Dynamic approach to predict pH profiles of biologically relevant buffers

Recently, dynamic approach has been applied to determine the steady state concentrations of multiple ionic species present in complex buffers at equilibrium. Here, we have used the dynamic approach to explicitly model the pH profiles of biologically relevant phosphate buffer and universal buffer (a mixture of three tri-protic acids such as citric acid, boric acid and phosphoric acid). The results from dynamic approach are identical to that of the conventional algebraic approach, but with an added advantage that the dynamic approach, allow for the modelling of complex buffer systems relatively easy compared to that of algebraic method.     

Ryanodine receptor assembly: a novel systems biology approach to 3D mapping

Ryanodine receptors (RyRs) are intracellular Ca²⁺ release channels (CRCs) that play a pivotal role in cellular Ca²⁺ signaling. In striated muscles, RyR-mediated Ca²⁺ release from the sarcoplasmic reticulum (SR) induces elevation of cytosolic Ca²⁺ concentration and subsequent muscle contraction. Evidence from various sources suggests that RyRs in homo-tetrameric conformation form a large conductance Ca²⁺ permeable channel in the central pore and large cytoplasmic domains. RyRs form a large assembly with various cytosolic and luminal proteins. A number of papers have been published concerning the functions of RyRs and the regulation of the associated proteins, but the three dimensional (3D) structure of the assembly has not been addressed in detail. In this paper, we have attempted to establish a 3D-map for the assembly of RyRs by considering published cryo-EM data, available X-ray crystallographic information and molecular modeling methods.     

The first living systems: a bioenergetic perspective.

The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.     

Breeding systems in Angiosperms: novel inferences from a new analytical approach

A novel analytical approach to classify breeding systems in Angiosperms combining statistical and conceptual criteria is proposed, which will allow to describe and compare available mating system data in an unified form. Four breeding system indexes (BSI) were combined: Index of Agamospermy, Index of Spontaneous Self-Pollination (ISSP), Index of Self-Fertility (ISF), and Index of Self-incompatibility. Their values, ranging from 0 to ∞, were analyzed using t tests to discriminate experimental breeding index values from 0 and 1.0. For each index, five discrete categories were described. The composite of the four BSI assigned to a species represents an integrated characterization of its reproductive system. A magnitude measure (M) describes the strength of each BSI assigned to a species. Indexes of inbreeding and outbreeding depression were also examined for each species. Published data from 1908 taxa were used to determine composite breeding systems. Frequencies of breeding index categories across the four BSI for the entire data set were determined. Non-agamospermous species dominated. Non-spontaneous self-pollinating and xenogamous species were the most frequent categories observed for ISSP and ISF indexes, respectively. The largest group of species examined was partially self-incompatible. Actual number of composite breeding systems inferred based on our analysis represents a small fraction (8.9 %) of all mathematically possible ones. Similarly, the observed combinations between results obtained from the four pollination tests and estimates of natural reproductive efficiency were only 22.1 % of all mathematically possible combinations. Within Angiosperms, there is a marked trend toward evolution of partial self-incompatibility with significant inbreeding depression.     

Mass spectrometry as a novel approach to probe cooperativity in multimeric enzymatic systems

Investigating cooperativity in multimeric enzymes is of utmost interest to improve our understanding of the mechanism of enzymatic regulation. In the present article, we propose a novel approach based on mass spectrometry to probe cooperativity in the binding of a ligand to a multisubunit enzyme. This approach presents the selective advantage of giving a direct insight into all the subsequent ligation states that are formed in solution as the ligand is added to the enzyme. A quantitative interpretation of the electrospray ionization (ESI) mass spectra gives the relative abundance of all the distinct enzymatic species, which allows one to directly deduce the cooperativity of the system. The overall method is described for the addition of the oxidized cofactor nicotinamide adenine dinucleotide (NAD(+)) to a dimeric mutant of Bacillus stearothermophilus glyceraldehyde-3-phosphate dehydrogenase (GPDH). It is then applied to four tetrameric enzymes: sturgeon muscle GPDH, wild type and S48G mutant of GPDH from B. stearothermophilus, and alcohol dehydrogenase (ADH) from Bakers yeast. The results illustrate the possibilities offered by this new technique. First, mass spectrometry allows a control of the enzymes before the addition of NAD(+). Second, the cooperative behavior can be drawn from one single ESI mass spectrum, which makes the method highly attractive in terms of the amount of biological material required. Above all, the major benefit lies in the direct visualization of all the enzymatic species that are in equilibrium in solution. The direct measurement of cooperativity readily resolve the inconvenience of the classical approaches employed in this field, which all need to model the experimental data in order to get the cooperative behavior of the system.     

