Phenotypic diversity and chaos in a minimal cell model

Gánti's chemoton model (Gánti, T., 2002. On the early evolution of biological periodicity. Cell. Biol. Int. 26, 729) is considered as an iconic example of a minimal protocell including three key subsystems: membrane, metabolism and information. The three subsystems are connected through stoichiometrical coupling which ensures the existence of a replication cycle for the chemoton. Our detailed exploration of a version of this model indicates that it displays a wide range of complex dynamics, from regularity to chaos. Here, we report the presence of a very rich set of dynamical patterns potentially displayed by a protocell as described by this implementation of a chemoton-like model. The implications for early cellular evolution and synthesis of artificial cells are discussed.     

The Beta Workbench: a computational tool to study the dynamics of biological systems

We introduce the Beta Workbench (BWB), a scalable tool built on top of the newly defined BlenX language to model, simulate and analyse biological systems. We show the features and the incremental modelling process supported by the BWB on a running example based on the mitogen-activated kinase pathway. Finally, we provide a comparison with related approaches and some hints for future extensions.     

From geochemistry and biochemistry to prebiotic evolution...we necessarily enter into Gánti's fluid automata

The present study is just an overview of the opening of the geochemical stage for the appearance of life. But that opening would not have been sufficient for the intellectual discovery of the origin of life! The excellent works and many commendable efforts that advance this explanation have not shown the fundamental elements that participate in the theoretical frame of biological evolution. The latter imply the existence of evolutionary transitions and the production of new levels of organization. In this brief analysis we do not intend to introduce the audience to the philosophy of biology. But we do expect to provide a modest overview, in which the geochemical chemolithoautotrophic opening of the stage should be seen, at most, as the initial metabolism that enabled organic compounds to follow the road where a chemical fluid machinery was thus able to undertake the more "sublime" course of organic biological evolution. We think that Tibor Gánti's chemoton is the most significant contribution to theoretical biology, and the only course now available to comprehend the unit of evolution problem without the structuralist and functionalist conflict prevalent in theoretical biology. In our opinion Gánti's chemoton theory travels to the "locus" where evolutionary theory dares to extend itself to entities at many levels of structural organization, beyond the gene or the group above. Therefore, in this and subsequent papers on the prebiotic conditions for the eventual appearance of the genetic code, we explore the formation and the presence of metal sulfide minerals, from the assembly of metal sulfide clusters through the precipitation of nanocrystals and the further reactions resulting in bulk metal sulfide phases. We endeavor to characterize pristine reactions and the modern surfaces, utilizing traditional surface science techniques and computational methods. Moreover, mechanistic details of the overall oxidation of metal sulfide minerals are set forth. We hope that this paper will lead our audience to accept that in a chemically oscillating system the chemoton is a model fluid state automaton capable of growth and self-reproduction. This is not simply a matter of transmitting a pattern, as in inorganic crystals; such self-reproduction must be more complex than crystal growth. Indeed that is what Gánti's theoretical and abstract model offers to us all: we finally have a philosophy of evolutionary units in theoretical biology.     

Syntactic sequencing in Hebbian cell assemblies

Hebbian cell assemblies provide a theoretical framework for the modeling of cognitive processes that grounds them in the underlying physiological neural circuits. Recently we have presented an extension of cell assemblies by operational components which allows to model aspects of language, rules, and complex behaviour. In the present work we study the generation of syntactic sequences using operational cell assemblies timed by unspecific trigger signals. Syntactic patterns are implemented in terms of hetero-associative transition graphs in attractor networks which cause a directed flow of activity through the neural state space. We provide regimes for parameters that enable an unspecific excitatory control signal to switch reliably between attractors in accordance with the implemented syntactic rules. If several target attractors are possible in a given state, noise in the system in conjunction with a winner-takes-all mechanism can randomly choose a target. Disambiguation can also be guided by context signals or specific additional external signals. Given a permanently elevated level of external excitation the model can enter an autonomous mode, where it generates temporal grammatical patterns continuously.     

