How do the environmental extremes of Siberian permafrost soils shape the composition of the bacterial soil community?

Microbial communities in permafrost soils of the Siberian Arctic are exposed to extreme environmental conditions. The soils are frozen throughout the entire year except for the short summer period, when thawing of the uppermost 20 to 50 cm of the permafrost sediment allows for the formation of a so-called active layer. Active layers show steep temperature gradients between 10 to 18 °C near the surface and 0 to 1 °C near the permafrost table. Additionally, seasonal freezing and thawing processes lead to the formation of patterns of low-centered polygons. Low-centered polygons determine a pronounced small-scale heterogeneity with regard to their physical and chemical properties between the elevated polygon rims and the depressed polygon centers.Within the active layer of a polygon rim, vertical profiles of potential methane oxidation rates in respond to different temperatures indicated a shift in the temperature optimum from 21 °C near the surface to 4 °C near the permafrost table [1]. This temperature shift could not be shown in samples of the polygon center. Based on these results we used 16S rDNA clone libraries as well as in-situ cell counting to compare the bacterial, in particular the methane oxidizing, community near the surface and near the permafrost table in samples of the polygon rim. The phylogenetic analyses show that the composition of the bacterial community near the surface is significantly different from the bacterial community near the permafrost table. The results also show that bacterial diversity and abundance in Siberian permafrost soils are comparably high as in temperate terrestrial environments.[1] Liebner. S. and Wagner, D. (in press) Abundance, distribution and potential activity of methane oxidizing bacteria in permafrost soils from the Lena Delta, Siberia. Environmental Microbiology doi: 10.1111/j.1462-2920.2006.01120.

An Implementation of Bayesian Adaptive Regression Splines (BARS) in C with S and R Wrappers

BARS (DiMatteo, Genovese, and Kass 2001) uses the powerful reversible-jump MCMC engine to perform spline-based generalized nonparametric regression. It has been shown to work well in terms of having small mean-squared error in many examples (smaller than known competitors), as well as producing visually-appealing fits that are smooth (filtering out high-frequency noise) while adapting to sudden changes (retaining high-frequency signal). However, BARS is computationally intensive. The original implementation in S was too slow to be practical in certain situations, and was found to handle some data sets incorrectly. We have implemented BARS in C for the normal and Poisson cases, the latter being important in neurophysiological and other point-process applications. The C implementation includes all needed subroutines for fitting Poisson regression, manipulating B-splines (using code created by Bates and Venables), and finding starting values for Poisson regression (using code for density estimation created by Kooperberg). The code utilizes only freely-available external libraries (LAPACK and BLAS) and is otherwise self-contained. We have also provided wrappers so that BARS can be used easily within S or R.

An Account of the Loss of the Country Ship Forbes and Frazer Sinclair, Her Late Commander

This paper reports on the life of the English Country trader Captain Frazer Sinclair leading up to and following the loss of the Forbes in the Karimata Strait in 1806. It examines the adventure and tenuous times of trading around the Indonesian archipelago after the fall of the VOC and subsequent transfer to the British. Included are the details of Captain Sinclair\u27s trading history, multiple prizes as a privateer, and shipwrecks

Methane emissions from an alpine fen in central Switzerland

Methane emissions and below ground methane pore water concentrations were determined in an alpine fen at 1,915m a.s.l. in central Switzerland. The fen represented an acidic (pH 4.5-4.9), nutrient-poor to mesotrophic habitat dominated by Carex limosa, Carex rostrata, Trichophorum caespitosum and Sphagnum species. From late fall to late spring the fen was snow-covered. Throughout winter the temperatures never dropped below 0°C at 5cm below the vegetation surface. Methane emissions in June, July, August and September were in the range of 125 (±26)-313 (±71)mgCH4m−2day−1 with a tendency to decrease along the summer season. Mean methane pore water concentrations at a depth of 20-40cm below the vegetation surface were 526 (±32)μM in June and in the range of 144 (±10)-233 (±7)μM in July, August and September. At a depth of 0-20cm the mean methane pore water concentrations dropped back to <20μM with an almost linear decrease between 0 and 15cm. Oxygen pore water concentrations were close to air saturation in the first few centimeters and dropped back below detection limit at a depth of 20cm. In July and August the pore water concentrations of dissolved organic carbon (DOC) were in the range of 7.2-10.1mgCl−1 at all depths. The pore water concentrations of acetate, formate and oxalate were in the range of 2.0-8.2μM at all depths. Methanotrophic and methanogenic communities were quantified using pmoA and mcrA, respectively, as marker genes. The abundances of both communities showed a distinct peak at a depth of 10-15cm below the vegetation surfac

Endothelial Wnt/β-catenin signaling inhibits glioma angiogenesis and normalizes tumor blood vessels by inducing PDGF-B expression

