Chromatin reorganization during emergence of malignant Friend tumors: early changes in H2A and H2B variants and nucleosome repeat length

Serial examination of five newly derived Friend murine tumors during early subcutaneous passages showed continuing changes in chromatin composition and structure over the first 10 to 20 passages followed by a period of stabilization over the subsequent 20 passages. These changes were reflected in a decrease in two major histone variants, H2A.1 and H2B.2, with a coordinate increase in histone variants, H2A.2 and H2B.1, and a changing nucleosome repeat length (NRL). The absolute values differed among the five tumors, but all five showed the same general direction of change. There was no obvious relationship among the NRL, H2A, and H2B histone variant values. A low H2A.1/H2A.2 ratio was found in Friend tumors of high malignant potential. Cell lines derived in vitro also showed directional changes in the H2A and H2B variants similar to those of their tumor cell parents, but with different kinetics. Our findings suggest that Friend tumor establishment is accompanied by an early period of chromatin reorganization marked by changes in several parameters of chromatin structure.     

Seasonal dynamics of denitrification activity in two water meadows

Seasonal variation in denitrification activity was measured in twoflooded water meadows, one on peaty and one on sandy soil, over a three-yearperiod. Measurements were taken during flooded and drained periods, usingthe acetylene-blockage technique, and the rates were compared to massbalance estimates of nitrate removal in the percolating water.Denitrification activity was higher in sandy soil than in peaty soil. Higherwater infiltration rate and thereby higher nitrate load was considered to bethe cause of the higher denitrification in the sandy soil. Floodingsignificantly increased denitrification, and the rates were higher in autumnand winter than in spring. This was considered to be a result of highernitrogen concentration in inflowing stream water during winter. Annualdenitrification was estimated to 430–460 kg N ha^-1yr^-1 in the sandy soil meadow, and 220 kg N ha^-1yr^-1 in the peaty soil meadow. In the sandy soil there was alarge discrepancy between nitrate removal rates and denitrification rates,which can be explained by nitrification of ammonium released from the soil.In the peaty soil nitrate disappearance and denitrification correspondedfairly well.     

Production of nitrous oxide in artificially flooded and drained soils

Production of nitrous oxide (N₂O) was studied in one peaty and one sandy soil undergoing wetting and drying cycles. The background concentration of N₂O in the soil was compared with the N₂O produced during 4 hours of incubation with and without addition of acetylene. The concentration of N₂O in the soil under flooded conditions was relatively stable, and net consumption of N₂O was observed as often as net production. The reference area and drained soils showed somewhat different patterns compared to the flooded soils, which was probably an effect of intermediate soil water conditions. During flooding, the nitrous oxide made up less than 1% of total denitrification on 50% and 54% of the sampling occasions for the peaty and the sandy soil, respectively, and N₂O/(N₂O+N₂)-ratios exceeded 0.2 on only 6% and 3% of the sampling occasions. Under drained conditions and in the reference areas, the ratios showed a more even frequency distribution. Grouping the nitrous oxide production data for different seasons and field conditions, we found few seasonal trends. At the sandy site, mean production of N₂O was larger during the winter months. There were weak correlations between N₂O production and floodwater nitrate concentration, and between N₂O production and soil temperature. N₂O production in the reference area varied between consumption and 4.6 kg N ha^–1 month^–1 and in flooded and drained soil between consumption and 2.6 kg N ha^–1 month^–1.     

Development of Electrochemiluminescent Serology Assays to Measure the Humoral Response to Antigens of Respiratory Syncytial Virus

Sensitive and precise serology assays are needed to measure the humoral response to antigens of respiratory syncytial virus (RSV) following natural infection or vaccination. We developed and evaluated a collection of electrochemiluminescent (ECL) serology assays using four RSV antigens (F, N, Ga and Gb). To assess the merits of ECL technology, the four ECL serology assays were evaluated using a well-characterized “gold standard” panel of acute and convalescent serum samples from fifty-nine RSV-positive and thirty RSV-negative elderly subjects (≥65 years old). The combined results from the four ECL assays demonstrated good concordance to the “gold standard” diagnosis, reaching 95% diagnostic sensitivity and 100% diagnostic specificity. Additionally, a combination of ECL assays provided higher diagnostic sensitivity than a commercially available diagnostic ELISA or cell-based microneutralization assay. In summary, these data demonstrate the advantages of using ECL-based serology assays and highlight their use as a sensitive diagnostic approach to detect recent RSV infection in an elderly population.     

