Effect of flap modifications on human FEN1 cleavage.

The flap endonuclease, FEN1, plays a critical role in DNA replication and repair. Human FEN1 exhibits both a 5' to 3' exonucleolytic and a structure-specific endonucleolytic activity. On primer-template substrates containing an unannealed 5'-tail, or flap structure, FEN1 employs a unique mechanism to cleave at the point of annealing, releasing the 5'-tail intact. FEN1 appears to track along the full length of the flap from the 5'-end to the point of cleavage. Substrates containing structural modifications to the flap have been used to explore the mechanism of tracking. To determine whether the nuclease must recognize a succession of nucleotides on the flap, chemical linkers were used to replace an interior nucleotide. The nuclease could readily traverse this site. The footprint of the nuclease at the time of cleavage does not extend beyond 25 nucleotides on the flap. Eleven-nucleotide branches attached to the flap beyond the footprinted region do not prevent cleavage. Single- or double-thymine dimers also allow cleavage. cis-Platinum adducts outside the protected region are moderately inhibitory. Platinum-modified branch structures are completely inert to cleavage. These results show that some flap modifications can prevent or inhibit tracking, but the tracking mechanism tolerates a variety of flap modifications. FEN1 has a flexible loop structure through which the flap has been proposed to thread. However, efficient cleavage of branched structures is inconsistent with threading the flap through a hole in the protein.     

Methanogenesis from methanol in Methanosarcina barkeri studied using membrane inlet mass spectrometry

Abstract A mass spectrometer with membrane inlet was used to study methanol metabolism by Methanosarcina barkeri strain MS. The addition of methanol to methanol grown culture samples in the mass spectrometer vessel stimulated methanogenesis and hydrogen production. The apparent K _s for methanol was determined as 0.5 mM and the V _max as 8.14 mmol g (dry weight) h⁻¹. The V _max for methane production was fairly constant during growth of the culture on methanol implying that growth is tightly coupled to methanogenesis. The addition of methanol to culture samples in the mass spectrometer vessel stimulated methanogenesis with no lag which indicated that methanogenesis can be uncoupled from growth. Exposure of the culture sample in the mass spectrometer vessel to an atmosphere of 2 kPa oxygen for 80 min resulted in a decrease in the rate of methanogenesis from methanol but on returning the atmosphere to nitrogen the addition of further methanol stimulated methanogenesis. The effect of other inhibitors of methanogenesis (2-bromoethane sulphonate and monensin); K _j values 21.5 μM and 0.3 mM, respectively) were also studied.     

Revisiting the use of Iprodione and Trichoderma in the integrated management of onion white rot

The biocontrol properties of Trichoderma species are well documented, but their effectiveness in antagonism of the problematic Sclerotium cepivorum, the causal agent of white rot in Allium species, appears limited with reports of significant control only relating to deliberately-mutated strains of Trichoderma. Our previous studies have indicated the possibility of using selected naturally-occurring strains of the antagonist in the suppression of other diseases; now in vitro and controlled environment in vivo studies have indicated that a degree of control of Onion White Rot is possible, and that the selected antagonist strains can be used in integrated treatments with Iprodione to good effect. The possible value of such treatments is considered in light of other approaches to the suppression of this continuing problem.     

A web server to locate periodicities in a sequence

Summary : FT is a tool written in C++, which implements the Fourier analysis method to locate periodicities in aminoacid or DNA sequences. It is provided for free public use on a WWW server with a Java interface. Availability : The server address is http://o2.db. uoa.gr/FT Contact : shamodr@atlas.uoa.gr      

Advantages of using microbial technology over traditional chemical technology in removal of black crusts from stone surfaces of historical monuments

This study compares two cleaning methods, one involving an ammonium carbonate-EDTA mixture and the other involving the sulfate-reducing bacterium Desulfovibrio vulgaris subsp. vulgaris ATCC 29579, for the removal of black crust (containing gypsum) on marble of the Milan Cathedral (Italy). In contrast to the chemical cleaning method, the biological procedure resulted in more homogeneous removal of the surface deposits and preserved the patina noble under the black crust. Whereas both of the treatments converted gypsum to calcite, allowing consolidation, the chemical treatment also formed undesirable sodium sulfate.     

