Crosslinked agarose encapsulated sorbents resistant to steam sterilization. Preparation and mechanical properties

The application of agarose in hemoperfusion is hampered by the lack of a suitable sterilization method. A technique has been developed for the crosslinking of agarose encapsulated sorbents by the reaction with 1,3-dichloro-2-propanol (DCP) under strong alkaline conditions. A twofold molar excess of DCP with respect to agarose and an equimolar amount of sodium hydroxide at a concentration of 0.3 mol/L with a reaction time of 1-4 h at 50°C are found to be the optimal conditions. The compressive strength of crosslinked beads is increased by a factor of 4. Agarose capsules are found to degrade by the influence of Y radiation, but are resistant to steam sterilization at 134°C during at least 30 min when crosslinked

Measurement of Oxygen Consumption Rate (OCR) and Extracellular Acidification Rate (ECAR) in Culture Cells for Assessment of the Energy Metabolism

Mammalian cells generate ATP by mitochondrial (oxidative phosphorylation) and non-mitochondrial (glycolysis) metabolism. Cancer cells are known to reprogram their metabolism using different strategies to meet energetic and anabolic needs (Koppenol et al., 2011; Zheng, 2012). Additionally, each cancer tissue has its own individual metabolic features. Mitochondria not only play a key role in energy metabolism but also in cell cycle regulation of cells. Therefore, mitochondria have emerged as a potential target for anticancer therapy since they are structurally and functionally different from their non-cancerous counterparts (D'Souza et al., 2011). We detail a protocol for measurement of oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) measurements in living cells, utilizing the Seahorse XF24 Extracellular Flux Analyzer (Figure 1). The Seahorse XF24 Extracellular Flux Analyzer continuously measures oxygen concentration and proton flux in the cell supernatant over time (Wu et al., 2007). These measurements are converted in OCR and ECAR values and enable a direct quantification of mitochondrial respiration and glycolysis. With this protocol, we sought to assess basal mitochondrial function and mitochondrial stress of three different cancer cell lines in response to the cytotoxic test lead compound mensacarcin in order to investigate its mechanism of action. Cells were plated in XF24 cell culture plates and maintained for 24 h. Prior to analysis, the culture media was replaced with unbuffered DMEM pH 7.4 and cells were then allowed to equilibrate in a non-CO2 incubator immediately before metabolic flux analysis using the Seahorse XF to allow for precise measurements of Milli-pH unit changes. OCR and ECAR were measured under basal conditions and after injection of compounds through drug injection ports. With the described protocol we assess the basic energy metabolism profiles of the three cell lines as well as key parameters of mitochondrial function in response to our test compound and by sequential addition of mitochondria perturbing agents oligomycin, FCCP and rotenone/antimycin A. [GRAPHICS]

Nonparametric longitudinal allele-sharing model

Basically no methods are available for the analysis of quantitative traits in longitudinal genetic epidemiological studies. We introduce a nonparametric factorial design for longitudinal data on independent sib pairs, modelling the phenotypic quadratic differences as the dependent variable. Factors are the number of alleles shared identically by descent (IBD) and the age categories at which the dependent variable is measured, allowing for dependence due to age. To identify a linked marker a rank statistic tests the influence of IBD group on phenotypic quadratic differences. No assumptions are made on normality or variances of the dependent variable. We apply our method to 71 sib pairs from the Framingham Heart Study data provided at the Genetic Analysis Workshop 13. For all 15 available markers on chromosome 17 we analyzed the influence on systolic blood pressure. In addition, different selection strategies to sample from the whole data are discussed

Development of a Antibacterial Disc Diffusion Assay to Differentiate Fusarin C from Non-Fusarin C activity in Early Screening of Mutant Fusarium graminearum Extracts

The discovery of novel compounds with antibacterial properties continues to be critically important.3 One potential source of such compounds is the cryptic genome of fungi known to produce biologically active molecules. A kmt6 mutant of the cereal pathogen Fusarium graminearum was previously developed through a histone H3 lysine 27 methyltransferase gene knockout, and has been shown to express hundreds of additional genes compared to wild type under the same growth conditions.1 Both the kmt6 mutant and the wild type F. graminearum produce the biologically active metabolite fusarin C, shown in Figure 1, and its analogs. Activity due to fusarin C can mask any activity of non-fusarin C compounds during early screening of extracts. Using a broad panel of bacteria, two samples were tested for differentiating activity profiles. These included an ethyl acetate extract of kmt6 growth media (i.e., the “160001E” fraction), and a more purified flash column fraction containing fusarin C and its analogs (i.e., the “fusarin C isolate”). Intriguingly, both Bacillus cereus and Staphylococcus aureus were inhibited by the 160001E extract, but were not inhibited by the fusarin C isolate. This indicates that activity from the 160001E fraction is not due to fusarin C or its analogs, but rather due to non-fusarin C compounds. With these results, a panel of 5 bacteria, including both gram negative and gram positive strains, has been developed as an early screening tool to differentiate activity between fusarin C isolates and non-fusarin C compounds from kmt6 mutant F. graminearum. This will aid in the bioassay-guided fractionation of extracts exhibiting antibacterial activity due to non-fusarin C compounds and toward the important aim of identifying novel compounds with antibacterial activity

