Quantifying above‐ and belowground biomass carbon loss with forest conversion in tropical lowlands of Sumatra (Indonesia)

Natural forests in South‐East Asia have been extensively converted into other land‐use systems in the past decades and still show high deforestation rates. Historically, lowland forests have been converted into rubber forests, but more recently, the dominant conversion is into oil palm plantations. While it is expected that the large‐scale conversion has strong effects on the carbon cycle, detailed studies quantifying carbon pools and total net primary production (NPP_total) in above‐ and belowground tree biomass in land‐use systems replacing rainforest (incl. oil palm plantations) are rare so far. We measured above‐ and belowground carbon pools in tree biomass together with NPP_total in natural old‐growth forests, ‘jungle rubber’ agroforests under natural tree cover, and rubber and oil palm monocultures in Sumatra. In total, 32 stands (eight plot replicates per land‐use system) were studied in two different regions. Total tree biomass in the natural forest (mean: 384 Mg ha^?1) was more than two times higher than in jungle rubber stands (147 Mg ha^?1) and >four times higher than in monoculture rubber and oil palm plantations (78 and 50 Mg ha^?1). NPP_total was higher in the natural forest (24 Mg ha^?1 yr^?1) than in the rubber systems (20 and 15 Mg ha^?1 yr^?1), but was highest in the oil palm system (33 Mg ha^?1 yr^?1) due to very high fruit production (15–20 Mg ha^?1 yr^?1). NPP_total was dominated in all systems by aboveground production, but belowground productivity was significantly higher in the natural forest and jungle rubber than in plantations. We conclude that conversion of natural lowland forest into different agricultural systems leads to a strong reduction not only in the biomass carbon pool (up to 166 Mg C ha^?1) but also in carbon sequestration as carbon residence time (i.e. biomass‐C:NPP‐C) was 3–10 times higher in the natural forest than in rubber and oil palm plantations.     

Verteporfin, photofrin II, and merocyanine 540 as PDT photosensitizers against melanoma cells

The efficiency of photodynamic effect (PDE) for Photofrin II (PfII), Verteporfin, and Merocyanine 540 (MC540) was compared against neoplastic cells. Triplet state lifetimes and singlet molecular oxygen quantum yields were correlated with biological effect. PfII triplet lifetime was two times longer than that of Verteporfin, however, its singlet molecular oxygen quantum yield was two times lower in comparison with Verteporfin. High singlet molecular oxygen quantum yield of Verteporfin resulted in high biological efficacy. To achieve 50% mortality of cells four times lower light dose and five times lower concentration of Verteporfin were applied in comparison with PfII. The same level of cell damage was reached using 10 times higher light dose and two times higher concentration of MC540 in comparison with PfII. Our results confirm that singlet molecular oxygen based mechanism, prevalent for Verteporfin and PfII, was highly effective against melanoma cells. Verteporfin can be used at small doses with high cellular damage efficiency.     

Expression of HSP27, HSP72 and MRP proteins in <Emphasis Type="Italic">in vitro</Emphasis> co-culture of colon tumour cell spheroids with normal cells after incubation with rhTGF-<Emphasis Type="Italic">β</Emphasis>1 and/or CPT-11

We studied the expression of inducible heat shock protein (HSP27, HSP72) and multidrug-resistance protein (MRP) in co-cultures of human colon carcinoma cell spheroids obtained from different grades of tumour with normal human colon epithelium, myofibroblast and endothelial cell monolayers. We also measured the influence of recombinant human transforming growth factor β1 (rhTGF-β1) and camptothecin (CPT-11), added as single agents or in combination, on the levels of the HSPs, MRP, interleukin (IL)-6 and nitric oxide (NO). An immunoblotting analysis with densitometry showed that rhTGF-β1 and/or CPT-11 increased HSP27, HSP72 and MRP expression in tumour cells and myofibroblasts, as well as in co-cultures compared with appropriate controls. By contrast, in colonic epithelium, inhibition of HSPs and MRP was comparable with that of the control. In endothelial cells, HSP72 was undetectable.     

The influence of the bolus-surface distance on the dose distribution in the build-up region

Aim

The aim of the paper is to examine the relation between the increase of the photon dose in water in the region of electronic disequilibrium – so-called build-up region – and the distance of the bolus from the water surface for the applied parameters of X-ray beams.

Materials and methods

PDD measurements were carried out using the plane-parallel ionization chamber Markus in the automatic water phantom IBA BluePhantom with OmniPro-Accept V7 (IBA Dosimetry GmbH, Schwarzenbruck, Germany). All measurements were performed for different field sizes and for 6 MV and 15 MV X-ray beams, respectively. A water-equivalent RW3 slab (Goettingen White Water) produced by PTW was used as a bolus.

Results

Placing a bolus in an irradiated field changes the shape of the PDD curve in the build-up region in comparison with the one obtained for an open field. All results has been inserted in tables and figures.

Conclusion

The closer the bolus is to the water surface, the smaller the depth of the maximum dose in the phantom for all investigated fields and energies. The changes in the build-up region are important, even if the bolus does not touch the surface of the water phantom. The influence of the bolus can be ignored when the bolus-surface distance equals 25 cm for 6MV X-ray beams and 39 cm for 15 MV X-ray beams.     

