Dynamical behaviour of biological regulatory networks—II. Immunity control in bacteriophage lambda

A number of bacterial and viral genes take part in the decision between lysis and lysogenization in temperate bacteriophages. In the lambda case, at least five viral genes (cI, cro, cII, N and cIII) and several bacterial genes are involved. Several attempts have been made to model this complex regulatory network. Our approach is based on a logical method described in the first paper of the series which formalizes the interactions between the elements of a regulatory network in terms of discrete variables, functions and parameters. In this paper two models are described and discussed, the first (two-variable model) focused on cI and cro interactions, the second (four-variable model) considering, in addition, genes cII and N. The treatment presented emphasizes the roles of positive and negative feedback loops and their interactions in the development of the phage. The role of the loops between cI and cro, and of cI on itself (which both have to be positive loops) was discovered earlier; this group's contribution to this aspect mainly deals with the possibility of treating these loops as parts of a more extended network. In contrast, the role of the negative loop of cro on itself had apparently remained unexplained. We realized that this loop buffers the expression of genes cro itself, cII, O and P against the inflation due to the rapid replication of the phage. More generally negative auto-control of a gene appears an efficient way to render its expression insensitive (or less sensitive) to gene dosage, whereas a simple negative control would not provide this result.     

The secant condition for instability in biochemical feedback control—I. The role of cooperativity and saturability

This paper concerns oscillations arising in a sequence of biochemical reactions      

Dynamics of small autocatalytic reaction networks—I. bifurcations,permanence and exclusion

Catalysis in replication networks has become an important issue in biophysics and other areas of biology. Examples are RNA catalysis, idiotype recognition in the immune response and dynamical models of Maynard-Smith games in sociobiology. Chemical reaction networks describing catalysed, template-induced reproduction of three species are analysed in full generality. The nine-dimensional parameter space is reduced to three relevant angular coordinates which determine completely the phase portraits (PPs) and the bifurcation patterns. All cases are classified and all generic as well as most of the nongeneric transitions are listed and described. This paper has been reproduced directly from disc using a LA-T_EX system.     

Infant monkeys’ concept of animacy: the role of eyes and fluffiness

Both human and nonhuman primates have been suggested to possess some essential knowledge about animate entities, but it remains unclear whether the concept of animacy is shared across species, which properties are used as an "animacy marker," and whether such ability is present at birth. We investigated infant Japanese monkeys' looking responses towards novel objects varying in both physical appearance and self-propelled motion, with the aim of depicting the role of eyes and fluffiness in the early recognition of animacy. Presented with an inanimate natural stone, three-month-old monkeys showed longer looking times at the stone's self-propelled motion than at its baseline still posture. This effect became significantly smaller when artificial fur was attached to the stone, while adding artificial eyes did not elicit a departing pattern in their looking behavior. In contrast, one-month-old monkeys showed no systematic differences in their looking behavior. This suggests that the concept of animacy in terms of self-propelledness may develop between one and three?months of age, with sensitivity to texture emerging by three?months. Development of biological knowledge is discussed in relation to social knowledge from both ontogenetic and phylogenetic perspectives.     

Anhydrobiosis in nematodes—I. The role of glycerol myo-inositol and trehalose during desiccation

• 1.1. The concentrations of free glycerol, inositol and trehalose in five species of nematodes were determined. Analyses of total inositol content were also made.
• 2.2. Significant differences in free and bound sugar levels were found between the two good anhydrobiotes Anguina tritici and Ditylenchus dipsaci and the three poor survivors Pangrellus redivivus, D. myceliophagous and Turbatrix aceti.
• 3.3. Highest trehalose contents were found in desiccated A. tritici and D. dipsaci, but glycerol levels were low.
• 4.4. P. redivivus and T. aceti contained high concentrations of free glycerol.
• 5.5. Desiccated A. tritici larvae contained more free and bound inositol than all other species studied, but desiccated D. dipsaci larvae had higher levels of bound inositol than P. redivivus, D. myceliophagous and T. aceti.
• 6.6. Dramatic reductions in inositol and trehalose contents were found in revived A. tritici larvae and freshly extracted D. dipsaci larvae. This was accompanied by an increase in glycerol content.
• 7.7. The results are discussed in relation to the possible biochemical adaptations employed by anhydrobiotes during desiccation.

