Reversible redox- and zinc-dependent dimerization of the Escherichia coli fur protein

Fur is a bacterial regulator using iron as a cofactor to bind to specific DNA sequences. This protein exists in solution as several oligomeric states, of which the dimer is generally assumed to be the biologically relevant one. We describe the equilibria that exist between dimeric Escherichia coli Fur and higher oligomers. The dissociation constant for the dimer-tetramer equilibrium is estimated to be in the millimolar range. Oligomerization is enhanced at low ionic strength and pH. The as-isolated monomeric form of Fur is not in equilibrium with the dimer and contains two disulfide bridges (C92-C95 and C132-C137). Binding of the monomer to DNA is metal-dependent and sequence specific with an apparent affinity 5.5 times lower than that of the dimer. Size exclusion chromatography, EDC cross-linking, and CD spectroscopy show that reconstitution of the dimer from the monomer requires reduction of the disulfide bridges and coordination of Zn2+. Reduction of the disulfide bridges or Zn2+ alone does not promote dimerization. EDC and DMA cross-links reveal that the N-terminal NH2 group of one subunit is in an ionic interaction with acidic residues of the C-terminal tail and close to Lys76 and Lys97 of the other. Furthermore, the yields of cross-link drastically decrease upon binding of metal in the activation site, suggesting that the N-terminus is involved in the conformational change. Conversely, oxidizing reagents, H2O2 or diamide, disrupt the dimeric structure leading to monomer formation. These results establish that coordination of the zinc ion and the redox state of the cysteines are essential for holding E. coli Fur in a dimeric state.     

Market Failure and the Environmental Policies of Firms: Economic Rationales for "Beyond Compliance" Behavior

This paper is an inquiry into the circumstances under which the voluntary provision of environmental public goods might be sensible from a firm's point of view. If environmental externalities were the only departure from the economic assumptions of perfect competition, and if no firms had preferential access to superior (low-cost) stocks of natural resources, firms that volunteered to internalize costs could not survive. But because externalities coexist with other departures from the competitive paradigm, such as asymmetric information and oligopoly competition, firms may find it in their shareholders' interests to provide environmental public goods to a greater degree than required by law. A number of firms, especially in Europe and North America, assert that they are pursuing "beyond-compliance" environmental policies. From the perspective of a firm's shareholders, it makes sense to pursue such policies if they increase the firm's expected value or if they appropriately manage business risk.
This paper discusses economically rational explanations for such policies. It analyzes the ways in which a firm's chances of financial success in pursuing any one of them are influenced by the firm's market position and organizational capabilities and by the basic structure of the industry in which it competes.     

Evidence for regulation of amelogenin gene expression by 1,25‐dihydroxyvitamin D3 in vivo

The unique hereditary enamel defect clearly related to the disturbance of one enamel matrix protein is X‐linked amelogenesis imperfecta (AI), in which several mutations of amelogenin gene have been identified. The clinical phenotype of many of these subjects shows similarities with enamel defects related to rickets. Therefore, we hypothesized that rachitic dental dysplasia is related to disturbances in the amelogenin pathway. In order to test this hypothesis, combined qualitative and quantitative studies in experimental vitamin D‐deficient (−D) rat model systems were performed. First, Western blot analysis of microdissected enamel matrix (secretion and maturation stages) showed no clear evidence of dysregulation of amelogenin protein processing in −D rats as compared with the controls. Second, the ultrastructural investigation permitted identification of the internal tissular defect of rachitic enamel, the irregular absence of intraprismatic enamel observed in −D animals, suggesting a possible link between prism morphogenesis and vitamin D. In addition, the steady‐state levels of amelogenin mRNAs measured in microdissected dental cells was decreased in −D rats and up‐regulated by an unique injection of 1,25‐dihydroxyvitamin D₃ (1,25(OH)₂D₃). The present study shows evidences that amelogenin expression is regulated by vitamin D. This is the first study of an hormonal regulation of tooth‐specific genes. J. Cell. Biochem. 76:194–205, 1999. © 1999 Wiley‐Liss, Inc.     