Chance vs. necessity in living systems: a false antinomy

The concepts of order and randomness are crucial to understand 'living systems' structural and dynamical rules. In the history of biology, they lay behind the everlasting debate on the relative roles of chance and determinism in evolution. Jacques Monod [1970] built a theory where chance (randomness) and determinism (order) were considered as two complementary aspects of life. In the present paper, we will give an up to date version of the problem going beyond the dichotomy between chance and determinism. To this end, we will first see how the view on living systems has evolved from the mechanistic one of the 19th century to the one stemming from the most recent literature, where they emerge as complex systems continuously evolving through multiple interactions among their components and with the surrounding environment. We will then report on the ever increasing evidence of "friendly" co-existence in living beings between a number of "variability generators", fixed by evolution, and the "spontaneous order" derived from interactions between components. We will propose that the "disorder" generated is "benevolent" because it allows living systems to rapidly adapt to changes in the environment by continuously changing, while keeping their internal harmony.     

pH gradients generated by polyprotic buffers. II. Experimental validation

The experimental validation refers to the computer program reported in the companion paper, able to simulate the course of pH, buffering power (beta) and ionic strength (I) of polyprotic buffers (either singly or in a mixture) titrated over any pH range. With simple oligoamines (up to five nitrogens) it is shown that it is impossible to generate linear pH gradients in the pH 4-10 interval, unless they are mixed in appropriate ratios. With pentaethylene hexamine, when used alone, it is possible to create a linear pH 4-10 interval, provided the molarity ratios are altered in the two chambers of the gradient mixer. The general rule operating for generation of linear pH intervals is constancy of buffering power throughout the titration. Local minima of beta produce steeper gradients, while local beta maxima flatten it. The ideal delta pK to arrange for linear pH gradients during titration is centred around 1 pH unit; thus polyprotic buffers with very large delta pK values (e.g., EDTA) appear to be totally useless for this purpose. The present computing algorithms should be quite efficient for optimizing existing buffer recipes for chromatofocusing or ampholyte displacement chromatography or for creating new, properly tailored, buffer mixtures.     

Neuroendocrine control of thyroid secretion in living systems: A feedback control system model

A model of the regulation of thyroid hormone in the bloodstream of living systems is formulated and analyzed. The portion of this model defined as theregulator includes components representing the thyroid, anterior pituitary and hypothalamic organs and their intercommunicating channels, that is, the peripheral plasma and hypophysial portal circulations and certain neuro-secretory connections. The loss of hormones from the plasma in the living system associated with physiological mechanisms within the peripheral tissue space and the excretory pathways is represented in the model by a lumpedload on the regulator. The model is reduced to a system of differential equations involving eleven parameters and variables, all of which are identified with certain physiological structures and states. Five of these are currently observable by available laboratory techniques and two others are computable explicity from the equations of the model; the remaining four can be computed in the same way to within a multiplicative constant. Procedires for carrying out ten of these measurements and calculations are suggested. On the basis of the equations and parameters of the model, a discussion of the normal behavior and the response of this system to certain types of disturbances is presented. A systematic effort has been made in the development of this model to include all relevant physiological data and relationships reported in the biological literature. A summary of this literature, reflecting the views and interpretations made by the authors of this paper, is included for completeness and ease of reference.     

