RNA quality in frozen breast cancer samples and the influence on gene expression analysis – a comparison of three evaluation methods using microcapillary electrophoresis traces

Background  

Assessing RNA quality is essential for gene expression analysis, as the inclusion of degraded samples may influence the interpretation of expression levels in relation to biological and/or clinical parameters. RNA quality can be analyzed by agarose gel electrophoresis, UV spectrophotometer, or microcapillary electrophoresis traces, and can furthermore be evaluated using different methods. No generally accepted recommendations exist for which technique or evaluation method is the best choice. The aim of the present study was to use microcapillary electrophoresis traces from the Bioanalyzer to compare three methods for evaluating RNA quality in 24 fresh frozen invasive breast cancer tissues: 1) Manual method = subjective evaluation of the electropherogram, 2) Ratio Method = the ratio between the 28S and 18S peaks, and 3) RNA integrity number (RIN) method = objective evaluation of the electropherogram. The results were also related to gene expression profiling analyses using 27K oligonucleotide microarrays, unsupervised hierarchical clustering analysis and ontological mapping.     

Mass transfer effects on the reaction rate for heterogeneously distributed immobilized yeast cells

Here we examine the efficiency of different immobilized cell gradients applied to immobilized Saccharomyces cerevisiae fermenting glucose to ethanol. We developed a simulation model to fully study the competing effects of mass transfer hindrance and kinetics. It is based on a diffusion-reaction model and can be used to analyze the different cell concentration profiles inside an immobilized gel bead, in terms of effectiveness factors, productivity, and mass flux. The internal diffusion coefficient, which varies with the local cell concentration, as well as the external mass transfer, is taken into account when describing the efficiency. Although the diffusion hindrance is greater at higher cell concentrations, high cell concentration is still advantageous in the present case because the increase in reaction rate outweighs the diffusion hindrance. Thus, high cell concentrations contribute to increased productivity. The influence of the cell concentration gradient on the efficiency of the beads is negligible. Within the range of cell profiles studied it has been established that the location of the cells within the bead is of lesser importance. However, a steep cell gradient increases the importance of the external mass transfer.     

Loss of Hda activity stimulates replication initiation from I-box, but not R4 mutant origins in Escherichia coli

Initiation of chromosome replication in Escherichia coli is limited by the initiator protein DnaA associated with ATP. Within the replication origin, binding sites for DnaA associated with ATP or ADP (R boxes) and the DnaA^ATP specific sites (I-boxes, τ-boxes and 6-mer sites) are found. We analysed chromosome replication of cells carrying mutations in conserved regions of oriC . Cells carrying mutations in DnaA-boxes I2, I3, R2, R3 and R5 as well as FIS and IHF binding sites resembled wild-type cells with respect to origin concentration. Initiation of replication in these mutants occurred in synchrony or with slight asynchrony only. Furthermore, lack of Hda stimulated initiation in all these mutants. The DnaA^ATP containing complex that leads to initiation can therefore be formed in the absence of several of the origin DnaA binding sites including both DnaA^ATP specific I-boxes. However, competition between I-box mutant and wild-type origins , revealed a positive role of I-boxes on initiation. On the other hand, mutations affecting DnaA-box R4 were found to be compromised for initiation and could not be augmented by an increase in cellular DnaA^ATP/DnaA^ADP ratio. Compared with the sites tested here, R4 therefore seems to contribute to initiation most critically.     

Lack of CCR7 induces pulmonary hypertension involving perivascular leukocyte infiltration and inflammation

The chemokine receptor CCR7 regulates lymphocyte trafficking, and CCR7 deficiency induces infiltration of T and B cells adjacent to vessels in mouse lungs. Perivascular infiltration of T and B cells has also been found in human pulmonary arterial hypertension, and downregulation of the CCR7 receptor in circulating leukocytes of such patients has been observed. To investigate whether changes in the CCR7 system contribute to the pathogenesis of pulmonary hypertension, we utilized mice deficient of the CCR7 receptor. The cardiopulmonary and inflammatory responses of CCR7 depletion were evaluated in CCR7-deficient and wild-type mice. Measurements of cytokines upregulated in the animal model were also performed in patients with pulmonary hypertension and controls and in vascular smooth muscle cells. We found that mice lacking CCR7 had increased right ventricular systolic pressure, reduced pulmonary artery acceleration time, increased right ventricular/tibial length ratio, Rho kinase-mediated pulmonary vasoconstriction, and increased muscularization of distal arteries, indicating pulmonary hypertension. These mice also showed increased perivascular infiltration of leukocytes, consisting mainly of T and B cells, and increased mRNA levels of the inflammatory cytokines interleukin-12 and CX3CL1 within pulmonary tissue. Increased serum levels of interleukin-12 and CX3CL1 were also observed in patients with pulmonary hypertension, particularly in those with pulmonary hypertension associated with connective tissue disorder. In smooth muscle cells, interleukin-12 induced secretion of the angiogenic cytokine interleukin-8. We conclude that these results suggest a role for CCR7 in the development of pulmonary arterial hypertension, at least in some subgroups, possibly via pulmonary infiltration of lymphocytes and secretion of interleukin-12 and CX3CL1.     