Ecto-alkaline phosphatase considered as levamisole-sensitive phosphohydrolase at physiological pH range during mineralization in cultured fetal calvaria cells

Alkaline phosphatase (ALP) activity expressed on the external surface of cultured fetal rat calvaria cells and its relationship with mineral deposition were investigated under pH physiological conditions. After replacement of culture medium by assay buffer and addition of p-nitrophenyl phosphate (pNPP), the rate of substrate hydrolysis catalyzed by whole cells remained constant for up to seven successive incubations of 10 min and was optimal over the pH range 7.6–8.2. It was decreased by levamisole by a 90% inhibition at 1 mM which was reversible within 10 min, dexamisole having no effect. Values of apparent Km for pNPP were close to 0.1 mM, and inhibition of pNPP hydrolysis by levamisole was uncompetitive (K_i = 45 μM). Phosphatidylinositol-specific phospholipase C (PI-PLC) produced the release into the medium of a p-nitrophenyl phosphatase (pNPPase) sensitive to levamisole at pH 7.8. The released activity whose rate was constant up to 75 min represented after 15 min 60% of the value of ecto-pNPPase activity. After 75 min of PI-PLC treatment the ecto-pNPPase activity remained unchanged despite the 30% decrease in Nonidet P-40-extractable ALP activity. High levels of ⁴⁵Ca incorporation into cell layers used as index of mineral deposition were decreased by levamisole in a stereospecific manner after 4 h, an effect which was reversed within 4 h after inhibitor removal, in accordance with ecto-pNPPase activity variations. These results evidenced the levamisole-sensitive activity of a glycosylphosphatidylinositol-anchored pNPPase consistent with ALP acting as an ecto-enzyme whose functioning under physiological conditions was correlated to ⁴⁵Ca incorporation and permit the prediction of the physiological importance of the enzyme dynamic equilibrium at the cell surface in cultured fetal calvaria cells. © 1996 Wiley-Liss, Inc.     

The effects of paternal reproductive tactic and rearing environment on juvenile variation in growth as mediated through aggression and foraging behaviours of Chinook salmon (Oncorhynchus tshawytscha)

In species with indeterminate growth, differential growth rates can lead to animals adopting alternative reproductive tactics such as sneak–guard phenotypes, which is partially predicted by variation in growth during the juvenile life‐history stage. To investigate sources of growth variation, we examined the independent and joint effects of paternal reproductive tactic (G) and rearing environment (E) on juvenile growth in Chinook salmon (Oncorhynchus tshawytscha), hypothesizing G and E effects are partially mediated through differences in behaviour such as aggressive interactions and resulting foraging behaviours. We created maternal half‐sibling families with one‐half of the female's eggs fertilized by the milt of a sneaker “jack” and the other half by a guarder “hooknose”. At the exogenous feeding stage, each split‐clutch family was then divided again and reared in a rationed diet or growth‐promotion diet environment for approximately 6 months, during which growth parameters were measured. Before saltwater transfer at 9 months of age, social interactions were observed in groups of six fish of various competitor origins. We found ration restricts growth rate and juvenile mass, and evidence of genetic effects on growth depensation, where jack‐sired individuals grew less uniformly over time. These growth‐related differences influenced an individual's level of aggression, with individuals raised on a restricted diet and those whose families experienced greatest growth being most aggressive. These individuals were more likely to feed than not and feed most often. Jack‐sired individuals were additionally aggressive in the absence of food, and when raised on a rationed diet outcompeted others to feed most. These results show how individuals may achieve higher growth rates via intrinsic (G) or induced (E) aggressive behavioural phenotypes, and eventually attain the threshold body size necessary during the saltwater phase to precociously sexually mature and adopt alternative reproductive phenotypes.     