Endothelial Wnt/β-catenin signaling is necessary for angiogenesis of the central nervous system and blood–brain barrier (BBB) differentiation, but its relevance for glioma vascularization is unknown. In this study, we show that doxycycline-dependent Wnt1 expression in subcutaneous and intracranial mouse glioma models induced endothelial Wnt/β-catenin signaling and led to diminished tumor growth, reduced vascular density, and normalized vessels with increased mural cell attachment. These findings were corroborated in GL261 glioma cells intracranially transplanted in mice expressing dominant-active β-catenin specifically in the endothelium. Enforced endothelial β-catenin signaling restored BBB characteristics, whereas inhibition by Dkk1 (Dickkopf-1) had opposing effects. By overactivating the Wnt pathway, we induced the Wnt/β-catenin–Dll4/Notch signaling cascade in tumor endothelia, blocking an angiogenic and favoring a quiescent vascular phenotype, indicated by induction of stalk cell genes. We show that β-catenin transcriptional activity directly regulated endothelial expression of platelet-derived growth factor B (PDGF-B), leading to mural cell recruitment thereby contributing to vascular quiescence and barrier function. We propose that reinforced Wnt/β-catenin signaling leads to inhibition of angiogenesis with normalized and less permeable vessels, which might prove to be a valuable therapeutic target for antiangiogenic and edema glioma therapy

Willingness of farmers to pay for reclaimed wastewater in Jordan and Tunisia.

Despite water scarcity and high agricultural water consumption in the Middle East and North Africa region, substantial amounts of treated wastewater are discharged into seas without proper utilization. This can be attributed to either farmers' unwillingness to use or to pay for reclaimed wastewater. Therefore, a field survey was conducted in Jordan and Tunisia, which are considered as representative to the MENA region, using a prepared and pilot tested questionnaire. This study applies the contingent valuation method to elicit the willingness of farmers to pay for reclaimed wastewater. Logistic regression analysis is applied in an attempt to build a model that correlates qualitative responses of farmers to monetary stimuli. The water price seriously affects farming profitability and farmers' willingness to pay for reclaimed wastewater. Farmers prove to be unwilling to pay more than 0.05 $/m3 of reclaimed wastewater primarily because of quality concerns, comparatively easy access to freshwater, and price

Wnt/beta-catenin signaling controls development of the blood–brain barrier

The blood–brain barrier (BBB) is confined to the endothelium of brain capillaries and is indispensable for fluid homeostasis and neuronal function. In this study, we show that endothelial Wnt/beta-catenin (beta-cat) signaling regulates induction and maintenance of BBB characteristics during embryonic and postnatal development. Endothelial specific stabilization of beta-cat in vivo enhances barrier maturation, whereas inactivation of beta-cat causes significant down-regulation of claudin3 (Cldn3), up-regulation of plamalemma vesicle-associated protein, and BBB breakdown. Stabilization of beta-cat in primary brain endothelial cells (ECs) in vitro by N-terminal truncation or Wnt3a treatment increases Cldn3 expression, BBB-type tight junction formation, and a BBB characteristic gene signature. Loss of beta-cat or inhibition of its signaling abrogates this effect. Furthermore, stabilization of beta-cat also increased Cldn3 and barrier properties in nonbrain-derived ECs. These findings may open new therapeutic avenues to modulate endothelial barrier function and to limit the devastating effects of BBB breakdown

Junctional adhesion molecule (JAM)-C deficient C57BL/6 mice develop a severe hydrocephalus

The junctional adhesion molecule (JAM)-C is a widely expressed adhesion molecule regulating cell adhesion, cell polarity and inflammation. JAM-C expression and function in the central nervous system (CNS) has been poorly characterized to date. Here we show that JAM-C−/− mice backcrossed onto the C57BL/6 genetic background developed a severe hydrocephalus. An in depth immunohistochemical study revealed specific immunostaining for JAM-C in vascular endothelial cells in the CNS parenchyma, the meninges and in the choroid plexus of healthy C57BL/6 mice. Additional JAM-C immunostaining was detected on ependymal cells lining the ventricles and on choroid plexus epithelial cells. Despite the presence of hemorrhages in the brains of JAM-C−/− mice, our study demonstrates that development of the hydrocephalus was not due to a vascular function of JAM-C as endothelial re-expression of JAM-C failed to rescue the hydrocephalus phenotype of JAM-C−/− C57BL/6 mice. Evaluation of cerebrospinal fluid (CSF) circulation within the ventricular system of JAM-C−/− mice excluded occlusion of the cerebral aqueduct as the cause of hydrocephalus development but showed the acquisition of a block or reduction of CSF drainage from the lateral to the 3rd ventricle in JAM-C−/− C57BL/6 mice. Taken together, our study suggests that JAM-C−/− C57BL/6 mice model the important role for JAM-C in brain development and CSF homeostasis as recently observed in humans with a loss-of-function mutation in JAM-C