247 results for qubit oscillator frequency
Polycyclic aromatic hydrocarbons and their quinones modulate the metabolic profile and induce DNA damage in human alveolar and bronchiolar cells
Contributors: Deepak Gurbani, Santosh Kumar Bharti, Ashutosh Kumar, Alok K. Pandey, Godson R.E.E. Ana, Ambrish Verma, Altaf Husain Khan, Devendra K. Patel, M.K.R. Mudiam, Swatantra K. Jain
... The release of particulate pollutants into the air through burning of coal, crude oil, diesel, coal tar, etc. raises concerns of potential health hazards to the exposed human population. Polycyclic aromatic hydrocarbons (PAHs) are major toxic constituents of particulate matter (PM), which upon ingestion get metabolized to even more toxic metabolites such as quinones. The PAHs levels were assessed in both respirable particulate matter (RSPM, 10μM size) of urban ambient air (UAA) and that of major contributors viz. diesel exhaust particles (DEPs) and coal tar combustions emissions (CTCE). Seven US Environmental Protection Agency (USEPA) prioritized PAHs in RSPM and 10 in SPM were detected in UAA. Ten and 15 prioritized PAHs, respectively, were also detected in diesel exhaust particles (DEP) and coal tar combustion emission (CTCE) evidencing their release in the air. These PM associated PAHs for UAA, DEP and CTCE showed significant increase (pDEP>UAA. Human lung alveolar (A549) and bronchiolar (BEAS-2B) cells when treated with PAH-metabolites viz. 1,4-benzoquinone (1,4-BQ), hydroquinone (HQ), 1,2-naphthoquinone (1,2-NQ), 1,4-naphthoquinone (1,4-NQ) and 9,10-phenanthroquinone (9,10-PQ) showed metabolic modulation in these cell lines with significant depletion of principal cellular metabolites viz. NADP, uracil, asparagines, glutamine, and histidine and accumulation of di-methyl amine and beta-hydroxybutyrate, identified using 1H NMR spectroscopy. These results suggest that PAH-quinones induce genotoxic effects by modulating the metabolic machinery inside the cells by a combined effect of oxidative stress and energy depletion. Our data for metabolic profiling of human lung cells could also help in understanding the mechanism of toxicity of other xenobiotics.
The evolving epidemiology of rotavirus gastroenteritis in central Portugal with modest vaccine coverage
Contributors: Fernanda Rodrigues, Miren Iturriza-Gómara, Robin Marlow, Jim Gray, Sameena Nawaz, Luís Januário, Adam Finn
... Rotavirus (RV) vaccines have been available on the private market in Portugal since 2006, with an estimated coverage rising from 16 to 42% between 2007 and 2010.
Contributors: Xianfeng Zhang, Mariko Kondo, Jing Chen, Hiroyuki Miyoshi, Hajime Suzuki, Takashi Ohashi, Hisatoshi Shida
... Tripartite motif-containing 5 isoform-α (TRIM5α), a host restriction factor, blocks infection of some retroviruses at a post-entry, pre-integration stage in a species-specific manner. A recent report by Sakuma et al. describes a second antiretroviral activity of rhesus macaque TRIM5α, which blocks HIV-1 production through rapid degradation of HIV-1 Gag polyproteins. Here, we find that human TRIM5α limits HIV-1 production. Transient expression of TRIM5α decreased HIV-1 production, whereas knockdown of TRIM5α in human cells increased virion release. A single amino acid substitution (R437C) in the SPRY domain diminished the restriction effect. Moderate levels of human wild-type TRIM5α and a little amount of R437C mutant were incorporated into HIV-1 virions. The R437C mutant also lost restriction activity against N-tropic murine leukemia virus infection. However, the corresponding R to C mutation in rhesus macaque TRIM5α had no effect on the restriction ability. Our findings suggest human TRIM5α is an intrinsic immunity factor against HIV-1 infection. The importance of arginine at 437 aa in SPRY domain for the late restriction is species-specific.
