicochemical and operational parameters of the carrier oligomers might be optimized by fine-tuning of synthesis conditions. The decreased vapor pressure and increased lipophilicity of the studied materials could reduce the risk exposure of the operational personnel, as well as, a decrease the environmental pollution. Acknowledgments The authors would like to thank the Polish Ministry of Science and Higher Education for supporting this work through the grant No. NN 310 303039. References [1] S. Dubey, V. Jhelum, P.K. Patanjali, Controlled release agrochemical formulations: A review, J. Scientific &Industrial Research (India) 70 (2011) 105-112. [2] W. J. Kowalski, I. Romanowska, M. Smol, A. Silowiecki, M. Głazek, Synthesis and evaluation of effectiveness of a controlled release preparation 2,4-D: a reduction of risk of pollution and exposure of workers, Archiv. Environm. Protect., 38 (2012) 119. [3 ] W. J. Kowalski, M.Glazek, A. Silowiecki, M. M, Kowalczuk I. Romanowska, D. Wloka, Controlled Release of 2,4-D and Dicamba 3-Hydroxybutyric Acid Oligomers, 32 nd ASTM Symposium on Pesticide Formulations and Delivery Systems, 01-03 Nov 2011, Tampa FL USA. Sponsored by ASTM Committee E-35.22. [4] European and Mediterranean Plant Protection Organization, EPPO Standards on plant protection products, Efficacy Evaluation of Plant Protection Products (PP1).

Neutral dipole-dipole dimers: A new field in science

NASA Astrophysics Data System (ADS)

Kosower, Edward M.; Borz, Galina

2018-03-01

Dimer formation with dipole neutralization produces species such as low polarity water (LPW) compatible with hydrophobic surfaces (Phys. Chem. Chem. Phys. 2015, 17, 24895-24900) Dimerization and dipole neutralization occurs for N-methylacetamide on polyethylene, a behavior drastically different from its contortions in acetonitrile on AgBr:AgCl planar crystals (AgX) (ChemPhysChem 2014, 15, 3598-3607). The weak infrared absorption of the amide dimer on polyethylene is shown experimentally. Dimerization of palmitic acid is shown along with some of the many ramifications for intracellular systems. Polyoligomers of water are present on polyethylene surfaces. Some high resolution spectra of three of the polyoligomers of water are shown along with a mechanistic scheme for polyoligomer formation and dissolution. The structures of some of the oligomers are known from spectroscopic studies of water on AgX. The scope of the article begins with PE, generally accepted as hydrophobic. The IR of PE revealed not only that water was present but that it appeared in two forms, oligomers (O) and polyoligomers (PO). How did we recognize what they were? These species had been observed as especially strong "marker" peaks in the spectra1 of water placed on planar AgX, a platform developed by Katzir and his coworkers [6]. But there was a problem: the proximity to PE of oligomers with substantial (calculated) dipole moments and thus polarity, including cyclic hexamers of water (chair and boat forms), the cyclic pentamer, the books I and II, and the cyclic trimer [7a]. Another link was needed, a role perfectly fit by the already cited low polarity water (LPW). The choice was experimentally supported by the detection of low intensity absorption in the bending region.Some important generalities flow from these results. What other dimers might be present in the biological or chemical world? Palmitic acid dimer (PAD) would be a candidate for decreasing the polarity of the acid (PA). Another possibility might be N-methylacylamides of which we have noted N-methylacetamide (NMA). We had found that NMA in a polar solvent on AgX was very acrobatic, forming first a 310-helix, an α-helix, a π-helix and a planar form in succession. In sharp contrast, we discovered that NMA forms a dimer (NMAD) and becomes immiscible with the water present on the PE surface. One may vary the acyl group and even include functional groups. Another aspect of the surface behavior of water is the formation of oligomers and polyoligomers. We will show a diagram that explains the formation of polyoligomers from oligomers and their ultimate formation of oligomers with apposed dipoles. This Scope summary should make it easier to follow the description of the varied phenomena found for the PE-water system.

α/β-Peptide Foldamers Targeting Intracellular Protein-Protein Interactions with Activity in Living Cells

PubMed Central

Checco, James W.; Lee, Erinna F.; Evangelista, Marco; Sleebs, Nerida J.; Rogers, Kelly; Pettikiriarachchi, Anne; Kershaw, Nadia J.; Eddinger, Geoffrey A.; Belair, David G.; Wilson, Julia L.; Eller, Chelcie H.; Raines, Ronald T.; Murphy, William L.; Smith, Brian J.; Gellman, Samuel H.; Fairlie, W. Douglas

2015-01-01

Peptides can be developed as effective antagonists of protein-protein interactions, but conventional peptides (i.e., oligomers of L-α-amino acids) suffer from significant limitations in vivo. Short half-lives due to rapid proteolytic degradation and an inability to cross cell membranes often preclude biological applications of peptides. Oligomers that contain both α- and β-amino acid residues (“α/β-peptides”) manifest decreased susceptibility to proteolytic degradation, and when properly designed these unnatural oligomers can mimic the protein-recognition properties of analogous “α-peptides”. This report documents an extension of the α/β-peptide approach to target intracellular protein-protein interactions. Specifically, we have generated α/β-peptides based on a “stapled” Bim BH3 α-peptide, which contains a hydrocarbon crosslink to enhance α-helix stability. We show that a stapled α/β-peptide can structurally and functionally mimic the parent stapled α-peptide in its ability to enter certain types of cells and block protein-protein interactions associated with apoptotic signaling. However, the α/β-peptide is nearly 100-fold more resistant to proteolysis than is the parent α-peptide. These results show that backbone modification, a strategy that has received relatively little attention in terms of peptide engineering for biomedical applications, can be combined with more commonly deployed peripheral modifications such as side chain crosslinking to produce synergistic benefits. PMID:26317395

α/β-Peptide Foldamers Targeting Intracellular Protein-Protein Interactions with Activity in Living Cells.

PubMed

Checco, James W; Lee, Erinna F; Evangelista, Marco; Sleebs, Nerida J; Rogers, Kelly; Pettikiriarachchi, Anne; Kershaw, Nadia J; Eddinger, Geoffrey A; Belair, David G; Wilson, Julia L; Eller, Chelcie H; Raines, Ronald T; Murphy, William L; Smith, Brian J; Gellman, Samuel H; Fairlie, W Douglas

2015-09-09

Peptides can be developed as effective antagonists of protein-protein interactions, but conventional peptides (i.e., oligomers of l-α-amino acids) suffer from significant limitations in vivo. Short half-lives due to rapid proteolytic degradation and an inability to cross cell membranes often preclude biological applications of peptides. Oligomers that contain both α- and β-amino acid residues ("α/β-peptides") manifest decreased susceptibility to proteolytic degradation, and when properly designed these unnatural oligomers can mimic the protein-recognition properties of analogous "α-peptides". This report documents an extension of the α/β-peptide approach to target intracellular protein-protein interactions. Specifically, we have generated α/β-peptides based on a "stapled" Bim BH3 α-peptide, which contains a hydrocarbon cross-link to enhance α-helix stability. We show that a stapled α/β-peptide can structurally and functionally mimic the parent stapled α-peptide in its ability to enter certain types of cells and block protein-protein interactions associated with apoptotic signaling. However, the α/β-peptide is nearly 100-fold more resistant to proteolysis than is the parent stapled α-peptide. These results show that backbone modification, a strategy that has received relatively little attention in terms of peptide engineering for biomedical applications, can be combined with more commonly deployed peripheral modifications such as side chain cross-linking to produce synergistic benefits.

Solvent-free, microwave-assisted synthesis of thiophene oligomers via Suzuki coupling.

PubMed

Melucci, Manuela; Barbarella, Giovanna; Sotgiu, Giovanna

2002-12-13

The purpose of this study was to obtain a rapid, efficient, and environmentally friendly methodology for the synthesis of highly pure thiophene oligomers. The solvent-free, microwave-assisted coupling of thienyl boronic acids and esters with thienyl bromides, using aluminum oxide as the solid support, allowed us to rapidly check the reaction trends on changing times, temperature, catalyst, and base and easily optimize the experimental conditions to obtain the targeted product in fair amounts. This procedure offers a novel, general, and very rapid route to the preparation of soluble thiophene oligomers. Thus, for example, quaterthiophene was obtained in 6 min by reaction of 2-bromo-2,2'-bithiophene with bis(pinacolato)diboron (isolated yield 65%), whereas quinquethiophene was obtained in 11 min by reaction of dibromoterthiophene with thienylboronic acid (isolated yield 74%). The synthesis of new chiral 2,2'-bithiophenes is reported. The detailed analysis of the byproducts of some reactions allowed us to elucidate a few aspects of reaction mechanisms. While the use of microwaves proved to be very convenient for the coupling between conventional thienyl moieties, the same was not true for the coupling of thienyl rings to thienyl-S,S-dioxide moieties. Indeed, in this case, the targeted product was obtained in low yields because of the competitive, accelerated, Diels-Alder reaction that affords a variety of condensation products.

Molecular Insights into the Effects of Media-Drug and Carrier-Drug Interactions on pH-Responsive Drug Carriers.

PubMed

Katiyar, Ratna S; Jha, Prateek K

2018-05-10

We have performed two sets of all atom molecular dynamics (MD) simulations of poly(acrylic acid) (PAA) oligomers, considered as a model pH-responsive drug carrier. In the first set, multiple oligomers of PAA are simulated in model gastric and intestinal fluids, where the degree of deprotonation of PAA oligomers is varied with the medium pH. Since the gastric fluid has a pH substantially lower than that of intestinal fluid, PAA is relatively lesser ionized in gastric fluid and forms aggregates. In the second set, we simulated multiple oligomers of PAA with multiple molecules of a cationic anticancer drug, doxorubicin (DOX), for a range of pH values representative of various physiological conditions. The diffusion coefficient of DOX decreases with an increase in pH due to an increase in the ionic complexation of PAA with DOX, despite a decrease in PAA aggregation. Our findings are in agreement with recent experimental reports on pH-triggered targeting of tumor cells by the PAA-DOX system. Results of these two sets of studies establish that both carrier aggregation and carrier-drug interactions are competing influences that together determine the drug release from pH-responsive polymers.

Impact of pectin esterification on the antimicrobial activity of nisin-loaded pectin particles.

PubMed

Krivorotova, Tatjana; Staneviciene, Ramune; Luksa, Juliana; Serviene, Elena; Sereikaite, Jolanta

2017-01-01

The relationship between pectin structure and the antimicrobial activity of nisin-loaded pectin particles was examined. The antimicrobial activity of five different nisin-loaded pectin particles, i.e., nisin-loaded high methoxyl pectin, low methoxyl pectin, pectic acid, dodecyl pectin with 5.4 and 25% degree of substitution were tested in the pH range of 4.0-7.0 by agar-diffusion assay and agar plate count methods. It was found that the degree of esterification of carboxyl group of galacturonic acid in pectin molecule is important for the antimicrobial activity of nisin-loaded pectin particles. Nisin-loaded particles prepared using pectic acid or the pectin with low degree of esterification exhibit higher antimicrobial activity than nisin-loaded high methoxyl pectin particles. Pectins with free carboxyl groups or of low degree of esterification are the most suitable for particles preparation. Moreover, nisin-loaded pectin particles were active at close to neutral or neutral pH values. Therefore, they could be effectively applied for food preservation. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:245-251, 2017. © 2016 American Institute of Chemical Engineers.

Dietary fibre components and pectin chemical features of peels during ripening in banana and plantain varieties.

PubMed

Happi Emaga, Thomas; Robert, Christelle; Ronkart, Sébastien N; Wathelet, Bernard; Paquot, Michel

2008-07-01

The effects of the ripeness stage of banana (Musa AAA) and plantain (Musa AAB) peels on neutral detergent fibre, acid detergent fibre, cellulose, hemicelluloses, lignin, pectin contents, and pectin chemical features were studied. Plantain peels contained a higher amount of lignin but had a lower hemicellulose content than banana peels. A sequential extraction of pectins showed that acid extraction was the most efficient to isolate banana peel pectins, whereas an ammonium oxalate extraction was more appropriate for plantain peels. In all the stages of maturation, the pectin content in banana peels was higher compared to plantain peels. Moreover, the galacturonic acid and methoxy group contents in banana peels were higher than in plantain peels. The average molecular weights of the extracted pectins were in the range of 132.6-573.8 kDa and were not dependant on peel variety, while the stage of maturation did not affect the dietary fibre yields and the composition in pectic polysaccharides in a consistent manner. This study has showed that banana peels are a potential source of dietary fibres and pectins.

Monosaccharide composition of acidic gum exudates from Indian Acacia tortilis ssp. raddiana (Savi) Brenan.

PubMed

Lakhera, Ajeet Kumar; Kumar, Vineet

2017-01-01

Acacia tortilis ssp. raddiana (Savi) Brenan commonly known as Israeli Babool has contributed immensely for sand dunes management in Indian desert leading to wind erosion control and increased biological productivity. The species is extensively used in traditional medicine system for a number of therapeutic applications and as nutraceutical. The polysaccharide was isolated in 43.6% yield from gum exudates. The monosaccharides, L-arabinose, D-galactose D-glucose, L-rhamnose and D-mannose were determined in molar ratio of 78.1%, 18.64%, 0.60%, 1.71% and 0.74% respectively. The molar ratio of uronic acids was studied using diverse spectrophotometric methods and compared with GLC. The content of D-galacturonic acid and D-glucuronic was determined as 3.88% and 4.35% respectively by GLC. The results were compared with the spectrophotometric methods. The results using DMP as chromogenic reagent are closer to that obtained by GLC. Structural analysis of the polysaccharide may provide scientific basis for nutraceutical, pharmaceutical and biological applications of gum exudates from A. tortilis, which is extensively planted in India. Copyright © 2016 Elsevier B.V. All rights reserved.

Electrooxidation of pyrrole-terminated self-assembled lipoic acid derivatives

NASA Astrophysics Data System (ADS)

Cabrita, Joana F.; Viana, Ana S.; Eberle, Christoph; Montforts, Franz-Peter; Mourato, Ana; Abrantes, Luisa M.

2009-08-01

New pyrrole derivatives, pyrrolyl lipoic acid (Py-LA 3) and dipyrrolyl lipoic acid (Py 2-LA 2) have been used for surface attachment and immobilisation on gold surfaces, by self-assembly. The electrooxidation of the surface-confined pyrroles was analysed by cyclic voltammetry and the modified electrodes morphological and thickness changes addressed by scanning probe microscopy and ellipsometry. The data support the formation of oligomers as a result of the pendant-pyrrolyl units ease oxidation but provide no evidence of an effective subsequent polymerisation.

Methods of introducing nucleic acids into cellular DNA

DOEpatents

Lajoie, Marc J.; Gregg, Christopher J.; Mosberg, Joshua A.; Church, George M.

2017-06-27

A method of introducing a nucleic acid sequence into a cell is provided where the cell has impaired or inhibited or disrupted DnaG primase activity or impaired or inhibited or disrupted DnaB helicase activity, or larger or increased gaps or distance between Okazaki fragments or lowered or reduced frequency of Okazaki fragment initiation, or the cell has increased single stranded DNA (ssDNA) on the lagging strand of the replication fork including transforming the cell through recombination with a nucleic acid oligomer.

5[prime] to 3[prime] nucleic acid synthesis using 3[prime]-photoremovable protecting group

DOEpatents

Pirrung, M.C.; Shuey, S.W.; Bradley, J.C.

1999-06-01

The present invention relates, in general, to a method of synthesizing a nucleic acid, and, in particular, to a method of effecting 5[prime] to 3[prime] nucleic acid synthesis. The method can be used to prepare arrays of oligomers bound to a support via their 5[prime] end. The invention also relates to a method of effecting mutation analysis using such arrays. The invention further relates to compounds and compositions suitable for use in such methods.

A protease-resistant exo-polygalacturonase from Klebsiella sp. Y1 with good activity and stability over a wide pH range in the digestive tract.

PubMed

Yuan, Peng; Meng, Kun; Wang, Yaru; Luo, Huiying; Shi, Pengjun; Huang, Huoqing; Bai, Yingguo; Yang, Peilong; Yao, Bin

2012-11-01

Polygalacturonases are important feed and food additives. In the present study an exo-polygalacturonase gene (pgu B) was cloned from Klebsiella sp. Y1 CGMCC 4433 and expressed in Escherichia coli BL21 (DE3). pgu B encodes a 658-amino acid polypeptide belonging to Glycoside Hydrolase Family 28. The optimal pH and temperature of exo-PGU B activity were 6.0 and 40-50°C, respectively. The enzyme exhibited >35% of maximum activity within the pH range of 2.0-12.0. Exo-PGU B or an exo-PGU B/ endo-polygalacturonase mixture reduced the viscosity of polygalacturonic acid (1.0%, w/v) by 15.6 and 39.4%, respectively. Under simulated alimentary tract conditions, exo-PGU B was very stable (>25% activity from pH 1.5 to 6.8) and active, releasing 53.7 and 109.6μg of galacturonic acid from 400 to 800μg of polygalacturonic acid, respectively. These properties make exo-PGU B a potentially valuable additive for applications in feed and food. Copyright © 2012 Elsevier Ltd. All rights reserved.

Structure and function of small heat shock/alpha-crystallin proteins: established concepts and emerging ideas.

PubMed

MacRae, T H

2000-06-01

Small heat shock/alpha-crystallin proteins are defined by conserved sequence of approximately 90 amino acid residues, termed the alpha-crystallin domain, which is bounded by variable amino- and carboxy-terminal extensions. These proteins form oligomers, most of uncertain quaternary structure, and oligomerization is prerequisite to their function as molecular chaperones. Sequence modelling and physical analyses show that the secondary structure of small heat shock/alpha-crystallin proteins is predominately beta-pleated sheet. Crystallography, site-directed spin-labelling and yeast two-hybrid selection demonstrate regions of secondary structure within the alpha-crystallin domain that interact during oligomer assembly, a process also dependent on the amino terminus. Oligomers are dynamic, exhibiting subunit exchange and organizational plasticity, perhaps leading to functional diversity. Exposure of hydrophobic residues by structural modification facilitates chaperoning where denaturing proteins in the molten globule state associate with oligomers. The flexible carboxy-terminal extension contributes to chaperone activity by enhancing the solubility of small heat shock/alpha-crystallin proteins. Site-directed mutagenesis has yielded proteins where the effect of the change on structure and function depends upon the residue modified, the organism under study and the analytical techniques used. Most revealing, substitution of a conserved arginine residue within the alpha-crystallin domain has a major impact on quaternary structure and chaperone action probably through realignment of beta-sheets. These mutations are linked to inherited diseases. Oligomer size is regulated by a stress-responsive cascade including MAPKAP kinase 2/3 and p38. Phosphorylation of small heat shock/alpha-crystallin proteins has important consequences within stressed cells, especially for microfilaments.

Template-directed synthesis and selective adsorption of oligoadenylates in hydroxyapatite

NASA Technical Reports Server (NTRS)

Gibbs, D.; Lohrmann, R.; Orgel, L. E.

1980-01-01

Polyuridylic acid is adsorbed completely from aqueous solution by hydroxyapatite under conditions that permit template-directed synthesis of oligoadenylates in free solution. The yield of oligoadenylates is enhanced to almost the same extent by poly(U) in the presence or the absence of hydroxyapatite. Under very similar conditions small quantities of hydroxyapatite adsorb higher-molecular-weight oligoadenylates selectively from a mixture of oligomers. On the basis of these results a mechanism for prebiotic oligonucleotide formation is proposed in which selective adsorption on hydroxyapatite or some other immobilized anion-exchanging material plays a major role. Monomers are released from the surface for reactivation, while oligomers are retained in a protected environment by adsorption to the apatite surface.

Sequence dependent N-terminal rearrangement and degradation of peptide nucleic acid (PNA) in aqueous solution

NASA Technical Reports Server (NTRS)

Eriksson, M.; Christensen, L.; Schmidt, J.; Haaima, G.; Orgel, L.; Nielsen, P. E.

1998-01-01

The stability of the PNA (peptide nucleic acid) thymine monomer inverted question markN-[2-(thymin-1-ylacetyl)]-N-(2-aminoaminoethyl)glycine inverted question mark and those of various PNA oligomers (5-8-mers) have been measured at room temperature (20 degrees C) as a function of pH. The thymine monomer undergoes N-acyl transfer rearrangement with a half-life of 34 days at pH 11 as analyzed by 1H NMR; and two reactions, the N-acyl transfer and a sequential degradation, are found by HPLC analysis to occur at measurable rates for the oligomers at pH 9 or above. Dependent on the amino-terminal sequence, half-lives of 350 h to 163 days were found at pH 9. At pH 12 the half-lives ranged from 1.5 h to 21 days. The results are discussed in terms of PNA as a gene therapeutic drug as well as a possible prebiotic genetic material.

Inactivation of lipoprotein lipase occurs on the surface of THP-1 macrophages where oligomers of angiopoietin-like protein 4 are formed

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makoveichuk, Elena; Sukonina, Valentina; Kroupa, Olessia

2012-08-24

Highlights: Black-Right-Pointing-Pointer Lipoprotein lipase (LPL) activity is controlled by ANGPTL4 in THP-1 macrophages. Black-Right-Pointing-Pointer Both LPL and ANGPTL4 bind to THP-1 macrophages in a heparin-releasable fashion. Black-Right-Pointing-Pointer Only monomers of ANGPTL4 are present within THP-1 macrophages. Black-Right-Pointing-Pointer Covalent oligomers of ANGPTL4 appear on cell surface and in medium. Black-Right-Pointing-Pointer Inactivation of LPL coincide with ANGPTL4 oligomer formation on cell surfaces. -- Abstract: Lipoprotein lipase (LPL) hydrolyzes triglycerides in plasma lipoproteins causing release of fatty acids for metabolic purposes in muscles and adipose tissue. LPL in macrophages in the artery wall may, however, promote foam cell formation and atherosclerosis. Angiopoietin-like proteinmore » (ANGPTL) 4 inactivates LPL and ANGPTL4 expression is controlled by peroxisome proliferator-activated receptors (PPAR). The mechanisms for inactivation of LPL by ANGPTL4 was studied in THP-1 macrophages where active LPL is associated with cell surfaces in a heparin-releasable form, while LPL in the culture medium is mostly inactive. The PPAR{delta} agonist GW501516 had no effect on LPL mRNA, but increased ANGPTL4 mRNA and caused a marked reduction of the heparin-releasable LPL activity concomitantly with accumulation of inactive, monomeric LPL in the medium. Intracellular ANGPTL4 was monomeric, while dimers and tetramers of ANGPTL4 were present in the heparin-releasable fraction and medium. GW501516 caused an increase in the amount of ANGPTL4 oligomers on the cell surface that paralleled the decrease in LPL activity. Actinomycin D blocked the effects of GW501516 on ANGPTL4 oligomer formation and prevented the inactivation of LPL. Antibodies against ANGPTL4 interfered with the inactivation of LPL. We conclude that inactivation of LPL in THP-1 macrophages primarily occurs on the cell surface where oligomers of ANGPTL4 are formed.« less

The Impact of HA Oligomer Content on Physical, Mechanical, and Biologic Properties of Divinyl Sulfone-Crosslinked HA Hydrogels

PubMed Central

Ibrahim, Samir; Kang, Qian K; Ramamurthi, Anand

2009-01-01

In recent studies, we showed that exogenous hyaluronic acid oligomers (HA-o) stimulate functional endothelialization, though native long-chain HA is more bioinert and possibly more biocompatible. Thus, in this study, hydrogels containing high molecular weight (HMW) HA (1×106 Da) and HA oligomer mixtures (HA-o: 0.75–10 kDa) were created by crosslinking with divinyl sulfone (DVS). The incorporation of HA oligomers was found to compromise the physical and mechanical properties of the gels (rheology, apparent crosslinking density, swelling ratio, degradation) and to very mildly enhance inflammatory cell recruitment in vivo; increasing the DVS crosslinker content within the gels in general, had the opposite effect, though the relatively high concentration of DVS within these gels (necessary to create a solid gel) also stimulated a mild sub-cutaneous inflammatory response in vivo and VCAM-1 expression by ECs cultured atop; ICAM-expression levels remained very low irrespective extent of DVS crosslinking or HA-o content. The greatest EC attachment and proliferation (MTT assay) was observed on gels that contained the highest amount of HA-o. The study shows that the beneficial EC response to HA oligomers and biocompatibility of HA is mostly unaltered by their chemical derivatization and crosslinking into a hydrogel. However, the study also demonstrates that the relatively high concentrations of DVS, necessary to create solid gels, compromises their biocompatibility. Moreover, the poor mechanics of even these heavily crosslinked gels, in the context of vascular implantation, necessitates the investigation of other, more appropriate crosslinking agents. Alternately, the outcomes of this study may be used to guide an approach based on chemical immobilization and controlled surface-presentation of both bioactive HA oligomers and more biocompatible HMW HAon synthetic or tissue engineered grafts already in use, without the use of a crosslinker, so that improved, predictable, and functional endothelialization can be achieved, and the need to create a mechanically compliant biomaterial for standalone use, circumvented. PMID:20186732

Exopolysaccharide production by a marine Pseudoalteromonas sp. strain isolated from Madeira Archipelago ocean sediments.

PubMed

Roca, Christophe; Lehmann, Mareen; Torres, Cristiana A V; Baptista, Sílvia; Gaudêncio, Susana P; Freitas, Filomena; Reis, Maria A M

2016-06-25

Exopolysaccharides (EPS) are polymers excreted by some microorganisms with interesting properties and used in many industrial applications. A new Pseudoalteromonas sp. strain, MD12-642, was isolated from marine sediments and cultivated in bioreactor in saline culture medium containing glucose as carbon source. Its ability to produce EPS under saline conditions was demonstrated reaching an EPS production of 4.4g/L within 17hours of cultivation, corresponding to a volumetric productivity of 0.25g/Lh, the highest value so far obtained for Pseudoalteromonas sp. strains. The compositional analysis of the EPS revealed the presence of galacturonic acid (41-42mol%), glucuronic acid (25-26mol%), rhamnose (16-22mol%) and glucosamine (12-16mol%) sugar residues. The polymer presents a high molecular weight (above 1000kDa). These results encourage the biotechnological exploitation of strain MD12-642 for the production of valuable EPS with unique composition, using saline by-products/wastes as feedstocks. Copyright © 2016 Elsevier B.V. All rights reserved.

Characterization and biological activities of a novel polysaccharide isolated from raspberry (Rubus idaeus L.) fruits.

PubMed

Yu, Zeyuan; Liu, Lu; Xu, Yaqin; Wang, Libo; Teng, Xin; Li, Xingguo; Dai, Jing

2015-11-05

A water-soluble polysaccharide namely RCP-II from raspberry fruits was obtained by complex enzyme method followed by successive purification using macroporous resin D4020 and Sephadex G-100 columns. RCP-II was an acidic heteropolysaccharide and the characteristic structure of polysaccharide was determined. The carbohydrate of RCP-II was composed with galacturonic acid, rhamnose, arabinose, xylose, glucose and galactose in a molar ratio of 1.00:0.55:1.19:0.52:0.44:1.90 and the average molecular weight was estimated to be 4013 Da, based on dextran standards. RCP-II presented high scavenging activity toward DPPH•, HO•, O2(•-) in a concentration-dependent manner. The determination of the inhibitory activity on protein glycation showed that in 14 days of incubation the inhibitory ability of RCP-II was more effective on the development of non-enzymatic glycation reaction at early phase than that at the following two phases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Extraction and Characterization of Highly Gelling Low Methoxy Pectin from Cashew Apple Pomace

PubMed Central

Yapo, Beda M.; Koffi, Kouassi L.

2013-01-01

Investigation on the pectic substances of cashew (Anacardium occidentale L.) apple under different acid-extraction conditions (pH 1.0, 1.5, and 2.0) showed that more than 10%–25% of A. occidentale pectins (AOP) could be extracted, depending on the extractant strength. The extracted AOP contained high amounts of galacturonic acid (GalA: 69.9%–84.5%) with some neutral sugars of which rhamnose (Rha: 1.3%–2.5%), arabinose (Ara: 2.6%–5.4%), and galactose (Gal: 4.7%–8.6%) were the main constituents. The degree of methoxylation (DM) was in the range of 28%–46% and was only slightly affected by the extractant strength, thereby indicating isolation of naturally low methoxy pectins (LMP). In terms of gelling capability, AOP yielded firmer Ca2+-mediated LMP gels than commercial citrus LMP with comparable DM. Cashew apple pomace, therefore, appears to be a potentially viable source for possible production of “non-chemically or enzymatically-tailored” LMP. PMID:28234301

Hypolipidemic effects of crude green tea polysaccharide on rats, and structural features of tea polysaccharides isolated from the crude polysaccharide.

PubMed

Nakamura, Michiko; Miura, Sayaka; Takagaki, Akiko; Nanjo, Fumio

2017-05-01

Crude tea polysaccharide (crude TPS) was prepared from instant green tea by ethanol precipitation followed by ultrafiltration membrane treatment and its effects on blood lipid, liver lipid, and fecal lipid levels were examined with Sprague-Dawley rats fed a high-fat diet. Although crude TPS showed no effects on the serum lipid levels, it suppressed the liver lipid accumulation and increased the fecal excretion of dietary fat. Then, the structural features of crude TPS were investigated. After separation of crude TPS by DEAE-cellulose and gel-filtration column chromatography, two kinds of neutral tea polysaccharides (NTPS-LP and NTPS-HH) and an acidic polysaccharide (ATPS-MH) were obtained. According to monosaccharide composition, methylation, and NMR analyses, NTPS-LP, NPTS-HH, and ATPS-MH were presumed to be starch, arabinogalactan with β-1,3-linked galactosyl backbone blanched at position 6 and with 1,5-linked arabinofuranosyl residues, and α-1,4-linked galacturonic acid backbone with arabinogalactan region, respectively.

Protease and Hemicellulase Assisted Extraction of Dietary Fiber from Wastes of Cynara cardunculus

PubMed Central

Santo Domingo, Cinthia; Soria, Marcelo; Rojas, Ana M.; Fissore, Eliana N.; Gerschenson, Lía N.

2015-01-01

The action of protease and hemicellulase for the extraction of fractions enriched in soluble fiber from bracts and stems of Cynara cardunculus was evaluated. Using a two-factor simplex design comprising protease amounts of 0–200 μL and hemicellulase amounts of 0–200 mg for 5 g of material, we explored the effect of a 5 h enzymatic treatment at 40 °C on the chemical composition and yield of the fractions isolated. The fractions contained inulin and pectin. In general, the protein, inulin, and polyphenol contents and also the yields were higher for fractions obtained from stems. The most marked effects were observed when enzymes were used at higher concentrations, especially for hemicellulase. The inclusion of a pre-heating step increased the yield and the inulin content for fractions isolated from bracts and stems and decreased the protein and polyphenol contents, and the galacturonic acid for bracts. These fractions, in general, contained the polyphenolic compounds monocaffeoylquinic acid, apigenin, and pinoresinol. PMID:25809605

Optimization of polysaccharides extraction from watermelon rinds: Structure, functional and biological activities.

PubMed

Romdhane, Molka Ben; Haddar, Anissa; Ghazala, Imen; Jeddou, Khawla Ben; Helbert, Claire Boisset; Ellouz-Chaabouni, Semia

2017-02-01

In the present work, optimization of hot water extraction, structural characteristics, functional properties, and biological activities of polysaccharides extracted from watermelon rinds (WMRP) were investigated. The physicochemical characteristics and the monosaccharide composition of these polysaccharides were then determined using chemical composition analysis, Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and gas chromatography-flame ionization detection (GC-FID). SEM images showed that extracted polysaccharides had a rough surface with many cavities. GC-FID results proved that galactose was the dominant sugar in the extracted polysaccharides, followed by arabinose, glucose, galacturonic acid, rhamnose, mannose, xylose and traces of glucuronic acid. The findings revealed that WMRP displayed excellent antihypertensive and antioxidant activities. Those polysaccharides had also a protection effect against hydroxyl radical-induced DNA damage. Functional properties of extracted polysaccharides were also evaluated. WMRP showed good interfacial dose-dependent proprieties. Overall, the results suggested that WMRP presents a promising natural source of antioxidants and antihypertensive agents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Kinetic modeling of batch fermentation for Populus hydrolysate tolerant mutant and wild type strains of Clostridium thermocellum.

PubMed

Linville, Jessica L; Rodriguez, Miguel; Mielenz, Jonathan R; Cox, Chris D

2013-11-01

The extent of inhibition of two strains of Clostridium thermocellum by a Populus hydrolysate was investigated. A Monod-based model of wild type (WT) and Populus hydrolysate tolerant mutant (PM) strains of the cellulolytic bacterium C. thermocellum was developed to quantify growth kinetics in standard media and the extent of inhibition to a Populus hydrolysate. The PM was characterized by a higher growth rate (μmax=1.223 vs. 0.571 h(-1)) and less inhibition (KI,gen=0.991 vs. 0.757) in 10% v/v Populus hydrolysate compared to the WT. In 17.5% v/v Populus hydrolysate inhibition of PM increased slightly (KI,gen=0.888), whereas the WT was strongly inhibited and did not grow in a reproducible manner. Of the individual inhibitors tested, 4-hydroxybenzoic acid was the most inhibitory, followed by galacturonic acid. The PM did not have a greater ability to detoxify the hydrolysate than the WT. Copyright © 2013 Elsevier Ltd. All rights reserved.

Reaction Kinetic Model of Dilute Acid-Catalyzed Hemicellulose Hydrolysis of Corn Stover under High-Solid Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Suan; Guan, Wenjian; Kang, Li

High solid conditions are desirable in pretreatment of lignocellulosic biomass. An advanced dilute-acid pretreatment reactor has been developed at National Renewable Energy Laboratory (NREL). It is a continuous auger-driven reactor that can be operated with high-solid charge at high temperature and with short residence time resulting high productivity and high sugar concentration. Here, we investigated the kinetics of the reactions associated with dilute-acid pretreatment of corn stover, covering the reaction conditions of the NREL reactor operation: 155-185 C, 1-2 wt% sulfuric acid concentration, and 1:2 solid to liquid ratio. The experimental data were fitted to a first-order biphasic model whichmore » assumes that xylan is comprised of two different fragments: fast and slow reacting fractions. Due to the high solid loading condition, significant amount of xylose oligomers was observed during the pretreatment. We also included the oligomers as an intermediate entity in the kinetic model. The effect of acid concentration was incorporated into the pre-exponential factor of Arrhenius equation. The kinetic model with bestfit kinetic parameters has shown good agreement with experimental data. The kinetic parameter values of the proposed model were noticeably different from those previously reported. The activation energies of xylan hydrolysis are lower and the acid exponents are higher than the average of literature values. The proposed model can serve as a useful tool for design and operation of pretreatment system pertaining to corn stover.« less

Reaction Kinetic Model of Dilute Acid-Catalyzed Hemicellulose Hydrolysis of Corn Stover under High-Solid Conditions

DOE PAGES

Shi, Suan; Guan, Wenjian; Kang, Li; ...

2017-09-13

High solid conditions are desirable in pretreatment of lignocellulosic biomass. An advanced dilute-acid pretreatment reactor has been developed at National Renewable Energy Laboratory (NREL). It is a continuous auger-driven reactor that can be operated with high-solid charge at high temperature and with short residence time resulting high productivity and high sugar concentration. Here, we investigated the kinetics of the reactions associated with dilute-acid pretreatment of corn stover, covering the reaction conditions of the NREL reactor operation: 155-185 C, 1-2 wt% sulfuric acid concentration, and 1:2 solid to liquid ratio. The experimental data were fitted to a first-order biphasic model whichmore » assumes that xylan is comprised of two different fragments: fast and slow reacting fractions. Due to the high solid loading condition, significant amount of xylose oligomers was observed during the pretreatment. We also included the oligomers as an intermediate entity in the kinetic model. The effect of acid concentration was incorporated into the pre-exponential factor of Arrhenius equation. The kinetic model with bestfit kinetic parameters has shown good agreement with experimental data. The kinetic parameter values of the proposed model were noticeably different from those previously reported. The activation energies of xylan hydrolysis are lower and the acid exponents are higher than the average of literature values. The proposed model can serve as a useful tool for design and operation of pretreatment system pertaining to corn stover.« less

Formation of periodic γ-turns in α/β-hybrid peptides: DFT and NMR experimental evidence.

PubMed

Chandrasekhar, Srivari; Rao, Kakita Veera Mohana; Seenaiah, Mallikanti; Naresh, Police; Devi, Ambure Sharada; Jagadeesh, Bharatam

2014-02-01

Hybrid peptidic oligomers comprising natural and unnatural amino acid residues that can exhibit biomolecular folding and hydrogen-bonding mimicry have attracted considerable interest in recent years. While a variety of hybrid peptidic helices have been reported in the literature, other secondary structural patterns such as γ-turns and ribbons have not been well explored so far. The present work reports the design of novel periodic γ-turns in the oligomers of 1:1 natural-α/unnatural trans-β-norborenene (TNAA) amino acid residues. Through DFT, NMR, and MD studies, it is convincingly shown that, in the mixed conformational pool, the heterogeneous backbone of the hybrid peptides preferentially adopt periodic 8-membered (pseudo γ-turn)/7-membered (inverse γ-turn) hydrogen bonds in both polar and non-polar solvent media. It is observed that the stereochemistry and local conformational preference of the β-amino acid building blocks have a profound influence on accessing the specific secondary fold. These findings may be of significant relevance for the development of molecular scaffolds that facilitate desired positioning of functional side-chains. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Processing and properties of fiber reinforced polymeric matrix composites: I. IM7/LARC(TM)-PETI-7 polyimide composites

NASA Technical Reports Server (NTRS)

Hou, Tan-Hung

1995-01-01

A phenylethynyl terminated imide oligomer formed from the reaction of benzophenone tetracarboxylic acid dianhydride, an 75:25 molar ratio of 4,4'-oxydianiline and meta-phenylenediamine and 4-phenylethynylphthalic anhydride as the endcapper at a theoretical number average molecular weight (Mn) of approximately 3,700 g/mol was evaluated as a composite resin matrix. A glass transition temperature (Tg) of 315 deg C was reached after 250 deg C/1 hr annealing of the matrix resin. Unidirectional prepreg was made by coating an N-methylpyrrolidinone solution of the amide acid oligomer onto unsized IM7 graphite fibers. The thermal and rheological properties and the solvent/volatile depletion rates of the amide acid/NMP system were determined. This information was used to successfully design a molding cycle for composite fabrication. Composites molded under 800 Psi at 371 C consistently yielded good consolidation as measured by C-scan and optical photomicrography. The composite's short beam shear strength (SBS), longitudinal and transverse flexural strengths and moduli were measured at various temperatures. These composites exhibited excellent room temperature (RT) longitudinal flexural strength and modulus and RT SBS strength retention at 177 C.

Validation and Characterization of a Novel Peptide That Binds Monomeric and Aggregated β-Amyloid and Inhibits the Formation of Neurotoxic Oligomers.

PubMed

Barr, Renae K; Verdile, Giuseppe; Wijaya, Linda K; Morici, Michael; Taddei, Kevin; Gupta, Veer B; Pedrini, Steve; Jin, Liang; Nicolazzo, Joseph A; Knock, Erin; Fraser, Paul E; Martins, Ralph N

2016-01-08

Although the formation of β-amyloid (Aβ) deposits in the brain is a hallmark of Alzheimer disease (AD), the soluble oligomers rather than the mature amyloid fibrils most likely contribute to Aβ toxicity and neurodegeneration. Thus, the discovery of agents targeting soluble Aβ oligomers is highly desirable for early diagnosis prior to the manifestation of a clinical AD phenotype and also more effective therapies. We have previously reported that a novel 15-amino acid peptide (15-mer), isolated via phage display screening, targeted Aβ and attenuated its neurotoxicity (Taddei, K., Laws, S. M., Verdile, G., Munns, S., D'Costa, K., Harvey, A. R., Martins, I. J., Hill, F., Levy, E., Shaw, J. E., and Martins, R. N. (2010) Neurobiol. Aging 31, 203-214). The aim of the current study was to generate and biochemically characterize analogues of this peptide with improved stability and therapeutic potential. We demonstrated that a stable analogue of the 15-amino acid peptide (15M S.A.) retained the activity and potency of the parent peptide and demonstrated improved proteolytic resistance in vitro (stable to t = 300 min, c.f. t = 30 min for the parent peptide). This candidate reduced the formation of soluble Aβ42 oligomers, with the concurrent generation of non-toxic, insoluble aggregates measuring up to 25-30 nm diameter as determined by atomic force microscopy. The 15M S.A. candidate directly interacted with oligomeric Aβ42, as shown by coimmunoprecipitation and surface plasmon resonance/Biacore analysis, with an affinity in the low micromolar range. Furthermore, this peptide bound fibrillar Aβ42 and also stained plaques ex vivo in brain tissue from AD model mice. Given its multifaceted ability to target monomeric and aggregated Aβ42 species, this candidate holds promise for novel preclinical AD imaging and therapeutic strategies. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

miR-20a inhibition using locked nucleic acid (LNA) technology and its effects on apoptosis of human macrophages infected by Toxoplasma gondii RH strain.

PubMed

Rezaei, Fatemeh; Daryani, Ahmad; Sharifi, Mohammadreza; Sarvi, Shahabeddin; Jafari, Narjes; Pagheh, Abdol Sattar; Hashemi, Nooshin; Hejazi, Seyed Hossein

2018-05-22

Toxoplasma gondii is a ubiquitous and infectious parasite that multiplies in any nucleated cell of warm-blooded animals and humans worldwide. This parasite has intricate mechanisms to reciprocate host-cell apoptosis to exist in the host cell. So far, the details of the parasite interactions with host cells are not well known. MicroRNAs (miRNAs) are one of the small noncoding RNAs that are now considered as a key mechanism of gene regulation. They are important in physiological and pathological processes such as apoptosis. In this study a Real Time quantitative PCR technique was used to evaluate the levels of miR-20a of miRNAs family in human macrophage during T. gondii infection to determine the role of miR-20a in apoptosis. Then, the inhibition of miR-20a function through interaction with transfection of Locked Nucleic Acid (LNA) antisense oligomer was studied. Furthermore, it was examined whether miR-20a is involved in apoptosis of human macrophages with T. gondii infected cells using flow cytometry. We found that miR-20a expression is up-regulated in human macrophages following T. gondii infection. After LNA anti miR-20a oligomer transfection, miR-20a inhibition was evaluated by quantitative reverse transcriptase polymerase chain reaction. Flow cytometry results showed that LNA anti-miR20a oligomer increased apoptosis. In agreement with this result, we found that specific LNA oligonucleotides prevent the functional activity of miR-20a and promotion of human macrophages apoptosis with T. gondii infection by inhibition of this miRNAs gene. Also, the results support the concept that LNA oligomer antisense may be used as a therapeutic implement for blocking detrimental miRNAs overexpressed in infections. Copyright © 2018 Elsevier Ltd. All rights reserved.

Assembly mechanism of the oligomeric streptolysin O pore: the early membrane lesion is lined by a free edge of the lipid membrane and is extended gradually during oligomerization.

PubMed

Palmer, M; Harris, R; Freytag, C; Kehoe, M; Tranum-Jensen, J; Bhakdi, S

1998-03-16

Streptolysin O (SLO) is a bacterial exotoxin that binds to cell membranes containing cholesterol and then oligomerizes to form large pores. Along with rings, arc-shaped oligomers form on membranes. It has been suggested that each arc represents an incompletely assembled oligomer and constitutes a functional pore, faced on the opposite side by a free edge of the lipid membrane. We sought functional evidence in support of this idea by using an oligomerization-deficient, non-lytic mutant of SLO. This protein, which was created by chemical modification of a single mutant cysteine (T250C) with N-(iodoacetaminoethyl)-1-naphthylamine-5-sulfonic acid, formed hybrid oligomers with active SLO on membranes. However, incorporation of the modified T250C mutant inhibited subsequent oligomerization, so that the hybrid oligomers were reduced in size. These appeared as typical arc lesions in the electron microscope. They formed pores that permitted passage of NaCl and calcein but restricted permeation of large dextran molecules. The data indicate that the SLO pore is formed gradually during oligomerization, implying that pores lined by protein on one side and an edge of free lipid on the other may be created in the plasma membrane. Intentional manipulation of the pore size may extend the utility of SLO as a tool in cell biological experiments.

An Open-Circuit Voltage and Power Conversion Efficiency Study of Fullerene Ternary Organic Solar Cells Based on Oligomer/Oligomer and Oligomer/Polymer.

PubMed

Zhang, Guichuan; Zhou, Cheng; Sun, Chen; Jia, Xiaoe; Xu, Baomin; Ying, Lei; Huang, Fei; Cao, Yong

2017-07-01

Variations in the open-circuit voltage (V oc ) of ternary organic solar cells are systematically investigated. The initial study of these devices consists of two electron-donating oligomers, S2 (two units) and S7 (seven units), and the electron-accepting [6,6]-phenyl C71 butyric acid methyl ester (PC 71 BM) and reveals that the V oc is continuously tunable due to the changing energy of the charge transfer state (E ct ) of the active layers. Further investigation suggests that V oc is also continuously tunable upon change in E ct in a ternary blend system that consists of S2 and its corresponding polymer (P11):PC 71 BM. It is interesting to note that higher power conversion efficiencies can be obtained for both S2:S7:PC 71 BM and S2:P11:PC 71 BM ternary systems compared with their binary systems, which can be ascribed to an improved V oc due to the higher E ct and an improved fill factor due to the improved film morphology upon the incorporation of S2. These findings provide a new guideline for the future design of conjugated polymers for achieving higher performance of ternary organic solar cells. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Light-absorbing oligomer formation in secondary organic aerosol from reactive uptake of isoprene epoxydiols.

