A declarative constraint-based method for analyzing discrete genetic regulatory networks

Dynamical modeling has proven useful for understanding how complex biological processes emerge from the many components and interactions composing genetic regulatory networks (GRNs). However, the development of models is hampered by large uncertainties in both the network structure and parameter values. To remedy this problem, the models are usually developed through an iterative process based on numerous simulations, confronting model predictions with experimental data and refining the model structure and/or parameter values to repair the inconsistencies. In this paper, we propose an alternative to this generate-and-test approach. We present a four-step method for the systematic construction and analysis of discrete models of GRNs by means of a declarative approach. Instead of instantiating the models as in classical modeling approaches, the biological knowledge on the network structure and its dynamics is formulated in the form of constraints. The compatibility of the network structure with the constraints is queried and in case of inconsistencies, some constraints are relaxed. Common properties of the consistent models are then analyzed by means of dedicated languages. Two such languages are introduced in the paper. Removing questionable constraints or adding interesting ones allows to further analyze the models. This approach allows to identify the best experiments to be carried out, in order to discriminate sets of consistent models and refine our knowledge on the system functioning. We test the feasibility of our approach, by applying it to the re-examination of a model describing the nutritional stress response in the bacterium Escherichia coli.     

Expression of the <Emphasis Type="Italic">yggE</Emphasis> gene protects <Emphasis Type="Italic">Escherichia coli</Emphasis> from potassium tellurite-generated oxidative stress

Potassium tellurite is highly toxic to most forms of life and specific bacterial tellurite defense mechanisms are not fully understood to date. Recent evidence suggests that tellurite would exert its toxic effects, at least in part, through the generation of superoxide anion that occurs concomitantly with intracellular tellurite (Te⁴⁺) reduction to elemental tellurium (Te^o). In this work the putative antioxidant role of YggE from Escherichia coli, a highly conserved protein in several bacterial species and whose function is still a matter of speculation, was studied. When exposed to tellurite, E. coli lacking yggE exhibited increased activity of superoxide dismutase and fumarase C, augmented levels of reactive oxygen species and high concentration of carbonyl groups in proteins. Upon genetic complementation with the homologous yggE gene these values were restored to those observed in the parental, isogenic, wild type strain, suggesting a direct participation of YggE in E. coli tolerance to tellurite.     

Involvement of digalactosyldiacylglycerol in cellular thermotolerance in <Emphasis Type="Italic">Synechocystis</Emphasis> sp. PCC 6803

The effects of digalactosyldiacylglycerol (DGDG) deficiency on photosynthesis at high temperatures were examined using a dgdA mutant of Synechocystis sp. PCC 6803 incapable of DGDG biosynthesis. The dgdA mutant cells showed significant growth retardation when the temperature was increased from 30 to 38°C, although wild-type cells grew normally. The degree of growth retardation was enhanced by increasing light intensity. In addition, dgdA mutant cells showed increased sensitivity to the photoinhibition of photosynthesis when illuminated at 38°C. Analysis of photosynthesis in intact cells suggested that the inhibition of repair processes and accelerated photodamage resulted in growth retardation in dgdA mutant cells at high temperatures.     

SLP‐2 is required for stress‐induced mitochondrial hyperfusion

Mitochondria are dynamic organelles, the morphology of which results from an equilibrium between two opposing processes, fusion and fission. Mitochondrial fusion relies on dynamin‐related GTPases, the mitofusins (MFN1 and 2) in the outer mitochondrial membrane and OPA1 (optic atrophy 1) in the inner mitochondrial membrane. Apart from a role in the maintenance of mitochondrial DNA, little is known about the physiological role of mitochondrial fusion. Here we report that mitochondria hyperfuse and form a highly interconnected network in cells exposed to selective stresses. This process precedes mitochondrial fission when it is triggered by apoptotic stimuli such as UV irradiation or actinomycin D. Stress‐induced mitochondrial hyperfusion (SIMH) is independent of MFN2, BAX/BAK, and prohibitins, but requires L‐OPA1, MFN1, and the mitochondrial inner membrane protein SLP‐2. In the absence of SLP‐2, L‐OPA1 is lost and SIMH is prevented. SIMH is accompanied by increased mitochondrial ATP production and represents a novel adaptive pro‐survival response against stress.     

Visualization of body thermoregulation by infrared imaging

This paper analyzes two mechanisms applied on the human body in order to study the thermoregulatory system according to heat generation and heat loss. Two approaches are presented. The first approach is based on plethysmography, where an armband is placed on the forearm in order to modulate the blood flow. The second approach uses a cold stimulation. The visualization is achieved using infrared imaging devices. The resulting images reveal a temperature balance between the stimulated and the non-stimulated hands. The thermal behavior and typical thermographic recordings on each subject are discussed and analyzed in response to different stimulations.     

Differential effects of nitrogen and phosphorus enrichment on growth of dwarf Avicennia marina mangroves

The effects of N and P enrichment were investigated on growth and physiological responses of dwarf Avicennia marina mangroves in a hypersaline (58 ± 8 psu) field site in Richards Bay, South Africa. It was hypothesized that at high salinities mangroves allocate more resources to roots than shoots, and that nutrient enrichment with N and P will shift resource allocation to shoots and enhance growth and productivity. In unvegetated areas of the dwarf zone, 1-year-old A. marina seedlings were planted in pots and enriched bimonthly with N, P, N + P, or remained unfertilized (control-C), and growth and morphology of plants were monitored for 2 years. Enrichment with N and N + P shifted resource allocation to shoots from 38% to 55%, and increased dry biomass accumulation by over 500%, compared to the control treatment. In the N and N + P treatments, plant height, number of leaves, leaf chlorophyll content and photosynthesis increased by over 50%, 330%, 30% and 30%, respectively, compared to the C and P treatments. Enrichment with N and N + P increased N concentrations in roots by over 60% (from 1.0 ± 0.1% to 1.6 ± 0.2% of dry mass) and in shoots by over 100% (from 1.3 ± 0.1% to 2.7 ± 02% of dry mass). Plants enriched with P alone were similar to those of the control. This study has demonstrated that dwarf A. marina in Richards Bay is N limited, and that N enrichment shifts resource allocation from roots to shoots and increases growth and productivity.     

内质网应激与心肌肥大

肌浆网是调控心肌细胞钙稳态、蛋白质合成和细胞凋亡的重要亚细胞器。内质网应激是指内质网理化环境改变和过负荷等因素导致未折叠/误折叠蛋白在内质网聚集和钙稳态失衡等内质网功能紊乱状态。适度的内质网应激有利于心肌细胞代偿,持续而严重的内质网应激则触发内质网应激相关细胞凋亡,造成肥大心肌由代偿转向衰竭,是影响心肌肥大发生、发展的重要因素。本文综述了内质网应激反应在心肌肥大发生、发展中的作用。