Combined effects of heterogeneity, anisotropy, and saturation on steady state flow and transport: A laboratory sand tank experiment

Field soils show rather different spreading behavior at different water saturations, frequently caused by layering of the soil material. We performed tracer experiments in a laboratory sand tank. Such experiments complement and help comprehension of field investigations. We estimated, by image analysis, the first two moments of small plumes traveling through a two-dimensional, heterogeneous medium with strongly anisotropic correlation structure. Three steady state regimes were analyzed. Two main conclusions were drawn. First, low saturation led to very large heterogeneity and to strong preferential flow. Thus the description of the flow paths and the prediction of the solute arrival times require, in this case, more accurate knowledge about the topological structure. Second, saturation-dependent macroscopic anisotropy is an essential element of transport in unsaturated media. For this reason, small structural soil features should be properly upscaled to give appropriate effective soil parameters to be input in transport models.

Primer extension based quantitative polymerase chain reaction reveals consistent differences in the methylation status of the MGMT promoter in diffusely infiltrating gliomas (WHO grade II-IV) of adults

Diffusely infiltrating gliomas (WHO grade II-IV) are the most common primary brain tumours in adults. These tumours are not amenable to cure by surgery alone, so suitable biomarkers for adjuvant modalities are required to guide therapeutic decision-making. Epigenetic silencing of the O(6)-methylguanine-DNA methyltransferase (MGMT) gene by promoter methylation has been associated with longer survival of patients with high-grade gliomas who receive alkylating chemotherapy; and molecular testing for the methylation status of the MGMT promoter sequence is regarded as among the most relevant of such markers. We have developed a primer extension-based assay adapted to formalin-fixed paraffin-embedded tissues that enables quantitative assessment of the methylation status of the MGMT promoter. The assay is very sensitive, highly reproducible, and provides valid test results in nearly 100% of cases. Our results indicate that oligodendrogliomas, empirically known to have a relatively favourable prognosis, are also the most homogeneous entities in terms of MGMT promoter methylation. Conversely, astrocytomas, which are more prone to spontaneous progression to higher grade malignancy, are significantly more heterogeneous. In addition, we show that the degree of promoter methylation correlates with the prevalence of loss of heterozygosity on chromosome arm 1p in the oligodendroglioma group, but not the astrocytoma group. Our results may have potentially important implications for clinical molecular diagnosis.

Mutation screening of the medium-chain acyl-CoA dehydrogenase (MCAD) and the ornithine transcarbamylase (OTC) genes by multiplex PCR amplification and sequencing

BACKGROUND: Sequencing based mutation screening assays of genes encompassing large numbers of exons could be substantially optimized by multiplex PCR, which enables simultaneous amplification of many targets in one reaction. In the present study, a multiplex PCR protocol originally developed for fragment analysis was evaluated for sequencing based mutation screening of the ornithine transcarbamylase (OTC) and the medium-chain acyl-CoA dehydrogenase (MCAD) genes. METHODS: Single exon and multiplex PCR protocols were applied to generate PCR templates for subsequent DNA sequencing of all exons of the OTC and the MCAD genes. For each PCR protocol and using the same DNA samples, 66 OTC and 98 MCAD sequence reads were generated. The sequences derived from the two different PCR methods were compared at the level of individual signal-to-noise ratios of the four bases and the proportion of high-quality base-signals. RESULTS: The single exon and the multiplex PCR protocol gave qualitatively comparable results for the two genes. CONCLUSIONS: Many existing sequencing based mutation analysis protocols may be easily optimized with the proposed method, since the multiplex PCR protocol was successfully applied without any re-design of the PCR primers and other optimization steps for generating sequencing templates for the OTC and MCAD genes, respectively.

Root Foraging Increases Performance of the Clonal Plant Potentilla reptans in Heterogeneous Nutrient Environments

Background Plastic root-foraging responses have been widely recognized as an important strategy for plants to explore heterogeneously distributed resources. However, the benefits and costs of root foraging have received little attention. Methodology/Principal Findings In a greenhouse experiment, we grew pairs of connected ramets of 22 genotypes of the stoloniferous plant Potentilla reptans in paired pots, between which the contrast in nutrient availability was set as null, medium and high, but with the total nutrient amount kept the same. We calculated root-foraging intensity of each individual ramet pair as the difference in root mass between paired ramets divided by the total root mass. For each genotype, we then calculated root-foraging ability as the slope of the regression of root-foraging intensity against patch contrast. For all genotypes, root-foraging intensity increased with patch contrast and the total biomass and number of offspring ramets were lowest at high patch contrast. Among genotypes, root-foraging intensity was positively related to production of offspring ramets and biomass in the high patch-contrast treatment, which indicates an evolutionary benefit of root foraging in heterogeneous environments. However, we found no significant evidence that the ability of plastic foraging imposes costs under homogeneous conditions (i.e. when foraging is not needed). Conclusions/Significance Our results show that plants of P. reptans adjust their root-foraging intensity according to patch contrast. Moreover, the results show that the root foraging has an evolutionary advantage in heterogeneous environments, while costs of having the ability of plastic root foraging were absent or very small.

