Indicating Soil Acidity Using Vegetation Relevés in Spatially Limited Areas – Case Study from the Považský Inovec, Slovakia

A fine-scaled approach for predicting soil acidity using plant species in a spatially limited area (?epú?ky Nature Reserve, Slovakia) is presented here. This approach copes with some specific limitations: i) a limited pool of vegetation data may make the predictions too sensitive to the lack of species information, and ii) the predictions may be sensitive to the narrow pH gradient. Vegetation relevés and soil reaction (pH-H₂O and pH-CaCl₂) were systematically recorded. A set of species indicator values and amplitudes was calibrated with physical pH data using the Weighted Averaging (WA), HOF modelling and Non-Metric Multidimensional Scaling (NMDS) methods, along with Ellenberg indicator values. Two prediction methods were tested: i) WA and ii) Amplitude Overlap (AO). WA prediction with Ellenberg’s and WA-calibrated species indicator values were the most powerful technique (R ²?=?68.4–68.7% and 53.4–59.1% for pH-CaCl₂ and pH-H₂O, respectively). WA-prediction with HOF-based indicator values was less effective (R ²?=?61.7% and 50.7%) due to the decrease in species’ information because with HOF modelling many species are assumed indifferent or too rare. The NMDS method does not bring any significant gain to the calibration, though it avoids the lack of species information. The AO method was proven to be less powerful under studied circumstances, because it is sensitive both to the lack of species’ information and to the truncation of species responses. The results prove that a spatially explicit approach can provide significant indices to estimate changes in soil acidity – pH-CaCl₂ better than pH-H₂O.     

Defining the DNA mismatch repair-dependent apoptotic pathway in primary cells: Evidence for p53-independence and involvement of centrosomal caspase 2

Many studies have shown that DNA mismatch repair (MMR) has a role beyond that of repair in response to several types of DNA damage, including ultraviolet radiation (UV). We have demonstrated previously that the MMR-dependent component of UVB-induced apoptosis is integral to the suppression of UVB-induced tumorigenesis. Here we demonstrate that Msh6-dependent UVB-induced apoptotic pathway is both activated via the mitochondria and p53-independent. In addition, we have shown for the first time that caspase 2, an initiator caspase, localizes to the centrosomes in mitotic primary mouse embryonic fibroblasts, irrespective of MMR status and UVB treatment.     

Quantitative characterizations of proteome: dependence on the number of proteins considered

We consider the sensitivity of numerical characterizations of proteome on the number of proteins considered in the analysis. We examined data on proteomics maps belonging to the liver cells of mice subject to four proliferators. We varied the number of proteins considered for quantitative analysis from 25 up to 1000 proteins. For each case, we have compared the similarity/dissimilarity results when different number of proteins has been considered. We found that proteins maps based on a set of about 300 most abundant proteins spots suffice for satisfactory numerical characterization of corresponding proteome.     

Acute alcohol administration inhibits the refeeding response after starvation in rat skeletal muscle

This study determined whether an acute alcohol dose could inhibit the refeeding response in starved muscle. Rats starved for 24 h were pretreated with alcohol or saline before refeeding by intragastric or intravenous infusion of enteral diet (ENT), total parenteral nutrition (TPN), or saline. Refeeding by TPN or ENT stimulated increases in the fractional rate of protein synthesis (k(s)) in skeletal muscle. Alcohol prevented the increase in k(s) when refeeding occurred intragastrically (TPN or ENT) (P < 0.001) but not intravenously (TPN). Upon intragastric refeeding, alcohol inhibited the increase in both eukaryotic initiation factor 4E-binding protein-1 (4E-BP1) and p70 S6 kinase (p70(S6K)) phosphorylation in plantaris but caused only partial inhibition in soleus muscle (ENT only). When rats were refed intravenously, alcohol had no effect on the increased 4E-BP1 or p70(S6K) phosphorylation in either muscle. Plasma insulin levels were augmented by alcohol. Alcohol-related changes in plasma amino acid concentrations were similar irrespective of the route of feeding, whereas IGF-I levels showed differential changes. This is the first study to demonstrate that acute alcohol ingestion impedes the starved-to-fed response in skeletal muscle.     