Emissions of greenhouse gases from ponds constructed for nitrogen removal

Methane and carbon dioxide emission from three constructed ponds were monitored during an annual cycle. Water temperature was a good predictor of methane emission in all three ponds. In the most intensively studied pond, nitrate concentration in the bottom water could further explain the amount of methane emitted. When water temperature exceeded 15 °C between 1 and 54 mg, CH₄ m⁻² h⁻¹ was emitted on all occasions, while at temperatures below 10 °C, less than 0.6 mg CH₄ m⁻² h⁻¹ was emitted. The flux of carbon dioxide differed between the ponds and no consistent patterns were found. In a laboratory study at 20 °C, we showed that high, but naturally occurring, nitrate concentrations (8 and 16 mg NO₃⁻–N l⁻¹) constrained the production of methane compared to the treatment with no nitrate addition. Nitrous oxide production was positively correlated with nitrate concentration. Carbon dioxide production was highest at the highest nitrate concentration, which indicates that increased nitrate loading on ponds and wetlands will stimulate organic matter decomposition rates. Our conclusion is that these ponds constructed for nitrate removal emit greenhouse gases comparable to lakes in the temperate region.     

Genetic inheritance of gene expression in human cell lines

Combining genetic inheritance information, for both molecular profiles and complex traits, is a promising strategy not only for detecting quantitative trait loci (QTLs) for complex traits but for understanding which genes, pathways, and biological processes are also under the influence of a given QTL. As a primary step in determining the feasibility of such an approach in humans, we present the largest survey to date, to our knowledge, of the heritability of gene-expression traits in segregating human populations. In particular, we measured expression for 23,499 genes in lymphoblastoid cell lines for members of 15 Centre d'Etude du Polymorphisme Humain (CEPH) families. Of the total set of genes, 2,340 were found to be expressed, of which 31% had significant heritability when a false-discovery rate of 0.05 was used. QTLs were detected for 33 genes on the basis of at least one P value <.000005. Of these, 13 genes possessed a QTL within 5 Mb of their physical location. Hierarchical clustering was performed on the basis of both Pearson correlation of gene expression and genetic correlation. Both reflected biologically relevant activity taking place in the lymphoblastoid cell lines, with greater coherency represented in Kyoto Encyclopedia of Genes and Genomes database (KEGG) pathways than in Gene Ontology database pathways. However, more pathway coherence was observed in KEGG pathways when clustering was based on genetic correlation than when clustering was based on Pearson correlation. As more expression data in segregating populations are generated, viewing clusters or networks based on genetic correlation measures and shared QTLs will offer potentially novel insights into the relationship among genes that may underlie complex traits.     

Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes

Modern medicine faces the challenge of developing safer and more effective therapies to treat human diseases. Many drugs currently in use were discovered without knowledge of their underlying molecular mechanisms. Understanding their biological targets and modes of action will be essential to design improved second-generation compounds. Here, we describe the use of a genome-wide pool of tagged heterozygotes to assess the cellular effects of 78 compounds in Saccharomyces cerevisiae. Specifically, lanosterol synthase in the sterol biosynthetic pathway was identified as a target of the antianginal drug molsidomine, which may explain its cholesterol-lowering effects. Further, the rRNA processing exosome was identified as a potential target of the cell growth inhibitor 5-fluorouracil. This genome-wide screen validated previously characterized targets or helped identify potentially new modes of action for over half of the compounds tested, providing proof of this principle for analyzing the modes of action of clinically relevant compounds.