Isolation and chemical characterization of lipopolysaccharides from four Mycoplana species (M. bullata,M. segnis,M. ramosa and M. dimorpha)

Lipopolysaccharides (LPS), isolated from four Mycoplana species, i.e. the type strains of M. bullata, M. segnis, M. ramosa and M. dimorpha, were characterized onto their chemical composition and their respective lipid A-types. Those of M. bullata and M. segnis showed on DOC-PAGE an R-type character and had lipid A's of the Lipid A_DAG-type which exclusively contained 2,3-diamino-2,3-dideoxy-d-glucose as lipid A sugar. LPS's of M. ramosa and M. dimorpha showed, although only weakly expressed, ladder-like patterns on DOC-PAGE indicating some S-type LPS's and lipid A of the d-glucosamine type (Lipid A_GlcN). M. bullata LPS contained mannose and glucose in major amounts and additionally l-glycero-d-mannoheptose, whereas M. segnis LPS was composed of rhamnose, mannose and glucose together with both, d-glycero-d-manno- and l-glycero-d-manno-heptoses in a molar ratio of 1:2. All LPS's contained 2-keto-3-deoxy-octonic acid (Kdo), phosphate and an unidentified acidic component X. In addition to X, M. segnis LPS contained glucuronic and galacturonic acids, whereas M. ramosa LPS contained only galacturonic acid. Acetic acid hydrolysis of the LPS resulted in splitting off lipid A moieties, very rich in 3-hydroxy fatty acids, in particular in 3-OH-12:0 (in Lipid A_DAG), or in 3-OH-14:0 (in Lipid A_GlcN). Analysis of the 3-acyloxyacyl residues revealed major amounts of amide-linked 3-OH(3-OH-13:0)12:0 in lipid A of M. bullata and 3-OH(12:0)12:0 in lipid A of M. segnis. The rare 4-oxo-myristic acid (4-oxo-14:0) was observed only in M. bullata LPS, where it is ester-linked. Amide linked diesters could not be traced in M. ramosa and M. dimorpha. All four lipid A's lacked erster-bound acyloxyacyl residues.Non-standard abbreviations DAG 2,3-diamino-2,3-dideoxy-d-glucose - Kdo 2-keto-3-deoxy-octonate - LPS lipopolysaccharide - PITC phenyl isothiocyanate - NANA N-acetyl neuraminic acid     

Enhancing the structural diversity between forest patches—A concept and real-world experiment to study biodiversity,multifunctionality and forest resilience across spatial scales

Intensification of land use by humans has led to a homogenization of landscapes and decreasing resilience of ecosystems globally due to a loss of biodiversity, including the majority of forests. Biodiversity–ecosystem functioning (BEF) research has provided compelling evidence for a positive effect of biodiversity on ecosystem functions and services at the local (α-diversity) scale, but we largely lack empirical evidence on how the loss of between-patch β-diversity affects biodiversity and multifunctionality at the landscape scale (γ-diversity). Here, we present a novel concept and experimental framework for elucidating BEF patterns at α-, β-, and γ-scales in real landscapes at a forest management-relevant scale. We examine this framework using 22 temperate broadleaf production forests, dominated by Fagus sylvatica. In 11 of these forests, we manipulated the structure between forest patches by increasing variation in canopy cover and deadwood. We hypothesized that an increase in landscape heterogeneity would enhance the β-diversity of different trophic levels, as well as the β-functionality of various ecosystem functions. We will develop a new statistical framework for BEF studies extending across scales and incorporating biodiversity measures from taxonomic to functional to phylogenetic diversity using Hill numbers. We will further expand the Hill number concept to multifunctionality allowing the decomposition of γ-multifunctionality into α- and β-components. Combining this analytic framework with our experimental data will allow us to test how an increase in between patch heterogeneity affects biodiversity and multifunctionality across spatial scales and trophic levels to help inform and improve forest resilience under climate change. Such an integrative concept for biodiversity and functionality, including spatial scales and multiple aspects of diversity and multifunctionality as well as physical and environmental structure in forests, will go far beyond the current widely applied approach in forestry to increase resilience of future forests through the manipulation of tree species composition.     

