Redox Fluctuations Frame Microbial Community Impacts on N-cycling Rates in a Humid Tropical Forest Soil

Fluctuating soil redox regimes may facilitate the co-occurrence of microbial nitrogen transformations with significantly different sensitivities to soil oxygen availability. In an upland humid tropical forest, we explored the impact of fluctuating redox regimes on gross nitrogen cycling rates and microbial community composition. Our results suggest that the rapidly fluctuating redox conditions that characterize these upland soils allow anoxic and oxic N processing to co-occur. Gross nitrogen mineralization was insensitive to soil redox fluctuations. In contrast, nitrifiers in this soil were directly affected by low redox periods, yet retained some activity even after 3–6 weeks of anoxia. Dissimilatory nitrate reduction to ammonium (DNRA) was less sensitive to oxygen exposure than expected, indicating that the organisms mediating this reductive process were also tolerant of unfavorable (oxic) conditions. Denitrification was a stronger sink for NO₃⁻ in consistently anoxic soils than in variable redox soils. Microbial biomass and community composition were maintained with redox fluctuation, but biomass decreased and composition changed under static oxic and anoxic soil regimes. Bacterial community structure was significantly correlated with rates of nitrification, denitrification and DNRA, suggesting that redox-control of soil microbial community structure was an important determinant of soil N-cycling rates. Specific nitrogen cycling functional groups in this environment (such as nitrifiers, DNRA organisms, and denitrifiers) appear to have adapted to nutrient resources that are spatially and temporally variable. In soils where oxygen is frequently depleted and re-supplied, characteristics of microbial tolerance and resilience can frame N cycling patterns.     

Richness and structure of plant communities in temporary pools from western Morocco: influence of human activities

Temporary pools are numerous in coastal plains of Atlantic Morocco and have a rich and diverse flora. These habitats are increasingly under pressure by man impact through grazing by domestic livestock and the development of annual crops in their catchments. The objectives of this work were to evaluate the species richness and the species composition of the vegetation of a sample of 30 pools in this region, in order to assess the structure of the vegetation within pools and to evaluate the role of environmental and anthropogenic factors in their richness and species composition. The results highlighted the species richness of the pools with 300 species found among which annual species were heavily dominant. The structure of the vegetation varied within pools according to a topographical/flooding gradient and between pools in relation with the land use in the surrounding areas. Three vegetation belts were recognized from the centre to the periphery of the pool. The total species richness per pool was not found significantly related to environmental or anthropogenic factors. The species characteristics of the pools were found mostly in the centre and their number affected by hydrological factors and land use in the pool and in the surrounding areas. The species characteristics of woodland habitats and of agriculture crops were found mostly in the peripheral zone. Temporary pools maintain specific communities of both aquatic and amphibious species, probably because of the selection induced by water level variations. The peripheral zone, although often dominated by terrestrial species, is clearly interpreted as part of the pool. It contains amphibious species highly characteristic of the pool for which the irregular flooding is a key environmental factor which decreases competition.     

Changes in the free-radical state and the level of free iron during the development of drug resistance in tumor cells

The free-radical state of K562 human erythroleukemia cells changes during the development of resistance to doxorubicin, an antitumor antibiotic with prooxidant action widely used in oncology. It was found that the level of superoxide anion in the resistant cells decreased. The addition of doxorubicin to the culture medium induced a much smaller increase in O ₂ ^? generation in the resistant cells than in the sensitive cells. Again, the semiquinone-type EPR signal with a g-factor of 2.006 considerably decreased in the resistant cells grown without doxorubicin as compared with the sensitive cells under the same conditions. The EPR study has shown that the level of paramagnetic nitrosyl complexes of nonheme iron in the resistant cells decreased, which indicates that the content of free nonheme iron declined in development of drug resistance. In addition, we have found with the use of RT-PCR that the level of mRNA of the transferrin receptor decreased in the resistant cells. The data suggest that the suppression of free-radical processes during the development of resistance of K562 cells to doxorubicin is a coordinated redox-dependent adaptive response.     

Rab4 GTP/GDP modulates amiloride-sensitive sodium channel (ENaC) function in colonic epithelia

The sodium-selective amiloride-sensitive epithelial sodium channel (ENaC) mediates electrogenic sodium re-absorption in tight epithelia. ENaC expression at the plasma membrane requires regulated transport, processing, and macromolecular assembly of subunit proteins in a defined and highly compartmentalized manner. Ras-related Rab GTPases monitor these processes in a highly regulated sequence of events. In order to evaluate the role of Rab proteins in ENaC function, Rab4 wild-type (WT), the GTPase-deficient mutant Rab4Q67L, and the dominant negative GDP-locked mutant Rab4S22N were over-expressed in the colon cancer cell line, HT-29 and amiloride-sensitive currents were recorded. Rab4 over-expression inhibited amiloride-sensitive currents. The effect was reversed by introducing Rab4-neutralizing antibody and Rab4 specific SiRNA. The GDP-locked Rab4 mutant inhibited, while GTPase-deficient mutant moderately stimulated amiloride-sensitive currents. Active status of Rab4 was confirmed by GTP overlay assay, while its expression was verified by Western blotting. Immunoprecipitation and pull-down assay suggest protein-protein interaction between Rab4 and ENaC. In addition, the functional modulation coincides with concomitant changes in ENaC expression at the cell surface and in intracellular pool. We propose that Rab4 is a critical element that regulates ENaC function by mechanisms that include GTP-GDP status, recycling, and expression level. Our observations imply that channel expression in apical membranes of epithelial cell system incorporates RabGTPase as an essential determinant of channel function and adds an exciting paradigm to ENaC therapeutics.     

