Dynamic simulation of regulatory networks using SQUAD

Background  

The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology.     

Benthic foraminiferal assemblages in the severely polluted coastal environment of Drapetsona-Keratsini,Saronikos Gulf (Greece)

Surface sediments were collected from the coastal zone of Drapetsona–Keratsini (Saronikos Gulf, Greece) in December 2012 for determining the local benthic foraminiferal community, identifying their spatial distribution patterns, and evaluating the response of foraminiferal species to geochemical composition through the hierarchical cluster analysis, principal component analysis and Spearman's rho correlation. Foraminifera can be classified into three distinct assemblages associated with the granulometry, elemental geochemistry, particulate organic carbon content and degree of sediment contamination. A relatively low-diversity assemblage, dominated by stress-tolerant taxa with Ammonia tepida Bolivina spathulata and Bulimina elongata being the prevailing species, is characteristic of the silty seabed of the main part of Drapetsona coastal zone and the Keratsini Port central basin, where organic carbon content, aliphatic and polycyclic aromatic hydrocarbons concentrations and trace metal loads are greatly elevated. On the sandy bottom of the investigated area, relatively high frequencies of miliolids prevail. An epiphytic rotaliid-dominated assemblage is recorded in the slightly-polluted sedimentary bottom of the inner and western part of the Keratsini Port.     

Functional analysis of LHCSR1, a protein catalyzing NPQ in mosses,by heterologous expression in Arabidopsis thaliana

Photosynthesis Research - Non-photochemical quenching, NPQ, of chlorophyll fluorescence regulates the heat dissipation of chlorophyll excited states and determines the efficiency of the oxygenic...     

Stage-specific regulation of programmed cell death during oogenesis of the medfly Ceratitis capitata (Diptera, Tephritidae)

In the present study, we describe novel features of programmed cell death in developing egg chambers occurring during mid- and late-oogenesis of the medfly Ceratitis capitata. During mid-oogenesis, the spontaneously degenerated egg chambers exhibit typical characteristics of apoptotic cell death. Their nurse cells contain fragmented DNA and fragmented actin, as revealed by TUNEL assay and immunolabelling, respectively. In vitro caspase activity assays and immunostaining procedures demonstrated that the atretic egg chambers acquired high levels of caspase activity. Distinct features of autophagic cell death were also observed during C. capitata mid-oogenesis, as revealed by the monodansylcadaverine staining approach and ultrastructural examination performed by transmission electron microscopy. Additionally, atretic egg chambers exhibit an upregulation of lysosomal proteases, as demonstrated by a procathepsin L immunolabelling procedure. At the late stages of C. capitata oogenesis, apoptosis and autophagy coexist, manifesting cell death features that are similar to the ones mentioned above, being also chaperoned by the involvement of an altered cytochrome c conformational display. We propose that apoptosis and autophagy operate synergistically during C. capitata oogenesis for a more efficient elimination of the degenerated nurse cells and abnormal egg chambers.     

Serum copper and zinc concentrations in healthy children aged 3–14 years in greece

Zinc (Zn) and copper (Cu) are essential trace elements in people, being required for functional activity of several enzyme systems. In this study, we determined Cu and Zn concentrations in the serum of 105 healthy children randomly selected, aged 3–14 yr, residing in a region of Greece (Thrace), and we investigated their association with children's gender, age, height, weight, and nutritional habits. The mean levels of Zn and Cu were 15.01±2.95 μmol/L and 26.18±5.47 μmol/L, respectively, with no significant difference between boys and girls. A significant positive correlation was found between age and Zn levels, and a negative one was found between age and Cu levels. Both Zn and Cu levels tended to increase with height, whereas Zn levels significantly decreased with increasing body mass indent (BMI). The consumption of meat, milk, and eggs were independent determinants for higher Zn levels, and the consumption of legumes and fruits were independent determinants for higher Cu levels. A significant negative correlation was found between Zn and Cu levels. In conclusion, our study, the first one evaluating the serum status of Cu and Zn in healthy Greek children, identified significant correlations of Zn and Cu levels with their age, height, BMI, and nutritional habits.     