Reduction of potassium tellurite to elemental tellurium and its effect on the plasma membrane redox components of the facultative phototroph Rhodobacter capsulatus

Summary.  Anaerobically light-grown cells of Rhodobacter capsulatus B100 are highly resistant to the toxic oxyanion tellurite (TeO₃ ²⁻; minimal inhibitory concentration, 250 μg/ml). This study examines, for the first time, some structural and biochemical features of cells and plasma membrane fragments of this facultative phototroph grown in the presence of 50μg of K₂TeO₃ per ml. Through the use of transmission microscopy and X-ray microanalysis we show that several “needlelike” shaped granules of elemental tellurium are accumulated into the cytosol near the intracytoplasmic membrane system. Flash-spectroscopy, oxygen consumption measurements, and difference spectra analysis indicated that membrane vesicles (chromatophores) isolated from tellurite-grown cells are able to catalyze both photosynthetic and respiratory electron transport activities, although they are characterized by a low c-type cytochrome content (mostly soluble cytochrome c ₂). This feature is paralleled by a low cytochrome c oxidase activity and with an NADH-dependent respiration which is catalyzed by a pathway leading to a quinol oxidase (Qox) inhibited by high (millimolar) concentrations of cyanide (CN⁻). Conversely, membranes from R. capsulatus B100 cells grown in the absence of tellurite are characterized by a branched respiratory chain in which the cytochrome c oxidase pathway (blocked by CN⁻ in the micromolar range) accounts for 35–40% of the total NADH-dependent oxygen consumption, while the remaining activity is catalyzed by the quinol oxidase pathway. These data have been interpreted to show that tellurite resistance of R. capsulatus B100 is characterized by the presence of a modified plasma-membrane-associated electron transport system. Received May 2, 2002; accepted July 26, 2002; published online May 21, 2003 RID="*" ID="*" Correspondence and reprints: Department of Biology, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy.     

Coupling of angiotensin II AT1 receptors to neuronal NHE activity and carrier-mediated norepinephrine release in myocardial ischemia

In ischemia, cardiac sympathetic nerve endings (cSNE) release excessive amounts of norepinephrine (NE) via the nonexocytotic Na(+)-dependent NE transporter (NET). NET, normally responsible for NE reuptake into cSNE, reverses in myocardial ischemia, releasing pathological amounts of NE. This carrier-mediated NE release can be triggered by elevated intracellular Na(+) levels in the axoplasm. The fact that ischemia activates the intracellular pH regulatory Na(+)/H(+) exchanger (NHE) in cSNE is pivotal in increasing intraneuronal Na(+) and thus activating carrier-mediated NE release. Angiotensin (ANG) II levels are also significantly elevated in the ischemic heart. However, the effects of ANG II on cSNE, which express the ANG II receptor, AT(1)R, are poorly understood. We hypothesized that ANG II-induced AT(1)R activation in cSNE may be positively coupled to NHE activity and thereby facilitate the pathological release of NE associated with myocardial ischemia. We tested this hypothesis in a cSNE model, human neuroblastoma cells stably transfected with rat recombinant AT(1A) receptor (SH-SY5Y-AT(1A)). SH-SY5Y-AT(1A) constitutively expresses amiloride-sensitive NHE and the NET. NHE activity was assayed in BCECF-loaded SH-SY5Y-AT(1A) as the rate of the Na(+)-dependent alkalinization in response to an acute acidosis. ANG II activation of AT(1)R markedly increased NHE activity in SH-SY5Y-AT(1A) via a Ca(2+)-dependent pathway and promoted carrier-mediated NE release. In addition, in guinea pig cSNE expressing native AT(1)R, ANG II elicited carrier-mediated NE release. In SH-SY5Y-AT(1A) and cSNE, amiloride inhibited the ANG II-mediated release of NE. Our results provide a link between AT(1)R and NHE in cSNE, which can exacerbate carrier-mediated NE release during protracted myocardial ischemia.     