     

Can proton pumping by SERCA enhance the regulatory role of phospholamban and sarcolipin?

The effect of the incorporation of phosphorylated phospholamban (pPLN) and sarcolipin (SLN) in mercury-supported self-assembled lipid monolayers and in lipid bilayers tethered to mercury via a hydrophilic spacer was investigated by voltammetric techniques and electrochemical impedance spectroscopy. It was shown that pPLN and SLN do not permeabilize lipid bilayers toward ions at physiological pH. However, they exert a permeabilizing action toward inorganic monovalent cations such as K⁺ and Tl⁺, but not toward divalent cations such as Ca²⁺ and Cd^2 +, following a small decrease in pH. This behavior can be associated with their regulatory action on the Ca-ATPase of the sarcoplasmic reticulum (SERCA). SERCA pumps two Ca²⁺ ions from the cytosol to the lumen of the sarcoplasmic reticulum (SR) and two protons in the opposite direction, causing a transient decrease of pH in the immediate vicinity of its cytoplasmic domain. This decrease is expected to activate the liberated pPLN molecules and SLN to make the SR membrane leakier toward K⁺ and Na⁺ and the SLN ion channel to translocate small inorganic anions, such as Cl⁻. The effect of pPLN and SLN, which becomes synergic when they are both present in the SR membrane, is expected to favor a rapid equilibration of ions on both sides of the membrane.     

Hatching of the Anostracan Branchiopod Chirocephalus diaphanus Prévost I. Osmotic processes and the possible role of glycerol

An osmotic hatching mechanism is proposed for the Anostracan Branchiopod Chirocephalus diaphanus, Prevost. In this mechanism, glycerol is thought to accumulate in the egg as a result of the metabolism of the embryo. The osmotic pressure exerted by the egg, largely due to this glycerol accumulation, causes water to enter from the environment. Eventually the hydrostatic pressure thus generated is sufficient to cause rupture of the eggshell. It is recognised that hatching in this Anostracan is a two-staged phenomenon, a process of “breaking”, in which glycerol is involved, preceding true “hatching”, in which glycerol is not involved. The egg is described and the physiology and ecological significance of the proposed hatching mechanism are discussed.     

Biodiesel production—current state of the art and challenges

Biodiesel is a clean-burning fuel produced from grease, vegetable oils, or animal fats. Biodiesel is produced by transesterification of oils with short-chain alcohols or by the esterification of fatty acids. The transesterification reaction consists of transforming triglycerides into fatty acid alkyl esters, in the presence of an alcohol, such as methanol or ethanol, and a catalyst, such as an alkali or acid, with glycerol as a byproduct. Because of diminishing petroleum reserves and the deleterious environmental consequences of exhaust gases from petroleum diesel, biodiesel has attracted attention during the past few years as a renewable and environmentally friendly fuel. Since biodiesel is made entirely from vegetable oil or animal fats, it is renewable and biodegradable. The majority of biodiesel today is produced by alkali-catalyzed transesterification with methanol, which results in a relatively short reaction time. However, the vegetable oil and alcohol must be substantially anhydrous and have a low free fatty acid content, because the presence of water or free fatty acid or both promotes soap formation. In this article, we examine different biodiesel sources (edible and nonedible), virgin oil versus waste oil, algae-based biodiesel that is gaining increasing importance, role of different catalysts including enzyme catalysts, and the current state-of-the-art in biodiesel production. JIMB 2008: BioEnergy—special issue.     