PubMed

Lin, Ying-Hsuan; Budisulistiorini, Sri Hapsari; Chu, Kevin; Siejack, Richard A; Zhang, Haofei; Riva, Matthieu; Zhang, Zhenfa; Gold, Avram; Kautzman, Kathryn E; Surratt, Jason D

2014-10-21

Secondary organic aerosol (SOA) produced from reactive uptake and multiphase chemistry of isoprene epoxydiols (IEPOX) has been found to contribute substantially (upward of 33%) to the fine organic aerosol mass over the Southeastern U.S. Brown carbon (BrC) in rural areas of this region has been linked to secondary sources in the summer when the influence of biomass burning is low. We demonstrate the formation of light-absorbing (290 < λ < 700 nm) SOA constituents from reactive uptake of trans-β-IEPOX onto preexisting sulfate aerosols as a potential source of secondary BrC. IEPOX-derived BrC generated in controlled chamber experiments under dry, acidic conditions has an average mass absorption coefficient of ∼ 300 cm(2) g(-1). Chemical analyses of SOA constituents using UV-visible spectroscopy and high-resolution mass spectrometry indicate the presence of highly unsaturated oligomeric species with molecular weights separated by mass units of 100 (C5H8O2) and 82 (C5H6O) coincident with the observations of enhanced light absorption, suggesting such oligomers as chromophores, and potentially explaining one source of humic-like substances (HULIS) ubiquitously present in atmospheric aerosol. Similar light-absorbing oligomers were identified in fine aerosol collected in the rural Southeastern U.S., supporting their atmospheric relevance and revealing a previously unrecognized source of oligomers derived from isoprene that contributes to ambient fine aerosol mass.

Electrostatic Forces as Dominant Interactions Between Proteins and Polyanions: an ESI MS Study of Fibroblast Growth Factor Binding to Heparin Oligomers

NASA Astrophysics Data System (ADS)

Minsky, Burcu Baykal; Dubin, Paul L.; Kaltashov, Igor A.

2017-04-01

The interactions between fibroblast growth factors (FGFs) and their receptors (FGFRs) are facilitated by heparan sulfate (HS) and heparin (Hp), highly sulfated biological polyelectrolytes. The molecular basis of FGF interactions with these polyelectrolytes is highly complex due to the structural heterogeneity of HS/Hp, and many details still remain elusive, especially the significance of charge density and minimal chain length of HS/Hp in growth factor recognition and multimerization. In this work, we use electrospray ionization mass spectrometry (ESI MS) to investigate the association of relatively homogeneous oligoheparins (octamer, dp8, and decamer, dp10) with acidic fibroblast growth factor (FGF-1). This growth factor forms 1:1, 2:1, and 3:1 protein/heparinoid complexes with both dp8 and dp10, and the fraction of bound protein is highly dependent on protein/heparinoid molar ratio. Multimeric complexes are preferentially formed on the highly sulfated Hp oligomers. Although a variety of oligomers appear to be binding-competent, there is a strong correlation between the affinity and the overall level of sulfation (the highest charge density polyanions binding FGF most strongly via multivalent interactions). These results show that the interactions between FGF-1 and Hp oligomers are primarily directed by electrostatics, and also demonstrate the power of ESI MS as a tool to study multiple binding equilibria between proteins and structurally heterogeneous polyanions.

Poliovirus 2C protein forms homo-oligomeric structures required for ATPase activity.

PubMed

Adams, Peter; Kandiah, Eaazhisai; Effantin, Grégory; Steven, Alasdair C; Ehrenfeld, Ellie

2009-08-14

The poliovirus protein 2C plays an essential role in viral RNA replication, although its precise biochemical activities or structural requirements have not been elucidated. The protein has several distinctive properties, including ATPase activity and membrane and RNA binding, that are conserved among orthologs of many positive-strand RNA viruses. Sequence alignments have placed these proteins in the SF3 helicase family, a subset of the AAA+ ATPase superfamily. A feature common to AAA+ proteins is the formation of oligomeric rings that are essential for their catalytic functions. Here we show that a recombinant protein, MBP-2C, in which maltose-binding protein was fused to 2C, formed soluble oligomers and that ATPase activity was restricted to oligomer-containing fractions from gel-filtration chromatography. The active fraction was visualized by negative-staining electron microscopy as ring-like particles composed of 5-8 protomers. This conclusion was confirmed by mass measurements obtained by scanning transmission electron microscopy. Mutation of amino acid residues in the 2C nucleotide-binding domain demonstrated that loss of the ability to bind or hydrolyze ATP did not affect oligomerization. Co-expression of active MBP-2C and inactive mutant proteins generated mixed oligomers that exhibited little ATPase activity, suggesting that incorporation of inactive subunits eliminates the function of the entire particle. Finally, deletion of the N-terminal 38 amino acids blocked oligomerization of the fusion protein and eliminated ATPase activity, despite retention of an unaltered nucleotide-binding domain.

Poliovirus 2C Protein Forms Homo-oligomeric Structures Required for ATPase Activity*

PubMed Central

Adams, Peter; Kandiah, Eaazhisai; Effantin, Grégory; Steven, Alasdair C.; Ehrenfeld, Ellie

2009-01-01

The poliovirus protein 2C plays an essential role in viral RNA replication, although its precise biochemical activities or structural requirements have not been elucidated. The protein has several distinctive properties, including ATPase activity and membrane and RNA binding, that are conserved among orthologs of many positive-strand RNA viruses. Sequence alignments have placed these proteins in the SF3 helicase family, a subset of the AAA+ ATPase superfamily. A feature common to AAA+ proteins is the formation of oligomeric rings that are essential for their catalytic functions. Here we show that a recombinant protein, MBP-2C, in which maltose-binding protein was fused to 2C, formed soluble oligomers and that ATPase activity was restricted to oligomer-containing fractions from gel-filtration chromatography. The active fraction was visualized by negative-staining electron microscopy as ring-like particles composed of 5–8 protomers. This conclusion was confirmed by mass measurements obtained by scanning transmission electron microscopy. Mutation of amino acid residues in the 2C nucleotide-binding domain demonstrated that loss of the ability to bind or hydrolyze ATP did not affect oligomerization. Co-expression of active MBP-2C and inactive mutant proteins generated mixed oligomers that exhibited little ATPase activity, suggesting that incorporation of inactive subunits eliminates the function of the entire particle. Finally, deletion of the N-terminal 38 amino acids blocked oligomerization of the fusion protein and eliminated ATPase activity, despite retention of an unaltered nucleotide-binding domain. PMID:19520852

H2CO3(s): a new candidate for CO2 capture and sequestration.

PubMed

Tossell, J A

2009-04-01

To reduce the magnitude of anthropogenic global warming it is necessary to remove CO2(g) from the effluent streams of coal-fired power plants and to sequester the CO2 either as a liquid or by reaction with other compounds. A major difficulty in achieving this goal arises from the very weak acidity of CO2(g), causing it to react only incompletely with weak bases, although this weak interaction does provide a means for "stripping" the CO2 from the acid-base complex at high temperatures. Reaction with strong bases like Na0H yields more stable complexes, but massive amounts of chemical reactants would need to be purchased and chemical products like NaHCO3 then stored. However, when gas-phase CO2 reacts with the weak base water (or when bicarbonate reacts with strong acid) the unstable product monomeric "H2CO3" can be formed. The free energy required is about 16 kcal/mol in the gas phase and about 10 kcal/mol in aqueous solution. This energy can be supplied by particle or photon excitation and is only a small fraction ofthe energy released when a mole of CH4 is converted to a mole of CO2. Although this monomeric compound is highly unstable, its oligomers are considerably more stable, due to internal H-bonding, with free energies for the larger oligomers in the gas phase which are about 4 kcal/(mol of H2CO3) lower, only about 6 kcal/mol H2CO3 higher than the gas-phase combination of CO2 and H2O at room temperature. Also, at lower temperature the entropic penalty for the oligomer is less and oligomeric H2CO3 becomes stable around the sublimation temperature of dry ice. This indicates that it may be possible to capture gas-phase CO2 directly, using only cheap and abundant H2O as a reactant, and to store the resulting (H2CO3)n as a oligomeric solid at only moderately cold temperatures. These conclusions are based on quantum computations that accurately reproduce the structures, spectra, and stabilities of H2CO3 oligomers. Methods for producing and characterizing the H2CO3 oligomers are discussed. However, some aspects of the proposed scheme are quite speculative and will require additional investigation. Several important questions need to be answered before the feasibility of this procedure on a planetary scale can be assessed, particularly those involving the vapor pressure curve, heat of sublimation, density, and compressibility of (H2CO3)n.

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth

PubMed Central

Foley, Joseph; Hill, Shannon E.; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-01-01

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the entire cascade of aggregation intermediates formed along each pathway. PMID:24089713

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth

NASA Astrophysics Data System (ADS)

Foley, Joseph; Hill, Shannon E.; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-09-01

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the entire cascade of aggregation intermediates formed along each pathway.

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth.

PubMed

Foley, Joseph; Hill, Shannon E; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-09-28

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the entire cascade of aggregation intermediates formed along each pathway.

Isohelical DNA-Binding Oligomers: Antiviral Activity and Application for the Design of Nanostructured Devices

NASA Astrophysics Data System (ADS)

Gursky, Georgy; Nikitin, Alexei; Surovaya, Anna; Grokhovsky, Sergey; Andronova, Valeria; Galegov, Georgy

We performed a systematic search for new structural motifs isohelical to double-stranded DNA and found five motifs that can be used for the design and synthesis of new DNA-binding oligomers. Some of the DNA-binding oligomers can be equipped with fluorescence chromophores and metal-chelating groups and may serve as conductive wires in nano-scaled electric circuits. A series of new DNA-binding ligands were synthesized by a modular assembly of pyrrole carboxamides and novel pseudopeptides of the form (XY)n. Here, Y is a glycine residue; n is the degree of polymerization. X is an unusual amino acid residue containing a five-membered aromatic ring. Antiviral activity of bis-linked netropsin derivatives is studied. Bis-netropsins containing 15 and 31 lysine residues at the N-termini inhibit most effectively reproduction of the herpes virus type 1 in the Vero cell culture, including virus variants resistant to acyclovir and its analogues. Antiviral activity of bis-linked netropsin derivatives is correlated with their ability to interact with long clusters of AT-base pairs in the origin of replication of the viral DNA.

Labile conjugation of a hydrophilic drug to PLA oligomers to modify a drug delivery system: cephradin in a PLAGA matrix.

PubMed

Ustariz-Peyret, C; Coudane, J; Vert, M; Kaltsatos, V; Boisramené, B

2000-01-01

The physical entrapment of a hydrophilic drug within degradable microspheres is generally difficult because of poor entrapment yield and/or fast release, depending on the microsphere fabrication method. In order to counter the effects of drug hydrophilicity, it is proposed to covalently attach the drug to lactic acid oligomers, with the aim of achieving temporary hydrophobization and slower release controlled by the separation of the drug from the degradable link within the polymer matrix. This strategy was tested on microspheres of the antibiotic cephradin. As the prodrug form, the entrapment of the drug was almost quantitative. The prodrug did degrade in an aqueous medium, modelling body fluids, but cleavage did not occur at the drug-oligomer junction and drug molecules bearing two lactyl residual units were released. When the prodrug is entrapped within a PLAGA matrix, no release was observed within the experimental time period. However, data suggest that conjugation via a bond more sensitive to hydrolysis than the main chain PLA ester bonds should make the system work as desired.

Time-resolved studies define the nature of toxic IAPP intermediates, providing insight for anti-amyloidosis therapeutics

PubMed Central

Abedini, Andisheh; Plesner, Annette; Cao, Ping; Ridgway, Zachary; Zhang, Jinghua; Tu, Ling-Hsien; Middleton, Chris T; Chao, Brian; Sartori, Daniel J; Meng, Fanling; Wang, Hui; Wong, Amy G; Zanni, Martin T; Verchere, C Bruce; Raleigh, Daniel P; Schmidt, Ann Marie

2016-01-01

Islet amyloidosis by IAPP contributes to pancreatic β-cell death in diabetes, but the nature of toxic IAPP species remains elusive. Using concurrent time-resolved biophysical and biological measurements, we define the toxic species produced during IAPP amyloid formation and link their properties to induction of rat INS-1 β-cell and murine islet toxicity. These globally flexible, low order oligomers upregulate pro-inflammatory markers and induce reactive oxygen species. They do not bind 1-anilnonaphthalene-8-sulphonic acid and lack extensive β-sheet structure. Aromatic interactions modulate, but are not required for toxicity. Not all IAPP oligomers are toxic; toxicity depends on their partially structured conformational states. Some anti-amyloid agents paradoxically prolong cytotoxicity by prolonging the lifetime of the toxic species. The data highlight the distinguishing properties of toxic IAPP oligomers and the common features that they share with toxic species reported for other amyloidogenic polypeptides, providing information for rational drug design to treat IAPP induced β-cell death. DOI: http://dx.doi.org/10.7554/eLife.12977.001 PMID:27213520

Purification of an Exopolygalacturonase from Penicillium viridicatum RFC3 Produced in Submerged Fermentation.

PubMed

Gomes, Eleni; Leite, Rodrigo Simões Ribeiro; da Silva, Roberto; Silva, Dênis

2009-01-01

An exo-PG obtained from Penicillium viridicatum in submerged fermentation was purified to homogeneity. The apparent molecular weight of the enzyme was 92 kDa, optimum pH and temperature for activity were pH 5 and 50-55 degrees C. The exo-PG showed a profile of an exo-polygalacturonase, releasing galacturonic acid by hydrolysis of pectin with a high degree of esterification (D.E.). Ions Ca(2+) enhanced the stability of enzyme and its activity by 30%. The K(m) was 1.30 in absence of Ca(2+) and 1.16 mg mL(-1) in presence of this ion. In relation to the V(max) the presence of this ion increased from 1.76 to 2.07 mumol min(-1)mg(-1).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Xiangmei; Mort, Andrew

A comore » mmercial apple pectin was sequentially digested with the cloned enzymes endopolygalacturonase, galactanase, arabinofuranosidase, xylogalacturonase, and rhamnogalacturonan hydrolase. The rhamnogalacturonan hydrolase-generated oligosaccharides were separated by ultrafiltration, anion exchange, and size-exclusion chromatography. Fractions from the ion exchange chromatography were pooled, lyophilized, and screened by MALDI-TOF MS. An oligosaccharide (RGP14P3) was identified and its structure, α -D-Gal p A- ( 1 → 2 ) - α -L-Rha p - ( 1 → 4 ) - α -D-Gal p A- ( 1 → 2 ) - α -L-Rha p - ( 1 → 4 ) - α -D-Gal p A, determined by 1D and 2D NMR spectrometry. This oligosaccharide probably represents a direct connection between homogalacturonan and rhamnogalacturonan in pectin. Alternatively, it could indicate that the nonreducing end of rhamnogalacturonan starts with a galacturonic acid residue.« less

Component analysis and free radicals scavenging activity of Cicer arietinum L. husk pectin.

PubMed

Urias-Orona, Vania; Huerta-Oros, Joselina; Carvajal-Millán, Elizabeth; Lizardi-Mendoza, Jaime; Rascón-Chu, Agustin; Gardea, Alfonso A

2010-10-11

A pectin (CAP) was extracted from the husk of Cicer arietinum L. Monosaccharide analysis of CAP revealed the dominance of galacturonic acid and smaller amounts of galactose, arabinose, rhamnose, glucose, xylose and mannose. Viscosimetric analysis showed that the intrinsic viscosity ([η]) and the molecular weight (MW) of CAP were 296 mL/g and 105 kDa, respectively. The degree of esterification (DE = 10%) was determined by FTIR spectroscopy. CAP exhibited a dose-dependent free radical scavenging activity, as shown by its DPPH radical inhibition. At 1.0 mg/mL CAP exhibited a scavenging rate of 29% on DPPH radicals. The evaluation of antioxidant activity suggested that CAP had good potential for DPPH radical scavenging activity and should be explored as a novel potential antioxidant.

Structure of a pectin methylesterase from Yersinia enterocolitica.

PubMed

Boraston, Alisdair B; Abbott, D Wade

2012-02-01

Pectin methylesterases (PMEs) are family 8 carbohydrate esterases (CE8s) which remove the methyl group from methylesterified galacturonic acid (GalA) residues within pectin. Although the role of pectinases such as PMEs within dedicated phytopathogens has been well established, the significance of homologous enzymes found within the genomes of human enteropathogens remains to be determined. Presented here is the low-resolution (3.5 Å) structure of the CE8 from Yersinia enterocolitica (YeCE8). The high degree of structural conservation in the topology of the active-site cleft and catalytic apparatus that is shared with a characterized PME from a bacterial phytopathogen (i) indicates that YeCE8 is active on methylated pectin and (ii) highlights a more prominent role for pectin utilization in Yersinia than in other enteropathogenic species.

Electrode compositions

DOEpatents

Block, Jacob; Fan, Xiyun

1998-01-01

An electrode composition for use as an electrode in a non-aqueous battery system. The electrode composition contains an electrically active powder in a solid polymer and, as a dispersant, a C.sub.8 -C.sub.15 alkyl capped oligomer of a hexanoic acid that is electrochemically inert at 2.5-4.5 volts.

Electrode compositions

DOEpatents

Block, J.; Fan, X.

1998-10-27

An electrode composition is described for use as an electrode in a non-aqueous battery system. The electrode composition contains an electrically active powder in a solid polymer and, as a dispersant, a C{sub 8}-C{sub 15} alkyl capped oligomer of a hexanoic acid that is electrochemically inert at 2.5--4.5 volts.

Tau Oligomers as Pathogenic Seeds: Preparation and Propagation In Vitro and In Vivo.

PubMed

Gerson, Julia E; Sengupta, Urmi; Kayed, Rakez

2017-01-01

Tau oligomers have been shown to be the main toxic tau species in a number of neurodegenerative disorders. In order to study tau oligomers both in vitro and in vivo, we have established methods for the reliable preparation, isolation, and detection of tau oligomers. Methods for the seeding of tau oligomers, isolation of tau oligomers from tissue, and detection of tau oligomers using tau oligomer-specific antibodies by biochemical and immunohistochemical methods are detailed below.

Cacao pod husks as a source of low-methoxyl, highly acetylated pectins able to gel in acidic media.

PubMed

Vriesmann, Lúcia Cristina; de Oliveira Petkowicz, Carmen Lúcia

2017-08-01

Cacao pod husks, the main by-product from cocoa production, have been investigated for pectin isolation. In the present study, the rheological properties of two low-methoxyl (LM) pectins isolated from cacao pod husks using different extraction conditions were evaluated. One pectin was obtained from optimized conditions employing aqueous nitric acid as an extractant, and the other one was extracted with boiling water. Pectin gels (0.99% galacturonic acid equivalent, w/w) were prepared at pH 2.5-3.0 in the presence of 60% sucrose (w/w) and subjected to rheological analysis. Dynamic oscillatory experiments at 25°C indicated that better gels were obtained at the lowest pH (2.5). Steady shear measurements revealed a shear-thinning behavior. The apparent viscosities of the samples increased as pH decreased. Gelation with calcium ions was not observed for either of the highly acetylated LM pectins analyzed. The rheological analysis results showed that despite their high acetyl content, LM pectins extracted by different methods from cacao pod husks were able to form gels at low pH under reduced water activity, suggesting a possible application in acidic products. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural Analysis and Immuno-Stimulating Activity of an Acidic Polysaccharide from the Stems of Dendrobium nobile Lindl.

PubMed

Wang, Jun-Hui; Zuo, Shu-Rong; Luo, Jian-Ping

2017-04-10

Dendrobium nobile Lindl., an epiphytic herb distributed in the Southeast Asia, is used as a tonic and antipyretic herbal medicine in China. In this study, a water-soluble acidic heteropolysaccharide, DNP-W4, containing mannose, glucose, galactose, xylose, rhamnose, and galacturonic acid, in the molar ratios of 1.0:4.9:2.5:0.5:1.0:0.9, was obtained from the stems of Dendrobium nobile Lindl. Using methylation analysis, partial acid hydrolysis, pectolyase treatment, NMR, and ESI-MS, the structure of DNP-W4 was elucidated. The obtained data indicated that DNP-W4 was a complex heteropolysaccharide and possessed a backbone composed of (1→4)-linked β-d-Glcp, (1→6)-linked β-d-Glcp, and (1→6)-linked β-d-Galp, with substitutes at O-4/6 of Glcp residues and O-3 of Galp. The branches of DNP-W4 were composed of terminal Manp, (1→6)-linked β-d-Manp, (1→3)-linked β-d-Glcp, β-d-Glcp, β-d-Galp, (1→4)-linked α-d-GalAp, (1→2)-linked α-L-Rhap, and Xylp. DNP-W4 had little immunological activities, but its derivatives had immuno-stimulating activities to some extent.

Effect of heat-generated product from uronic acids on the physiological activities of microbial cells and its application.

PubMed

Aoyagi, Hideki; Ishii, Hideki; Ugwu, Charles U; Tanaka, Hideo

2008-07-01

Filtered samples of monogalacturonic (GA) and monoglucuronic acids (GL) that were prepared using millipore filter (pore size=0.2 microm) slightly inhibited the growth of Escherichia coli while the autoclaved (at 121 degrees C for 20 min) samples of GA and GL completely inhibited the growth of E. coli. The most effective substance generated upon autoclave treatment was isolated and characterized as trans-4,5-dihydroxy-2-cyclopenten-1-one (DHCP). The optimal conditions for DHCP generation were also established by autoclaving GA (pH 2.3) at 121 degrees C for 3h. DHCP completely inhibited the growth of E. coli. However, the growth of E. coli was restored when superoxide dismutase and catalase were added to the culture broth that contained DHCP. It was thought that DHCP might have induced the release of active oxygen, which resulted in the inhibition of microbial growth. In the case of gram-positive bacteria (Bacillus cereus, Bacillus subtilis and Staphylococcus aureus) and yeast (Saccharomyces cerevisiae and Candida brassicae), DHCP inhibited the cell growth. Based on our results, methods for preparation of food preservatives that contained pectin degraded products (oligo-galacturonic acid and monogalacturonic acid) and DHCP were developed. The preservatives were very effective in inhibiting the growth of E. coli and S. cerevisiae.

Characterization of gold kiwifruit pectin from fruit of different maturities and extraction methods.

PubMed

Yuliarti, Oni; Matia-Merino, Lara; Goh, Kelvin K T; Mawson, John; Williams, Martin A K; Brennan, Charles

2015-01-01

Studies on gold kiwifruit pectins are limited. In this work, the characterization of pectin isolated from two different stages of maturity of gold kiwifruit, namely early harvested fruit (EHF) and main harvested fruit (MHF) isolated by three methods (acid, water, enzymatic) was carried out. Pectins isolated from MHF were higher in galacturonic acid content (52-59% w/w) and weight-average molecular weights (Mw, 1.7-3.8 × 10(6)g/mol) compared with EHF pectins (29-49% w/w and 0.2-1.7 × 10(6)g/mol respectively). Enzymatic treatment gave the highest yield but lowest in Mw, viscosity and mechanical spectra for both maturities. The pectin of both maturities was classified as high-methoxyl pectin with the degree of esterification ranged from 82% to 90%. Water-extracted MHF pectin molecules had the highest RMS radius (182.7 nm) and Mw (3.75 × 10(6)g/mol). The water extraction method appeared to retain the native state of pectin molecules compared with acid and enzymatic extraction methods based on the Mw and viscosity data. Copyright © 2014 Elsevier Ltd. All rights reserved.

Purification and Biochemical and Kinetic Properties of an Endo-Polygalacturonase from the Industrial Fungus Aspergillus sojae.

PubMed

Fratebianchi, Dante; Cavello, Ivana Alejandra; Cavalitto, Sebastián Fernando

2017-01-01

An endo-polygalacturonase secreted by Aspergillus sojae was characterized after being purified to homogeneity from submerged cultures with orange peel as the sole carbon source by gel filtration and ion-exchange chromatographies. According to SDS-PAGE and analytical isoelectric focusing analyses, the enzyme presents a molecular weight of 47 kDa and pI value of 4.2. This enzyme exhibits considerable stability under highly acidic to neutral conditions (pH 1.5-6.5) and presents a half-life of 2 h at 50°C. Besides its activity towards pectin and polygalacturonic acid, the enzyme displays pectin-releasing activity, acting best in a pH range of 3.3-5.0. Thin-layer chromatographic analysis revealed that tri-galacturonate is the main enzymatic end product of polygalacturonic acid hydrolysis, indicating that it is an endo-polygalacturonase. The enzyme exhibits Michaelis-Menten kinetics, with KM and VMAX values of 0.134 mg/mL and 9.6 µmol/mg/min, respectively, and remained stable and active in the presence of SO2, ethanol, and various cations assayed except Hg2+. © 2017 S. Karger AG, Basel.

A polygalacturonase localized in the Golgi apparatus in Pisum sativum.

PubMed

Ohashi, Takao; Jinno, Jun; Inoue, Yoshiyuki; Ito, Shoko; Fujiyama, Kazuhito; Ishimizu, Takeshi

2017-09-01

Pectin is a plant cell wall constituent that is mainly composed of polygalacturonic acid (PGA), a linear α1,4-d-galacturonic acid (GalUA) backbone. Polygalacturonase (PG) hydrolyzes the α1,4-linkages in PGA. Nearly all plant PGs identified thus far are secreted as soluble proteins. Here we describe the microsomal PG activity in pea (Pisum sativum) epicotyls and present biochemical evidence that it was localized to the Golgi apparatus, where pectins are biosynthesized. The microsomal PG was purified, and it was enzymatically characterized. The purified enzyme showed maximum activity towards pyridylaminated oligogalacturonic acids with six degrees of polymerization (PA-GalUA6), with a Km value of 11 μM for PA-GalUA6. The substrate preference of the enzyme was complementary to that of PGA synthase. The main PG activity in microsomes was detected in the Golgi fraction by sucrose density gradient ultracentrifugation. The activity of the microsomal PG was lower in rapidly growing epicotyls, in contrast to the high expression of PGA synthase. The role of this PG in the regulation of pectin biosynthesis or plant growth is discussed. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Synthesis and characterization of L-lactide and polylactic acid (PLA) from L-lactic acid for biomedical applications

NASA Astrophysics Data System (ADS)

Rahmayetty, Sukirno, Prasetya, Bambang; Gozan, Misri

2017-02-01

Lactide is the monomer for the polymer polylactic acid (PLA) from lactic acid through polycondensation and depolymerization process. The properties of PLA strongly depend on the quality of the lactide monomer from which it is synthesized. Optical purity of lactide produced in depolymerization process confirmed to be L-lactide. The highest yield of crude lactide was 38.5% at temperature 210 °C with average molecular weight (Mn) of oligomer was 2389. Ring opening polymerization of lactide using Candida rugosa lipase as biocatalyst to PLLA synthesis has been achieved to generate useful biomedical materials free from heavy metal.

Left-handed helical preference in an achiral peptide chain is induced by an L-amino acid in an N-terminal type II β-turn.

PubMed

De Poli, Matteo; De Zotti, Marta; Raftery, James; Aguilar, Juan A; Morris, Gareth A; Clayden, Jonathan

2013-03-15

Oligomers of the achiral amino acid Aib adopt helical conformations in which the screw-sense may be controlled by a single N-terminal residue. Using crystallographic and NMR techniques, we show that the left- or right-handed sense of helical induction arises from the nature of the β-turn at the N terminus: the tertiary amino acid L-Val induces a left-handed type II β-turn in both the solid state and in solution, while the corresponding quaternary amino acid L-α-methylvaline induces a right-handed type III β-turn.

Acidic pH retards the fibrillization of human Islet Amyloid Polypeptide due to electrostatic repulsion of histidines.

PubMed

Li, Yang; Xu, Weixin; Mu, Yuguang; Zhang, John Z H

2013-08-07

The human Islet Amyloid Polypeptide (hIAPP) is the major constituent of amyloid deposits in pancreatic islets of type-II diabetes. IAPP is secreted together with insulin from the acidic secretory granules at a low pH of approximately 5.5 to the extracellular environment at a neutral pH. The increased accumulation of extracellular hIAPP in diabetes indicates that changes in pH may promote amyloid formation. To gain insights and underlying mechanisms of the pH effect on hIAPP fibrillogenesis, all-atom molecular dynamics simulations in explicit solvent model were performed to study the structural properties of five hIAPP protofibrillar oligomers, under acidic and neutral pH, respectively. In consistent with experimental findings, simulation results show that acidic pH is not conducive to the structural stability of these oligomers. This provides a direct evidence for a recent experiment [L. Khemtemourian, E. Domenech, J. P. F. Doux, M. C. Koorengevel, and J. A. Killian, J. Am. Chem. Soc. 133, 15598 (2011)], which suggests that acidic pH inhibits the fibril formation of hIAPP. In addition, a complementary coarse-grained simulation shows the repulsive electrostatic interactions among charged His18 residues slow down the dimerization process of hIAPP by twofold. Besides, our all-atom simulations reveal acidic pH mainly affects the local structure around residue His18 by destroying the surrounding hydrogen-bonding network, due to the repulsive interactions between protonated interchain His18 residues at acidic pH. It is also disclosed that the local interactions nearby His18 operating between adjacent β-strands trigger the structural transition, which gives hints to the experimental findings that the rate of hIAPP fibril formation and the morphologies of the fibrillar structures are strongly pH-dependent.

Inactivation of lipoprotein lipase occurs on the surface of THP-1 macrophages where oligomers of angiopoietin-like protein 4 are formed.

PubMed

Makoveichuk, Elena; Sukonina, Valentina; Kroupa, Olessia; Thulin, Petra; Ehrenborg, Ewa; Olivecrona, Thomas; Olivecrona, Gunilla

2012-08-24

Lipoprotein lipase (LPL) hydrolyzes triglycerides in plasma lipoproteins causing release of fatty acids for metabolic purposes in muscles and adipose tissue. LPL in macrophages in the artery wall may, however, promote foam cell formation and atherosclerosis. Angiopoietin-like protein (ANGPTL) 4 inactivates LPL and ANGPTL4 expression is controlled by peroxisome proliferator-activated receptors (PPAR). The mechanisms for inactivation of LPL by ANGPTL4 was studied in THP-1 macrophages where active LPL is associated with cell surfaces in a heparin-releasable form, while LPL in the culture medium is mostly inactive. The PPARδ agonist GW501516 had no effect on LPL mRNA, but increased ANGPTL4 mRNA and caused a marked reduction of the heparin-releasable LPL activity concomitantly with accumulation of inactive, monomeric LPL in the medium. Intracellular ANGPTL4 was monomeric, while dimers and tetramers of ANGPTL4 were present in the heparin-releasable fraction and medium. GW501516 caused an increase in the amount of ANGPTL4 oligomers on the cell surface that paralleled the decrease in LPL activity. Actinomycin D blocked the effects of GW501516 on ANGPTL4 oligomer formation and prevented the inactivation of LPL. Antibodies against ANGPTL4 interfered with the inactivation of LPL. We conclude that inactivation of LPL in THP-1 macrophages primarily occurs on the cell surface where oligomers of ANGPTL4 are formed. Copyright © 2012 Elsevier Inc. All rights reserved.

Supplementation with xylanase and β-xylosidase to reduce xylo-oligomer and xylan inhibition of enzymatic hydrolysis of cellulose and pretreated corn stover

PubMed Central

2011-01-01

Background Hemicellulose is often credited with being one of the important physical barriers to enzymatic hydrolysis of cellulose, and acts by blocking enzyme access to the cellulose surface. In addition, our recent research has suggested that hemicelluloses, particularly in the form of xylan and its oligomers, can more strongly inhibit cellulase activity than do glucose and cellobiose. Removal of hemicelluloses or elimination of their negative effects can therefore become especially pivotal to achieving higher cellulose conversion with lower enzyme doses. Results In this study, cellulase was supplemented with xylanase and β-xylosidase to boost conversion of both cellulose and hemicellulose in pretreated biomass through conversion of xylan and xylo-oligomers to the less inhibitory xylose. Although addition of xylanase and β-xylosidase did not necessarily enhance Avicel hydrolysis, glucan conversions increased by 27% and 8% for corn stover pretreated with ammonia fiber expansion (AFEX) and dilute acid, respectively. In addition, adding hemicellulase several hours before adding cellulase was more beneficial than later addition, possibly as a result of a higher adsorption affinity of cellulase and xylanase to xylan than glucan. Conclusions This key finding elucidates a possible mechanism for cellulase inhibition by xylan and xylo-oligomers and emphasizes the need to optimize the enzyme formulation for each pretreated substrate. More research is needed to identify advanced enzyme systems designed to hydrolyze different substrates with maximum overall enzyme efficacy. PMID:21702938

Influence of Picual olive ripening on virgin olive oil alteration and stability during potato frying.

PubMed

Olivero-David, Raul; Mena, Carmen; Pérez-Jimenez, M Angeles; Sastre, Blanca; Bastida, Sara; Márquez-Ruiz, Gloria; Sánchez-Muniz, Francisco J

2014-12-03

Ripening modifies oil attributes and composition. However, the influence of olive ripening on virgin olive oil (VOO) thermal oxidative stability on food-frying has not been studied yet. Oils from Picual olives of low (VOO1), medium (VOO2), and high (VOO3) ripeness were obtained, and their thermal oxidative stability during 40 potato-fryings was tested. Unused VOO1 showed higher antioxidant content and oxidative stability than VOO2 and VOO3. Polar compounds (PC), oligomers, and altered fatty acid methyl esters (polar-FAME) increased, whereas linoleic acid, polyphenols, and tocopherols decreased in the three VOOs through frying. The alteration was lower in VOO1, followed by VOO2 (0.105, 0.117, and 0.042 g/100 g oil less of PC, oligomers and polar-FAME per frying, respectively, in VOO1 than in VOO3). In conclusion, VOO obtained from low-ripeness Picual olives should be preferred when frying fresh-potatoes due to its higher thermal and oxidative stability, permitting a higher number of potato-frying uses.

A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal† †Electronic supplementary information (ESI) available. CCDC X-ray crystal data for 1a and 1b have been deposited with the CCDC, deposition numbers 1518806 and 1518807. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc05474a Click here for additional data file. Click here for additional data file.

PubMed Central

Tomsett, Michael; Maffucci, Irene; Le Bailly, Bryden A. F.; Byrne, Liam; Bijvoets, Stefan M.; Lizio, M. Giovanna; Raftery, James; Butts, Craig P.; Webb, Simon J.; Contini, Alessandro

2017-01-01

Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion. PMID:28451368

Evidence of Liquid Crystal-Assisted Abiotic Ligation of Nucleic Acids

NASA Astrophysics Data System (ADS)

Fraccia, Tommaso P.; Zanchetta, Giuliano; Rimoldi, Valeria; Clark, Noel A.; Bellini, Tommaso

2015-06-01

The emergence of early life must have been marked by the appearance in the prebiotic era of complex molecular structures and systems, motivating the investigation of conditions that could not only facilitate appropriate chemical synthesis, but also provide the mechanisms of molecular selection and structural templating necessary to pilot the complexification toward specific molecular patterns. We recently proposed and demonstrated that these functions could be afforded by the spontaneous ordering of ultrashort nucleic acids oligomers into Liquid Crystal (LC) phases. In such supramolecular assemblies, duplex-forming oligomers are held in average end-to-end contact to form chemically discontinuous but physically continuous double helices. Using blunt ended duplexes, we found that LC formation could both provide molecular selection mechanisms and boost inter-oligomer ligation. This paper provides an essential extension to this notion by investigating the catalytic effects of LC ordering in duplexes with mutually interacting overhangs. Specifically, we studied the influence of LC ordering of 5'-hydroxy-3'-phosphate partially self-complementary DNA 14mers with 3'-CG sticky-ends, on the efficiency of non-enzymatic ligation reaction induced by water-soluble carbodiimide EDC as condensing agent. We investigated the ligation products in mixtures of DNA with poly-ethylene glycol (PEG) at three PEG concentrations at which the system phase separates creating DNA-rich droplets that organize into isotropic, nematic LC and columnar LC phases. We observe remarkable LC-enhanced chain lengthening, and we demonstrate that such lengthening effectively promotes and stabilizes LC domains, providing the kernel of a positive feedback cycle by which LC ordering promotes elongation, in turn stabilizing the LC ordering.

High Boron-loaded DNA-Oligomers as Potential Boron Neutron Capture Therapy and Antisense Oligonucleotide Dual-Action Anticancer Agents.

PubMed

Kaniowski, Damian; Ebenryter-Olbińska, Katarzyna; Sobczak, Milena; Wojtczak, Błażej; Janczak, Sławomir; Leśnikowski, Zbigniew J; Nawrot, Barbara

2017-08-23

Boron cluster-modified therapeutic nucleic acids with improved properties are of interest in gene therapy and in cancer boron neutron capture therapy (BNCT). High metallacarborane-loaded antisense oligonucleotides (ASOs) targeting epidermal growth factor receptor (EGFR) were synthesized through post-synthetic Cu (I)-assisted "click" conjugation of alkyne-modified DNA-oligonucleotides with a boron cluster alkyl azide component. The obtained oligomers exhibited increased lipophilicity compared to their non-modified precursors, while their binding affinity to complementary DNA and RNA strands was slightly decreased. Multiple metallacarborane residues present in the oligonucleotide chain, each containing 18 B-H groups, enabled the use of IR spectroscopy as a convenient analytical method for these oligomers based on the diagnostic B-H signal at 2400-2650 cm -1 . The silencing activity of boron cluster-modified ASOs used at higher concentrations was similar to that of unmodified oligonucleotides. The screened ASOs, when used in low concentrations (up to 50 μM), exhibited pro-oxidative properties by inducing ROS production and an increase in mitochondrial activities in HeLa cells. In contrast, when used at higher concentrations, the ASOs exhibited anti-oxidative properties by lowering ROS species levels. In the HeLa cells (tested in the MTT assay) treated (without lipofectamine) or transfected with the screened compounds, the mitochondrial activity remained equal to the control level or only slightly changed (±30%). These findings may be useful in the design of dual-action boron cluster-modified therapeutic nucleic acids with combined antisense and anti-oxidant properties.

Membrane omega-3 fatty acids modulate the oligomerisation kinetics of adenosine A2A and dopamine D2 receptors

NASA Astrophysics Data System (ADS)

Guixà-González, Ramon; Javanainen, Matti; Gómez-Soler, Maricel; Cordobilla, Begoña; Domingo, Joan Carles; Sanz, Ferran; Pastor, Manuel; Ciruela, Francisco; Martinez-Seara, Hector; Selent, Jana

2016-01-01

Membrane levels of docosahexaenoic acid (DHA), an essential omega-3 polyunsaturated fatty acid (ω-3 PUFA), are decreased in common neuropsychiatric disorders. DHA modulates key cell membrane properties like fluidity, thereby affecting the behaviour of transmembrane proteins like G protein-coupled receptors (GPCRs). These receptors, which have special relevance for major neuropsychiatric disorders have recently been shown to form dimers or higher order oligomers, and evidence suggests that DHA levels affect GPCR function by modulating oligomerisation. In this study, we assessed the effect of membrane DHA content on the formation of a class of protein complexes with particular relevance for brain disease: adenosine A2A and dopamine D2 receptor oligomers. Using extensive multiscale computer modelling, we find a marked propensity of DHA for interaction with both A2A and D2 receptors, which leads to an increased rate of receptor oligomerisation. Bioluminescence resonance energy transfer (BRET) experiments performed on living cells suggest that this DHA effect on the oligomerisation of A2A and D2 receptors is purely kinetic. This work reveals for the first time that membrane ω-3 PUFAs play a key role in GPCR oligomerisation kinetics, which may have important implications for neuropsychiatric conditions like schizophrenia or Parkinson’s disease.

Acetylene terminated aspartimides and resins therefrom

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor); Havens, Stephen J. (Inventor)

1989-01-01

Acetylene terminated aspartimides are prepared using two methods. In the first, an amino-substituted aromatic acetylene is reacted with an aromatic bismaleimide in a solvent of glacial acetic acid and/or m-cresol. In the second method, an aromatic diamine is reacted with an ethynyl containing maleimide, such an N-(3-ethynyl phenyl) maleimide, in a solvent of glacial acetic acid and/or m-cresol. In addition, acetylene terminated aspartimides are blended with various acetylene terminated oligomers and polymers to yield composite materials exhibiting improved mechanical properties.

N-(3-ethynylphenyl)maleimide

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor); Havens, Stephen J. (Inventor)

1990-01-01

Acetylene terminated aspartimides are prepared using two methods. In the first, an amino-substituted aromatic acetylene is reacted with an aromatic bismaleimide in a solvent of glacial acetic acid and/or m-cresol. In the second method, an aromatic diamine is reacted with an ethynyl containing maleimide, such as N-(3-ethynylphenyl) maleimide, in a solvent of glacial acetic acid and/or m-cresol. In addition, acetylene terminated aspartimides are blended with various acetylene terminated oligomers and polymers to yield composite materials exhibiting improved mechanical properties.

Surface monolayers of well-defined amphiphilic block copolymer composed of poly(acrylic acid) or poly(oxyethylene) and poly(styrene). Interpolymer complexation at the air-water interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niwa, Masazo; Hayashi, Takehiro; Higashi, Nobuyuki

1990-01-01

Amphiphilic block polymers (2,3) composed of poly(acrylic acid) (PAA) or poly(oxyethylene) (POE) and chain length controlled poly(styrene) (PSt) have been prepared by using a catalytic system of tribromomethyl-terminated oligomer and manganese carbonyl. All the amphiphilic materials formed well-behaved surface monolayers, and the II-A curves for them expanded systematically with an increase of the PSt chain length.

Pentavalent Bismuth-Mediated Glycosylation Methods to Activate Sialic and Uronic Acids and the Incorporation of Sialic Acids Into Insulin

NASA Astrophysics Data System (ADS)

Kabotso, Daniel Elorm Kwame

The negative charge at physiological pH of carboxylic acid-containing monosaccharides modulate the properties of many natural biomolecules such as oligosaccharides and glycoconjugates. Unfortunately, these altered electronic properties also make the incorporation of such acidic sugars more challenging as compared to the more commonly studied neutral sugars. Herein are reported the first demonstration of glycosylation reactions mediated by triphenylbis(1,1,1-trifluoromethanesulfonato)-bismuth with thioglycosides containing carboxylic acid substituents protected as esters. Unlike with many neutral sugar substrates, the addition of 1-propanethiol to the reactions proved critical to obtaining good yields of the desired glycosylation products using sialic acid, galacturonic acid, and glucuronic acid. The protocol was demonstrated to be amenable to automation using a liquid-handling platform. The consequences of artificially incorporating carboxylic-acid-containing sugars into proteins were tested by the design of a linker containing 1 to 4 sialic acids--a sugar found in many human proteins and brain tissues--that was attached via reductive amination of trityl thiopropylaldehyde at the phenyl alanine terminal end of the protein insulin produced through solid-phase peptide synthesis. Removal of the trityl group with neat trifluoroacetic acid furnished the thiol-free modified insulin that was ligated via a disulfide bond to the peptide scaffold bearing acetyl protected sialic acids. A 14-15% ammonium hydroxide solution was found to be effective in deprotecting the acetyl groups without degradation of the disulfide bond. In addition to maintaining the potency and bioactivity of insulin, the sialic acid-containing linker rendered insulin more resistant to aggregation due to heat and mechanical agitation compared to the unmodified protein.

Biomass pre-treatment for co-production of high-concentration C5- and C6-carbohydrates and their derivatives

DOEpatents

Dumesic, James A.; Martin Alonso, David; Luterbacher, Jeremy Scott

2016-06-07

Described is a method of processing biomass to separate it into a liquid fraction enriched in solubilized C5-sugar-containing oligomers and C-5 sugar monomers and a solid fraction enriched in substantially insoluble cellulose and C6-sugar-containing oligomers. The method includes the steps of reacting biomass with a solvent system comprising water, at least one lactone, or at least one furan, or at least one cyclic ether, and at least one acid, for a time and at a temperature to yield the liquid and solid fractions. The liquid and solid fractions may then be separated. Gamma-valeroloactone is a preferred lactone for use in the solvent system. Tetrahydrofuran is a preferred furan species for use in the solvent system.

Efficacy of peptide nucleic acid and selected conjugates against specific cellular pathologies of amyotrophic lateral sclerosis.