On peptide bond formation, translocation, nascent protein progression and the regulatory properties of ribosomes. Derived on 20 October 2002 at the 28th FEBS Meeting in Istanbul.

High-resolution crystal structures of large ribosomal subunits from Deinococcus radiodurans complexed with tRNA-mimics indicate that precise substrate positioning, mandatory for efficient protein biosynthesis with no further conformational rearrangements, is governed by remote interactions of the tRNA helical features. Based on the peptidyl transferase center (PTC) architecture, on the placement of tRNA mimics, and on the existence of a two-fold related region consisting of about 180 nucleotides of the 23S RNA, we proposed a unified mechanism integrating peptide bond formation, A-to-P site translocation, and the entrance of the nascent protein into its exit tunnel. This mechanism implies sovereign, albeit correlated, motions of the tRNA termini and includes a spiral rotation of the A-site tRNA-3' end around a local two-fold rotation axis, identified within the PTC. PTC features, ensuring the precise orientation required for the A-site nucleophilic attack on the P-site carbonyl-carbon, guide these motions. Solvent mediated hydrogen transfer appears to facilitate peptide bond formation in conjunction with the spiral rotation. The detection of similar two-fold symmetry-related regions in all known structures of the large ribosomal subunit, indicate the universality of this mechanism, and emphasizes the significance of the ribosomal template for the precise alignment of the substrates as well as for accurate and efficient translocation. The symmetry-related region may also be involved in regulatory tasks, such as signal transmission between the ribosomal features facilitating the entrance and the release of the tRNA molecules. The protein exit tunnel is an additional feature that has a role in cellular regulation. We showed by crystallographic methods that this tunnel is capable of undergoing conformational oscillations and correlated the tunnel mobility with sequence discrimination, gating and intracellular regulation.     

Mesoderm-specific B104 expression in the Drosophila embryo is mediated by internal cis-acting elements of the transposon

The Drosophila melanogaster genome contains about 100 copies of the B104 transposable element, which is strongly expressed during embryogenesis. Here we show that B104 expression is restricted to the esophageal and amnioproctodeal regions of the embryo and to the developing mesoderm. Mesoderm-specific B104 expression requires the activity of the mesoderm-determining factors twist and snail. Virtually the same expression patterns were observed in Drosophila yakuba, a species that a separated from D. melanogaster by some 15 million years of evolution. We show that B104 expression is directed by internal sequences of the retrotransposon that are capable of acting as a cis-acting regulatory element in front of a heterologous Drosophila promoter. Our findings suggest that retrotransposon insertions can affect the expression patterns of endogenous genes by adding and distributing specific cis-acting control elements throughout the host genome. We therefore propose that transposable elements in addition to reducing the fitness of their hosts may also provide a rich pool of cis-acting sequences that contribute to the long-term evolutionary potential of the population in a beneficial manner.     

d-Ribulose 1,5-bisphosphate carboxylase and polyhedral inclusion bodies in Nitrosomonas spec

Polydedral inclusion bodies were isolated from exponentially grown cells of Nitrosomonas spec. The bodies contained d-ribulose, 1,5-bisphosphate carboxylase. The specific activity of the enzyme was 0.0122 mol CO₂ fixed per min per mg of protein.     

Cloning and characterization of the CYS3 (CYI1) gene of Saccharomyces cerevisiae.

A DNA fragment containing the Saccharomyces cerevisiae CYS3 (CYI1) gene was cloned. The clone had a single open reading frame of 1,182 bp (394 amino acid residues). By comparison of the deduced amino acid sequence with the N-terminal amino acid sequence of cystathionine gamma-lyase, CYS3 (CYI1) was concluded to be the structural gene for this enzyme. In addition, the deduced sequence showed homology with the following enzymes: rat cystathionine gamma-lyase (41%), Escherichia coli cystathionine gamma-synthase (36%), and cystathionine beta-lyase (25%). The N-terminal half of it was homologous (39%) with the N-terminal half of S. cerevisiae O-acetylserine and O-acetylhomoserine sulfhydrylase. The cloned CYS3 (CYI1) gene marginally complemented the E. coli metB mutation (cystathionine gamma-synthase deficiency) and conferred cystathionine gamma-synthase activity as well as cystathionine gamma-lyase activity to E. coli; cystathionine gamma-synthase activity was detected when O-succinylhomoserine but not O-acetylhomoserine was used as substrate. We therefore conclude that S. cerevisiae cystathionine gamma-lyase and E. coli cystathionine gamma-synthase are homologous in both structure and in vitro function and propose that their different in vivo functions are due to the unavailability of O-succinylhomoserine in S. cerevisiae and the scarceness of cystathionine in E. coli.     