Ataxia-telangiectasia-mutated (ATM) and NBS1-dependent phosphorylation of Chk1 on Ser-317 in response to ionizing radiation

In mammals, the ATM (ataxia-telangiectasia-mutated) and ATR (ATM and Rad3-related) protein kinases function as critical regulators of the cellular DNA damage response. The checkpoint functions of ATR and ATM are mediated, in part, by a pair of checkpoint effector kinases termed Chk1 and Chk2. In mammalian cells, evidence has been presented that Chk1 is devoted to the ATR signaling pathway and is modified by ATR in response to replication inhibition and UV-induced damage, whereas Chk2 functions primarily through ATM in response to ionizing radiation (IR), suggesting that Chk2 and Chk1 might have evolved to channel the DNA damage signal from ATM and ATR, respectively. We demonstrate here that the ATR-Chk1 and ATM-Chk2 pathways are not parallel branches of the DNA damage response pathway but instead show a high degree of cross-talk and connectivity. ATM does in fact signal to Chk1 in response to IR. Phosphorylation of Chk1 on Ser-317 in response to IR is ATM-dependent. We also show that functional NBS1 is required for phosphorylation of Chk1, indicating that NBS1 might facilitate the access of Chk1 to ATM at the sites of DNA damage. Abrogation of Chk1 expression by RNA interference resulted in defects in IR-induced S and G(2)/M phase checkpoints; however, the overexpression of phosphorylation site mutant (S317A, S345A or S317A/S345A double mutant) Chk1 failed to interfere with these checkpoints. Surprisingly, the kinase-dead Chk1 (D130A) also failed to abrogate the S and G(2) checkpoint through any obvious dominant negative effect toward endogenous Chk1. Therefore, further studies will be required to assess the contribution made by phosphorylation events to Chk1 regulation. Overall, the data presented in the study challenge the model in which Chk1 only functions downstream from ATR and indicate that ATM does signal to Chk1. In addition, this study also demonstrates that Chk1 is essential for IR-induced inhibition of DNA synthesis and the G(2)/M checkpoint.     

An experimental and theoretical structural study of 5-amino-3-methylisoxazolo-4-carboxylic acid<Emphasis Type="Italic"> p</Emphasis>-chlorophenylamide

Experimental and theoretical structural studies of 5-amino-3-methylisoxazolo-4-carboxylic acid p-chlorophenylamide were performed. This compound belongs to a new class of isoxazole derivatives exhibiting promising immunological activity. The crystallographic structure was measured and compared with theoretical calculations for the investigated compound. The theoretical analyses were performed using Kohn-Sham density functional theory (DFT) with the B3LYP hybrid exchange-correlation energy functional and 6-311+G(d,p) basis set. The solvent effect was included using the SCRF/PCM method with water (epsilon=78) as a solvent. Topological analysis was performed in terms of Bader's theory of atoms in molecules, yielding molecular parameters for quantum molecular similarity investigations. Figure The SCRF/PCM map of electrostatic potential around the molecule: light grey isosurface at +0.5 a.u., dark grey at -0.05 a.u.     

The genetic structure of natural and reintroduced roe deer (Capreolus capreolus) populations in the Alps and central Italy,with reference to the mitochondrial DNA phylogeography of Europe

The first hypervariable fragment (HVI) of the mitochondrial DNA control region was sequenced in 90 individuals of the European roe deer (Capreolus capreolus) from the Alps, central Italy and Spain. Pooling these data with 70 published sequences from several European regions, we were able to identify patterns of divergence within the Italian peninsula, and in Europe in general. The results we obtained can be summarized as follows. First, the genetic structure of European roe deer populations is substantial (PhiST values around 0.6). Second, the divergence between some central Italian populations, the Alpine group (which is genetically close to the French, the Spanish and the Norwegian samples) and the Eastern European populations seems to reflect Upper Pleistocene subdivisions, possibly related to three southern European refugia. Third, a different group of central Italian individuals probably diverged more recently from the Alpine group, and their attribution to the subspecies C. c. italicus does not appear justified. Fourth, the analysis of mitochondrial DNA in the roe deer can be used to identify recently reintroduced animals in the western Alps which clearly cluster within the Eastern European group, thus providing an important tool for conservation and management strategies for this species.