N‐acetylcysteine increases susceptibility of HeLa cells to bacterial invasion

Serratia grimesii are non‐pathogenic bacteria capable, however, to invade eukaryotic cells provided that they synthesize intracellular metalloprotease grimelysin (Bozhokina et al. [2011] Cell. Biol. Int. 35: 111–118). To elucidate how invasion of grimelysin containing bacteria depends on physiological state of host cells, we studied the effect of N‐acetylcysteine (NAC) on susceptibility of HeLa cells to invasion by the wild‐type S. grimesii and recombinant E. coli expressing grimelysin gene. Incubation of HeLa cells with 10 mM NAC resulted in changes of cell morphology and disassembly of actin cytoskeleton that were reversed when NAC was removed from the culture medium. Both in the presence of NAC and upon its removal, the entry of grimelysin producing bacteria increased by a factor of 1.5–2 and 3–3.5 for wild‐type S. grimesii and recombinant E. coli, respectively. This effect does not correlate with cytoskeleton rearrangements but may be due to the NAC‐induced up‐regulation of cell surface receptors playing a role in cell adhesion and cell–cell junctions. A twofold difference in the efficiency of S. grimesii and recombinant E. coli to enter the NAC‐treated cells suggests that the entry of the wild‐type and recombinant bacteria occurs via different receptors which activity is differently affected by NAC. J. Cell. Biochem. 114: 1568–1574, 2013. © 2013 Wiley Periodicals, Inc.     

Complexes assembled from TMV-derived spherical particles and entire virions of heterogeneous nature

Previously, we described some structural features of spherical particles (SPs) generated by thermal remodelling of the tobacco mosaic virus. The SPs represent a universal platform that could bind various proteins. Here, we report that entire isometric virions of heterogeneous nature bind non-specifically to the SPs. Formaldehyde (FA) was used for covalent binding of a virus to the SPs surface for stabilizing the SP—virus complexes. Transmission and high resolution scanning electron microscopy showed that the SPs surface was covered with virus particles. The architecture of SP–virion complexes was examined by immunologic methods. Mean diameters of SPs and SP–human enterovirus C and SP–cauliflower mosaic virus (CaMV) compositions were determined by nanoparticle tracking analysis (NTA) in liquid. Significantly, neither free SPs nor individual virions were detected by NTA in either FA-crosslinked or FA-untreated compositions. Entirely, all virions were bound to the SPs surface and the SP sites within the SP–CaMV complexes were inaccessible for anti-SP antibodies. Likewise, the SPs immunogenicity within the FA-treated SPs–CaMV compositions was negligible. Apparently, the SP antigenic sites were hidden and masked by virions within the compositions. Previously, we reported that the SPs exhibited adjuvant activity when foreign proteins/epitopes were mixed with or crosslinked to SPs. We found that immunogenicity of entire CaMV crosslinked to SP was rather low which could be due to the above-mentioned masking of the SPs booster. Contrastingly, immunogenicity of the FA-untreated compositions increased significantly, presumably, due to partial release of virions and unmasking of some SPs-buster sites after animals immunization.     

Permafrost and fire as regulators of stream chemistry in basins of the Central Siberian Plateau

Stream chemistry in permafrost regions is regulated by a variety of drivers that affect hydrologic flowpaths and watershed carbon and nutrient dynamics. Here we examine the extent to which seasonal dynamics of soil active layer thickness and wildfires regulate solute concentration in streams of the continuous permafrost region of the Central Siberian Plateau. Samples were collected from 2006 to 2012 during the frost-free season (May–September) from sixteen watersheds with fire histories ranging from 3 to 120 years. The influence of permafrost was evident through significantly higher dissolved organic carbon (DOC) concentrations in the spring, when only the organic soil horizon was accessible to runoff. As the active layer deepened through the growing season, water was routed deeper through the underlying mineral horizon where DOC underwent adsorption and concentrations decreased. In contrast, mean concentrations of major cations (Ca²⁺ > Na⁺ > Mg²⁺ > K⁺) were significantly higher in the summer, when contact with mineral horizons in the active zone provided a source of cations. Wildfire caused significantly lower concentrations of DOC in more recently burned watersheds, due to removal of a source of DOC through combustion of the organic layer. An opposite trend was observed for dissolved inorganic carbon and major cations in more recently burned watersheds. There was also indication of talik presence in three of the larger watersheds evidenced by Cl^? concentrations that were ten times higher than those of other watersheds. Because climate change affects both fire recurrence intervals as well as rates of permafrost degradation, delineating their combined effects on solute concentration allows forecasting of the evolution of biogeochemical cycles in this region in the future.     

