Daily dynamics of cellulase activity in arable soils depending on management practices

The daily dynamics of cellulase activity was studied during 27 days by the cellophane membrane method on soils managed using the conventional high-input farming system (application of mineral fertilizers and pesticides) and the biological conservation farming system (application of organic fertilizers alone) in a microfield experiment. The regular oscillatory dynamics of the cellulase activity were revealed and confirmed by the harmonic (Fourier) analysis. The oscillatory dynamics of the cellulase activity had a self-oscillatory nature and was not directly caused by the disturbing impacts of both the uncontrolled (natural) changes in the temperature and moisture (rainfall) and the controlled ones (the application of different fertilizers). The disturbing impacts affected the oscillation amplitude of the cellulase activity but not the frequency (periods) of the oscillations. The periodic oscillations of the cellulase activity were more significant in the soil under the high-input management compared to the soil under the biological farming syste

Organo-mineral imprints in fossil cyanobacterial mats of an Antarctic lake

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ALKALOHALOPHILIC BACTERIA OF THE FAMILY BACILLACEAE IN THE LAKES OF THE BADAIN JARAN DESERT (CHINA)

The Badain Jaran desert is located in the western part of Inner Mongolia (China) in the Alashan Highland. The investigated soda-salt lakes combine high pH (more than 9) and mineralization (up to 400 g/dm3), where conditions for the development of an alkali-halophilic microbial community are created. The purpose of our work was to isolate and study pure alkali-halophilic microorganisms in the lakes of the Badain Jaran desert. From the accumulative cultures of the cortex salt and the microbial mats of the lakes of the Badain Jaran desert, pure cultures belonging to the family Bacillaceae (the phylum Firmicutes) were isolated and described. With the help of biochemical methods, the ecological and physiological properties of the isolated bacteria were determined. The isolated bacteria exhibit the properties of alkalophiles and obligate alkalophiles and develop at pH 7–10.5, the optima ranging from 9 to 10. With respect to the concentration of NaCl, the strains showed the properties of obligate halophiles and extreme halophiles. With respect to temperature, the isolated microorganisms are mesophiles growing at 10–50 °C, the optimal growth being at 30–40 °C. With respect to the substrates used, the isolated cultures are noted for extensive metabolic activity and, when in their natural habitats, are supposedly active participants of the destruction of organic matter. To study the hydrochemical indicators of water, the following methods were used: atomic emission spectrometry with inductively coupled plasma, ion chromatography and capillary electrophoresis. As a result, it was found that a sodium cation and anions of carbonate, bicarbonate of chlorine and sulphate dominate in the soda-salt lakes of the Badain Jaran desert in a multicomponent composition. The results obtained broaden the notion of the diversity and ecological significance of bacteria in the extreme natural ecosystems of the Badain Jaran desert. The isolated strains are of interest for biotechnology as producers of enzymes resistant to high pH and mineralization

Inter-subunit interactions that coordinate Rad51's activities

Rad51 is the central catalyst of homologous recombination in eukaryotes and is thus critical for maintaining genomic integrity. Recent crystal structures of filaments formed by Rad51 and the closely related archeal RadA and eubacterial RecA proteins place the ATPase site at the protomeric interface. To test the relevance of this feature, we mutated conserved residues at this interface and examined their effects on key activities of Rad51: ssDNA-stimulated ATP hydrolysis, DNA binding, polymerization on DNA substrates and catalysis of strand-exchange reactions. Our results show that the interface seen in the crystal structures is very important for nucleoprotein filament formation. H352 and R357 of yeast Rad51 are essential for assembling the catalytically competent form of the enzyme on DNA substrates and coordinating its activities. However, contrary to some previous suggestions, neither of these residues is critical for ATP hydrolysis

Description of a new species of soil algae, Parietochloris grandis sp. nov., and study of its fatty acid profiles under different culturing conditions

© 2018 Elsevier B.V. The new species Parietochloris grandis sp. nov. is described from forest soil in the Dnipropetrovsk region, Ukraine. The description is based on morphological features and the phylogenetic analysis of partial SSU rDNA and rbcL genes. Phylogenetic analysis places P. grandis in the Parietochloris clade, within the family Trebouxiophyceae. The novel strain formed a strongly supported monophyletic lineage with the type species of Parietochloris, P. alveolaris. P. grandis differed from other species in the Parietochloris clade by the size and form of vegetative cells and the large number of zoospores in zoosporangia. A number of experiments with different phosphates and nitrates concentrations were conducted to evaluate changes in fatty acid profile and biomass. The dominant fatty acids during cultivation on standard BG-11 medium, as well as with the phosphates concentrations ranged from 0.22 to 2 mM, were linoleic acid (24–25%), palmitic acid (12–14%), linolenic acid (9–12%), and oleic acid (7–11%). The content of arachidonic acid and eicosapentaenoic acid ranged from 3.5 to 4.5% and 0.7% to 0.8%, respectively. The fatty acid profile and total fatty acids varied significantly under different nutrient deficiency. The greatest variation was found for oleic acid (9–46%) and linolenic acid (2–13%). The percentage of arachidonic acid was the highest with a standard nitrates concentration in the medium (5%) and the lowest in the absence of phosphates and nitrates (1.3–1.5%), but the absolute content in dry biomass was similar in all variants of the experiment (6.5–9.3 mg g−1 dry weight). The absence of nitrogen and both nitrogen and phosphorus led to a 3–fold increase in TFA in comparison with the control. Thus, this strain can be considered in biotechnological application as a potential producer of the essential linoleic acid or oleic acid

