Rarity,ecological memory,rate of floral change in phytoplankton—and the mystery of the Red Cock

In this article, we attempt to estimate the contemporary phytoplankton species pool of a particular lake, by assessing the rate of floral change over a period of 15 years. Phytoplankton time series data from Lake Stechlin, an oligo-mesotrophic lake in the Baltic Lake District (Germany) were used. Of the 254 algal species recorded during the 15-year of studies with roughly biweekly sampling, 212 species were planktonic. In the individual plankton years, the recorded total number of species changed between 97 and 122, of which the number of dominants (>1% contribution to the annual average of total biomass) was only 10–19. The 15-year cumulative number of species exhibited an almost linear increase after an initial saturation phase. This increase was attributed to two reasons: increase of sample size and immigration of species new to the flora. Based on a probabilistic model developed in this study, we estimated the number of co-existing planktonic species of the lake as some 180, and the rate of floral change as 1–2 species per year. Of these co-existing species, only few maintain the matter–energy processing ecosystem functions in any particular plankton year. Selection of these dominants is probably driven by mesoclimatic cycles, coupled with human-induced forcing, like eutrophication. All others are hiding as an ecological memory, in the sense of the capacity or experiences of past states to influence present or future responses of the community. Data analyses suggest that selection of the ‘memory species’ that show temporary abundance increases over shorter (several years) periods are largely dependent upon the dominants. These results show that interspecific interactions and the particular autecological features of the dominants, together with their effects on the whole ecosystem, act as a major organizing force. Some phytoplankton species, like Planktothrix rubescens, are efficient ecosystem engineers with cascading effects of both a top-down and bottom-up nature. Historical scientific data on Planktothrix blooms in Lake Stechlin suggest cyclic patterns in long-term development of phytoplankton which, as the legend of the Red Cock suggests, dates back much further than scientific archives.     

Colonization factors of diarrheagenicE. coli and their intestinal receptors

WhileEscherichia coli is common as a commensal organism in the distal ileum and colon, the presence of colonization factors (CF) on pathogenic strains ofE. coli facilitates attachment of the organism to intestinal receptor molecules in a species- and tissue-specific fashion. After the initial adherence, colonization occurs, and the involvement of additional virulence determinants leads to illness. EnterotoxigenicE. coli (ETEC) is the most extensively studied of the five categories ofE. coli that cause diarrheal disease, and has the greatest impact on health worldwide. ETEC can be isolated from domestic animals and humans. The biochemistry, genetics, epidemiology, antigenic characteristics, and cell and receptor binding properties of ETEC have been extensively described. Another major category, enteropathogenicE. coli (EPEC), has virulence mechanisms, primarily effacement and cytoskeletal rearrangement of intestinal brush borders, that are distinct from ETEC. An EPEC CF receptor has been purified and characterized as a sialidated transmembrane glycoprotein complex directly attached to actin, thereby associating CF-binding with host-cell response. Three, additional categories ofE. coli diarrheal disease, their colonization factors and their host cell receptors are discussed. It appears that biofilms exist in the intestine in a manner similar to oral bacterial biofilms, and thatE. coli is part of these biofilms as both commensals and pathogens.Abbreviations CF colonization factor - CFA Colonization Factor Antigen - CS coli-surface-associated antigen - EAggEC enteroaggregativeE. coli - ECDD E. coli diarrheal disease - EHEC enterohemorrhagicE. coli - EIEC enteroinvasiveE. coli - EPEC enteropathogenicE. coli - ETEC enterotoxigenicE. coli - Gal galactose - GalNAc N-acetyl galactosamine - LT heat-labile toxin - NeuAc N-acetyl neuraminic acid - PCF Putative colonization factor - RBC red blood cells - SLT Shiga-like toxin - ST heat-stable toxin     

Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics

The main limiting factor in Bayesian MCMC analysis of phylogeny is typically the efficiency with which topology proposals sample tree space. Here we evaluate the performance of seven different proposal mechanisms, including most of those used in current Bayesian phylogenetics software. We sampled 12 empirical nucleotide data sets--ranging in size from 27 to 71 taxa and from 378 to 2,520 sites--under difficult conditions: short runs, no Metropolis-coupling, and an oversimplified substitution model producing difficult tree spaces (Jukes Cantor with equal site rates). Convergence was assessed by comparison to reference samples obtained from multiple Metropolis-coupled runs. We find that proposals producing topology changes as a side effect of branch length changes (LOCAL and Continuous Change) consistently perform worse than those involving stochastic branch rearrangements (nearest neighbor interchange, subtree pruning and regrafting, tree bisection and reconnection, or subtree swapping). Among the latter, moves that use an extension mechanism to mix local with more distant rearrangements show better overall performance than those involving only local or only random rearrangements. Moves with only local rearrangements tend to mix well but have long burn-in periods, whereas moves with random rearrangements often show the reverse pattern. Combinations of moves tend to perform better than single moves. The time to convergence can be shortened considerably by starting with a good tree, but this comes at the cost of compromising convergence diagnostics based on overdispersed starting points. Our results have important implications for developers of Bayesian MCMC implementations and for the large group of users of Bayesian phylogenetics software.     

The cellular prion protein and its role in Alzheimer disease

The cellular prion protein (PrP^C) is a membrane-bound glycoprotein especially abundant in the central nervous system (CNS). The scrapie prion protein (PrP^Sc, also termed prions) is responsible of transmissible spongiform encephalopathies (TSE), a group of neurodegenerative diseases which affect humans and other mammal species, although the presence of PrP^C is needed for the establishment and further evolution of prions.The present work compares the expression and localization of PrP^C between healthy human brains and those suffering from Alzheimer disease (AD).In both situations we have observed a rostrocaudal decrease in the amount of PrP^C within the CNS, both by immunoblotting and immunohistochemistry techniques. PrP^C is higher expressed in our control brains than in AD cases. There was a neuronal loss and astogliosis in our AD cases. There was a tendency of a lesser expression of PrP^C in AD cases than in healthy ones. And in AD cases, the intensity of the expression of the unglycosylated band is higher than the di- and monoglycosylated bands.With regards to amyloid plaques, those present in AD cases were positively labeled for PrP^C, a result which is further supported by the presence of PrP^C in the amyloid plaques of a transgenic line of mice mimicking AD.The work was done according to Helsinki Declaration of 1975, and approved by the Ethics Committee of the Faculty of Medicine of the University of Navarre.Key words: cellular prion protein, Alzheimer disease, transgenic mice     

Tempo and mode of early gene loss in endosymbiotic bacteria from insects

Background  

Understanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode (size and types of deletions) of gene losses. In this study, we analysed five endosymbiotic genome sequences of the gamma-proteobacteria (three different Buchnera aphidicola strains, Wigglesworthia glossinidia, Blochmannia floridanus) to test if gene loss could be driven by the selective importance of genes. We used a parsimony method to reconstruct a minimal ancestral genome of insect endosymbionts and quantified gene loss along the branches of the phylogenetic tree. To evaluate the selective or functional importance of genes, we used a parameter that measures the level of adaptive codon bias in E. coli (i.e. codon adaptive index, or CAI), and also estimates of evolutionary rates (Ka) between pairs of orthologs either in free-living bacteria or in pairs of symbionts.     

