Exploring the environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era

The class Kinetoplastea encompasses both free-living and parasitic species from awide range of hosts. Several representatives of this group are responsible for severehuman diseases and for economic losses in agriculture and livestock. While this groupencompasses over 30 genera, most of the available information has been derived fromthe vertebrate pathogenic genera LeishmaniaandTrypanosoma. Recent studies of the previously neglected groups ofKinetoplastea indicated that the actual diversity is much higher than previouslythought. This article discusses the known segment of kinetoplastid diversity and howgene-directed Sanger sequencing and next-generation sequencing methods can help todeepen our knowledge of these interesting protists.     

New sulfate-reducing bacteria isolated from Buryatian alkaline brackish lakes: description of Desulfonatronum buryatense sp. nov

New strains of sulfate-reducing bacteria were isolated from two alkaline brackish lakes located in the Siberian region of Russia, namely in the Southern Transbaikalia, Buriatia. The article presents data describing morphology, physiology, and biochemical characteristics of the isolated strains. These strains Ki4, Ki5, and Su2 were mesophilic and alkaliphilic with optimal growth at pH 8.9, 9.4, and 10.0, respectively. All isolated strains utilized lactate, formate, and ethanol in the presence of sulfate for growth and sulfidogenesis accompanied with formation of acetate and CO₂. Strains Ki5 and Su2 were able to reduce Fe(III). The DNA G + C content in strains Ki4, Ki5 and Su2 was 56.3, 48.8 and 59.6 mol%, respectively. According to phylogenetic analysis of 16S rRNA sequences, the new strains were clustered within the genus Desulfonatronum, and the closest relative D. lacustre Z-7951^T (=DSM 10312^T) showed 99.3–99.6 % similarity. DNA–DNA relatedness values of the strains Ki4, Ki5, and Su2 with D. lacustre Z-7951^T were 89, 53, and 79 %, respectively. Polyphasic taxonomy data suggest that strain Ki5^T is representative of the proposed novel species Desulfonatronum buryatense sp. nov.     

A Reversible Histone H3 Acetylation Cooperates with Mismatch Repair and Replicative Polymerases in Maintaining Genome Stability

Mutations are a major driving force of evolution and genetic disease. In eukaryotes, mutations are produced in the chromatin environment, but the impact of chromatin on mutagenesis is poorly understood. Previous studies have determined that in yeast Saccharomyces cerevisiae, Rtt109-dependent acetylation of histone H3 on K56 is an abundant modification that is introduced in chromatin in S phase and removed by Hst3 and Hst4 in G2/M. We show here that the chromatin deacetylation on histone H3 K56 by Hst3 and Hst4 is required for the suppression of spontaneous gross chromosomal rearrangements, base substitutions, 1-bp insertions/deletions, and complex mutations. The rate of base substitutions in hst3Δ hst4Δ is similar to that in isogenic mismatch repair-deficient msh2Δ mutant. We also provide evidence that H3 K56 acetylation by Rtt109 is important for safeguarding DNA from small insertions/deletions and complex mutations. Furthermore, we reveal that both the deacetylation and acetylation on histone H3 K56 are involved in mutation avoidance mechanisms that cooperate with mismatch repair and the proofreading activities of replicative DNA polymerases in suppressing spontaneous mutagenesis. Our results suggest that cyclic acetylation and deacetylation of chromatin contribute to replication fidelity and play important roles in the protection of nuclear DNA from diverse spontaneous mutations.     

Convective tissue movements play a major role in avian endocardial morphogenesis

Endocardial cells play a critical role in cardiac development and function, forming the innermost layer of the early (tubular) heart, separated from the myocardium by extracellular matrix (ECM). However, knowledge is limited regarding the interactions of cardiac progenitors and surrounding ECM during dramatic tissue rearrangements and concomitant cellular repositioning events that underlie endocardial morphogenesis. By analyzing the movements of immunolabeled ECM components (fibronectin, fibrillin-2) and TIE1 positive endocardial progenitors in time-lapse recordings of quail embryonic development, we demonstrate that the transformation of the primary heart field within the anterior lateral plate mesoderm (LPM) into a tubular heart involves the precise co-movement of primordial endocardial cells with the surrounding ECM. Thus, the ECM of the tubular heart contains filaments that were associated with the anterior LPM at earlier developmental stages. Moreover, endocardial cells exhibit surprisingly little directed active motility, that is, sustained directed movements relative to the surrounding ECM microenvironment. These findings point to the importance of large-scale tissue movements that convect cells to the appropriate positions during cardiac organogenesis.     