Histological Observations of Rotylenchulus reniformis on Gossypium longicalyx and Interspecific Cotton Hybrids

Observations on the development of reniform nematode (Rotylenchulus reniformis) on roots of Gossypium longicalyx, G. hirsutum, and two interspecific hybrids derived from them were made by light microscopy. Gossypium longicalyx is reported to be immune to reniform nematode, but the mechanism(s) for resistance are unknown. Penetration of G. longicalyx roots by female nematodes was confirmed, and incipient swelling of the females, indicating initiation of maturation of the reproductive system, was observed. Female maturation occurred up to the formation of a single embryo inside the female body but not beyond this point. In both hybrids, development was inhibited but progressed further than in the immune parent. Reactions ranged from highly compatible, with the formation of active syncytia and full development of females, to incompatible with little or no development of the female. Compatible plants showed characteristic hypertrophied cells, enlarged nuclei, dense cytoplasm, and partial dissolution of cell walls, whereas incompatible plant reactions included lignification of the cells adjacent to the nematode head, or the complete collapse and necrosis of the cells involved. The need to characterize reactions and to carefully select among the plants descended from the hybrids during the introgression process, as well as the importance of combining the results of reproduction tests with histological observation of the plant-nematode interactions, is discussed.     

Phosphoproteomics: unraveling the signaling web

In recent years, phosphoproteomic technologies have increased our understanding of cellular signaling networks. Here, we frame recent phosphoproteomics-based advances in the context of the DNA damage response and ErbB receptor family signaling and offer a perspective on how the molecular insights arising from the integration of such proteomic approaches might be used for clinical applications.     

Calibrating the Tree of Life: fossils, molecules and evolutionary timescales

Background

Molecular dating has gained ever-increasing interest since the molecular clock hypothesis was proposed in the 1960s. Molecular dating provides detailed temporal frameworks for divergence events in phylogenetic trees, allowing diverse evolutionary questions to be addressed. The key aspect of the molecular clock hypothesis, namely that differences in DNA or protein sequence between two species are proportional to the time elapsed since they diverged, was soon shown to be untenable. Other approaches were proposed to take into account rate heterogeneity among lineages, but the calibration process, by which relative times are transformed into absolute ages, has received little attention until recently. New methods have now been proposed to resolve potential sources of error associated with the calibration of phylogenetic trees, particularly those involving use of the fossil record.

Scope and Conclusions

The use of the fossil record as a source of independent information in the calibration process is the main focus of this paper; other sources of calibration information are also discussed. Particularly error-prone aspects of fossil calibration are identified, such as fossil dating, the phylogenetic placement of the fossil and the incompleteness of the fossil record. Methods proposed to tackle one or more of these potential error sources are discussed (e.g. fossil cross-validation, prior distribution of calibration points and confidence intervals on the fossil record). In conclusion, the fossil record remains the most reliable source of information for the calibration of phylogenetic trees, although associated assumptions and potential bias must be taken into account.     

Identification and genomic location of a reniform nematode (Rotylenchulus reniformis) resistance locus (Renari) introgressed from Gossypium aridum into upland cotton (G. hirsutum)

In this association mapping study, a tri-species hybrid, [Gossypium arboreum × (G. hirsutum × G. aridum)²], was crossed with MD51ne (G. hirsutum) and progeny from the cross were used to identify and map SSR markers associated with reniform nematode (Rotylenchulus reniformis) resistance. Seventy-six progeny (the 50 most resistant and 26 most susceptible) plants were genotyped with 104 markers. Twenty-five markers were associated with a resistance locus that we designated Ren ^ari and two markers, BNL3279_132 and BNL2662_090, mapped within 1 cM of Ren ^ari . Because the SSR fragments associated with resistance were found in G. aridum and the bridging line G 371, G. aridum is the likely source of this resistance. The resistance is simply inherited, possibly controlled by a single dominant gene. The markers identified in this project are a valuable resource to breeders and geneticists in the quest to produce cotton cultivars with a high level of resistance to reniform nematode.