Hexagonal crystal structure of the A-DNA octamer d(GTGTACAC) and its comparison with the tetragonal structure: correlated variations in helical parameters

The alternating DNA octamer d(GTGTACAC) has been grown in a novel hexagonal crystal form. The structure has been determined and refined to a 2-A resolution, with 51 water molecules. The A-DNA conformation is a variant of that observed for the tetragonal form of the same sequence (Jain et al., 1989) containing a bound spermine. The crystals belong to the space group P6(1)22, a = b = 32.40 A and c = 79.25 A, with one strand in the asymmetric unit. The new hexagonal structure was solved by rotation and translation searches in direct space and refined to a final R value of 12.7% by using 1561 unique reflections greater than 1.5 sigma (I). The electron density clearly shows that the penultimate A7 sugar had flipped into the alternative C2'-endo pucker. This dent in the molecule can be attributed to close intermolecular contacts. In contrast, in the tetragonal structure, the DNA is distorted in the central TA step, where the A5 backbone bonds C4'-C5' and O5'-P assume trans conformations. The hexagonal double helix more closely resembles the fiber diffraction A-DNA, compared to the tetragonal form. For instance, the tilt angle is higher (16 degrees vs 10 degrees), which is correlated with a larger displacement from the helix axis (3.5 vs 3.3), a lower rise per residue (2.9 vs 3.2), and a smaller major-groove width (6.1 vs 8.7), thus indicating that the variations in these global helical parameters are correlated. The propeller twist angles in both forms are higher for the G-C base pairs (15.3 degrees, 12.14 degrees) than for the A-T base pairs (10.8 degrees, 9.1 degrees), which is the reverse of the expected order. Unlike the tetragonal structure, the hexagonal crystal structure interestingly does not contain a bound spermine molecule. Our analysis reveals that the conformational differences between the tetragonal and hexagonal forms are not entirely due to the spermine binding, and crystal packing seems to play an important role.     

Ecoengineering high rate anaerobic digestion systems: analysis of improved syntrophic biomethanation catalysts

High performance biomethanation granules with operational specific COD removal rates of 7 kg COD removed/kg SS/d were obtained by ecoengineering conventional, granular, UASB digester sludge using a designed protocol of starvation and selection on a defined volatile fatty acid (VFA) based mineral medium. Addition of low (0.15 mM) sulfate levels to this VFA medium increased the maximum shock-load COD removal rate of the ecoengineered biomethanation granules to 9 kg COD/kg SS/d with specific acetate, propionate, and butyrate removal rates of 111, 28, and 64 mol/g SS/d. Addition of moderate (26 mM) calcium levels inhibited growth and altered the structure of granules. The general cellular, growth, stability, and performance features of these ecoengineered granules are described and discussed in relation to their use as improved biomethanation starter cultures.     

Use of benzyl 2-acetamido-2-deoxy-3-O-(2-O-methyl-beta-D-galactosyl)-beta- D-glucopyranoside [2'-O-methyllacto-N-biose I beta Bn] as a specific acceptor for GDP-fucose: N-acetylglucosaminide alpha(1----4)-L-fucosyltransferase

A synthetic substrate, benzyl 2-acetamido-2-deoxy-3-O-(2-O-methyl-beta-D- galactopyranosyl)-beta-D-glucopyranoside, was demonstrated to be a specific acceptor for the Lewis blood group-specified alpha(1----4)-L-fucosyltransferase from human saliva and stomach mucosa. The fucosyl linkage of the product resulting from the use of this substrate isolated by paper chromatography was characterized by hydrolysis with specific alpha(1----3)/(1----4)-L- fucosidase. The product can be separated by adsorption onto the reverse-phase cartridge and recovered by one-step elution with methanol. The enzymatic properties of alpha(1----4)-L-fucosyltransferase from saliva and stomach mucosa have also been examined using this substrate.     

Amylases during different stages of seed development in wheat

The β-Amylase activity was high in seeds of pre-Milk and milk stages but low in seeds of half seed and dough stages and very low at fully ripe stage of seed development. Zymogen (latent β-Amylase) was absent in half seed stage but appeared at pre-Milk stage. The content of zymogen increased progressively with advance in ripening time. No α-Amylase activity was detected at any stages of seed development in wheat.     

Population biology of Avena XI. Variation in peripheral isolates of A. barbata

Data on genetic polymorphism, scored at two morphological loci, showed peripheral, isolated roadside colonies of slender oat (Avena barbata) to be significantly less polymorphic than the large central populations in continuous stands. The role of random drift (founder effect) was evident in the genetic structure of such roadside colonies which were, however, not monomorphic. Multilocus associations also suggested large Hill-Robertson effect in generating gametic disequilibria. Such isolates with varying amounts of elapsed time since the founder events could offer useful material for a study of evolutionary processes including the selection-drift balance.     

Action of phospholipase A2 on unmodified phosphatidylcholine bilayers: Organizational defects are preferred sites of action

Summary The hydrolytic action of the bee venom phospholipase A₂ on phosphatidylcholine bilayers is studied under a variety of conditions that introduce alterations in the packing, such as those induced by sonication, gel to liquid crystalline phase transition, and osmotic shock. Two phases of hydrolysis could be resolved under a wide range of experimental conditions. With the various forms of the bilayers one observes only a partial hydrolysis of the total available substrate during the first phase. However, the fraction of the substrate hydrolyzed in the first phase changes with the form of the available substrate, with the amount of the enzyme added, with the temperature, with the phase transition characteristics of the substrate, and by the sonication of the substrate. The second phase of hydrolysis is generally observed when a certain concentration of the products has been produced during the first phase of hydrolysis. These observations are interpreted to suggest that the bee venom phospholipase A₂ preferentially catalyzes hydrolysis of the substrate available at or near the defects in the organization of the substrate in the bilayers.     

Removal of diacetyl from beer by adsorbants and diacetyl reductase

Removal of diacetyl from beer with adsorbants like cellulose, silica gel, activated charcoal, calcium phosphate gel, anion- and cation-exchange resins, and silicylic acid black soil bed (SABSB) was attempted in comparison with the enzyme diacetyl reductase (EC 1.1.1.5). Diacetyl could be removed from beer by the adsorbants but they had undesirable effect on the beer quality such as color, pH, and alcohol levels. These adverse effects were not observed with the use of diacetyl reductase. The results favor the enzymatic removal of diacetyl from beer as a superior approach.