Mitochondria as the target of the pro-apoptotic protein Bax

During apoptosis, engagement of the mitochondrial pathway involves the permeabilization of the outer mitochondrial membrane (OMM), which leads to the release of cytochrome c and other apoptogenic proteins such as Smac/DIABLO, AIF, EndoG, Omi/HtraA2 and DDP/TIMM8a. OMM permeabilization depends on activation, translocation and oligomerization of multidomain Bcl-2 family proteins such as Bax or Bak. Factors involved in Bax conformational change and the function(s) of the distinct domains controlling the addressing and the insertion of Bax into mitochondria are described in this review. We also discuss our current knowledge on Bax oligomerization and on the molecular mechanisms underlying the different models accounting for OMM permeabilization during apoptosis.     

Population responses to perturbations: the importance of trait-based analysis illustrated through a microcosm experiment

Environmental change continually perturbs populations from a stable state, leading to transient dynamics that can last multiple generations. Several long-term studies have reported changes in trait distributions along with demographic response to environmental change. Here we conducted an experimental study on soil mites and investigated the interaction between demography and an individual trait over a period of nonstationary dynamics. By following individual fates and body sizes at each life-history stage, we investigated how body size and population density influenced demographic rates. By comparing the ability of two alternative approaches, a matrix projection model and an integral projection model, we investigated whether consideration of trait-based demography enhances our ability to predict transient dynamics. By utilizing a prospective perturbation analysis, we addressed which stage-specific demographic or trait-transition rate had the greatest influence on population dynamics. Both body size and population density had important effects on most rates; however, these effects differed substantially among life-history stages. Considering the observed trait-demography relationships resulted in better predictions of a population's response to perturbations, which highlights the role of phenotypic plasticity in transient dynamics. Although the perturbation analyses provided comparable predictions of stage-specific elasticities between the matrix and integral projection models, the order of importance of the life-history stages differed between the two analyses. In conclusion, we demonstrate how a trait-based demographic approach provides further insight into transient population dynamics.     

Lost in space? Searching for directions in the spatial modelling of individuals,populations and species ranges

The workshop ‘Spatial models in animal ecology, management and conservation’ held at Silwood Park (UK), 9–11 March 2010, aimed to synthesize recent progress in modelling the spatial dynamics of individuals, populations and species ranges and to provide directions for research. It brought together marine and terrestrial researchers working on spatial models at different levels of organization, using empirical as well as theory-driven approaches. Different approaches, temporal and spatial scales, and practical constraints predominate at different levels of organization and in different environments. However, there are theoretical concepts and specific methods that can fruitfully be transferred across levels and systems, including: habitat suitability characterization, movement rules, and ways of estimating uncertainty.     

Effect of predation risk on the presence and persistence of yellow-bellied marmot (Marmota flaviventris) colonies

Habitat selection may have population level consequences and ultimately may influence a population's local persistence or extinction. We capitalized on a long-term study (1962–2004) of yellow-bellied marmots Marmota flaviventris in and around the Rocky Mountain Biological Laboratory, Gothic, Colorado, USA, and compared habitat characteristics associated with food availability and predation risk to explain variation in persistence of marmots at 27 sites, and their absence at 22 additional, randomly selected sites. We classified sites as persistent, intermittent or null based on whether there was a history of extinction; intermittent sites periodically went extinct and null sites never had marmots. Logistic regression analyses revealed that environmental variables associated with visibility and safety, rather than food, correctly classified sites as persistent or non-persistent as well as persistent or intermittent. Discriminant function analysis that included the null sites revealed that the same visibility-related characteristics predicted where marmots were found. These results highlight the importance of variation in safety among sites in predicting long-term population persistence, as well as a species' distribution.     

Cometabolic Degradation of Trichloroethylene by Single- and Two-Phase Systems

The cometabolic degradation of trichloroethylene (TCE) by Pseudomonas putida F1 (strain ATCC 700007) at different concentrations was studied in single- and two-phase systems using 2-undecanone as the second organic phase. Toluene vapors were used as the primary growth substrate for Pseudomonas putida F1. The effects of the biomass concentration and the phase ratio on the biodegradation process were investigated. The best biomass concentration and the most suitable phase ratio were found to be 0.462 and 0.025 g/L (v_org/v_aq), respectively. In the single-phase system, 36.5 mg/L TCE was degraded completely in 15 hours and only 78% of 55 mg/L TCE was degraded in 27 hours, while in the two-phase system 55 mg/L TCE was degraded completely in 14 hours. The use of the two-phase system not only decreased the biodegradation time of TCE but also prevented the inhibition effect of high concentrations of TCE on the microbial biomass.     