PubMed

Browne, Elisse C; Parakh, Sonam; Duncan, Luke F; Langford, Steven J; Atkin, Julie D; Abbott, Belinda M

2016-04-01

Cellular studies have been undertaken on a nonamer peptide nucleic acid (PNA) sequence, which binds to mRNA encoding superoxide dismutase 1, and a series of peptide nucleic acids conjugated to synthetic lipophilic vitamin analogs including a recently prepared menadione (vitamin K) analog. Reduction of both mutant superoxide dismutase 1 inclusion formation and endoplasmic reticulum stress, two of the key cellular pathological hallmarks in amyotrophic lateral sclerosis, by two of the prepared PNA oligomers is reported for the first time. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

Assessment of configurations and chemistries of bridged nucleic acids-containing oligomers as external guide sequences: a methodology for inhibition of expression of antibiotic resistance genes

PubMed Central

Jackson, Alexis; Jani, Saumya; Davies-Sala, Carol; Soler-Bistué, Alfonso J. C.; Zorreguieta, Angeles; Tolmasky, Marcelo E.

2016-01-01

External guide sequences (EGSs) are short antisense oligoribonucleotides that elicit RNase P-mediated cleavage of a target mRNA, which results in inhibition of gene expression. EGS technology is used to inhibit expression of a wide variety of genes, a strategy that may lead to development of novel treatments of numerous diseases, including multidrug-resistant bacterial and viral infections. Successful development of EGS technology depends on finding nucleotide analogs that resist degradation by nucleases present in biological fluids and the environment but still elicit RNase P-mediated degradation when forming a duplex with a target mRNA. Previous results suggested that locked nucleic acids (LNA)/DNA chimeric oligomers have these properties. LNA are now considered the first generation of compounds collectively known as bridged nucleic acids (BNAs) – modified ribonucleotides that contain a bridge at the 2ʹ,4ʹ-position of the ribose. LNA and the second-generation BNA, known as BNANC, differ in the chemical nature of the bridge. Chimeric oligomers containing LNA or BNANC and deoxynucleotide monomers in different configurations are nuclease resistant and could be excellent EGS compounds. However, not all configurations may be equally active as EGSs. RNase P cleavage assays comparing LNA/DNA and BNANC/DNA chimeric oligonucleotides that share identical nucleotide sequence but with different configurations were carried out using as target the amikacin resistance aac(6ʹ)-Ib mRNA. LNA/DNA gapmers with 5 and 3/4 LNA residues at the 5ʹ- and 3ʹ-ends, respectively, were the most efficient EGSs while all BNANC/DNA gapmers showed very poor activity. When the most efficient LNA/DNA gapmer was covalently bound to a cell-penetrating peptide, the hybrid compound conserved the EGS activity as determined by RNase P cleavage assays and reduced the levels of resistance to amikacin when added to Acinetobacter baumannii cells in culture, an indication of cellular uptake and biological activity. PMID:27857983

Functional Diversity of Isoamylase Oligomers: The ISA1 Homo-Oligomer Is Essential for Amylopectin Biosynthesis in Rice Endosperm1[W][OA

PubMed Central

Utsumi, Yoshinori; Utsumi, Chikako; Sawada, Takayuki; Fujita, Naoko; Nakamura, Yasunori

2011-01-01

Rice (Oryza sativa) endosperm has two isoamylase (ISA) oligomers, ISA1 homo-oligomer and ISA1-ISA2 hetero-oligomer. To examine their contribution to starch synthesis, expression of the ISA1 or ISA2 gene was differently regulated in various transgenic plants. Although suppression of ISA2 gene expression caused the endosperm to have only the homo-oligomer, no significant effects were detected on the starch phenotypes. In contrast, ISA2 overexpression led to endosperm having only the hetero-oligomer, and starch synthesis in the endosperm was drastically impaired, both quantitatively and qualitatively, because the starch was devoid of typical starch features, such as thermal and x-ray diffraction properties, and water-soluble highly branched maltodextrins were accumulated. In the ISA2 overexpressed line, about 60% to 70% of the ISA1-ISA2 hetero-oligomer was bound to starch, while the ISA homo- and hetero-oligomers from the wild type were mostly present in the soluble form at the early milking stage of the endosperm. Detailed analysis of the relative amounts of homo- and hetero-oligomers in various lines also led us to the conclusion that the ISA1 homo-oligomer is essential, but not the ISA1-ISA2 oligomer, for starch production in rice endosperm. The relative amounts of ISA1 and ISA2 proteins were shown to determine the ratio of both oligomers and the stoichiometry of both ISAs in the hetero-oligomer. It was noted when compared with the homo-oligomer that all the hetero-oligomers from rice endosperm and leaf and potato (Solanum tuberosum) tuber were much more stable at 40°C. This study provides substantial data on the structural and functional diversity of ISA oligomers between plant tissues and species. PMID:21436381

Purification of an Exopolygalacturonase from Penicillium viridicatum RFC3 Produced in Submerged Fermentation

PubMed Central

Gomes, Eleni; Leite, Rodrigo Simões Ribeiro; da Silva, Roberto; Silva, Dênis

2009-01-01

An exo-PG obtained from Penicillium viridicatum in submerged fermentation was purified to homogeneity. The apparent molecular weight of the enzyme was 92 kDa, optimum pH and temperature for activity were pH 5 and 50–55°C. The exo-PG showed a profile of an exo-polygalacturonase, releasing galacturonic acid by hydrolysis of pectin with a high degree of esterification (D.E.). Ions Ca2+ enhanced the stability of enzyme and its activity by 30%. The K m was 1.30 in absence of Ca2+ and 1.16 mg mL−1 in presence of this ion. In relation to the V max the presence of this ion increased from 1.76 to 2.07 μmol min−1mg−1. PMID:20148174

Structure of a Rhamnogalacturonan Fragment from Apple Pectin: Implications for Pectin Architecture

DOE PAGES

Wu, Xiangmei; Mort, Andrew

2014-01-01

A comore » mmercial apple pectin was sequentially digested with the cloned enzymes endopolygalacturonase, galactanase, arabinofuranosidase, xylogalacturonase, and rhamnogalacturonan hydrolase. The rhamnogalacturonan hydrolase-generated oligosaccharides were separated by ultrafiltration, anion exchange, and size-exclusion chromatography. Fractions from the ion exchange chromatography were pooled, lyophilized, and screened by MALDI-TOF MS. An oligosaccharide (RGP14P3) was identified and its structure, α -D-Gal p A- ( 1 → 2 ) - α -L-Rha p - ( 1 → 4 ) - α -D-Gal p A- ( 1 → 2 ) - α -L-Rha p - ( 1 → 4 ) - α -D-Gal p A, determined by 1D and 2D NMR spectrometry. This oligosaccharide probably represents a direct connection between homogalacturonan and rhamnogalacturonan in pectin. Alternatively, it could indicate that the nonreducing end of rhamnogalacturonan starts with a galacturonic acid residue.« less

Proteus mirabilis RMS 203 as a new representative of the O13 Proteus serogroup.

PubMed

Palusiak, Agata; Siwińska, Małgorzata; Zabłotni, Agnieszka

2015-01-01

The unique feature of some Proteus O-polysaccharides is occurrence of an amide of galacturonic acid with N(ε)-[(S/R)-1-Carboxyethyl]-L-lysine, GalA6(2S,8S/R-AlaLys). The results of the serological studies presented here, with reference to known O-antigens structures suggest that GalA6(2S,8S/R-AlaLys) or 2S,8R-AlaLys contribute to cross-reactions of O13 Proteus antisera, and Proteeae LPSs. It was also revealed that the Proteus mirabilis RMS 203 strain can be classified into the O13 serogroup, represented so far by two strains: Proteus mirabilis 26/57 and Proteus vulgaris 8344. The O13 LPS is a serologically important antigen with a fragment common to LPSs of different species in the Proteeae tribe.

Anatomical, chemical, and biochemical characterization of cladodes from prickly pear [Opuntia ficus-indica (L.) Mill.].

PubMed

Ginestra, Giovanna; Parker, Mary L; Bennett, Richard N; Robertson, Jim; Mandalari, Giuseppina; Narbad, Arjan; Lo Curto, Rosario B; Bisignano, Giuseppe; Faulds, Craig B; Waldron, Keith W

2009-11-11

Opuntia ficus-indica cladodes represent the green stem of the plant and are generally used as animal feed or disposed of in landfills. The present work investigated the anatomical and chemical composition of Opuntia cladodes, which form the basis of their pharmacological effects. Glucose and galacturonic acid were the main sugars of Opuntia cladodes, whereas high-performance liquid chromatography (HPLC) analysis showed the presence of mainly kaempherol and isorhamnetin glycosides (glucoside and rhamnoside). The presence of high amounts of calcium oxalate crystals was demonstrated by light microscopy on fresh and lyophilized cladodes. No antimicrobial activity was observed even after enzymatic treatment. O. ficus-indica cladodes may retain material tightly associated with cell-wall components, and this property will have the potential to greatly reduce the bioavailability of bioactive compounds.

Structure of a pectin methylesterase from Yersinia enterocolitica

PubMed Central

Boraston, Alisdair B.; Abbott, D. Wade

2012-01-01

Pectin methylesterases (PMEs) are family 8 carbohydrate esterases (CE8s) which remove the methyl group from methylesterified galacturonic acid (GalA) residues within pectin. Although the role of pectinases such as PMEs within dedicated phytopathogens has been well established, the significance of homologous enzymes found within the genomes of human enteropathogens remains to be determined. Presented here is the low-resolution (3.5 Å) structure of the CE8 from Yersinia enterocolitica (YeCE8). The high degree of structural conservation in the topology of the active-site cleft and catalytic apparatus that is shared with a characterized PME from a bacterial phytopathogen (i) indicates that YeCE8 is active on methylated pectin and (ii) highlights a more prominent role for pectin utilization in Yersinia than in other enteropathogenic species. PMID:22297983

Identification and characterisation of water and alkali soluble oligosaccharides from hazelnut skin (Corylus avellana L.).

PubMed

Montella, Rosa; Coïsson, Jean Daniel; Travaglia, Fabiano; Locatelli, Monica; Bordiga, Matteo; Meyrand, Mickael; Barile, Daniela; Arlorio, Marco

2013-10-15

Hazelnut skins are a good example of agricultural by-product with the potential to become a valuable source of functional ingredients. In this work, the fibre from hazelnut skins was extracted by using water and alkali solution and characterised by a suite of analytical tools (MALDI-FTICR, nano LC-Chip-Q-ToF and gas chromatography). Over thirty complex free oligosaccharides, composed mainly of galacturonic acid and N-acetylgalactosamine, were characterised for the first time in the present study. Their concentration ranged between 16 and 34mg per g of extract. The oligosaccharides isolated from this agricultural by-product are mainly hexose oligosaccharides (potentially galacto-oligosaccharides,) and xyloglucans. The identified composition could justify the bioactive activity of the extracts, namely prebiotic activity, previously demonstrated. Copyright © 2013 Elsevier Ltd. All rights reserved.

Extraction Optimization, Purification and Physicochemical Properties of Polysaccharides from Gynura medica.

PubMed

Li, Fengwei; Gao, Jian; Xue, Feng; Yu, Xiaohong; Shao, Tao

2016-03-23

Extraction of polysaccharides from Gynura medica (GMPs) was optimized by response surface methodology (RSM). A central composition design including three parameters, namely extraction temperature (X₁), ratio of water to raw material (X₂) and extraction time (X₃), was used. The best conditions were extraction temperature of 91.7 °C, extraction time of 4.06 h and ratio of water to raw material of 29.1 mL/g. Under the optimized conditions, the yield of GMPs was 5.56%, which was similar to the predicted polysaccharides yield of 5.66%. A fraction named GMP-1 was obtained after isolation and purification by DEAE-52 and Sephadex G-100 gel chromatography, respectively. GMP-1, with a molecular weight of 401 kDa, mainly consisted of galacturonic acid (GalA), xylose (Xyl), glucose (Glu). Infrared spectroscopy was used to characterize the major functional groups of GMP-1 and the results indicated that it was an acidic polysaccharide. The antioxidant and α-glucosidase inhibitory activities of GMPs and GMP-1 were determined in vitro. The results indicated that GMPs and GMP-1 show potential for use in functional foods or medicines.

Combined action of the major secreted exo- and endopolygalacturonases is required for full virulence of Fusarium oxysporum.

PubMed

Bravo Ruiz, Gustavo; Di Pietro, Antonio; Roncero, M Isabel G

2016-04-01

The genome of the tomato pathogen Fusarium oxysporum f. sp. lycopersici encodes eight different polygalacturonases (PGs): four endoPGs and four exoPGs. Quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) revealed that endoPGs pg1 and pg5 and exoPGs pgx4 and pgx6 are expressed at significant levels during growth on citrus pectin, polygalacturonic acid or the monomer galacturonic acid, as well as during the infection of tomato plants. The remaining PG genes exhibit low expression levels under all the conditions tested. Secreted PG activity was decreased significantly during growth on pectin in the single deletion mutants lacking either pg1 or pgx6, as well as in the double mutant. Although the single deletion mutants did not display a significant virulence reduction on tomato plants, the Δpg1Δpgx6 double mutant was significantly attenuated in virulence. The combined action of exoPGs and endoPGs is thus essential for plant infection by the vascular wilt fungus F. oxysporum. © 2015 BSPP and John Wiley & Sons Ltd.

Further analysis of the structure and immunological activity of an RG-I type pectin from Panax ginseng.

PubMed

Zhang, Xu; Li, Shanshan; Sun, Lin; Ji, Li; Zhu, Jingjing; Fan, Yuying; Tai, Guihua; Zhou, Yifa

2012-06-20

In this paper, we further analysed the structure of a type I rhamnogalacturonan (RG-I) pectin (WGPA-2-RG) fractionated from ginseng polysaccharides. Methylation and periodate oxidation analyses showed that WGPA-2-RG has a backbone consisting of alternating rhamnose (Rha) and galacturonic acid (GalA) residues and side chains consisting of type II arabinogalactan (AG-II). Partial acidic hydrolysis for 6h completely removed arabinose (Ara), partial galactose (Gal), but little GalA and Rha. During partial hydrolysis, the molecular weight of WGPA-2-RG decreased smoothly, suggesting that the Ara and cleavable Gal residues exist on the surface of the molecule, while GalA and Rha residues exist in the core of the molecule. The bioactivity assay showed that the arabinogalactan side chains of WGPA-2-RG are essential structures for stimulating NO secretion and lymphocyte proliferation. However, removal of the Ara and Gal residues through hydrolysis did not appreciably affect the ability of WGPA-2-RG to enhance macrophage phagocytosis. Copyright © 2012 Elsevier Ltd. All rights reserved.

A Novel Acid-Stable Endo-Polygalacturonase from Penicillium oxalicum CZ1028: Purification, Characterization, and Application in the Beverage Industry.

PubMed

Cheng, Zhong; Chen, Dong; Lu, Bo; Wei, Yutuo; Xian, Liang; Li, Yi; Luo, Zhenzhen; Huang, Ribo

2016-06-28

Acidic endo-polygalacturonases are the major part of pectinase preparations and extensively applied in the clarification of fruits juice, vegetables extracts, and wines. However, most of the reported fungal endo-polygalacturonases are active and stable under narrow pH range and low temperatures. In this study, an acidic endo-polygalacturonase (EPG4) was purified and characterized from a mutant strain of Penicillium oxalicum. The N-terminal amino acid sequence of EPG4 (ATTCTFSGSNGAASASKSQT) was different from those of reported endopolygalacturonases. EPG4 displayed optimal pH and temperature at 5.0 and 60-70°C towards polygalacturonic acid (PGA), respectively, and was notably stable at pH 2.2-7.0. When tested against pectins, EPG4 showed enzyme activity over a broad acidic pH range (>15.0% activity at pH 2.2-6.0 towards citrus pectin; and >26.6% activity at pH 2.2-7.0 towards apple pectin). The Km and Vmax values were determined as 1.27 mg/ml and 5,504.6 U/mg, respectively. The enzyme hydrolyzed PGA in endo-manner, releasing oligo-galacturonates from PGA, as determined by TLC. Addition of EPG4 (3.6 U/ml) significantly reduced the viscosity (by 42.4%) and increased the light transmittance (by 29.5%) of the papaya pulp, and increased the recovery (by 24.4%) of the papaya extraction. All of these properties make the enzyme a potential application in the beverage industry.

Stabilization, Characterization, and Selective Removal of Cystatin C Amyloid Oligomers*

PubMed Central

Östner, Gustav; Lindström, Veronica; Hjort Christensen, Per; Kozak, Maciej; Abrahamson, Magnus; Grubb, Anders

2013-01-01

The pathophysiological process in amyloid disorders usually involves the transformation of a functional monomeric protein via potentially toxic oligomers into amyloid fibrils. The structure and properties of the intermediary oligomers have been difficult to study due to their instability and dynamic equilibrium with smaller and larger species. In hereditary cystatin C amyloid angiopathy, a cystatin C variant is deposited in arterial walls and cause brain hemorrhage in young adults. In the present investigation, we use redox experiments of monomeric cystatin C, stabilized against domain swapping by an intramolecular disulfide bond, to generate stable oligomers (dimers, trimers, tetramers, decamers, and high molecular weight oligomers). These oligomers were characterized concerning size by gel filtration, polyacrylamide gel electrophoresis, and mass spectrometry, shape by electron and atomic force microscopy, and, function by assays of their capacity to inhibit proteases. The results showed the oligomers to be highly ordered, domain-swapped assemblies of cystatin C and that the oligomers could not build larger oligomers, or fibrils, without domain swapping. The stabilized oligomers were used to induce antibody formation in rabbits. After immunosorption, using immobilized monomeric cystatin C, and elution from columns with immobilized cystatin C oligomers, oligomer-specific antibodies were obtained. These could be used to selectively remove cystatin C dimers from biological fluids containing both dimers and monomers. PMID:23629649

Differential metabolic responses of perennial grass Cynodon transvaalensis×Cynodon dactylon (C₄) and Poa Pratensis (C₃) to heat stress.

PubMed

Du, Hongmei; Wang, Zhaolong; Yu, Wenjuan; Liu, Yimin; Huang, Bingru

2011-03-01

Differential metabolic responses to heat stress may be associated with variations in heat tolerance between cool-season (C₃) and warm-season (C₄) perennial grass species. The main objective of this study was to identify metabolites associated with differential heat tolerance between C₄ bermudagrass and C₃ Kentucky bluegrass by performing metabolite profile analysis using gas chromatography-mass spectrometry. Plants of Kentucky bluegrass (Poa Pratensis'Midnight') and hybrid bermudagrass (Cynodon transvaalensis x Cynodon dactylon'Tifdwarf') were grown under optimum temperature conditions (20/15 °C for Kentucky bluegrass and 30/25 °C for bermudagrass) or heat stress (35/30 °C for Kentucky bluegrass and 45/40 °C for bermudagrass). Physiological responses to heat stress were evaluated by visual rating of grass quality, measuring photochemical efficiency (variable fluorescence to maximal fluorescence) and electrolyte leakage. All of these parameters indicated that bermudagrass exhibited better heat tolerance than Kentucky bluegrass. The metabolite analysis of leaf polar extracts revealed 36 heat-responsive metabolites identified in both grass species, mainly consisting of organic acids, amino acids, sugars and sugar alcohols. Most metabolites showed higher accumulation in bermudagrass compared with Kentucky bluegrass, especially following long-term (18 days) heat stress. The differentially accumulated metabolites included seven sugars (sucrose, fructose, galactose, floridoside, melibiose, maltose and xylose), a sugar alcohol (inositol), six organic acids (malic acid, citric acid, threonic acid, galacturonic acid, isocitric acid and methyl malonic acid) and nine amino acids (Asn, Ala, Val, Thr, γ-aminobutyric acid, IIe, Gly, Lys and Met). The differential accumulation of those metabolites could be associated with the differential heat tolerance between C₃ Kentucky bluegrass and C₄ bermudagrass. Copyright © Physiologia Plantarum 2010.

Piperazine-based nucleic acid analogs

DOEpatents

Schmidt, Jurgen; Silks, Louis A.; Michalczyk, Ryszard

2005-01-11

A novel nucleoside analog is disclosed which comprises a piperazine ring in the place of the ring ribose or deoxyribose sugar. Monomers utilizing a broad variety of nucleobases are disclosed, as well as oligomers comprising the monomers disclosed herein linked by a variety of linkages, including amide, phosphonamide, and sulfonamide linkages. A method of synthesizing the nucleoside analogs is also disclosed.

Recent advances in peptide nucleic acid for cancer bionanotechnology.

PubMed

Wu, Jun-Chen; Meng, Qing-Chun; Ren, Hong-Mei; Wang, Hong-Tao; Wu, Jie; Wang, Qi

2017-06-01

Peptide nucleic acid (PNA) is an oligomer, in which the phosphate backbone has been replaced by a pseudopeptide backbone that is meant to mimic DNA. Peptide nucleic acids are of the utmost importance in the biomedical field because of their ability to hybridize with neutral nucleic acids and their special chemical and biological properties. In recent years, PNAs have emerged in nanobiotechnology for cancer diagnosis and therapy due to their high affinity and sequence selectivity toward corresponding DNA and RNA. In this review, we summarize the recent progresses that have been made in cancer detection and therapy with PNA biotechnology. In addition, we emphasize nanoparticle PNA-based strategies for the efficient delivery of drugs in anticancer therapies.

Rubisco oligomers composed of linked small and large subunits assemble in tobacco plastids and have higher affinities for CO2 and O2.

PubMed

Whitney, Spencer Michael; Kane, Heather Jean; Houtz, Robert L; Sharwood, Robert Edward

2009-04-01

Manipulation of Rubisco within higher plants is complicated by the different genomic locations of the large (L; rbcL) and small (S; RbcS) subunit genes. Although rbcL can be accurately modified by plastome transformation, directed genetic manipulation of the multiple nuclear-encoded RbcS genes is more challenging. Here we demonstrate the viability of linking the S and L subunits of tobacco (Nicotiana tabacum) Rubisco using a flexible 40-amino acid tether. By replacing the rbcL in tobacco plastids with an artificial gene coding for a S40L fusion peptide, we found that the fusions readily assemble into catalytic (S40L)8 and (S40L)16 oligomers that are devoid of unlinked S subunits. While there was little or no change in CO2/O2 specificity or carboxylation rate of the Rubisco oligomers, their Kms for CO2 and O2 were reduced 10% to 20% and 45%, respectively. In young maturing leaves of the plastome transformants (called ANtS40L), the S40L-Rubisco levels were approximately 20% that of wild-type controls despite turnover of the S40L-Rubisco oligomers being only slightly enhanced relative to wild type. The reduced Rubisco content in ANtS40L leaves is partly attributed to problems with folding and assembly of the S40L peptides in tobacco plastids that relegate approximately 30% to 50% of the S40L pool to the insoluble protein fraction. Leaf CO2-assimilation rates in ANtS40L at varying pCO2 corresponded with the kinetics and reduced content of the Rubisco oligomers. This fusion strategy provides a novel platform to begin simultaneously engineering Rubisco L and S subunits in tobacco plastids.

β-Hairpin-Mediated Formation of Structurally Distinct Multimers of Neurotoxic Prion Peptides

PubMed Central

Gill, Andrew C.

2014-01-01

Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109–122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109–122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109–122 peptide (A117V, associated with familial prion disease) increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106–126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an important new atomic-level model for the formation of oligomers and fibrils of the prion protein and suggest that stabilization of β-hairpin structure may enhance cellular toxicity by altering the balance between oligomeric and fibrillar protein assemblies. PMID:24498083

Capping of Aβ42 Oligomers by Small Molecule Inhibitors

PubMed Central

2015-01-01

Aβ42 peptides associate into soluble oligomers and protofibrils in the process of forming the amyloid fibrils associated with Alzheimer’s disease. The oligomers have been reported to be more toxic to neurons than fibrils, and have been targeted by a wide range of small molecule and peptide inhibitors. With single touch atomic force microscopy (AFM), we show that monomeric Aβ42 forms two distinct types of oligomers, low molecular weight (MW) oligomers with heights of 1–2 nm and high MW oligomers with heights of 3–5 nm. In both cases, the oligomers are disc-shaped with diameters of ∼10–15 nm. The similar diameters suggest that the low MW species stack to form the high MW oligomers. The ability of Aβ42 inhibitors to interact with these oligomers is probed using atomic force microscopy and NMR spectroscopy. We show that curcumin and resveratrol bind to the N-terminus (residues 5–20) of Aβ42 monomers and cap the height of the oligomers that are formed at 1–2 nm. A second class of inhibitors, which includes sulindac sulfide and indomethacin, exhibit very weak interactions across the Aβ42 sequence and do not block the formation of the high MW oligomers. The correlation between N-terminal interactions and capping of the height of the Aβ oligomers provides insights into the mechanism of inhibition and the pathway of Aβ aggregation. PMID:25422864

Tandem mass spectrometric analysis of aspergillus niger pectin methylesterase: mode of action on fully methyl-esterified oligogalacturonates.

PubMed

Kester, H C; Benen, J A; Visser, J; Warren, M E; Orlando, R; Bergmann, C; Magaud, D; Anker, D; Doutheau, A

2000-03-01

The substrate specificity and the mode of action of Aspergillus niger pectin methylesterase (PME) was determined using both fully methyl-esterified oligogalacturonates with degrees of polymerization (DP) 2-6 and chemically synthesized monomethyl trigalacturonates. The enzymic activity on the different substrates and a preliminary characterization of the reaction products were performed by using high-performance anion-exchange chromatography at neutral pH. Electrospray ionization tandem MS (ESI-MS/MS) was used to localize the methyl esters on the (18)O-labelled reaction products during the course of the enzymic reaction. A. niger PME is able to hydrolyse the methyl esters of fully methyl-esterified oligogalacturonates with DP 2, and preferentially hydrolyses the methyl esters located on the internal galacturonate residues, followed by hydrolysis of the methyl esters towards the reducing end. This PME is unable to hydrolyse the methyl ester of the galacturonate moiety at the non-reducing end.

Direct Correlation Between Ligand-Induced α-Synuclein Oligomers and Amyloid-like Fibril Growth

PubMed Central

Nors Perdersen, Martin; Foderà, Vito; Horvath, Istvan; van Maarschalkerweerd, Andreas; Nørgaard Toft, Katrine; Weise, Christoph; Almqvist, Fredrik; Wolf-Watz, Magnus; Wittung-Stafshede, Pernilla; Vestergaard, Bente

2015-01-01

Aggregation of proteins into amyloid deposits is the hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease. The suggestion that intermediate oligomeric species may be cytotoxic has led to intensified investigations of pre-fibrillar oligomers, which are complicated by their transient nature and low population. Here we investigate alpha-synuclein oligomers, enriched by a 2-pyridone molecule (FN075), and the conversion of oligomers into fibrils. As probed by leakage assays, the FN075 induced oligomers potently disrupt vesicles in vitro, suggesting a potential link to disease related degenerative activity. Fibrils formed in the presence and absence of FN075 are indistinguishable on microscopic and macroscopic levels. Using small angle X-ray scattering, we reveal that FN075 induced oligomers are similar, but not identical, to oligomers previously observed during alpha-synuclein fibrillation. Since the levels of FN075 induced oligomers correlate with the amounts of fibrils among different FN075:protein ratios, the oligomers appear to be on-pathway and modeling supports an ‘oligomer stacking model’ for alpha-synuclein fibril elongation. PMID:26020724

Tobacco class I cytosolic small heat shock proteins are under transcriptional and translational regulations in expression and heterocomplex prevails under the high-temperature stress condition in vitro.

PubMed

Park, Soo Min; Kim, Keun Pill; Joe, Myung Kuk; Lee, Mi Ok; Koo, Hyun Jo; Hong, Choo Bong

2015-04-01

Seven genomic clones of tobacco (Nicotiana tabacum W38) cytosolic class I small heat shock proteins (sHSPs), probably representing all members in the class, were isolated and found to have 66 to 92% homology between their nucleotide sequences. Even though all seven sHSP genes showed heat shock-responsive accumulation of their transcripts and proteins, each member showed discrepancies in abundance and timing of expression upon high-temperature stress. This was mainly the result of transcriptional regulation during mild stress conditions and transcriptional and translational regulation during strong stress conditions. Open reading frames (ORFs) of these genomic clones were expressed in Escherichia coli and the sHSPs were purified from E. coli. The purified tobacco sHSPs rendered citrate synthase and luciferase soluble under high temperatures. At room temperature, non-denaturing pore exclusion polyacrylamide gel electrophoresis on three sHSPs demonstrated that the sHSPs spontaneously formed homo-oligomeric complexes of 200 ∼ 240 kDa. However, under elevated temperatures, hetero-oligomeric complexes between the sHSPs gradually prevailed. Atomic force microscopy showed that the hetero-oligomer of NtHSP18.2/NtHSP18.3 formed a stable oligomeric particle similar to that of the NtHSP18.2 homo-oligomer. These hetero-oligomers positively influenced the revival of thermally inactivated luciferase. Amino acid residues mainly in the N-terminus are suggested for the exchange of the component sHSPs and the formation of dominant hetero-oligomers under high temperatures. © 2014 John Wiley & Sons Ltd.

Capillary electrophoresis for aluminum ion speciation: Optimized separation conditions for complex polycation mixtures.

PubMed

Ouadah, Nesrine; Moire, Claudine; Brothier, Fabien; Kuntz, Jean-François; Deschaume, Olivier; Bartic, Carmen; Cottet, Hervé

2018-06-01

Aluminum chlorohydrates (ACH) are used in numerous applications and commercial products on a global scale including water treatment, catalysis or antiperspirants. They are complex mixtures of water soluble aluminum polycations of different degrees of polymerization, that are difficult to separate and quantify due to their susceptibility to depolymerize in solution when placed out of equilibrium, which is inherent to any separation process. We recently achieved the first capillary electrophoresis separation and characterization of ACH oligomers using 4-morpholineethanesulfonic acid (MES) as background electrolyte counter-ion. MES stabilizes the separated ACH oligomers during the electrophoretic process leading to highly repeatable and fast separations. In this work, the separation of ACH oligomers was further studied and perfected by varying the ionic strength, MES concentration and pH of the background electrolyte. Complex electrophoretic behavior is reported for the separation of Al 13 , Al 30 and Na + ions according to these experimental parameters. The transformation of the electropherograms in effective mobility scale and the use of the slope-plot approach are used to better understand the observed changes in selectivity/resolution. Optimal conditions (700 mM MES at 25 mM ionic strength containing 0.1 mM didodecyldimethylammonium bromide for dynamic capillary coating, pH 4.8) obtained for the separation of ACH oligomers are used for the baseline separation of samples difficult to analyze with other methods, including different molecular, aggregated and colloidal forms of aluminum from the Al 13 , Al 30 and Na + mixture, validating the rationale of the approach. Copyright © 2018. Published by Elsevier B.V.

Amyloid β oligomers induce interleukin-1β production in primary microglia in a cathepsin B- and reactive oxygen species-dependent manner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taneo, Jun; Adachi, Takumi; Yoshida, Aiko

2015-03-13

Amyloid β (Aβ) peptide, a causative agent of Alzheimer's disease, forms two types of aggregates: oligomers and fibrils. These aggregates induce inflammatory responses, such as interleukin-1β (IL-1β) production by microglia, which are macrophage-like cells located in the brain. In this study, we examined the effect of the two forms of Aβ aggregates on IL-1β production in mouse primary microglia. We prepared Aβ oligomer and fibril from Aβ (1–42) peptide in vitro. We analyzed the characteristics of these oligomers and fibrils by electrophoresis and atomic force microscopy. Interestingly, Aβ oligomers but not Aβ monomers or fibrils induced robust IL-1β production in themore » presence of lipopolysaccharide. Moreover, Aβ oligomers induced endo/phagolysosome rupture, which released cathepsin B into the cytoplasm. Aβ oligomer-induced IL-1β production was inhibited not only by the cathepsin B inhibitor CA-074-Me but also by the reactive oxygen species (ROS) inhibitor N-acetylcysteine. Random chemical crosslinking abolished the ability of the oligomers to induce IL-1β. Thus, multimerization and fibrillization causes Aβ oligomers to lose the ability to induce IL-1β. These results indicate that Aβ oligomers, but not fibrils, induce IL-1β production in primary microglia in a cathepsin B- and ROS-dependent manner. - Highlights: • We prepared amyloid β (Aβ) fibrils with minimum contamination of Aβ oligomers. • Primary microglia (MG) produced IL-1β in response to Aβ oligomers, but not fibrils. • Only Aβ oligomers induced leakage of cathepsin B from endo/phagolysosomes. • IL-1β production in response to Aβ oligomers depended on both cathepsin B and ROS. • Crosslinking reduced the ability of the Aβ oligomers to induce IL-1β from MG.« less

Design of multi-phase dynamic chemical networks

NASA Astrophysics Data System (ADS)

Chen, Chenrui; Tan, Junjun; Hsieh, Ming-Chien; Pan, Ting; Goodwin, Jay T.; Mehta, Anil K.; Grover, Martha A.; Lynn, David G.

2017-08-01

Template-directed polymerization reactions enable the accurate storage and processing of nature's biopolymer information. This mutualistic relationship of nucleic acids and proteins, a network known as life's central dogma, is now marvellously complex, and the progressive steps necessary for creating the initial sequence and chain-length-specific polymer templates are lost to time. Here we design and construct dynamic polymerization networks that exploit metastable prion cross-β phases. Mixed-phase environments have been used for constructing synthetic polymers, but these dynamic phases emerge naturally from the growing peptide oligomers and create environments suitable both to nucleate assembly and select for ordered templates. The resulting templates direct the amplification of a phase containing only chain-length-specific peptide-like oligomers. Such multi-phase biopolymer dynamics reveal pathways for the emergence, self-selection and amplification of chain-length- and possibly sequence-specific biopolymers.

Phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions

NASA Astrophysics Data System (ADS)

Gibard, Clémentine; Bhowmik, Subhendu; Karki, Megha; Kim, Eun-Kyong; Krishnamurthy, Ramanarayanan

2018-02-01

Prebiotic phosphorylation of (pre)biological substrates under aqueous conditions is a critical step in the origins of life. Previous investigations have had limited success and/or require unique environments that are incompatible with subsequent generation of the corresponding oligomers or higher-order structures. Here, we demonstrate that diamidophosphate (DAP)—a plausible prebiotic agent produced from trimetaphosphate—efficiently (amido)phosphorylates a wide variety of (pre)biological building blocks (nucleosides/tides, amino acids and lipid precursors) under aqueous (solution/paste) conditions, without the need for a condensing agent. Significantly, higher-order structures (oligonucleotides, peptides and liposomes) are formed under the same phosphorylation reaction conditions. This plausible prebiotic phosphorylation process under similar reaction conditions could enable the systems chemistry of the three classes of (pre)biologically relevant molecules and their oligomers, in a single-pot aqueous environment.

Phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions

NASA Astrophysics Data System (ADS)

Gibard, Clémentine; Bhowmik, Subhendu; Karki, Megha; Kim, Eun-Kyong; Krishnamurthy, Ramanarayanan

2017-11-01

Prebiotic phosphorylation of (pre)biological substrates under aqueous conditions is a critical step in the origins of life. Previous investigations have had limited success and/or require unique environments that are incompatible with subsequent generation of the corresponding oligomers or higher-order structures. Here, we demonstrate that diamidophosphate (DAP)-a plausible prebiotic agent produced from trimetaphosphate - efficiently (amido)phosphorylates a wide variety of (pre)biological building blocks (nucleosides/tides, amino acids and lipid precursors) under aqueous (solution/paste) conditions, without the need for a condensing agent. Significantly, higher-order structures (oligonucleotides, peptides and liposomes) are formed under the same phosphorylation reaction conditions. This plausible prebiotic phosphorylation process under similar reaction conditions could enable the systems chemistry of the three classes of (pre)biologically relevant molecules and their oligomers, in a single-pot aqueous environment.

The hunt for brain Aβ oligomers by peripherally circulating multi-functional nanoparticles: Potential therapeutic approach for Alzheimer disease.

PubMed

Mancini, Simona; Minniti, Stefania; Gregori, Maria; Sancini, Giulio; Cagnotto, Alfredo; Couraud, Pierre-Olivier; Ordóñez-Gutiérrez, Lara; Wandosell, Francisco; Salmona, Mario; Re, Francesca

2016-01-01

We previously showed the ability of liposomes bi-functionalized with phosphatidic acid and an ApoE-derived peptide (mApoE-PA-LIP) to reduce brain Aβ in transgenic Alzheimer mice. Herein we investigated the efficacy of mApoE-PA-LIP to withdraw Aβ peptide in different aggregation forms from the brain, using a transwell cellular model of the blood-brain barrier and APP/PS1 mice. The spontaneous efflux of Aβ oligomers (Aβo), but not of Aβ fibrils, from the 'brain' side of the transwell was strongly enhanced (5-fold) in presence of mApoE-PA-LIP in the 'blood' compartment. This effect is due to a withdrawal of Aβo exerted by peripheral mApoE-PA-LIP by sink effect, because, when present in the brain side, they did not act as Aβo carrier and limit the oligomer efflux. In vivo peripheral administration of mApoE-PA-LIP significantly increased the plasma Aβ level, suggesting that Aβ-binding particles exploiting the sink effect can be used as a therapeutic strategy for Alzheimer disease. From the Clinical Editor: Alzheimer disease (AD) at present is an incurable disease, which is thought to be caused by an accumulation of amyloid-β (Aβ) peptides in the brain. Many strategies in combating this disease have been focused on either the prevention or dissolving these peptides. In this article, the authors showed the ability of liposomes bi-functionalized with phosphatidic acid and with an ApoE- derived peptide to withdraw amyloid peptides from the brain. The data would help the future design of more novel treatment for Alzheimer disease. Copyright © 2015 Elsevier Inc. All rights reserved.

Preparation and Surface Property of Fluoroalkyl End-Capped Vinyltrimethoxysilane Oligomer/Talc Composite-Encapsulated Organic Compounds: Application for the Separation of Oil and Water.

PubMed

Oikawa, Yuri; Saito, Tomoya; Yamada, Satoshi; Sugiya, Masashi; Sawada, Hideo

2015-07-01

Fluoroalkyl end-capped vinyltrimethoxysilane oligomer [R(F)-(CH2-CHSi(OMe)3)n-R(F); n = 2, 3; R(F) = CF(CF3)OC3F7 (R(F)-VM oligomer)] can undergo the sol-gel reaction in the presence of talc particles under alkaline conditions at room temperature to provide the corresponding fluorinated oligomeric silica/talc nanocomposites (RF-VM-SiO2/Talc). A variety of guest molecules such as 2-hydroxy-4-methoxybenzophenone (HMB), bisphenol A (BPA), bisphenol AF, 3-(hydroxysilyl)-1-propanesulfonic acid (THSP), and perfluoro-2-methyl-3-oxahexanoic acid (R(F)-COOH) are effectively encapsulated into the R(F)-VM-SiO2/Talc composite cores to afford the corresponding fluorinated nanocomposites-encapsulated these guest molecules. The R(F)-VM-SiO2/Talc composites encapsulated low molecular weight aromatic compounds such as HMB and BPA can exhibit a superoleophilic-superhydrophobic characteristic on the surfaces; however, the R(F)-VM-SiO2/Talc composite-encapsulated THSP and R(F)-COOH exhibit a superoleophobic-superhydrophilic characteristic on the modified surfaces. In these nanocomposites, the R(F)-VM-SiO2/Talc/THSP composites are applicable to the surface modification of polyester fabric, and the modified polyester fabric possessing a superoleophobic-superhydrophilic characteristic on the surface can be used for the membrane for oil (dodecane)/water separation. In addition, the R(F)-VM-SiO2/Talc composites-encapsulated micrometer-size controlled cross-linked polystyrene particles can be also prepared under similar conditions, and the obtained composite white-colored particle powders are applied to the packing material for the column chromatography to separate water-in-oil (W/O) emulsion.

Polymerization of amino acids containing nucleotide bases

NASA Technical Reports Server (NTRS)

Ben Cheikh, Azzouz; Orgel, Leslie E.

1990-01-01

The nucleoamino acids 1-(3'-amino,3'-carboxypropyl)uracil (3) and 9-(3'-amino,3'-carboxypropyl)adenine (4) have been prepared as (L)-en-antiomers and as racemic mixtures. When 3 or 4 is suspended in water and treated with N,N'-carbon-yldiimidazole, peptides are formed in good yield. The products formed from the (L)-enantiomers are hydrolyzed to the monomeric amino acids by pronase. Attempts to improve the efficiency of these oligomerizations by including a polyuridylate template in the reaction mixture were not successful. Similarly, oligomers derived from the (L)-enantiomer of 3 did not act as templates to facilitate the oligomerization of 4.

Determination of the chemical structure of the capsular polysaccharide of strain B33, a fast-growing soya bean-nodulating bacterium isolated from an arid region of China.

PubMed Central

Rodríguez-Carvajal, M A; Tejero-Mateo, P; Espartero, J L; Ruiz-Sainz, J E; Buendía-Clavería, A M; Ollero, F J; Yang, S S; Gil-Serrano, A M

2001-01-01

We have determined the structure of a polysaccharide from strain B33, a fast-growing bacterium that forms nitrogen-fixing nodules with Asiatic and American soya bean cultivars. On the basis of monosaccharide analysis, methylation analysis, one-dimensional 1H- and 13C-NMR and two-dimensional NMR experiments, the structure was shown to consist of a polymer having the repeating unit -->6)-4-O-methyl-alpha-D-Glcp-(1-->4)-3-O-methyl-beta-D-GlcpA-(1--> (where GlcpA is glucopyranuronic acid and Glcp is glucopyranose). Strain B33 produces a K-antigen polysaccharide repeating unit that does not have the structural motif sugar-Kdx [where Kdx is 3-deoxy-D-manno-2-octulosonic acid (Kdo) or a Kdo-related acid] proposed for different Sinorhizobium fredii strains, all of them being effective with Asiatic soya bean cultivars but unable to form nitrogen-fixing nodules with American soya bean cultivars. Instead, it resembles the K-antigen of S. fredii strain HH303 (rhamnose, galacturonic acid)n, which is also effective with both groups of soya bean cultivars. Only the capsular polysaccharide from strains B33 and HH303 have monosaccharide components that are also present in the surface polysaccharide of Bradyrhizobium elkanii strains, which consists of a 4-O-methyl-D-glucurono-L-rhamnan. PMID:11439101

Lipid oxidation. Part. 1. Effect of free carboxyl group on the decomposition of lipid hydroperoxide.

PubMed

Pokorný, J; Rzepa, J; Janícek, G

1976-01-01

Hydroperoxido butyl oleate was decomposed by heating in excess palmitic acid at 60-120 degrees C. The decomposition followed the kinetics of a first order reaction with formation of both monomeric and oligomeric secondary products. The proportions of oligomers slightly increased with increasing reaction temperature and decreased with increasing concentration of hydroperoxide. The activation energy was 70.4 kJ/mol +/- 4.7 kJ/mol. The decomposition of hydroperoxides proceeded partially by monomolecular cleavage, partially by formation of esters with palmitic acid.

Amyloid β-protein oligomers and Alzheimer’s disease

PubMed Central

2013-01-01

The oligomer cascade hypothesis, which states that oligomers are the initiating pathologic agents in Alzheimer’s disease, has all but supplanted the amyloid cascade hypothesis, which suggested that fibers were the key etiologic agents in Alzheimer’s disease. We review here the results of in vivo, in vitro and in silico studies of amyloid β-protein oligomers, and discuss important caveats that should be considered in the evaluation of these results. This article is divided into four sections that mirror the main approaches used in the field to better understand oligomers: (1) attempts to locate and examine oligomers in vivo in situ; that is, without removing these species from their environment; (2) studies involving oligomers extracted from human or animal tissues and the subsequent characterization of their properties ex vivo; (3) studies of oligomers that have been produced synthetically and studied using a reductionist approach in relatively simple in vitro biophysical systems; and (4) computational studies of oligomers in silico. These multiple orthogonal approaches have revealed much about the molecular and cell biology of amyloid β-protein. However, as informative as these approaches have been, the amyloid β-protein oligomer system remains enigmatic. PMID:24289820

[Analysis of monosaccharides and uronic acids in polysaccharides by pre-column derivatization with p-aminobenzoic acid and high performance liquid chromatography].

PubMed

Hao, Guitang; Chen, Shangwei; Zhu, Song; Yin, Hongping; Dai, Jun; Cao, Yuhua

2007-01-01

An ion-pair reversed-phase high performance liquid chromatographic (RP-HPLC) method for the simultaneous determination of carbohydrate and uronic acids was developed. p-Aminobenzoic acid (p-AMBA) was used for pre-column derivatization of the analytes, enabling fluorescence (lambda(ex) = 313 nm, lambda(em) = 358 nm) or ultraviolet (UV at 303 nm) detection. Reaction conditions such as reaction temperature and reaction time were optimized. Atlantis dC18 column with hydrophilic end capping was selected for the separation of derivatives. Effects of mobile phase compositions such as ion pairs and their concentrations and pH on the retention behaviors and separation results of 9 monosaccharides and 2 uronic acids were investigated. Derivatives of fructose, galactose, glucose, mannose, xylose, arabinose, ribose, galacturonic acid, fucose, glucuronic acid and rhamnose were separated within 42 min, applying tetrabutyl ammonium hydrogen bisulfate (TBAHSO4) as the ion pair reagent. The detection limits were between 3.38 x 10(-8) mol/L and 176 x 10(-8) mol/L for fluorescence detection and between 2.55 x 10(-7) mol/L and 13.4 x 10(-7) mol/L for UV detection. Good linearities were obtained with correlation coefficients (r2) above 0.99. The relative standard deviations (RSDs) of the peak area of the derivatives in 12 - 51 h after derivatization were from 2.5% to 3.9%. This method has been applied for the determination of mono-/disaccharides and uronic acids in spirulina polysaccharide after dissolved in trifluoroacetic acid solution (2 mol/L). The results showed this method is suitable for the analysis of monosaccharide compositions in polysaccharides.

