A real-time qPCR assay for the detection of the nifH gene of Methanobrevibacter smithii, a potential indicator of sewage pollution

Aims: To degrade ether‐type polyurethane (ether‐PUR), ether‐PUR–degrading micro‐organism was isolated. Moreover, ether‐PUR–degrading mechanisms were analysed using model compounds of ether‐PUR. Methods and Results: A fungus designated as strain PURDK2, capable of changing the configuration of ether‐PUR, has been isolated. This isolated fungus was identified as Alternaria sp. Using a scanning electron microscope, the grid structure of ether‐PUR was shown to be melted and disrupted by the fungus. The degradation of ether‐PUR by the fungus was analysed, and the ether‐PUR was degraded by the fungus by about 27·5%. To analyse the urethane‐bond degradation by the fungus, a degraded product of ethylphenylcarbamate was analysed using GC/MS. Aniline and ethanol were detected by degradation with the supernatant, indicating that the fungus secreted urethane‐bond–degrading enzyme(s). PURDK2 also degraded urea bonds when diphenylmethane‐4,4′‐dibutylurea was used as a substrate. Conclusions: The enzyme(s) from PURDK2 degraded urethane and urea bonds to convert the high molecular weight structure of ether‐PUR to small molecules; and then the fungus seems to use the small molecules as an energy source. Significance and Impact of the Study: Ether‐PUR–degrading fungus, strain PURDK2, was isolated, and the urethane‐ and urea‐bonds–degrading enzymes from strain PURDK2 could contribute to the material recycling of ether‐PUR.     

A fluorimetric method for determination of calcineurin activity

Calcineurin is a calcium-dependent, serine/threonine phosphatase that is involved in a variety of signaling pathways. Calcineurin is distinct among phosphatases because its activity requires calcium and is not sensitive to inhibition by compounds that block the related phosphatases PP1A and PP2A. Therefore, the most common methods to measure calcineurin activity rely on calcium-dependent dephosphorylation of a substrate derived from the RII subunit of protein kinase A in the presence of PP1A/PP2A inhibitors. However, current techniques quantify activity by measurement of released radioactive phosphate or detection of free phosphate with malachite green. Both methods involve technical challenges and have undesirable features. We report a new calcineurin fluorimetric assay that utilizes a fluorescently labeled phosphopeptide substrate and separation of dephosphorylated peptide product by titanium-oxide. The method is rapid, quantitative, involves no radioactivity and is suitable for high throughput assays. Furthermore, with the use of a standard curve, precise measurements of calcineurin activity can be obtained.     

Genbank accession #: AF111812

Plant Molecular Biology -     

Rhythms of differentiation and diacylglycerol in Neurospora.

Although the fungus Neurospora crassa is a relatively simple lower eukaryote, its circadian system may be more complex than previously thought. In this paper we review evidence suggesting that there may be several output pathways coupled in complex ways to a single oscillator, or that there may be more than one oscillator driving independent output pathways. We have described two new rhythms in Neurospora that are not tightly coupled to the rhythm of conidiation bands that is the standard assay for the state of the Neurospora circadian clock. The first is a rhythm in the timing of differentiation, i.e. the production of aerial hyphae and spores. Large regions of the mycelium differentiate synchronously, as if responding to a spatially widespread signal. This rhythm may be distinct from the timer that sets the determination switch controlling the spatial pattern of conidiation bands. The second new rhythm is an oscillation in the levels of the neutral lipid diacylglycerol (DAG). This rhythm is found in all regions of a colony and is not always in phase with the rhythm of conidiation bands. The DAG rhythm shares some characteristics with the differentiation rhythm and has the potential to act as the signal that induces rhythmic differentiation.     

Cellular autonomy of theGonyaulax circadian clock

Because of the long term persistence of free-running circadian rhythms in populations of unicells, several investigators have considered, but not demonstrated, a possible role for intercellular interaction in maintaining synchrony between individual cells. The experiments described here were designed to test more critically the possibility that there is interaction between cells, including those possessing only small phase differences. None was detected; the bioluminescent glow of the mixed cultures matched the algebraic sum of the independent control cultures.     

Molecular evolution of P transposable elements in the genus Drosophila. III. The melanogaster species group

Phylogenetic relationships were determined for 76 partial P-element sequences from 14 species of the melanogaster species group within the Drosophila subgenus Sophophora. These results are examined in the context of the phylogeny of the species from which the sequences were isolated. Sequences from the P-element family fall into distinct subfamilies, or clades, which are often characteristic for particular species subgroups. When examined locally among closely related species, the evolution of P elements is characterized by vertical transmission, whereby the P-element phylogeny traces the species phylogeny. On a broader scale, however, the P-element phylogeny is not congruent with the species phylogeny. One feature of P-element evolution in the melanogaster group is the presence of more than one P-element subfamily, differing by as much as 36%, in the genomes of some species. Thus, P elements from several individual species are not monophyletic, and a likely explanation for the incongruence between P-element and species phylogenies is provided by the comparison of paralogous sequences. In certain instances, horizontal transfer seems to be a valid alternative explanation for lack of congruence between species and P-element phylogenies. The canonical P-element subfamily, which represents the active, autonomous transposable element, is restricted to D. melanogaster. Thus, its origin clearly lies outside of the melanogaster species group, consistent with the earlier conclusion of recent horizontal transfer.      

Mechanical stimulation of tissue engineered tendon constructs: effect of scaffold materials

Our group has shown that numerous factors can influence how tissue engineered tendon constructs respond to in vitro mechanical stimulation. Although one study showed that stimulating mesenchymal stem cell (MSC)-collagen sponge constructs significantly increased construct linear stiffness and repair biomechanics, a second study showed no such effect when a collagen gel replaced the sponge. While these results suggest that scaffold material impacts the response of MSCs to mechanical stimulation, a well-designed intra-animal study was needed to directly compare the effects of type-I collagen gel versus type-I collagen sponge in regulating MSC response to a mechanical stimulus. Eight constructs from each cell line (n=8 cell lines) were created in specially designed silicone dishes. Four constructs were created by seeding MSCs on a type-I bovine collagen sponge, and the other four were formed by seeding MSCs in a purified bovine collagen gel. In each dish, two cell-sponge and two cell-gel constructs from each line were then mechanically stimulated once every 5 min to a peak strain of 2.4%, for 8 h/day for 2 weeks. The other dish remained in an incubator without stimulation for 2 weeks. After 14 days, all constructs were failed to determine mechanical properties. Mechanical stimulation significantly improved the linear stiffness (0.048+/-0.009 versus 0.015+/-0.004; mean+/-SEM (standard error of the mean ) N/mm) and linear modulus (0.016+/-0.004 versus 0.005+/-0.001; mean+/-SEM MPa) of cell-sponge constructs. However, the same stimulus produced no such improvement in cell-gel construct properties. These results confirm that collagen sponge rather than collagen gel facilitates how cells respond to a mechanical stimulus and may be the scaffold of choice in mechanical stimulation studies to produce functional tissue engineered structures.