Building on piles in floodplains

Last year in the Netherlands 15 locations were allocated along the Rhine branches where – under strong restrictions - it was allowed to build in floodplains. Building in floodplains may lead to a water level rise during floods and moreover, the river bed morphology may be disturbed (erosion/sedimentation). A potential building location on a floodplain of the river IJssel near Deventer (Wilpsche Klei) is used as a fictitious case to investigate these processes

Encapsulation of DNA by cationic diblock copolymer vesicles

Encapsulation of dsDNA fragments (contour length 54 nm) by the cationic diblock copolymer poly(butadiene-b-N-methyl 4-vinyl pyridinium) [PBd-b-P4VPQ] has been studied with phase contrast, polarized light, and fluorescence microscopy, as well as scanning electron microscopy. Encapsulation was achieved with a single emulsion technique. For this purpose, an aqueous DNA solution is emulsified in an organic solvent (toluene) and stabilized by the amphiphilic diblock copolymer. The PBd block forms an interfacial brush, whereas the cationic P4VPQ block complexes with DNA. A subsequent change of the quality of the organic solvent results in a collapse of the PBd brush and the formation of a capsule. Inside the capsules, the DNA is compacted as shown by the appearance of birefringent textures under crossed polarizers and the increase in fluorescence intensity of labeled DNA. The capsules can also be dispersed in aqueous medium to form vesicles, provided they are stabilized with an osmotic agent (polyethylene glycol) in the external phase. It is shown that the DNA is released from the vesicles once the osmotic pressure drops below 105 N/m2 or if the ionic strength of the supporting medium exceeds 0.1 M. The method has also proven to be efficient to encapsulate pUC18 plasmid in sub-micron sized vesicles and the general applicability of the method has been demonstrated by the preparation of the charge inverse system: cationic poly(ethylene imine) encapsulated by the anionic diblock poly(styrene-b-acrylic acid).Comment: 35 pages, 11 figures, accepted for publication in Langmui

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.Comment: 38 pages, 10 figures, accepted for publication in The Journal of Chemical Physic

Synthesis of highly branched alpha-glucans with different structures using GH13 and GH57 glycogen branching enzymes

Glycogen branching enzymes (GBEs) convert starch into branched alpha-glucan polymers. To explore if the amylose content of substrates effects the structure of the branched alpha-glucans, mixtures of amylose and amylopectin were converted by four thermophilic GBEs. The degree of branching and molecular weight of the products increased with an increasing percentage of amylose with the GH57 GBEs of Thermus thermophilus and Thermococcus kodakarensis, and the GH13 GBEs of Rhodothermus marinas and Petrotoga mobilis. The only exception is that the degree of branching of the Petrotoga mobilis GBE products is not influenced by the amylose content. A second difference is the relatively high hydrolytic activity of two GH57 GBEs, while the two GH13 GBEs have almost no hydrolytic activity. Moreover, the two GH13 GBEs synthesize branched alpha-glucans with a narrow molecular weight distribution, while the two GH57 GBEs products consist of two or three molecular weight fractions

Effect of light and preservatives on the stability of the phycocyanin from the extremophilic red microalgae Cyanidioschyzon merolae

Synthetic dyes are replaced more and more in food products by natural pigments. A growing number of consumers are concerned with the potential health risk and behavior problems related to synthetic dyes. The phycocyanin of the cyanobacterium Arthospira platensis is the only natural blue pigment commercially available. The thermoacidophilic red microalgae Cuanidioschyzon merolae could provide an alternative phycocyanin source. As C. merolae grows at relatively high temperatures (45 to 56°C), the phycocyanin has a high thermostability even at relatively low pH. The stability of the C. merolae phycocyanin was determined for several products of relevant parameters. Average daylight (300-500 Lux) did not significantly affect the stability, while intense light (20,000 Lux) reduced the half-life to 35 hours. The preservatives such as glucose, sucrose, fructose, and sorbitol improved the stability of C. merolae phycocyanin considerably, with 20% glucose resulting in no loss of color at all. The results show that C. merolae phycocyanin can be used in various food products as a natural blue colorant

The influence of amylose content on the modification of starches by glycogen branching enzymes

Glycogen branching enzymes (GBEs) have been used to generate new branches in starches for producing slowly digestible starches. The aim of this study was to expand the knowledge about the mode of action of these enzymes by identifying structural aspects of starchy substrates affecting the products generated by different GBEs. The structures obtained from incubating five GBEs (three from glycoside hydrolase family (GH) 13 and two from GH57) on five different substrates exhibited minor but statistically significant correlations between the amount of longer chains (degree of polymerization (DP) 9-24) of the product and both the amylose content and the degree of branching of the substrate (Pearson correlation coefficient of ≤-0.773 and ≥0.786, respectively). GH57 GBEs mainly generated large products with long branches (100-700 kDa and DP 11-16) whereas GH13 GBEs produced smaller products with shorter branches (6-150 kDa and DP 3-10)

