Hyperfine Interactions in the NV-13C Quantum Registers in Diamond Grown from the Azaadamantane Seed.

Nanostructured diamonds hosting optically active paramagnetic color centers (NV, SiV, GeV, etc.) and hyperfine-coupled with them quantum memory 13C nuclear spins situated in diamond lattice are currently of great interest to implement emerging quantum technologies (quantum information processing, quantum sensing and metrology). Current methods of creation such as electronic-nuclear spin systems are inherently probabilistic with respect to mutual location of color center electronic spin and 13C nuclear spins. A new bottom-up approach to fabricate such systems is to synthesize first chemically appropriate diamond-like organic molecules containing desired isotopic constituents in definite positions and then use them as a seed for diamond growth to produce macroscopic diamonds, subsequently creating vacancy-related color centers in them. In particular, diamonds incorporating coupled NV-13C spin systems (quantum registers) with specific mutual arrangements of NV and 13C can be obtained from anisotopic azaadamantane molecule. Here we predict the characteristics of hyperfine interactions (hfi) for the NV-13C systems in diamonds grown from various isotopically substituted azaadamantane molecules differing in 13C position in the seed, as well as the orientation of the NV center in the post-obtained diamond. We used the spatial and hfi data simulated earlier for the H-terminated cluster C510[NV]-H252. The data obtained can be used to identify (and correlate with the seed used) the specific NV-13C spin system by measuring, e.g., the hfi-induced splitting of the mS = ±1 sublevels of the NV center in optically detected magnetic resonance (ODMR) spectra being characteristic for various NV-13C systems.

Flax (Linum usitatissimum L.) response to non-optimal soil acidity and zinc deficiency.

BACKGROUND: Flax (Linum usitatissimum L.) is grown for fiber and seed production. Unfavorable environments, such as nutrient deficiency and non-optimal soil acidity, decrease the quantity and quality of yield. Cultivation of tolerant to stress varieties can significantly reduce the crop losses. Understanding the mechanisms of flax response to the stresses and identification of resistance gene candidates will help in breeding of improved cultivars. In the present work, the response of flax plants to increased pH level and zinc (Zn) deficiency was studied. RESULTS: We performed high-throughput transcriptome sequencing of two flax cultivars with diverse tolerance to increased pH level and Zn deficiency: Norlin (tolerant) and Mogilevsky (sensitive). Sixteen cDNA libraries were created from flax plants grown under control conditions, increased pH level, Zn deficiency, and both stresses simultaneously, and about 35 million reads were obtained for each experiment type. Unfavorable pH resulted in significantly stronger gene expression alterations compared to Zn deficiency. Ion homeostasis, oxidoreductase activity, cell wall, and response to stress Gene Ontology terms were the most affected by unfavorable pH and Zn deficiency both in tolerant and sensitive flax cultivars. Upregulation of genes encoding metal transporters was identified under increased pH level, Zn deficiency, and both stresses simultaneously. Under Zn deficiency, only in tolerant cultivar Norlin, we revealed the induction of several photosynthesis-related genes and, in this way, this tolerant genotype could overcome unfavorable effects of reduced Zn content. CONCLUSIONS: We identified genes with expression alterations in flax under non-optimal soil acidity and Zn deficiency based on high-throughput sequencing data. These genes are involved in diverse processes, including ion transport, cell wall biogenesis, and photosynthesis, and could play an important role in flax response to the studied stresses. Moreover, genes with distinct expression changes between examined tolerant and sensitive genotypes could determine the mechanisms of flax tolerance to non-optimal soil acidity and Zn deficiency.

Evidence of T-helper cell 2 cytokine regulation of chronic otitis media with effusion.