Tissue-Specific Differences in DNA Modifications (5-Hydroxymethylcytosine, 5-Formylcytosine, 5-Carboxylcytosine and 5-Hydroxymethyluracil) and Their Interrelationships

Background

Replication-independent active/enzymatic demethylation may be an important process in the functioning of somatic cells. The most plausible mechanisms of active 5-methylcytosine demethylation, leading to activation of previously silenced genes, involve ten-eleven translocation (TET) proteins that participate in oxidation of 5-methylcytosine to 5-hydroxymethylcytosine which can be further oxidized to 5-formylcytosine and 5-carboxylcytosine. Recently, 5-hydroxymethylcytosine was demonstrated to be a relatively stable modification, and the previously observed substantial differences in the level of this modification in various murine tissues were shown to depend mostly on cell proliferation rate. Some experimental evidence supports the hypothesis that 5-hydroxymethyluracil may be also generated by TET enzymes and has epigenetic functions.

Results

Using an isotope-dilution automated online two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry, we have analyzed, for the first time, all the products of active DNA demethylation pathway: 5-methyl-2′-deoxycytidine, 5-hydroxymethyl-2′-deoxycytidine, 5-formyl-2′-deoxycytidine and 5-carboxyl-2′-deoxycytidine, as well as 5-hydroxymethyl-2′-deoxyuridine, in DNA isolated from various rat and porcine tissues. A strong significant inverse linear correlation was found between the proliferation rate of cells and the global level of 5-hydroxymethyl-2′-deoxycytidine in both porcine (R² = 0.88) and rat tissues (R² = 0.83); no such relationship was observed for 5-formyl-2′-deoxycytidine and 5-carboxyl-2′-deoxycytidine. Moreover, a substrate-product correlation was demonstrated for the two consecutive steps of iterative oxidation pathway: between 5-hydroxymethyl-2′-deoxycytidine and its product 5-formyl-2′-deoxycytidine, as well as between 5-formyl-2′-deoxycytidine and 5-carboxyl-2′-deoxycytidine (R² = 0.60 and R² = 0.71, respectively).

Conclusions

Good correlations within the substrate-product sets of iterative oxidation pathway may suggest that a part of 5-formyl-2′-deoxycytidine and/or 5-carboxyl-2′-deoxycytidine can be directly linked to a small portion of 5-hydroxymethyl-2′-deoxycytidine which defines the active demethylation process.     

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon‐date and calibration error into Bayesian phylogenetic analyses of ancient DNA

Studies of DNA from ancient samples provide a valuable opportunity to gain insight into past evolutionary and demographic processes. Bayesian phylogenetic methods can estimate evolutionary rates and timescales from ancient DNA sequences, with the ages of the samples acting as calibrations for the molecular clock. Sample ages are often estimated using radiocarbon dating, but the associated measurement error is rarely taken into account. In addition, the total uncertainty quantified by converting radiocarbon dates to calendar dates is typically ignored. Here, we present a tool for incorporating both of these sources of uncertainty into Bayesian phylogenetic analyses of ancient DNA. This empirical calibrated radiocarbon sampler (ECRS) integrates the age uncertainty for each ancient sequence over the calibrated probability density function estimated for its radiocarbon date and associated error. We use the ECRS to analyse three ancient DNA data sets. Accounting for radiocarbon‐dating and calibration error appeared to have little impact on estimates of evolutionary rates and related parameters for these data sets. However, analyses of other data sets, particularly those with few or only very old radiocarbon dates, might be more sensitive to using artificially precise sample ages and should benefit from use of the ECRS.     

Accumulation Pattern of Inorganic Elements in Scaly Tooth Mushroom (Sarcodon imbricatus) from Northern Poland

Several studies have documented contamination levels and daily intake of metallic elements from foodstuffs including rice, maize, pulses, vegetables, fruits, fish, meat, egg, milk etc., however, limited literature is available on metal contamination levels in wild growing mushrooms and possible human exposure via consumption of it. Sarcodon imbricatus is an edible mushroom, commonly consumed in many parts of the world. Very few studies have been conducted on inorganic elemental composition in fruiting bodies (edible part) of this fungus. In this study, elements such as silver (Ag), aluminum (Al), barium (Ba), calcium (Ca), cadmium (Cd), cobalt (Co,) chromium (Cr), copper (Cu), iron (Fe), mercury (Hg), potassium (K), magnesium (Mg), manganese (Mn), sodium (Na), nickel (Ni), phosphorous (P), lead (Pb), rubidium (Rb), strontium (Sr) and zinc (Zn) were measured in caps and stems of fruiting bodies of S. imbricatus collected from the Wdzydze forests in Central and the Augustowska Primeval forest in Eastern Poland. Results revealed that a wide variation in concentrations of various metals in caps and stems samples collected from the two forests. Toxic metallic elements such as Cd and Hg showed preferential accumulation in caps than stems samples from both the forests. However, the concentrations of Cd, Hg and Pb in the mushroom samples were below the established weekly intake tolerance limits.