Designing Polyamide Inhibitors of TWIST 1 for Prosenescence Therapy

DTIC Science & Technology

2014-09-01

Pyrrole -Imidazole Polyamides; TWIST1; KRAS; non-small cell lung cancer (NSCLC); senescence 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF... Pyrrole -Imidazole Polyamides (PIP) are a class of cell permeable programmable small-molecule heterocyclic amino acid oligomers that can be designed...The original specific aims are below: Specific Aim#1. Design and synthesize a TWIST1-inhibitory specific Pyrrole -Imidazole Polyamides (PIP

Nucleotide Oligomers

DTIC Science & Technology

2001-01-01

translated is ensured. For example, autosomal dominant retinitis pigmentosa (ADRP) is a genetic disorder that results in the degeneration of night and...GLOSSARY A adenosine ADRP Autosomal Dominant Retinitis Pigmentosa C cytidine DNA deoxyribonucleic acid G guanosine mRNA messenger RNA OH hydroxyl PCR...peripheral vision. The genetic defect lies in one, or both copies of a gene required for normal retinal structure and vision, rhodopsin. Triplex

Pectin-modifying enzymes and pectin-derived materials: applications and impacts.

PubMed

Bonnin, Estelle; Garnier, Catherine; Ralet, Marie-Christine

2014-01-01

Pectins are complex branched polysaccharides present in primary cell walls. As a distinctive feature, they contain high amount of partly methyl-esterified galacturonic acid and low amount of rhamnose and carry arabinose and galactose as major neutral sugars. Due to their structural complexity, they are modifiable by many different enzymes, including hydrolases, lyases, and esterases. Their peculiar structure is the origin of their physicochemical properties. Among others, their remarkable gelling properties make them a key additive for food industries. Pectin-degrading enzymes and -modifying enzymes may be used in a wide variety of applications to modulate pectin properties or produce pectin derivatives and oligosaccharides with functional as well as nutritional interests. This paper reviews the scientific information available on pectin structure, pectin-modifying enzymes, and the use of enzymes to produce pectin with controlled structure or pectin-derived oligosaccharides, with functional or nutritional interesting properties.

High-performance liquid chromatography of methanol released from pectins after its oxidation to formaldehyde and condensation with 2,4-dinitrophenylhydrazine.

PubMed

Zegota, H

1999-11-26

A procedure was developed to measure the content of methanol in pectins after the base-catalysed hydrolysis of galacturonic acid methyl esters and oxidation of released methanol with potassium permanganate followed by condensation of the resulting formaldehyde (HCHO) with 2,4-dinitrophenylhydrazine (DNPH) dissolved in acetonitrile. The constant yields of resultant formaldehyde 2,4-dinitrophenylhydrazone (HCHO-DNPH derivative) were obtained at molar ratios of DNPH/HCHO higher than 5. The separation of the HCHO-DNPH derivative from DNPH reagent was achieved by isocratic reversed-phase HPLC equipped with the spectrophotometric detector set at a wavelength of 351 nm. The calibration curve was linear in the methanol concentration range between 0.04 and 15 micromol/ml (R=0.9995). The total recovery from pectin solutions spiked with methanol was equal to 100.6+/-5.1%.

Composition of the sheath produced by the green alga Chlorella sorokiniana.

PubMed

Watanabe, K; Imase, M; Sasaki, K; Ohmura, N; Saiki, H; Tanaka, H

2006-05-01

To investigate the chemical characterization of the mucilage sheath produced by Chlorella sorokiniana. Algal mucilage sheath was hydrolysed with NaOH, containing EDTA. The purity of the hydrolysed sheath was determined by an ATP assay. The composition of polysaccharide in the sheath was investigated by high-performance anion-exchange chromatography with pulsed amperometric detection. Sucrose, galacturonic acid, xylitol, inositol, ribose, mannose, arabinose, galactose, rhamnose and fructose were detected in the sheath as sugar components. Magnesium was detected in the sheath as a divalent cation using inductively coupled argon plasma. The sheath matrix also contained protein. It appears that the sheath is composed of sugars and metals. Mucilage sheath contains many kinds of saccharides that are produced as photosynthetic metabolites and divalent cations that are contained in the culture medium. This is the first report on chemical characterization of the sheath matrix produced by C. sorokiniana.

Intact carbohydrate structures as part of the melanoidin skeleton.

PubMed

Cämmerer, Bettina; Jalyschko, Walentina; Kroh, Lothar W

2002-03-27

Model melanoidins from monomeric, oligomeric, and polymeric carbohydrates, and amino acids formed under aqueous as well as water-free reaction conditions, were submitted to acidic catalyzed hydrolysis. Their degradation products were detected qualitatively and quantitatively by HPTLC and HPLC-DAD. A considerable amount of monomer carbohydrates from hydrolysis of model melanoidins formed under water-free reaction conditions was detected. It can be seen clearly that the amount of carbohydrates released increased with increasing degree of polymerization of the carbohydrates used as starting material. In comparison, the hydrolysis of melanoidins formed in aqueous condition resulted in only a small glucose release. It seems that in the Maillard reaction under water-free conditions, a significant amount of di- and oligomer carbohydrates were incorporated into the melanoidin skeleton as complete oligomer with intact glycosidic bond, forming side chains at the melanoidin skeleton. Additional side chains could be formed by transglycosylation reactions. With increasing water content, hydrothermolytic as well as retro-aldol reactions of the starting carbonyl components became significant, and therefore the possibility of forming side chains decreased. The results are consistent with the postulated melanoidin structure being built up mainly from sugar degradation products, probably branched via amino compounds.

Mechanism by which DHA inhibits the aggregation of KLVFFA peptides: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Zhou, Hong; Liu, Shengtang; Shao, Qiwen; Ma, Dongfang; Yang, Zaixing; Zhou, Ruhong

2018-03-01

Docosahexaenoic acid (DHA) is one of the omega-3 polyunsaturated fatty acids, which has shown promising applications in lowering Aβ peptide neurotoxicity in vitro by preventing aggregation of Aβ peptides and relieving accumulation of Aβ fibrils. Unfortunately, the underlying molecular mechanisms of how DHA interferes with the aggregation of Aβ peptides remain largely enigmatic. Herein, aggregation behaviors of amyloid-β(Aβ)16-21 peptides (KLVFFA) with or without the presence of a DHA molecule were comparatively studied using extensive all-atom molecular dynamics simulations. We found that DHA could effectively suppress the aggregation of KLVFFA peptides by redirecting peptides to unstructured oligomers. The highly hydrophobic and flexible nature of DHA made it randomly but tightly entangled with Leu-17, Phe-19, and Phe-20 residues to form unstructured but stable complexes. These lower-ordered unstructured oligomers could eventually pass through energy barriers to form ordered β-sheet structures through large conformational fluctuations. This study depicts a microscopic picture for understanding the role and mechanism of DHA in inhibition of aggregation of Aβ peptides, which is generally believed as one of the important pathogenic mechanisms of Alzheimer's disease.

RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids

PubMed Central

Sample, Paul J.; Gaston, Kirk W.; Alfonzo, Juan D.; Limbach, Patrick A.

2015-01-01

Ribosomal ribonucleic acid (RNA), transfer RNA and other biological or synthetic RNA polymers can contain nucleotides that have been modified by the addition of chemical groups. Traditional Sanger sequencing methods cannot establish the chemical nature and sequence of these modified-nucleotide containing oligomers. Mass spectrometry (MS) has become the conventional approach for determining the nucleotide composition, modification status and sequence of modified RNAs. Modified RNAs are analyzed by MS using collision-induced dissociation tandem mass spectrometry (CID MS/MS), which produces a complex dataset of oligomeric fragments that must be interpreted to identify and place modified nucleosides within the RNA sequence. Here we report the development of RoboOligo, an interactive software program for the robust analysis of data generated by CID MS/MS of RNA oligomers. There are three main functions of RoboOligo: (i) automated de novo sequencing via the local search paradigm. (ii) Manual sequencing with real-time spectrum labeling and cumulative intensity scoring. (iii) A hybrid approach, coined ‘variable sequencing’, which combines the user intuition of manual sequencing with the high-throughput sampling of automated de novo sequencing. PMID:25820423

Growth of fluorescence gold clusters using photo-chemically activated ligands

NASA Astrophysics Data System (ADS)

Mishra, Dinesh; Aldeek, Fadi; Michael, Serge; Palui, Goutam; Mattoussi, Hedi

2016-03-01

Ligands made of lipoic acid (LA) appended with a polyethylene glycol (PEG) chain have been used in the aqueous phase growth of luminescent gold clusters with distinct emission from yellow to near-IR, using two different routes. In the first route, the gold-ligand complex was chemically reduced using sodium borohydride in alkaline medium, which gave near- IR luminescent gold clusters with maximum emission around 745 nm. In the second method, LA-PEG ligand was photochemically modified to a mixture of thiols, oligomers and oxygenated species under UV-irradiation, which was then used as both reducing agent and stabilizing ligand. By adjusting the pH, temperature, and time of the reaction, we were able to obtain clusters with two distinct emission properties. Refluxing the gold-ligand complex in alkaline medium in the presence of excess ligand gave yellow emission within the first two hours and the emission shifted to red after overnight reaction. Mass spectrometry and chemical assay were used to understand the photo-chemical transformation of Lipoic Acid (LA). Mass spectroscopic studies showed the photo-irradiated product contains thiols, oligomers (dimers, trimers and tetramers) as well as oxygenated species. The amount of thiol formed under different conditions of irradiation was estimated using Ellman's assay.

Adsorption and condensation of amino acids and nucleotides with soluble mineral salts

NASA Technical Reports Server (NTRS)

Orenberg, J.; Lahav, N.

1986-01-01

The directed synthesis of biopolymers in an abiotic environment is presumably a cyclic sequence of steps which may be realized in a fluctuating environment such as a prebiotic pond undergoing wetting-drying cycles. Soluble mineral salts have been proposed as an essential component of this fluctuating environment. The following sequence may be considered as a most primitive mechanism of information transfer in a fluctuating environment: (1) adsorption of a biomolecule onto a soluable mineral salt surface to act as an adsorbed template; (2) specific adsorption of biomonomers onto the adsorbed template; (3) condensation of the adsorbed biomonomers; and (4) desorption of the elongated oligomer. In this investigation, the salts selected for study were CaSO4.2H2O(gypsum), SrSO4, and several other metal sulfates and chlorides. Adsorption of the monomeric species, gly, 5'AMP 5'GMP, and 5'CMP was investigated. The adsorbed template biopolymers used were Poly-A, Poly-G, Poly-C, and Poly-U. The results of studies involving these experimental participants, the first two steps of the proposed primitive information transfer mechanism, and condensation of amino acids to form oligomers in a fluctuating environment are to be reported.

Amine-reactive forms of a luminescent diethylenetriaminepentaacetic acid chelate of terbium and europium: attachment to DNA and energy transfer measurements.

PubMed

Li, M; Selvin, P R

1997-01-01

An isothiocyanate form of a lanthanide chelate which is highly luminescent when bound to terbium or europium has been synthesized. The chelate consists of diethylenetriaminepentaacetic acid (DTPA) covalently joined to a chromophore, 7-amino-4-methyl-2(1H)-quinolinone (cs124), and to L-p-aminophenylalanine, in which the aromatic amine was further converted to an isothiocyanate group. Ethylenediamine was also used in place of aminophenylalanine, but the isothiocyanate formed from the aliphatic amine was significantly less reactive. Site-specific attachments to triglycine and to the 5' ends of amine-modified DNA oligomers have been made. In addition, as an alternative method of coupling to macromolecules, DTPA anhydride-cs124 can be used to react specifically with a 5' amine group on base-deprotected synthetic DNA oligomers. Synthesis and purification is relatively straightforward in both cases, and luminescent properties are favorable for several applications, including as nonisotopic labels, as long-lifetime alternatives to fluorophores in imaging and diagnostics and particularly as donors in luminescence resonance energy transfer. Energy transfer measurements are consistent with previously reported measurements using different attachment mechanisms.

Isolation, characterization, and aggregation of a structured bacterial matrix precursor.

PubMed

Chai, Liraz; Romero, Diego; Kayatekin, Can; Akabayov, Barak; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

2013-06-14

Biofilms are surface-associated groups of microbial cells that are embedded in an extracellular matrix (ECM). The ECM is a network of biopolymers, mainly polysaccharides, proteins, and nucleic acids. ECM proteins serve a variety of structural roles and often form amyloid-like fibers. Despite the extensive study of the formation of amyloid fibers from their constituent subunits in humans, much less is known about the assembly of bacterial functional amyloid-like precursors into fibers. Using dynamic light scattering, atomic force microscopy, circular dichroism, and infrared spectroscopy, we show that our unique purification method of a Bacillus subtilis major matrix protein component results in stable oligomers that retain their native α-helical structure. The stability of these oligomers enabled us to control the external conditions that triggered their aggregation. In particular, we show that stretched fibers are formed on a hydrophobic surface, whereas plaque-like aggregates are formed in solution under acidic pH conditions. TasA is also shown to change conformation upon aggregation and gain some β-sheet structure. Our studies of the aggregation of a bacterial matrix protein from its subunits shed new light on assembly processes of the ECM within bacterial biofilms.

Ultrasound-assisted extraction of pectins from grape pomace using citric acid: a response surface methodology approach.

PubMed

Minjares-Fuentes, R; Femenia, A; Garau, M C; Meza-Velázquez, J A; Simal, S; Rosselló, C

2014-06-15

An ultrasound-assisted procedure for the extraction of pectins from grape pomace with citric acid as the extracting agent was established. A Box-Behnken design (BBD) was employed to optimize the extraction temperature (X1: 35-75°C), extraction time (X2: 20-60 min) and pH (X3: 1.0-2.0) to obtain a high yield of pectins with high average molecular weight (MW) and degree of esterification (DE) from grape pomace. Analysis of variance showed that the contribution of a quadratic model was significant for the pectin extraction yield and for pectin MW whereas the DE of pectins was more influenced by a linear model. An optimization study using response surface methodology was performed and 3D response surfaces were plotted from the mathematical model. According to the RSM model, the highest pectin yield (∼32.3%) can be achieved when the UAE process is carried out at 75°C for 60 min using a citric acid solution of pH 2.0. These pectic polysaccharides, composed mainly by galacturonic acid units (<97% of total sugars), have an average MW of 163.9 kDa and a DE of 55.2%. Close agreement between experimental and predicted values was found. These results suggest that ultrasound-assisted extraction could be a good option for the extraction of functional pectins with citric acid from grape pomace at industrial level. Copyright © 2014 Elsevier Ltd. All rights reserved.

Structural and technological characterisation of pectin extracted with sodium citrate and nitric acid from sunflower heads.

PubMed

Muñoz-Almagro, Nerea; Rico-Rodriguez, Fabián; Wilde, Peter J; Montilla, Antonia; Villamiel, Mar

2018-05-18

An optimisation of temperature, time and extracting agent concentration of pectin extraction from sunflower heads using sodium citrate and nitric acid (SP-SC and SP-NA) was carried out. At optimal conditions, the yield of extraction with nitric acid (SPO-NA) was 2-fold greater than the corresponding with sodium citrate (SPO-SC) (14.3 vs 7.7%, respectively). Regarding pectin structure, the galacturonic acid (GalA) content in both, SPO-SC and SPO-NA, was similar (∼85%). However, SPO-NA showed lower molecular weight (Mw) (88.9 kDa) and neutral sugar content (4%) than SPO-SC (464 kDa, 9%), indicating that nitric acid deeply degraded pectin structure. These differences derived into dissimilar behaviour in their technological functionality. SPO-SC showed higher viscosity and better emulsifying capacity than SPO-NA, although any of them were able to stabilise the oil/water emulsion. Both sunflower pectins formed gels with Ca 2+ (75 mg/g of pectin) at pH 3.0. However, when sucrose was added, the gels formed by SP-SC and 20% sucrose presented the same hardness as those of SP-NA with 40% sucrose. These results suggest that the pectin extracted with sodium citrate, an eco-friendly agent, could be a promising ingredient, with good thickening and gelling properties. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

[Mode of action and inhibition of polygalacturonase covalently bound to polysaccharide and glass carriers].

PubMed

Bock, W; Krause, M; Göbel, H; Anger, H; Schawaller, H J; Flemming, C; Gabert, A

1978-01-01

Endo-polygalacturonase (EC 3.2.1.15.) from Aspergillus spec. is much changed as far as its mode of action and the interaction with vegetable inhibitors of pectinase (from green beans and cucumbers) are concerned when it is covalently bound to insoluble carriers (Sepharose, cellulose powder, macroporous glass and nonporous ballotinis). Whereas a 2% degradation of substrate by the soluble enzyme caused a 50% decrease of viscosity of citrus pectic acid, the comparable degradation of substrate was increased to a level of about 10% with the investigated polygalacturonase carrier complexes apparently independent of the properties of the carriers and the kind of binding of the enzyme. In contrast to this the higher degradation of substrate of 15 and 20% respectively which was further stated at a 50% decrease of viscosity is unambiguously connected with the carriers and is in direct correlation with the specific activity of the polygalacturonase carrier complexes. Contrary to the soluble enzyme the covalently bound enzyme produces more lower oligomerous galacturonic acids by an exo-mechanism or by multiple attack already at the beginning of the hydrolysis of pectic acid. During the final stage there is an enrichment of trigalacturonic acid besides mono- and digalacturonic acids independent of the state of solution of the enzyme. It could further be stated that the strong inhibition of the soluble endo-polygalacturonase by selected pectinase inhibitors which was described earlier is reduced by degrees with the enzyme covalently bound to the insoluble carriers.

Understanding the native Californian diet: Identification of condensed and hydrolyzable tannins in tanoak acorns (Lithocarpus densiflorus).

PubMed

Meyers, Katherine J; Swiecki, Tedmund J; Mitchell, Alyson E

2006-10-04

The tanoak (Lithocarpus densiflorus) acorn was a staple food in the Native American diet and is still used in traditional dishes. Acorns from the genus Quercus have been shown to contain a large range of hydrolyzable tannins. However, neither hydrolyzable nor condensed tannins have been characterized in tanoak acorns. The aim of this study was to identify the full range of hydrolyzable and condensed tannins in extracts of tanoak acorns using liquid chromatography/electrospray ionization-mass spectrometry/mass spectrometry. Condensed tannins were identified as B type oligomers of (epi)-catechin (procyanidins) with a degree of polymerization up to six. Oligomers up to and including tetramers were identified by UV spectra and MS detection whereas pentamers and hexamers were detected only by MS. The total concentration of condensed tannins was 464 mg/100 g acorn pericarp. The concentration of propocyanidin monomers, dimers, trimers, and tetramers in acorn pericarp (mg/100 g acorn pericarp) were 95 +/- 10.9, 148 +/- 35.0, 90 +/- 17.9, and 131 +/- 1.9, respectively. No procyanidins were found in the acorn cotyledon tissue. A total of 22 hydrolyzable tannins were identified in methanolic extracts of acorn cotyledon tissue. Gallic acid derivatives predominated and included galloylated esters of glucose, hexahydrodiphenoyl esters of glucose, and methylated gallates. Galloylated esters of glucose were present as isomers of galloyl glucose, digalloyl glucose, and trigalloyl glucose. Mass spectral fragmentation patterns indicate the presence of one gallic acid-galloyl glucose isomer and two gallic acid-digalloyl-glucose isomers. No isomers of tetragalloyl glucose and pentagalloyl glucose were identified. Ellagic acid and ellagic acid pentoside were also identified.

Assessment of renal response with urinary exosomes in patients with AL amyloidosis: A proof of concept.

PubMed

Ramirez-Alvarado, Marina; Barnidge, David R; Murray, David L; Dispenzieri, Angela; Marin-Argany, Marta; Dick, Christopher J; Cooper, Shawna A; Nasr, Samih H; Ward, Christopher J; Dasari, Surendra; Jiménez-Zepeda, Víctor H; Leung, Nelson

2017-06-01

Immunoglobulin light chain (AL) amyloidosis is a fatal complication of B-cell proliferation secondary to deposition of amyloid fibrils in various organs. Urinary exosomes (UEX) are the smallest of the microvesicles excreted in the urine. Previously, we found UEX of patients with AL amyloidosis contained immunoglobulin light chain (LC) oligomers that patients with multiple myeloma did not have. To further explore the role of the LC oligomers, UEX was isolated from an AL amyloidosis patient with progressive renal disease despite achieving a complete response. LC oligomers were identified. Mass spectrometry (MS) of the UEX and serum identified two monoclonal lambda LCs. Proteomics of the trypsin digested amyloid fragments in the kidney by laser microdissection and MS analysis identified a λ6 LC. The cDNA from plasma cell clone was from the IGLV- 6-57 family and it matched the amino acid sequences of the amyloid peptides. The predicted mass of the peptide product of the cDNA matched the mass of one of the two LCs identified in the UEX and serum. UEX combined with MS were able to identify 2 monoclonal lambda LCs that current clinical methods could not. It also identified the amyloidogenic LC which holds potential for response assessment in the future. © 2017 Wiley Periodicals, Inc.

Repetition as the essence of life on this earth: music and genes.

PubMed

Ohno, S

1987-01-01

In prebiotic nucleic acid replication, templates appear to have been in short supply. A single round of tandem duplication of existing oligomers assured progressive extension of templates to the length adequate for encoding of polypeptide chains. Thus, the first set of coding sequences had to be repeats of base oligomers encoding polypeptide chains of various periodicities. On one hand, the readiness of these periodical polypeptide chains to assume alpha-helical and/or beta-sheet secondary structures contributed to the extremely rapid initial functional diversification of these polypeptide chains. It would be recalled that most, if not all, of the sugar-metabolizing enzymes had already achieved the inviolable functional competence before the division of prokaryotes from eukaryotes. On the other hand, a certain (dipeptidic?) of the peptidic periodicities was apparently chosen as the timekeeping unit by the biological clock. Musical compositions too apparently evolved originally as a timekeeping device. Accordingly, repetitiousness is evident in all musical compositions. Evolution of musical compositions from the early Baroque to the late Romantic parallels that of coding sequences from rather exact repeats of base oligomers to more complex modern coding sequences in which repetitious elements are less conspicuous and more varied. Inasmuch as the earth is governed by the hierarchy of periodicities (days, months and years), such reliance on periodicities is rather expected.

Tau Oligomers as Potential Targets for Alzheimer’s Diagnosis and Novel Drugs

PubMed Central

Guzmán-Martinez, Leonardo; Farías, Gonzalo A.; Maccioni, Ricardo Benjamin

2013-01-01

A cumulative number of approaches have been carried out to elucidate the pathogenesis of Alzheimer’s disease (AD). Tangles formation has been identified as a major event involved in the neurodegenerative process, due to the conversion of either soluble peptides or oligomers into insoluble filaments. Most of recent studies share in common the observation that formation of tau oligomers and the subsequent pathological filaments arrays is a critical step in AD etiopathogenesis. Oligomeric tau species appear to be toxic for neuronal cells, and therefore appear as an appropriate target for the design of molecules that may control morphological and functional alterations leading to cognitive impairment. Thus, current therapeutic strategies are aimed at three major types of molecules: (1) inhibitors of protein kinases and phosphatases that modify tau and that may control neuronal degeneration, (2) methylene blue, and (3) natural phytocomplexes and polyphenolics compounds able to either inhibit the formation of tau filaments or disaggregate them. Only a few polyphenolic molecules have emerged to prevent tau aggregation. In this context, fulvic acid (FA), a humic substance, has potential protective activity cognitive impairment. In fact, formation of paired helical filaments in vitro, is inhibited by FA affecting the length of fibrils and their morphology. PMID:24191153

Aerosol-Forming Reactions of Glyoxal, Methylglyoxal and Amino Acids in Clouds

NASA Astrophysics Data System (ADS)

de Haan, D. O.; Smith, K. W.; Stroik, D. R.; Corrigan, A. L.; Lee, F. E.; Phan, J. T.; Conley, A. C.

2008-12-01

Glyoxal and methylglyoxal are two common aldehydes present in fog and cloud water. Amino acids are present in clouds at similar concentrations. Here we present bulk and aerosol mass spectroscopic data demonstrating that irreversible reactions between glyoxal and amino acids, triggered by droplet evaporation, produce N-derivatized imidazole compounds along with deeply colored Maillard reaction products. These reactions can occur in the dark and in the absence of oxidants. Reactions between methylglyoxal and amino acids produce analogous methylated products plus oligomers with masses up to m/z = 1000. These reactions, which go to completion on the 10-min-timescale of cloud processing, could be significant sources of secondary organic aerosol and humic-like substances (HULIS or brown carbon).

The Role of the Local Conformation of a Cyclically Constrained β-AMINO Acid in the Secondary Structures of a Mixed α/β Diastereomer Pair

NASA Astrophysics Data System (ADS)

Blodgett, Karl N.; Zwier, Timothy S.

2017-06-01

Synthetic foldamers are non-natural polymers designed to fold into unique secondary structures that either mimic nature's preferred secondary structures, or expand their possibilities. Among the most studied synthetic foldamers are β-peptides, which lengthen the distance between amide groups from the single substituted carbon spacer in α-peptides by one (β) additional carbon. Cyclically constrained β-amino acids can impart rigidity to the secondary structure of oligomers by locking in a particular conformation. The β-residue cis-2-aminocyclohexanecarboxylic acid (cis-ACHC) is one such amino acid which has been shown to drive vastly different secondary structures as a function of the local conformation of the cyclohexane ring. We present data on two diastereomers of the mixed α/β tri-peptide Ac-Ala-β_{ACHC}-Ala-NHBn which differ from one another by the chirality along the ACHC residue (SRSS vs. SSRS). The first oligomer is known to crystallize to a 9/11 mixed helix while the second forms no intramolecular hydrogen bonds in the crystal state. This talk will describe the conformation-specific IR and UV spectroscopy of the above two diastereomers under jet cooled conditions in the gas phase. Assignments based on comparison with calculations show the presence of incipient 9/11 mixed helices and competing structures containing more tightly folded hydrogen-bonded networks. The calculated global minimum structures are observed in each case, and in each case these folded structures are reminiscent of a β-turn.

Structural Characteristics of the Alpha-Synuclein Oligomers Stabilized By the Flavonoid Baicalein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, D.-P.; Fink, A.L.; Uversky, V.N.

The flavonoid baicalein inhibits fibrillation of alpha-synuclein, which is a major component of Lewy bodies in Parkinson's disease. It has been known that baicalein induces the formation of alpha-synuclein oligomers and consequently prevents their fibrillation. In order to evaluate the structural properties of baicalein-stabilized oligomers, we purified oligomer species by HPLC and examined their stability and structure by CD, Fourier transform infrared spectroscopy, size exclusion chromatography HPLC, small-angle X-ray scattering, and atomic force microscopy. Baicalein-stabilized oligomers are beta-sheet-enriched according to CD and Fourier transform infrared spectroscopy analyses. They did not form fibrils even after very prolonged incubation. From small-angle X-raymore » scattering data and atomic force microscopy images, the oligomers were characterized as quite compact globular species. Oligomers were extremely stable, with a GdmCl C(m)=3.3 M. This high stability explains the previously observed inhibition properties of baicalein against alpha-synuclein fibrillation. These baicalein-stabilized oligomers, added to the solution of aggregating alpha-synuclein, were able to noticeably inhibit its fibrillation. After prolonged coincubation, short fibrils were formed, suggesting an effective interaction of oligomers with monomeric alpha-synuclein. Membrane permeability tests suggested that the baicalein-stabilized oligomers had a mild effect on the integrity of the membrane surface. This effect was rather similar to that of the monomeric protein, suggesting that targeted stabilization of certain alpha-synuclein oligomers might offer a potential strategy for the development of novel Parkinson's disease therapies.« less

Acidic pH retards the fibrillization of human islet amyloid polypeptide due to electrostatic repulsion of histidines

NASA Astrophysics Data System (ADS)

Li, Yang; Xu, Weixin; Mu, Yuguang; Zhang, John Z. H.

2013-08-01

The human Islet Amyloid Polypeptide (hIAPP) is the major constituent of amyloid deposits in pancreatic islets of type-II diabetes. IAPP is secreted together with insulin from the acidic secretory granules at a low pH of approximately 5.5 to the extracellular environment at a neutral pH. The increased accumulation of extracellular hIAPP in diabetes indicates that changes in pH may promote amyloid formation. To gain insights and underlying mechanisms of the pH effect on hIAPP fibrillogenesis, all-atom molecular dynamics simulations in explicit solvent model were performed to study the structural properties of five hIAPP protofibrillar oligomers, under acidic and neutral pH, respectively. In consistent with experimental findings, simulation results show that acidic pH is not conducive to the structural stability of these oligomers. This provides a direct evidence for a recent experiment [L. Khemtemourian, E. Domenech, J. P. F. Doux, M. C. Koorengevel, and J. A. Killian, J. Am. Chem. Soc. 133, 15598 (2011)], 10.1021/ja205007j, which suggests that acidic pH inhibits the fibril formation of hIAPP. In addition, a complementary coarse-grained simulation shows the repulsive electrostatic interactions among charged His18 residues slow down the dimerization process of hIAPP by twofold. Besides, our all-atom simulations reveal acidic pH mainly affects the local structure around residue His18 by destroying the surrounding hydrogen-bonding network, due to the repulsive interactions between protonated interchain His18 residues at acidic pH. It is also disclosed that the local interactions nearby His18 operating between adjacent β-strands trigger the structural transition, which gives hints to the experimental findings that the rate of hIAPP fibril formation and the morphologies of the fibrillar structures are strongly pH-dependent.

Poly(fumaric-co-sebacic anhydride). A degradation study as evaluated by FTIR, DSC, GPC and X-ray diffraction.

PubMed

Santos, C A; Freedman, B D; Leach, K J; Press, D L; Scarpulla, M; Mathiowitz, E

1999-06-28

The degradation of three poly(fumaric-co-sebacic anhydride) [P(FA:SA)] copolymers is examined in a composition of microspheres made by the hot melt encapsulation process. The emergence of low molecular weight oligomers occurs during degradation of the copolymer microspheres, as evidenced by a variety of characterization methods. Characterization was conducted to determine the extent of degradation of the polyanhydride microspheres using Fourier-transform infrared spectroscopy (FTIR), gel permeation chromatography (GPC), differential scanning calorimetry (DSC) and X-ray diffraction. It is demonstrated that degradation of P(FA:SA) is greatly accelerated at basic pH, yet there is little difference between degradation in neutral and acidic buffers. A good correlation exists between the results of each characterization method, which allows a better understanding of the degradation process and the resulting formation of low molecular weight oligomers in poly(fumaric-co-sebacic anhydride).

Production of clean pyrolytic sugars for fermentation.

PubMed

Rover, Marjorie R; Johnston, Patrick A; Jin, Tao; Smith, Ryan G; Brown, Robert C; Jarboe, Laura

2014-06-01

This study explores the separate recovery of sugars and phenolic oligomers produced during fast pyrolysis with the effective removal of contaminants from the separated pyrolytic sugars to produce a substrate suitable for fermentation without hydrolysis. The first two stages from a unique recovery system capture "heavy ends", mostly water-soluble sugars and water-insoluble phenolic oligomers. The differences in water solubility can be exploited to recover a sugar-rich aqueous phase and a phenolic-rich raffinate. Over 93 wt % of the sugars is removed in two water washes. These sugars contain contaminants such as low-molecular-weight acids, furans, and phenols that could inhibit successful fermentation. Detoxification methods were used to remove these contaminants from pyrolytic sugars. The optimal candidate is NaOH overliming, which results in maximum growth measurements with the use of ethanol-producing Escherichia coli. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Procyanidins (Condensed Tannins) in Green Cell Suspension Cultures of Douglas Fir Compared with Those in Strawberry and Avocado Leaves by Means of C18-Reversed-phase Chromatography 1

PubMed Central

Stafford, Helen A.; Lester, Hope H.

1980-01-01

The procyanidins (the most common type of proanthocyanidin or condensed tannin) from cell suspension cultures derived from cotyledons of Douglas Fir have been compared with those isolated from leaves of strawberry and avocado. Seventy per cent methanol (v/v) extracts from 100 milligrams fresh weight samples were analyzed by a combination of C18-reversed-phase columns with high-performance liquid chromatography, and normal phase paper chromatography. (−)-Epicatechin and its oligomers were generally retarded longer on C18 columns than the corresponding units made of (+)-catechin when eluted with solvents made up of 5% acetic acid alone or mixed with methanol up to 15% (v/v). Douglas fir preparations contained the most complex set of procyanidins and consisted of oligomers of catechin and epicatechin, whereas strawberry and avocado contained mainly (+)-catechin and (−)-epicatechin derivatives, respectively. PMID:16661581

Ketimine modifications as a route to novel amorphous and derived semicrystalline poly(arylene ether ketone) homo- and copolymers

NASA Technical Reports Server (NTRS)

Mohanty, D. K.; Lowery, R. C.; Lyle, G. D.; Mcgrath, J. E.

1987-01-01

A series of amine terminal amorphous poly(arylene ether ketone) oligomers of controlled molecular weights (2-15 K) were synthesized. These oligomers have been found to undergo 'self-crosslinking' reactions upon heating above 220 C, via the reaction of the terminal amine groups with the in-chain keto carbonyl functionalities. The resulting networks are ductile, chemically resistant, and nonporous. The networks obtained via generated ketimine functionality were characterized by solid state NMR. They have also been found to be remarkably stable toward hydrolysis. Ketimine functional bishalide monomers have also been synthesized. Such monomers have been utilized to synthesize a wide variety of amorphous poly(arylene ether) ketimine polymers. A high molecular weight hydroquinone functional poly(arylene ether) ketimine has been acid treated to regenerate a poly(arylene ether ketone) backbone in solution. This novel procedure thus allows for the synthesis of important matrix resins under relatively mild conditions.

Tracking the Growth Transitions of A Solvent-Charged Model Globular Protein

NASA Astrophysics Data System (ADS)

Babcock, Jeremiah; Friday, Jacob; Brancaleon, Lorenzo

2011-03-01

Biophysical studies have shown that solutes like proteins undergo aggregation through specific pathways that often lead to long polymeric structures called fibrils. The knowledge of the size of early-stage protein aggregates (oligomers) has an important bearing on the elucidation of the dynamics of the process of protein unit combinations. In this study, bovine serum albumin, a well-characterized model protein known to polymerize in alkaline and acidic conditions in the normal (N) to basic (B) or (N) to (E) transition, was incubated at pH 9.0 and pH 3.1 for longer than eight days. Particle growth in solution was monitored by absorption, fluorescence and circular dichroism spectroscopy and concurrently measured by atomic force microscopy (AFM) methods to yield BSA oligomer size distributions. Results show that the BSA aggregation pathway is concentration-dependent and rapidly forms spherical aggregates, which preferentially come together to form flexible polymers.

Prion Protein-mediated Toxicity of Amyloid-β Oligomers Requires Lipid Rafts and the Transmembrane LRP1*

PubMed Central

Rushworth, Jo V.; Griffiths, Heledd H.; Watt, Nicole T.; Hooper, Nigel M.

2013-01-01

Soluble oligomers of the amyloid-β (Aβ) peptide cause neurotoxicity, synaptic dysfunction, and memory impairments that underlie Alzheimer disease (AD). The cellular prion protein (PrPC) was recently identified as a high affinity neuronal receptor for Aβ oligomers. We report that fibrillar Aβ oligomers recognized by the OC antibody, which have been shown to correlate with the onset and severity of AD, bind preferentially to cells and neurons expressing PrPC. The binding of Aβ oligomers to cell surface PrPC, as well as their downstream activation of Fyn kinase, was dependent on the integrity of cholesterol-rich lipid rafts. In SH-SY5Y cells, fluorescence microscopy and co-localization with subcellular markers revealed that the Aβ oligomers co-internalized with PrPC, accumulated in endosomes, and subsequently trafficked to lysosomes. The cell surface binding, internalization, and downstream toxicity of Aβ oligomers was dependent on the transmembrane low density lipoprotein receptor-related protein-1 (LRP1). The binding of Aβ oligomers to cell surface PrPC impaired its ability to inhibit the activity of the β-secretase BACE1, which cleaves the amyloid precursor protein to produce Aβ. The green tea polyphenol (−)-epigallocatechin gallate and the red wine extract resveratrol both remodeled the fibrillar conformation of Aβ oligomers. The resulting nonfibrillar oligomers displayed significantly reduced binding to PrPC-expressing cells and were no longer cytotoxic. These data indicate that soluble, fibrillar Aβ oligomers bind to PrPC in a conformation-dependent manner and require the integrity of lipid rafts and the transmembrane LRP1 for their cytotoxicity, thus revealing potential targets to alleviate the neurotoxic properties of Aβ oligomers in AD. PMID:23386614

Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth.

PubMed

Forsythe, Jay G; Yu, Sheng-Sheng; Mamajanov, Irena; Grover, Martha A; Krishnamurthy, Ramanarayanan; Fernández, Facundo M; Hud, Nicholas V

2015-08-17

Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides-oligomers with a combination of ester and amide linkages-in model prebiotic reactions that are driven by wet-cool/dry-hot cycles. Through a combination of ester-amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Asp 58 modulates lens αA-crystallin oligomer formation and chaperone function.

PubMed

Takata, Takumi; Nakamura-Hirota, Tooru; Inoue, Rintaro; Morishima, Ken; Sato, Nobuhiro; Sugiyama, Masaaki; Fujii, Noriko

2018-06-01

Senile cataract onset is caused by insolubilization of lens proteins. The lens crystallin protein family correctly orders the formation of homo- or hetero-oligomers in lens fiber cells. Because lens fiber cells do not divide, covalent post-translational modifications, such as isomerization of aspartate residues, accumulate with aging. Although many isomerization sites of αA-crystallin have been reported, their structural and functional contributions have never been identified. In this study, αA-crystallin was extracted from aged human lens and separated into each oligomeric state by size exclusion chromatography and electrophoresis. The novel combination methodology of in-solution/gel tryptic digestion with liquid chromatography equipped with mass spectrometry (LC-MS/MS) was used to evaluate the isomerization of Asp 58. The contributions of isomerization to assembly, solubility, and chaperone functions of αA-crystallin were estimated using a series of mutations of Asp 58 in αA-crystallin. The results indicated that the isomerization of Asp 58 depended on the oligomer size and age of the lens. The substitution of Asp 58 for hydrophobic residues increased αA-crystallin oligomer size and decreased solubility. All substitutions decreased the chaperone function of αA-crystallin for aggregates of bovine βL-crystallin and alcohol dehydrogenase. The data indicated that Asp 58 in αA-crystallin was critical for intermolecular interactions in the lens. Our results also suggested that LC-MS/MS-based isomerization analyses of in-gel-digested products could be useful for investigating the isomerization of Asp residues in oligomeric states. This method could also be used to analyze d/l ratios of amino acid residues in soluble protein aggregates. © 2018 Federation of European Biochemical Societies.

Interaction of a novel peptoid enhancer--arginine oligomer with bovine submaxillary mucin.

PubMed

Liang, Wei; Davalian, Dariush; Torchilin, Vladimir P

2004-12-01

To determine the thermodynamics of binding reaction of arginine oligomer (R8) to bovine submaxillary mucin (BSM) in order to provide the foundation for understanding the influence of mucin on transport of macromolecules through mucosa mediated by arginine oligomer. Ultracentrifugation sedimentation was employed to investigate the interaction of BSM-R8. The mixtures of R8 with variable concentration and constant volume of BSM were placed on a shaker under oscillation at 25 degrees C to achieve equilibriums of binding reaction, and then centrifuged. The fluorescence intensity of the supernatant was measured by spectrofluorometer. The data were described by two types of binding sites model, the binding parameters of BSM-R8 were obtained by Scatchard plots. At the low pH values < or = 4.5 and ionic strength > or = 0.2 mol x L(-1), the BSM-R8 interaction was principally electrostatic interaction, the five primary binding sites (n1) predominantly were supplied by sulfate groups, the secondary binding sites apparently depended on pH, in that percent ionization of sialic acid residues (n2) in BSM. At the low ionic strength < or = 0.2 mol x L(-1) and pH 7.0, the BSM-R8 interaction was exceedingly complex, hydrogen bonds, hydrophobic interaction and electrostatic forces were involved in the interaction between R8 and BSM, the binding sites of BSM bound R8 were markedly increased. There existed evidence that R8 interacted with BSM. The pH and the ionic strength of the binding solution strongly affected the interaction of BSM with R8. The results suggested that the enhancing efficacy of the arginine oligomer for the transport of macromolecules through different site mucosa in body might be variable.

Chemical characterization of SOA formed from aqueous-phase reactions of phenols with the triplet excited state of carbonyl and hydroxyl radical

DOE PAGES

Yu, L.; Smith, J.; Laskin, A.; ...

2014-08-19

Phenolic compounds, which are emitted in significant amounts from biomass burning, can undergo fast reactions in atmospheric aqueous phases to form secondary organic aerosol (aqSOA). In this study, we investigate the reactions of phenol and two methoxy-phenols (syringol and guaiacol) with two major aqueous phase oxidants – the triplet excited states of an aromatic carbonyl ( 3C*) and hydroxyl radical (·OH). We thoroughly characterize the low-volatility species produced from these reactions and interpret their formation mechanisms using aerosol mass spectrometry (AMS), nanospray desorption electrospray ionization mass spectrometry (nano-DESI MS), and ion chromatography (IC). A large number of oxygenated molecules aremore » identified, including oligomers containing up to six monomer units, functionalized monomer and oligomers with carbonyl, carboxyl, and hydroxyl groups, and small organic acid anions (e.g., formate, acetate, oxalate, and malate). The average atomic oxygen-to-carbon (O / C) ratios of phenolic aqSOA are in the range of 0.85–1.23, similar to those of low-volatility oxygenated organic aerosol (LV-OOA) observed in ambient air. The aqSOA compositions are overall similar for the same precursor, but the reactions mediated by 3C* are faster than ·OH-mediated reactions and produce more oligomers and hydroxylated species at the point when 50% of the phenol had reacted. Profiles determined using a thermodenuder indicate that the volatility of phenolic aqSOA is influenced by both oligomer content and O / C ratio. In addition, the aqSOA shows enhanced light absorption in the UV-vis region, suggesting that aqueous-phase reactions of phenols are likely an important source of brown carbon in the atmosphere, especially in regions influenced by biomass burning.« less

Alzheimer's Therapeutics Targeting Amyloid Beta 1–42 Oligomers II: Sigma-2/PGRMC1 Receptors Mediate Abeta 42 Oligomer Binding and Synaptotoxicity

PubMed Central

Izzo, Nicholas J.; Xu, Jinbin; Zeng, Chenbo; Kirk, Molly J.; Mozzoni, Kelsie; Silky, Colleen; Rehak, Courtney; Yurko, Raymond; Look, Gary; Rishton, Gilbert; Safferstein, Hank; Cruchaga, Carlos; Goate, Alison; Cahill, Michael A.; Arancio, Ottavio; Mach, Robert H.; Craven, Rolf; Head, Elizabeth; LeVine, Harry; Spires-Jones, Tara L.; Catalano, Susan M.

2014-01-01

Amyloid beta (Abeta) 1–42 oligomers accumulate in brains of patients with Mild Cognitive Impairment (MCI) and disrupt synaptic plasticity processes that underlie memory formation. Synaptic binding of Abeta oligomers to several putative receptor proteins is reported to inhibit long-term potentiation, affect membrane trafficking and induce reversible spine loss in neurons, leading to impaired cognitive performance and ultimately to anterograde amnesia in the early stages of Alzheimer's disease (AD). We have identified a receptor not previously associated with AD that mediates the binding of Abeta oligomers to neurons, and describe novel therapeutic antagonists of this receptor capable of blocking Abeta toxic effects on synapses in vitro and cognitive deficits in vivo. Knockdown of sigma-2/PGRMC1 (progesterone receptor membrane component 1) protein expression in vitro using siRNA results in a highly correlated reduction in binding of exogenous Abeta oligomers to neurons of more than 90%. Expression of sigma-2/PGRMC1 is upregulated in vitro by treatment with Abeta oligomers, and is dysregulated in Alzheimer's disease patients' brain compared to age-matched, normal individuals. Specific, high affinity small molecule receptor antagonists and antibodies raised against specific regions on this receptor can displace synthetic Abeta oligomer binding to synaptic puncta in vitro and displace endogenous human AD patient oligomers from brain tissue sections in a dose-dependent manner. These receptor antagonists prevent and reverse the effects of Abeta oligomers on membrane trafficking and synapse loss in vitro and cognitive deficits in AD mouse models. These findings suggest sigma-2/PGRMC1 receptors mediate saturable oligomer binding to synaptic puncta on neurons and that brain penetrant, small molecules can displace endogenous and synthetic oligomers and improve cognitive deficits in AD models. We propose that sigma-2/PGRMC1 is a key mediator of the pathological effects of Abeta oligomers in AD and is a tractable target for small molecule disease-modifying therapeutics. PMID:25390692

Purified high molecular weight synthetic Aβ(1-42) and biological Aβ oligomers are equipotent in rapidly inducing MTT formazan exocytosis.