Cytokine and cellular patterns of effusions may reflect stages of middle ear inflammation. The local interplay between IL-2 and -4 is likely to play a crucial role in the switching of inflammation in the chronic stage. The T-helper cell 2 (Th2) cytokines IL-4, -5 and -13 and the Th2/Th1 cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) regulate the cellular and molecular processes of chronic inflammation in the middle ear and therefore the chronic condition of otitis media with effusion (OME). Early identification of the cytokine and cellular patterns of effusions can be helpful in directing the clinical treatment of OME.We hypothesized that IL-2 and the group of Th2 cytokines regulate chronic inflammation in the middle ear and chronic OME. Effusions from children with persistent OME were analysed to determine the presence of cytokines (the Th1 cytokine IL-2, the Th2 cytokines IL-4, -5 and -13 and the Th1/Th2 cytokine GM-CSF), inflammatory cells (CD4+ T cells, eosinophils, macrophages and neutrophils) and mucin. Cytokines were evaluated by means of a quantitative "sandwich"-type ELISA, inflammatory cells by means of alkaline phosphatase-anti-alkaline phosphatase immunocytostaining and mucin by means of a modified periodic acid-Schiff method based on a slot-blot technique. The cytokine pattern in effusions varied from patient to patient. GM-CSF correlated positively and IL-4 inversely with IL-2 and the increased level of IL-4 may have had an inhibitory effect on IL-2. IL-5 and -13 correlated with IL-4. Inflammatory cells correlated with cytokines as follows: CD4+ T cells with IL-2 and -4; macrophages and neutrophils with GM-CSF; and eosinophils with IL-5. Some cytokine-cellular correlations in effusions were reflected at the clinical level. The mucin content of effusions correlated with the concentrations of IL-4 (>10 pg/ml) and -13, suggesting involvement of IL-4 and -13 in upregulation of the middle ear mucin metabolism.

The immunoregulatory and allergy-associated cytokines in the aetiology of the otitis media with effusion.

Inflammation in the middle ear mucosa, which can be provoked by different primary factors such as bacterial and viral infection, local allergic reactions and reflux, is the crucial event in the pathogenesis of otitis media with effusion (OME). Unresolved acute inflammatory responses or defective immunoregulation of middle inflammation can promote chronic inflammatory processes and stimulate the chronic condition of OME. Cytokines are the central molecular regulators of middle ear inflammation and can switch the acute phase of inflammation in the chronic stage and induce molecular-pathological processes leading to the histopathological changes accompanying OME. In this review we present cytokines identified in otitis media, immunoregulatory [interleukin (IL)-2, IL-10, transforming growth factor-beta]) and allergy associated (IL-4, IL-5, granulocyte-macrophage colony-stimulating factor), as crucial molecular regulators, responsible for chronic inflammation in the middle ear and the chronic condition of OME.

Effects of tumor-associated mutations on Rad54 functions.

Yeast RAD54 gene, a member of the RAD52 epistasis group, plays an important role in homologous recombination and DNA double strand break repair. Rad54 belongs to the Snf2/Swi2 protein family, and it possesses a robust DNA-dependent ATPase activity, uses free energy from ATP hydrolysis to supercoil DNA, and cooperates with the Rad51 recombinase in DNA joint formation. There are two RAD54-homologous genes in human cells, hRAD54 and RAD54B. Mutations in these human genes have been found in tumors. These tumor-associated mutations map to conserved regions of the hRad54 and hRad54B proteins. Here we introduced the equivalent mutations into the Saccharomyces cerevisiae RAD54 gene in an effort to examine the functional consequences of these gene changes. One mutant, rad54 G484R, showed sensitivity to DNA-damaging agents and reduced homologous recombination rates, indicating a loss of function. Even though the purified rad54 G484R mutant protein retained the ability to bind DNA and interact with Rad51, it was nearly devoid of ATPase activity and was similarly defective in DNA supercoiling and D-loop formation. Two other mutants, rad54 N616S and rad54 D442Y, were not sensitive to genotoxic agents and behaved like the wild type allele in homologous recombination assays. Consistent with the mild phenotype associated with the rad54 N616S allele, its encoded protein was similar to wild type Rad54 protein in biochemical attributes. Because dysfunctional homologous recombination gives rise to genome instability, our results are consistent with the premise that tumor-associated mutations in hRad54 and Rad54B could contribute to the tumor phenotype or enhance the genome instability seen in tumor cells.

Role of the error-free damage bypass postreplication repair pathway in the maintenance of genomic stability.

