Dark matter in archaeal genomes: a rich source of novel mobile elements,defense systems and secretory complexes

Microbial genomes encompass a sizable fraction of poorly characterized, narrowly spread fast-evolving genes. Using sensitive methods for sequences comparison and protein structure prediction, we performed a detailed comparative analysis of clusters of such genes, which we denote “dark matter islands”, in archaeal genomes. The dark matter islands comprise up to 20 % of archaeal genomes and show remarkable heterogeneity and diversity. Nevertheless, three classes of entities are common in these genomic loci: (a) integrated viral genomes and other mobile elements; (b) defense systems, and (c) secretory and other membrane-associated systems. The dark matter islands in the genome of thermophiles and mesophiles show similar general trends of gene content, but thermophiles are substantially enriched in predicted membrane proteins whereas mesophiles have a greater proportion of recognizable mobile elements. Based on this analysis, we predict the existence of several novel groups of viruses and mobile elements, previously unnoticed variants of CRISPR-Cas immune systems, and new secretory systems that might be involved in stress response, intermicrobial conflicts and biogenesis of novel, uncharacterized membrane structures.     

Dynamics of abundance of antifungal strains of Pseudomonas in the rhizosphere of hydroponic cucumbers grown on greenhouse mineral substrate

Data were obtained on the dynamics of the abundance of the biocontrol strains of Pseudomonas chlororaphis SPB1217 and Pseudomonas fluorescens SPB2137 with antifungal activity. These strains are able to develop in the rhizosphere of cucumbers grown on mineral substrate under hydroponic conditions in industrial greenhouses. After four weeks of vegetation of plants, the abundance of the inoculated strains was 19-28% of the total bacterial numbers determined by inoculation onto solid medium. The investigated strains spread together with the young, actively growing and exudating roots; they reached a stable level of abundance in deep layers of the greenhouse substrate. A significant difference in the abundance of fungi in the tested variants was observed after 20 days of vegetation: the abundance of fungi in the control was two times higher than in the variant inoculated with strain SPB2137.     

Genetic polymorphism in GST, NAT2, and MTRR and susceptibility to childhood acute leukemia

It is known that presence of xenobiotic-metabolizing gene polymorphisms in some cases correlates with hereditary predisposition to the oncological diseases. In the present work the frequencies of xenobiotic-metabolizing gene polymorphisms in 332 children with the diagnosis acute lymphoblastic leukemia (ALL), 71 children with the diagnosis acute myeloblastic leukemia (AML) and 490 healthy donors have been determined using allele-specific hybridization on the biochip. Statistically significant increase in the frequency of GSTT1 "null" genotype (OR = 1.9, p = 4.7E-5) and GSTT1/GSTM1 double "null" genotype (OR = 3.1, p = 2.5E-8) in children with acute leukemia relative to healthy donors group has been revealed. Also 1.8-fold increase in the frequency of NAT2 genotype 341T/T, 481C/C, 590G/G in children with acute leukemia relative to healthy donors group (p = 0.026) has been recognized. Analysis of gene-gene interactions has showed that in patients with acute leukemia genotype NAT2 341T/T, 481C/C, 590G/G in combination with GSTT1 "null" and/or GSTM1 "null" genotype is significantly more frequent than in population control. Besides the reduction of MTRR genotype 66G/G frequency in girls with acute leukemia relative to female healthy donors has been found (OR = 0.50, p = 0.0015). Analysis of gene-gene interactions has shown that the presence of GSTT1 "null" and/or GSTM1 "null" genotype in combination with MTRR genotype 66A/- may consider as risk factor of acute leukemia in girls. Thus, the studied polymorphic variants of genes GSTT1, GSTM1, NAT2 and MTRR can modulate the risk of childhood acute leukemia, residents of European part of Russia.     

Possible pathways for destruction of polyaromatic hydrocarbons by some oil-degrading bacteria isolated from plant endosphere and rhizosphere

Six strains of oil-degrading bacteria isolated from the endosphere and rhizosphere of plants growing on oil polluted soils of the Irkutsk region were studied to determine the pathways for biodestruction of polyaromatic oil hydrocarbons. All strains were able to efficiently degrade polyaromatic hydrocarbons with the formation of pyrocatechin as a final product; strains 90, 108, and 112 additionally formed protocathechuic acid. The culture broth of the studied strains contained ferulic, n-coumaric, n-oxybenzoic, vanillic, and lilac acids, which probably represent metabolites of cinnamic alcohol, cinnamic aldehyde, and benzoic acid presenting in oil and metabolized by bacteria.     

Interaction of Rhizospheric Bacteria and Nonrhizobial Endophytic Bacteria Moving from the Roots to the Rhizosphere of Pea Plants (Pisum sativum)

Applied Biochemistry and Microbiology - Six of 11 strains of endophytic bacteria from pea (Pisum sativum L.) seeds were found in an aqueous medium of seedling-root growth under hydroculture...     

Morphology and electrostatics play active role in neuronal differentiation processes on flexible conducting substrates

This commentary discusses and summarizes the key highlights of our recently reported work entitled “Neuronal Differentiation of Embryonic Stem Cell Derived Neuronal Progenitors Can Be Regulated by Stretchable Conducting Polymers.” The prospect of controlling the mechanical-rigidity and the surface conductance properties offers a unique combination for tailoring the growth and differentiation of neuronal cells. We emphasize the utility of transparent elastomeric substrates with coatings of electrically conducting polymer to realize the desired substrate-characteristics for cellular development processes. Our study showed that neuronal differentiation from ES cells is highly influenced by the specific substrates on which they are growing. Thus, our results provide a better strategy for regulated neuronal differentiation by using such functional conducting surfaces.     

Beetles (Insecta,Coleoptera) in the arctic fauna: Communication 1. Faunal composition

Coleoptera, the largest insect order, appears to be subordinate to Diptera in the extent of colonization of the Arctic environment. Beetles comprise about 13% of the insect fauna of the tundra zone, yet in the high latitudes several of their families retain considerable levels of species diversity and play significant cenotic roles. The present communication reviews the circumpolar beetle fauna of the Arctic. Based on original data, literature sources and museum collections, with the use of extrapolations and analogies, the taxonomic and ecological diversity patterns of the suborders, series and families of Coleoptera are distinguished, the latitude-zonal distribution and the northernmost range limits of the species are analyzed, and their adaptations and cenotic relations are characterized.     

RNA-binding properties of the plant protein Nt-4/1

The tobacco α-helical protein Nt-4/1 with unknown function forms ribonucleoprotein (RNP) complexes in vitro. Results obtained by retardation of RNP complexes in agarose gel were confirmed by Western-Northern hybridization. Several deletion and point mutants of Nt-4/1 were constructed, and the RNA-binding site was mapped in a positively charged region of the C-terminal domain of the protein. The results of this study and those described earlier support our hypothesis of the participation of Nt-4/1 protein in spreading RNA-containing pathogens in the plant.