The conserved Fanconi anemia nuclease Fan1 and the SUMO E3 ligase Pli1 act in two novel Pso2-independent pathways of DNA interstrand crosslink repair in yeast

DNA interstrand cross-links (ICLs) represent a physical barrier to the progression of cellular machinery involved in DNA metabolism. Thus, this type of adduct represents a serious threat to genomic stability and as such, several DNA repair pathways have evolved in both higher and lower eukaryotes to identify this type of damage and restore the integrity of the genetic material. Human cells possess a specialized ICL-repair system, the Fanconi anemia (FA) pathway. Conversely yeasts rely on the concerted action of several DNA repair systems. Recent work in higher eukaryotes identified and characterized a novel conserved FA component, FAN1 (Fanconi anemia-associated nuclease 1, or FANCD2/FANCI-associated nuclease 1). In this study, we characterize Fan1 in the yeast Schizosaccharomyces pombe. Using standard genetics, we demonstrate that Fan1 is a key component of a previously unidentified ICL-resolution pathway. Using high-throughput synthetic genetic arrays, we also demonstrate the existence of a third pathway of ICL repair, dependent on the SUMO E3 ligase Pli1. Finally, using sequence-threaded homology models, we predict and validate key residues essential for Fan1 activity in ICL repair

Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach

We have developed a novel DNA microarray-based approach for identification of the sequence-specificity of single-stranded nucleic-acid-binding proteins (SNABPs). For verification, we have shown that the major cold shock protein (CspB) from Bacillus subtilis binds with high affinity to pyrimidine-rich sequences, with a binding preference for the consensus sequence, 5′-GTCTTTG/T-3′. The sequence was modelled onto the known structure of CspB and a cytosine-binding pocket was identified, which explains the strong preference for a cytosine base at position 3. This microarray method offers a rapid high-throughput approach for determining the specificity and strength of ss DNA–protein interactions. Further screening of this newly emerging family of transcription factors will help provide an insight into their cellular function

Real-time assembly and disassembly of human RAD51 filaments on individual DNA molecules

The human DNA repair protein RAD51 is the crucial component of helical nucleoprotein filaments that drive homologous recombination. The molecular mechanistic details of how this structure facilitates the requisite DNA strand rearrangements are not known but must involve dynamic interactions between RAD51 and DNA. Here, we report the real-time kinetics of human RAD51 filament assembly and disassembly on individual molecules of both single- and double-stranded DNA, as measured using magnetic tweezers. The relative rates of nucleation and filament extension are such that the observed filament formation consists of multiple nucleation events that are in competition with each other. For varying concentration of RAD51, a Hill coefficient of 4.3 ± 0.5 is obtained for both nucleation and filament extension, indicating binding to dsDNA with a binding unit consisting of multiple (≥4) RAD51 monomers. We report Monte Carlo simulations that fit the (dis)assembly data very well. The results show that, surprisingly, human RAD51 does not form long continuous filaments on DNA. Instead each nucleoprotein filament consists of a string of many small filament patches that are only a few tens of monomers long. The high flexibility and dynamic nature of this arrangement is likely to facilitate strand exchange

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

We have achieved the ability to synthesize thousands of unique, long oligonucleotides (150mers) in fmol amounts using parallel synthesis of DNA on microarrays. The sequence accuracy of the oligonucleotides in such large-scale syntheses has been limited by the yields and side reactions of the DNA synthesis process used. While there has been significant demand for libraries of long oligos (150mer and more), the yields in conventional DNA synthesis and the associated side reactions have previously limited the availability of oligonucleotide pools to lengths <100 nt. Using novel array based depurination assays, we show that the depurination side reaction is the limiting factor for the synthesis of libraries of long oligonucleotides on Agilent Technologies’ SurePrint® DNA microarray platform. We also demonstrate how depurination can be controlled and reduced by a novel detritylation process to enable the synthesis of high quality, long (150mer) oligonucleotide libraries and we report the characterization of synthesis efficiency for such libraries. Oligonucleotide libraries prepared with this method have changed the economics and availability of several existing applications (e.g. targeted resequencing, preparation of shRNA libraries, site-directed mutagenesis), and have the potential to enable even more novel applications (e.g. high-complexity synthetic biology)