Absence of an embryonic stem cell DNA methylation signature in human cancer.

BackgroundDifferentiated cells that arise from stem cells in early development contain DNA methylation features that provide a memory trace of their fetal cell origin (FCO). The FCO signature was developed to estimate the proportion of cells in a mixture of cell types that are of fetal origin and are reminiscent of embryonic stem cell lineage. Here we implemented the FCO signature estimation method to compare the fraction of cells with the FCO signature in tumor tissues and their corresponding nontumor normal tissues.MethodsWe applied our FCO algorithm to discovery data sets obtained from The Cancer Genome Atlas (TCGA) and replication data sets obtained from the Gene Expression Omnibus (GEO) data repository. Wilcoxon rank sum tests, linear regression models with adjustments for potential confounders and non-parametric randomization-based tests were used to test the association of FCO proportion between tumor tissues and nontumor normal tissues. P-values of < 0.05 were considered statistically significant.ResultsAcross 20 different tumor types we observed a consistently lower FCO signature in tumor tissues compared with nontumor normal tissues, with 18 observed to have significantly lower FCO fractions in tumor tissue (total n = 6,795 tumor, n = 922 nontumor, P < 0.05). We replicated our findings in 15 tumor types using data from independent subjects in 15 publicly available data sets (total n = 740 tumor, n = 424 nontumor, P < 0.05).ConclusionsThe results suggest that cancer development itself is substantially devoid of recapitulation of normal embryologic processes. Our results emphasize the distinction between DNA methylation in normal tightly regulated stem cell driven differentiation and cancer stem cell reprogramming that involves altered methylation in the service of great cell heterogeneity and plasticity

Springtime phytoplankton dynamics in Arctic Krossfjorden and Kongsfjorden (Spitsbergen) as a function of glacier proximity

The hydrographic properties of the Kongsfjorden-Krossfjorden system (79 degrees N, Spitsbergen) are affected by Atlantic water incursions as well as glacier meltwater runoff. This results in strong physical gradients (temperature, salinity and irradiance) within the fjords. Here, we tested the hypothesis that glaciers affect phytoplankton dynamics as early as the productive spring bloom period. During two campaigns in 2007 (late spring) and 2008 (early spring) we studied hydrographic characteristics and phytoplankton variability along two transects in both fjords, using high-performance liquid chromatography (HPLC)-CHEMTAX pigment fingerprinting, molecular fingerprinting (denaturing gradient gel electrophoresis, or DGGE) and sequencing of 18S rRNA genes. The sheltered inner fjord locations remained colder during spring as opposed to the outer locations. Vertical light attenuation coefficients increased from early spring onwards, at all locations, but in particular at the inner locations. In late spring meltwater input caused stratification of surface waters in both fjords. The inner fjord locations were characterized by overall lower phytoplankton biomass. Furthermore HPLC-CHEMTAX data revealed that diatoms and Phaeocystis sp. were replaced by small nano-and picophytoplankton during late spring, coinciding with low nutrient availability. The innermost stations showed higher relative abundances of nano-and picophytoplankton throughout, notably of cyanophytes and cryptophytes. Molecular fingerprinting revealed a high similarity between inner fjord samples from early spring and late spring samples from all locations, while outer samples from early spring clustered separately. We conclude that glacier influence, mediated by early meltwater input, modifies phytoplankton biomass and composition already during the spring bloom period, in favor of low biomass and small cell size communities. This may affect higher trophic levels especially when regional warming further increases the period and volume of meltwater

Variability of protistan and bacterial communities in two Arctic fjords (Spitsbergen)