The postreplication repair pathway (PRR) is composed of error-free and error-prone sub-pathways that allow bypass of DNA damage-induced replication-blocking lesions. The error-free sub-pathway is also used for bypass of spontaneous DNA damage and functions in cooperation with recombination pathways. In diploid yeast cells, error-free PRR is needed to prevent genomic instability, which is manifest as loss of heterozygosity (LOH) events of increased chromosome loss and recombination. Homologous recombination acts synergistically with the error-free damage avoidance branch of PRR to prevent chromosome loss. The DNA damage checkpoint gene MEC1 acts synergistically with the PRR pathway in maintaining genomic stability. Integration of the PRR pathway with other cellular pathways for preventing genomic instability is discussed. In diploid strains, the most dramatic increase is in the abnormality of chromosome loss when a repair or damage detection pathway is defective.

LPS up-regulates mucin and cytokine mRNA expression and stimulates mucin and cytokine secretion in goblet cells.

Bacterial inflammation in mucosa is accompanied by morphological and proliferative changes in goblet cells and mucin hypersecretion. Main stimulators of bacterial inflammation are bacterial lipopolysaccharides (LPS). In vitro investigation of the LPS effect on the molecular processes in goblet cells, using the human mucin-secreting goblet cell line HT29-MTX, showed the following results. LPS up-regulated mucin and cytokine mRNA expression and secretion in goblet cells in a concentration and time-dependent manner, with a maximum output at an LPS concentration of 100 ng/ml. LPS (100 ng/ml) increased mRNA expression of MUC5AC (2.4x), MUC5B (2.1x), and IL-8 (2.3x) and stimulated secretion of mucins (MUC5AC up to 39%, MUC5B up to 31%) and the inflammatory cytokine IL-8 (up to 10x). A significant correlation was found between the LPS-induced IL-8 secretion and secretion of mucins. These results suggest: (1) goblet cells, responding to the direct stimulation of bacterial LPS by two inflammatory-related processes such as production and secretion of the gel-forming mucins and the inflammatory cytokine IL-8, can be considered as an important part of mucosal immunity and (2) LPS- induced goblet cell mucin secretion can occur partly via IL-8-dependent pathway.

Role of the pro-inflammatory cytokines tumor necrosis factor-alpha, interleukin-1 beta, interleukin-6 and interleukin-8 in the pathogenesis of the otitis media with effusion.

Inflammation in the middle ear mucosa, caused usually by bacterial and viral pathogens, is the primary event in the middle ear predisposing the development of otitis media with effusion (OME). Numerous inflammatory mediators have been identified in OME. However, cytokines play a central role as initiators, mediators and regulators of middle ear inflammation and subsequent molecular-pathological processes in middle ear tissues, leading to histopathological changes in the middle ear cavity and the pathogenesis of OME. In this article, we aim to present an overview of current research developments in the pro-inflammatory cytokine involvement in the aetiology of otitis media with effusion.

In vitro study of IL-8 and goblet cells: possible role of IL-8 in the aetiology of otitis media with effusion.

One of the main characteristics of otitis media with effusion (OME) is the differentiation of basal cells into goblet cells with subsequent proliferation in a modified respiratory epithelium leading to the formation of mucin-rich effusion in the middle ear cleft. In order to determine the effect of pro-inflammatory cytokines identified in OME, e.g. IL-1beta, tumour necrosis factor (TNF)-alpha, IL-6 and IL-8, on goblet cells, and to clarify the role of IL-8 in particular, we used the human goblet cell line HT29-MTX, which secretes two OME-related mucins: MUC5AC and MUC5B. IL-1beta and TNF-alpha stimulated the secretion of IL-8 in HT29-MTX goblet cells. Dose- (2-200 ng/ml) and time- (0-5 days) response studies of IL-8-induced mucin secretion were carried out. IL-8 upregulated the secretion of MUC5AC and MUC5B mucins in a concentration-dependent manner, with a maximum response at an IL-8 concentration of 20 ng/ml. IL-8 (20 ng/ml)-mediated mucin secretion persisted for up to 5 days, with a peak response 72 h after the addition of cytokine. These results suggest that: (i) goblet cells are target cells for the pro-inflammatory cytokines IL-1beta, TNF-alpha and IL-8 and can contribute to the pathogenesis of OME by increasing both the concentration of IL-8 and the secretion of mucin; and (ii) IL-8 stimulates prolonged mucin secretion from goblet cells and may be involved in the maintenance of the disease in the chronic stage.