STEPP--Search Tool for Exploration of Petri net Paths: a new tool for Petri net-based path analysis in biochemical networks

To understand biochemical processes caused by, e. g., mutations or deletions in the genome, the knowledge of possible alternative paths between two arbitrary chemical compounds is of increasing interest for biotechnology, pharmacology, medicine, and drug design. With the steadily increasing amount of data from high-throughput experiments new biochemical networks can be constructed and existing ones can be extended, which results in many large metabolic, signal transduction, and gene regulatory networks. The search for alternative paths within these complex and large networks can provide a huge amount of solutions, which can not be handled manually. Moreover, not all of the alternative paths are generally of interest. Therefore, we have developed and implemented a method, which allows us to define constraints to reduce the set of all structurally possible paths to the truly interesting path set. The paper describes the search algorithm and the constraints definition language. We give examples for path searches using this dedicated special language for a Petri net model of the sucrose-to-starch breakdown in the potato tuber.     

Hylomorphism and the Metabolic Closure Conception of Life

This paper examines three exemplary theories of living organization with respect to their common feature of defining life in terms of metabolic closure: autopoiesis, (M, R) systems, and chemoton theory. Metabolic closure is broadly understood to denote the property of organized chemical systems that each component necessary for the maintenance of the system is produced from within the system itself, except for an input of energy. It is argued that two of the theories considered—autopoiesis and (M, R) systems—participate in a hylomorphist pattern of thinking which separates the “form” of the living system from its “matter.” The analysis and critique of hylomorphism found in the work of the philosopher Gilbert Simondon is then applied to these two theories, and on the basis of this critique it is argued that the chemoton model offers a superior theory of minimal life which overcomes many of the problems associated with the other two. Throughout, the relationship between hylomorphism and the understanding of living things as machines is explored. The paper concludes by considering how hylomorphism as a background ontology for theories of life fundamentally influences the way life is defined.     

Protocell self-reproduction in a spatially extended metabolism-vesicle system

Cellular life requires the presence of a set of biochemical mechanisms in order to maintain a predictable process of growth and division. Several attempts have been made towards the building of minimal protocells from a top-down approach, i.e. by using available biomolecules. This type of synthetic approach has so far been only partially successful, and appropriate models of the synthetic protocell cycle might be needed to guide future experiments. In this paper, we present a simple biochemically and physically feasible model of cell replication involving a discrete semi-permeable vesicle with an internal minimal metabolism involving two reactive centers. It is shown that such a system can effectively undergo a whole cell replication cycle. The model can be used as a basic framework to model whole protocell dynamics including more complex sets of reactions. The possible implementation of our design in future synthetic protocells is outlined.     

HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns

The database, called HyPaLib (for Hybrid Pattern Library), contains annotated structural elements characteristic for certain classes of structural and/or functional RNAs. These elements are described in a language specifically designed for this purpose. The language allows convenient specification of hybrid patterns, i.e. motifs consisting of sequence features and structural elements together with sequence similarity and thermodynamic constraints. We are currently developing software tools that allow a user to search sequence databases for any pattern in HyPaLib, thus providing functionality which is similar to PROSITE, but dedicated to the more complex patterns in RNA sequences. HyPaLib is available at http://bibiserv. techfak.uni-bielefeld.de/HyPa/.     

A mechanomolecular model for the movement of chromosomes during mitosis driven by a minimal kinetochore bicyclic cascade

During mitosis chromosomes use a complex network of dynamic microtubules to find the cell equator in preparation for division signals. The roles of cellular chemical signals in mechanisms driving mitotic chromosomal movements are not well understood. In this paper we propose a mathematical model of this process which incorporates a molecular scale model of kinetochore-microtubule interactions into a negative feedback loop between spindle forces and local kinetochore biochemical reactions. This system allows kinetochore biochemical reactions to control and coordinate chromosome movement thus providing a direct connection between mechanical signals and mitosis chemical species. Our feedback control model can recreate chromosome movement from prometaphase to anaphase in good agreement with experimental data.     