Cardiovascular events in early RA are a result of inflammatory burden and traditional risk factors: a five year prospective study

Introduction  

Co-morbidity and mortality due to cardiovascular disease (CVD) are increased in patients with rheumatoid arthritis (RA). Most published studies in this field are retrospective or cross sectional. We investigated the presence of traditional and disease related risk factors for CVD at the onset of RA and during the first five years following diagnosis. We also evaluated their potential for predicting a new cardiovascular event (CVE) during the five-year follow-up period and the modulatory effect of pharmacological treatment.     

Large scale experimental effects of three levels of sheep densities on an alpine ecosystem

Plant–herbivore dynamics is a major topic in ecological research, but empirical knowledge on the ecological effects of different densities of large grazers from fully replicated experiments is rare. Previous studies have focused on grazing vs no grazing, and our understanding of the extent to which different levels of grazing alter vegetation composition, and how quickly such effects can be measured, is therefore limited. We performed a fully replicated, short‐term (four‐year) experiment using large enclosures (each ～0.3 km²) with three different sheep densities (no grazing, low grazing and high grazing, respectively) in an alpine environment with summer grazing in southern Norway to address these issues. Sheep grazing mainly affected plant species at high densities of sheep as compared to no sheep after a four‐year treatment; few effects of low sheep densities were detectable. Highly selected herbs, herbs suggested vulnerable to trampling, and woody species decreased, while most graminoids, one ruderal, one prostrate species and two bryophyte taxa increased at high sheep densities. We found contrasting responses within main functional groups highlighting that fine details of plant life histories need to be known for responses to grazing to be successfully predicted. Vascular plant cover and bare soil responded to sheep density after two years of treatment, but only for one of the species was frequency change observed at this stage. Overall, plants in low grazing plots were found to be almost unaffected. Changes in abundance were mainly found at the no grazing and high grazing treatments. Plant species that decreased at high grazing generally increased at no grazing and vice versa, suggesting a response to both cessation of grazing and enhanced grazing respectively. Our study demonstrates, beyond a simple comparison of heavily grazed and non‐grazed sites, that herbivore effects on plants are typically non‐linearly related to herbivore density, and that the speed of plant responses will depend both on the plant property examined and the grazing pressure.     

Phosphorus effects on metabolic processes in monoxenic arbuscular mycorrhiza cultures

The influence of external phosphorus (P) on carbon (C) allocation and metabolism as well as processes related to P metabolism was studied in monoxenic arbuscular mycorrhiza cultures of carrot (Daucus carota). Fungal hyphae of Glomus intraradices proliferated from the solid minimal medium containing the colonized roots into C-free liquid minimal medium with different P treatments. The fungus formed around three times higher biomass in P-free liquid medium than in medium with 2.5 mM inorganic P (high-P). Mycelium in the second experiment was harvested at an earlier growth stage to study metabolic processes when the mycelium was actively growing. P treatment influenced the root P content and [(13)C]glucose administered to the roots 7 d before harvest gave a negative correlation between root P content and (13)C enrichment in arbuscular mycorrhiza fungal storage lipids in the extraradical hyphae. Eighteen percent of the enriched (13)C in extraradical hyphae was recovered in the fatty acid 16:1omega5 from neutral lipids. Polyphosphate accumulated in hyphae even in P-free medium. No influence of P treatment on fungal acid phosphatase activity was observed, whereas the proportion of alkaline-phosphatase-active hyphae was highest in high-P medium. We demonstrated the presence of a motile tubular vacuolar system in G. intraradices. This system was rarely seen in hyphae subjected to the highest P treatment. We concluded that the direct responses of the extraradical hyphae to the P concentration in the medium are limited. The effects found in hyphae seemed instead to be related to increased availability of P to the host root.