Testing generalized allometries in allocation modeling within an individual-based simulation framework

The allocation of carbohydrates from photosynthesis to various plant compartments is a key process in ecophysiology and consequently an important element in process-based ecosystem modeling. In this study, we tested generalized empirical equations in a widely applied partitioning concept based on compartment-specific biomass allometries. For an 88-year chronosequence of European beech (Fagus sylvatica L.) in Austria, we used the individual-based hybrid forest model PICUS v1.4 to compare simulations employing foliage biomass functions at different levels of generalization against runs with site-specific parameterization and observations. Sensitivities of the individual tree model were generally in line with the original stand-level partitioning concept and ecological process understanding. While stand-level leaf area increased with increasing allocation to foliage, net primary productivity showed no significant response due to saturated radiation interception in the dense chronosequence stands. Strong sensitivities were revealed at the individual tree level, where favoring allocation to the foliage compartment resulted in increasing asymmetry of competition and height–diameter relationships. Applying a generalized parameterization based on data from the full range of continental species distribution resulted in a significant overestimation of mean tree height and subsequently standing volume stock at the chronosequence. At a lower hierarchical level of generality, however, simulations with a representative regional parameterization performed satisfactorily compared to model runs using the site-specific allometry. In relation to common accuracy demands, e.g., in forest management decision support, the study suggests the rejection of a generic parameterization while corroborating the use of regional generalizations in ecosystem models.     

ABA-dependent amine oxidases-derived H2O2 affects stomata conductance

Recently we showed that ABA is at least partly responsible for the induction of the polyamine exodus pathway in Vitis vinifera plants. Both sensitive and tolerant plants employ this pathway to orchestrate stress responses, differing between stress adaptation and programmed cell death. Herein we show that ABA is an upstream signal for the induction of the polyamine catabolic pathway in Vitis vinifera. Thus, amine oxidases are producing H₂O₂ which signals stomata closure. Moreover, the previously proposed model for the polyamine catabolic pathway is updated and discussed.Key words: plant growth, abscissic acid, polyamines, amine oxidases, signaling, oxidative stress, programmed cell deathWe have shown that tobacco salinity induces an exodus of the polyamine (PA) spermidine (Spd) into the apoplast where it is oxidized by polyamine oxidase (PAO) generating hydrogen peroxide (H₂O₂). Depending on the size of H₂O₂, it signals either tolerance-effector genes or the programmed cell death syndrome¹ (PCD). PAs are ubiquitous and biologically active molecules. In the recent years remarkable progress has been accomplished regarding the regulation of PAs biosynthesis and catalysis, not only under normal physiological but also under stress conditions.¹ The most studied PAs are the diamine Putrescine (Put) and its derivatives the triamine Spd and the tetramine spermine (Spm). They are present in the cells in soluble form (S), or conjugated either to low molecular weight compounds (soluble hydrolyzed form, SH) or to “macro” molecules or cell walls (pellet hydrolyzed form, PH). In higher plants, Put is synthesized either directly from ornithine via ornithine decarboxylase (ODC; EC 4.1.1.17) or indirectly from arginine via arginine decarboxylase (ADC; EC 4.1.1.19). Spd and Spm are synthesized via Spd synthase (EC 2.5.1.16, SPDS) and Spm synthase (EC 2.5.1.22, SPMS), respectively, by sequential addition of aminopropyl groups to Put, catalyzed by S-adenosyl-L-methionine decarboxylase (SAMDC; EC 4.1.1.50).^2,3 In plants, PAs are present in the cytoplasm, as well as in cellular organelles.⁴ Recently it was shown that during stress, they are secreted into the apoplast where they are oxidized by amine oxidases (AOs), such as diamine oxidase for Put (DAO, E.C. 1.4.3.6) and polyamine oxidase (PAO, E.C. 1.4.3.4) for Spd and Spm.^1,5,6 Oxidation of PAs generates, amongst other products, H₂O₂^1,7,8 which is involved in cell signaling processes coordinated by abscissic acid (ABA),⁹ but also acts as efficient oxidant and, at high concentration, orchestrates the PCD syndrome.^6,10 Two types of PA catabolism by PAO are known in plants: the terminal and the back-conversion pathways. The terminal one takes place in the apoplast, produces except H₂O₂, 1,3-diaminopropane and an aldehyde depending on the species. On the other hand, the back-conversion pathway is intracellular (cytoplasm and peroxisomes) resulting to the production of H₂O₂ and the sequential production of Put by Spm via Spd.^1,7 Now we have shown that PA exodus also occurs in Vitis vinifera and this phenomenon is at least partially induced by abscissic acid (ABA).¹¹ Thus, exogenous application of ABA results to PA exodus into the apoplast of grapevine. PA is oxidized by an AO resulting to production of H₂O₂. When the titer of H₂O₂ is below a threshold, expression of tolerance-effector genes is induced, while when it exceeds this threshold the programmed cell death (PCD) syndrome is induced.     