Demonstration of T cell and macrophage progenitors in carp (Cyprinus carpio) kidney hematopoietic tissues. Development of clonal assay system for carp hematopoietic cells
Contributors: Fumihiko Katakura, Takuya Yamaguchi, Miyuki Yoshida, Tadaaki Moritomo, Teruyuki Nakanishi
... Single hematopoietic cells from carp (Cyprinus carpio) kidney were seeded to each well of 96-well plates and cultured in the presence of a supporting cell layer and conditioned media (CM). The CM were obtained from bulk-cultured carp hematopoietic cells, in which T and macrophage-lineage cells rapidly proliferated as previously reported. After 2–3 weeks, colony formation was found in 0–4 wells of each plate. Three different morphological types of colonies were observed: “type I colonies”, “type II colonies” and “mixed-type colonies”. Type I colony cells were interpreted as composed by macrophage-lineage cells, since they expressed a specific macrophage marker, M-CSFR/csf1r gene, and most of them phagocytosed latex particles. Type II colony cells were interpreted as composed by T lineage cells, since they expressed several T cell marker genes including gata3, lck and TCRβ, but did not engulf latex particles. Mixed-type colonies were interpreted as composed by both macrophages and T lineage cells. They expressed not only the M-CSFR gene but also a T cell marker gene, gata3, but not other T cell markers, such as lck and TCRβ. These results indicated that the mixed-type colonies were developed from immature common progenitors of macrophage and T cell. In contrast, type I and type II colonies were developed from more mature and mono-potent progenitors of macrophage and T cell, respectively.
Applying a field spectroscopy technique for assessing successional trends of biological soil crusts in a semi-arid environment
Contributors: E. Zaady, A. Karnieli, M. Shachak
... We studied the successional stages of biological soil crusts (BSCs) by using in-situ spectroscopic techniques during 6 years of recovery following scraping-sterilization and scraping-crumbling disturbances on north- and south-facing slopes and in plots with and without overland water runoff barriers. Two spectral indices, the Brightness Index (BI) and the Normalized Difference Vegetation Index (NDVI), were used as indicators for evaluating BSC succession, with special attention to differences between the north- and the south-facing slopes. We found that BSC succession could be expressed as linear regressions of the above-mentioned indicators during the experimental years for the different treatments. Both indicators were found to be significantly different in each of the experimental years: BI values decreased while NDVI values increased for each of the three treatments. Thus, the BI can serve as a good indicator during the early years following disturbance while the NDVI can be useful after crusts have become established. We conclude that spectral reflectance measurements of BSCs can be a useful monitoring technique for studying the regeneration of the soil surface without direct disturbance.
CRACC-targeting Fc-fusion protein induces activation of NK cells and DCs and improves T cell immune responses to antigenic targets
Contributors: Yasser A. Aldhamen, David P.W. Rastall, Weimin Chen, Sergey S. Seregin, Cristiane Pereira-Hicks, Sarah Godbehere, Norbert E. Kaminski, Andrea Amalfitano
Development of CRACC-Fc fusion protein. (A) Plasmid encoding CRACC-ECD/mIgG1-Fc was transiently transfected into 100ml suspension HEK 293-6E cell culture. CRACC-Fc protein was captured from the cell culture supernatant by HiTrapTM Mabselect 5ml column and followed by buffer exchange and SDS-PAGE and Western blot analysis. Lane M: protein marker. Lane R: reducing conditions. Lane N: non-reducing conditions. Lane P: mouse IgG1, Kappa (B and C) RAW264.7 cells (300,000cells/well) were plated in quadruplicate in 24-well plate and then stimulated for 24h with LPS (1μg/ml). After 24h, cells were harvested and incubated with escalating doses of CRACC-Fc fusion protein for 2h. After 2h, cells were then washed and stained with APC-conjugated anti-CRACC antibody and CRACC expression was evaluated by flow cytometry. (B) Representative flow cytometry figures for CRACC expression on LPS-stimulated RAW264.7 cells in the presence or absence of CRACC-Fc fusion protein. (C) Frequency of CRACC expression on LPS-stimulated RAW264.7 cells in the presence of escalating doses of CRACC-Fc fusion protein. (D) Immunoprecipitation analysis for EAT-2 expression in RAW264.7 cells following LPS stimulation in the presence or absence of CRACC-Fc (10μg/ml). (E) Quantification of EAT-2 protein levels