Modeling the heterogeneous ice and gas coma of Comet 103P/Hartley 2

The spectacular images of Comet 103P/Hartley 2 recorded by the Medium Resolution Instrument (MRI) and High Resolution Instrument (HRI) on board of the Extrasolar Planet Observation and Deep Impact Extended Investigation (EPOXI) spacecraft, as the Deep Impact extended mission, revealed that its bi-lobed very active nucleus outgasses volatiles heterogeneously. Indeed, CO2 is the primary driver of activity by dragging out chunks of pure ice out of the nucleus from the sub-solar lobe that appear to be the main source of water in Hartley 2's coma by sublimating slowly as they go away from the nucleus. However, water vapor is released by direct sublimation of the nucleus at the waist without any significant amount of either CO2 or icy grains. The coma structure for a comet with such areas of diverse chemistry differs from the usual models where gases are produced in a homogeneous way from the surface. We use the fully kinetic Direct Simulation Monte Carlo model of Tenishev et al. (Tenishev, V.M., Combi, M.R., Davidsson, B. [2008]. Astrophys. J. 685, 659-677; Tenishev, V.M., Combi, M.R., Rubin, M. [2011]. Astrophys. J. 732, 104-120) applied to Comet 103P/Hartley 2 including sublimating icy grains to reproduce the observations made by EPOXI and ground-based measurements. A realistic bi-lobed nucleus with a succession of active areas with different chemistry was included in the model enabling us to study in details the coma of Hartley 2. The different gas production rates from each area were found by fitting the spectra computed using a line-by-line non-LTE radiative transfer model to the HRI observations. The presence of icy grains with long lifetimes, which are pushed anti-sunward by radiation pressure, explains the observed OH asymmetry with enhancement on the night side of the coma.

Bone-Conditioned Medium Changes Gene Expression in Bone-Derived Fibroblasts.

PURPOSE Autologous bone is used for augmentation in the course of oral implant placement. Bone grafts release paracrine signals that can modulate mesenchymal cell differentiation in vitro. The detailed genetic response of the bone-derived fibroblasts to these paracrine signals has remained elusive. Paracrine signals accumulate in bone-conditioned medium (BCM) prepared from porcine cortical bone chips. MATERIALS AND METHODS In this study, bone-derived fibroblasts were exposed to BCM followed by a whole genome expression profiling and downstream quantitative reverse transciptase polymerase chain reaction of the most strongly regulated genes. RESULTS The data show that ADM, IL11, IL33, NOX4, PRG4, and PTX3 were differentially expressed in response to BCM in bone-derived fibroblasts. The transforming growth factor beta (TGF-β) receptor 1 antagonist SB431542 blocked the effect of BCM on the expression of the gene panel, except for IL33. CONCLUSION These in vitro results extend existing evidence that cortical bone chips release paracrine signals that provoke a robust genetic response in mesenchymal cells that is not exclusively mediated via the TGF-β receptor. The present data provide further insights into the process of graft consolidation.

Breakdown of chlorophyll: A nonenzymatic reaction accounts for the formation of the colorless "nonfluorescent" chlorophyll catabolites

Senescent higher plants degrade their chlorophylls (Chls) to polar colorless tetrapyrrolic Chl catabolites, which accumulate in the vacuoles. In extracts from degreened leaves of the tree Cercidiphyllum japonicum an unpolar catabolite of this type was discovered. This tetrapyrrole was named Cj-NCC-2 and was found to be identical with the product of a stereoselective nonenzymatic isomerization of a “fluorescent” Chl catabolite. This (bio-mimetic) formation of the “nonfluorescent” catabolite Cj-NCC-2 took place readily at ambient temperature and at pH 4.9 in aqueous solution. The indicated nonenzymatic process is able to account for a crucial step during Chl breakdown in senescent higher plants. Once delivered to the acidic vacuoles, the fluorescent Chl catabolites are due to undergo a rapid, stereoselective isomerization to the ubiquitous nonfluorescent catabolites. The degradation of the Chl macrocycle is thus indicated to rely on just two known enzymes, one of which is senescence specific and cuts open the chlorin macroring. The two enzymes supply the fluorescent Chl catabolites, which are “programmed” to isomerize further rapidly in an acidic medium, as shown here. Indeed, only small amounts of the latter are temporarily observable during senescence in higher plants.