Identification of a Novel Self-Sufficient Styrene Monooxygenase from Rhodococcus opacus 1CP

Sequence analysis of a 9-kb genomic fragment of the actinobacterium Rhodococcus opacus 1CP led to identification of an open reading frame encoding a novel fusion protein, StyA2B, with a putative function in styrene metabolism via styrene oxide and phenylacetic acid. Gene cluster analysis indicated that the highly related fusion proteins of Nocardia farcinica IFM10152 and Arthrobacter aurescens TC1 are involved in a similar physiological process. Whereas 413 amino acids of the N terminus of StyA2B are highly similar to those of the oxygenases of two-component styrene monooxygenases (SMOs) from pseudomonads, the residual 160 amino acids of the C terminus show significant homology to the flavin reductases of these systems. Cloning and functional expression of His₁₀-StyA2B revealed for the first time that the fusion protein does in fact catalyze two separate reactions. Strictly NADH-dependent reduction of flavins and highly enantioselective oxygenation of styrene to (S)-styrene oxide were shown. Inhibition studies and photometric analysis of recombinant StyA2B indicated the absence of tightly bound heme and flavin cofactors in this self-sufficient monooxygenase. StyA2B oxygenates a spectrum of aromatic compounds similar to those of two-component SMOs. However, the specific activities of the flavin-reducing and styrene-oxidizing functions of StyA2B are one to two orders of magnitude lower than those of StyA/StyB from Pseudomonas sp. strain VLB120.The incorporation of one atom of oxygen during hydroxylation, epoxidation, sulfoxidation, or Baeyer-Villiger oxidation is a common initial step of the aerobic degradation of aromatic compounds by microorganisms. In bacteria, these reactions are most frequently catalyzed by inducible flavoprotein monooxygenases (EC 1.14.13 [57]). The majority of these enzymes (so-called single-component flavoprotein monooxygenases) utilize electrons from NAD(P)H, which are transferred to a non-covalently bound flavin adenine dinucleotide (FAD) in order to activate molecular oxygen as a flavin (hydro)peroxide. Depending on the protonation of this intermediate and the type of substrate, an oxygen atom is then incorporated by nucleophilic or electrophilic attack. More recently, different two-component flavoprotein monooxygenases have been characterized (57). These systems cover an NAD(P)H-dependent flavin reductase in order to generate reduced flavin and an oxygenase that utilizes this cofactor for the activation of oxygen.The exquisite regio- and stereoselectivities of oxygen insertion by flavoprotein monooxygenases favor these enzymes for biocatalytic applications (23, 24, 33). This is especially true because chemical synthesis approaches by hetero- or homogenic catalysis often do not yield a sufficiently high enantiomeric excess for the production of pharmaceuticals and their chiral building blocks. The use of oxygen as an inexpensive nontoxic oxidant and mild reaction conditions are additional advantages with the potential for increasing the environmental sustainability of oxygenase-catalyzed biotransformations.The necessity for expensive cofactors is perhaps the most striking drawback limiting the industrial application of flavoprotein monooxygenases. Different electrochemical and enzymatic procedures for in vitro cofactor regeneration are available (20, 21, 32, 52, 56), but these systems are currently lacking long-term stability. As a consequence, the practical application of flavoprotein monooxygenases is virtually restricted to in vivo systems in which cofactor regeneration is mediated by the metabolism of the expression host (45, 49). The limitations of whole-cell-mediated biotransformations by substrate and/or product toxicity can be overcome by means of two-phase systems, as was recently shown for the two-component styrene monooxygenase (SMO) from Pseudomonas sp. strain VLB120 (45).Two-component flavoprotein monooxygenases present additional challenges for biocatalytic applications. The need for two separate protein components may hamper attempts at recombinant enzyme expression, the application of immobilized enzymes in cell-free systems, and the detection of novel oxygenases during activity-based metagenome-screening approaches. Moreover, and as was already shown for the two-component SMO from Pseudomonas sp. strain VLB120 (44), the interprotein transfer of reduced FAD is accompanied to a certain extent by the auto-oxidative formation of reactive oxygen species such as hydrogen peroxide (Fig. ​(Fig.1).1). Auto-oxidation of reduced FAD not only decreases the efficiency of the oxygenation process but also negatively interferes with the physiological conditions of the cell. The extent of oxidative stress is considerably increased when FAD oxidoreductase activity exceeds oxygenase activity and uncoupling becomes dominant.Open in a separate windowFIG. 1.Catalytic mechanism of two-component SMOs and the formation of oxidative stress by uncoupling between FAD oxidoreductase (StyB) and oxygenase (StyA) (adapted from reference 36). FAD_OX and FAD_RED, oxidized and reduced forms of FAD, respectively.Presently the details of reduced-FAD transfer between the oxygenase and FAD oxidoreductase components of SMOs are not known. Recent kinetic studies have indicated that reduced FAD is transferred by a mixed mechanism in which direct contact of both proteins and free diffusion of the reduced cofactor play a role (25). This hypothesis is supported by the work of Otto and coworkers in which the formation of hydrogen peroxide was shown to be reciprocally proportional to the concentration of active oxygenase StyA (44). The high level of efficiency of self-sufficient cytochrome P450 enzymes compared to that of multicomponent types is attributed to the closer location between the heme-containing P450 domain (oxygenase) and a reductase domain (FAD/flavin mononucleotide [FMN] and NADH binding site), which should also promote the efficiency of diffusive transfer (38). These self-sufficient P450 systems are of high biocatalytic interest (8, 34, 39), and it is likely that other types of self-sufficient monooxygenases (e.g., flavoenzymes) behave in a similar way.Members of the gram-positive genus Rhodococcus are characterized by their exceptionally high level of metabolic versatility toward a broad range of organic substrates (31). Large genome sizes, the presence of megaplasmids, and a distinct gene redundancy (multiple enzyme homologs) favor these organisms as a promising source for novel enzymes (59). Moreover, several studies have provided evidence of functionally convergent evolution of the catabolic activities of rhodococci and proteobacteria (12, 37). Since most research on bacterial catabolic activities has so far been performed on the latter group, novel enzymes and mechanisms are likely to be identified in gram-positive bacteria.The nocardioform actinobacterium Rhodococcus opacus 1CP was originally isolated from contaminated soil by enrichment with 4-chloro- and 2,4-dichlorophenol as the sole carbon sources (18). To solve questions related to the enzymes involved in chlorophenol mineralization, an R. opacus 1CP clone library was generated, leading to the identification of a 9-kb genomic fragment harboring genes with a presumed function in styrene metabolism. Sequence analysis indicated the presence of an open reading frame (ORF) encoding a fusion protein composed of an oxygenase and a reductase subunit with a high level of similarity to the corresponding subunits of two-component SMOs from pseudomonads. Recombinant expression and biochemical characterization confirmed that it has enantioselective styrene epoxidation ability and showed that StyA2B is the first representative of a new class of NADH- and flavin-dependent single-component flavoprotein monooxygenases.     