A database system for the analysis of biochemical pathways

To provide support for the analysis of biochemical pathways a database system based on a model that represents the characteristics of the domain is needed. This domain has proven to be difficult to model by using conventional data modelling techniques. We are building an ontology for biochemical pathways, which acts as the basis for the generation of a database on the same domain, allowing the definition of complex queries and complex data representation. The ontology is used as a modelling and analysis tool which allows the expression of complex semantics based on a first-order logic representation language. The induction capabilities of the system can help the scientist in formulating and testing research hypotheses that are difficult to express with the standard relational database mechanisms. An ontology representing the shared formalisation of the knowledge in a scientific domain can also be used as data integration tool clarifying the mapping of concepts to the developers of different databases. In this paper we describe the general structure of our system, concentrating on the ontology-based database as the key component of the system.     

Semiempirical configuration interaction calculations in biochemical environments: parametrization and application to γD-crystallin, an eye-lens protein

We approach the problem of optical excitations in molecular aggregates in complex biochemical environments from a computational, all-atom perspective. The system is divided into a π orbital part described by a Pariser-Parr-Pople model with configuration interaction using singly excited Slater determinants (PPP-CIS). It is coupled to the protein and water charges of a classical force field. Strategies for a high-accuracy reparameterization and an efficient computational solution are presented. For γD-crystallin, a band edge consisting of charge-transfer states emerges for a coupled molecular aggregate compared to the uncoupled residues. The energies of some charge-transfer states strongly depend on the dielectric properties of the model, giving a first insight into the potential temporal evolution of these excitations. Possible biochemical implications are discussed.     

Eap1p, an adhesin that mediates Candida albicans biofilm formation in vitro and in vivo

Candida albicans is the leading cause of systemic fungal infections in immunocompromised humans. The ability to form biofilms on surfaces in the host or on implanted medical devices enhances C. albicans virulence, leading to antimicrobial resistance and providing a reservoir for infection. Biofilm formation is a complex multicellular process consisting of cell adhesion, cell growth, morphogenic switching between yeast form and filamentous states, and quorum sensing. Here we describe the role of the C. albicans EAP1 gene, which encodes a glycosylphosphatidylinositol-anchored, glucan-cross-linked cell wall protein, in adhesion and biofilm formation in vitro and in vivo. Deleting EAP1 reduced cell adhesion to polystyrene and epithelial cells in a gene dosage-dependent manner. Furthermore, EAP1 expression was required for C. albicans biofilm formation in an in vitro parallel plate flow chamber model and in an in vivo rat central venous catheter model. EAP1 expression was upregulated in biofilm-associated cells in vitro and in vivo. Our results illustrate an association between Eap1p-mediated adhesion and biofilm formation in vitro and in vivo.     

Knowledge representation of signal transduction pathways

MOTIVATIONS: Signal transduction is the common term used to define a diverse topic that encompasses a large body of knowledge about the biochemical mechanisms. Since most of the knowledge of signal transduction resides in scientific articles and is represented by texts in natural language or by diagrams, there is the need of a knowledge representation model for signal transduction pathways that can be as readily processed by a computer as it is easily understood by humans. RESULTS: A signal transduction pathway representation model is presented. It is based on a compound graph structure and is designed to handle the diversity and hierarchical structure of pathways. A prototype knowledge base was implemented on a deductive database and a number of biological queries are demonstrated on it.     

X-ray scattering study of activated Arp2/3 complex with bound actin-WCA

Previous structures of Arp2/3 complex, determined in the absence of a nucleation-promoting factor and actin, reveal its inactive conformation. The study of the activated structure has been hampered by uncontrollable polymerization. We have engineered a stable activated complex consisting of Arp2/3 complex, the WCA activator region of N-WASP, and one actin monomer, and studied its structure in solution by small angle X-ray scattering (SAXS). The scattering data support a model in which the first actin subunit binds at the barbed end of Arp2, and disqualify an alternative model that places the first actin subunit at the barbed end of Arp3. This location of the first actin and bound W motif constrains the binding site of the C motif to subunits Arp2 and ARPC1, from where the A motif can reach subunits Arp3 and ARPC3. The results support a model of activation that is consistent with most of the biochemical observations.     