Globally consistent climate sensitivity of natural disturbances across boreal and temperate forest ecosystems

Disturbance regimes are changing in forests across the world in response to global climate change. Despite the profound impacts of disturbances on ecosystem services and biodiversity, assessments of disturbances at the global scale remain scarce. Here, we analyzed natural disturbances in boreal and temperate forest ecosystems for the period 2001–2014, aiming to 1) quantify their within- and between-biome variation and 2) compare the climate sensitivity of disturbances across biomes. We studied 103 unmanaged forest landscapes with a total land area of 28.2 × 10⁶ ha, distributed across five continents. A consistent and comprehensive quantification of disturbances was derived by combining satellite-based disturbance maps with local expert knowledge of disturbance agents. We used Gaussian finite mixture models to identify clusters of landscapes with similar disturbance activity as indicated by the percent forest area disturbed as well as the size, edge density and perimeter–area-ratio of disturbed patches. The climate sensitivity of disturbances was analyzed using Bayesian generalized linear mixed effect models and a globally consistent climate dataset. Within-biome variation in natural disturbances was high in both boreal and temperate biomes, and disturbance patterns did not vary systematically with latitude or biome. The emergent clusters of disturbance activity in the boreal zone were similar to those in the temperate zone, but boreal landscapes were more likely to experience high disturbance activity than their temperate counterparts. Across both biomes high disturbance activity was particularly associated with wildfire, and was consistently linked to years with warmer and drier than average conditions. Natural disturbances are a key driver of variability in boreal and temperate forest ecosystems, with high similarity in the disturbance patterns between both biomes. The universally high climate sensitivity of disturbances across boreal and temperate ecosystems indicates that future climate change could substantially increase disturbance activity.     

Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids.

The evolution of 2 tandemly repeated sequences Spelt1 and Spelt52 was studied in Triticum species representing 2 evolutionary lineages of wheat and in Aegilops sect. Sitopsis, putative donors of their B/G genomes. Using fluorescence in situ hybridization we observed considerable polymorphisms in the hybridization patterns of Spelt1 and Spelt52 repeats between and within Triticum and Aegilops species. Between 2 and 28 subtelomeric sites of Spelt1 probe were detected in Ae. speltoidies, depending on accession. From 8 to 12 Spelt1 subtelomeric sites were observed in species of Timopheevi group (GAt genome), whereas the number of signals in emmer/aestivum accessions was significantly less (from 0 to 6). Hybridization patterns of Spelt52 in Ae. speltoides, Ae. longissima, and Ae. sharonensis were species specific. Subtelomeric sites of Spelt52 repeat were detected only in T. araraticum (T. timopheevii), and their number and chromosomal location varied between accessions. Superimposing copy number data onto our phylogenetic scheme constructed from RAPD data suggests 2 major independent amplifications of Spelt52 and 1 of Spelt1 repeats in Aegilops divergence. It is likely that the Spelt1 amplification took place in the ancient Ae. speltoides before the divergence of polyploid wheats. The Spelt52 repeat was probably amplified in the lineage of Ae. speltoides prior to divergence of the allopolyploid T. timopheevii but after the divergence of T. durum. In a separate amplification event, Spelt52 copy number expanded in the common ancestor of Ae. longissima and Ae. sharonensis.     