Structural requirements of carbohydrates to bind Agaricus bisporus lectin

Galbeta1-3GalNAc (T-disaccharide) and related molecules were assayed to describe the structural requirements of carbohydrates to bind Agaricus bisporus lectin (ABL). Results provide insight into the most relevant regions of T-disaccharide involved in the binding of ABL. It was found that monosaccharides bind ABL weakly indicating a more extended carbohydrate-binding site as compared to those involvedin the T- disaccharide specific lectins such as jacalin and peanut agglutinin. Lacto-N-biose (Galbeta1-3GlcNAc) unlike T-disaccharide, is unable to inhibit the ABL interaction, thus showing the great importance of the position of the axial C-4 hydroxyl group of GalNAc in T-disaccharide. This finding could explain the inhibitory ability of Galbeta1-6GlcNAc and lactose because C-4 and C-3 hydroxyl groups of reducing Glc, respectively, occupy a similar position as reported by conformational analysis. From the comparison of different glycolipids bearing terminal T-disaccharide bound to different linkages, it can be seen than ABL binding is even more impaired by an adjacent C-6 residual position than by the anomeric influence of T-disaccharide. Furthermore, the addition of beta-GlcNAc to the terminal T-disaccharide in C-3 position of Gal does not affect the ABL binding whereas if an anionic group such as glucuronic acid is added to C-3, the binding is partially affected. These findings demonstrate that ABL holds a particular binding nature different from that of other T-disaccharide specific lectins.