Characterization of composted olive mill wastes to predict potential plant disease suppressiveness

Despite its proven agronomic value, the plant disease suppressive effect of composts from olive waste has not been adequately investigated. In the present study, the disease suppressive potential of two olive waste (OW) composts against soil-borne plant pathogens was investigated. Both OW composts showed sizeable, active microbial populations, which were able to grow actively on chitin and cellulose. In plate inhibition trials, OW compost water extracts (CWEs) exerted a significant inhibitory effect on the growth of the pathogens Fusarium oxysporum f.sp. lycopersici (Fol), Pythium ultimum, Phytophtora infestans, Sclerotina sclerotiorum and Verticillium dahliae; and in pot experiments, the OW composts significantly reduced P. ultimum damping-off and Fol wilt diseases on tomato seedlings. The disease suppressive effect of OW composts seems to be due to the combined effects of suppression phenomena caused by the presence of microorganisms competing for both nutrients and space as well as by the activity of specific antagonistic microorganisms.     

Improved methodology for bioremoval of black crusts on historical stone artworks by use of sulfate-reducing bacteria

An improved methodology to remove black crusts from stone by using Desulfovibrio vulgaris subsp. vulgaris ATCC 29579, a sulfate-reducing bacterium, is presented. The strain removed 98% of the sulfates of the crust in a 45-h treatment. Precipitation of black iron sulfide was avoided using filtration of a medium devoid of iron. Among three cell carriers, Carbogel proved to be superior to both sepiolite and Hydrobiogel-97, as it allowed an easy application of the bacteria, kept the system in a state where microbial activity was maintained, and allowed easy removal of the cells after the treatment.     

Effects of low electric current (LEC) treatment on pure bacterial cultures

AIMS: This research focused on the effects of low electric current (LEC) on the cell viability and metabolic activity of Escherichia coli and Bacillus cereus. METHODS AND RESULTS: Different LEC intensities at fixed amperage were applied, employing either graphite or copper electrode pairs, and the effects were determined by conventional cultural methods and bioindicators. On E. coli, the LEC with graphite electrodes at 5 and 10 mA led to no significant variation, but at 20 and 40 mA there was increasing inhibition of both the enzymatic activities and growth, and a reduction in ATP content. On B. cereus, similar experiments at the lower amperages did not have any inhibitor effects, however, the 40 mA current stimulated growth, ATP content and some enzymatic activities. The LEC treatment using copper electrodes caused, already at 5 mA, inhibition of bacterial growth and metabolic and enzymatic activities in both E. coli and B. cereus. CONCLUSIONS: On the basis of the obtained results using different amperages and electrodes, we can conclude that E. coli seem to be more sensitive compared with B. cereus. SIGNIFICANCE AND IMPACT OF THE STUDY: The study increases the knowledge on LEC treatment effects on the pure bacterial cultures.     

Biocleaning on Cultural Heritage: new frontiers of microbial biotechnologies

Over the last two decades, the biotechnologies applied to Cultural heritage (CH) have become a successful novel alternative to the traditional approaches in the CH conservation and preservation. From these new perspectives, microorganisms and their metabolisms can be used for the safeguarding of artworks. Biocleaning is a field with a growing interest, based on eco-friendly processes and safe procedures, where biological reactions occurring in natural habitats are optimized in artificial conditions with the aim of CH conservation. This represents a new tool and opportunity for the development and improvement of the sector, with a great advantage for the CH conservation-restoration, in terms of safety, effectiveness, costs and environmental sustainability. This review focuses on the use of microbes and enzymes involved in biocleaning of CH artworks. The aim is to provide a comprehensive, critical and chronological view of the scientific works published until now where ‘virtuous’ microorganisms are applied on different CH materials, pointing out strength and drawback of the biocleaning treatments.