Krossfjorden and Kongsfjorden are Arctic fjords on the western side of Spitsbergen. These fjords share a common mouth to the open sea, and both are influenced by the input of sediment-rich glacial meltwater leading to decreased surface salinity, increased turbidity and decreased light penetration during summer. Earlier classical taxonomic studies had described the pelagic protistan composition of the Kongsfjorden during summer, revealing the dominance of flagellates of often unresolved taxonomic origin. Only little information existed on microbial eukaryote composition of the Krossfjorden as well as the bacterial composition of both fjords. The aim of the present study was to analyze and compare surface summertime protistan and bacterial communities in both fjords, using molecular approaches (16S and 18S rRNA DGGE, sequencing). Samples were collected three times a week from the central Kongsfjorden over a 1-month period. Additionally, 10 marine and 2 freshwater sites were sampled within a 1-week period in both Kongsfjorden and Krossfjorden. The central Kongsfjorden revealed a relatively stable protistan community over time with dinoflagellates, chlorophytes and small heterotrophs dominating. In contrast, the bacterial community varied over time and appeared to be correlated with the inflow of glacial meltwater. The Kongsfjorden and Krossfjorden were found to harbor distinctive bacterial and eukaryotic communities. We speculate that differences in glacial meltwater composition and fjord bathymetry affect the surface water properties and therefore the observed spatial variability in the community fingerprints.</p

Description of Atmospheric Conditions at the Pierre Auger Observatory Using Meteorological Measurements and Models

Atmospheric conditions at the site of a cosmic ray observatory must be known well for reconstructing observed extensive air showers, especially when measured using the fluorescence technique. For the Pierre Auger Observatory, a sophisticated network of atmospheric monitoring devices has been conceived. Part of this monitoring was a weather balloon program to measure atmospheric state variables above the Observatory. To use the data in reconstructions of air showers, monthly models have been constructed. Scheduled balloon launches were abandoned and replaced with launches triggered by high-energetic air showers as part of a rapid monitoring system. Currently, the balloon launch program is halted and atmospheric data from numerical weather prediction models are used. A description of the balloon measurements, the monthly models as well as the data from the numerical weather prediction are presented

The Central Laser Facility at the Pierre Auger Observatory

The Central Laser Facility is located near the middle of the Pierre Auger Observatory in Argentina. It features a UV laser and optics that direct a beam of calibrated pulsed light into the sky. Light scattered from this beam produces tracks in the Auger optical detectors which normally record nitrogen fluorescence tracks from cosmic ray air showers. The Central Laser Facility provides a "test beam" to investigate properties of the atmosphere and the fluorescence detectors. The laser can send light via optical fiber simultaneously to the nearest surface detector tank for hybrid timing analyses. We describe the facility and show some examples of its many uses.Comment: 4 pages, 5 figures, submitted to 29th ICRC Pune Indi

Macroalgae

Research on Antarctic macroalgae began with the expeditions of Gaudichaud, Bory, Montagne, Hooker and Harvey as early as 1817 (Godley 1965). A second notable period in the exploration of macroalgae from the Southern Ocean and the cold-temperate regions of South America was around the turn of the 19th to the 20th century. The most important studies during this time were conducted by Hariot, Reinsch, Gain, Skottsberg and Kylin (Wiencke & Clayton 2002). These taxonomic and biogeographical studies enabled Papenfuss (1964) to produce the first catalogue of Antarctic and sub-Antarctic benthic marine macroalgae. The introduction of SCUBA diving into the methodological portfolio by Neushul (1965), Zaneveld (1966a, b, 1968) and Delépine et al. (1966) opened a new era. Later on, Moe (Moe & DeLaca 1976), Lamb & Zimmermann (1976), Amsler (Amsler et al., 1995) and Klöser and co-workers (Klöser et al. 1996) conducted numerous diving studies allowing for the first time more precise descriptions of the depth distribution of Antarctic macroalgae. In subsequent years a major attempt was made to investigate the life history of Antarctic species (Wiencke et al. 2007). In this period scientific knowledge of Antarctic macroalgae was considerably broadened and the first monograph of these ecologically important species was compiled (Wiencke & Clayton 2002). Moreover, in-depth studies on the physiological thallus anatomy (Wiencke et al. 2007), phenology (Wiencke et al. 2011) as well as on the temperature and light requirements (Gómez et al. 2011, Wiencke & Amsler 2012) of Antarctic species became possible. Detailed investigations on trophic relations between macroalgae and herbivores began in the last decade of the 20th century (Iken 1996, 1999). Recent studies focus on the defenses between macroalgae and herbivores, defences against diatom fouling (Amsler et al. 2005a, 2008, 2011, Iken et al. 2011, Wiencke & Amsler 2012) as well as on the effect of global climate changes on geographic distribution (Müller et al. 2011) and depth zonation (Zacher et al. 2007a, Campana et al. 2011)