after normalization to the 55kDa loading protein. Densitometric analysis was done using Image J software. Cells were plated in quadruplicate. The bars represent mean±SD. ...Frequency of T and B lymphocytes following rAd5-Null and CRACC-Fc co-administration. (A) Flow cytometry analysis for the percentages of CD8+ CD3+ T cells (A), CD8− CD3+ T cells (B), and CD19+ CD3− B cells (C) 12 days following rAd5-Null and either CRACC-Fc or control IgG co-administration. Statistical analysis was completed using a Student's t-test, p<0.05 was deemed as a statistically significant difference. ...CRACC-Fc fusion protein has an innate immunostimulatory activity. Male C57BL/6 mice (n=5) were i.p. injected with a mixture of rAd5-Null (2×1010vps/mouse) and 200μg of CRACC-Fc fusion protein [rAd5-Null+ CRACC-Fc) or control IgG [Ad-Null+ Control IgG]. After 12h, mice were sacrificed and splenocytes were prepared. (A) Frequency of IFNγ expressing NK cells (CD3-NK1.1+) derived from Ad-Null+ CRACC-Fc or Ad-Null+ Control IgG co-injected mice. (B and C) DCs (CD11c+, CD11b+, F4/80−) maturation was evaluated by assessing the expression levels of CD80, CD86, and I-A/I-E molecules. Expression of CD80 (B), CD86 (C), and I-A/I-E (D) on CD11c+, CD11b+, F4/80− DCs is shown. Data are presented as mean±SD. Statistical analysis was completed using a one-way analysis of variance (ANOVA) with a Student–Newman–Keuls post hoc test, p<0.05 was deemed as a statistically significant difference. *** denotes p<0.001, statistically different from naive animals. ...Cytokines secretion profiles of Gag-specific CD8+ T cells derived from rAd5-HIV/Gag and CRACC-Fc co-vaccination. Splenocytes (2×106cells/well) derived from naives (n=4) or vaccinated mice (n=7) were stimulated with the HIV-Gag immunogenic peptide, AMQMLKETI and FACS ICS analysis was performed. The Cytokines secretion profiles of HIV-Gag-specific CD8+ T cells elicited by the rAd5-HIV/Gag and CRACC-Fc co-vaccination regimen were determined by multiparameter intercellular staining assay. Gate were set based on negative control (naïve) and placed consistently across samples. The total frequency of splenic CD8+ T cells derived from naïve or vaccinated mice expressing IFNγ (A), TNFα (B), IL-2 (C), IFNγ/TNFα (D), IFNγ/IL-2 (E), or TNFα/IL-2 (F). Data are presented as mean±SD. Statistical analysis was completed using a one-way analysis of variance (ANOVA) with a Student–Newman–Keuls post hoc test, p<0.05 was deemed as a statistically significant difference. **, *** denotes p<0.01, p<0.001 statistically different from naive animals. Data are representative of three independent experiments with similar results. ...CRACC-Fc co-vaccination alters the elicited CD8+ T cells toward TEM phenotype. Phenotypic analysis of HIV-Gag-specific CD8+ T cells elicited after rAd5-HIV/Gag and CRACC-Fc co-vaccination at 42dpi. Multiparameter Gag-tetramer binding assays were performed in PBMCs (A) or splenocytes (B) of naives (n=4) or vaccinated mice (n=6) to enumerate the frequency of Gag-specific tetramer positive effector memory (CD62Llow CD127high) CD8+ T cells. Data are presented as mean±SD. Statistical analysis was completed using a one-way analysis of variance (ANOVA) with a Student–Newman–Keuls post hoc test, p<0.05 was deemed as a statistically significant difference. **, *** denotes p<0.01, p<0.001 statistically different from naive animals. Data are representative of three independent experiments with similar results. ...Increased breadth of Gag-specific CD8+ T cell responses following rAd5-HIV/Gag and CRACC-Fc co-vaccination. Splenocytes (2×106cells/well) derived from naives (n=4) or vaccinated mice (n=7) were stimulated with Gag-peptide pool# 17 (identified in Fig. 4C) and FACS ICS analysis for IFNγ-, TNFα- and IL-2-expressing CD8+ T cells was performed. The total frequency of splenic CD8+ T cells expressing IFNγ (A), TNFα (B), IL-2 (C), IFNγ/TNFα (D), IFNγ/IL-2 (E), or TNFα/IL-2 (F) are shown. Data are presented as mean±SD. Statistical analysis was completed using a one-way analysis of variance (ANOVA) with a Student–Newman–Keuls post-hoc test, p<0.05 was deemed as a statistically significant difference. **, *** denotes p<0.01, p<0.001 statistically different from naive animals. Data are representative of two independent experiments with similar results. ...CRACC-Fc fusion protein has an innate immunostimulatory activity. Male C57BL/6 mice (n=5) were i.p. injected with a mixture of rAd5-Null (2×1010vps/mouse) and 200μg of CRACC-Fc fusion protein [rAd5-Null+ CRACC-Fc) or control IgG [Ad-Null+ Control IgG]. After 12h, mice were sacrificed and splenocytes were prepared. (A) Frequency