PubMed

Weidner, Adam M; Housley, Molly; Murphy, M Paul; Levine, Harry

2011-06-15

Synthetic soluble Aβ oligomers are often used as a surrogate for biologic material in a number of model systems. We compared the activity of Aβ oligomers (synthetic and cell culture media derived) on the human SH-SY5Y neuroblastoma and C2C12 mouse myoblast cell lines in a novel, modified MTT assay. Separating oligomers from monomeric peptide by size exclusion chromatography produced effects at peptide concentrations approaching physiologic levels (10-100 nM). Purified oligomers, but not monomers or fibrils, elicited an increase of a detergent-insoluble form of MTT formazan within 2h as opposed to a control toxin (H(2)O(2)). This effect was comparable for biological and synthetic peptide in both cell types. Monomeric Aβ attenuated the effect of soluble oligomers. This study suggests that the activities of biological and synthetic oligomers are indistinguishable during early stages of Aβ oligomer-cell interaction. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Amyloid-β oligomer detection by ELISA in cerebrospinal fluid and brain tissue.

PubMed

Bruggink, Kim A; Jongbloed, Wesley; Biemans, Elisanne A L M; Veerhuis, Rob; Claassen, Jurgen A H R; Kuiperij, H Bea; Verbeek, Marcel M

2013-02-15

Amyloid-β (Aβ) deposits are important pathological hallmarks of Alzheimer's disease (AD). Aβ aggregates into fibrils; however, the intermediate oligomers are believed to be the most neurotoxic species and, therefore, are of great interest as potential biomarkers. Here, we have developed an enzyme-linked immunosorbent assay (ELISA) specific for Aβ oligomers by using the same capture and (labeled) detection antibody. The ELISA predominantly recognizes relatively small oligomers (10-25 kDa) and not monomers. In brain tissue of APP/PS1 transgenic mice, we found that Aβ oligomer levels increase with age. However, for measurements in human samples, pretreatment to remove human anti-mouse antibodies (HAMAs) was required. In HAMA-depleted human hippocampal extracts, the Aβ oligomer concentration was significantly increased in AD compared with nondemented controls. Aβ oligomer levels could also be quantified in pretreated cerebrospinal fluid (CSF) samples; however, no difference was detected between AD and control groups. Our data suggest that levels of small oligomers might not be suitable as biomarkers for AD. In addition, we demonstrate the importance of avoiding HAMA interference in assays to quantify Aβ oligomers in human body fluids. Copyright © 2012 Elsevier Inc. All rights reserved.

An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain.

PubMed Central

Chartrand, P; Harvey, S C; Ferbeyre, G; Usman, N; Cedergren, R

1995-01-01

A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oligomers shows that, although the all-deoxyribonucleotide oligomer is less efficient in catalysis, the DNA/substrate complex shares many of the properties of the all-RNA hammerhead domain such as multiple turnover kinetics and dependence on Mg2+ concentration. On the other hand, the values of kinetic parameters distinguish the DNA oligomer from the all-RNA oligomer. In addition, an analog of the oligomer having a single ribonucleotide in a strongly conserved position of the hammerhead domain is associated with more efficient catalysis than the all-RNA oligomer. Images PMID:7479070

Combinatorial control of gene expression in Aspergillus niger grown on sugar beet pectin.

PubMed

Kowalczyk, Joanna E; Lubbers, Ronnie J M; Peng, Mao; Battaglia, Evy; Visser, Jaap; de Vries, Ronald P

2017-09-27

Aspergillus niger produces an arsenal of extracellular enzymes that allow synergistic degradation of plant biomass found in its environment. Pectin is a heteropolymer abundantly present in the primary cell wall of plants. The complex structure of pectin requires multiple enzymes to act together. Production of pectinolytic enzymes in A. niger is highly regulated, which allows flexible and efficient capture of nutrients. So far, three transcriptional activators have been linked to regulation of pectin degradation in A. niger. The L-rhamnose-responsive regulator RhaR controls the production of enzymes that degrade rhamnogalacturonan-I. The L-arabinose-responsive regulator AraR controls the production of enzymes that decompose the arabinan and arabinogalactan side chains of rhamnogalacturonan-II. The D-galacturonic acid-responsive regulator GaaR controls the production of enzymes that act on the polygalacturonic acid backbone of pectin. This project aims to better understand how RhaR, AraR and GaaR co-regulate pectin degradation. For that reason, we constructed single, double and triple disruptant strains of these regulators and analyzed their growth phenotype and pectinolytic gene expression in A. niger grown on sugar beet pectin.

Purification, characterization and anti-proliferation activities of polysaccharides extracted from Viscum coloratum (Kom.) Nakai.

PubMed

Chai, Yangyang; Zhao, Min

2016-09-20

Three polysaccharides, VCP1, VCP2 and VCP3 were isolated from Viscum coloratum (Kom.) Nakai using DEAE-cellulose chromatography. VCP1 (32KDa) was composed of glucose, galactose, arabinose, rhamnose and mannose, while VCP2 (280KDa) and VCP3 (21KDa) were consisted of glucose, galactose, arabinose, rhamnose, mannose, glucuronic acid and galacturonic acid. The optical rotation was measured at 20+1°C. The characteristic absorptive bands of purified fraction were determined by FT-IR. (13)C NMR spectroscopy analysis showed that VCP1 was a neutral polysaccharide, and VCP2 and VCP3 were RG-I type pectin. The linkage patterns of VCP2 were evaluated by methylation analysis: 1,5-linked Araf, 1,4-linked Galp, 1,2-linked Rhap, and 1,2,4-linked Rhap. The degree of esterification was 50%. The anti-proliferation ability against HepG2 cells and HepG2.2.15 cells of VCP2 was stronger than VCP1 and VCP3. So the polysaccharides from Viscum coloratum (Kom.) Nakai could be used as potential natural sources with inhibiting tumor cells proliferation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Isomer separation and effect of the degree of polymerization on the gas-phase structure of chondroitin sulfate oligosaccharides analyzed by ion mobility and tandem mass spectrometry.

PubMed

Poyer, Salomé; Lopin-Bon, Chrystel; Jacquinet, Jean-Claude; Salpin, Jean-Yves; Daniel, Régis

2017-12-15

Chondroitin sulfate (CS) glycosaminoglycans are bioactive sulfated polysaccharides comprising repeating units of uronic acid and N-acetyl galactose sulfated at various positions. The optimal length and sulfation pattern of the CS bioactive sequences remain elusive so that structure-activity relationships cannot be easily established. Development of efficient analytical methods allowing the differentiation of the various sulfation patterns of CS sequences is therefore of particular importance to correlate their biological functions to the sulfation pattern. Discrimination of different oligomers (dp2 to dp6) of synthetic chondroitin sulfate isomers was evaluated by electrospray ionization tandem mass spectrometry (ESI-MS/MS) in the negative-ion mode from deprotonated and alkali adduct species. In addition, ion mobility mass spectrometry (IMS-MS) was used to study the influence of both the degree of polymerization and sulfate group location on the gas-phase conformation of CS oligomers. ESI-MS/MS spectra of chondroitin sulfate isomers show characteristic product ions exclusively from alkali adduct species (Li, Na, K and Cs). Whatever the alkali adducts studied, MS/MS of chondroitin oligosaccharides sulfated at position 6 yields a specific product ion at m/z 139 while CS oligosaccharides sulfated at position 4 show a specific product ion at m/z 154. Being observed for the different CS oligomers di-, tetra- and hexasaccharides, these fragment ions are considered as diagnostic ions for chondroitin 6-O-sulfate and chondroitin 4-O-sulfate, respectively. IMS-MS experiments reveal that collision cross-sections (CCS) of CS oligomers with low charge states evolved linearly with degrees of polymerization indicating a similar gas-phase conformation. This study allows the fast and unambiguous differentiation of CS isomers sulfated at position 6 or 4 for both saturated and unsaturated analogues from MS/MS experiments. In addition, the CCS linear evolution of CS oligomers in function of the degree of polymerization indicates that no folding occurs even for hexasaccharides. Copyright © 2017 John Wiley & Sons, Ltd.

Isolation, Purification, Characterization and Effect upon HepG2 Cells of Anemaran from Rhizome Anemarrhena.

PubMed

Jiang, Qian-Qian; Zhao, Yun-Ping; Gao, Wen-Yuan; Li, Xia; Huang, Lu-Qi; Xiao, Pei-Gen

2013-01-01

The rhizome of Anemarrhena asphodeloides is used as food and traditional Chinese medicine for its hypoglycemic effect. The aim of this study was to investigate the isolation, purification and hypoglycemic activity of Anemaran as the active component. The influence factors (isolation duration, ratio of residuals to water and extracting times) during the isolation process were evaluated. The optimal conditions for NA and AA were extraction temperature 90ºC and 100ºC, duration 1h and 1.5 h, extraction time 3 and 3, and the solid-liquor ratio 1:20 and 1:15, respectively. Neutral and acid Anemaran (NA and AA) were isolated from the rhizome of Anemarrhena asphodeloides. Five fractions of NA-1, NA-2, NA-3, AA-1 and AA-2 were obtained after crude neutral and acid Anemaran purified through DEAE- 52 cellulose anion-exchange column. The characterizations of Anemaran and its different fractions were both analyzed by Fourier transform infrared spectroscopy (FT-IR) and scanning electron micrographs (SEM). Structural properties of different fractions were examined by FT-IR. Strong characteristic absorption peaks were observed at around 1744 cm(-1)and 1650 cm(-1) caused by the C=O group of uronic acids, and the band between 1440 cm(-1) and 1395 cm(-1) associated with the stretching vibration of C-O of galacturonic acid. Neither the crude neutral, nor the acid anemaran significantly inhibited the growth of HepG2 cells in-vitro, which indicated the low cytotoxicity of the anemaran. Furthermore, both neutral and acid anemaran showed hypoglycemic effect. The hypoglycemic effect of neutral anemaran was much higher than that of acid anemaran.

Electrografting of conductive oligomers and polymers using diazonium electroreduction

NASA Astrophysics Data System (ADS)

Lacroix, Jean Christophe; Trippe-Allard, Gaelle; Ghilane, Jalal; Martin, Pascal

2014-03-01

This paper describes the attachment of conjugated oligomers onto electrode surface through the reduction of diazonium compounds. In this connection some properties of conjugated oligomers and of layers grafted through diazonium electroreduction will first be briefly presented. The electrochemical behavior of conjugated oligomers grafted on a surface using diazonium electroreduction will then be discussed.

Structural and functional properties of prefibrillar α-synuclein oligomers.

PubMed

Pieri, Laura; Madiona, Karine; Melki, Ronald

2016-04-14

The deposition of fibrillar alpha-synuclein (α-syn) within inclusions (Lewy bodies and Lewy neurites) in neurons and glial cells is a hallmark of synucleinopathies. α-syn populates a variety of assemblies ranging from prefibrillar oligomeric species to fibrils whose specific contribution to neurodegeneration is still unclear. Here, we compare the specific structural and biological properties of distinct soluble prefibrillar α-syn oligomers formed either spontaneously or in the presence of dopamine and glutaraldehyde. We show that both on-fibrillar assembly pathway and distinct dopamine-mediated and glutaraldehyde-cross-linked α-syn oligomers are only slightly effective in perturbing cell membrane integrity and inducing cytotoxicity, while mature fibrils exhibit the highest toxicity. In contrast to low-molecular weight and unstable oligomers, large stable α-syn oligomers seed the aggregation of soluble α-syn within reporter cells although to a lesser extent than mature α-syn fibrils. These oligomers appear elongated in shape. Our findings suggest that α-syn oligomers represent a continuum of species ranging from unstable low molecular weight particles to mature fibrils via stable elongated oligomers composed of more than 15 α-syn monomers that possess seeding capacity.

Heat Resistant Characteristics of Major Royal Jelly Protein 1 (MRJP1) Oligomer

PubMed Central

Moriyama, Takanori; Ito, Aimi; Omote, Sumire; Miura, Yuri; Tsumoto, Hiroki

2015-01-01

Soluble royal jelly protein is a candidate factor responsible for mammiferous cell proliferation. Major royal jelly protein 1 (MRJP1), which consists of oligomeric and monomeric forms, is an abundant proliferative protein in royal jelly. We previously reported that MRJP1 oligomer has biochemical heat resistance. Therefore, in the present study, we investigated the effects of several heat treatments (56, 65 and 96°C) on the proliferative activity of MRJP1 oligomer. Heat resistance studies showed that the oligomer molecular forms were slightly maintained until 56℃, but the molecular forms were converted to macromolecular heat-aggregated MRJP1 oligomer at 65℃ and 96℃. But, the growth activity of MRJP1 oligomer treated with 96°C was slightly attenuated when compared to unheated MRJP1 oligomer. On the other hand, the cell proliferation activity was preserved until 96℃ by the cell culture analysis of Jurkat cells. In contrast, those of IEC-6 cells were not preserved even at 56°C. The present observations suggest that the bioactive heat-resistance properties were different by the origin of the cells. The cell proliferation analysis showed that MRJP1 oligomer, but not MRJP2 and MRJP3, significantly increased cell numbers, suggesting that MRJP1 oligomer is the predominant proliferation factor for mammiferous cells. PMID:26020775

Enzymatic production of defined chitosan oligomers with a specific pattern of acetylation using a combination of chitin oligosaccharide deacetylases

NASA Astrophysics Data System (ADS)

Hamer, Stefanie Nicole; Cord-Landwehr, Stefan; Biarnés, Xevi; Planas, Antoni; Waegeman, Hendrik; Moerschbacher, Bruno Maria; Kolkenbrock, Stephan

2015-03-01

Chitin and chitosan oligomers have diverse biological activities with potentially valuable applications in fields like medicine, cosmetics, or agriculture. These properties may depend not only on the degrees of polymerization and acetylation, but also on a specific pattern of acetylation (PA) that cannot be controlled when the oligomers are produced by chemical hydrolysis. To determine the influence of the PA on the biological activities, defined chitosan oligomers in sufficient amounts are needed. Chitosan oligomers with specific PA can be produced by enzymatic deacetylation of chitin oligomers, but the diversity is limited by the low number of chitin deacetylases available. We have produced specific chitosan oligomers which are deacetylated at the first two units starting from the non-reducing end by the combined use of two different chitin deacetylases, namely NodB from Rhizobium sp. GRH2 that deacetylates the first unit and COD from Vibrio cholerae that deacetylates the second unit starting from the non-reducing end. Both chitin deacetylases accept the product of each other resulting in production of chitosan oligomers with a novel and defined PA. When extended to further chitin deacetylases, this approach has the potential to yield a large range of novel chitosan oligomers with a fully defined architecture.

Heat Resistant Characteristics of Major Royal Jelly Protein 1 (MRJP1) Oligomer.

PubMed

Moriyama, Takanori; Ito, Aimi; Omote, Sumire; Miura, Yuri; Tsumoto, Hiroki

2015-01-01

Soluble royal jelly protein is a candidate factor responsible for mammiferous cell proliferation. Major royal jelly protein 1 (MRJP1), which consists of oligomeric and monomeric forms, is an abundant proliferative protein in royal jelly. We previously reported that MRJP1 oligomer has biochemical heat resistance. Therefore, in the present study, we investigated the effects of several heat treatments (56, 65 and 96°C) on the proliferative activity of MRJP1 oligomer. Heat resistance studies showed that the oligomer molecular forms were slightly maintained until 56℃, but the molecular forms were converted to macromolecular heat-aggregated MRJP1 oligomer at 65℃ and 96℃. But, the growth activity of MRJP1 oligomer treated with 96°C was slightly attenuated when compared to unheated MRJP1 oligomer. On the other hand, the cell proliferation activity was preserved until 96℃ by the cell culture analysis of Jurkat cells. In contrast, those of IEC-6 cells were not preserved even at 56°C. The present observations suggest that the bioactive heat-resistance properties were different by the origin of the cells. The cell proliferation analysis showed that MRJP1 oligomer, but not MRJP2 and MRJP3, significantly increased cell numbers, suggesting that MRJP1 oligomer is the predominant proliferation factor for mammiferous cells.

Capillary electrophoresis of chitooligosaccharides in acidic solution: simple determination using a quaternary-ammonium-modified column and indirect photometric detection with crystal violet.

PubMed

Hattori, Toshiaki; Anraku, Nobuhiro; Kato, Ryo

2010-02-01

Five chitosan oligosaccharides were separated in acidic aqueous solution by capillary electrophoresis (CE) with indirect photometric detection using a positively coated capillary. Electrophoretic mobility of the chitooligosaccharides (COSs) depended on the number of monomer units in acidic aqueous solution, similar to other polyelectrolyte oligomers. The separation was developed in nitric acid aqueous solution at pH 3.0 with 1 mM Crystal Violet, using a capillary positively coated with N-trimethoxypropyl-N,N,N-trimethylammonium chloride. The limit of the detection for chitooligosaccharides with two to six saccharide chains was less than 5 microM. CE determination of an enzymatically hydrolyzed COS agreed with results from HPLC. 2009 Elsevier B.V. All rights reserved.

Glycyrrhiza and Uncaria Hook contribute to protective effect of traditional Japanese medicine yokukansan against amyloid β oligomer-induced neuronal death.

PubMed

Kanno, Hitomi; Kawakami, Zenji; Iizuka, Seiichi; Tabuchi, Masahiro; Mizoguchi, Kazushige; Ikarashi, Yasushi; Kase, Yoshio

2013-08-26

Yokukansan, a traditional Japanese (Kampo) medicine, composed of seven medicinal herbs has been traditionally used to treat neurosis, insomnia, and night crying and irritability in children. Recently, this medicine has been reported to improve the behavioral and psychological symptoms of dementia (BPSD) that often become problematic in patients with Alzheimer's disease (AD). Amyloid β (Aβ) oligomers, which are extremely toxic to neurons, are involved in neurodegeneration in AD. In animals, yokukansan has been proven to improve memory impairments and BPSD-like behavior in transgenic mice overexpressing amyloid precursor protein and mice intracerebroventricularly injected with Aβ oligomers. These results suggest that yokukansan is potentially able to reduce the neurotoxicity of Aβ oligomers. Therefore, the present study aimed to explore the improving effects brought by yokukansan that consists of seven herbs for Aβ oligomer-induced neurotoxicity in vitro and to identify the candidate herbs in yokukansan's action. Primary cultured rat cortical neurons were used. Neurotoxicity induced by Aβ oligomers (3µM) and improving effects of yokukansan (300-1000 µg/mL) and its constituent herbs were evaluated in MTT assay, DNA fragmentation analysis, and electron microscopic analysis at 48h after treatment with Aβ oligomers and drugs. Moreover, changes in expression of genes related to endoplasmic reticulum (ER) stress and in caspase-3 activity that is the enzyme closely related to apoptosis were analyzed to investigate the underlying mechanisms. Yokukansan ameliorated Aβ oligomer-induced neuronal damage in a dose-dependent manner in the MTT assay. This drug also suppressed DNA fragmentation caused by Aβ oligomers. Electron microscopic analysis suggested that yokukansan reduced karyopyknosis and the expansion of rough ER caused by Aβ oligomers. However, neither Aβ oligomers nor yokukansan affected the mRNA expression of any ER stress-related genes, including CHOP and GRP78. On the other hand, yokukansan dose-dependently suppressed Aβ oligomer-induced activation of caspase-3. Among the seven constituents of yokukansan, Glycyrrhiza and Uncaria Hook (60-200 µg/mL) suppressed Aβ oligomer-induced neuronal damage, DNA fragmentation, karyopyknosis, and caspase-3 activation to almost the same extent as yokukansan. The present results suggest that yokukansan possesses an ameliorative effect against Aβ oligomer-induced neuronal apoptosis through the suppression of caspase-3 activation. Glycyrrhiza and Uncaria Hook may, at least in part, contribute to the neuroprotective effect of yokukansan. These mechanisms may underlie the improving effects of yokukansan on memory impairment and BPSD-like behaviors induced by Aβ oligomers. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Effects of Glycine, Water, Ammonia, and Ammonium Bicarbonate on the Oligomerization of Methionine

NASA Astrophysics Data System (ADS)

Huang, Rui; Furukawa, Yoshihiro; Otake, Tsubasa; Kakegawa, Takeshi

2017-06-01

The abiotic oligomerization of amino acids may have created primordial, protein-like biological catalysts on the early Earth. Previous studies have proposed and evaluated the potential of diagenesis for the amino acid oligomerization, simulating the formation of peptides that include glycine, alanine, and valine, separately. However, whether such conditions can promote the formation of peptides composed of multiple amino acids remains unclear. Furthermore, the chemistry of pore water in sediments should affect the oligomerization and degradation of amino acids and oligomers, but these effects have not been studied extensively. In this study, we investigated the effects of water, ammonia, ammonium bicarbonate, pH, and glycine on the oligomerization and degradation of methionine under high pressure (150 MPa) and high temperature conditions (175 °C) for 96 h. Methionine is more difficult to oligomerize than glycine and methionine dimer was formed in the incubation of dry powder of methionine. Methionine oligomers as long as trimers, as well as methionylglycine and glycylmethionine, were formed under every condition with these additional compounds. Among the compounds tested, the oligomerization reaction rate was accelerated by the presence of water and by an increase in pH. Ammonia also increased the oligomerization rate but consumed methionine by side reactions and resulted in the rapid degradation of methionine and its peptides. Similarly, glycine accelerated the oligomerization rate of methionine and the degradation of methionine, producing water, ammonia, and bicarbonate through its decomposition. With Gly, heterogeneous dimers (methionylglycine and glycylmethionine) were formed in greater amounts than with other additional compounds although smaller amount of these heterogeneous dimers were formed with other additional compounds. These results suggest that accelerated reaction rates induced by water and co-existing reactive compounds promote the oligomerization of less reactive amino acids during diagenesis and enhance the formation of peptides composed of multiple amino acids.

Monounsaturated fatty acid ether oligomers formed during heating of virgin olive oil show agglutination activity against human red blood cells.

PubMed

Patrikios, Ioannis S; Mavromoustakos, Thomas M

2014-01-29

The present work focuses on the characterization of molecules formed when virgin olive oil is heated at 130 °C for 24 h open in air, which are found to be strong agglutinins. The hemagglutinating activity of the newly formed molecule isolated from the heated virgin olive oil sample was estimated against human red blood cells (RBCs). Dimers and polymers (high molecular weight molecules) were identified through thin layer chromatography (TLC) of the oil mixture. (1)H and (13)C nuclear magnetic resonance (NMR) and gas chromatography-mass spectroscopy (GC-MS) were the methods used for structural characterization. Among others, oligomerization of at least two monounsaturated fatty acids (FA) by an ether linkage between the hydrocarbon chains is involved. Light microscopy was used to characterize and visualize the agglutination process. Agglutination without fusion or lysis was observed. It was concluded that the heating of virgin olive oil open in air, among other effects, produces oligomerization as well as polymerization of unsaturated FA, possibly of monohydroxy, monounsaturated FA that is associated with strong hemagglutinating activity against human RBCs. The nutritional value and the effects on human health of such oligomers are not discussed in the literature and remain to be investigated.

Impaired trafficking of human kidney anion exchanger (kAE1) caused by hetero-oligomer formation with a truncated mutant associated with distal renal tubular acidosis.

PubMed

Quilty, Janne A; Cordat, Emmanuelle; Reithmeier, Reinhart A F

2002-12-15

Autosomal dominant distal renal tubular acidosis (dRTA) has been associated with several mutations in the anion exchanger AE1 gene. The effect of an 11-amino-acid C-terminal dRTA truncation mutation (901 stop) on the expression of kidney AE1 (kAE1) and erythroid AE1 was examined in transiently transfected HEK-293 cells. Unlike the wild-type proteins, kAE1 901 stop and AE1 901 stop mutants exhibited impaired trafficking from the endoplasmic reticulum to the plasma membrane as determined by immunolocalization, cell-surface biotinylation, oligosaccharide processing and pulse-chase experiments. The 901 stop mutants were able to bind to an inhibitor affinity resin, suggesting that these mutant membrane proteins were not grossly misfolded. Co-expression of wild-type and mutant kAE1 or AE1 resulted in intracellular retention of the wild-type proteins in a pre-medial Golgi compartment. This dominant negative effect was due to hetero-oligomer formation of the mutant and wild-type proteins. Intracellular retention of kAE1 in the alpha-intercalated cells of the kidney would account for the impaired acid secretion into the urine characteristic of dRTA.

Poly(amido-amine)-based hydrogels with tailored mechanical properties and degradation rates for tissue engineering.

PubMed

Martello, Federico; Tocchio, Alessandro; Tamplenizza, Margherita; Gerges, Irini; Pistis, Valentina; Recenti, Rossella; Bortolin, Monica; Del Fabbro, Massimo; Argentiere, Simona; Milani, Paolo; Lenardi, Cristina

2014-03-01

Poly(amido-amine) (PAA) hydrogels containing the 2,2-bisacrylamidoacetic acid-4-amminobutyl guanidine monomeric unit have a known ability to enhance cellular adhesion by interacting with the arginin-glycin-aspartic acid (RGD)-binding αVβ3 integrin, expressed by a wide number of cell types. Scientific interest in this class of materials has traditionally been hampered by their poor mechanical properties and restricted range of degradation rate. Here we present the design of novel biocompatible, RGD-mimic PAA-based hydrogels with wide and tunable degradation rates as well as improved mechanical and biological properties for biomedical applications. This is achieved by radical polymerization of acrylamide-terminated PAA oligomers in both the presence and absence of 2-hydroxyethylmethacrylate. The degradation rate is found to be precisely tunable by adjusting the PAA oligomer molecular weight and acrylic co-monomer concentration in the starting reaction mixture. Cell adhesion and proliferation tests on Madin-Darby canine kidney epithelial cells show that PAA-based hydrogels have the capacity to promote cell adhesion up to 200% compared to the control. Mechanical tests show higher compressive strength of acrylic chain containing hydrogels compared to traditional PAA hydrogels. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Quantification of DNA using the luminescent oxygen channeling assay.

PubMed

Patel, R; Pollner, R; de Keczer, S; Pease, J; Pirio, M; DeChene, N; Dafforn, A; Rose, S

2000-09-01

Simplified and cost-effective methods for the detection and quantification of nucleic acid targets are still a challenge in molecular diagnostics. Luminescent oxygen channeling assay (LOCI(TM)) latex particles can be conjugated to synthetic oligodeoxynucleotides and hybridized, via linking probes, to different DNA targets. These oligomer-conjugated LOCI particles survive thermocycling in a PCR reaction and allow quantified detection of DNA targets in both real-time and endpoint formats. The endpoint DNA quantification format utilized two sensitizer bead types that are sensitive to separate illumination wavelengths. These two bead types were uniquely annealed to target or control amplicons, and separate illuminations generated time-resolved chemiluminescence, which distinguished the two amplicon types. In the endpoint method, ratios of the two signals allowed determination of the target DNA concentration over a three-log range. The real-time format allowed quantification of the DNA target over a six-log range with a linear relationship between threshold cycle and log of the number of DNA targets. This is the first report of the use of an oligomer-labeled latex particle assay capable of producing DNA quantification and sequence-specific chemiluminescent signals in a homogeneous format. It is also the first report of the generation of two signals from a LOCI assay. The methods described here have been shown to be easily adaptable to new DNA targets because of the generic nature of the oligomer-labeled LOCI particles.

Structural and functional properties of prefibrillar α-synuclein oligomers

PubMed Central

Pieri, Laura; Madiona, Karine; Melki, Ronald

2016-01-01

The deposition of fibrillar alpha-synuclein (α-syn) within inclusions (Lewy bodies and Lewy neurites) in neurons and glial cells is a hallmark of synucleinopathies. α-syn populates a variety of assemblies ranging from prefibrillar oligomeric species to fibrils whose specific contribution to neurodegeneration is still unclear. Here, we compare the specific structural and biological properties of distinct soluble prefibrillar α-syn oligomers formed either spontaneously or in the presence of dopamine and glutaraldehyde. We show that both on-fibrillar assembly pathway and distinct dopamine-mediated and glutaraldehyde-cross-linked α-syn oligomers are only slightly effective in perturbing cell membrane integrity and inducing cytotoxicity, while mature fibrils exhibit the highest toxicity. In contrast to low-molecular weight and unstable oligomers, large stable α-syn oligomers seed the aggregation of soluble α-syn within reporter cells although to a lesser extent than mature α-syn fibrils. These oligomers appear elongated in shape. Our findings suggest that α-syn oligomers represent a continuum of species ranging from unstable low molecular weight particles to mature fibrils via stable elongated oligomers composed of more than 15 α-syn monomers that possess seeding capacity. PMID:27075649

Antiparallel Triple-strand Architecture for Prefibrillar Aβ42 Oligomers*

PubMed Central

Gu, Lei; Liu, Cong; Stroud, James C.; Ngo, Sam; Jiang, Lin; Guo, Zhefeng

2014-01-01

Aβ42 oligomers play key roles in the pathogenesis of Alzheimer disease, but their structures remain elusive partly due to their transient nature. Here, we show that Aβ42 in a fusion construct can be trapped in a stable oligomer state, which recapitulates characteristics of prefibrillar Aβ42 oligomers and enables us to establish their detailed structures. Site-directed spin labeling and electron paramagnetic resonance studies provide structural restraints in terms of side chain mobility and intermolecular distances at all 42 residue positions. Using these restraints and other biophysical data, we present a novel atomic-level oligomer model. In our model, each Aβ42 protein forms a single β-sheet with three β-strands in an antiparallel arrangement. Each β-sheet consists of four Aβ42 molecules in a head-to-tail arrangement. Four β-sheets are packed together in a face-to-back fashion. The stacking of identical segments between different β-sheets within an oligomer suggests that prefibrillar oligomers may interconvert with fibrils via strand rotation, wherein β-strands undergo an ∼90° rotation along the strand direction. This work provides insights into rational design of therapeutics targeting the process of interconversion between toxic oligomers and non-toxic fibrils. PMID:25118290

Characteristics of fucose-containing polysaccharides from submerged fermentation of Agaricus blazei Murill.

PubMed

Wang, Hsueh-Ting; Yang, Li-Chan; Yu, Hui-Ching; Chen, Miaw-Ling; Wang, Huei-Ju; Lu, Ting-Jang

2018-04-01

Fucose is one of important residues of recognition pattern for many immune cells. In this study, we characterized bioactive fucose-containing acidic polysaccharides from submerged fermentation of Agaricus blazei Murill. We obtained the polysaccharides through a cell-based activity-guided strategy, and used carbohydrate recognition monoclonal antibodies based Enzyme-Linked Immuno Sorbent Assay (ELISA) along with methylation and NMR analyses to investigate the structural characteristics of the polysaccharides. The polysaccharides had Mw of 3.5 × 10 5  Da. The major sugars were l-fucose, l-arabinose, d-galactose, d-xylose, and d-galacturonic acid in the molar ratio of 6.4, 15.5, 28.5, 14.7, and 25.0% with a small amount of d-glucose, d-mannose, l-rhamnose, and d-glucuronic acid. Results indicated that the bioactive polysaccharides consisted of a (1,4)-Galp and (1,4)-GalAp back bone; (1,2)-Xyl and (1,2)-Rha might also comprise backbone or constitute side chain; linkage (1,5)-Ara and terminal fucosyl residues were also involved in the polysaccharides. Regarding bioactivity, removal of the terminal l-fucosyl residues reduced the TNF-α cytokine stimulating activity of the polysaccharides in a RAW 264.7 macrophage cell-line test, whereas NF-κB and TLR4 affected the polysaccharide-induced TNF-α production. Copyright © 2017. Published by Elsevier B.V.

The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Zilian; Chen, Yi; Wang, Rui

Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that bacterial EPS rich in uronic acid is resistant to mineralization by microbes and thus has a long residence time in global oceans. To confirm this hypothesis, bacterial EPS rich in galacturonic acid was isolated from Alteromonas sp. JL2810. The EPS was used to amend natural seawater to investigate the bioavailability of this EPS by native populations, in the presence and absence of ammonium and phosphate amendment. The data indicated that the bacterial EPS could not bemore » completely consumed during the cultivation period and that the bioavailability of EPS was not only determined by its intrinsic properties, but was also determined by other factors such as the availability of inorganic nutrients. During the experiment, the humic-like component of fluorescent dissolved organic matter (FDOM) was freshly produced. Bacterial community structure analysis indicated that the class Flavobacteria of the phylum Bacteroidetes was the major contributor for the utilization of EPS. This report is the first to indicate that Flavobacteria are a major contributor to bacterial EPS degradation. Finally, the fraction of EPS that could not be completely utilized and the FDOM (e.g., humic acid-like substances) produced de novo may be refractory and may contribute to the carbon storage in the oceans.« less

Physicochemical properties of water-soluble polysaccharides from black cumin seeds.

PubMed

Trigui, Ines; Yaich, Héla; Sila, Assaâd; Cheikh-Rouhou, Salma; Bougatef, Ali; Blecker, Christophe; Attia, Hamadi; Ayadi, M A

2018-06-01

In the present work, water-soluble polysaccharides were isolated from black cumin seeds. Polysaccharides were characterized by their carbohydrate composition, molecular weight, thermal stability and by FTIR, NMR spectroscopy and X-ray diffraction. The surface, the functional and the antioxidant properties of black cumin water-soluble polysaccharides (BCWSP) were also investigated. BCWSP consisted mainly of galacturonic acid (30.20%), glucuronic acid (17.66%) and neutral sugar (22.99%). BCWSP was composed of high peak molecular weight. The FTIR spectrum obtained for BCWSP showed two most important absorptions, at 1659 and 1085 cm -1 , which corresponded to COO - of uronic acids and pyranose form, respectively. NMR spectroscopy data suggested that the BCWSP is probably a rhamnogalacturonan backbone with galactan and arabinan side chains. X-ray pattern revealed the semi-crystalline behavior of BCWSP. WHC and OHC of BCWSP were relatively high and varied with temperatures. The polysaccharide zeta potential was greatly affected by pH. Results indicated that the decrease of surface tension has influenced foaming and emulsifying capacities. The DPPH radical scavenging activity of the BCWSP was 63.25% at 1 mg/mL. The BCWSP displayed moderate reductive, β carotene bleaching and chelating abilities. Overall, our results suggested that BCWSP could be used as alternative additives in food and non-food products. Copyright © 2017. Published by Elsevier B.V.

Sequential ultrasound-microwave assisted acid extraction (UMAE) of pectin from pomelo peels.

PubMed

Liew, Shan Qin; Ngoh, Gek Cheng; Yusoff, Rozita; Teoh, Wen Hui

2016-12-01

This study aims to optimize sequential ultrasound-microwave assisted extraction (UMAE) on pomelo peel using citric acid. The effects of pH, sonication time, microwave power and irradiation time on the yield and the degree of esterification (DE) of pectin were investigated. Under optimized conditions of pH 1.80, 27.52min sonication followed by 6.40min microwave irradiation at 643.44W, the yield and the DE value of pectin obtained was respectively at 38.00% and 56.88%. Based upon optimized UMAE condition, the pectin from microwave-ultrasound assisted extraction (MUAE), ultrasound assisted extraction (UAE) and microwave assisted extraction (MAE) were studied. The yield of pectin adopting the UMAE was higher than all other techniques in the order of UMAE>MUAE>MAE>UAE. The pectin's galacturonic acid content obtained from combined extraction technique is higher than that obtained from sole extraction technique and the pectin gel produced from various techniques exhibited a pseudoplastic behaviour. The morphological structures of pectin extracted from MUAE and MAE closely resemble each other. The extracted pectin from UMAE with smaller and more regular surface differs greatly from that of UAE. This has substantiated the highest pectin yield of 36.33% from UMAE and further signified their compatibility and potentiality in pectin extraction. Copyright © 2016 Elsevier B.V. All rights reserved.

The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities

DOE PAGES

Zhang, Zilian; Chen, Yi; Wang, Rui; ...

2015-11-16

Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that bacterial EPS rich in uronic acid is resistant to mineralization by microbes and thus has a long residence time in global oceans. To confirm this hypothesis, bacterial EPS rich in galacturonic acid was isolated from Alteromonas sp. JL2810. The EPS was used to amend natural seawater to investigate the bioavailability of this EPS by native populations, in the presence and absence of ammonium and phosphate amendment. The data indicated that the bacterial EPS could not bemore » completely consumed during the cultivation period and that the bioavailability of EPS was not only determined by its intrinsic properties, but was also determined by other factors such as the availability of inorganic nutrients. During the experiment, the humic-like component of fluorescent dissolved organic matter (FDOM) was freshly produced. Bacterial community structure analysis indicated that the class Flavobacteria of the phylum Bacteroidetes was the major contributor for the utilization of EPS. This report is the first to indicate that Flavobacteria are a major contributor to bacterial EPS degradation. Finally, the fraction of EPS that could not be completely utilized and the FDOM (e.g., humic acid-like substances) produced de novo may be refractory and may contribute to the carbon storage in the oceans.« less

Apoptosis induced by islet amyloid polypeptide soluble oligomers is neutralized by diabetes-associated specific antibodies

PubMed Central

Bram, Yaron; Frydman-Marom, Anat; Yanai, Inbal; Gilead, Sharon; Shaltiel-Karyo, Ronit; Amdursky, Nadav; Gazit, Ehud

2014-01-01

Soluble oligomeric assemblies of amyloidal proteins appear to act as major pathological agents in several degenerative disorders. Isolation and characterization of these oligomers is a pivotal step towards determination of their pathological relevance. Here we describe the isolation of Type 2 diabetes-associated islet amyloid polypeptide soluble cytotoxic oligomers; these oligomers induced apoptosis in cultured pancreatic cells, permeated model lipid vesicles and interacted with cell membranes following complete internalization. Moreover, antibodies which specifically recognized these assemblies, but not monomers or amyloid fibrils, were exclusively identified in diabetic patients and were shown to neutralize the apoptotic effect induced by these oligomers. Our findings support the notion that human IAPP peptide can form highly toxic oligomers. The presence of antibodies identified in the serum of diabetic patients confirms the pathological relevance of the oligomers. In addition, the newly identified structural epitopes may also provide new mechanistic insights and a molecular target for future therapy. PMID:24589570

A native interactor scaffolds and stabilizes toxic ATAXIN-1 oligomers in SCA1

PubMed Central

Lasagna-Reeves, Cristian A; Rousseaux, Maxime WC; Guerrero-Muñoz, Marcos J; Park, Jeehye; Jafar-Nejad, Paymaan; Richman, Ronald; Lu, Nan; Sengupta, Urmi; Litvinchuk, Alexandra; Orr, Harry T; Kayed, Rakez; Zoghbi, Huda Y

2015-01-01

Recent studies indicate that soluble oligomers drive pathogenesis in several neurodegenerative proteinopathies, including Alzheimer and Parkinson disease. Curiously, the same conformational antibody recognizes different disease-related oligomers, despite the variations in clinical presentation and brain regions affected, suggesting that the oligomer structure might be responsible for toxicity. We investigated whether polyglutamine-expanded ATAXIN-1, the protein that underlies spinocerebellar ataxia type 1, forms toxic oligomers and, if so, what underlies their toxicity. We found that mutant ATXN1 does form oligomers and that oligomer levels correlate with disease progression in the Atxn1154Q/+ mice. Moreover, oligomeric toxicity, stabilization and seeding require interaction with Capicua, which is expressed at greater ratios with respect to ATXN1 in the cerebellum than in less vulnerable brain regions. Thus, specific interactors, not merely oligomeric structure, drive pathogenesis and contribute to regional vulnerability. Identifying interactors that stabilize toxic oligomeric complexes could answer longstanding questions about the pathogenesis of other proteinopathies. DOI: http://dx.doi.org/10.7554/eLife.07558.001 PMID:25988806

Monomeric and polymeric forms of ependymin: a brain extracellular glycoprotein implicated in memory consolidation processes.

PubMed

Shashoua, V E

1988-07-01

Ependymin, a brain extracellular glycoprotein that appears to be implicated in neural circuit modifications associated with the process of memory consolidation, can rapidly polymerize into fibrous aggregates when the Ca2+ concentration in solution is reduced by the addition of EGTA or by dialysis. Such aggregates, once formed, could not be redissolved in boiling 1% SDS in 6 M urea, acetic acid, saturated aqueous potassium thiocyanate, and trifluoroacetic acid. They were, however, soluble in formic acid. Investigations of the immunological properties of ependymin indicated that various monomers, oligomers and polymers of the molecule with differing carbohydrate contents can be obtained. The polymerization properties of the ependymins may play an important role in their functions in memory consolidation mechanisms.

Nitric oxide-induced interstrand cross-links in DNA.

PubMed

Caulfield, Jennifer L; Wishnok, John S; Tannenbaum, Steven R

2003-05-01

The DNA damaging effects of nitrous acid have been extensively studied, and the formation of interstrand cross-links have been observed. The potential for this cross-linking to occur through a common nitrosating intermediate derived from nitric oxide is investigated here. Using a HPLC laser-induced fluorescence (LIF) system, the amount of interstrand cross-link formed on nitric oxide treatment of the 5'-fluorescein-labeled oligomer ATATCGATCGATAT was determined. This self-complimentary sequence contains two 5'-CG sequences, which is the preferred site for nitrous acid-induced cross-linking. Nitric oxide was delivered to an 0.5 mM oligomer solution at 15 nmol/mL/min to give a final nitrite concentration of 652 microM. The resulting concentration of the deamination product, xanthine, in this sample was found to be 211 +/- 39 nM, using GC/MS, and the amount of interstrand cross-link was determined to be 13 +/- 2.5 nM. Therefore, upon nitric oxide treatment, the cross-link is found at approximately 6% of the amount of the deamination product. Using this system, detection of the cross-link is also possible for significantly lower doses of nitric oxide, as demonstrated by treatment of the same oligomer with NO at a rate of 18 nmol/mL/min resulting in a final nitrite concentration of 126 microM. The concentration of interstrand cross-link was determined to be 3.6 +/- 0.1 nM in this sample. Therefore, using the same dose rate, when the total nitric oxide concentration delivered drops by a factor of approximately 5, the concentration of cross-link drops by a factor of about 4-indicating a qausi-linear response. It may now be possible to predict the number of cross-links in a small genome based on the number of CpG sequences and the yield of xanthine derived from nitrosative deamination.

Polymerization on the rocks: beta-amino acids and arginine

NASA Technical Reports Server (NTRS)

Liu, R.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1998-01-01

We have studied the accumulation of long oligomers of beta-amino acids on the surface of minerals using the 'polymerization on the rocks' protocol. We find that long oligopeptides of beta-glutamic acid which cannot be formed in homogeneous aqueous solution are accumulated efficiently on the surface of hydroxylapatite using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDAC) as condensing agent. The EDAC-induced oligomerization of aspartic acid on hydroxylapatite proceeds even more efficiently. Hydroxylapatite can also facilitate the ligation of the tripeptide (glu)3. The 'polymerization on the rocks' scenario is not restricted to negatively-charged amino acids. Oligoarginines are accumulated on the surface of illite using carbonyldiimidizole (CDI) as condensing agent. We find that FeS2 catalyzes the CDI-induced oligomerization of arginine, although it does not adsorb oligoarginines. These results are relevant to the formation of polypeptides on the primitive earth.

Cashew apple juice as microbial cultivation medium for non-immunogenic hyaluronic acid production.

PubMed

Oliveira, Adriano H; Ogrodowski, Cristiane C; de Macedo, André C; Santana, Maria Helena A; Gonçalves, Luciana R B

2013-12-01

In this work, natural cashew apple juice was used as cultivation medium as an alternative to substitute brain heart infusion medium. The effect of aeration and juice supplementation with yeast extract on the production of hyaluronic acid in batch fermentation was also investigated. Similar levels of cell mass were obtained in inoculum using cashew apple juice supplemented with yeast extract or the conventional brain heart infusion medium. Fermentation in Erlenmeyer flasks produced low biomass and hyaluronic acid concentrations. The hyaluronic acid concentration and viscosity increased from 0.15 g/L and 3.87 cP (no aeration or medium supplementation) to 1.76 g/L and 107 cP, when aeration (2 vvm) and 60 g/L of yeast extract were used. The results suggest the production of low-molecular weight hyaluronic acid oligomers instead of the high molecular weight polymer.

Cashew apple juice as microbial cultivation medium for non-immunogenic hyaluronic acid production

PubMed Central

Oliveira, Adriano H.; Ogrodowski, Cristiane C.; de Macedo, André C.; Santana, Maria Helena A.; Gonçalves, Luciana R.B.