Immobilized cycling enzyme active transport systems. pH feedback control

Active transport can be induced by applying a pH gradient across a membrane containing a homogeneous mixture of two cycling enzymes. When the two reactions are inversely 'pH active', one producing protons and the other consuming them, a pH feedback control of the functional structure occurs and the active transport function of the membrane can be either stabilized or inhibited according to whether the endogenic pH modifications tend to enhance or reduce the exergonic pH gradient. When it is stabilized, the system looks like a thin active layer surrounded by two diffusive layers, leading to a fairly good model for biological transport systems. Under particular conditions, signals can be emitted.     

Light-independent conidiation in Trichoderma spp.: a novel approach to microcycle conidiation

Microcycle conidiation in Trichoderma hamatum and T. harzianum has been achieved in complete darkness for the first time. The time required for mass conidiation without intervening vegetative growth was decreased to 24 h instead of 6 to 7 days. The conidia produced by microcycle conidiation were viable and had pigmentation and antagonistic behaviour similar to those of the parental stock cultures.N. Khurana, R.K. Saxena, R. Gupta and R.C. Kuhad are with the Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India.     

The analysis of distributed control and information processing in adaptive systems: a biologically motivated approach.

Biological systems have evolved hierarchical, distributed control structures that greatly enhance their adaptability. Two important determinants of biological adaptability considered here are: (i) the pattern of distribution of self-control capabilities; (ii) the degree of programmability of information processing. In this paper we model organizations as goal-oriented, adaptive systems, possessing properties similar to those of biological systems. We use the notion of implicit control (defined as the capability of self-control that is embedded in a system's own dynamics) in the analysis of the impact of specific patterns of distribution of control and information processing on the adaptability of organizations. A principle of design of organizational information systems, that captures important aspects of adaptability-preserving strategies of information processing in biological systems, is stated in terms of the implicit control concept.     

Complex systems in pulmonary medicine: a systems biology approach to lung disease

The lung is a highly complex organ that can only be understood by integrating the many aspects of its structure and function into a comprehensive view. Such a view is provided by a systems biology approach, whereby the many layers of complexity, from the molecular genetic, to the cellular, to the tissue, to the whole organ, and finally to the whole body, are synthesized into a working model of understanding. The systems biology approach therefore relies on the expertise of many disciplines, including genomics, proteomics, metabolomics, physiomics, and, ultimately, clinical medicine. The overall structure and functioning of the lung cannot be predicted from studying any one of these systems in isolation, and so this approach highlights the importance of emergence as the fundamental feature of systems biology. In this paper, we will provide an overview of a systems biology approach to lung disease by briefly reviewing the advances made at many of these levels, with special emphasis on recent work done in the realm of pulmonary physiology and the analysis of clinical phenotypes.     

Intravital microscopy: a novel tool to study cell biology in living animals

Intravital microscopy encompasses various optical microscopy techniques aimed at visualizing biological processes in live animals. In the last decade, the development of non-linear optical microscopy resulted in an enormous increase of in vivo studies, which have addressed key biological questions in fields such as neurobiology, immunology and tumor biology. Recently, few studies have shown that subcellular processes can be imaged dynamically in the live animal at a resolution comparable to that achieved in cell cultures, providing new opportunities to study cell biology under physiological conditions. The overall aim of this review is to give the reader a general idea of the potential applications of intravital microscopy with a particular emphasis on subcellular imaging. An overview of some of the most exciting studies in this field will be presented using resolution as a main organizing criterion. Indeed, first we will focus on those studies in which organs were imaged at the tissue level, then on those focusing on single cells imaging, and finally on those imaging subcellular organelles and structures.     