DNA polymerases ζ and Rev1 mediate error-prone bypass of non-B DNA structures

DNA polymerase ζ (Pol ζ) and Rev1 are key players in translesion DNA synthesis. The error-prone Pol ζ can also participate in replication of undamaged DNA when the normal replisome is impaired. Here we define the nature of the replication disturbances that trigger the recruitment of error-prone polymerases in the absence of DNA damage and describe the specific roles of Rev1 and Pol ζ in handling these disturbances. We show that Pol ζ/Rev1-dependent mutations occur at sites of replication stalling at short repeated sequences capable of forming hairpin structures. The Rev1 deoxycytidyl transferase can take over the stalled replicative polymerase and incorporate an additional ‘C’ at the hairpin base. Full hairpin bypass often involves template-switching DNA synthesis, subsequent realignment generating multiply mismatched primer termini and extension of these termini by Pol ζ. The postreplicative pathway dependent on polyubiquitylation of proliferating cell nuclear antigen provides a backup mechanism for accurate bypass of these sequences that is primarily used when the Pol ζ/Rev1-dependent pathway is inactive. The results emphasize the pivotal role of noncanonical DNA structures in mutagenesis and reveal the long-sought-after mechanism of complex mutations that represent a unique signature of Pol ζ.     

Effects of organic solvent vapors on the protochlorophyllic complex from etiolated leaves. Conditions for reversible and irreversible destruction]

The spectral properties and the ability of etyolated leaves pigments treated with organic solvent vapours (OS) for phototransformations were studied by measuring low temperature fluorescence spectra (-196 degrees C). Under the effects of OS the fluorescence at 655 nm was gradually decreased and that at 630--640 nm was increased. The effects of OS depended on the partial pressure of OS. The ability of the pigments for phototransformations was decreased with an increase in fluorescence at 630 nm. The emission maximum of fluorescence of the pigment formed in the light was shifted by 10--18 nm towards the shortwave region. Partial reversibility of the destroying effects of diethyl ester was found. A removal of the ester vapours resulted in a relative increase of fluorescence in the etyolated leaves at 640--645 nm and a decrease of the amount of "photo-inactive" pigment. The maximum of fluorescence of the pigment formed in the light was shifted towards the long-wave region (approximately 5 nm) as compared to the leaves irradiated in the presence of the ester. Partial functional reconstitution indicates that at least part of the pigment molecules are able to form a protochlorophyllide (protochlorophyll) -- protein complex, similar to the native one.     

Significance of determining novobiocin sensitivity in the taxonomy of staphylococci

Novobiocin sensitivity of 96 strains belonging to various staphylococcal species was studied. It was noted that Staph. saprophyticus significantly differed from Staph. aureus and Staph. epidermidis with respect to the above antibiotic. The MIC up to 2 micrograms/ml and the growth inhibition zones of 26--35 mm in diameter were characteristic of Staph. aureau and Staph. epidermidis, while the respective figures for most of the strains of Staph. saprophyticus were 32--64 micrograms/ml and 12--17 mm. However, 28 percent of the strains of Staph. saprophyticus did not differ with respect to their movobiocin sensitivity from the other 2 species. It is concluded that the "novobiocin test" may be used for differentiation of staphylococci, within the genera. At the same time it was shown that the method of the paper sensitivity discs compares very favourably with the method of serial dilutions in agar not only because of its simplicity and convenience of manipulation with single strains, but also of the possibility of identifying the population heterogenicity with respect to novobiocin sensitivity.     

Iron-Reducing Microbial Communities of the Lake Baikal Low-Temperature Bottom Sediments

Microbiology - Psychroactive enrichment cultures reducing anthraquinone 2,6-disulfonate (AQDS) and soluble complexes of ferric iron at 5–20°C were isolated from the samples of Lake...     

Immune Checkpoints of the B7 Family. Part 2. Representatives of the B7 Family B7-H3, B7-H4, B7-H5, B7-H6, B7-H7, and ILDR2 and Their Receptors

Russian Journal of Bioorganic Chemistry - Immune checkpoints regulate polarity, strength, and termination of the immune response. The leading roles in these processes are played by molecules of the...