The novel method for isolating chitinolytic bacteria and its application in screening for hyperchitinase producing mutant of Alcaligenes xylosoxydans

AIMS: To develop a novel, rapid and effective screening method for chitinase producing bacteria. METHODS AND RESULTS: A simple and rapid technique for screening of potential chitinolytic bacteria has been developed using the chitin binding dye calcofluor white M2R in chitin agar. Microorganisms possessing high chitinolytic potential gave a clear zone under ultraviolet light after 24-48 h of incubation. This method was successfully applied for isolating the hyperchitinase mutant of Alcaligenes xylosoxydans. The mutant Alc. xylosoxydans EMS 33 was found to produce 3.4 times more chitinase than the wild type. CONCLUSIONS: In this study, the screening method for chitinase producing bacteria has been developed and it was applied to screen chitinase-overproducing mutant of Alc. xylosoxydans. SIGNIFICANCE AND IMPACT OF THE STUDY: The novel screening method for chitinase producer is more sensitive, rapid, user-friendly and reliable, which can also be used for screening of recombinants having chitinase gene.     

Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions

Molecular dynamics (MD) simulations of the activation domain of porcine procarboxypeptidase B (ADBp) were performed to examine the effect of using the particle-particle particle-mesh (P3M) or the reaction field (RF) method for calculating electrostatic interactions in simulations of highly charged proteins. Several structural, thermodynamic, and dynamic observables were derived from the MD trajectories, including estimated entropies and solvation free energies and essential dynamics (ED). The P3M method leads to slightly higher atomic positional fluctuations and deviations from the crystallographic structure, along with somewhat lower values of the total energy and solvation free energy. However, the ED analysis of the system leads to nearly identical results for both simulations. Because of the strong similarity between the results, both methods appear well suited for the simulation of highly charged globular proteins in explicit solvent. However, the lower computational demand of the RF method in the present implementation represents a clear advantage over the P3M method.     

Crystal structures of a pantothenate synthetase from M. tuberculosis and its complexes with substrates and a reaction intermediate

Pantothenate biosynthesis is essential for the virulence of Mycobacterium tuberculosis, and this pathway thus presents potential drug targets against tuberculosis. We determined the crystal structure of pantothenate synthetase (PS) from M. tuberculosis, and its complexes with AMPCPP, pantoate, and a reaction intermediate, pantoyl adenylate, with resolutions from 1.6 to 2 A. PS catalyzes the ATP-dependent condensation of pantoate and beta-alanine to form pantothenate. Its structure reveals a dimer, and each subunit has two domains with tight association between domains. The active-site cavity is on the N-terminal domain, partially covered by the C-terminal domain. One wall of the active site cavity is flexible, which allows the bulky AMPCPP to diffuse into the active site to nearly full occupancy when crystals are soaked in solutions containing AMPCPP. Crystal structures of the complexes with AMPCPP and pantoate indicate that the enzyme binds ATP and pantoate tightly in the active site, and brings the carboxyl oxygen of pantoate near the alpha-phosphorus atom of ATP for an in-line nucleophilic attack. When crystals were soaked with, or grown in the presence of, both ATP and pantoate, a reaction intermediate, pantoyl adenylate, is found in the active site. The flexible wall of the active site cavity becomes ordered when the intermediate is in the active site, thus protecting it from being hydrolyzed. Binding of beta-alanine can occur only after pantoyl adenylate is formed inside the active site cavity. The tight binding of the intermediate pantoyl adenylate suggests that nonreactive analogs of pantoyl adenylate may be inhibitors of the PS enzyme with high affinity and specificity.     

Clonal diversity and genetic differentiation in Ilex leucoclada M. patches in an old-growth beech forest

We investigated clonal diversity within patches of Ilex leucoclada and genetic variation within and among patches using random amplified polymorphic DNA (RAPD) markers in a 1-ha plot within an old-growth beech forest. We found 38 patches that exhibited a clumped distribution in the middle of the plot. We identified a total of 166 RAPD phenotypes among the 215 stems sampled from 27 patches that were completely within the plot. The population showed high clonal diversity within patches (mean number of genets relative to number of stems = 0.79; mean Simpson's D = 0.89). Variation in RAPD phenotypes among patches was highly significant (PhiST in the molecular variance analysis = 0.316, P < 0.001), indicating genetic differentiation among patches. Pairwise genetic distances, PhiST, among patches did not correlate with geographical distances among patches. The cluster analysis based on the genetic distances showed few clear clusters of patches, indicating no spatial genetic structure among patches. High levels of clonal diversity both within patches and within the population may be explained by multiple founders, seedling recruitment during patch-formation, and somatic mutation. The significant genetic differentiation among patches may be caused by separate founding events and/or kin structuring within patches.     