Enhanced nitrogen removal in bio-electrochemical systems by pH control

Microbial fuel cells can be designed to remove nitrogenous compounds out of wastewater, but their performance is at present limited to 0.33 kg NO₃ ⁻-Nm⁻³ net cathode compartment (NCC) d⁻¹. By maintaining the pH in the cathode at 7.2, nitrogen removal was increased from 0.22 to 0.50 kg NO₃ ⁻-Nm⁻³ NCC d⁻¹. Bio-electrochemical active microorganisms seem to struggle with the deterioration of their own environment due to slow proton fluxes. Therefore, the results suggest that an appropriate pH adjustment strategy is necessary to allow a sustained and enhanced biological activity in bio-electrochemical systems.     

pH gradients generated by polyprotic buffers. I. Theory and computer simulation

This paper presents the general equations for computing pH, dissociation coefficients, buffering power and ionic strength of pure polyelectrolyte solutions (polyacids, polybases and zwitterionic species with any number of dissociable groups) and mixtures of any number of these species. A program has been written for simulating the behaviour of mixtures containing up to 50 species (including buffers and titrants), each of them with up to 10 dissociable groups. This allowed one to check the equations with the available data on a few oligoprotic species.     

Aqueous two-phase systems: a novel approach for the separation of proteose peptones

Poly(ethylene glycol) and dextran aqueous two-phase systems (ATPS) were developed to facilitate the separation of components of the proteose peptone fraction of bovine milk, which are mostly large casein derived peptides or glycoproteins. These have proved difficult to purify using conventional chromatographic procedures. ATPS exploit differences in hydrophobicity, size and ionic properties of the proteose peptones with a view to developing methods for future large scale preparations of the individual components of this whey protein fraction.     

Effects of pH control with phthalate buffers on hot-water extraction of hemicelluloses from spruce wood

Ground spruce wood was extracted with water at 170 °C at four different pH levels (3.8, 4.0, 4.2 and 4.4) achieved by using phthalate buffers. Static batch extractions were carried out in an accelerated solvent extractor (ASE-300). The extracted non-cellulosic carbohydrates, predominantly galactoglucomannans (GGMs), were characterised mainly by sugar unit analysis and molar mass determination. Compared to extraction with plain water, extractions with phthalate buffer solutions gave similar yields of non-cellulosic carbohydrates, but gave up to 70% less monosaccharides, and consequently higher molar masses of extracted GGMs. Moreover, at these pH levels, the hydrolysis of acetyl groups were decreased by 40% compared to extraction with plain water, thus maintaining the water solubility of GGMs. It is concluded that hot water extraction of hemicelluloses in high-molar-mass form (average Mw about 10 kDa) from wood in good yields (8% of wood) demands appropriate control of pH, to a level of about 4.     

GATHER: a systems approach to interpreting genomic signatures

MOTIVATION: Understanding the full meaning of the biology captured in molecular profiles, within the context of the entire biological system, cannot be achieved with a simple examination of the individual genes in the signature. To facilitate such an understanding, we have developed GATHER, a tool that integrates various forms of available data to elucidate biological context within molecular signatures produced from high-throughput post-genomic assays. RESULTS: Analyzing the Rb/E2F tumor suppressor pathway, we show that GATHER identifies critical features of the pathway. We further show that GATHER identifies common biology in a series of otherwise unrelated gene expression signatures that each predict breast cancer outcome. We quantify the performance of GATHER and find that it successfully predicts 90% of the functions over a broad range of gene groups. We believe that GATHER provides an essential tool for extracting the full value from molecular signatures generated from genome-scale analyses. AVAILABILITY: GATHER is available at http://gather.genome.duke.edu/     

Threshold policies control for predator-prey systems using a control Liapunov function approach

The stability of predator-prey models, in the context of exploitation of renewable resources, subject to threshold policies (TP) is studied in this paper using the idea of backstepping and control Liapunov functions (CLF) well known in control theory, as well as the concept of virtual equilibria. TPs are defined and analysed for different types of one and two species predator-prey models. The models studied are the single species Noy-Meir herbivore-vegetation model, in a grazing management context, as well as the Rosenzweig-MacArthur two species predator-prey model, in a fishery management context. TPs are shown to be versatile and useful in managing renewable resources, being simple to design and implement, and also yielding advantages in situations of overexploitation.