AP endonuclease paralogues with distinct activities in DNA repair and bacterial pathogenesis

Oxidative stress is a principal cause of DNA damage, and mechanisms to repair this damage are among the most highly conserved of biological processes. Oxidative stress is also used by phagocytes to attack bacterial pathogens in defence of the host. We have identified and characterised two apurinic/apyrimidinic (AP) endonuclease paralogues in the human pathogen Neisseria meningitidis. The presence of multiple versions of DNA repair enzymes in a single organism is usually thought to reflect redundancy in activities that are essential for cellular viability. We demonstrate here that these two AP endonuclease paralogues have distinct activities in DNA repair: one is a typical Neisserial AP endonuclease (NApe), whereas the other is a specialised 3'-phosphodiesterase Neisserial exonuclease (NExo). The lack of AP endonuclease activity of NExo is shown to be attributable to the presence of a histidine side chain, blocking the abasic ribose-binding site. Both enzymes are necessary for survival of N. meningitidis under oxidative stress and during bloodstream infection. The novel functional pairing of NExo and NApe is widespread among bacteria and appears to have evolved independently on several occasions.     

Effect of temperature on ethanol tolerance of a thermophilic anaerobic ethanol producer Thermoanaerobacter A10: modeling and simulation

The low ethanol tolerance of thermophilic anaerobic bacteria (<2%, v/v) is a major obstacle for their industrial exploitation for ethanol production. The ethanol tolerance of the thermophilic anaerobic ethanol-producing strain Thermoanaerobacter A10 was studied during batch tests of xylose fermentation at a temperature range of 50-70 degrees C with exogenously added ethanol up to approximately 6.4% (v/v). At the optimum growth temperature of 70 degrees C, the strain was able to tolerate 4.7% (v/v) ethanol, and growth was completely inhibited at 5.6% (v/v). A higher ethanol tolerance was found at lower temperatures. At 60 degrees C, the strain was able to tolerate at least 5.1% (v/v) ethanol. A generalized form of Monod kinetic equation proposed by Levenspiel was used to describe the ethanol (product) inhibition. The model predicted quite well the experimental data for the temperature interval 50-70 degrees C, and the maximum specific growth rate and the toxic power (n), which describes the order of ethanol inhibition at each temperature, were estimated. The toxic power (n) was 1.33 at 70 degrees C, and corresponding critical inhibitory product concentration (P(crit)) above which no microbial growth occurs was determined to be 5.4% (v/v). An analysis of toxic power (n) and P(crit) showed that the optimum temperature for combined microbial growth and ethanol tolerance was 60 degrees C. At this temperature, the toxic power (n), and P(crit) were 0.50, and 6.5% (v/v) ethanol, respectively. From a practical point of view, the model may be applied to compare the ethanol inhibition (ethanol tolerance) on microbial growth of different thermophilic anaerobic bacterial strains.     

The 3BP2 adapter protein is required for optimal B-cell activation and thymus-independent type 2 humoral response

3BP2 is a pleckstrin homology domain- and Src homology 2 (SH2) domain-containing adapter protein that is mutated in the rare human bone disorder cherubism and which has also been implicated in immunoreceptor signaling. However, a function for this protein has yet to be established. Here we show that mice lacking 3BP2 exhibited a perturbation in the peritoneal B1 and splenic marginal-zone B-cell compartments and diminished thymus-independent type 2 antigen response. 3BP2(-/-) B cells demonstrated a proliferation defect in response to antigen receptor cross-linking and a heightened sensitivity to B-cell receptor-induced death via a caspase-3-dependent apoptotic pathway. We show that 3BP2 binds via its SH2 domain to the CD19 signaling complex and is required for optimum Syk phosphorylation and calcium flux.