of IFNγ expressing NK cells (CD3-NK1.1+) derived from Ad-Null+ CRACC-Fc or Ad-Null+ Control IgG co-injected mice. (B and C) DCs (CD11c+, CD11b+, F4/80−) maturation was evaluated by assessing the expression levels of CD80, CD86, and I-A/I-E molecules. Expression of CD80 (B), CD86 (C), and I-A/I-E (...Increased breadth of Gag-specific CD8+ T cell responses following rAd5-HIV/Gag and CRACC-Fc co-vaccination. Splenocytes (2×106cells/well) derived from naives (n=4) or vaccinated mice (n=7) were stimulated with Gag-peptide pool# 17 (identified in Fig. 4C) and FACS ICS analysis for IFNγ-, TNFα- and IL-2-expressing CD8+ T cells was performed. The total frequency of splenic CD8+ T cells expressing IFNγ (A), TNFα (B), IL-2 (C), IFNγ/TNFα (D), IFNγ/IL-2 (E), or TNFα/IL-2 (F) are shown. Data are presented as mean±SD. Statistical analysis was completed using a one-way analysis of variance (ANOVA) with a Student–Newman–Keuls post-hoc test, psimilar results. ... The CD2-like receptor activating cytotoxic cell (CRACC) receptor is a member of the SLAM family of receptors that are found on several types of immune cells. We previously demonstrated that increasing the abundance of the adaptor protein EAT-2 during vaccination enhanced innate and adaptive immune responses to vaccine antigens. Engagement of the CRACC receptor in the presence of the EAT-2 adaptor generally results in immune cell activation, while activating CRACC signaling in cells that lack EAT-2 adaptor inhibits their effector and regulatory functions. As EAT-2 is the only SAP adaptor that interacts with the CRACC receptor, we hypothesized that technologies that specifically modulate CRACC signaling during vaccination may also improve antigen specific adaptive immune responses. To test this hypothesis, we constructed a CRACC-targeting Fc fusion protein and included it in vaccination attempts. Indeed, mice co-vaccinated with the CRACC-Fc fusion protein and an adenovirus vaccine expressing the HIV-Gag protein had improved Gag-specific T cell responses, as compared to control mice. These responses are characterized by increased numbers of Gag-specific tetramer+ CD8+ T cells and increases in production of IFNγ, TNFα, and IL2, by Gag-specific CD8+ T cells. Moreover, our results revealed that use of the CRACC-Fc fusion protein enhances vaccine-elicited innate immune responses, as characterized by increased dendritic cells (DCs) maturation and IFNγ production from NK cells. This study highlights the importance of CRACC signaling during the induction of an immune response generally, and during vaccinations specifically, and also lends insight into the mechanisms underlying our prior results noting EAT-2-dependent improvements in vaccine efficacy.
Contributors: Petrizzo, Annacarmen, Tagliamonte, Maria, Mauriello, Angela, Costa, Valerio, Aprile, Marianna, Esposito, Roberta, Caporale, Andrea, Luciano, Antonio, Arra, Claudio, Tornesello, Maria Lina
... Background: A novel prediction algorithm is needed for the identification of effective tumor associated mutated neoantigens. Only those with no homology to self wild type antigens are true predicted neoantigens (TPNAs) and can elicit an antitumor T cell response, not attenuated by central tolerance. To this aim, the mutational landscape was evaluated in HCV-associated hepatocellular carcinoma.Methods: Liver tumor biopsies and adjacent non-tumor liver tissues were obtained from 9 HCV-chronically infected subjects and subjected to RNA-Seq analysis. Mutant peptides were derived from single nucleotide variations and TPNAs were predicted using two prediction servers (e.g. NetTepi and NetMHCstabpan) by comparison with corresponding wild-type sequences, non-related self and pathogen-related antigens. Immunological confirmation was obtained in preclinical as well as clinical setting.Results: The development of such an improved algorithm resulted in a handful of TPNAs despite the large number of predicted neoantigens. Furthermore, TPNAs may share homology to pathogen's antigens and be targeted by a pre-existing T cell immunity. Cross-reactivity between such antigens was confirmed in an experimental pre-clinical setting. Finally, TPNAs homologous to pathogen's antigens were found in the only HCC long-term survival patient, suggesting a correlation between the pre-existing T cell immunity specific for these TPNAs and the favourable clinical outcome.Conclusions: The new algorithm allowed the identification of the very few TPNAs in cancer cells, and those targeted by a pre-existing immunity strongly correlated with long-term survival. Only such TPNAs represent the optimal candidates for immunotherapy strategies.