Enhancing Science Teaching through Performing Marbling Art Using Basic Solutions and Base Indicators

Basic solutions are an indispensable part of our daily life. Basic solutions are commonly used in industries such as the textile industry, oil refineries, the fertilizer industry, and pharmaceutical products. Most cleaning agents, such as soap, detergent, and bleach, and some of our foods, such as chocolate and eggs, include bases. Bases are the fundamental concepts of chemistry. Indicators are chemical compounds that can be added to solution to determine whether it is a base or not. This article describes an activity whose primary aim is to teach base indicators to preservice elementary teachers. In this activity, the authors turned the traditional art of marbling into something achievable with the chemical substances that are the basic solutions and base indicators found in nearly all chemistry laboratories. Therefore, this activity can be called chemical marbling. The preservice elementary teachers learned the base indicators and basic solutions throughout this activity. The purpose of the study is not only to teach the science concepts to the preservice elementary teachers with fun but also to promote the development of their attitudes toward science, creativity, and aesthetic feelings. Suggestions stress that chemical marbling might be a good tool to acquire the preservice elementary teachers’ cognitive and affective learning outcomes.     

Synthetic antisense oligodeoxynucleotides to transiently suppress different nucleus- and chloroplast-encoded proteins of higher plant chloroplasts

Selective inhibition of gene expression by antisense oligodeoxynucleotides (ODNs) is widely applied in gene function analyses; however, experiments with ODNs in plants are scarce. In this work, we extend the use of ODNs in different plant species, optimizing the uptake, stability, and efficiency of ODNs with a combination of molecular biological and biophysical techniques to transiently inhibit the gene expression of different chloroplast proteins. We targeted the nucleus-encoded phytoene desaturase (pds) gene, encoding a key enzyme in carotenoid biosynthesis, the chlorophyll a/b-binding (cab) protein genes, and the chloroplast-encoded psbA gene, encoding the D1 protein. For pds and psbA, the in vivo stability of ODNs was increased by phosphorothioate modifications. After infiltration of ODNs into juvenile tobacco (Nicotiana benthamiana) leaves, we detected a 25% to 35% reduction in mRNA level and an approximately 5% decrease in both carotenoid content and the variable fluorescence of photosystem II. In detached etiolated wheat (Triticum aestivum) leaves, after 8 h of greening, the mRNA level, carotenoid content, and variable fluorescence were inhibited up to 75%, 25%, and 20%, respectively. Regarding cab, ODN treatments of etiolated wheat leaves resulted in an up to 59% decrease in the amount of chlorophyll b, a 41% decrease of the maximum chlorophyll fluorescence intensity, the cab mRNA level was reduced to 66%, and the protein level was suppressed up to 85% compared with the control. The psbA mRNA and protein levels in Arabidopsis (Arabidopsis thaliana) leaves were inhibited by up to 85% and 72%, respectively. To exploit the potential of ODNs for photosynthetic genes, we propose molecular design combined with fast, noninvasive techniques to test their functional effects.     

Genetic characterization of pomegranate (Punica granatum L.) genotypes by AFLP markers

The Coruh Valley, located in Northeastern Turkey, is one of the most important centers of diversity in pomegranate in Turkey. In this study, we attempted to characterize 19 promising pomegranate genotypes originating from the Coruh Valley in using fluorescent dye AFLP markers and capillary electrophoresis. Four AFLP primer combinations were used, generating a total of 297 fragments, 213 of which were polymorphic (73.0%). Resolving powers of the AFLP primers ranged from 0.700 to 1.018, with a total of 3.440, while polymorphism information contents ranged from 0.707 to 0.837 with an average of 0.764. UPGMA clustering of the genotypes showed two major groups. Most of the fruit characteristics of the genotypes within the same group were variable. Therefore, the results showed that molecular characterization is necessary to get reliable relationships among pomegranate genotypes and AFLP markers can be used effectively in pomegranate.