Systems biology and the origins of life? Part I. Are biochemical networks possible ancestors of living systems? Reproduction,identity and sensitivity to signals of biochemical networks

The set of these two theoretical papers offers an alternative to the hypothesis of a primordial RNA-world. The basic idea of these papers is to consider that the first prebiotic systems could have been networks of catalysed reactions encapsulated by a membrane. In order to test this hypothesis it was attempted to list the main obligatory features of living systems and see whether encapsulated biochemical networks could possibly display these features. The traits of living systems are the following: the ability they have to reproduce; the fact they possess an identity; the fact that biological events should be considered in the context of a history; the fact that living systems are able to evolve by selection of alterations of their structure and self-organization. The aim of these two papers is precisely to show that encapsulated biochemical networks can possess these properties and can be considered good candidates for the first prebiotic systems. In the present paper it is shown that if the proteinoids are not very specific catalysts and if some of the reactions of the network are autocatalytic whereas others are not, the resulting system does not reach a steady-state and tends to duplicate. In the same line, these biochemical networks possess an identity, viz. an information, defined from the probability of occurrence of these nodes. Moreover interaction of two ligands can increase, or decrease, this information. In the first case, the system is defined as emergent, in the second case it is considered integrated. Another property of living systems is that their behaviour is defined in the context of a time-arrow. For instance, they are able to sense whether the intensity of a signal is reached after an increase, or a decrease. This property can be mimicked by a simple physico-chemical system made up of the diffusion of a ligand followed by its chemical transformation catalysed by a proteinoid displaying inhibition by excess substrate. Under these conditions the system reacts differently depending on whether the same ligand concentration is reached after an increase or a decrease.     

Biological monitoring of fish and crustaceans in the Wadden Sea — potential and problems

Monitoring of fish and crustaceans in the Wadden Sea (WS) must cope with rapid changes in distribution patterns, access to certain areas and gear efficiency. Application and limitations of a variety of fishing devices (fyke nets, gill nets, enclosures, stow nets, purse seines, beam trawls, push nets, beach seines, bottom trawls, pelagic trawls) are discussed with regard to different objectives of monitoring. Furthermore, the validity of data from three current monitoring programmes is also discussed. Presented at the VI International Wadden Sea Symposium (Biologische Anstalt Helgoland, Wattenmeerstation Sylt, D-2282 List, FRG, 1–4 November 1988)     

Biological waste gas treatment with a modified rotating biological contactor. Ι. Control of biofilm growth and long-term performance

In this work, we introduce a modified rotating biological contactor (RBC) system and demonstrate its feasibility by applying the newly devised process to the biological treatment of artificial waste gas. In the proposed system, the waste gas is introduced to the bioreactor in the spacings between the rotating discs through a hollow shaft, thus allowing for intimate gas–liquid contact. A 91-l modified RBC containing 20 biofilm support discs 40 cm in diameter was used in the experiments. Toluene was used as the model pollutant, and the system was operated under standard operating conditions for more than one year in order to investigate its long-term performance and assess its ability to control the growth of the biofilm. It was demonstrated that the proposed system allows to efficiently control the growth of the biofilm, thus overcoming the clogging problem inherent in most conventional methods for the biological treatment of waste gas. Moreover, the system was shown to exhibit stationary long-term performance for a period of more than one year, hence indicating its feasibility for industrial application.     

A model of the role of natural killer cells in immune surveillance — I

Summary The theory of immune surveillance of Thomas and Burnet stated in part that antigenic differences between neoplastic and normal cells provide the stimulus for their destruction by cells of the immune system. Burnet pointed to the T lymphocyte as the cell which mediated this surveillance. The existence of some form of surveillance in cases of no T lymphocyte functioning presents the possibility that surveillance, if present at all, is mediated by non T cells.Cells identified as naturally cytotoxic killer (NK) cells appear to have properties required of a surveillance effector population. This paper utilizes properties of NK cells and the effects of interferon on this population to construct a mathematical model of the characteristics that an NK cell surveillance would have. A two level theory of immune surveillance is proposed.This research has been supported in part by the National Science Foundation under grant #NSF-Eng. 7904852