Succession of mycorrhizal fungi in stands of Pinus sylvestris in the Netherlands

The mycorrhizal mycoflora was investigated in 35 stands of Pinus sylvestris in three types of young (4-13 yr) and three of old (50-80 yr) stands in the Netherlands, differing in number of rotations and soil type. A plot of 1050 m² (30 m x 35 m) within each stand was searched for carpophores during the autumns of 1986 and 1987. 10 soil samples per plot were taken in October 1987 in order to assess the mycorrhizal status of the tree roots. The composition of mycorrhizal mycoflora in the different plots was subjected to TWINSPAN cluster analysis and Detrended Correspondence Analysis. Plot groupings generated by these analyses largely parallelled the stand types, indicating that each stand type has its own mycoflora. Differences in myco-floristic composition between stand types were parallelled by differences in the composition of green vegetation. The young stand types had 3.5–27 x more carpophores and 1.4–6.8 x more species than two of the old stand types One old stand type was intermediate. Considerable differences in species composition between the young stand types were observed. It is concluded that the succession of mycorrhizal fungi is not primarily influenced by ageing of the trees, but rather by changes in the soil. The results were compared with data on changes in the occurrence of fruiting species of mycorrhizal fungi in the Netherlands during this century. It appeared that species which have declined according to these data were more frequent in the young plots than in the old plots. However, these species are reported to be frequent in old stands of P. sylvestris in Estonia and Finland. It is argued that this difference is related to the high nitrogen deposition in the Netherlands.     

Application of fluorescence internal transcribed spacer-PCR (f-ITS) for the cluster analysis of bacteria isolated from air and deteriorated fresco surfaces

The aim of this work was the evaluation of fluorescence ITS-PCR (f-ITS) as a molecular tool to analyze the microbial community involved in the biodeterioration of cultural heritage surfaces. As a case study we analyzed by f-ITS ninety-two bacterial strains isolated from a medieval fresco and the surrounding air environment. The internal transcribed spacer between the 16S and 23S rRNA genes was amplified, and then the fluorescently labeled PCR products were separated by capillary electrophoresis. Bacterial strains were identified by 16S rDNA sequencing. The f-ITS electropherograms showed different profiles coherent with the affiliation of the strains at the genus and species levels. Among the isolates obtained from the fresco surface, those belonging to the genus Bacillus were the most prevailing exhibiting 8 different f-ITS profiles. The airborne bacilli exhibited only 2 of these 8 profiles. Staphylococcus were mostly isolated from air and produced 4 different profiles. Pseudomonas isolates presented 3 different profiles, and one of them was typical of Pseudomonas putida. Members of the other genera produced their distinctive profiles. Our results show that f-ITS is a promising molecular tool for the rapid selection and clustering of strains isolated from different sources.     

Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes

Hox genes are key regulators of anterior-posterior axis patterning and have a major role in hindbrain development. The zebrafish Hox4 paralogs have strong overlapping activities in hindbrain rhombomeres 7 and 8, in the spinal cord and in the pharyngeal arches. With the aim to predict enhancers that act on the hoxa4a, hoxb4a, hoxc4a and hoxd4a genes, we used sequence conservation around the Hox4 genes to analyze all fish:human conserved non-coding sequences by reporter assays in stable zebrafish transgenesis. Thirty-four elements were functionally tested in GFP reporter gene constructs and more than 100 F1 lines were analyzed to establish a correlation between sequence conservation and cis-regulatory function, constituting a catalog of Hox4 CNEs. Sixteen tissue-specific enhancers could be identified. Multiple alignments of the CNEs revealed paralogous cis-regulatory sequences, however, the CNE sequence similarities were found not to correlate with tissue specificity. To identify ancestral enhancers that direct Hox4 gene activity, genome sequence alignments of mammals, teleosts, horn shark and the cephalochordate amphioxus, which is the most basal extant chordate possessing a single prototypical Hox cluster, were performed. Three elements were identified and two of them exhibited regulatory activity in transgenic zebrafish, however revealing no specificity. Our data show that the approach to identify cis-regulatory sequences by genome sequence alignments and subsequent testing in zebrafish transgenesis can be used to define enhancers within the Hox clusters and that these have significantly diverged in their function during evolution.     

Reaction of a bulky phosphite with [Ru3(CO)12]: The molecular structure of one of the decomposition products

Mono- and bis-substituted phosphite complexes [Ru₃(CO)_12−x L_x] (L = tris(2,4-di-tert-butylphenyl) phosphite; x = 1, 2) were synthesized by simple substitution reactions, and were characterized by spectroscopic methods. The monosubstituted ruthenium complex disproportionates in acetone producing a mononuclear ruthenium complex as one of the decomposition products. Single crystal X-ray diffraction analysis established the molecular structure of this new compound.     