Biochemical systems theory: operational differences among variant representations and their significance

An appropriate language or formalism for the analysis of complex biochemical systems has been sought for several decades. The necessity for such a formalism results from the large number of interacting components in biochemical systems and the complex non-linear character of these interactions. The Power-Law Formalism, an example of such a language, underlies several recent attempts to develop an understanding of integrated biochemical systems. It is the simplest representation of integrated biochemical systems that has been shown to be consistent with well-known growth laws and allometric relationships--the most regular, quantitative features that have been observed among the systemic variables of complex biochemical systems. The Power-Law Formalism provides the basis for Biochemical Systems Theory, which includes several different strategies of representation. Among these, the synergistic-system (S-system) representation is the most useful, as judged by a variety of objective criteria. This paper first describes the predominant features of the S-system representation. It then presents detailed comparisons between the S-system representation and other variants within Biochemical Systems Theory. These comparisons are made on the basis of objective criteria that characterize the efficiency, power, clarity and scope of each representation. Two of the variants within Biochemical Systems Theory are intimately related to other approaches for analyzing biochemical systems, namely Metabolic Control Theory and Flux-Oriented Theory. It is hoped that the comparisons presented here will result in a deeper understanding of the relationships among these variants. Finally, some recent developments are described that demonstrate the potential for further growth of Biochemical Systems Theory and the underlying Power-Law Formalism on which it is based.     

Acceleration of neuronal precursors differentiation induced by substrate nanotopography

Embryonic stem (ES) cell differentiation in specific cell lineages is a major issue in cell biology particularly in regenerative medicine. Differentiation is usually achieved by using biochemical factors and it is not clear whether mechanical properties of the substrate over which cells are grown can affect proliferation and differentiation. Therefore, we produced patterns in polydimethylsiloxane (PDMS) consisting of groove and pillar arrays of sub-micrometric lateral resolution as substrates for cell cultures. We analyzed the effect of different nanostructures on differentiation of ES-derived neuronal precursors into neuronal lineage without adding biochemical factors. Neuronal precursors adhered on PDMS more effectively than on glass coverslips. We demonstrated that neuronal yield was enhanced by increasing pillars height from 35 to 400 nm. On higher pillar neuronal differentiation reaches ～80% 96 h after plating and the largest differentiation enhancement of pillars over flat PDMS was observed during the first 6 h of culture. We conclude that PDMS nanopillars accelerate and increase neuronal differentiation.     

The nuclear pore complex

The nuclear pore complex is the largest supramolecular complex that assembles in the eukaryotic cell. This structure is highly dynamic and must disassemble prior to mitosis and reassemble after the event. The directed movement of macromolecules into and out of the nucleus occurs through the nuclear pore complex, a potentially regulatory point for translocation. Using biochemical and genetic approaches, several nuclear pore complex proteins from yeast and vertebrates have been well characterized. Although very little is known about plant nuclear pore proteins, research is providing new information that indicates that plant nuclear pore complexes may have some unique features.     

The Scribble and Par complexes in polarity and migration: friends or foes?

The Par complex [consisting of Bazooka (also called Par3), Par6 and aPKC] is a well-described regulator of cell polarity whose role in many aspects of cell morphogenesis is under intense investigation. Recently, another set of proteins known as the Scribble complex (consisting of Scribble, Discs large and Lethal giant larvae) has also been shown to be important in polarity regulation in several settings. Here, we describe the current status of Scribble in polarity and review evidence from various model systems that indicates an essential but context-dependent role for the Scribble and Par complexes in directed cell migration. Based on the known interactions of Scribble and Par complexes with each other and with other signalling pathways, we propose models by which Par and Scribble might interact to regulate cell migration.