Formulation of competition between sexual and selfing forms

In a recent issue, Rausch and Morgan (2005) analyzed the role of selfing in the autopolyploidization process theoretically based on the formulation of Felber (1991), although they did not explicitly model a pollen pool. This paper reformulates the male contribution to outcrossing in terms of gamete frequencies within a pollen pool. This is a general issue when considering competition between sexual and selfing or asexual forms in a single population, which must be considered in theoretical treatments.     

Observation of single-stranded DNA on mica and highly oriented pyrolytic graphite by atomic force microscopy

Atomic force microscopy was used to image single-stranded DNA (ssDNA) adsorbed on mica modified by Mg(2+), by 3-aminopropyltriethoxysilane or on modified highly oriented pyrolytic graphite (HOPG). ssDNA molecules on mica have compact structures with lumps, loops and super twisting, while on modified HOPG graphite ssDNA molecules adopt a conformation without secondary structures. We have shown that the immobilization of ssDNA under standard conditions on modified HOPG eliminates intramolecular base-pairing, thus this method could be important for studying certain processes involving ssDNA in more details.     

Biology and mycovirus-assisted biological control of Sclerotinia sclerotiorum infecting vegetable and oilseed crops

Abstract

Plant disease caused by pathogenic fungal infection causes maximum crop damage. Among different fungal diseases, rot caused by Sclerotinia spp.; is a primary concern for vegetables and oilseed industry. Disease management using Chemical fungicides is a potential hazard and leads to the development of many fungicide-resistant strains. Hypovirulence associated mycoviruses is a possible environment-friendly solution, and current studies are aiming to exploit their potential as biocontrol agents. The use of the mycovirus mediated hypovirulent approach has emerged as a new technique to identify successful biocontrol agents. Most mycoviruses are known to have RNA genomes, double-stranded RNA (dsRNA) or single-stranded RNA (ssRNA). A total of six dsRNA mycoviruses and a one ssDNA mycovirus have been reported from Sclerotinia sclerotiorum till date which includes the most recent entry as published by Hamid and his group in 2018. In contrast to dsRNA mycovirus, ssDNA mycovirus reported from Sclerotinia sclerotiorum has significant potential to be used as a biocontrol agent in the fields. Despite several reports on mycoviruses of Sclerotinia, not much could be done to explore its commercial importance. The present review describes the recent developments in the area of mycoviruses of Sclerotinia sclerotiorum and associated biocontrol potential.     

Modulation of T4 gene 32 protein DNA binding activity by the recombination mediator protein UvsY

Bacteriophage T4 UvsY is a recombination mediator protein that promotes assembly of the UvsX-ssDNA presynaptic filament. UvsY helps UvsX to displace T4 gene 32 protein (gp32) from ssDNA, a reaction necessary for proper formation of the presynaptic filament. Here we use DNA stretching to examine UvsY interactions with single DNA molecules in the presence and absence of gp32 and a gp32 C-terminal truncation (*I), and show that in both cases UvsY is able to destabilize gp32-ssDNA interactions. In these experiments UvsY binds more strongly to dsDNA than ssDNA due to its inability to wrap ssDNA at high forces. To support this hypothesis, we show that ssDNA created by exposure of stretched DNA to glyoxal is strongly wrapped by UvsY, but wrapping occurs only at low forces. Our results demonstrate that UvsY interacts strongly with stretched DNA in the absence of other proteins. In the presence of gp32 and *I, UvsY is capable of strongly destabilizing gp32-DNA complexes in order to facilitate ssDNA wrapping, which in turn prepares the ssDNA for presynaptic filament assembly in the presence of UvsX. Thus, UvsY mediates UvsX binding to ssDNA by converting rigid gp32-DNA filaments into a structure that can be strongly bound by UvsX.     

Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method

The C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP) contains a potential RNA-binding region in its N-terminal portion and also serves as a dimerization domain by forming a homodimer with a molecular mass of 28 kDa. So far, the structure determination of the SARS-CoV NP CTD in solution has been impeded by the poor quality of NMR spectra, especially for aromatic resonances. We have recently developed the stereo-array isotope labeling (SAIL) method to overcome the size problem of NMR structure determination by utilizing a protein exclusively composed of stereo- and regio-specifically isotope-labeled amino acids. Here, we employed the SAIL method to determine the high-quality solution structure of the SARS-CoV NP CTD by NMR. The SAIL protein yielded less crowded and better resolved spectra than uniform ¹³C and ¹⁵N labeling, and enabled the homodimeric solution structure of this protein to be determined. The NMR structure is almost identical with the previously solved crystal structure, except for a disordered putative RNA-binding domain at the N-terminus. Studies of the chemical shift perturbations caused by the binding of single-stranded DNA and mutational analyses have identified the disordered region at the N-termini as the prime site for nucleic acid binding. In addition, residues in the β-sheet region also showed significant perturbations. Mapping of the locations of these residues onto the helical model observed in the crystal revealed that these two regions are parts of the interior lining of the positively charged helical groove, supporting the hypothesis that the helical oligomer may form in solution.