Synthesis of tetravalent LacNAc-glycoclusters as high-affinity cross-linker against Erythrina cristagalli agglutinin

Four kinds of tetravalent double-headed glycoclusters [(LacNAc)₄-DHGs] were designed with linkers of varying lengths consisting of alkanedioic carboxyamido groups (C₆, C₁₂, C₁₈ and C₂₄) between two bi-antennary LacNAc-glycosides. These glycoclusters served as high-affinity cross-linking ligands for the LacNAc-binding lectin Erythrina cristagalli agglutinin (ECA). The binding activity and cross-linking between each ligand and ECA were characterized by a hemagglutination inhibition (HI) assay, isothermal titration calorimetry (ITC), a quantitative precipitation assay and dynamic light scattering (DLS). For the precipitation assay and DLS measurement, the synthesized (LacNAc)₄-DHGs were found to be capable of binding and precipitating the ECA as multivalent ligands. ITC analysis indicated the binding of (LacNAc)₄-DHGs was driven by a favorable enthalpy change. Furthermore, the entropy penalty from binding (LacNAc)₄-DHGs clearly decreased in a spacer length-dependent manner. The binding affinities of flexible (LacNAc)₄-DHGs (C₁₈ and C₂₄) with long spacers were found to be more favorable than those of the clusters having short spacers (C₆ and C₁₂). These results were supported by molecular dynamics simulations with explicit water molecules for the tetravalent glycoclusters with ECA. We concluded that the subtle modification in the epitope-presenting scaffolds exerts the significant effect in the recognition efficiency involved in the LacNAc moieties by ECA.     

A new bonding mode for the bicyclic guanidinate, [hpp], in the tetrametallic yttrium oxide cluster, Y4(hpp)8Cl2(μ4-O)

Oxygen incorporation in the product of the reaction between YCl₃ and the lithium salt of 1,3,4,6,7,8-hexahydro-2Hpyrimido[1,2-a]pyrimidine (hppH) afforded the tetrametallic cluster Y₄(hpp)₈Cl₂(μ₄-O), in which four of the guanidinate anions are involved in a previously unreported μ,η²,η²-bridging mode between two metal centres.     

Evolution of tryptophan biosynthetic pathway in microbial genomes: a comparative genetic study

Biosynthetic pathway evolution needs to consider the evolution of a group of genes that code for enzymes catalysing the multiple chemical reaction steps leading to the final end product. Tryptophan biosynthetic pathway has five chemical reaction steps that are highly conserved in diverse microbial genomes, though the genes of the pathway enzymes show considerable variations in arrangements, operon structure (gene fusion and splitting) and regulation. We use a combined bioinformatic and statistical analyses approach to address the question if the pathway genes from different microbial genomes, belonging to a wide range of groups, show similar evolutionary relationships within and between them. Our analyses involved detailed study of gene organization (fusion/splitting events), base composition, relative synonymous codon usage pattern of the genes, gene expressivity, amino acid usage, etc. to assess inter- and intra-genic variations, between and within the pathway genes, in diverse group of microorganisms. We describe these genetic and genomic variations in the tryptophan pathway genes in different microorganisms to show the similarities across organisms, and compare the same genes across different organisms to find the possible variability arising possibly due to horizontal gene transfers. Such studies form the basis for moving from single gene evolution to pathway evolutionary studies that are important steps towards understanding the systems biology of intracellular pathways.     

Immunoregulatory effect of mesenchymal stem cell via mitochondria signaling pathways in allergic asthma

Asthma is a complicated lung disease, which has increased morbidity and mortality rates in worldwide. There is an overlap between asthma pathophysiology and mitochondrial dysfunction and MSCs may have regulatory effect on mitochondrial dysfunction and treats asthma. Therefore, immune-modulatory effect of MSCs and mitochondrial signaling pathways in asthma was studied.After culturing of MSCs and producing asthma animal model, the mice were treated with MSCs via IV via IT. BALf's eosinophil Counting, The levels of IL-4, −5, −13, −25, –33, INF-γ, Cys-LT, LTB4, LTC4, mitochondria genes expression of COX-1, COX-2, ND1, Nrf2, Cytb were measured and lung histopathological study were done.BALf's eosinophils, the levels of IL-4, −5, −13, −25, –33, LTB4, LTC4, Cys-LT, the mitochondria genes expression (COX-1, COX-2, Cytb and ND-1), perivascular and peribronchial inflammation, mucus hyper-production and hyperplasia of the goblet cell in pathological study were significantly decreased in MSCs-treated asthma mice and reverse trend was found about Nrf-2 gene expression, IFN-γ level and ratio of the INF-γ/IL-4.MSC therapy can control inflammation, immune-inflammatory factors in asthma and mitochondrial related genes, and prevent asthma immune-pathology.     

Preparation and structures of the cluster dimers consisting of Rh2Mo2S4 single-cubane units connected by two bidentate N-donor ligands

Reactions of a single-cubane cluster [{Rh(cod)}₂{MoCl(dtc)}₂(μ₃-S)₄] (cod = 1,5-cyclooctadiene, dtc = diethyldithiocarbamate) with 1 equiv. of L (L = pyrazine, 4,4′-bipyridyl, trans-1,2-bis(4-pyridyl)ethylene) in the presence of 2 equiv. of AgBF₄ in CH₂Cl₂ gave doubly bridged double-cubane clusters [({Rh(cod)}₂{Mo(dtc)}₂(μ₃-S)₄)₂(μ-L)₂][BF₄]₄, whose structures were determined by the single-crystal X-ray analysis.