The genomic underpinnings of apoptosis in Strongylocentrotus purpuratus

Programmed cell death through apoptosis is a pan-metazoan character involving intermolecular signaling networks that have undergone substantial lineage-specific evolution. A survey of apoptosis-related proteins encoded in the sea urchin genome provides insight into this evolution while revealing some interesting novelties, which we highlight here. First, in addition to a typical CARD-carrying Apaf-1 homologue, sea urchins have at least two novel Apaf-1-like proteins that are each linked to a death domain, suggesting that echinoderms have evolved unique apoptotic signaling pathways. Second, sea urchins have an unusually large number of caspases. While the set of effector caspases (caspases-3/7 and caspase-6) in sea urchins is similar to that found in other basal deuterostomes, signal-responsive initiator caspase subfamilies (caspases-8/10 and 9, which are respectively linked to DED and CARD adaptor domains) have undergone echinoderm-specific expansions. In addition, there are two groups of divergent caspases, one distantly related to the vertebrate interleukin converting enzyme (ICE)-like subfamily, and a large clan that does not cluster with any of the vertebrate caspases. Third, the complexity of proteins containing an anti-apoptotic BIR domain and of Bcl-2 family members approaches that of vertebrates, and is greater than that found in protostome model systems such as Drosophila or Caenorhabditis elegans. Finally, the presence of Death receptor homologues, previously known only in vertebrates, in both Strongylocentrotus purpuratus and Nematostella vectensis suggests that this family of apoptotic signaling proteins evolved early in animals and was subsequently lost in the nematode and arthropod lineage(s). Our results suggest that cell survival is contingent upon a diverse array of signals in sea urchins, more comparable in complexity to vertebrates than to arthropods or nematodes, but also with unique features that may relate to specific requirements imposed by the biphasic life cycle and/or immunological idiosyncrasies of this organism.     

Forces driving the binding of homeodomains to DNA

Homeodomains are helix-turn-helix type DNA-binding domains that exhibit sequence-specific DNA binding by insertion of their "recognition" alpha helices into the major groove and a short N-terminal arm into the adjacent minor groove without inducing substantial distortion of the DNA. The stability and DNA binding of four representatives of this family, MATalpha2, engrailed, Antennapedia, and NK-2, and truncated forms of the last two lacking their N-terminal arms have been studied by a combination of optical and microcalorimetric methods at different temperatures and salt concentrations. It was found that the stability of the free homeodomains in solution is rather low and, surprisingly, is reduced by the presence of the N-terminal arm for the Antennapedia and NK-2 domains. Their stabilities depend significantly upon the presence of salt: strongly for NaCl but less so for NaF, demonstrating specific interactions with chloride ions. The enthalpies of association of the homeodomains with their cognate DNAs are negative, at 20 degrees C varying only between -12 and -26 kJ/mol for the intact homeodomains, and the entropies of association are positive; i.e., DNA binding is both enthalpy- and entropy-driven. Analysis of the salt dependence of the association constants showed that the electrostatic component of the Gibbs energy of association resulting from the entropy of mixing of released ions dominates the binding, being about twice the magnitude of the nonelectrostatic component that results from dehydration of the protein/DNA interface, van der Waals interactions, and hydrogen bonding. A comparison of the effects of NaCl/KCl with NaF showed that homeodomain binding results in a release not only of cations from the DNA phosphates but also of chloride ions specifically associated with the proteins. The binding of the basic N-terminal arms in the minor groove is entirely enthalpic with a negative heat capacity effect, i.e., is due to sequence-specific formation of hydrogen bonds and hydrophobic interactions rather than electrostatic contacts with the DNA phosphates.     

Diindolilmethane (DIM) selectively inhibits cancer stem cells

Epidemiologic studies repeatedly have shown chemopreventive effects of cruciferous vegetables. Indole-3-carbinol (I3C) and its metabolite diindolylmethane (DIM) were identified in these plants as active ingredients and theirs anti-tumor activities were confirmed in multiple in vitro and in vivo experiments. Here, we demonstrate that DIM is a selective and potent inhibitor of cancer stem cells (CSCs). In several cancer cell lines, DIM inhibited tumor sphere formation at the concentrations 30-300 times lower than concentrations required for growth inhibition of parental cells cultured as adherent culture. We also found that treatment with DIM overcomes chemoresistance of CSCs to cytotoxics, such as paclitaxel, doxorubicin, and SN-38. Pre-treatment of tumor spheres with DIM before implantation to mice significantly retarded the growth of primary tumors compared to tumors formed by untreated tumor spheres. The concentrations of DIM required to suppress CSCs formation are in the close range to those achievable in human plasma after oral dosing of the compound. Therefore, DIM can potentially be used in cancer patients, either alone, or in combinations with existing drugs.