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

(Per)chlorate-reducing bacteria can utilize aerobic and anaerobic pathways of aromatic degradation with (per)chlorate as an electron acceptor.

UnlabelledThe pathways involved in aromatic compound oxidation under perchlorate and chlorate [collectively known as (per)chlorate]-reducing conditions are poorly understood. Previous studies suggest that these are oxygenase-dependent pathways involving O2 biogenically produced during (per)chlorate respiration. Recently, we described Sedimenticola selenatireducens CUZ and Dechloromarinus chlorophilus NSS, which oxidized phenylacetate and benzoate, two key intermediates in aromatic compound catabolism, coupled to the reduction of perchlorate or chlorate, respectively, and nitrate. While strain CUZ also oxidized benzoate and phenylacetate with oxygen as an electron acceptor, strain NSS oxidized only the latter, even at a very low oxygen concentration (1%, vol/vol). Strains CUZ and NSS contain similar genes for both the anaerobic and aerobic-hybrid pathways of benzoate and phenylacetate degradation; however, the key genes (paaABCD) encoding the epoxidase of the aerobic-hybrid phenylacetate pathway were not found in either genome. By using transcriptomics and proteomics, as well as by monitoring metabolic intermediates, we investigated the utilization of the anaerobic and aerobic-hybrid pathways on different electron acceptors. For strain CUZ, the results indicated utilization of the anaerobic pathways with perchlorate and nitrate as electron acceptors and of the aerobic-hybrid pathways in the presence of oxygen. In contrast, proteomic results suggest that strain NSS may use a combination of the anaerobic and aerobic-hybrid pathways when growing on phenylacetate with chlorate. Though microbial (per)chlorate reduction produces molecular oxygen through the dismutation of chlorite (ClO2(-)), this study demonstrates that anaerobic pathways for the degradation of aromatics can still be utilized by these novel organisms.ImportanceS. selenatireducens CUZ and D. chlorophilus NSS are (per)chlorate- and chlorate-reducing bacteria, respectively, whose genomes encode both anaerobic and aerobic-hybrid pathways for the degradation of phenylacetate and benzoate. Previous studies have shown that (per)chlorate-reducing bacteria and chlorate-reducing bacteria (CRB) can use aerobic pathways to oxidize aromatic compounds in otherwise anoxic environments by capturing the oxygen produced from chlorite dismutation. In contrast, we demonstrate that S. selenatireducens CUZ is the first perchlorate reducer known to utilize anaerobic aromatic degradation pathways with perchlorate as an electron acceptor and that it does so in preference over the aerobic-hybrid pathways, regardless of any oxygen produced from chlorite dismutation. D. chlorophilus NSS, on the other hand, may be carrying out anaerobic and aerobic-hybrid processes simultaneously. Concurrent use of anaerobic and aerobic pathways has not been previously reported for other CRB or any microorganisms that encode similar pathways of phenylacetate or benzoate degradation and may be advantageous in low-oxygen environments

Movements, connectivity, and space use of immature green turtles within coastal habitats of the Culebra Archipelago, Puerto Rico: implications for conservation

Juvenile green turtles occupy coastal marine habitats important for their ontogeny; however, the details of their movement, connectivity, and space use in these developmental habitats are still poorly understood. Given that these areas are often threatened by human disturbance, additional information on green turtle spatial ecology is needed to meet conservation end- points for this endangered species. For this study, we used fixed passive acoustic telemetry to (1) describe movement patterns and connectivity of immature green turtles within, outside, and across 2 bays, Manglar and Tortuga bays, on Culebra and Culebrita islands, Puerto Rico; and (2) determine spatio-temporal drivers of the presence and absence of turtles within Manglar Bay. Network analysis used to quantify movement patterns showed that turtles in our study exhibited differential space use with little to no connectivity across the 2 bays. In addition, turtles exhibited high site fidelity, with larger turtles leaving on brief trips. We applied a presence−absence Bayesian binomial model on a subset of 9 turtles at an hourly temporal scale and showed that turtles within Manglar Bay occupied areas of lagoon and seagrass habitats at night and were rarely using areas of macroalgae habitat. The parameter estimates from the model enabled us to predict the space use of turtles across Manglar Bay, and the hourly probability distributions highlighted predictive diel movement patterns across the bay. Considering the importance of juvenile and subadult life stages for population viability, we recommend continued protection of these critical juvenile turtle developmental habitats to ensure recruitment into the adult life stage

Solar Carbon Monoxide, Thermal Profiling, and the Abundances of C, O, and their Isotopes

