Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks

We generalize random Boolean networks by softening the hard binary discretization into multiple discrete states. These multistate networks are generic models of gene regulatory networks, where each gene is known to assume a finite number of functionally different expression levels. We analytically determine the critical connectivity that separates the biologically unfavorable frozen and chaotic regimes. This connectivity is inversely proportional to a parameter which measures the heterogeneity of the update rules. Interestingly, the latter does not necessarily increase with the mean number of discrete states per node. Still, allowing for multiple states decreases the critical connectivity as compared to random Boolean networks, and thus leads to biologically unrealistic situations.Therefore, we study two approaches to increase the critical connectivity. First, we demonstrate that each network can be kept in its frozen regime by sufficiently biasing the update rules. Second, we restrict the randomly chosen update rules to a subclass of biologically more meaningful functions. These functions are characterized based on a thermodynamic model of gene regulation. We analytically show that their usage indeed increases the critical connectivity. From a general point of view, our thermodynamic considerations link discrete and continuous models of gene regulatory networks.     

Rheology and dynamic light scattering of octa-ethyleneglycol-monododecylether/chitosan solutions

In this work we used rheometry and DLS to probe relaxation phenomena in solutions of chitosan and octa-ethyleneglycol-monododecylether. The dispersions had a marked pseudoplastic behavior, which became less evident, as surfactant concentration was increased. Arrhenius plots showed that systems with surfactant presented a characteristic temperature at which apparent enthalpy of activation (varying from 3 to 40 kJ mol⁻¹) changed: this change was correlated to a possible transition of colloidal aggregates to a wormlike configuration. DLS intensity correlation functions were described by KWW equation: pure chitosan solutions had relaxation rate distributions centered at a characteristic relaxation rate around 4.6 × 10⁻⁶ μS⁻¹; as surfactant was added, a new component, with a faster characteristic relaxation rate with a magnitude order of 10⁻³ μs⁻¹, appeared. It was shown that the dependence between these relaxation rates and surfactant concentration could be used to describe DLS-related relaxation phenomena as an Arrhenius-activated process, agreeing with results obtained using rheometry.     

Crosstalk between mitochondria and peroxisomes

Mitochondria and peroxisomes are small ubiquitous organelles. They both play major roles in cell metabolism,especially in terms of fatty acid metabolism,reactive oxygen species(ROS) production,and ROS scavenging,and it is now clear that they metabolically interact with each other. These two organelles share some properties,such as great plasticity and high potency to adapt their form and number according to cell requirements. Their functions are connected,and any alteration in the function of mitochondria may induce changes inperoxisomal physiology. The objective of this paper was to highlight the interconnection and the crosstalk existing between mitochondria and peroxisomes. Special emphasis was placed on the best known connections between these organelles:origin,structure,and metabolic interconnections.     

Effects of size on Vervet (Cercopithecus aethiops) gait parameters: A cross-sectional approach

A comparison of the values of certain temporal and spatial locomotor parameters was made among ten different-aged (sized) vervet monkeys locomoting at nine identical speeds. Cycle and stance durations decreased across speed for all the animals; at any one speed both parameters also varied directly with body size. Stride length increased with speed for all the animals and was greater in the larger animals. Swing duration and hindlimb support length tended to be relatively consistent for each animal across speed, but varied among the animals directly with body size. Hindlimb duty factor decreased with speed for any one animal but showed no direct correlation with size. Hindlimb angular excursion also showed no correlation with size, nor did it show a simple relationship with speed. In terms of gaits and gait transitions, the data indicate that vervets use a very wide variety of gait types, which are not easily correlated with speed or body size. Furthermore, the data suggest the existence of a run–gallop transition zone of speeds for these animals, rather than the existence of a specific transition speed. Finally, the data were used to test intraspecifically the elastic and dynamic similarity models, both of which predict how locomotor parameters will change with size in animals. The results are generally consistent with the dynamic model.     

Reconstructing a recycling and nonauxotroph biosynthetic pathway in Escherichia coli toward highly efficient production of L-citrulline

L-citrulline is a high-value amino acid with promising application in medicinal and food industries. Construction of highly efficient microbial cell factories for L-citrulline production is still an open issue due to complex metabolic flux distribution and L-arginine auxotrophy. In this study, we constructed a nonauxotrophic cell factory in Escherichia coli for high-titer L-citrulline production by coupling modular engineering strategies with dynamic pathway regulation. First, the biosynthetic pathway of L-citrulline was enhanced after blockage of the degradation pathway and introduction of heterologous biosynthetic genes from Corynebacterium glutamicum. Specifically, a superior recycling biosynthetic pathway was designed to replace the native linear pathway by deleting native acetylornithine deacetylase. Next, the carbamoyl phosphate and L-glutamate biosynthetic modules, the NADPH generation module, and the efflux module were modified to increase L-citrulline titer further. Finally, a toggle switch that responded to cell density was designed to dynamically control the expression of the argG gene and reconstruct a nonauxotrophic pathway. Without extra supplement of L-arginine during fermentation, the final CIT24 strain produced 82.1 g/L L-citrulline in a 5-L bioreactor with a yield of 0.34 g/g glucose and a productivity of 1.71 g/(L ⋅ h), which were the highest values reported by microbial fermentation. Our study not only demonstrated the successful design of cell factory for high-level L-citrulline production but also provided references of coupling the rational module engineering strategies and dynamic regulation strategies to produce high-value intermediate metabolites.     

Rebalancing microbial carbon distribution for L-threonine maximization using a thermal switch system

In metabolic engineering, unbalanced microbial carbon distribution has long blocked the further improvement in yield and productivity of high-volume natural metabolites. Current studies mostly focus on regulating desired biosynthetic pathways, whereas few strategies are available to maximize L-threonine efficiently. Here, we present a strategy to guarantee the supply of reduced cofactors and actualize L-threonine maximization by regulating cellular carbon distribution in central metabolic pathways. A thermal switch system was designed and applied to divide the whole fermentation process into two stages: growth and production. This system could rebalance carbon substrates between pyruvate and oxaloacetate by controlling the heterogenous expression of pyruvate carboxylase and oxaloacetate decarboxylation that responds to temperature. The system was tested in an L-threonine producer Escherichia coli TWF001, and the resulting strain TWF106/pFT24rp overproduced L-threonine from glucose with 111.78% molar yield. The thermal switch system was then employed to switch off the L-alanine synthesis pathway, resulting in the highest L-threonine yield of 124.03%, which exceeds the best reported yield (87.88%) and the maximum available theoretical value of L-threonine production (122.47%). This inducer-free genetic circuit design can be also developed for other biosynthetic pathways to increase product conversion rates and shorten production cycles.     

Effect of a pesticide,pentachlorophenol (PCP) on soil microflora

Although pentachlorophenol (PCP) retarded the initial increase in total viable bacteria and gram-negative bacteria in the percolated soil, populations exceeded those in the percolated soils without the addition of PCP at a later period. This seems to be a phenomenon similar to “the partial sterilization effect”. On the other hand, spore counts were continuously lower in the percolated soils when PCP had been added. Ammonification of glycine was also slightly inhibited, but nitrification of ammonium was strongly depressed by PCP. Other physicochemical changes of the percolate proceeded according to those of bacterial populations and biochemical reactions.