Integrated miRNA and mRNA profiling of tumor-educated macrophages identifies prognostic subgroups in estrogen receptor-positive breast cancer
Contributors: Annalen Bleckmann, Andreas Leha, Stephan Artmann, Kerstin Menck, Gabriela Salinas-Riester, Claudia Binder, Tobias Pukrop, Tim Beissbarth, Florian Klemm
Stable feature selection of miR-iTEM in breast cancer datasets. List of stably selected miRNAs from the different miRNA sets (miR-iTEM list, miR-Oxford ER + list, all miRNAs list) and their corresponding inclusion frequencies (in % of all cross validation runs) for the two external breast cancer datasets. “-“ indicates that this miRNA was not present in the respective list of miRNAs. ...Stable feature selection of miR-iTEM in breast cancer datasets. List of stably selected miRNAs from the different miRNA sets (miR-iTEM list, miR-Oxford ER + list, all miRNAs list) and their corresponding inclusion frequencies (in % of all cross validation runs) for the two external breast cancer datasets. “-“ indicates that this miRNA was not present in the respective list of miRNAs. ... Various studies have identified aberrantly expressed miRNAs in breast cancer and demonstrated an association between distinct miRNAs and malignant progression as well as metastasis. Even though tumor-associated macrophages (TAM) are known mediators of these processes, little is known regarding their miRNA expression upon education by malignant cells in vivo.
Brief communication - Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa
Contributors: Mallikarjuna Rao Kovi, Gaurav Sablok, XuFeng Bai, Micael Wendell, Odd-Arne Rognli, HuiHui Yu, YongZhong Xing
... In plants, flowering is a major biological phenomenon, which is regulated by an array of interactions occurring between biotic and abiotic factors. In our study, we have compared the expression profiles of flowering genes involved in the flowering pathway, which are influenced by conditions like photoperiod and temperature from seedling to heading developmental stages in two Oryza sativa indica varieties, viz., Zhenshan 97 and Minghui 63 using a expression network approach. Using the network expression approach, we found 17 co-expressed genes having the same expression profile pattern as three key photoperiod flowering genes Hd1, Ehd1 and Hd3a. We also demonstrated that these three co-expressed genes have a similar simulation pattern as temperature flowering genes. Based on our observations, we hypothesize that photoperiod and temperature regulate flowering pathways independently. The present study provides a basis for understanding the network of co-expressed genes involved in flowering pathway and presents a way to demonstrate the behavior of specific gene sets in specific cultivars.
The regulation of focal adhesion complex formation and salivary gland epithelial cell organization by nanofibrous PLGA scaffolds
Contributors: Sharon J. Sequeira, David A. Soscia, Basak Oztan, Aaron P. Mosier, Riffard Jean-Gilles, Anand Gadre, Nathaniel C. Cady, Bülent Yener, James Castracane, Melinda Larsen
... Nanofiber scaffolds have been useful for engineering tissues derived from mesenchymal cells, but few studies have investigated their applicability for epithelial cell-derived tissues. In this study, we generated nanofiber (250 nm) or microfiber (1200 nm) scaffolds via electrospinning from the polymer, poly-l-lactic-co-glycolic acid (PLGA). Cell-scaffold contacts were visualized using fluorescent immunocytochemistry and laser scanning confocal microscopy. Focal adhesion (FA) proteins, such as phosphorylated FAK (Tyr397), paxillin (Tyr118), talin and vinculin were localized to FA complexes in adult cells grown on planar surfaces but were reduced and diffusely localized in cells grown on nanofiber surfaces, similar to the pattern observed in adult mouse salivary gland tissues. Significant differences in epithelial cell morphology and cell clustering were also observed and quantified, using image segmentation and computational cell-graph analyses. No statistically significant differences in scaffold stiffness between planar PLGA film controls compared to nanofibers scaffolds were detected using nanoindentation with atomic force microscopy, indicating that scaffold topography rather than mechanical properties accounts for changes in cell attachments and cell structure. Finally, PLGA nanofiber scaffolds could support the spontaneous self-organization and branching of dissociated embryonic salivary gland cells. Nanofiber scaffolds may therefore have applicability in the future for engineering an artificial salivary gland.