Expression of a Structural Protein of the Mycovirus FgV-ch9 Negatively Affects the Transcript Level of a Novel Symptom Alleviation Factor and Causes Virus Infection-Like Symptoms in Fusarium graminearum

Infections of fungi by mycoviruses are often symptomless but sometimes also fatal, as they perturb sporulation, growth, and, if applicable, virulence of the fungal host. Hypovirulence-inducing mycoviruses, therefore, represent a powerful means to defeat fungal epidemics on crop plants. Infection with Fusarium graminearum virus China 9 (FgV-ch9), a double-stranded RNA (dsRNA) chrysovirus- like mycovirus, debilitates Fusarium graminearum, the causal agent of fusarium head blight. In search for potential symptom alleviation or aggravation factors in F. graminearum, we consecutively infected a custom-made F. graminearum mutant collection with FgV-ch9 and found a mutant with constantly elevated expression of a gene coding for a putative mRNA-binding protein that did not show any disease symptoms despite harboring large amounts of virus. Deletion of this gene, named virus response 1 (vr1), resulted in phenotypes identical to those observed in the virus-infected wild type with respect to growth, reproduction, and virulence. Similarly, the viral structural protein coded on segment 3 (P3) caused virus infection-like symptoms when expressed in the wild type but not in the vr1 overexpression mutant. Gene expression analysis revealed a drastic downregulation of vr1 in the presence of virus and in mutants expressing P3. We conclude that symptom development and severity correlate with gene expression levels of vr1. This was confirmed by comparative transcriptome analysis, showing a large transcriptional overlap between the virus-infected wild type, the vr1 deletion mutant, and the P3-expressing mutant. Hence, vr1 represents a fundamental host factor for the expression of virus-related symptoms and helps us understand the underlying mechanism of hypovirulence. IMPORTANCE Virus infections of phytopathogenic fungi occasionally impair growth, reproduction, and virulence, a phenomenon referred to as hypovirulence. Hypovirulence-inducing mycoviruses, therefore, represent a powerful means to defeat fungal epidemics on crop plants. However, the poor understanding of the molecular basis of hypovirulence induction limits their application. Using the devastating fungal pathogen on cereal crops, Fusarium graminearum, we identified an mRNA binding protein (named virus response 1, vr1) which is involved in symptom expression. Downregulation of vr1 in the virus-infected fungus and vr1 deletion evoke virus infection-like symptoms, while constitutive expression overrules the cytopathic effects of the virus infection. Intriguingly, the presence of a specific viral structural protein is sufficient to trigger the fungal response, i.e., vr1 downregulation, and symptom development similar to virus infection. The advancements in understanding fungal infection and response may aid biological pest control approaches using mycoviruses or viral proteins to prevent future Fusarium epidemics

Combining Independent, Weighted P-Values: Achieving Computational Stability by a Systematic Expansion with Controllable Accuracy

Given the expanding availability of scientific data and tools to analyze them, combining different assessments of the same piece of information has become increasingly important for social, biological, and even physical sciences. This task demands, to begin with, a method-independent standard, such as the -value, that can be used to assess the reliability of a piece of information. Good's formula and Fisher's method combine independent -values with respectively unequal and equal weights. Both approaches may be regarded as limiting instances of a general case of combining -values from groups; -values within each group are weighted equally, while weight varies by group. When some of the weights become nearly degenerate, as cautioned by Good, numeric instability occurs in computation of the combined -values. We deal explicitly with this difficulty by deriving a controlled expansion, in powers of differences in inverse weights, that provides both accurate statistics and stable numerics. We illustrate the utility of this systematic approach with a few examples. In addition, we also provide here an alternative derivation for the probability distribution function of the general case and show how the analytic formula obtained reduces to both Good's and Fisher's methods as special cases. A C++ program, which computes the combined -values with equal numerical stability regardless of whether weights are (nearly) degenerate or not, is available for download at our group website http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/CoinedPValues.html