2013-01-01

In this work, natural cashew apple juice was used as cultivation medium as an alternative to substitute brain heart infusion medium. The effect of aeration and juice supplementation with yeast extract on the production of hyaluronic acid in batch fermentation was also investigated. Similar levels of cell mass were obtained in inoculum using cashew apple juice supplemented with yeast extract or the conventional brain heart infusion medium. Fermentation in Erlenmeyer flasks produced low biomass and hyaluronic acid concentrations. The hyaluronic acid concentration and viscosity increased from 0.15 g/L and 3.87 cP (no aeration or medium supplementation) to 1.76 g/L and 107 cP, when aeration (2 vvm) and 60 g/L of yeast extract were used. The results suggest the production of low-molecular weight hyaluronic acid oligomers instead of the high molecular weight polymer. PMID:24688498

Synthesis and characterization of oligobenzimidazoles: Electrochemical, electrical, optical, thermal and rectification properties

NASA Astrophysics Data System (ADS)

Anand, Siddeswaran; Muthusamy, Athianna

2018-03-01

A series of benzimidazole monomers, (2-(2, 4-dihydroxyphenyl)-1H-benzimidazol-5-yl)(phenyl) methanone (BIKH), 2-(3-ethoxy-2-hydroxyphenyl)-1H-benzo [d]imidazole-5-yl) (phenyl) methanone (BIKE) and 2-(5-bromo-2-hydroxyphenyl)-1H-benzo [d]imidazole-5-yl) (phenyl) methanone (BIKB) were prepared by condensing three substituted aromatic aldehydes with 3, 4-diaminobenzophenone. In aqueous alkaline medium the benzimidazoles were converted in to oligomers by oxidative polycondensation using NaOCl as oxidant. The formation of monomers and oligomers were confirmed with 1H, 13C NMR, FT-IR, and UV-visible spectroscopic techniques. The oligomers were investigated for their optical, electrical, electrochemical and thermal properties. The electrochemical and optical band gaps of monomers and oligomers were calculated using both UV-visible spectroscopy and cyclic voltametry respectively. The band gap values of monomers are compared with band gap values obtained from quantum theoretical calculations with DFT. The electrical conductivity studies of iodine doped and undoped oligomers were done using two point probe technique. It is found that these values are showing good correlation with the charge densities on imidazole nitrogen obtained from Huckel method. The conductivity of oligomers increases with increase in iodine vapour contact time. The dielectric properties of oligomers have been investigated at different temperature and frequency. The dielectric measurement data were used to calculate the AC conductivity and activation energy of oligomers. Oligomer OBIKH is having greater thermal stability due to its number of chain propagation sites than other oligomers and is shown by its high carbines residue of around 60% at 600 °C in thermogravimetric analysis. I-V characteristics of oligobenzimidazole p-n diodes have shown good rectifying nature in the range -4 to 4 V.

Alzheimer's amyloid-β oligomers rescue cellular prion protein induced tau reduction via the Fyn pathway.

PubMed

Chen, Rong-Jie; Chang, Wei-Wei; Lin, Yu-Chun; Cheng, Pei-Lin; Chen, Yun-Ru

2013-09-18

Amyloid-β (Aβ) and tau are the pathogenic hallmarks in Alzheimer's disease (AD). Aβ oligomers are considered the actual toxic entities, and the toxicity relies on the presence of tau. Recently, Aβ oligomers have been shown to specifically interact with cellular prion protein (PrP(C)) where the role of PrP(C) in AD is still not fully understood. To investigate the downstream mechanism of PrP(C) and Aβ oligomer interaction and their possible relationships to tau, we examined tau expression in human neuroblastoma BE(2)-C cells transfected with murine PrP(C) and studied the effect under Aβ oligomer treatment. By Western blotting, we found that PrP(C) overexpression down-regulated tau protein and Aβ oligomer binding alleviated the tau reduction induced by wild type but not M128V PrP(C), the high AD risk polymorphic allele in human prion gene. PrP(C) lacking the Aβ oligomer binding site was incapable of rescuing the level of tau reduction. Quantitative RT-PCR showed the PrP(C) effect was attributed to tau reduction at the transcription level. Treatment with Fyn pathway inhibitors, Fyn kinase inhibitor PP2 and MEK inhibitor U0126, reversed the PrP(C)-induced tau reduction and Aβ oligomer treatment modulated Fyn kinase activity. The results suggested Fyn pathway regulated Aβ-PrP(C)-tau signaling. Overall, our results demonstrated that PrP(C) down-regulated tau via the Fyn pathway and the effect can be regulated by Aβ oligomers. Our study facilitated the understanding of molecular mechanisms among PrP(C), tau, and Aβ oligomers.

Laccase-Catalyzed Synthesis of Low-Molecular-Weight Lignin-Like Oligomers and their Application as UV-Blocking Materials.

PubMed

Lim, Jieyan; Sana, Barindra; Krishnan, Ranganathan; Seayad, Jayasree; Ghadessy, Farid J; Jana, Satyasankar; Ramalingam, Balamurugan

2018-02-02

The laccase-catalyzed oxidative polymerization of monomeric and dimeric lignin model compounds was carried out with oxygen as the oxidant in aqueous medium. The oligomers were characterized by using gel permeation chromatography (GPC) and matrix-assisted laser desorption ionization time-of-flight mass spectroscopy (MALDI-TOF MS) analysis. Oxidative polymerization led to the formation of oligomeric species with a number-average molecular weight (M n ) that ranged from 700 to 2300 Da with a low polydispersity index. Spectroscopic analysis provided insight into the possible modes of linkages present in the oligomers, and the oligomerization is likely to proceed through the formation of C-C linkages between phenolic aromatic rings. The oligomers were found to show good UV light absorption characteristics with high molar extinction coefficient (5000-38 000 m -1  cm -1 ) in the UV spectral region. The oligomers were blended independently with polyvinyl chloride (PVC) by using solution blending to evaluate the compatibility and UV protection ability of the oligomers. The UV/Vis transmittance spectra of the oligomer-embedded PVC films indicated that these lignin-like oligomers possessed a notable ability to block UV light. In particular, oligomers obtained from vanillyl alcohol and the dimeric lignin model were found to show good photostability in accelerated UV weathering experiments. The UV-blocking characteristics and photostability were finally compared with the commercial low-molecular-weight UV stabilizer 2,4-dihydroxybenzophenone. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Kinetic Study of DDGS Hemicellulose Acid Hydrolysis and NMR Characterization of DDGS Hydrolysate.

PubMed

Chen, Hanchi; Liu, Shijie

2015-09-01

Liquid hot water (LHW) extraction was used as a pretreatment method to separate the hemicellulose fraction from dried distiller's grain with solubles (DDGS) into liquid phase. Acid hydrolysis using 3.264 % w/w sulfuric acid at 130 °C was performed to convert polysaccharides in LHW extract to monosaccharides. The structure characterization of DDGS in anomeric carbon region based on proton NMR and heteronuclear single quantum coherence (HSQC) during acid hydrolysis was studied in this work. It reveals that the sugar units in DDGS hemicelluloses are constructed with (1-4)-β-D-xylopyranose and α-L-arabinofuranosyl residues. A kinetic model is included to explain the changing concentration of monomer, oligomer, and sugar units. The model was further tested based on the changing concentration of five carbon sugar units during hydrolysis.

Preventing iron(ii) precipitation in aqueous systems using polyacrylic acid: some molecular insights.

PubMed

Artola, Pierre-Arnaud; Rousseau, Bernard; Clavaguéra, Carine; Roy, Marion; You, Dominique; Plancque, Gabriel

2018-06-22

We present molecular dynamics simulations of aqueous iron(ii) systems in the presence of polyacrylic acid (PAA) under the extreme conditions that take place in the secondary coolant circuit of a nuclear power plant. The aim of this work is to understand how the oligomer can prevent iron(ii) deposits, and to provide molecular interpretation. We show how, to this end, not only the complexant ability is necessary, but also the chain length compared to iron(ii) concentration. When the chain is long enough, a hyper-complexation phenomenon occurs that can explain the specific capacity of the polymer to prevent iron(ii) precipitation.

Detection of chitinase activity by 2-aminobenzoic acid labeling of chito-oligosaccharides.

PubMed

Ghauharali-van der Vlugt, Karen; Bussink, Anton P; Groener, Johanna E M; Boot, Rolf G; Aerts, Johannes M F G

2009-01-01

Chitinases are hydrolases capable of hydrolyzing the abundant natural polysaccharide chitin. Next to artificial fluorescent substrates, more physiological chito-oligomers are commonly used in chitinase assays. Analysis of chito-oligosaccharides products is generally accomplished by UV detection. However, the relatively poor sensitivity poses a serious limitation. Here we report on a novel, much more sensitive assay for the detection of chito-oligosaccharide reaction products released by chitinases, based on fluorescent detection, following chemical labeling by 2-aminobenzoic acid. Comparison with existing UV-based assays, shows that the novel assay offers the same advantages yet allows detection of chito-oligosaccharides in the low picomolar range.

Separation of 2-aminobenzoic acid-derivatized glycosaminoglycans and asparagine-linked glycans by capillary electrophoresis.

PubMed

Sato, Kae; Sato, Kiichi; Okubo, Akira; Yamazaki, Sunao

2005-01-01

A capillary electrophoresis method was developed for the analysis of oligosaccharides combined with derivatization with 2-aminobenzoic acid. Glycosaminoglycan delta-disaccharides were effectively resolved on a fused-silica capillary tube using 150 mM borate, pH 8.5, as a running electrolyte solution. This analytical method was applied to the identification of glycosaminoglycan in combination with enzymatic digestion. The separation of N-glycans or glucose-oligomers was performed with a phosphate buffer containing polyethylene glycol or borate as an electrolyte solution. This method is expected to be useful in the determination of oligosaccharide structures in a glycoprotein.

Fluorene- and benzofluorene-cored oligomers as low threshold and high gain amplifying media

NASA Astrophysics Data System (ADS)

Kazlauskas, Karolis; Kreiza, Gediminas; Bobrovas, Olegas; AdomÄ--nienÄ--, Ona; AdomÄ--nas, Povilas; Jankauskas, Vygintas; JuršÄ--nas, Saulius

2015-07-01

Deliberate control of intermolecular interactions in fluorene- and benzofluorene-cored oligomers was attempted via introduction of different-length alkyl moieties to attain high emission amplification and low amplified spontaneous emission (ASE) threshold at high oligomer concentrations. Containing fluorenyl peripheral groups decorated with different-length alkyl moieties, the oligomers were found to express weak concentration quenching of emission, yet excellent carrier drift mobilities (close to 10-2 cm2/V/s) in the amorphous films. Owing to the larger radiative decay rates (>1.0 × 109 s-1) and smaller concentration quenching, fluorene-cored oligomers exhibited down to one order of magnitude lower ASE thresholds at higher concentrations as compared to those of benzofluorene counterparts. The lowest threshold (300 W/cm2) obtained for the fluorene-cored oligomers at the concentration of 50 wt % in polymer matrix is among the lowest reported for solution-processed amorphous films in ambient conditions, what makes the oligomers promising for lasing application. Great potential in emission amplification was confirmed by high maximum net gain (77 cm-1) revealed for these compounds. Although the photostability of the oligomers was affected by photo-oxidation, it was found to be comparable to that of various organic lasing materials including some commercial laser dyes evaluated under similar excitation conditions.

Amyloid Oligomers and Protofibrils, but Not Filaments, Self-Replicate from Native Lysozyme

PubMed Central

2015-01-01

Self-assembly of amyloid fibrils is the molecular mechanism best known for its connection with debilitating human disorders such as Alzheimer’s disease but is also associated with various functional cellular responses. There is increasing evidence that amyloid formation proceeds along two distinct assembly pathways involving either globular oligomers and protofibrils or rigid monomeric filaments. Oligomers, in particular, have been implicated as the dominant molecular species responsible for pathogenesis. Yet the molecular mechanisms regulating their self-assembly have remained elusive. Here we show that oligomers/protofibrils and monomeric filaments, formed along distinct assembly pathways, display critical differences in their ability to template amyloid growth at physiological vs denaturing temperatures. At physiological temperatures, amyloid filaments remained stable but could not seed growth of native monomers. In contrast, oligomers and protofibrils not only remained intact but were capable of self-replication using native monomers as the substrate. Kinetic data further suggested that this prion-like growth mode of oligomers/protofibrils involved two distinct activities operating orthogonal from each other: autocatalytic self-replication of oligomers from native monomers and nucleated polymerization of oligomers into protofibrils. The environmental changes to stability and templating competence of these different amyloid species in different environments are likely to be important for understanding the molecular mechanisms underlying both pathogenic and functional amyloid self-assembly. PMID:24884889

Amyloid oligomers and protofibrils, but not filaments, self-replicate from native lysozyme.

PubMed

Mulaj, Mentor; Foley, Joseph; Muschol, Martin

2014-06-25

Self-assembly of amyloid fibrils is the molecular mechanism best known for its connection with debilitating human disorders such as Alzheimer's disease but is also associated with various functional cellular responses. There is increasing evidence that amyloid formation proceeds along two distinct assembly pathways involving either globular oligomers and protofibrils or rigid monomeric filaments. Oligomers, in particular, have been implicated as the dominant molecular species responsible for pathogenesis. Yet the molecular mechanisms regulating their self-assembly have remained elusive. Here we show that oligomers/protofibrils and monomeric filaments, formed along distinct assembly pathways, display critical differences in their ability to template amyloid growth at physiological vs denaturing temperatures. At physiological temperatures, amyloid filaments remained stable but could not seed growth of native monomers. In contrast, oligomers and protofibrils not only remained intact but were capable of self-replication using native monomers as the substrate. Kinetic data further suggested that this prion-like growth mode of oligomers/protofibrils involved two distinct activities operating orthogonal from each other: autocatalytic self-replication of oligomers from native monomers and nucleated polymerization of oligomers into protofibrils. The environmental changes to stability and templating competence of these different amyloid species in different environments are likely to be important for understanding the molecular mechanisms underlying both pathogenic and functional amyloid self-assembly.

Hypoglycemic activities of A- and B-type procyanidin oligomer-rich extracts from different Cinnamon barks.

PubMed

Lu, Zhaolian; Jia, Qi; Wang, Rui; Wu, Ximin; Wu, Yingchun; Huang, Caiguo; Li, Yiming

2011-02-15

Procyanidin oligomers in Cinnamon are thought to be responsible for the biological activity in the treatment of diabetes mellitus (DM). To clarify types of procyanidin oligomers in different Cinnamon species and investigate their different effects, the present study investigated procyanidin oligomers in polyphenolic oligomer-rich extracts of three Cinnamon samples by LC-MS methods, and their hypoglycemic activities were detected in vivo and in vitro. The results showed that two of the three samples from Cinnamomum cassia were rich in B-type procyanidin oligomers, and the other sample was rich in A-type procyanidin oligomers. The Cinnamon extracts were administered at doses of 200 and 300 mg/kg body wt. in high-fat diet-fed and low-dose streptozotocin (STZ)-induced diabetic mice for 14 days. The results showed that blood glucose concentrations were significantly decreased in all Cinnamon extract groups compared with the control group (p<0.05). Administration of the Cinnamon extracts significantly increased the consumption of extracellular glucose in insulin-resistant HepG2 cells and normal HepG2 cells compared with the control group. These results suggest that both A- and B-type procyanidin oligomers in different Cinnamon species have hypoglycemic activities and may improve insulin sensitivity in type 2 DM. Copyright © 2010 Elsevier GmbH. All rights reserved.

wALADin benzimidazoles differentially modulate the function of porphobilinogen synthase orthologs.

PubMed

Lentz, Christian S; Halls, Victoria S; Hannam, Jeffrey S; Strassel, Silke; Lawrence, Sarah H; Jaffe, Eileen K; Famulok, Michael; Hoerauf, Achim; Pfarr, Kenneth M

2014-03-27

The heme biosynthesis enzyme porphobilinogen synthase (PBGS) is a potential drug target in several human pathogens. wALADin1 benzimidazoles have emerged as species-selective PBGS inhibitors against Wolbachia endobacteria of filarial worms. In the present study, we have systematically tested wALADins against PBGS orthologs from bacteria, protozoa, metazoa, and plants to elucidate the inhibitory spectrum. However, the effect of wALADin1 on different PBGS orthologs was not limited to inhibition: several orthologs were stimulated by wALADin1; others remained unaffected. We demonstrate that wALADins allosterically modulate the PBGS homooligomeric equilibrium with inhibition mediated by favoring low-activity oligomers, while 5-aminolevulinic acid, Mg(2+), or K(+) stabilized high-activity oligomers. Pseudomonas aeruginosa PBGS could be inhibited or stimulated by wALADin1 depending on these factors and pH. We have defined the wALADin chemotypes responsible for either inhibition or stimulation, facilitating the design of tailored PBGS modulators for potential application as antimicrobial agents, herbicides, or drugs for porphyric disorders.

wALADin Benzimidazoles Differentially Modulate the Function of Porphobilinogen Synthase Orthologs

PubMed Central

2015-01-01

The heme biosynthesis enzyme porphobilinogen synthase (PBGS) is a potential drug target in several human pathogens. wALADin1 benzimidazoles have emerged as species-selective PBGS inhibitors against Wolbachia endobacteria of filarial worms. In the present study, we have systematically tested wALADins against PBGS orthologs from bacteria, protozoa, metazoa, and plants to elucidate the inhibitory spectrum. However, the effect of wALADin1 on different PBGS orthologs was not limited to inhibition: several orthologs were stimulated by wALADin1; others remained unaffected. We demonstrate that wALADins allosterically modulate the PBGS homooligomeric equilibrium with inhibition mediated by favoring low-activity oligomers, while 5-aminolevulinic acid, Mg2+, or K+ stabilized high-activity oligomers. Pseudomonas aeruginosa PBGS could be inhibited or stimulated by wALADin1 depending on these factors and pH. We have defined the wALADin chemotypes responsible for either inhibition or stimulation, facilitating the design of tailored PBGS modulators for potential application as antimicrobial agents, herbicides, or drugs for porphyric disorders. PMID:24568185

Design and UV-curable behaviour of boron based reactive diluent for epoxy acrylate oligomer used for flame retardant wood coating

PubMed Central

Chambhare, Sachin U.; Lokhande, Gunawant P.; Jagtap, Ramanand N.

2017-01-01

Abstract Difunctional boron-containing reactive flame retardant for UV-curable epoxy acrylate oligomer was synthesized from phenyl boronic acid and glycidyl methacrylate. The synthesized reactive diluent was utilized to formulate ultraviolet (UV)-curable wood coatings. The weight fractions of reactive diluent in coatings formulation was varied from 5 to 25 wt % with constant photoinitiator concentration. The molecular structure of reactive flame retardant was confirmed by Fourier-transform infrared, Nuclear magnetic resonance (NMR) and 11B NMR spectral analysis. Further, the efficacy of flame retardant behaviour of coatings was evaluated using limiting oxygen index and UL-94 vertical burning test. Thermal stability of cured coatings films were estimated from thermogravimetric and differential scanning calorimetry analysis. The effects of varying concentration of reactive diluent on the viscosity of coatings formulation along with optical, mechanical and chemical resistance properties of coatings were also evaluated. The coatings gel content, water absorption behaviour, contact angle analysis and stain resistance were also studied. PMID:29491786

Porous Cross-Linked Polyimide-Urea Networks

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B. (Inventor); Nguyen, Baochau N. (Inventor)

2015-01-01

Porous cross-linked polyimide-urea networks are provided. The networks comprise a subunit comprising two anhydride end-capped polyamic acid oligomers in direct connection via a urea linkage. The oligomers (a) each comprise a repeating unit of a dianhydride and a diamine and a terminal anhydride group and (b) are formulated with 2 to 15 of the repeating units. The subunit was formed by reaction of the diamine and a diisocyanate to form a diamine-urea linkage-diamine group, followed by reaction of the diamine-urea linkage-diamine group with the dianhydride and the diamine to form the subunit. The subunit has been cross-linked via a cross-linking agent, comprising three or more amine groups, at a balanced stoichiometry of the amine groups to the terminal anhydride groups. The subunit has been chemically imidized to yield the porous cross-linked polyimide-urea network. Also provided are wet gels, aerogels, and thin films comprising the networks, and methods of making the networks.

An enzyme cascade synthesis of ε-caprolactone and its oligomers.

PubMed

Schmidt, Sandy; Scherkus, Christian; Muschiol, Jan; Menyes, Ulf; Winkler, Till; Hummel, Werner; Gröger, Harald; Liese, Andreas; Herz, Hans-Georg; Bornscheuer, Uwe T

2015-02-23

Poly-ε-caprolactone (PCL) is chemically produced on an industrial scale in spite of the need for hazardous peracetic acid as an oxidation reagent. Although Baeyer-Villiger monooxygenases (BVMO) in principle enable the enzymatic synthesis of ε-caprolactone (ε-CL) directly from cyclohexanone with molecular oxygen, current systems suffer from low productivity and are subject to substrate and product inhibition. The major limitations for such a biocatalytic route to produce this bulk chemical were overcome by combining an alcohol dehydrogenase with a BVMO to enable the efficient oxidation of cyclohexanol to ε-CL. Key to success was a subsequent direct ring-opening oligomerization of in situ formed ε-CL in the aqueous phase by using lipase A from Candida antarctica, thus efficiently solving the product inhibition problem and leading to the formation of oligo-ε-CL at more than 20 g L(-1) when starting from 200 mM cyclohexanol. This oligomer is easily chemically polymerized to PCL. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Direct observation of ultrafast coherent exciton dynamics in helical π-stacks of self-assembled perylene bisimides

PubMed Central

Sung, Jooyoung; Kim, Pyosang; Fimmel, Benjamin; Würthner, Frank; Kim, Dongho

2015-01-01

Ever since the discovery of dye self-assemblies in nature, there have been tremendous efforts to exploit biomimetic supramolecular assemblies for tailored artificial photon processing materials. This feature necessarily has resulted in an increasing demand for understanding exciton dynamics in the dye self-assemblies. In a sharp contrast with J-type aggregates, however, the detailed observation of exciton dynamics in H-type aggregates has remained challenging. In this study, as we succeed in measuring transient fluorescence from Frenkel state of π-stacked perylene tetracarboxylic acid bisimide dimer and oligomer aggregates, we present an experimental demonstration on Frenkel exciton dynamics of archetypal columnar π–π stacks of dyes. The analysis of the vibronic peak ratio of the transient fluorescence spectra reveals that unlike the simple π-stacked dimer, the photoexcitation energy in the columnar π-stacked oligomer aggregates is initially delocalized over at least three molecular units and moves coherently along the chain in tens of femtoseconds, preceding excimer formation process. PMID:26492820

Intensification of steam explosion and structural intricacies impacting sugar recovery.

PubMed

Gaur, Ruchi; Semwal, Surbhi; Raj, Tirath; Yadav Lamba, Bhawna; Ramu, E; Gupta, Ravi P; Kumar, Ravindra; Puri, Suresh K

2017-10-01

Dilute acid (DA) pretreatment at pilot level failed for cotton stalk (CS) due to the technical issues posed by its inherent nature. Reasonable glucan conversion has been reported via two-stage pretreatment but adds on to the process cost. Proposed herewith is a single-stage steam explosion (SE) process preceded by water extraction resulting in high sugar recovery from CS. Raising the extraction temperature to 80°C increased the glucan conversion from 37.9 to 52.4%. Further improvement up to 68.4% was achieved when DA was incorporated during the room temperature extraction. LC-MS revealed the formation of xylo-oligomers limiting the glucan conversion in proportion to the length of xylo-oligomers. Varying extraction conditions induced structural alterations in biomass after SE evident by compositional analysis, Infrared Spectroscopy, X-Ray Diffraction and Scanning Electron Microscopy. Overall glucose recovery, i.e. 75.8-76.7% with and without DA extraction respectively was achieved. Copyright © 2017 Elsevier Ltd. All rights reserved.

Preparation and characterization of dutasteride-loaded nanostructured lipid carriers coated with stearic acid-chitosan oligomer for topical delivery.

PubMed

Noor, Norhayati Mohamed; Sheikh, Khalid; Somavarapu, Satyanarayana; Taylor, Kevin M G

2017-08-01

Dutasteride, used for treating benign prostate hyperplasia (BPH), promotes hair growth. To enhance delivery to the hair follicles and reduce systemic effects, in this study dutasteride has been formulated for topical application, in a nanostructured lipid carrier (NLC) coated with chitosan oligomer-stearic acid (CSO-SA). CSO-SA has been successfully synthesized, as confirmed using 1 H NMR and FTIR. Formulation of dutasteride-loaded nanostructured lipid carriers (DST-NLCs) was optimized using a 2 3 full factorial design. This formulation was coated with different concentrations of stearic acid-chitosan solution. Coating DST-NLCs with 5% SA-CSO increased mean size from 187.6±7.0nm to 220.1±11.9nm, and modified surface charge, with zeta potentials being -18.3±0.9mV and +25.8±1.1mV for uncoated and coated DST-NLCs respectively. Transmission electron microscopy showed all formulations comprised approximately spherical particles. DST-NLCs, coated and uncoated with CSO-SA, exhibited particle size stability over 60days, when stored at 4-8°C. However, NLCs coated with CSO (without conjugation) showed aggregation when stored at 4-8°C after 30days. The measured particle size for all formulations stored at 25°C suggested aggregation, which was greatest for DST-NLCs coated with 10% CSO-SA and 5% CSO. All nanoparticle formulations exhibited rapid release in an in vitro release study, with uncoated NLCs exhibiting the fastest release rate. Using a Franz diffusion cell, no dutasteride permeated through pig ear skin after 48h, such that it was not detected in the receptor chamber for all samples. The amount of dutasteride in the skin was significantly different (p<0.05) for DST-NLCs (6.09±1.09μg/cm 2 ) without coating and those coated with 5% CSO-SA (2.82±0.40μg/cm 2 ), 10% CSO-SA (2.70±0.35μg/cm 2 ) and CSO (2.11±0.64μg/cm 2) . There was a significant difference (p<0.05) in the cytotoxicity (IC 50 ) between dutasteride alone and in the nanoparticles. DST-NLCs coated and uncoated with CSO-SA increased the maximum non-toxic concentration by 20-fold compared to dutasteride alone. These studies indicate that a stearic acid-chitosan conjugate was successfully prepared, and modified the surface charge of DST-NLCs from negative to positive. These stable, less cytotoxic, positively-charged dutasteride-loaded nanostructured lipid carriers, with stearic acid-chitosan oligomer conjugate, are appropriate for topical delivery and have potential for promotion of hair growth. Copyright © 2017. Published by Elsevier B.V.

SDS-PAGE analysis of Aβ oligomers is disserving research into Alzheimer´s disease: appealing for ESI-IM-MS

NASA Astrophysics Data System (ADS)

Pujol-Pina, Rosa; Vilaprinyó-Pascual, Sílvia; Mazzucato, Roberta; Arcella, Annalisa; Vilaseca, Marta; Orozco, Modesto; Carulla, Natàlia

2015-10-01

The characterization of amyloid-beta peptide (Aβ) oligomer forms and structures is crucial to the advancement in the field of Alzheimer´s disease (AD). Here we report a critical evaluation of two methods used for this purpose, namely sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), extensively used in the field, and ion mobility coupled to electrospray ionization mass spectrometry (ESI-IM-MS), an emerging technique with great potential for oligomer characterization. To evaluate their performance, we first obtained pure cross-linked Aβ40 and Aβ42 oligomers of well-defined order. Analysis of these samples by SDS-PAGE revealed that SDS affects the oligomerization state of Aβ42 oligomers, thus providing flawed information on their order and distribution. In contrast, ESI-IM-MS provided accurate information, while also reported on the chemical nature and on the structure of the oligomers. Our findings have important implications as they challenge scientific paradigms in the AD field built upon SDS-PAGE characterization of Aβ oligomer samples.

Aqueous extraction of pectin from sour orange peel and its preliminary physicochemical properties.

PubMed

Hosseini, Seyed Saeid; Khodaiyan, Faramarz; Yarmand, Mohammad Saeid

2016-01-01

Sour orange peel, a by-product of the fruit juice industry, was used as a source of pectin. The effects of temperature (75-95°C), time (30-90 min), and liquid-solid ratio (20-40, v/w) were investigated on yield, methoxylation degree (DE), and galacturonic acid content using a Box-Behnken design and response surface methodology. The highest extraction yield (17.95 ± 0.3%) was obtained at temperature of 95°C, time of 90 min, and liquid-solid ratio of 25 (v/w). The DE values for the pectin ranged from 17% to 30.5%, indicating that the pectin was low in methoxyle. The emulsifying activity of pectin extracted under optimal conditions was 45%. The emulsions were 86.6% stable at 4°C and 71.4% at 23°C after 30 days of storage. The pectin exhibited Newtonian flow at low concentrations (≤ 1.0%, w/v); as the concentration increased, pseudoplastic flow became dominant. Copyright © 2015 Elsevier B.V. All rights reserved.

Pectinolytic enzymes of anaerobic fungi.

PubMed

Kopecný, J; Hodrová, B

1995-05-01

Pectinolytic enzymes of four rumen fungi have been described. Three fungal species were monocentric Neocallimastix spp. H15, JL3 and OC2, and one isolate was a polycentric strain of Orpinomyces joyonii, A4. They differed in degree of pectin degradation and utilization. Only the strain Neocallimastix sp. H15 and partially Orpinomyces joyonii A4 were able to utilize pectin to a higher extent. The most important pectinolytic activity in all these isolates represented pectin lyase (EC 4.2.2.10) and polygalacturonase (EC 3.2.1.15). Their specific activities were in the range of 100-900 and 10-450 micrograms galacturonic acid h-1 mg protein-1 for pectin lyase and polygalacturonase, respectively. Polygalacturonase, located mainly in the endocellular fraction, was inhibited by calcium ions and had the main pH optimum at pH 6.0. All strains produced pectate lyase (EC 4.2.2.2). None of the strains tested produced pectinesterase (EC 3.1.1.11).

Polysaccharides from Arctium lappa L.: Chemical structure and biological activity.

PubMed

Carlotto, Juliane; de Souza, Lauro M; Baggio, Cristiane H; Werner, Maria Fernanda de P; Maria-Ferreira, Daniele; Sassaki, Guilherme L; Iacomini, Marcello; Cipriani, Thales R

2016-10-01

The plant Arctium lappa L. is popularly used to relieve symptoms of inflammatory disorders. A crude polysaccharide fraction (SAA) resulting of aqueous extraction of A. lappa leaves showed a dose dependent anti-edematogenic activity on carrageenan-induced paw edema, which persisted for up to 48h. Sequential fractionation by ultrafiltration at 50kDa and 30kDa cut-off membranes yielded three fractions, namely RF50, RF30, and EF30. All these maintained the anti-edematogenic effect, but RF30 showed a more potent action, inhibiting 57% of the paw edema at a dose of 4.9mg/kg. The polysaccharide RF30 contained galacturonic acid, galactose, arabinose, rhamnose, glucose, and mannose in a 7:4:2:1:2:1 ratio and had a Mw of 91,000g/mol. Methylation analysis and NMR spectroscopy indicated that RF30 is mainly constituted by a type I rhamnogalacturonan branched by side chains of types I and II arabinogalactans, and arabinan. Copyright © 2016 Elsevier B.V. All rights reserved.

Antioxidant and immunological activities of polysaccharides from Gentiana scabra Bunge roots.

PubMed

Wang, Zhanyong; Wang, Chenyu; Su, Tingting; Zhang, Jing

2014-11-04

Two polysaccharide fractions, GSP I-a and GSP II-b, were isolated from Gentiana scabra Bunge roots. Both GSP I-a and GSP II-b comprised seven monosaccharides: fructose, mannose, rhamnose, galacturonic acid, glucose, galactose, and fucose. Ultraviolet and infrared analyses show that GSP I-a and GSP II-b are proteoglycans. In vitro evaluation of the antioxidant activity suggests that GSP I-a and GSP II-b scavenge 1,1-diphenyl-2-picrylhydrazyl radicals. However, the scavenging activity of the latter is stronger than that of the former. GSP I-a and GSP II-b have relatively low reducing powers and scavenging activities toward superoxide anions and hydroxyls. GSP I-a and GSP II-b significantly increase lymphocyte proliferation when lipopolysaccharide is used as a mitogen for lymphocytes, but only GSP I-a can significantly increase lymphocyte proliferation within the test-dosage range when concanavalin A is used as a mitogen. Copyright © 2014 Elsevier Ltd. All rights reserved.

Optimization and antioxidant activity of polysaccharides from Plantago depressa.

PubMed

Han, Na; Wang, Lin; Song, Zehai; Lin, Junyu; Ye, Chun; Liu, Zhihui; Yin, Jun

2016-12-01

Polysaccharide from the herb of Plantago depressa (PDP) was obtained through ethanol precipitation preceded by a water extraction step. The optimum extraction yield of 5.68±0.46% was obtained with the treatment of raw material in water (w/v, 1:25.34) at 80.44°C during 1.97h, 3.28 times. Under these conditions, obtained yield value was in total agreement with value predicted by the model executed by Box-Behnken design (BBD). Following analysis by IR, HPLC-UV, MS and 1 H NMR, the composition of PDP was found to be l-rhamnose, galactose, arabinose, glucose and d-galacturonic acid. The maximum tolerated dose of PDP was 10g/kg. The antioxidant activity of PDP was investigated using five tests and it was found that PDP was able to scavenge hydroxyl, DPPH and ABTS radicals, besides their β-carotene bleaching inhibitory activity. In particular, in the test of β-carotene bleaching inhibition, PDP displayed higher activity than Vitamin C. Copyright © 2016 Elsevier B.V. All rights reserved.

Application of response surface methodology for optimization of polygalacturonase production by Aspergillus niger.

PubMed

Yadav, Kaushlesh K; Garg, Neelima; Kumar, Devendra; Kumar, Sanjay; Singh, Achal; Muthukumar, M

2015-01-01

Polygalacturonase (PG) degrades pectin into D-galacturonic acid monomers and is used widely in food industry especially for juice clarification. In the present study,. fermentation conditions for polygalacturonase production by Asgergillus niger NAIMCCF-02958, using mango peel as substrate, were optimized using the 2(3) factorial design with central composite rotatable experimental design (CCRD) of response surface methodology (RSM). The maximum PG activity 723.66 U g(-1) was achieved under pH 4.0, temperature 30 degrees C and 2% inoculum by response surface curve. The experimental value of PG activity wkas higher 607.65 U g(-1) than the predicted value 511.75 U g(-1). Under the proposed optimized conditions, the determination coefficient (R2) was equal to 0.66 indicating that the model could explain 66% of the total variation as well as establish the relationship between the variables and the responses. ANOVA analysis and the three dimensional plots also confirmed interactions among the parameters.

Characterization of Two Homogalacturonan Pectins with Immunomodulatory Activity from Green Tea

PubMed Central

Wang, Huijun; Wei, Guodong; Liu, Fei; Banerjee, Gautam; Joshi, Manoj; Bligh, S. W. Annie; Shi, Songshan; Lian, Hui; Fan, Hongwei; Gu, Xuelan; Wang, Shunchun

2014-01-01

Two natural homogalacturonan (HG) pectins (MW ca. 20 kDa) were isolated from green tea based on their immunomodulatory activity. The crude tea polysaccharides (TPS1 and TPS2) were obtained from green tea leaves by hot water extraction and followed by 40% and 70% ethanol precipitation, respectively. Two homogenous water soluble polysaccharides (TPS1-2a and TPS1-2b) were obtained from TPS1 after purification with gel permeation, which gave a higher phagocytic effect than TPS2. A combination of composition, methylation and configuration analyses, as well as NMR (nuclear magnetic resonance) spectroscopy revealed that TPS1-2a and TPS1-2b were homogalacturonan (HG) pectins consisting of a backbone of 1,4-linked α-d-galacturonic acid (GalA) residues with 28.4% and 26.1% of carboxyl groups as methyl ester, respectively. The immunological assay results demonstrated that TPS1-2, which consisted mainly of HG pectins, showed phagocytosis-enhancing activity in HL-60 cells. PMID:24901527

Bacterial succession and metabolite changes during flax (Linum usitatissimum L.) retting with Bacillus cereus HDYM-02.

PubMed

Zhao, Dan; Liu, Pengfei; Pan, Chao; Du, Renpeng; Ping, Wenxiang; Ge, Jingping

2016-09-02

High-throughput sequencing and GC-MS (gas chromatography-mass spectrometry) were jointly used to reveal the bacterial succession and metabolite changes during flax (Linum usitatissimum L.) retting. The inoculation of Bacillus cereus HDYM-02 decreased bacterial richness and diversity. This inoculum led to the replacement of Enterobacteriaceae by Bacillaceae. The level of aerobic Pseudomonadaceae (mainly Azotobacter) and anaerobic Clostridiaceae_1 gradually increased and decreased, respectively. Following the addition of B. cereus HDYM-02, the dominant groups were all degumming enzyme producers or have been proven to be involved in microbial retting throughout the entire retting period. These results could be verified by the metabolite changes, either degumming enzymes or their catalytic products galacturonic acid and reducing sugars. The GC-MS data showed a clear separation between flax retting with and without B. cereus HDYM-02, particularly within the first 72 h. These findings reveal the important bacterial groups that are involved in fiber retting and will facilitate improvements in the retting process.

An artificial molecular machine that builds an asymmetric catalyst

NASA Astrophysics Data System (ADS)

De Bo, Guillaume; Gall, Malcolm A. Y.; Kuschel, Sonja; De Winter, Julien; Gerbaux, Pascal; Leigh, David A.

2018-05-01

Biomolecular machines perform types of complex molecular-level tasks that artificial molecular machines can aspire to. The ribosome, for example, translates information from the polymer track it traverses (messenger RNA) to the new polymer it constructs (a polypeptide)1. The sequence and number of codons read determines the sequence and number of building blocks incorporated into the biomachine-synthesized polymer. However, neither control of sequence2,3 nor the transfer of length information from one polymer to another (which to date has only been accomplished in man-made systems through template synthesis)4 is easily achieved in the synthesis of artificial macromolecules. Rotaxane-based molecular machines5-7 have been developed that successively add amino acids8-10 (including β-amino acids10) to a growing peptide chain by the action of a macrocycle moving along a mono-dispersed oligomeric track derivatized with amino-acid phenol esters. The threaded macrocycle picks up groups that block its path and links them through successive native chemical ligation reactions11 to form a peptide sequence corresponding to the order of the building blocks on the track. Here, we show that as an alternative to translating sequence information, a rotaxane molecular machine can transfer the narrow polydispersity of a leucine-ester-derivatized polystyrene chain synthesized by atom transfer radical polymerization12 to a molecular-machine-made homo-leucine oligomer. The resulting narrow-molecular-weight oligomer folds to an α-helical secondary structure13 that acts as an asymmetric catalyst for the Juliá-Colonna epoxidation14,15 of chalcones.

Preparation of Imide Oligomers via Concurrent Reactive Extrusion

NASA Technical Reports Server (NTRS)

Avakian, Roger W. (Inventor); Hu, Ling (Inventor)

2018-01-01

Reactive extrusion can be used in a continuous, solvent-less preparation of imide oligomers involving two competing reactions among three ingredients, the first reaction between a dianhydride and a diamine and the second reaction between an endcap and the same diamine. The imide oligomer can form a composite via conventional production methods or via formation of a film from imide oligomer re-melted in an extruder before being impregnated into tape or fabric.

Large α-synuclein oligomers inhibit neuronal SNARE-mediated vesicle docking

PubMed Central

Choi, Bong-Kyu; Choi, Mal-Gi; Kim, Jae-Yeol; Yang, Yoosoo; Lai, Ying; Kweon, Dae-Hyuk; Lee, Nam Ki; Shin, Yeon-Kyun

2013-01-01

Parkinson disease and dementia with Lewy bodies are featured with the formation of Lewy bodies composed mostly of α-synuclein (α-Syn) in the brain. Although evidence indicates that the large oligomeric or protofibril forms of α-Syn are neurotoxic agents, the detailed mechanisms of the toxic functions of the oligomers remain unclear. Here, we show that large α-Syn oligomers efficiently inhibit neuronal SNARE-mediated vesicle lipid mixing. Large α-Syn oligomers preferentially bind to the N-terminal domain of a vesicular SNARE protein, synaptobrevin-2, which blocks SNARE-mediated lipid mixing by preventing SNARE complex formation. In sharp contrast, the α-Syn monomer has a negligible effect on lipid mixing even with a 30-fold excess compared with the case of large α-Syn oligomers. Thus, the results suggest that large α-Syn oligomers function as inhibitors of dopamine release, which thus provides a clue, at the molecular level, to their neurotoxicity. PMID:23431141

Diverse mechanisms of antidiabetic effects of the different procyanidin oligomer types of two different cinnamon species on db/db mice.

PubMed

Chen, Liang; Sun, Peng; Wang, Ting; Chen, Kaixian; Jia, Qi; Wang, Heyao; Li, Yiming

2012-09-12

The procyanidin oligomers are thought to be responsible for the antidiabetic activity of cinnamon. To investigate the hypoglycemic effects of different procyanidin oligomer types, the procyanidin oligomer-rich extracts were prepared from two different cinnamon species. Using high-performance liquid chromatography with purified procyanidin oligomers as reference compounds, we found that the Cinnamomum cassia extract (CC-E) and Cinnamomum tamala extract (CT-E) were rich in B- and A-type procyanidin oligomers, respectively. In the experiment, 8-week-old diabetic (db/db) mice were gavaged with CC-E and CT-E (both 200 mg/kg per day) for 4 weeks. Both CC-E and CT-E exhibited antidiabetic effects. Moreover, histopathological studies of the pancreas, liver, and adipose tissue showed that CC-E promoted lipid accumulation in the adipose tissue and liver, whereas CT-E mainly improved the insulin concentration in the blood and pancreas.

Computer simulations and theoretical aspects of the depletion interaction in protein-oligomer mixtures.

PubMed

Boncina, M; Rescic, J; Kalyuzhnyi, Yu V; Vlachy, V

2007-07-21

The depletion interaction between proteins caused by addition of either uncharged or partially charged oligomers was studied using the canonical Monte Carlo simulation technique and the integral equation theory. A protein molecule was modeled in two different ways: either as (i) a hard sphere of diameter 30.0 A with net charge 0, or +5, or (ii) as a hard sphere with discrete charges (depending on the pH of solution) of diameter 45.4 A. The oligomers were pictured as tangentially jointed, uncharged, or partially charged, hard spheres. The ions of a simple electrolyte present in solution were represented by charged hard spheres distributed in the dielectric continuum. In this study we were particularly interested in changes of the protein-protein pair-distribution function, caused by addition of the oligomer component. In agreement with previous studies we found that addition of a nonadsorbing oligomer reduces the phase stability of solution, which is reflected in the shape of the protein-protein pair-distribution function. The value of this function in protein-protein contact increases with increasing oligomer concentration, and is larger for charged oligomers. The range of the depletion interaction and its strength also depend on the length (number of monomer units) of the oligomer chain. The integral equation theory, based on the Wertheim Ornstein-Zernike approach applied in this study, was found to be in fair agreement with Monte Carlo results only for very short oligomers. The computer simulations for a model mimicking the lysozyme molecule (ii) are in qualitative agreement with small-angle neutron experiments for lysozyme-dextran mixtures.

Tau Oligomers Associate with Inflammation in the Brain and Retina of Tauopathy Mice and in Neurodegenerative Diseases

PubMed Central

Nilson, Ashley N.; English, Kelsey C.; Gerson, Julia E.; Barton Whittle, T.; Nicolas Crain, C.; Xue, Judy; Sengupta, Urmi; Castillo-Carranza, Diana L.; Zhang, Wenbo; Gupta, Praveena; Kayed, Rakez

2016-01-01

It is well-established that inflammation plays an important role in Alzheimer’s disease (AD) and frontotemporal lobar dementia (FTLD). Inflammation and synapse loss occur in disease prior to the formation of larger aggregates, but the contribution of tau to inflammation has not yet been thoroughly investigated. Tau pathologically aggregates to form large fibrillar structures known as tangles. However, evidence suggests that smaller soluble aggregates, called oligomers, are the most toxic species and form prior to tangles. Furthermore, tau oligomers can spread to neighboring cells and between anatomically connected brain regions. In addition, recent evidence suggests that inspecting the retina may be a window to brain pathology. We hypothesized that there is a relationship between tau oligomers and inflammation, which are hallmarks of early disease. We conducted immunofluorescence and biochemical analyses on tauopathy mice, FTLD, and AD subjects. We showed that oligomers co-localize with astrocytes, microglia, and HMGB1, a pro-inflammatory cytokine. Additionally, we show that tau oligomers are present in the retina and are associated with inflammatory cells suggesting that the retina may be a valid non-invasive biomarker for brain pathology. These results suggest that there may be a toxic relationship between tau oligomers and inflammation. Therefore, the ability of tau oligomers to spread may initiate a feed-forward cycle in which tau oligomers induce inflammation, leading to neuronal damage, and thus more inflammation. Further mechanistic studies are warranted in order to understand this relationship, which may have critical implications for improving the treatment of tauopathies. PMID:27716675

Chemical characterization of SOA formed from aqueous-phase reactions of phenols with the triplet excited state of carbonyl and hydroxyl radical

DOE PAGES

Yu, L.; Smith, J.; Laskin, A.; ...