Biomass and phycocyanin content of heterotrophic Galdieria sulphuraria 074G under maltodextrin and granular starches-feeding conditions

A major disadvantage of microalgal cultivation is limited biomass yields due to the autotrophic lifestyle of most microalgal species. Heterotrophic growth on a suitable carbon source and oxygen can overcome such limitations. The red microalga Galdieria sulphuraria strain 074G grows heterotrophically on glucose and a number of other carbon sources while constitutively producing photopigments, including the blue-colored phycocyanin, a natural food colorant. Galdieria sulphuraria strain 074G grew well on maltodextrins as well as on granular starch in combination with the enzyme cocktail Stargen002. The maltodextrin cultures produced 2 mg phycocyanin per gram substrate, being slightly more than on glucose. The phycocyanin extracted from maltodextrin-grown cultures was thermostable up to 55 °C. Maltodextrins can be a cheap alternative to glucose syrups for the production of phycocyanin as natural food colorant

Rational transformation of Lactobacillus reuteri 121 reuteransucrase into a dextransucrase

Glucansucrase or glucosyltransferase (GTF) enzymes of lactic acid bacteria display high sequence similarity but catalyze synthesis of different α-glucans (e.g., dextran, mutan, alternan, and reuteran) from sucrose. The variations in glucosidic linkage specificity observed in products of different glucansucrase enzymes appear to be based on relatively small differences in amino acid sequences in their sugar-binding acceptor subsites. This notion was derived from mutagenesis of amino acids of GTFA (reuteransucrase) from Lactobacillus reuteri strain 121 putatively involved in acceptor substrate binding. A triple amino acid mutation (N1134S:N1135E:S1136V) in a region immediately next to the catalytic Asp1133 (putative transition state stabilizing residue) converted GTFA from a mainly α-(1→4) (∼45%, reuteran) to a mainly α-(1→6) (∼80%, dextran) synthesizing enzyme. The subsequent introduction of mutation P1026V:I1029V, involving two residues located in a region next to the catalytic Asp1024 (nucleophile), resulted in synthesis of an α-glucan containing only a very small percentage of α-(1→4) glucosidic linkages (∼5%) and a further increased percentage of α-(1→6) glucosidic linkages (∼85%). This changed glucosidic linkage specificity was also observed in the oligosaccharide products synthesized by the different mutant GTFA enzymes from (iso)maltose and sucrose. Amino acids crucial for glucosidic linkage type specificity of reuteransucrase have been identified in this report. The data show that a combination of mutations in different regions of GTF enzymes influences the nature of both the glucan and oligosaccharide products. The amino acids involved most likely contribute to sugar-binding acceptor subsites in glucansucrase enzymes. © 2005 American Chemical Society. Chemicals / CAS: 1,4 alpha glucan branching enzyme, 9001-97-2; dextransucrase, 9032-14-8; glucosyltransferase, 9031-48-5; maltose, 16984-36-4, 69-79-4; sucrose, 122880-25-5, 57-50-1; Bacterial Proteins; dextransucrase, EC 2.4.1.5; Glucans; Glucose, 50-99-7; Glucosyltransferases, EC 2.4.1.-; Isomaltose, 499-40-1; Maltose, 69-79-4; Sucrase, EC 3.2.1.48; Sucrose, 57-50-

Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles

The filamentous ascomycete Aspergillus niger is well known for its ability to produce a large variety of enzymes for the degradation of plant polysaccharide material. A major carbon and energy source for this soil fungus is starch, which can be degraded by the concerted action of α-amylase, glucoamylase and α-glucosidase enzymes, members of the glycoside hydrolase (GH) families 13, 15 and 31, respectively. In this study we have combined analysis of the genome sequence of A. niger CBS 513.88 with microarray experiments to identify novel enzymes from these families and to predict their physiological functions. We have identified 17 previously unknown family GH13, 15 and 31 enzymes in the A. niger genome, all of which have orthologues in other aspergilli. Only two of the newly identified enzymes, a putative α-glucosidase (AgdB) and an α-amylase (AmyC), were predicted to play a role in starch degradation. The expression of the majority of the genes identified was not induced by maltose as carbon source, and not dependent on the presence of AmyR, the transcriptional regulator for starch degrading enzymes. The possible physiological functions of the other predicted family GH13, GH15 and GH31 enzymes, including intracellular enzymes and cell wall associated proteins, in alternative α-glucan modifying processes are discussed