Gelation of xanthan with trivalent metal ions

In-situ gelation of semidilute xanthan solutions with trivalent chromium, aluminum or iron ions was studied by rheology and UV-spectroscopy. Measurements of the elastic modulus of xanthan gel cylinders prepared by dialysis against the complexing ion at pH values from 2 to 6 indicate that monomeric species of the ion are ineffective, whereas dimeric or higher oligomeric species are effective in crosslinking the polysaccharide. When chromium was used as the crosslinking species, the dependence of the gelation rate on the ionic concentration followed a power law with a coefficient of 1·7. The gelation time and the gelation rate were found to extrapolate to zero at 1 m Cr for 2·5 mg/ml xanthan. The limiting concentration of xanthan needed for gelation with 5 m Cr(III) at 20°C was estimated as 0·35 mg/ml. This critical xanthan concentration is close to the overlap concentration c^* estimated from the experimentally determined intrinsic viscosity [η] using c^* = 1·4/[η]. An apparent activation energy for crosslinking of xanthan was calculated as E_a = 42 kJ/mol and E_a = 108 kJ/mol for Cr and Al ions, respectively. The fractal dimensionality of xanthan-Cr at the sol-gel transition was estimated as 1·3 applying the Chambon-Winter criterion for gelation, thus indicating that this gelation criterion is applicable also to stiff-chain polysaccharides such as xanthan.     

Small‐scale genetic structure and mating patterns in an extensive sessile oak forest (Quercus petraea (Matt.) Liebl.)

Oaks (Quercus) are major components of temperate forest ecosystems in the Northern Hemisphere where they form intermediate or climax communities. Sessile oak (Quercus petraea) forests represent the climax vegetation in eastern Germany and western Poland. Here, sessile oak forms pure stands or occurs intermixed with Scots Pine (Pinus sylvestris). A large body of research is available on gene flow, reproduction dynamics, and genetic structure in fragmented landscapes and mixed populations. At the same time, our knowledge regarding large, contiguous, and monospecific populations is considerably less well developed. Our study is an attempt to further develop our understanding of the reproduction ecology of sessile oak as an ecologically and economically important forest tree by analyzing mating patterns and genetic structure within adult trees and seedlings originating from one or two reproduction events in an extensive, naturally regenerating sessile oak forest. We detected positive spatial genetic structure up to 30 meters between adult trees and up to 40 meters between seedlings. Seed dispersal distances averaged 8.4 meters. Pollen dispersal distances averaged 22.6 meters. In both cases, the largest proportion of the dispersal occurred over short distances. Dispersal over longer distances was more common for pollen but also appeared regularly for seeds. The reproductive success of individual trees was highly skewed. Only 41 percent of all adult trees produced any offspring while the majority did not participate in reproduction. Among those trees that contributed to the analyzed seedling sample, 80 percent contributed 1–3 gametes. Only 20 percent of all parent trees contributed four or more gametes. However, these relatively few most fertile trees contributed 51 percent of all gametes within the seedling sample. Vitality and growth differed significantly between reproducing and nonreproducing adult trees with reproducing trees being more vital and vigorous than nonreproducing individuals. Our study demonstrates that extensive, apparently homogenous oak forests are far from uniform on the genetic level. On the contrary, they form highly complex mosaics of remarkably small local neighborhoods. This counterbalances the levelling effect of long‐distance dispersal and may increase the species’ adaptive potential. Incorporating these dynamics in the management, conservation, and restoration of oak forests can support the conservation of forest genetic diversity and assist those forests in coping with environmental change.