2014-12-23

Phenolic compounds, which are emitted in significant amounts from biomass burning, can undergo fast reactions in atmospheric aqueous phases to form secondary organic aerosol (aqSOA). In this study, we investigate the reactions of phenol (compound with formula C 6H 5OH)), guaiacol (2-methoxyphenol), and syringol (2,6-dimethoxyphenol) with two major aqueous-phase oxidants – the triplet excited states of an aromatic carbonyl ( 3C *) and hydroxyl radical (· OH). We thoroughly characterize the low-volatility species produced from these reactions and interpret their formation mechanisms using aerosol mass spectrometry (AMS), nanospray desorption electrospray ionization mass spectrometry (nano-DESI MS), and ion chromatography (IC). Amore » large number of oxygenated molecules are identified, including oligomers containing up to six monomer units, functionalized monomer and oligomers with carbonyl, carboxyl, and hydroxyl groups, and small organic acid anions (e.g., formate, acetate, oxalate, and malate). The average atomic oxygen-to-carbon (O / C) ratios of phenolic aqSOA are in the range of 0.85–1.23, similar to those of low-volatility oxygenated organic aerosol (LV-OOA) observed in ambient air. The aqSOA compositions are overall similar for the same precursor, but the reactions mediated by 3C * are faster than · OH-mediated reactions and produce more oligomers and hydroxylated species at the point when 50% of the phenolic compound has reacted. Profiles determined using a thermodenuder indicate that the volatility of phenolic aqSOA is influenced by both oligomer content and O / C ratio. In addition, the aqSOA shows enhanced light absorption in the UV–visible region, suggesting that aqueous-phase reactions of phenols may contribute to formation of secondary brown carbon in the atmosphere, especially in regions influenced by biomass burning.« less

Overexpression in Escherichia coli, folding, purification, and characterization of the first three short consensus repeat modules of human complement receptor type 1.

PubMed

Dodd, I; Mossakowska, D E; Camilleri, P; Haran, M; Hensley, P; Lawlor, E J; McBay, D L; Pindar, W; Smith, R A

1995-12-01

We have developed a simple expression, isolation, and folding protocol for an SCR oligomer comprising the first three SCRs of complement receptor Type 1 (C3b/C4b receptor, CD35). A T7 RNA polymerase expression system in Escherichia coli was used to express the oligomer as inclusion bodies. The oligomer was recovered from solubilized inclusion bodies using batch adsorption on SP-Sepharose. The oligomer was folded by one-step dilution in 20 mM ethanolamine/1 mM EDTA supplemented with 1 mM GSH/0.5 mM GSSG. The folded material was processed to a concentrated (> 20 mg/ml), usable product of greater than 98% purity using a combination of ultrafiltration, ammonium sulfate treatment, hydrophobic interaction, and size-exclusion chromatography. The yield of folded material varied between 6 and 15 mg/liter culture. The oxidation states of the 12 cysteine residues in SCR(1-3) were identified by HPLC of peptide fragments from a tryptic digest using dual UV/fluorescence detection, collection of selected peaks, and N-terminal sequencing. This methodology confirmed the expected location of disulfide bridges. Equilibrium and velocity sedimentation studies are interpreted in terms of a single sedimenting species with molecular weights of 21,629 and 21,063 by these respective techniques. These values compare to the predicted molecular weight, from amino acid composition, of 21,817. The hydrodynamic properties of the molecule indicate that it is asymmetric with an axial ratio of 1:5.2 or equivalent dimensions of 21 x 110 A. SCR(1-3) has an unusual CD spectrum exhibiting a broad maximum at 220-230 nm and a minimum at 190 nm. There was little evidence of classical secondary structure. The product exhibited concentration-dependent inhibition of complement-mediated lysis of sensitized sheep red blood cells.

Alzheimer brain-derived tau oligomers propagate pathology from endogenous tau.

PubMed

Lasagna-Reeves, Cristian A; Castillo-Carranza, Diana L; Sengupta, Urmi; Guerrero-Munoz, Marcos J; Kiritoshi, Takaki; Neugebauer, Volker; Jackson, George R; Kayed, Rakez

2012-01-01

Intracerebral injection of brain extracts containing amyloid or tau aggregates in transgenic animals can induce cerebral amyloidosis and tau pathology. We extracted pure populations of tau oligomers directly from the cerebral cortex of Alzheimer disease (AD) brain. These oligomers are potent inhibitors of long term potentiation (LTP) in hippocampal brain slices and disrupt memory in wild type mice. We observed for the first time that these authentic brain-derived tau oligomers propagate abnormal tau conformation of endogenous murine tau after prolonged incubation. The conformation and hydrophobicity of tau oligomers play a critical role in the initiation and spread of tau pathology in the naïve host in a manner reminiscent of sporadic AD.

Calculation of density functional theory (DFT) vibrational parameters of nucleotides for use in theoretical optical calculations: Herein applied to circular dichroism (CD) and absorption of polynucleotides

NASA Astrophysics Data System (ADS)

Ferber, Steven Dwight

2005-11-01

The Vibrational Circular Dichroism (VCD) of Nucleic Acids is a sensitive function of their conformation. DeVoe's classically derived polarizability theory allows the calculation of polymer absorption and circular dichroism spectra in any frequency range. Following the approach of Tinoco and Cech as modified by Moore and Self, calculations were done in the infrared (IR) region with theoretically derived monomer input parameters. Presented herein are calculated absorption and CD spectra for nucleic acid oligomers and polymers. These calculations improve upon earlier attempts, which utilized frequencies, intensities and normal modes from empirical analysis of the nitrogenous base of the monomers. These more complete input polarizability parameters include all contributions to specific vibrational normal modes for the entire nucleotide structure. They are derived from density functional theory (DFT) vibrational analysis on quasi-nucleotide monomers using the GAUSSIAN '98/'03 program. The normal modes are "integrated" for the first time into single virtual (DeVoe) oscillators by incorporating "fixed partial charges" in the manner of Schellman. The results include the complete set of monomer normal modes. All of these modes may be analyzed, in a manner similar to those demonstrated here (for the 1500-1800 cm-1 region). A model is utilized for the polymer/oligomer monomers which maintains the actual electrostatic charge on the adjacent protonated phosphoryl groups (hydrogen phosphate, a mono-anion). This deters the optimization from "collapsing" into a hydrogen-bonded "ball" and thereby maintains the extended (polymer-like) conformation. As well, the precise C2 "endo" conformation of the sugar ring is maintained in the DNA monomers. The analogous C3 "endo" conformation is also maintained for the RNA monomers, which are constrained by massive "anchors" at the phosphates. The complete IR absorbance spectra (0-4,000 cm-1) are calculated directly in Gaussian. Calculated VCD and Absorbance Spectra for the eight standard Ribonucleic and Deoxy-ribonucleic acid homo-polymers in the nitrogenous base absorbing region 1550-1750 cm-1 are presented. These spectra match measured spectra at least as well as spectra calculated from empirical parameters. These results demonstrate that the purely theoretical calculation, an example given herein, should serve to provide more transferable, universal parameters for the polarizability treatment of the optical properties of oligomers and polymers.

DFT Modeling of Cross-Linked Polyethylene: Role of Gold Atoms and Dispersion Interactions.

PubMed

Blaško, Martin; Mach, Pavel; Antušek, Andrej; Urban, Miroslav

2018-02-08

Using DFT modeling, we analyze the concerted action of gold atoms and dispersion interactions in cross-linked polyethylene. Our model consists of two oligomer chains (PEn) with 7, 11, 15, 19, or 23 carbon atoms in each oligomer cross-linked with one to three Au atoms through C-Au-C bonds. In structures with a single gold atom the C-Au-C bond is located in the central position of the oligomer. Binding energies (BEs) with respect to two oligomer radical fragments and Au are as high as 362-489 kJ/mol depending on the length of the oligomer chain. When the dispersion contribution in PEn-Au-PEn oligomers is omitted, BE is almost independent of the number of carbon atoms, lying between 293 and 296 kJ/mol. The dispersion energy contributions to BEs in PEn-Au-PEn rise nearly linearly with the number of carbon atoms in the PEn chain. The carbon-carbon distance in the C-Au-C moiety is around 4.1 Å, similar to the bond distance between saturated closed shell chains in the polyethylene crystal. BEs of pure saturated closed shell PEn-PEn oligomers are 51-187 kJ/mol. Both Au atoms and dispersion interactions contribute considerably to the creation of nearly parallel chains of oligomers with reasonably high binding energies.

Single-molecule FRET studies on alpha-synuclein oligomerization of Parkinson’s disease genetically related mutants

NASA Astrophysics Data System (ADS)

Tosatto, Laura; Horrocks, Mathew H.; Dear, Alexander J.; Knowles, Tuomas P. J.; Dalla Serra, Mauro; Cremades, Nunilo; Dobson, Christopher M.; Klenerman, David

2015-11-01

Oligomers of alpha-synuclein are toxic to cells and have been proposed to play a key role in the etiopathogenesis of Parkinson’s disease. As certain missense mutations in the gene encoding for alpha-synuclein induce early-onset forms of the disease, it has been suggested that these variants might have an inherent tendency to produce high concentrations of oligomers during aggregation, although a direct experimental evidence for this is still missing. We used single-molecule Förster Resonance Energy Transfer to visualize directly the protein self-assembly process by wild-type alpha-synuclein and A53T, A30P and E46K mutants and to compare the structural properties of the ensemble of oligomers generated. We found that the kinetics of oligomer formation correlates with the natural tendency of each variant to acquire beta-sheet structure. Moreover, A53T and A30P showed significant differences in the averaged FRET efficiency of one of the two types of oligomers formed compared to the wild-type oligomers, indicating possible structural variety among the ensemble of species generated. Importantly, we found similar concentrations of oligomers during the lag-phase of the aggregation of wild-type and mutated alpha-synuclein, suggesting that the properties of the ensemble of oligomers generated during self-assembly might be more relevant than their absolute concentration for triggering neurodegeneration.

Protection against β-amyloid-induced synaptic and memory impairments via altering β-amyloid assembly by bis(heptyl)-cognitin

PubMed Central

Chang, Lan; Cui, Wei; Yang, Yong; Xu, Shujun; Zhou, Wenhua; Fu, Hongjun; Hu, Shengquan; Mak, Shinghung; Hu, Juwei; Wang, Qin; Pui-Yan Ma, Victor; Chung-lit Choi, Tony; Dik-lung Ma, Edmond; Tao, Liang; Pang, Yuanping; Rowan, Michael J.; Anwyl, Roger; Han, Yifan; Wang, Qinwen

2015-01-01

β-amyloid (Aβ) oligomers have been closely implicated in the pathogenesis of Alzheimer’s disease (AD). We found, for the first time, that bis(heptyl)-cognitin, a novel dimeric acetylcholinesterase (AChE) inhibitor derived from tacrine, prevented Aβ oligomers-induced inhibition of long-term potentiation (LTP) at concentrations that did not interfere with normal LTP. Bis(heptyl)-cognitin also prevented Aβ oligomers-induced synaptotoxicity in primary hippocampal neurons. In contrast, tacrine and donepezil, typical AChE inhibitors, could not prevent synaptic impairments in these models, indicating that the modification of Aβ oligomers toxicity by bis(heptyl)-cognitin might be attributed to a mechanism other than AChE inhibition. Studies by using dot blotting, immunoblotting, circular dichroism spectroscopy, and transmission electron microscopy have shown that bis(heptyl)-cognitin altered Aβ assembly via directly inhibiting Aβ oligomers formation and reducing the amount of preformed Aβ oligomers. Molecular docking analysis further suggested that bis(heptyl)-cognitin presumably interacted with the hydrophobic pockets of Aβ, which confers stabilizing powers and assembly alteration effects on Aβ. Most importantly, bis(heptyl)-cognitin significantly reduced cognitive impairments induced by intra-hippocampal infusion of Aβ oligomers in mice. These results clearly demonstrated how dimeric agents prevent Aβ oligomers-induced synaptic and memory impairments, and offered a strong support for the beneficial therapeutic effects of bis(heptyl)-cognitin in the treatment of AD. PMID:26194093

Experimental and Molecular Modeling Evaluation of the Physicochemical Properties of Proline-Based Deep Eutectic Solvents.

PubMed

van den Bruinhorst, Adriaan; Spyriouni, Theodora; Hill, Jörg-Rüdiger; Kroon, Maaike C

2018-01-11

The liquid range and applicability of deep eutectic solvents (DESs) are determined by their physicochemical properties. In this work, the physicochemical properties of glycolic acid:proline and malic acid:proline were evaluated experimentally and with MD simulations at five different ratios. Both DESs exhibited esterification upon preparation, which affected the viscosity in particular. In order to minimize oligomer formation and water release, three different experimental preparation methods were explored, but none could prevent esterification. The experimental and calculated densities of the DESs were found to be in good agreement. The measured and modeled glass transition temperature showed similar trends with composition, as did the experimental viscosity and the calculated diffusivities. The MD simulations provided additional insight at the atomistic level, showing that at acid-rich compositions, the acid-acid hydrogen bonding (HB) interactions prevail. Malic acid-based DESs show stronger acid-acid HB interactions than glycolic acid-based ones, possibly explaining its extreme viscosity. Upon the addition of proline, the interspecies interactions become predominant, confirming the formation of the widely assumed HB network between the DESs constituents in the liquid phase.

C9/12 Ribbon-Like Structures in Hybrid Peptides Alternating α- and Thiazole-Based γ-Amino Acids.

PubMed

Bonnel, Clément; Legrand, Baptiste; Simon, Matthieu; Martinez, Jean; Bantignies, Jean-Louis; Kang, Young Kee; Wenger, Emmanuel; Hoh, Francois; Masurier, Nicolas; Maillard, Ludovic T

2017-12-11

According to their restricted conformational freedom, heterocyclic γ-amino acids are usually considered to be related to Z-vinylogous γ-amino acids. In this context, oligomers alternating α-amino acids and thiazole-based γ-amino acids (ATCs) were expected to fold into a canonical 12-helical shape as described for α/γ-hybrid peptides composed of cis-α/β-unsaturated γ-amino acids. However, through a combination of X-ray crystallography, NMR spectroscopy, FTIR experiments, and DFT calculations, it was determined that the folding behavior of ATC-containing hybrid peptides is much more complex. The homochiral α/(S)-ATC sequences were unable to adopt a stable conformation, whereas the heterochiral α/(R)-ATC peptides displayed novel ribbon structures stabilized by unusual C 9/12 -bifurcated hydrogen bonds. These ribbon structures could be considered as a succession of pre-organized γ/α dipeptides and may provide the basis for designing original α-helix mimics. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Information transfer from peptide nucleic acids to RNA by template-directed syntheses

NASA Technical Reports Server (NTRS)

Schmidt, J. G.; Nielsen, P. E.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1997-01-01

Peptide nucleic acids (PNAs) are uncharged analogs of DNA and RNA in which the ribose-phosphate backbone is substituted by a backbone held together by amide bonds. PNAs are interesting as models of alternative genetic systems because they form potentially informational base paired helical structures. A PNA C10 oligomer has been shown to act as template for efficient formation of oligoguanylates from activated guanosine ribonucleotides. In a previous paper we used heterosequences of DNA as templates in sequence-dependent polymerization of PNA dimers. In this paper we show that information can be transferred from PNA to RNA. We describe the reactions of activated mononucleotides on heterosequences of PNA. Adenylic, cytidylic and guanylic acids were incorporated into the products opposite their complement on PNA, although less efficiently than on DNA templates.

Epimerization of Alanyl-Alanine Induced by γ-Rays Irradiation in Aqueous Solutions.

PubMed

Munegumi, Toratane

2017-03-01

Living organisms have homochiral L-amino acids in proteins and homochiral D-mononucleotides in nucleic acids. The chemical evolutionary process to protein homochirality has been discussed for many years. Although many scenarios have been proposed for homochirality in the monomeric compounds, homochirality in amino acids and mononucleotides does not always guarantee homochirality in polypeptides and polynucleotides. Integrated scenarios containing the pathways from monomer to polymer should be proposed because in the pathways oligomers and polymers as well as monomers racemize (or epimerize), degrade, and condense. This research addresses epimerization and degradation of dipeptides under γ-rays irradiation by a cobalt-60 ( 60 Co) radiation source. The different rate constants of epimerization between diastereomeric dipeptides in the research suggest that the potential pathway toward homochirality could be much more complex.

Dry/Wet Cycling and the Thermodynamics and Kinetics of Prebiotic Polymer Synthesis

PubMed Central

Ross, David S.; Deamer, David

2016-01-01

The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life’s origins: (i) how did the polymers arise in an aqueous prebiotic world; and (ii) once formed in some manner, how were they sufficiently persistent to engage in further chemistry. We propose here a quantitative resolution of these issues that evolved from recent accounts in which RNA-like polymers were produced in evaporation/rehydration cycles. The equilibrium Nm + Nn ↔ Nm+n + H2O is endoergic by about 3.3 kcal/mol for polynucleotide formation, and the system thus lies far to the left in the starting solutions. Kinetic simulations of the evaporation showed that simple Le Châtelier’s principle shifts were insufficient, but the introduction of oligomer-stabilizing factors of 5–10 kcal/mol both moved the process to the right and respectively boosted and retarded the elongation and hydrolysis rates. Molecular crowding and excluded volume effects in present-day cells yield stabilizing factors of that order, and we argue here that the crowded conditions in the evaporites generate similar effects. Oligomer formation is thus energetically preferred in those settings, but the process is thwarted in each evaporation step as diffusion becomes rate limiting. Rehydration dissipates disordered oligomer clusters in the evaporites, however, and subsequent dry/wet cycling accordingly “ratchets up” the system to an ultimate population of kinetically trappedthermodynamically preferred biopolymers. PMID:27472365

Bovine seminal ribonuclease triggers Beclin1-mediated autophagic cell death in pancreatic cancer cells.

PubMed

Fiorini, Claudia; Gotte, Giovanni; Donnarumma, Federica; Picone, Delia; Donadelli, Massimo

2014-05-01

Among the large number of variants belonging to the pancreatic-type secretory ribonuclease (RNase) superfamily, bovine pancreatic ribonuclease (RNase A) is the proto-type and bovine seminal RNase (BS-RNase) represents the unique natively dimeric member. In the present manuscript, we evaluate the anti-tumoral property of these RNases in pancreatic adenocarcinoma cell lines and in nontumorigenic cells as normal control. We demonstrate that BS-RNase stimulates a strong anti-proliferative and pro-apoptotic effect in cancer cells, while RNase A is largely ineffective. Notably, we reveal for the first time that BS-RNase triggers Beclin1-mediated autophagic cancer cell death, providing evidences that high proliferation rate of cancer cells may render them more susceptible to autophagy by BS-RNase treatment. Notably, to improve the autophagic response of cancer cells to BS-RNase we used two different strategies: the more basic (as compared to WT enzyme) G38K mutant of BS-RNase, known to interact more strongly than wt with the acidic membrane of cancer cells, or BS-RNase oligomerization (tetramerization or formation of larger oligomers). Both mutant BS-RNase and BS-RNase oligomers potentiated autophagic cell death as compared to WT native dimer of BS-RNase, while the various RNase A oligomers remained completely ineffective. Altogether, our results shed more light on the mechanisms lying at the basis of BS-RNase antiproliferative effect in cancer cells, and support its potential use to develop new anti-cancer strategies. Copyright © 2014 Elsevier B.V. All rights reserved.

Alzheimer's Therapeutics Targeting Amyloid Beta 1–42 Oligomers I: Abeta 42 Oligomer Binding to Specific Neuronal Receptors Is Displaced by Drug Candidates That Improve Cognitive Deficits

PubMed Central

Izzo, Nicholas J.; Staniszewski, Agnes; To, Lillian; Fa, Mauro; Teich, Andrew F.; Saeed, Faisal; Wostein, Harrison; Walko, Thomas; Vaswani, Anisha; Wardius, Meghan; Syed, Zanobia; Ravenscroft, Jessica; Mozzoni, Kelsie; Silky, Colleen; Rehak, Courtney; Yurko, Raymond; Finn, Patricia; Look, Gary; Rishton, Gilbert; Safferstein, Hank; Miller, Miles; Johanson, Conrad; Stopa, Edward; Windisch, Manfred; Hutter-Paier, Birgit; Shamloo, Mehrdad; Arancio, Ottavio; LeVine, Harry; Catalano, Susan M.

2014-01-01

Synaptic dysfunction and loss caused by age-dependent accumulation of synaptotoxic beta amyloid (Abeta) 1–42 oligomers is proposed to underlie cognitive decline in Alzheimer's disease (AD). Alterations in membrane trafficking induced by Abeta oligomers mediates reduction in neuronal surface receptor expression that is the basis for inhibition of electrophysiological measures of synaptic plasticity and thus learning and memory. We have utilized phenotypic screens in mature, in vitro cultures of rat brain cells to identify small molecules which block or prevent the binding and effects of Abeta oligomers. Synthetic Abeta oligomers bind saturably to a single site on neuronal synapses and induce deficits in membrane trafficking in neuronal cultures with an EC50 that corresponds to its binding affinity. The therapeutic lead compounds we have found are pharmacological antagonists of Abeta oligomers, reducing the binding of Abeta oligomers to neurons in vitro, preventing spine loss in neurons and preventing and treating oligomer-induced deficits in membrane trafficking. These molecules are highly brain penetrant and prevent and restore cognitive deficits in mouse models of Alzheimer's disease. Counter-screening these compounds against a broad panel of potential CNS targets revealed they are highly potent and specific ligands of the sigma-2/PGRMC1 receptor. Brain concentrations of the compounds corresponding to greater than 80% receptor occupancy at the sigma-2/PGRMC1 receptor restore cognitive function in transgenic hAPP Swe/Ldn mice. These studies demonstrate that synthetic and human-derived Abeta oligomers act as pharmacologically-behaved ligands at neuronal receptors - i.e. they exhibit saturable binding to a target, they exert a functional effect related to their binding and their displacement by small molecule antagonists blocks their functional effect. The first-in-class small molecule receptor antagonists described here restore memory to normal in multiple AD models and sustain improvement long-term, representing a novel mechanism of action for disease-modifying Alzheimer's therapeutics. PMID:25390368

Alzheimer's therapeutics targeting amyloid beta 1-42 oligomers I: Abeta 42 oligomer binding to specific neuronal receptors is displaced by drug candidates that improve cognitive deficits.

PubMed

Izzo, Nicholas J; Staniszewski, Agnes; To, Lillian; Fa, Mauro; Teich, Andrew F; Saeed, Faisal; Wostein, Harrison; Walko, Thomas; Vaswani, Anisha; Wardius, Meghan; Syed, Zanobia; Ravenscroft, Jessica; Mozzoni, Kelsie; Silky, Colleen; Rehak, Courtney; Yurko, Raymond; Finn, Patricia; Look, Gary; Rishton, Gilbert; Safferstein, Hank; Miller, Miles; Johanson, Conrad; Stopa, Edward; Windisch, Manfred; Hutter-Paier, Birgit; Shamloo, Mehrdad; Arancio, Ottavio; LeVine, Harry; Catalano, Susan M

2014-01-01

Synaptic dysfunction and loss caused by age-dependent accumulation of synaptotoxic beta amyloid (Abeta) 1-42 oligomers is proposed to underlie cognitive decline in Alzheimer's disease (AD). Alterations in membrane trafficking induced by Abeta oligomers mediates reduction in neuronal surface receptor expression that is the basis for inhibition of electrophysiological measures of synaptic plasticity and thus learning and memory. We have utilized phenotypic screens in mature, in vitro cultures of rat brain cells to identify small molecules which block or prevent the binding and effects of Abeta oligomers. Synthetic Abeta oligomers bind saturably to a single site on neuronal synapses and induce deficits in membrane trafficking in neuronal cultures with an EC50 that corresponds to its binding affinity. The therapeutic lead compounds we have found are pharmacological antagonists of Abeta oligomers, reducing the binding of Abeta oligomers to neurons in vitro, preventing spine loss in neurons and preventing and treating oligomer-induced deficits in membrane trafficking. These molecules are highly brain penetrant and prevent and restore cognitive deficits in mouse models of Alzheimer's disease. Counter-screening these compounds against a broad panel of potential CNS targets revealed they are highly potent and specific ligands of the sigma-2/PGRMC1 receptor. Brain concentrations of the compounds corresponding to greater than 80% receptor occupancy at the sigma-2/PGRMC1 receptor restore cognitive function in transgenic hAPP Swe/Ldn mice. These studies demonstrate that synthetic and human-derived Abeta oligomers act as pharmacologically-behaved ligands at neuronal receptors--i.e. they exhibit saturable binding to a target, they exert a functional effect related to their binding and their displacement by small molecule antagonists blocks their functional effect. The first-in-class small molecule receptor antagonists described here restore memory to normal in multiple AD models and sustain improvement long-term, representing a novel mechanism of action for disease-modifying Alzheimer's therapeutics.

Donor-acceptor-donor thienyl/bithienyl-benzothiadiazole/quinoxaline model oligomers: experimental and theoretical studies.

PubMed

Pina, João; de Melo, J Seixas; Breusov, D; Scherf, Ullrich

2013-09-28

A comprehensive spectral and photophysical investigation of four donor-acceptor-donor (DAD) oligomers consisting of electron-deficient 2,1,3-benzothiadiazole or quinoxaline moieties linked to electron-rich thienyl or bithienyl units has been undertaken. Additionally, a bis(dithienyl) substituted naphthalene was also investigated. The D-A-D nature of these oligomers resulted in the presence of an intramolecular charge transfer (ICT) state, which was further substantiated by solvatochromism studies (analysis with the Lippert-Mataga formalism). Hereby, significant differences have been obtained for the fluorescence quantum yields of the oligomers in the non-polar solvent methylcyclohexane vs. the polar ethanol. The study was further complemented with the determination of the optimized ground-state molecular geometries for the oligomers together with the prediction of the lowest vertical one-electron excitation energy and the relevant molecular orbital contours using DFT calculations. The electronic transitions show a clear HOMO to LUMO charge-transfer character. In contrast to the thiophene oligomers (the oligothiophenes with n = 1-7), where the intersystem crossing (ISC) yield decreases with n, the studied DAD oligomers were found to show an increase in the ISC efficiency with the number of (donor) thienyl units.

Proanthocyanidin Characterization, Antioxidant and Cytotoxic Activities of Three Plants Commonly Used in Traditional Medicine in Costa Rica: Petiveria alliaceae L., Phyllanthus niruri L. and Senna reticulata Willd.

PubMed Central

Navarro, Mirtha; Moreira, Ileana; Arnaez, Elizabeth; Quesada, Silvia; Azofeifa, Gabriela; Alvarado, Diego; Monagas, Maria J.

2017-01-01

The phenolic composition of aerial parts from Petiveria alliaceae L., Phyllanthus niruri L. and Senna reticulata Willd., species commonly used in Costa Rica as traditional medicines, was studied using UPLC-ESI-TQ-MS on enriched-phenolic extracts. Comparatively, higher values of total phenolic content (TPC), as measured by the Folin-Ciocalteau method, were observed for P. niruri extracts (328.8 gallic acid equivalents/g) than for S. reticulata (79.30 gallic acid equivalents/g) whereas P. alliaceae extract showed the lowest value (13.45 gallic acid equivalents/g). A total of 20 phenolic acids and proanthocyanidins were identified in the extracts, including hydroxybenzoic acids (benzoic, 4-hydroxybenzoic, gallic, prochatechuic, salicylic, syringic and vanillic acids); hydroxycinnamic acids (caffeic, ferulic, and p-coumaric acids); and flavan-3-ols monomers [(+)-catechin and (−)-epicatechin)]. Regarding proanthocyanidin oligomers, five procyanidin dimers (B1, B2, B3, B4, and B5) and one trimer (T2) are reported for the first time in P. niruri, as well as two propelargonidin dimers in S. reticulata. Additionally, P. niruri showed the highest antioxidant DPPH and ORAC values (IC50 of 6.4 μg/mL and 6.5 mmol TE/g respectively), followed by S. reticulata (IC50 of 72.9 μg/mL and 2.68 mmol TE/g respectively) and P. alliaceae extract (IC50 >1000 μg/mL and 1.32 mmol TE/g respectively). Finally, cytotoxicity and selectivity on gastric AGS and colon SW20 adenocarcinoma cell lines were evaluated and the best values were also found for P. niruri (SI = 2.8), followed by S. reticulata (SI = 2.5). Therefore, these results suggest that extracts containing higher proanthocyanidin content also show higher bioactivities. Significant positive correlation was found between TPC and ORAC (R2 = 0.996) as well as between phenolic content as measured by UPLC-DAD and ORAC (R2 = 0.990). These findings show evidence for the first time of the diversity of phenolic acids in P. alliaceae and S. reticulata, and the presence of proanthocyanidins as minor components in latter species. Of particular relevance is the occurrence of proanthocyanidin oligomers in phenolic extracts from P. niruri and their potential bioactivity. PMID:29048336

Oxidative Stress during the Progression of β-Amyloid Pathology in the Neocortex of the Tg2576 Mouse Model of Alzheimer's Disease.

PubMed

Porcellotti, Sara; Fanelli, Francesca; Fracassi, Anna; Sepe, Sara; Cecconi, Francesco; Bernardi, Cinzia; Cimini, AnnaMaria; Cerù, Maria Paola; Moreno, Sandra

2015-01-01

Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive neurodegeneration. Pathogenetic mechanisms, triggered by β-amyloid (Aβ) accumulation, include oxidative stress, derived from energy homeostasis deregulation and involving mitochondria and peroxisomes. We here addressed the oxidative stress status and the elicited cellular response at the onset and during the progression of Aβ pathology, studying the neocortex of Tg2576 model of AD. Age-dependent changes of oxidative damage markers, antioxidant enzymes, and related transcription factors were analysed in relation to the distribution of Aβ peptide and oligomers, by a combined molecular/morphological approach. Nucleic acid oxidative damage, accompanied by defective antioxidant defences, and decreased PGC1α expression are already detected in 3-month-old Tg2576 neurons. Conversely, PPARα is increased in these cells, with its cytoplasmic localization suggesting nongenomic, anti-inflammatory actions. At 6 months, when intracellular Aβ accumulates, PMP70 is downregulated, indicating impairment of fatty acids peroxisomal translocation and their consequent harmful accumulation. In 9-month-old Tg2576 neocortex, Aβ oligomers and acrolein deposition correlate with GFAP, GPX1, and PMP70 increases, supporting a compensatory response, involving astroglial peroxisomes. At severe pathological stages, when senile plaques disrupt cortical cytoarchitecture, antioxidant capacity is gradually lost. Overall, our data suggest early therapeutic intervention in AD, also targeting peroxisomes.

Temperature and Light modulate the trans-delta3-hexadecenoic acid content of phosphatidylglycerol: light-harvesting complex II organization and non-photochemical quenching.

PubMed

Gray, Gordon R; Ivanov, Alexander G; Król, Marianna; Williams, John P; Kahn, Mobashoher U; Myscich, Elizabeth G; Huner, Norman P A

2005-08-01

The interaction of light and temperature in the modulation of the trans-delta3-hexadecenoic acid (trans-16:1) content of phosphatidylglycerol (PG) in winter rye (Secale cereale L.) was assessed and related to the organization of light-harvesting complex II (LHCII). Increasing the growth irradiance from 50 to 800 micromol m(-2) s(-1) at 20 degrees C resulted in a 1.8-fold increase in the trans-16:1 content in PG which favoured a greater preponderance of oligomeric LHCII, measured in vitro as the ratio of oligomer : monomer. Similar irradiance-dependent increases were observed during growth at 5 degrees C; however, 1.4-fold lower trans-16:1 contents and lower LHCII oligomer : monomer ratios were observed compared with growth at 20 degrees C and the same irradiance. These trends were also observed under natural field conditions. Thus, the accumulation of trans-16:1, as well as the organization of LHCII are modulated by both growth irradiance and growth temperature in an independent but additive manner. We also examined how changes in the supramolecular organization of LHCII affected the capacity for non-photochemical quenching (q(N)) and photoprotection via antenna quenching (q(O)). While q(O) was positively correlated with q(N), there was no correlation with either LHCII organization or xanthophyll cycle activity under the steady-state growth conditions examined.

Efficient Cleavage of Lignin–Carbohydrate Complexes and Ultrafast Extraction of Lignin Oligomers from Wood Biomass by Microwave‐Assisted Treatment with Deep Eutectic Solvent

PubMed Central

Liu, Yongzhuang; Chen, Wenshuai; Xia, Qinqin; Guo, Bingtuo; Wang, Qingwen; Liu, Shouxin; Liu, Yixing; Li, Jian

2017-01-01

Abstract Lignocellulosic biomass is an abundant and renewable resource for the production of biobased value‐added fuels, chemicals, and materials, but its effective exploitation by an energy‐efficient and environmentally friendly strategy remains a challenge. Herein, a facile approach for efficiently cleaving lignin–carbohydrate complexes and ultrafast fractionation of components from wood by microwave‐assisted treatment with deep eutectic solvent is reported. The solvent was composed of sustainable choline chloride and oxalic acid dihydrate, and showed a hydrogen‐bond acidity of 1.31. Efficient fractionation of lignocellulose with the solvent was realized by heating at 80 °C under 800 W microwave irradiation for 3 min. The extracted lignin showed a low molecular weight of 913, a low polydispersity of 1.25, and consisted of lignin oligomers with high purity (ca. 96 %), and thus shows potential in downstream production of aromatic chemicals. The other dissolved matter mainly comprised glucose, xylose, and hydroxymethylfurfural. The undissolved material was cellulose with crystal I structure and a crystallinity of approximately 75 %, which can be used for fabricating nanocellulose. Therefore, this work promotes an ultrafast lignin‐first biorefinery approach while simultaneously keeping the undissolved cellulose available for further utilization. This work is expected to contribute to improving the economics of overall biorefining of lignocellulosic biomass. PMID:28054749

HAMLET forms annular oligomers when deposited with phospholipid monolayers.

PubMed

Baumann, Anne; Gjerde, Anja Underhaug; Ying, Ming; Svanborg, Catharina; Holmsen, Holm; Glomm, Wilhelm R; Martinez, Aurora; Halskau, Oyvind

2012-04-20

Recently, the anticancer activity of human α-lactalbumin made lethal to tumor cells (HAMLET) has been linked to its increased membrane affinity in vitro, at neutral pH, and ability to cause leakage relative to the inactive native bovine α-lactalbumin (BLA) protein. In this study, atomic force microscopy resolved membrane distortions and annular oligomers (AOs) produced by HAMLET when deposited at neutral pH on mica together with a negatively charged lipid monolayer. BLA, BAMLET (HAMLET's bovine counterpart) and membrane-binding Peptide C, corresponding to BLA residues 75-100, also form AO-like structures under these conditions but at higher subphase concentrations than HAMLET. The N-terminal Peptide A, which binds to membranes at acidic but not at neutral pH, did not form AOs. This suggests a correlation between the capacity of the proteins/peptides to integrate into the membrane at neutral pH-as observed by liposome content leakage and circular dichroism experiments-and the formation of AOs, albeit at higher concentrations. Formation of AOs, which might be important to HAMLET's tumor toxic action, appears related to the increased tendency of the protein to populate intermediately folded states compared to the native protein, the formation of which is promoted by, but not uniquely dependent on, the oleic acid molecules associated with HAMLET. Copyright © 2012 Elsevier Ltd. All rights reserved.

Substrate-induced growth and isolation of Acidobacteria from acidic Sphagnum peat.

PubMed

Pankratov, Timofei A; Serkebaeva, Yulia M; Kulichevskaya, Irina S; Liesack, Werner; Dedysh, Svetlana N

2008-05-01

Fluorescence in situ hybridization (FISH) was applied to estimate the population size of the poorly characterized phylum Acidobacteria in acidic peat sampled from nine different Sphagnum-dominated wetlands of Northern Russia. The cell numbers of these bacteria in oxic peat layers ranged from 0.4 x 10(6) to 1.3 x 10(7) cells per g of wet peat, comprising up to 4% of total bacterial cells. Substrate-induced growth of acidobacteria was observed after amendment of peat samples with glucose, pectin, xylan, starch, ethanol and methanol, while weak or no response was obtained for acetate, pyruvate, mannitol and cellobiose. Using low-nutrient media and FISH-mediated monitoring of the isolation procedure, we succeeded in obtaining nine strains of acidobacteria in pure cultures. These strains belonged to subdivisions 1 and 3 of the Acidobacteria and represented strictly aerobic, heterotrophic organisms. Except for methanol, the substrate utilization patterns of these isolates matched the results obtained in our substrate-amendment experiments with native peat. All strains were also capable of utilizing galacturonic acid, a characteristic component of the cell wall in Sphagnum spp, which is released during moss decomposition. Most isolates from subdivision 1 were truly acidophilic organisms with the growth optimum at pH 3.5-4.5, while the isolates from subdivision 3 grew optimally at pH 5.5-6.5. Another important phenotypic trait of novel strains was their capability of active growth at low temperatures. Both acidophily and low-temperature growth are consistent with the occurrence of acidobacteria in cold and acidic northern wetlands.

Lectin activity in mycelial extracts of Fusarium species.

PubMed

Bhari, Ranjeeta; Kaur, Bhawanpreet; Singh, Ram S

2016-01-01

Lectins are non-immunogenic carbohydrate-recognizing proteins that bind to glycoproteins, glycolipids, or polysaccharides with high affinity and exhibit remarkable ability to agglutinate erythrocytes and other cells. In the present study, ten Fusarium species previously not explored for lectins were screened for the presence of lectin activity. Mycelial extracts of F. fujikuroi, F. beomiformii, F. begoniae, F. nisikadoi, F. anthophilum, F. incarnatum, and F. tabacinum manifested agglutination of rabbit erythrocytes. Neuraminidase treatment of rabbit erythrocytes increased lectin titers of F. nisikadoi and F. tabacinum extracts, whereas the protease treatment resulted in a significant decline in agglutination by most of the lectins. Results of hapten inhibition studies demonstrated unique carbohydrate specificity of Fusarium lectins toward O-acetyl sialic acids. Activity of the majority of Fusarium lectins exhibited binding affinity to d-ribose, l-fucose, d-glucose, l-arabinose, d-mannitol, d-galactosamine hydrochloride, d-galacturonic acid, N-acetyl-d-galactosamine, N-acetyl-neuraminic acid, 2-deoxy-d-ribose, fetuin, asialofetuin, and bovine submaxillary mucin. Melibiose and N-glycolyl neuraminic acid did not inhibit the activity of any of the Fusarium lectins. Mycelial extracts of F. begoniae, F. nisikadoi, F. anthophilum, and F. incarnatum interacted with most of the carbohydrates tested. F. fujikuroi and F. anthophilum extracts displayed strong interaction with starch. The expression of lectin activity as a function of culture age was investigated. Most species displayed lectin activity on the 7th day of cultivation, and it varied with progressing of culture age. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Polyclonal antibody against a complement-activating pectin from the roots of Angelica acutiloba.

PubMed

Wang, N L; Kiyohara, H; Matsumoto, T; Otsuka, H; Hirano, M; Yamada, H

1994-10-01

Anti-sera against a complement-activating pectin (AR-2IIb), which was purified from the roots of Angelica acutiloba Kitagawa, were obtained by immunization of rabbits, and a polyclonal anti-AR-2IIb antibody of the IgG class was purified by affinity chromatography on AR-2IIb-immobilized Sepharose and Protein G-Sepharose. Periodate oxidation of AR-2IIb significantly reduced its inhibitory activity on the reactivity of AR-2IIb to anti-AR-2IIb-IgG, but pronase digestion of AR-2IIb did not affect its inhibitory activity. Other pharmacologically active pectins from A. autiloba, Bupleurum falcatum, and Glycyrrhiza uralensis and the complement-activating pectic arabinogalactan from A. autiloba also showed significant inhibitory activities on the reactivity of AR-2IIb to anti-AR-2IIb-IgG, but these inhibitory activities were lower than that of AR-2IIb. Other pectins, polygalacturonic acid, arabinogalactan, galactan, and araban tested had negligible inhibitory activity. Endo-a-(1-->4)-polygalacturonase digestion of AR-2IIb indicated that its "ramified" region (rhamnogalacturonan core possessing neutral oligosaccharide side-chains) contained epitopes for anti-AR-2IIb-IgG, but that 2-keto-3-deoxyoctulosonic acid (KDO)-containing regions and oligogalacturonides obtained from AR-2IIb were not recognized by anti-AR-2IIb-IgG. Although carboxyl-reduction of galacturonic acid in the "ramified" region decreased the inhibitory activity of the "ramified" on its reactivity to anti-AR-2IIb, an acidic tetrasaccharide unit in the rhamnogalacturonan core had negligible inhibitory activity.

Structural characterization and immunomodulatory effect of a polysaccharide HCP-2 from Houttuynia cordata.

PubMed

Cheng, Bao-Hui; Chan, Judy Yuet-Wa; Chan, Ben Chung-Lap; Lin, Huang-Quan; Han, Xiao-Qiang; Zhou, Xuelin; Wan, David Chi-Cheong; Wang, Yi-Fen; Leung, Ping-Chung; Fung, Kwok-Pui; Lau, Clara Bik-San

2014-03-15

Immunomodulation of natural polysaccharides has been the hot topic of research in recent years. In order to explore the immunomodulatory effect of Houttuynia cordata Thunb., the water extract was studied and a polysaccharide HCP-2 with molecular weight of 60,000 Da was isolated by chromatography using DEAE Sepharose CL-6B and Sephacryl S-500 [corrected] HR columns. The structure characterization of HCP-2 was performed by Fourier transform infrared spectroscopy (FTIR), acidic hydrolysis, PMP derivation, HPLC analysis and nuclear magnetic resonance spectra (NMR). HCP-2 was elucidated as a pectic polysaccharide with a linear chain of 1,4-linked α-D-galacturonic acid residues in which part of the 6-carboxyl groups were methyl esterified and part of 2-hydroxyl groups were acetylated. The bioactivity assays showed that HCP-2 could increase the secretions of interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), macrophage inhibitory protein-1α (MIP-1α), macrophage inhibitory protein-1β (MIP-1β), and RANTES (regulated on activation, normal T cell expressed and secreted) in human peripheral blood mononuclear cells (PBMCs), which play critical roles in the innate immune system and shape the adaptive immunity. Our results implied that HCP-2 could be an immune enhancer. Copyright © 2013 Elsevier Ltd. All rights reserved.

Elucidation of amyloid beta-protein oligomerization mechanisms: discrete molecular dynamics study.

PubMed

Urbanc, B; Betnel, M; Cruz, L; Bitan, G; Teplow, D B

2010-03-31

Oligomers of amyloid beta-protein (Abeta) play a central role in the pathology of Alzheimer's disease. Of the two predominant Abeta alloforms, Abeta(1-40) and Abeta(1-42), Abeta(1-42) is more strongly implicated in the disease. We elucidated the structural characteristics of oligomers of Abeta(1-40) and Abeta(1-42) and their Arctic mutants, [E22G]Abeta(1-40) and [E22G]Abeta(1-42). We simulated oligomer formation using discrete molecular dynamics (DMD) with a four-bead protein model, backbone hydrogen bonding, and residue-specific interactions due to effective hydropathy and charge. For all four peptides under study, we derived the characteristic oligomer size distributions that were in agreement with prior experimental findings. Unlike Abeta(1-40), Abeta(1-42) had a high propensity to form paranuclei (pentameric or hexameric) structures that could self-associate into higher-order oligomers. Neither of the Arctic mutants formed higher-order oligomers, but [E22G]Abeta(1-40) formed paranuclei with a similar propensity to that of Abeta(1-42). Whereas the best agreement with the experimental data was obtained when the charged residues were modeled as solely hydrophilic, further assembly from spherical oligomers into elongated protofibrils was induced by nonzero electrostatic interactions among the charged residues. Structural analysis revealed that the C-terminal region played a dominant role in Abeta(1-42) oligomer formation whereas Abeta(1-40) oligomerization was primarily driven by intermolecular interactions among the central hydrophobic regions. The N-terminal region A2-F4 played a prominent role in Abeta(1-40) oligomerization but did not contribute to the oligomerization of Abeta(1-42) or the Arctic mutants. The oligomer structure of both Arctic peptides resembled Abeta(1-42) more than Abeta(1-40), consistent with their potentially more toxic nature.

Liquid chromatography/tandem mass spectrometry method for quantitative estimation of polyethylene glycol 400 and its applications.

PubMed

Vijaya Bhaskar, V; Middha, Anil; Tiwari, Sudhir; Shivakumar, Savithiri

2013-05-01

A rapid sensitive and selective MRM based method for the determination of polyethylene glycol 400 (PEG 400) in rat plasma was developed using liquid chromatography/tandem mass spectrometry (LC-MS/MS). PEG 400 and telmisartan (Internal standard) were extracted from rat plasma with acetonitrile and analysed on C18 column (Waters Xbridge, 50×4.6 mm, 3.5 μm) with the mobile phase (A - 0.1% formic acid in water; B - methanol). A generic gradient method with a short run time of 3.5 min was developed for the analysis of PEG 400. A total of nine oligomers were identified for PEG 400. The most abundant ions corresponding to PEG 400 oligomers at m/z 327, 371, 432, 476, 520, 564, 608, 652 and 696 with daughter ion at m/z 89 were selected for multiple reaction monitoring (MRM) in electrospray mode of ionisation. Analyte peak area of the oligomers was summed up to calculate the plasma concentrations of total PEG 400. The standard curve was linear (0.9954) over the concentration range of 1.01-1013.40 μg/mL. The lower limit of quantitation for PEG 400 was 1.01 μg/mL using 50 μL plasma. The coefficient of variation and relative error for inter and intraassay at three QC levels were 2.31-13.34 and -7.99 to 0.37, respectively. The method was validated for various parameters such as extraction recovery, matrix effect, autosampler stability, benchtop stability, freeze thaw stability, long term stability and was proved to be consistent across three QC levels with overall %CV less than 15. The developed method was successfully applied to the absolute bioavailability study of PEG 400 in male Sprague Dawley rats. Plasma concentrations of PEG 400 was measured after administration through oral and intravenous routes in male Sprague Dawley rats at a dose of 3.38 g/kg. Pharmacokinetic (PK) parameters were characterised by performing the analysis using Phoenix Winnonlin software (v 6.3). PEG 400 has good oral bioavailability with mean absolute bioavailability of 47.23%. Plasma concentration profile/PK parameters of PEG 400 was established in both intravenous and oral routes, which helps to qualify the analytical batch of NCEs having spiky plasma concentration profiles/erratic results. Purity of the PEG 400 oligomers was estimated using ELSD detection. Differences in pharmacokinetics of oligomers was studied. It was found that with increase in molecular weight of the oligomer, a decrease in absolute bioavailability was observed. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

Effects of polyalkylene glycols and fatty acid soaps on properties of synthetic lubricating-cooling fluids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stulii, A.A.

