Blockage and recovery of nitrification in soils exposed to acetylene

Acetylene gas is very useful in laboratory and in situ assay procedures for nitrogen fixation and denitrification. There is concern, however, that measurements of denitrification may be underestimated because nitrification, a major source of nitrate, is inhibited by C 2 H 2 . The objective of this study was to examine the effects of C 2 H 2 partial pressure and length of exposure time on nitrification in soils. Acetylene partial pressures of 0.1, 1.0, and 10.0 kPa were found to effectively inhibit nitrification in soil samples incubated in the laboratory. Both the partial pressure of C 2 H 2 and the length of exposure time were found to affect the recovery time of nitrification in soil samples. Nitrification recovered within seven days in samples exposed to 0.1 and 1.0 kPa C 2 H 2 for only 24 hours. The recovery of nitrification in samples exposed to 10.0 kPa C 2 H 2 for 24 hours or to 0.1 and 1.0 kPa C 2 H 2 for 216 hours was delayed for an additional seven days, however.     

Potential use of Great Salt Lake water for lobster culture

Three experiments were conducted to determine if water from the Great Salt Lake altered in chemical composition and dilution can be used successfully to sustain a species of hermit crab Pagarus sp. and the American Lobster ( Homarus americanus ). Great Salt Lake water altered by freshwater dilution will not sustain the hermit crab or the American lobster. Great Salt Lake water can be altered chemically by dilution to support growth of the American lobster. American lobsters maintained in Instant Ocean synthetic sea water (control) grow at a more rapid rate than animals sustained in altered Great Salt Lake water. A plastic primer coat used for plastic tank repair appears to be a moult inhibitor for the American lobster. Lobsters afflicted by the primer coat are not able to reverse the damage by continued moults.     

European earwig, Forficula auricularia L. (Dermaptera: Forficulidae), at the Hanford Reach National Monument, Washington State

The European earwig, Forficula auricularia L., was surveyed using pitfall traps at 3 sites at the Hanford Reach National Monument in south central Washington State. Pitfall traps were collected weekly from April 2002 through April 2003. The earwig was consistently taken during all months of the year at a disturbed, weedy site along the Columbia River (White Bluffs Ferry site) but was rare or not collected in 2 less-disturbed shrubsteppe habitats. Highest numbers occurred during April–May, when immatures accounted for the majority of the catch; immatures reached the adult stage during mid-July, and the species is univoltine at the site. Possible reasons why earwigs have not colonized the monument’s shrubsteppe habitat include the arid climate with lack of available moisture, especially for breeding purposes, and a lack of burrow sites. La tijereta Europea, Forficula auricularia L., fue estudiada usando trampas de caída en tres sitios del Hanford Reach National Monument en el sur del estado de Washington. Se colectaron los contenidos de las trampas de caída semanalmente desde abril de 2002 hasta abril de 2003. La tijereta apareció constantemente durante todos los meses del año en un sitio perturbado de vegetación herbácea en la orilla del Río Columbia (el lugar del antiguo transbordador White Bluffs) pero su colecta fue escasa o nula en dos hábitats de estepa arbustiva menos perturbados. Los mayores números ocurrieron durante abril y mayo cuando los organismos inmaduros representaron la mayoría de los especímenes capturados; éstos alcanzaron la etapa adulta a mediados de julio y la especie es univoltina en este sitio. Posibles causas de que las tijeretas no hayan colonizado el hábitat de estepa arbustiva del Monumento podrían incluir su clima árido carente de agua disponible, especialmente para la reproducción, y una falta de sitios para madrigueras.     

Relationship between environmental and vegetational parameters for understory and open-area communities

Ten individuals from each of four tree species were selected, and their associated understory and adjacent open-area communities were sampled for both environmental and vegetational parameters, including light intensity, pH, litter depth, soil depth, and percentages of exposed rock, litter cover, living cover, shrubs, forbs, grasses, and annuals. The four tree species were ponderosa pine, Rocky Mountain juniper, Gambel oak, and snowbrush ceanothus. The study site was in the lower Uinta Mountains about 10 miles east of Kamas, Utah. Correlations among the various biotic and abiotic parameters were examined. The interplay of these factors in differentiating the understory and open-area communities is discussed.       

Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33

Genome-wide association studies (GWAS) have identified ten loci harboring common variants that influence risk of developing colorectal cancer (CRC). To enhance the power to identify additional CRC risk loci, we conducted a meta-analysis of three GWAS from the UK which included a total of 3,334 affected individuals (cases) and 4,628 controls followed by multiple validation analyses including a total of 18,095 cases and 20,197 controls. We identified associations at four new CRC risk loci: 1q41 (rs6691170, odds ratio (OR) = 1.06, P = 9.55 × 10?1? and rs6687758, OR = 1.09, P = 2.27 × 10??, 3q26.2 (rs10936599, OR = 0.93, P = 3.39 × 10??), 12q13.13 (rs11169552, OR = 0.92, P = 1.89 × 10?1? and rs7136702, OR = 1.06, P = 4.02 × 10??) and 20q13.33 (rs4925386, OR = 0.93, P = 1.89 × 10?1?). In addition to identifying new CRC risk loci, this analysis provides evidence that additional CRC-associated variants of similar effect size remain to be discovered.     

Evidence for an instructive mechanism of de novo methylation in cancer cells

DNA methylation has a role in the regulation of gene expression during normal mammalian development but can also mediate epigenetic silencing of CpG island genes in cancer and other diseases. Many individual genes (including tumor suppressors) have been shown to undergo de novo methylation in specific tumor types, but the biological logic inherent in this process is not understood. To decipher this mechanism, we have adopted a new approach for detecting CpG island DNA methylation that can be used together with microarray technology. Genome-wide analysis by this technique demonstrated that tumor-specific methylated genes belong to distinct functional categories, have common sequence motifs in their promoters and are found in clusters on chromosomes. In addition, many are already repressed in normal cells. These results are consistent with the hypothesis that cancer-related de novo methylation may come about through an instructive mechanism.     

Genome assembly comparison identifies structural variants in the human genome

Numerous types of DNA variation exist, ranging from SNPs to larger structural alterations such as copy number variants (CNVs) and inversions. Alignment of DNA sequence from different sources has been used to identify SNPs and intermediate-sized variants (ISVs). However, only a small proportion of total heterogeneity is characterized, and little is known of the characteristics of most smaller-sized (<50 kb) variants. Here we show that genome assembly comparison is a robust approach for identification of all classes of genetic variation. Through comparison of two human assemblies (Celera's R27c compilation and the Build 35 reference sequence), we identified megabases of sequence (in the form of 13,534 putative non-SNP events) that were absent, inverted or polymorphic in one assembly. Database comparison and laboratory experimentation further demonstrated overlap or validation for 240 variable regions and confirmed >1.5 million SNPs. Some differences were simple insertions and deletions, but in regions containing CNVs, segmental duplication and repetitive DNA, they were more complex. Our results uncover substantial undescribed variation in humans, highlighting the need for comprehensive annotation strategies to fully interpret genome scanning and personalized sequencing projects.     

A truncating mutation of HDAC2 in human cancers confers resistance to histone deacetylase inhibition

Disruption of histone acetylation patterns is a common feature of cancer cells, but very little is known about its genetic basis. We have identified truncating mutations in one of the primary human histone deacetylases, HDAC2, in sporadic carcinomas with microsatellite instability and in tumors arising in individuals with hereditary nonpolyposis colorectal cancer syndrome. The presence of the HDAC2 frameshift mutation causes a loss of HDAC2 protein expression and enzymatic activity and renders these cells more resistant to the usual antiproliferative and proapoptotic effects of histone deacetylase inhibitors. As such drugs may serve as therapeutic agents for cancer, our findings support the use of HDAC2 mutational status in future pharmacogenetic treatment of these individuals.