Gel purification of radiolabeled nucleic acids via phosphorimaging: Dip-N-Dot

RNA and DNA oligonucleotides radiolabeled with ³²P or ³³P often require gel electrophoresis to remove undesired side and/or degradation products. Common ways to visualize these molecules after electrophoresis are by ultraviolet (UV) shadowing, which necessarily reduces the specific activity of the oligonucleotide, and by autoradiography using film, which is cumbersome and increases the cost of generating the radiolabeled molecule. A more cost-effective method is to physically inject the gel with a “Dip-N-Dot” solution of dye and radionuclide after electrophoresis but prior to phosphorimaging. The gel can be overlaid on its computer-generated image, allowing the labeled molecules to be visualized quickly.     

ATP6V0C Knockdown in Neuroblastoma Cells Alters Autophagy-Lysosome Pathway Function and Metabolism of Proteins that Accumulate in Neurodegenerative Disease

ATP6V0C is the bafilomycin A1-binding subunit of vacuolar ATPase, an enzyme complex that critically regulates vesicular acidification. We and others have shown previously that bafilomycin A1 regulates cell viability, autophagic flux and metabolism of proteins that accumulate in neurodegenerative disease. To determine the importance of ATP6V0C for autophagy-lysosome pathway function, SH-SY5Y human neuroblastoma cells differentiated to a neuronal phenotype were nucleofected with non-target or ATP6V0C siRNA and following recovery were treated with either vehicle or bafilomycin A1 (0.3–100 nM) for 48 h. ATP6V0C knockdown was validated by quantitative RT-PCR and by a significant decrease in Lysostracker Red staining. ATP6V0C knockdown significantly increased basal levels of microtubule-associated protein light chain 3-II (LC3-II), α-synuclein high molecular weight species and APP C-terminal fragments, and inhibited autophagic flux. Enhanced LC3 and LAMP-1 co-localization following knockdown suggests that autophagic flux was inhibited in part due to lysosomal degradation and not by a block in vesicular fusion. Knockdown of ATP6V0C also sensitized cells to the accumulation of autophagy substrates and a reduction in neurite length following treatment with 1 nM bafilomycin A1, a concentration that did not produce such alterations in non-target control cells. Reduced neurite length and the percentage of propidium iodide-positive dead cells were also significantly greater following treatment with 3 nM bafilomycin A1. Together these results indicate a role for ATP6V0C in maintaining constitutive and stress-induced ALP function, in particular the metabolism of substrates that accumulate in age-related neurodegenerative disease and may contribute to disease pathogenesis.     

Catechol derivatives of aminopyrazine and cell protection against UVB-induced mortality

A series of 5-aryl- and 3,5-bis-aryl-2-amino-1,4-pyrazine derivatives 4 and 6, and related imidazolopyrazinones 7, has been synthesized, the aryl groups of which are catechol and/or phenol substituents. These compounds, tested against human keratinocyte cells stressed by UVB irradiation, showed high antioxidative properties. One compound (6f) was more active than EGCG/ECG (green tea extract) in reducing cell mortality.     

Pluronic F-68: an answer for shoot regeneration recalcitrance in microspore-derived <Emphasis Type="Italic">Brassica napus</Emphasis> embryos

Recalcitrance to tissue culture is observed in some genotypes of Brassica napus. Several studies have confirmed that Pluronic F-68 has growth-promoting effects on numerous tissue types. This work investigated the effect of the non-ionic surfactant Pluronic F-68 at four concentrations (0.1%, 0.25%, 0.5%, and 1% (w/v)) on the responsiveness of recalcitrant B. napus lines to tissue culture. Microspores from seven populations of B. napus were cultured on Nitsch and Nitsch medium with this compound. The embryos obtained were plated on solid B5 medium supplemented with zeatin for shoot induction. Pluronic F-68 had a highly significant effect on the proportion of shoot regeneration (P < 0.05) in some of the recalcitrant populations. However, no strong dose–response effect was observed. The estimated probability of a shoot occurring in the absence of Pluronic F-68 ranged from 0.04 to 0.31 depending on the genotype, while in the presence of Pluronic F-68, it ranged from 0.07 to 0.53, respectively.     

Forest productivity under elevated CO₂ and O₃: positive feedbacks to soil N cycling sustain decade-long net primary productivity enhancement by CO₂

The accumulation of anthropogenic CO? in the Earth's atmosphere, and hence the rate of climate warming, is sensitive to stimulation of plant growth by higher concentrations of atmospheric CO?. Here, we synthesise data from a field experiment in which three developing northern forest communities have been exposed to factorial combinations of elevated CO? and O?. Enhanced net primary productivity (NPP) (c. 26% increase) under elevated CO? was sustained by greater root exploration of soil for growth-limiting N, as well as more rapid rates of litter decomposition and microbial N release during decay. Despite initial declines in forest productivity under elevated O?, compensatory growth of O? -tolerant individuals resulted in equivalent NPP under ambient and elevated O?. After a decade, NPP has remained enhanced under elevated CO? and has recovered under elevated O? by mechanisms that remain un-calibrated or not considered in coupled climate-biogeochemical models simulating interactions between the global C cycle and climate warming.     

Biology and data-intensive scientific discovery in the beginning of the 21st century

The life sciences are poised at the beginning of a paradigm-changing evolution in the way scientific questions are answered. Data-Intensive Science (DIS) promise to provide new ways of approaching scientific challenges and answering questions. This article is a summary of the life sciences issues and challenges as discussed in the DIS workshop in Seattle, September 19-20, 2010.     

IL-21 and IL-6 are critical for different aspects of B cell immunity and redundantly induce optimal follicular helper CD4 T cell (Tfh) differentiation

Cytokines are important modulators of lymphocytes, and both interleukin-21 (IL-21) and IL-6 have proposed roles in T follicular helper (Tfh) differentiation, and directly act on B cells. Here we investigated the absence of IL-6 alone, IL-21 alone, or the combined lack of IL-6 and IL-21 on Tfh differentiation and the development of B cell immunity in vivo. C57BL/6 or IL-21^−/− mice were treated with a neutralizing monoclonal antibody against IL-6 throughout the course of an acute viral infection (lymphocytic choriomeningitis virus, LCMV). The combined absence of IL-6 and IL-21 resulted in reduced Tfh differentiation and reduced Bcl6 protein expression. In addition, we observed that these cytokines had a large impact on antigen-specific B cell responses. IL-6 and IL-21 collaborate in the acute T-dependent antiviral antibody response (90% loss of circulating antiviral IgG in the absence of both cytokines). In contrast, we observed reduced germinal center formation only in the absence of IL-21. Absence of IL-6 had no impact on germinal centers, and combined absence of both IL-21 and IL-6 revealed no synergistic effect on germinal center B cell development. Studying CD4 T cells in vitro, we found that high IL-21 production was not associated with high Bcl6 or CXCR5 expression. TCR stimulation of purified naïve CD4 T cells in the presence of IL-6 also did not result in Tfh differentiation, as determined by Bcl6 or CXCR5 protein expression. Cumulatively, our data indicates that optimal Tfh formation requires IL-21 and IL-6, and that cytokines alone are insufficient to drive Tfh differentiation.