Production of polysaccharides by Silene vulgaris callus culture depending on carbohydrates of the medium

Sources of carbohydrate nutrition such as sucrose, glucose, and galactose, with the exception of arabinose, were shown to influence positively callus growth and polysaccharide (pectin silenan and acidic arabinogalactan) biosynthesis. Galactose was found to cause a stimulatory effect on yield and productivity of arabinogalactan. Low concentrations of sucrose failed to support the cell growth and polysaccharide biosynthesis. Increasing sucrose concentrations led to biomass accumulation but failed to enhance efficiency of the substrate utilization. The optimal medium for the campion cell culture growth was found to be one containing 30 g/liter of sucrose or a mixture of sucrose with glucose (in 15 g/liter). Increasing sucrose concentrations in the medium from 30 to 100 g/liter failed to significantly influence the polysaccharide yields while the polysaccharide productivity per liter of the medium grew due to promotion of culture productivity in biomass. Variations of the carbon sources in the nutrient media were shown to influence insignificantly the biochemical characteristics of arabinogalactan and silenan while an increase in the sucrose concentration to 50-100 g/liter led to a diminution of the galacturonic acid content in silenan and to changes in contents of the neutral monosaccharide residues in silenan and arabinogalactan.     

Patterns of morphogenesis from cotyledon explants of pigeonpea

Summary Cotyledons excised from seedlings of Cajanus cajan (pigeonpea) were grown on media containing cytokinins (6-benzyladenine, zeatin, and zeatin riboside) and an allied compound, thidiazuron. With the exception of zeatin riboside, initial response in terms of induction of organized structures was very high. However, subsequent regeneration of shoots from cotyledon explants was very poor. Anatomical studies on the regenerating explants were undertaken to study the pattern of morphogenesis. Cytokinins and thidiazuron induced divisions in the epidermal and sub-epidermal cell layers leading to the formation of primary protrusions on the surface. This was followed by the development of foci of high meristematic activity either on the surface or within the primary protrusions. These foci differentiated into embryo-like structures or shoot meristem-like structures. Mostly aberrant shoots, with poorly developed apical meristems, regenerated from these structures.     

Transgenic pig expressing the enhanced green fluorescent protein produced by nuclear transfer using colchicine-treated fibroblasts as donor cells

Fetal-derived fibroblast cells were transduced with replication defective vectors containing the enhanced green fluorescent protein (EGFP). The transgenic cells were treated with colchicine, which theoretically would synchronize the cells into G2/M stage, and then used as donor nuclei for nuclear transfer. The donor cells were transferred into the perivitalline space of enucleated in vitro matured porcine oocytes, and fused and activated with electrical pulses. A total of 8.3% and 28.6% of reconstructed oocytes showed nuclear envelope breakdown and premature chromosome condensation 0.5 and 2 hr after activation, respectively. Percentage of pronuclear formation was 62.5, 12 hr after activation. Most (91.4%) of the 1-cell embryos with pronuclei did not extrude a polar body. Most (77.2%) embryos on day 5 were diploid. Within 2 hr after fusion, strong fluorescence was detectable in most reconstructed oocytes (92.3%). The fluorescence in all NT embryos became weak 15 hr after fusion and disappeared when culture to 48 hr. But from day 3, cleaved embryos at the 2- to 4-cell stage started to express EGFP again. On day 7, 85.8% of cleaved embryos expressed EGFP. A total of 9.4% of reconstructed embryos developed to blastocyst stage and 71.5% of the blastoctysts expressed EGFP. After 200 reconstructed 1-cell stage embryos were transferred into four surrogate gilts, three recipients were found to be pregnant. One of them maintained to term and delivered a healthy transgenic piglet expressing EGFP. Our data suggest that the combination of transduction of somatic cells by a replication defective vector with the nuclear transfer of colchicine-treated donors is an alternative to produce transgenic pigs. Furthermore, the tissues expressing EGFP from descendents of this pig may be very useful in future studies using pigs that require genetically marked cells.     

Research on photosynthetic reaction centers from 1932 to 1987

The history of research on photosynthetic reaction centers is outlined, starting with the implication of their existence through the discovery of the photosynthetic unit, as reported by R. Emerson and W. Arnold in 1932, and culminating in the crystallization and X-ray analysis of the anoxygenic bacterial reaction centers, reported by J. Deisenhofer, H. Michel, and coworkers, over the period 1982–1987. Reaction centers of purple photosynthetic bacteria have received the most attention because they have been well purified and characterized. Structures of cyanobacterial reaction centers of Photosystems I and II are now available from the laboratories of H. Witt and W. Saenger. This revised version was published online in June 2006 with corrections to the Cover Date.     

Organogenesis in the vine cactus Selenicereus megalanthus using thidiazuron

Segments of distal and proximal parts of the cotyledons, hypocotyls and epicotyls of yellow pitaya [Selenicereus megalanthus (Cactaceae)], were cultured on Murashige and Skoog (MS) medium supplemented with thidiazuron (TDZ). The proximal part of the cotyledons was found to be the most responsive tissue, maximal bud regeneration being achieved in the presence of 200 M thidiazuron. However, TDZ does not change the pattern of regeneration competence, which remains restricted to the proximal part of the cotyledons. The best medium for shoot elongation was found to be MS lacking plant growth regulators. Rooting was induced on MS medium supplemented with 5.3 M naphthaleneacetic acid. Rooted plantlets were transferred to a soil medium and acclimatized successfully in a greenhouse.