1983-01-01

The lack of any effect of the polyalkylene glycols on the series of properties of the fatty acid soaps was confirmed by replacing the PEG-35 in the synthetic lubricating-cooling fluid (LCF) by a polyethylene glycol with a molecular weight of 400 or 6000, a propylene oxide oligomer with a molecular weight of 700, or a copolymer of ethylene and propylene oxides (Pluronic 44, Pluriol PE-6400, Hydropol 200). Attempts to select surfactants and optimal concentrations in synthetic LCFs based on polyalkylene glycols. Indicates that of the studied soaps, those of the most interest are the triethanolamine soaps of individual C/sub 6/-C/submore » 10/ fatty acids and commercial mixed C/sub 7/-C/sub 9/ synthetic fatty acids. Finds that the polyalkylene glycols and the indicated soaps supplement each other, imparting the required set of properties to the LCF.« less

Detergent-dispersant additives based on high-molecular-weight alkylphenols

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kulieva, K.N.; Namazova, I.I.; Ismailova, N.D.

1988-09-01

This article describes the synthesis and investigation of Mannich bases produced for alkylphenols, obtained in turn from ethylene oligomers. These oligomers are the still bottoms from distillation products of high-temperature oligomerization of ethylene in the presence of triethylaluminum. Two narrow cuts obtained from the distillation of oligomer fraction were used to study the influence of ethylene oligomer molecular weight on the properties of the additives. The additives were blended in DS-11 oil to evaluate their detergency-dispersancy and other properties. Comparison blends were made with succinimide additives based on the same ethylene oligomers. The Mannich bases give improvements in the oxidationmore » resistance, anticorrosion properties, and detergency-dispersancy of the DS-11 diesel oil.« less

Effects of adding methacrylate monomers on viscosity and mechanical properties of experimental light-curing soft lining materials based on urethane (meth)acrylate oligomers.

PubMed

Kanie, Takahito; Kadokawa, Akihiko; Arikawa, Hiroyuki; Fujii, Koichi; Ban, Seiji

2008-11-01

We investigated the viscosity and mechanical properties of experimental light-curing soft lining materials based on six commercially available urethane (meth)acrylate oligomers. The viscosities of the six oligomers were 1.9, 20.6, 26.8, 144.0, 185.3, and 8803.4 Pa*s at 25 degrees C. Two monomers (ethyl- and butyl-methacrylate) were added at 20 wt% to these oligomers to decrease the viscosity, resulting in viscosity reductions of 0.2 to 13.6 Pa*s for the six oligomers. The mechanical properties (compressive modulus, Shore A hardness, and tensile strength) were measured after two times light-polymerization for 3 min. The addition of the monomers to the oligomers only slightly changed the mechanical properties, in contrast to the large viscosity changes. Based on these results, it appears that the addition of ethyl- or butyl-methacrylate monomers is useful for decreasing the viscosity of experimental light-curing soft lining materials without changing their mechanical properties.

Towards non-invasive diagnostic imaging of early-stage Alzheimer's disease

NASA Astrophysics Data System (ADS)

Viola, Kirsten L.; Sbarboro, James; Sureka, Ruchi; de, Mrinmoy; Bicca, Maíra A.; Wang, Jane; Vasavada, Shaleen; Satpathy, Sreyesh; Wu, Summer; Joshi, Hrushikesh; Velasco, Pauline T.; Macrenaris, Keith; Waters, E. Alex; Lu, Chang; Phan, Joseph; Lacor, Pascale; Prasad, Pottumarthi; Dravid, Vinayak P.; Klein, William L.

2015-01-01

One way to image the molecular pathology in Alzheimer's disease is by positron emission tomography using probes that target amyloid fibrils. However, these fibrils are not closely linked to the development of the disease. It is now thought that early-stage biomarkers that instigate memory loss are composed of Aβ oligomers. Here, we report a sensitive molecular magnetic resonance imaging contrast probe that is specific for Aβ oligomers. We attach oligomer-specific antibodies onto magnetic nanostructures and show that the complex is stable and binds to Aβ oligomers on cells and brain tissues to give a magnetic resonance imaging signal. When intranasally administered to an Alzheimer's disease mouse model, the probe readily reached hippocampal Aβ oligomers. In isolated samples of human brain tissue, we observed a magnetic resonance imaging signal that distinguished Alzheimer's disease from controls. Such nanostructures that target neurotoxic Aβ oligomers are potentially useful for evaluating the efficacy of new drugs and ultimately for early-stage Alzheimer's disease diagnosis and disease management.

Violation of the isolated square rule for group 13-15 oligomers: theoretical prediction of a new class of inorganic polymers.

PubMed

Timoshkin, Alexey Y; Schaefer, Henry F

2005-02-21

It is widely thought that the oligomer compounds [RMYR]n (M-group 13, Y-group 15 element) should obey the isolated square rule found for the boron-nitrogen cages. In contrast to these expectations, the needle-shaped oligomers, which violate this rule, are more stable compared to the cage (fullerene-like) oligomers for all MY pairs (M = B, Al, Ga, In; Y = N, P, As). The stability of the needle-shaped clusters improves with increasing oligomerization degree. Thus, the isolated square rule, which is analogous to the isolated pentagon rule widely applied for fullerenes, should not serve as the basis for searches for the most stable structures of the inorganic oligomers. Generation of the needle-shaped oligomers from the group 13 and 15 hydrides is thermodynamically favorable. A synthesis of novel inorganic polymers, formed by fusion of trimeric M3Y3 rings, is expected to be viable.

Transesterification of PHA to oligomers covalently bonded with (bio)active compounds containing either carboxyl or hydroxyl functionalities.

PubMed

Kwiecień, Iwona; Radecka, Iza; Kowalczuk, Marek; Adamus, Grażyna

2015-01-01

This manuscript presents the synthesis and structural characterisation of novel biodegradable polymeric controlled-release systems of pesticides with potentially higher resistance to weather conditions in comparison to conventional forms of pesticides. Two methods for the preparation of pesticide-oligomer conjugates using the transesterification reaction were developed. The first method of obtaining conjugates, which consist of bioactive compounds with the carboxyl group and polyhydroxyalkanoates (PHAs) oligomers, is "one-pot" transesterification. In the second method, conjugates of bioactive compounds with hydroxyl group and polyhydroxyalkanoates oligomers were obtained in two-step method, through cyclic poly(3-hydroxybutyrate) oligomers. The obtained pesticide-PHA conjugates were comprehensively characterised using GPC, 1H NMR and mass spectrometry techniques. The structural characterisation of the obtained products at the molecular level with the aid of mass spectrometry confirmed that both of the synthetic strategies employed led to the formation of conjugates in which selected pesticides were covalently bonded to PHA oligomers via a hydrolysable ester bond.

Development of Processible Electroactive Oligomers and Polymers

DTIC Science & Technology

1991-10-01

of structure and electroactive properties. Electroactive molecules including fused ring (ladder oligomers) dyes , squarylium -heterocyclic moieties...Electroactive molecules including fused ring (ladder oligomers) dyes , squarylium -heterocyclic moieties, phenylpolyenes, thienylpolyenes, carbocyanine dyes ...phenylpolyenes, thienylpolyenes, carbocyanine dyes , and tetraazaannulenes have also been synthetically incorporated into a variety of traditional

Water-soluble metal working fluids additives derived from the esters of acid anhydrides with higher alcohols for aluminum alloy materials.

PubMed

Yamamoto, Syutaro; Tomoda, Hideyuki; Watanabe, Shoji

2007-01-01

Water-soluble metal working fluids are used for processing of aluminum alloy materials. This short article describes properties of new additives in water-soluble metal working fluids for aluminum alloy materials. Many half esters or diesters were prepared from the reactions of higher alcohols with acid anhydrides. Interestingly, diesters of PTMG (tetrahydrofuran oligomer, MW = 650 and 1000) and polybutylene oxide (MW = 650) with maleic anhydride and succinic anhydride showed both of an excellent anti-corrosion property for aluminum alloy and a good hard water tolerance. The industrial soluble type processing oils including these additives also showed anti-corrosion property and hard water tolerance.

[Analysis of the bacterial community developing in the course of Sphagnum moss decomposition].

PubMed

Kulichevskaia, I S; Belova, S E; Kevbrin, V V; Dedysh, S N; Zavarzin, G A

2007-01-01

Slow degradation of organic matter in acidic Sphagnum peat bogs suggests a limited activity of organotrophic microorganisms. Monitoring of the Sphagnum debris decomposition in a laboratory simulation experiment showed that this process was accompanied by a shift in the water color to brownish due to accumulation of humic substances and by the development of a specific bacterial community with a density of 2.4 x 10(7) cells ml(-1). About half of these organisms are metabolically active and detectable with rRNA-specific oligonucleotide probes. Molecular identification of the components of this microbial community showed the numerical dominance of bacteria affiliated with the phyla Alphaproteobacteria, Actinobacteria, and Phanctomycetes. The population sizes of Firmicutes and Bacteroidetes, which are believed to be the main agents of bacterially-mediated decomposition in eutrophic wetlands, were low. The numbers of planctomycetes increased at the final stage of Sphagnum decomposition. The representative isolates of Alphaproteobacteria were able to utilize galacturonic acid, the only low-molecular-weight organic compound detected in the water samples; the representatives of Planctomycetes were able to decompose some heteropolysaccharides, which points to the possible functional role of these groups of microorganisms in the community under study. Thus, the composition of the bacterial community responsible for Sphagnum decomposition in acidic and low-mineral oligotrophic conditions seems to be fundamentally different from that of the bacterial community which decomposes plant debris in eutrophic ecosystems at neutral pH.

UUAT1 Is a Golgi-Localized UDP-Uronic Acid Transporter That Modulates the Polysaccharide Composition of Arabidopsis Seed Mucilage

DOE PAGES

Saez-Aguayo, Susana; Rautengarten, Carsten; Temple, Henry; ...

2017-01-01

UDP-glucuronic acid (UDP-GlcA) is the precursor of many plant cell wall polysaccharides and is required for production of seed mucilage. Following synthesis in the cytosol, it is transported into the lumen of the Golgi apparatus, where it is converted to UDP-galacturonic acid (UDP-GalA), UDP-arabinose, and UDP-xylose. To identify the Golgi-localized UDP-GlcA transporter, we screened Arabidopsis thaliana mutants in genes coding for putative nucleotide sugar transporters for altered seed mucilage, a structure rich in the GalA-containing polysaccharide rhamnogalacturonan I. As a result, we identified UUAT1, which encodes a Golgi-localized protein that transports UDP-GlcA and UDP-GalA in vitro. The seed coat ofmore » uuat1 mutants had less GalA, rhamnose, and xylose in the soluble mucilage, and the distal cell walls had decreased arabinan content. Cell walls of other organs and cells had lower arabinose levels in roots and pollen tubes, but no differences were observed in GalA or xylose contents. Furthermore, the GlcA content of glucuronoxylan in the stem was not affected in the mutant. Interestingly, the degree of homogalacturonan methylation increased in uuat1. These results suggest that this UDP-GlcA transporter plays a key role defining the seed mucilage sugar composition and that its absence produces pleiotropic effects in this component of the plant extracellular matrix.« less

UUAT1 Is a Golgi-Localized UDP-Uronic Acid Transporter That Modulates the Polysaccharide Composition of Arabidopsis Seed Mucilage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saez-Aguayo, Susana; Rautengarten, Carsten; Temple, Henry

UDP-glucuronic acid (UDP-GlcA) is the precursor of many plant cell wall polysaccharides and is required for production of seed mucilage. Following synthesis in the cytosol, it is transported into the lumen of the Golgi apparatus, where it is converted to UDP-galacturonic acid (UDP-GalA), UDP-arabinose, and UDP-xylose. To identify the Golgi-localized UDP-GlcA transporter, we screened Arabidopsis thaliana mutants in genes coding for putative nucleotide sugar transporters for altered seed mucilage, a structure rich in the GalA-containing polysaccharide rhamnogalacturonan I. As a result, we identified UUAT1, which encodes a Golgi-localized protein that transports UDP-GlcA and UDP-GalA in vitro. The seed coat ofmore » uuat1 mutants had less GalA, rhamnose, and xylose in the soluble mucilage, and the distal cell walls had decreased arabinan content. Cell walls of other organs and cells had lower arabinose levels in roots and pollen tubes, but no differences were observed in GalA or xylose contents. Furthermore, the GlcA content of glucuronoxylan in the stem was not affected in the mutant. Interestingly, the degree of homogalacturonan methylation increased in uuat1. These results suggest that this UDP-GlcA transporter plays a key role defining the seed mucilage sugar composition and that its absence produces pleiotropic effects in this component of the plant extracellular matrix.« less

UUAT1 Is a Golgi-Localized UDP-Uronic Acid Transporter That Modulates the Polysaccharide Composition of Arabidopsis Seed Mucilage[OPEN

PubMed Central

Saez-Aguayo, Susana; Rautengarten, Carsten; Temple, Henry; Sanhueza, Dayan; Ejsmentewicz, Troy; Sandoval-Ibañez, Omar; Parra-Rojas, Juan Pablo; Ebert, Berit; Reyes, Francisca C.

2017-01-01

UDP-glucuronic acid (UDP-GlcA) is the precursor of many plant cell wall polysaccharides and is required for production of seed mucilage. Following synthesis in the cytosol, it is transported into the lumen of the Golgi apparatus, where it is converted to UDP-galacturonic acid (UDP-GalA), UDP-arabinose, and UDP-xylose. To identify the Golgi-localized UDP-GlcA transporter, we screened Arabidopsis thaliana mutants in genes coding for putative nucleotide sugar transporters for altered seed mucilage, a structure rich in the GalA-containing polysaccharide rhamnogalacturonan I. As a result, we identified UUAT1, which encodes a Golgi-localized protein that transports UDP-GlcA and UDP-GalA in vitro. The seed coat of uuat1 mutants had less GalA, rhamnose, and xylose in the soluble mucilage, and the distal cell walls had decreased arabinan content. Cell walls of other organs and cells had lower arabinose levels in roots and pollen tubes, but no differences were observed in GalA or xylose contents. Furthermore, the GlcA content of glucuronoxylan in the stem was not affected in the mutant. Interestingly, the degree of homogalacturonan methylation increased in uuat1. These results suggest that this UDP-GlcA transporter plays a key role defining the seed mucilage sugar composition and that its absence produces pleiotropic effects in this component of the plant extracellular matrix. PMID:28062750

Liquid Crystalline Thermosets from Ester, Ester-Imide, and Ester-Amide Oligomers

NASA Technical Reports Server (NTRS)

Dingemans, Theodornus J. (Inventor); Weiser, Erik S. (Inventor); SaintClair, Terry L. (Inventor)

2005-01-01

Main chain thermotropic liquid crystal esters, ester-imides, and ester-amides were prepared from AA, BB, and AB type monomeric materials and were end-capped with phenylacetylene, phenylmaleimide, or nadimide reactive end-groups. The resulting reactive end-capped liquid crystal oligomers exhibit a variety of improved and preferred physical properties. The end-capped liquid crystal oligomers are thermotropic and have, preferably, molecular weights in the range of approximately 1000-15,OOO grams per mole. The end-capped liquid crystal oligomers have broad liquid crystalline melting ranges and exhibit high melt stability and very low melt viscosities at accessible temperatures. The end-capped liquid crystal oligomers are stable for up to an hour in the melt phase. These properties make the end-capped liquid crystal oligomers highly processable by a variety of melt process shape forming and blending techniques including film extrusion, fiber spinning, reactive injection molding (RIM), resin transfer molding (RTM), resin film injection (RFI), powder molding, pultrusion, injection molding, blow molding, plasma spraying and thermo-forming. Once processed and shaped, the end- capped liquid crystal oligomers were heated to further polymerize and form liquid crystalline thermosets (LCT). The fully cured products are rubbers above their glass transition temperatures. The resulting thermosets display many properties that are superior to their non-end-capped high molecular weight analogs.

Early and Selective Impairments in Axonal Transport Kinetics of Synaptic Cargoes Induced by Soluble Amyloid β-Protein Oligomers

PubMed Central

Tang, Yong; Scott, David A.; Das, Utpal; Edland, Steven D.; Radomski, Kryslaine; Koo, Edward H.; Roy, Subhojit

2013-01-01

The downstream targets of amyloid β (Aβ)-oligomers remain elusive. One hypothesis is that Aβ-oligomers interrupt axonal transport. Although previous studies have demonstrated Aβ-induced transport blockade, early effects of low-n soluble Aβ-oligomers on axonal transport remain unclear. Furthermore, the cargo selectivity for such deficits (if any) or the specific effects of Aβ on the motility kinetics of transported cargoes are also unknown. Toward this, we visualized axonal transport of vesicles in cultured hippocampal neurons treated with picomolar (pm) levels of cell-derived soluble Aβ-oligomers. We examined select cargoes thought to move as distinct organelles and established imaging parameters that allow organelle tracking with consistency and high fidelity – analyzing all data in a blinded fashion. Aβ-oligomers induced early and selective diminutions in velocities of synaptic cargoes but had no effect on mitochondrial motility, contrary to previous reports. These changes were N-methyl d-aspartate receptor/glycogen synthase kinase-3β dependent and reversible upon washout of the oligomers. Cluster-mode analyses reveal selective attenuations in faster-moving synaptic vesicles, suggesting possible decreases in cargo/motor associations, and biochemical experiments implicate tau phosphorylation in the process. Collectively, the data provide a biological basis for Aβ-induced axonal transport deficits. PMID:22309053

Liquid crystalline thermosets from ester, ester-imide, and ester-amide oligomers

NASA Technical Reports Server (NTRS)

Dingemans, Theodorous J. (Inventor); Weiser, Erik S. (Inventor); St. Clair, Terry L. (Inventor)

2005-01-01

Main chain thermotropic liquid crystal esters, ester-imides, and ester-amides were prepared from AA, BB, and AB type monomeric materials and were end-capped with phenylacetylene, phenylmaleimide, or nadimide reactive end-groups. The resulting reactive end-capped liquid crystal oligomers exhibit a variety of improved and preferred physical properties. The end-capped liquid crystal oligomers are thermotropic and have, preferably, molecular weights in the range of approximately 1000-15,000 grams per mole. The end-capped liquid crystal oligomers have broad liquid crystalline melting ranges and exhibit high melt stability and very low melt viscosities at accessible temperatures. The end-capped liquid crystal oligomers are stable for up to an hour in the melt phase. These properties make the end-capped liquid crystal oligomers highly processable by a variety of melt process shape forming and blending techniques including film extrusion, fiber spinning, reactive injection molding (RIM), resin transfer molding (RTM), resin film injection (RFI), powder molding, pultrusion, injection molding, blow molding, plasma spraying and thermo-forming. Once processed and shaped, the end-capped liquid crystal oligomers were heated to further polymerize and form liquid crystalline thermosets (LCT). The fully cured products are rubbers above their glass transition temperatures. The resulting thermosets display many properties that are superior to their non-end-capped high molecular weight analogs.

Adhesive Properties of Cured Phenylethynyl Containing Imides

NASA Technical Reports Server (NTRS)

Jensen, Brian J.; Chang, Alice C.

1997-01-01

Considerable attention has been directed towards acetylene terminated oligomers over the last 20 years' and recent work has focused on phenylethynyl terminated imide (PETI) oligomers. These reactive oligomers possess several features which make them attractive candidates for use as composite matrices and adhesives. The phenylethynyl group can be readily incorporated into many different functionalized oligomers. The reactive oligomers possess relatively low melt viscosities and thermally cure without the evolution of volatile by-products. Once cured, they typically display high glass transition temperatures (Tgs), excellent solvent resistance and high mechanical properties. new modified phenylethynyl-terminated imide (LaRC MPEI) oligomers were synthesized at various molecular weights utilizing a small amount of trifunctional amine. As long as the amount of triamine is relatively small, this approach produces a mixture of linear, star-shaped and branched polymer chains that has lower melt and solution viscosity than an equivalent molecular weight linear phenylethynyl terminated imide oligomers. The work reported herein involves the synthesis and characterization of a copolymer using this approach and the preparation of blends utilizing a phenylethynyl containing reactive plasticizer of lower molecular weight called LaRC LV-121. The chemistry and properties of this new MPEI as well as some blends of MPEI with LV-121, are presented and compared to the linear version, LARC-PETI-5.

Intracellular soluble α‐synuclein oligomers reduce pyramidal cell excitability

PubMed Central

Kaufmann, Timothy J.; Harrison, Paul M.; Richardson, Magnus J. E.; Pinheiro, Teresa J. T.

2016-01-01

Key points The presynaptic protein α‐synuclein forms aggregates during Parkinson's disease.Accumulating evidence suggests that the small soluble oligomers of α‐synuclein are more toxic than the larger aggregates appearing later in the disease.The link between oligomer toxicity and structure still remains unclear.In the present study, we have produced two structurally‐defined oligomers that have a similar morphology but differ in secondary structure.These oligomers were introduced into neocortical pyramidal cells during whole‐cell recording and, using a combination of experimentation and modelling, electrophysiological parameters were extracted.Both oligomeric species had similar effects on neuronal properties reducing input resistance, time constant and increasing capacitance. The net effect was a marked reduction in neuronal excitability that could impact on network activity. Abstract The presynaptic protein α‐synuclein (αSyn) aggregates during Parkinson's disease (PD) to form large proteinaceous amyloid plaques, the spread of which throughout the brain clinically defines the severity of the disease. During early stages of aggregation, αSyn forms soluble annular oligomers that show greater toxicity than much larger fibrils. These oligomers produce toxicity via a number of possible mechanisms, including the production of pore‐forming complexes that permeabilize membranes. In the present study, two well‐defined species of soluble αSyn oligomers were produced by different protocols: by polymerization of monomer and by sonication of fibrils. The two oligomeric species produced were morphologically similar, with both having an annular structure and consisting of approximately the same number of monomer subunits, although they differed in their secondary structure. Oligomeric and monomeric αSyn were injected directly into the soma of pyramidal neurons in mouse neocortical brain slices during whole‐cell patch clamp recording. Using a combined experimental and modelling approach, neuronal parameters were extracted to measure, for the first time in the neocortex, specific changes in neuronal electrophysiology. Both species of oligomer had similar effects: (i) a significant reduction in input resistance and the membrane time constant and (ii) an increase in the current required to trigger an action potential with a resultant reduction in the firing rate. Differences in oligomer secondary structure appeared to produce only subtle differences in the activity of the oligomers. Monomeric αSyn had no effect on neuronal parameters, even at high concentrations. The oligomer‐induced fall in neuronal excitability has the potential to impact both network activity and cognitive processing. PMID:26915902

Fluorometric detection of adenine in target DNA by exciplex formation with fluorescent 8-arylethynylated deoxyguanosine.

PubMed

Saito, Yoshio; Kugenuma, Kenji; Tanaka, Makiko; Suzuki, Azusa; Saito, Isao

2012-06-01

We demonstrated an intriguing method to discriminate adenine by incident appearance of an intense new emission via exciplex formation in hybridization of target DNA with newly designed fluorescent 8-arylethynylated deoxyguanosine derivatives. We described the synthesis of such highly electron donating fluorescent guanosine derivatives and their incorporation into DNA oligomers which may be used for the structural study and the fluorometric analysis of nucleic acids. Copyright © 2012 Elsevier Ltd. All rights reserved.

Determination of the size and degree of acetyl substitution of oligosaccharides from Neisseria meningitidis group A by ionspray mass spectrometry.

PubMed

Cescutti, P; Bigio, M; Guarnieri, V

1996-07-16

The capsular polysaccharide produced by Neisseria meningitidis group A has the following structure: [formula: see text] [formula: see text] This polysaccharide was partially hydrolysed with acetic acid, and the oligomers obtained were separated by fast performance liquid chromatography. Six fractions were collected and characterised by ionspray mass spectrometry in the positive ion mode. This soft ionisation technique established the size of the obtained oligosaccharides and the degree of O-acetyl substitution for each fraction.

Acidic processing of hemicellulosic saccharides from pine wood: product distribution and kinetic modeling.

PubMed

Rivas, Sandra; González-Muñoz, María Jesús; Santos, Valentín; Parajó, Juan Carlos

2014-06-01

Water soluble compounds were removed from Pinus pinaster wood by a mild aqueous extraction, and the treated wood was subjected to hydrothermal processing to convert most hemicelluloses into soluble saccharides (including low molecular weight polymers, oligomers and monosaccharides). The liquid phase containing hemicellulose-derived saccharides was acidified with sulfuric acid and heated up to 130-250°C to obtain furans and levulinic acid as major products. The concentration profiles of the major compounds participating in the reactions were interpreted by a kinetic model. A maximum conversion of pentoses into furfural near 80% was predicted at high temperature and short time, conditions leading to 24% conversion of hexoses into HMF. Production of levulinic acid was favored at low temperatures. Maximum molar conversion of hexoses into levulinic acid (66.7% at 130°C) needed a long reaction time (235 h). A value of 53.0% can be achieved at 170°C after 5 h. Copyright © 2014 Elsevier Ltd. All rights reserved.

Frying stability of high oleic sunflower oils as affected by composition of tocopherol isomers and linoleic acid content.

PubMed

Aladedunye, Felix; Przybylski, Roman

2013-12-01

The influence of linoleic acid content and tocopherol isomeric composition on the frying performance of high oleic sunflower oil was evaluated during a 14-day restaurant style frying operation. At equal linoleic acid content, no significant difference was observed between high oleic sunflower oil containing only α-tocopherol and the sample containing a mixture of α-, γ-, and δ-isomers as measured by the amount of total polar components, oligomers, anisidine value, and free fatty acids. On the contrary, at similar tocopherol isomeric composition, high oleic sunflower oil containing lower amount of linoleic acid showed superior frying stability compared to the sample with a higher content of linoleic acid, suggesting that the frying performance of high oleic sunflower oil is dictated primarily by the level of linoleic acid, with the tocopherol isomeric composition of the oil having no significant influence. In all oil samples, the loss of γ-tocopherol was higher than the corresponding loss of α-tocopherol. Copyright © 2013 Elsevier Ltd. All rights reserved.

Stabilization of neurotoxic Alzheimer amyloid-β oligomers by protein engineering

PubMed Central

Sandberg, Anders; Luheshi, Leila M.; Söllvander, Sofia; Pereira de Barros, Teresa; Macao, Bertil; Knowles, Tuomas P. J.; Biverstål, Henrik; Lendel, Christofer; Ekholm-Petterson, Frida; Dubnovitsky, Anatoly; Lannfelt, Lars; Dobson, Christopher M.; Härd, Torleif

2010-01-01

Soluble oligomeric aggregates of the amyloid-β peptide (Aβ) have been implicated in the pathogenesis of Alzheimer’s disease (AD). Although the conformation adopted by Aβ within these aggregates is not known, a β-hairpin conformation is known to be accessible to monomeric Aβ. Here we show that this β-hairpin is a building block of toxic Aβ oligomers by engineering a double-cysteine mutant (called Aβcc) in which the β-hairpin is stabilized by an intramolecular disulfide bond. Aβ40cc and Aβ42cc both spontaneously form stable oligomeric species with distinct molecular weights and secondary-structure content, but both are unable to convert into amyloid fibrils. Biochemical and biophysical experiments and assays with conformation-specific antibodies used to detect Aβ aggregates in vivo indicate that the wild-type oligomer structure is preserved and stabilized in Aβcc oligomers. Stable oligomers are expected to become highly toxic and, accordingly, we find that β-sheet-containing Aβ42cc oligomers or protofibrillar species formed by these oligomers are 50 times more potent inducers of neuronal apoptosis than amyloid fibrils or samples of monomeric wild-type Aβ42, in which toxic aggregates are only transiently formed. The possibility of obtaining completely stable and physiologically relevant neurotoxic Aβ oligomer preparations will facilitate studies of their structure and role in the pathogenesis of AD. For example, here we show how kinetic partitioning into different aggregation pathways can explain why Aβ42 is more toxic than the shorter Aβ40, and why certain inherited mutations are linked to protofibril formation and early-onset AD. PMID:20713699

Esculin and its oligomer fractions inhibit adhesion and migration of U87 glioblastoma cells and in vitro angiogenesis.

PubMed

Mokdad-Bzeouich, Imen; Kovacic, Hervé; Ghedira, Kamel; Chebil, Latifa; Ghoul, Mohamed; Chekir-Ghedira, Leila; Luis, José

2016-03-01

Cancer metastasis is the major cause of cancer-related death. Chemoprevention is defined as the use of natural or synthetic substances to prevent cancer formation or cancer progress. In the present study, we investigate the antitumor activity of esculin and its oligomer fractions in U87 glioblastoma cells. We showed that esculin and its oligomers reduced U87 cell growth in a dose dependent manner. They also inhibited cell adhesion to collagen IV and vitronectin by interfering with the function of their respective receptors α2β1 and αvβ5 integrins. Furthermore, the tested samples were able to reduce migration of U87 cells towards another extracellular matrix fibronectin. Moreover, esculin and its oligomer fractions inhibited in vitro angiogenesis of endothelial cells (HMEC-1). In summary, our data provide the first evidence that esculin and its oligomer fractions are able to reduce adhesion, migration of glioblastoma cells and in vitro angiogenesis. Esculin and its oligomers may thus exert multi-target functions against cancer cells.

Mitochondrial Ca2+ overload underlies Abeta oligomers neurotoxicity providing an unexpected mechanism of neuroprotection by NSAIDs.

PubMed

Sanz-Blasco, Sara; Valero, Ruth A; Rodríguez-Crespo, Ignacio; Villalobos, Carlos; Núñez, Lucía

2008-07-23

Dysregulation of intracellular Ca(2+) homeostasis may underlie amyloid beta peptide (Abeta) toxicity in Alzheimer's Disease (AD) but the mechanism is unknown. In search for this mechanism we found that Abeta(1-42) oligomers, the assembly state correlating best with cognitive decline in AD, but not Abeta fibrils, induce a massive entry of Ca(2+) in neurons and promote mitochondrial Ca(2+) overload as shown by bioluminescence imaging of targeted aequorin in individual neurons. Abeta oligomers induce also mitochondrial permeability transition, cytochrome c release, apoptosis and cell death. Mitochondrial depolarization prevents mitochondrial Ca(2+) overload, cytochrome c release and cell death. In addition, we found that a series of non-steroidal anti-inflammatory drugs (NSAIDs) including salicylate, sulindac sulfide, indomethacin, ibuprofen and R-flurbiprofen depolarize mitochondria and inhibit mitochondrial Ca(2+) overload, cytochrome c release and cell death induced by Abeta oligomers. Our results indicate that i) mitochondrial Ca(2+) overload underlies the neurotoxicity induced by Abeta oligomers and ii) inhibition of mitochondrial Ca(2+) overload provides a novel mechanism of neuroprotection by NSAIDs against Abeta oligomers and AD.

Binding of ATP by pertussis toxin and isolated toxin subunits

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hausman, S.Z.; Manclark, C.R.; Burns, D.L.

1990-07-03

The binding of ATP to pertussis toxin and its components, the A subunit and B oligomer, was investigated. Whereas, radiolabeled ATP bound to the B oligomer and pertussis toxin, no binding to the A subunit was observed. The binding of ({sup 3}H)ATP to pertussis toxin and the B oligomer was inhibited by nucleotides. The relative effectiveness of the nucleotides was shown to be ATP > GTP > CTP > TTP for pertussis toxin and ATP > GTP > TTP > CTP for the B oligomer. Phosphate ions inhibited the binding of ({sup 3}H)ATP to pertussis toxin in a competitive manner;more » however, the presence of phosphate ions was essential for binding of ATP to the B oligomer. The toxin substrate, NAD, did not affect the binding of ({sup 3}H)ATP to pertussis toxin, although the glycoprotein fetuin significantly decreased binding. These results suggest that the binding site for ATP is located on the B oligomer and is distinct from the enzymatically active site but may be located near the eukaryotic receptor binding site.« less

[Differences in oligomerization of nucleocapsid protein of epidemic human influenza A(H1N1), A(H1N2) and B viruses].

PubMed

Prokudina, E N; Semenova, N P; Chumakov, V M; Burtseva, E I; Slepushkin, A N

2003-01-01

A comparative analysis of involving the nucleocapsid protein (NP) into shaping-up of SDS-resistant oligomers was carried out presently in circulating epidemic strains of human influenza, viruses A and B. The study results of viral isolates obtained from clinical samples and recent standard strains revealed that the involvement of NP in the SDS-resistant oligomers, which are different in various subtypes of influenza A viruses. According to this sign, the human viruses A(9H3N2) are close to the avian ones, in which, as proved by us previously, virtually the entire NP transforms itself into the oligomers resistant to SDS. About 10-20% of NP are involved in shaping-up the virus influenza A(H1N1) of SDS-resistant oligomers. No SDS-resistant NP-oligomers were detected in influenza of type B. It is suggested that the prevalence of human viruses A(H3N2) in NP-oligomers are the peculiarities of NP structure and of the presence of the PB1 protein from avian influenza virus.

Chloroplast biogenesis at cold-hardening temperatures. Kinetics of trans-Δ3-hexadecenoic acid accumulation and the assembly of LHCII.

PubMed

Krol, M; Huner, N P; Williams, J P; Maissan, E

1988-02-01

Etiolated seedlings developed at cold-hardening temperatures (5°C) exhibited etioplasts with considerable vesiculation of internal membranes compared to etioplasts developed at 20°C regardless of the osmotic concentration employed during sample preparation. This vesiculation disappeared during exposure to continuous light at 5°C. This transformation of 5°C and 20°C etioplasts to chloroplasts under continuous light at 5° and 20°C respectively proceeded normally with the initial development of non-appressed lamellae and the subsequent appearance of granal stacks. However, chloroplasts developed at 5°C exhibited fewer lamellae per granum than chloroplasts developed at 20°C.Although the polypeptide complements of etioplasts and chloroplasts developed at 5° or 20°C were not significantly different, monomeric light harvesting complex (LHCII3) was assembled into oligomeric light harvesting complex (LHCII1) during chloroplast biogenesis at 20°C (oligomer:monomer =1.8) whereas monomeric LHCII predominated at 5°C (oligomer:monomer =0.3). Low temperature fluorescence emission spectra of isolated thylakoids indicated that both the F685/F735 and F695/F735 were significantly higher after greening at 5°C than at 20°C. In addition, chloroplast biogenesis at 5°C was associated with a low ratio of trans-Δ3-hexadecenoic acid (0.5) in phosphatidylglycerol whereas at 20°C biogenesis was associated with a high ratio (1.6). Comparative kinetics indicated that the maximization of the trans-Δ3-hexadecenoic acid level precedes the assembly of monomeric LHCII into oligomeric LHCII during biogenesis at 20°C. It is suggested that low developmental temperatures modulate the assembly of LHCII by reducing the trans-Δ3-hexadecenoic acid content of phosphatidylglycerol such that monomeric or some intermediate form of LHCII predominates.

Protection against peroxynitrite by cocoa polyphenol oligomers.

PubMed

Arteel, G E; Sies, H

1999-11-26

Flavonoids, natural plant constituents, protect against peroxynitrite and can thereby play a role in defense against this mediator of inflammation. Procyanidin oligomers of different size (monomer through nonamer), isolated from the seeds of Theobroma cacao, were examined for their ability to protect against peroxynitrite-dependent oxidation of dihydrorhodamine 123 and nitration of tyrosine. By molarity, oligomers were more effective than the monomeric epicatechin; the tetramer was particularly efficient at protecting against oxidation and nitration reactions. These results suggest that epicatechin oligomers found in cocoa powder and chocolate may be a potent dietary source for defense against peroxynitrite.

Oligomerization of mononucleotides on montmorillonite: A potential approach to the prebiotic synthesis of RNA. [Abstract only

NASA Technical Reports Server (NTRS)

Ferris, James P.; Ertem, Goezen; Ding, Zi Ping; Prabahar, Joseph

1994-01-01

The condensation of the 5'-phosphorimidazolide of adenosine (ImpA) on montmorillonite in a pH 8 aqueous solution yields oligomers containing up to 10 monomer units. The regiospecificity of 3',5'-phosphodiester bond formation is enhanced by addition of 10% diadenosine pyrophosphate (AppA) to the reaction mixture. A series of activated derivatives of 5'-AMP was prepared to investigate the effect of the leaving group on oligomer formation. The benzimidazole and p-dimethylamino-pyridine derivatives gave the best yields of oligomers. Factors important for oligomer formation is discussed.

Direct mass spectrometry approaches to characterize polyphenol composition of complex samples.

PubMed

Fulcrand, Hélène; Mané, Carine; Preys, Sébastien; Mazerolles, Gérard; Bouchut, Claire; Mazauric, Jean-Paul; Souquet, Jean-Marc; Meudec, Emmanuelle; Li, Yan; Cole, Richard B; Cheynier, Véronique

2008-12-01

Lower molecular weight polyphenols including proanthocyanidin oligomers can be analyzed after HPLC separation on either reversed-phase or normal phase columns. However, these techniques are time consuming and can have poor resolution as polymer chain length and structural diversity increase. The detection of higher molecular weight compounds, as well as the determination of molecular weight distributions, remain major challenges in polyphenol analysis. Approaches based on direct mass spectrometry (MS) analysis that are proposed to help overcome these problems are reviewed. Thus, direct flow injection electrospray ionization mass spectrometry analysis can be used to establish polyphenol fingerprints of complex extracts such as in wine. This technique enabled discrimination of samples on the basis of their phenolic (i.e. anthocyanin, phenolic acid and flavan-3-ol) compositions, but larger oligomers and polymers were poorly detectable. Detection of higher molecular weight proanthocyanidins was also restricted with matrix-assisted laser desorption ionization (MALDI) MS, suggesting that they are difficult to desorb as gas-phase ions. The mass distribution of polymeric fractions could, however, be determined by analyzing the mass distributions of bovine serum albumin/proanthocyanidin complexes using MALDI-TOF-MS.

Condensation of activated diguanylates on a Poly/C/ template. [prebiotic polynucleotide replication mechanism

NASA Technical Reports Server (NTRS)

Lohrmann, R.; Bridson, P. K.; Orgel, L. E.

1981-01-01

The metal-ion catalysis of the oligomerization of activated diguanylate isomers on a polycytidylic acid template is studied in an investigation of possible early prebiotic polynucleotide replication mechanisms. The 5'-imidazolides of diguanylates linked 2' to 5' or 3' to 5' were reacted with polyC in a 1-methylimidazole or a 2,6-lutidine buffer in the presence of a Zn(+2) or a Pb(+2) catalyst, and reaction products were determined by paper chromatography, paper electrophoresis and liquid chromatography. In the lutidine buffer, the presence of both the Zn(+2) catalyst and the polyC template is found to result in the production of 3'-5' linked oligomers with up to 10 diguanylate units, and from diguanylates in the presence of the monomer. In the reactions conducted in the 1-methylimidazole buffer, the addition of Pb(+2) is found to lead to less marked increases in oligomerization in the presence of template, with approximately equal proportions of 2'-5' and 3'-5' oligomers formed from the 2'-5' substrate and mainly 3'-5' bonds from the 3'-5' linked dimer.

Precipitation pathways for ferrihydrite formation in acidic solutions

DOE PAGES

Zhu, Mengqiang; Khalid, Syed; Frandsen, Cathrine; ...

2015-10-03

In this study, iron oxides and oxyhydroxides form via Fe 3+ hydrolysis and polymerization in many aqueous environments, but the pathway from Fe 3+ monomers to oligomers and then to solid phase nuclei is unknown. In this work, using combined X-ray, UV–vis, and Mössbauer spectroscopic approaches, we were able to identify and quantify the long-time sought ferric speciation over time during ferric oxyhydroxide formation in partially-neutralized ferric nitrate solutions ([Fe 3+] = 0.2 M, 1.8 < pH < 3). Results demonstrate that Fe exists mainly as Fe(H 2O) 6 3+, μ-oxo aquo dimers and ferrihydrite, and that with time, themore » μ-oxo dimer decreases while the other two species increase in their concentrations. No larger Fe oligomers were detected. Given that the structure of the μ-oxo dimer is incompatible with those of all Fe oxides and oxyhydroxides, our results suggest that reconfiguration of the μ-oxo dimer structure occurs prior to further condensation leading up to the nucleation of ferrihydrite. The structural reconfiguration is likely the rate-limiting step involved in the nucleation process.« less

MAPLE prepared heterostructures with oligoazomethine: Fullerene derivative mixed layer for photovoltaic applications

NASA Astrophysics Data System (ADS)

Stanculescu, A.; Rasoga, O.; Socol, M.; Vacareanu, L.; Grigoras, M.; Socol, G.; Stanculescu, F.; Breazu, C.; Matei, E.; Preda, N.; Girtan, M.

2017-09-01

Mixed layers of azomethine oligomers containing 2,5-diamino-3,4-dicyanothiophene as central unit and triphenylamine (LV5) or carbazol (LV4) at both ends as donor and fullerene derivative, [6,6]-phenyl-C61 butyric acid butyl ester ([C60]PCB-C4) as acceptor, have been prepared by Matrix Assisted Pulsed Laser Evaporation (MAPLE) on glass/ITO and Si substrates. The effect of weight ratio between donor and acceptor (1:1; 1:2) and solvent type (chloroform, dimethylsulphoxide) on the optical (UV-vis transmission/absorption, photoluminescence) and morphological properties of LV4 (LV5): [C60]PCB-C4 mixed layers has been evidenced. Dark and under illumination I-V characteristics of the heterostructures realized with these mixed layers sandwiched between ITO and Al electrodes have revealed a solar cell behavior for the heterostructures prepared with both LV4 and LV5 using chloroform as matrix solvent. The solar cell structure realized with oligomer LV5, glass/ITO/LV5: [C60]PCB-C4 (1:1) has shown the best parameters.

Peptoids: a modular approach to drug discovery.

PubMed Central

Simon, R J; Kania, R S; Zuckermann, R N; Huebner, V D; Jewell, D A; Banville, S; Ng, S; Wang, L; Rosenberg, S; Marlowe, C K

1992-01-01

Peptoids, oligomers of N-substituted glycines, are described as a motif for the generation of chemically diverse libraries of novel molecules. Ramachandran-type plots were calculated and indicate a greater diversity of conformational states available for peptoids than for peptides. The monomers incorporate t-butyl-based side-chain and 9-fluorenylmethoxy-carbonyl alpha-amine protection. The controlled oligomerization of the peptoid monomers was performed manually and robotically with in situ activation by either benzotriazol-1-yloxytris(pyrrolidino)phosphonium hexafluorophosphate or bromotris(pyrrolidino)phosphonium hexaflurophosphate. Other steps were identical to peptide synthesis using alpha-(9-fluorenylmethoxycarbonyl)amino acids. A total of 15 monomers and 10 oligomers (peptoids) are described. Preliminary data are presented on the stability of a representative oligopeptoid to enzymatic hydrolysis. Peptoid versions of peptide ligands of three biological systems (bovine pancreatic alpha-amylase, hepatitis A virus 3C proteinase, and human immunodeficiency virus transactivator-responsive element RNA) were found with affinities comparable to those of the corresponding peptides. The potential use of libraries of these compounds in receptor- or enzyme-based assays is discussed. PMID:1409642

quenched-smFISH: Counting small RNA in Pathogenic Bacteria

NASA Astrophysics Data System (ADS)

Shepherd, Douglas; Li, Nan; Micheva-Viteva, Sofiya; Munsky, Brian; Hong-Geller, Elizabeth; Werner, James

2014-03-01

Here, we present a modification to single-molecule fluorescence in situ hybridization, quenched smFISH (q-smFISH), that enables quantitative detection and analysis of small RNA (sRNA) expressed in bacteria. We show that short nucleic acid targets can be detected when the background of unbound singly dye-labeled DNA oligomers is reduced through hybridization with a set of complementary DNA oligomers labeled with a fluorescence quencher. Exploiting an automated, multi-color wide-field microscope and GPU-accelerated data analysis package, we analyzed the statistics of sRNA expression in thousands of individual Yersinia pseudotuberculosis and Yersinia pestis bacteria before and during a simulated infection. Before infection, we find only a small fraction of either bacteria express the small RNAs YSR35 or YSP8. The copy numbers of these RNA are increased during simulated infection, suggesting a role in pathogenesis. The ability to directly quantify expression level changes of sRNA in single cells as a function of external stimuli provides key information on the role of sRNA in bacterial regulatory networks.