The stratigraphy of the Middle Stone Age sediments at Pinnacle Point Cave 13B (Mossel Bay, Western Cape Province, South Africa)

Pinnacle Point Cave 13B (PP13B) has provided the earliest archaeological evidence for the exploitation of marine shellfish, along with very early evidence for use and modification of pigments and the production of bladelets, all dated to approximately 164?ka (Marean et?al., 2007). This makes PP13B a key site in studies of the origins of modern humans, one of a handful of sites in Africa dating to Marine Isotope Stage 6 (MIS 6), and the only site on the coast of South Africa with human occupation confidently dated to MIS 6. Along with this MIS 6 occupation there are rich archaeological sediments dated to MIS 5, and together these sediments are differentially preserved in three different areas of the cave. The sediments represent a complex palimpsest of geogenic, biogenic, and anthropogenic input and alteration that are described and interpreted through the use of a variety of macrostratigraphic, micromorphologic, and geochemical techniques. Three independent dating techniques allow us to constrain the age range of these sediments and together provide the stratigraphic context for the analyses of the material that follow in this special issue.     

PCR-Denaturing Gradient Gel Electrophoresis of Complex Microbial Communities: A Two-Step Approach to Address the Effect of Gel-to-Gel Variation and Allow Valid Comparisons Across a Large Dataset

Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology to profile complex microbial communities over time and in response to different stimuli. However, inherent gel-to-gel variability has always been a barrier toward meaningful interpretation of DGGE profiles obtained from multiple gels. To address this problem, we developed a two-step methodology to align DGGE profiles across a large dataset. The use of appropriate inter-gel standards was of vital importance since they provided the basis for efficient within- and between-gel alignment and a reliable means to evaluate the final outcome of the process. Pretreatment of DGGE profiles by a commercially available image analysis software package (TL120 v2006, Phoretix 1D Advanced) followed by a simple interpolation step in Matlab minimized the effect of gel-to-gel variation, allowing for comparisons between large numbers of samples with a high degree of confidence. At the same time, data were obtained in the form of whole densitometric curves, rather than as band presence/absence or intensity information, and could be readily analyzed by a collection of well-established multivariate methods. This work clearly demonstrates that there is still room for significant improvements as to the way large DGGE datasets are processed and statistically interrogated.     

Helicobacter pylori VacA Toxin/Subunit p34: Targeting of an Anion Channel to the Inner Mitochondrial Membrane

The vacuolating toxin VacA, released by Helicobacter pylori, is an important virulence factor in the pathogenesis of gastritis and gastroduodenal ulcers. VacA contains two subunits: The p58 subunit mediates entry into target cells, and the p34 subunit mediates targeting to mitochondria and is essential for toxicity. In this study we found that targeting to mitochondria is dependent on a unique signal sequence of 32 uncharged amino acid residues at the p34 N-terminus. Mitochondrial import of p34 is mediated by the import receptor Tom20 and the import channel of the outer membrane TOM complex, leading to insertion of p34 into the mitochondrial inner membrane. p34 assembles in homo-hexamers of extraordinary high stability. CD spectra of the purified protein indicate a content of >40% β-strands, similar to pore-forming β-barrel proteins. p34 forms an anion channel with a conductivity of about 12 pS in 1.5 M KCl buffer. Oligomerization and channel formation are independent both of the 32 uncharged N-terminal residues and of the p58 subunit of the toxin. The conductivity is efficiently blocked by 5-nitro-2-(3-phenylpropylamino)benzoic acid (NPPB), a reagent known to inhibit VacA-mediated apoptosis. We conclude that p34 essentially acts as a small pore-forming toxin, targeted to the mitochondrial inner membrane by a special hydrophobic N-terminal signal.     

Haloadaptation: insights from comparative modeling studies of halophilic archaeal DHFRs

Proteins of halophilic archaea function in high-salt concentrations that inactivate or precipitate homologous proteins from non-halophilic species. Haloadaptation and the mechanism behind the phenomenon are not yet fully understood. In order to obtain useful information, homology modeling studies of dihydrofolate reductases (DHFRs) from halophilic archaea were performed that led to the construction of structural models. These models were subjected to energy minimization, structural evaluation and analysis. Complementary approaches concerning calculations of the amino acid composition and visual inspection of the surfaces and cores of the models, as well as calculations of electrostatic surface potentials, in comparison to non-halophilic DHFRs were also performed. The results provide evidence that sheds some light on the phenomenon of haloadaptation: DHFRs from halophilic archaea may maintain their fold, in high-salt concentrations, by sharing highly negatively charged surfaces and weak hydrophobic cores.     