A solar photospheric "thermal profiling" analysis is presented, exploiting the infrared rovibrational bands of carbon monoxide (CO) as observed with the McMath-Pierce Fourier transform spectrometer (FTS) at Kitt Peak, and from above the Earth's atmosphere by the Shuttle-borne ATMOS experiment. Visible continuum intensities and center-limb behavior constrained the temperature profile of the deep photosphere, while CO center-limb behavior defined the thermal structure at higher altitudes. The oxygen abundance was self consistently determined from weak CO absorptions. Our analysis was meant to complement recent studies based on 3-D convection models which, among other things, have revised the historical solar oxygen (and carbon) abundance downward by a factor of nearly two; although in fact our conclusions do not support such a revision. Based on various considerations, an oxygen abundance of 700+/-100 ppm (parts per million relative to hydrogen) is recommended; the large uncertainty reflects the model sensitivity of CO. New solar isotopic ratios also are reported for 13C, 17O, and 18O.Comment: 90 pages, 19 figures (some with parts "a", "b", etc.); to be published in the Astrophysical Journal Supplement

Caridina nilotica in Lake Victoria: abundance, biomass, and diel vertical migration

Caridina nilotica (Decapoda: Atyidae) in offshore waters of Lake Victoria were investigated with both day and night sampling over a period of two years. Offshore populations are mainly planktonic rather than benthic, and the animals exhibit diel vertical migrations into near-surface waters at night. These changes in diel abundance as well as the size-frequency distribution of the migrating shrimp suggest that the migratory behavior is in response to visual planktivory, because only the very smallest individuals (2–4 mm) remain in surface waters during the day. During October 1992, abundances were estimated both by vertical net sampling and by underwater video transect methods. Concordance was established between abundances estimated by the two methods. Only about 9% (night) to 14% (day) of the Caridina population appeared to be epibenthic. We suggest that the behavior of the animal is consistent with the hypothesis that it is not a strict detritivore as previously reported; rather it may engage in facultative planktivory, especially at night.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42890/1/10750_2004_Article_BF00036467.pd

Warming seas increase cold-stunning events for Kemp’s ridley sea turtles in the northwest Atlantic

Since the 1970s, the magnitude of turtle cold-stun strandings have increased dramatically within the northwestern Atlantic. Here, we examine oceanic, atmospheric, and biological factors that may affect the increasing trend of cold-stunned Kemp’s ridleys in Cape Cod Bay, Massachusetts, United States of America. Using machine learning and Bayesian inference modeling techniques, we demonstrate higher cold-stunning years occur when the Gulf of Maine has warmer sea surface temperatures in late October through early November. Surprisingly, hatchling numbers in Mexico, a proxy for population abundance, was not identified as an important factor. Further, using our Bayesian count model and forecasted sea surface temperature projections, we predict more than 2,300 Kemp’s ridley turtles may cold-stun annually by 2031 as sea surface temperatures continue to increase within the Gulf of Maine. We suggest warmer sea surface temperatures may have modified the northerly distribution of Kemp’s ridleys and act as an ecological bridge between the Gulf Stream and nearshore waters. While cold-stunning may currently account for a minor proportion of juvenile mortality, we recommend continuing efforts to rehabilitate cold-stunned individuals to maintain population resiliency for this critically endangered species in the face of a changing climate and continuing anthropogenic threats

Evidence towards the involvement of nitric oxide in drought tolerance of sugarcane

© 2017 Elsevier Masson SAS Exogenous supply of nitric oxide (NO) increases drought tolerance in sugarcane plants. However, little is known about the role of NO produced by plants under water deficit. The aim of this study was to test the hypothesis that drought-tolerance in sugarcane is associated with NO production and metabolism, with the more drought-tolerant genotype presenting higher NO accumulation in plant tissues. The sugarcane genotypes IACSP95-5000 (drought-tolerant) and IACSP97-7065 (drought-sensitive) were submitted to water deficit by adding polyethylene glycol (PEG-8000) in nutrient solution to reduce the osmotic potential to−0.4MPa. To evaluate short-time responses to water deficit, leaf and root samples were taken after 24h under water deficit. The drought-tolerant genotype presented higher root extracellular NO content, which was accompanied by higher root nitrate reductase (NR) activity as compared to the drought-sensitive genotype under water deficit. In addition, the drought-tolerant genotype had higher leaf intracellular NO content than the drought-sensitive one. IACSP95-5000 exhibited decreases in root S-nitrosoglutathione reductase (GSNOR) activity under water deficit, suggesting that S-nitrosoglutathione (GSNO) is less degraded and that the drought-tolerant genotype has a higher natural reservoir of NO than the drought-sensitive one. Those differences in intracellular and extracellular NO contents and enzymatic activities were associated with higher leaf hydration in the drought-tolerant genotype as compared to the sensitive one under water deficit