Effects of basketball training on maximal oxygen uptake, muscle strength, and joint mobility in young basketball players

The purpose of this study was to examine the effects of prolonged basketball skills training on maximal aerobic power, isokinetic strength, joint mobility, and body fat percentage, in young basketball players, and controls of the same age. Twenty basketball players and 18 control boys participated in the study. Basketball players participated both in their school's physical education program and in a children's basketball team training program. Controls participated only in their school's physical education program. All subjects were tested every 6 months (18 months total, 11(1/2), 12, 12(1/2), 13 years old) for VO(2)max, peak torque values of the quadriceps and hamstrings at 180 and 300 degrees x s(-1) and range of motion of the knee and hip joints. Body fat percentage was assessed at the beginning and the end of the experimental period. Results showed that the basketball group had lower heart rate values in all ages and higher VO(2) values in the initial test compared with the control in submaximal intensity. The VO(2)max was altered in both groups on the final test, when compared to the initial test. However, the basketball group had a higher VO(2)max on each of the 6-month follow-up measurements, compared to the control group (p < 0.001). At the end of the 18-month follow-up period no significant differences were observed in isokinetic strength and joint mobility of the lower limbs between the 2 groups. On the contrary, the boys of the trained group had significantly lower percentage body fat values, compared to controls. In conclusion, regular basketball training increased aerobic power and decreased body fat percentage of prepubescent boys, while it did not affect muscle strength and joint mobility of the lower limbs. The major implication suggested by the findings of the present study is that, in order to improve the basic physical components, specific training procedures should be incorporated during the basketball training sessions. It is recommended that all children should be involved in some type of cardiovascular and resistance training program.     

A genotype calling algorithm for the Illumina BeadArray platform

MOTIVATION: Large-scale genotyping relies on the use of unsupervised automated calling algorithms to assign genotypes to hybridization data. A number of such calling algorithms have been recently established for the Affymetrix GeneChip genotyping technology. Here, we present a fast and accurate genotype calling algorithm for the Illumina BeadArray genotyping platforms. As the technology moves towards assaying millions of genetic polymorphisms simultaneously, there is a need for an integrated and easy-to-use software for calling genotypes. RESULTS: We have introduced a model-based genotype calling algorithm which does not rely on having prior training data or require computationally intensive procedures. The algorithm can assign genotypes to hybridization data from thousands of individuals simultaneously and pools information across multiple individuals to improve the calling. The method can accommodate variations in hybridization intensities which result in dramatic shifts of the position of the genotype clouds by identifying the optimal coordinates to initialize the algorithm. By incorporating the process of perturbation analysis, we can obtain a quality metric measuring the stability of the assigned genotype calls. We show that this quality metric can be used to identify SNPs with low call rates and accuracy. AVAILABILITY: The C++ executable for the algorithm described here is available by request from the authors.     

Hydrogen peroxide inhibits caspase-dependent apoptosis by inactivating procaspase-9 in an iron-dependent manner

Apoptosis represents a physiological form of cell death, the perturbation of which may contribute to the development of several diseases connected with accumulation of unwanted cells or excessive cell loss. We have previously shown that the continuous presence of low concentrations of H2O2 (generated by the action of glucose oxidase) was able to inhibit caspase-mediated apoptosis in Jurkat cells. The main purpose of the present study was to elucidate the exact molecular mechanism(s) underlying this inhibitory action of H2O2. The results presented show that events like outer mitochondrial membrane permeabilization, release of cytochrome c from mitochondria, oligomerization of Apaf-1, and recruitment of procaspase-9 to apoptosomes were taking place normally, but further advancement toward activation of the execution caspases was interrupted when H2O2 was present during the apoptotic process. From the results presented in this work, it emerges that the inhibition of procaspase-9 autoactivation was probably due to the reversible oxidation of sensitive cysteine residues in this molecule. Remarkably, caspase-9 activation and the ensuing caspase cascade proceeded normally in the presence of H2O2 under conditions of iron deprivation, indicating that the inhibition of procaspase-9 activation was an iron-dependent process. Collectively, these results highlighted the potential role of available intracellular iron ions in signaling mechanisms related to apoptotic cell death.