PubMed HealthSearch

Biomedical subjects

P Hogeweg

Publications and source records attributed to P Hogeweg.

At least 19 recordsLinked to original sources

Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure.

Protein-specific versus taxon-specific patterns of nucleotide frequencies were studied in histone genes. The third positions of codons have a (well-known) taxon-specific G+C level and a histone type-specific G/C ratio. This ratio counterbalances the G/C ratio in the first and second positions so that the overall G and C levels in the coding region become approximately equal. The compensation of the G/C ratio indicates a selection pressure at the mRNA level rather than a selection pressure or mutation bias at the DNA level or a selection pressure on codon usage. The structure of histone mRNAs is compatible with the hypothesis that the G/C compensation is due to selection pressures on mRNA secondary structure. Nevertheless, no specific motifs seem to have been selected, and the free energy of the secondary structures is only slightly lower than that expected on the basis of nucleotide frequencies.

Animals

Iterative character weighting based on mutation frequency: a new method for constructing phyletic trees.

In this paper we present an iterative character weighting method for the construction of phyletic trees. An initial tree is used to calculate the character weights, which are the number of mutations normalized so that the possible range is corrected for. The weights obtained are used to adjust the tree; this process is iterated until a stable tree is found. Using data generated according to a model tree, we show that the trees constructed by the iterative character weighting method converge to the true underlying tree. Using biological data, the trees become closer to the systematic classification of the species concerned, and patterns conflicting with the phylogenetic pattern can be singled out. The method involves a combination of minimal length methods and similarity methods, whereby the strict parsimony criterion is relaxed.

Animals

Structural analysis of a group II intron by chemical modifications and minimal energy calculations.

Folding of the yeast mitochondrial group II intron aI5c has been analysed by chemical modification of the in vitro synthesised RNA with dimethylsulfate and diethylpyrocarbonate. Computer calculations of the intron secondary structure through minimization of free energy were also performed in order to study thermodynamic properties of the intron and to relate these to data obtained from chemical modification. Comparison of the two sets of data with the current phylogenetic model structure of the intron aI5 reveals close agreement, thus lending strong support for the existence of a typical group II intron core structure comprising six neighbouring stem-loop domains. Local discrepancies between the experimental data and the model structures have been analyzed by reference to thermodynamic properties of the structure. This shows that use of the latest refined set of free energy values improves the structure calculation significantly.

Base Sequence

Idiotypic networks incorporating T-B cell co-operation. The conditions for percolation.

Previous work was concerned with symmetric immune networks of idiotypic interactions amongst B cell clones. The behaviour of these networks was contrary to expectations. This was caused by an extensive percolation of idiotypic signals. Idiotypic activation was thus expected to affect almost all (greater than 10(7] B cell clones. We here analyse whether the incorporation of helper T cells (Th) into these B cell models could cause a reduction in the percolation. Empirical work on idiotypic interactions between Th and B cells however, would suggest that two different idiotypic Th models should be developed: (1) a Th which recognises native B cell idiotypes, i.e. a non-MHC-restricted "ThId" model, and (2) a "classical" MHC-restricted helper T cell model. In the ThId model, the Th-B cell interaction is symmetric. A 2-D model of a Th and a B cell clone that interact idiotypically with each other accounts for various equilibria (i.e. one virgin and two immune states). Introduction of antigen does indeed lead to a state switch from the virgin to the immune state; such a system is thus able to "remember" its exposure to antigen. Idiotypic signals do however, percolate in ThId models via these "B-Th-B-Th" pathways: proliferating Th and B cell clones that interact idiotypically, will always activate each other reciprocally. In the MHC-restricted Th model, Th-B interactions are asymmetric. Because the B cell idiotypes are processed and subsequently presented by MHC molecules, the Th receptor and the native B cell receptor are not expected to be complementary. Thus the Th and the B cells are unable to activate each other reciprocally, and a 2-D Th-B cell model cannot account for idiotypic memory. In contrast to the ThId model, idiotypic activation cannot percolate via "B-Th-B-Th" interactions. Due to the assymmetry idiotypic activation stops at the first Th level. A Th clone cannot activate a subsequent B cell clone: if the B cells recognise the Th cells, they see idiotype but get no help; if the Th cells see the B cells, the B cells are helped but see no idiotype. The percolation along "B-B-B" pathways in these two models is next analysed. Two B cells clones, each helped by one Th clone, are connected by a symmetric idiotypic interaction. It turns out that in both models the second (i.e. anti-idiotypic) B cells (B2) never proliferate.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals

Pattern analysis of RNA secondary structure similarity and consensus of minimal-energy folding.

We describe an automated procedure to search for consensus structures or substructures in a set of homologous or related RNA molecules. The procedure is based on the calculation of optimal and sub-optimal secondary structures using thermodynamic rules for base-pairing by energy-minimization. A linear representation of the secondary structures of the related RNAs is used so that they can be compared and classified using standard alignment and clusterings programs. We illustrate the method by means of two sets of homologous small RNAs, U2 and U3, and a set of alpha-globin mRNAs and show that biologically interesting consensus structures are obtained.

Animals

Stability of symmetric idiotypic networks--a critique of Hoffmann's analysis.

Hoffmann (1982) analysed a very simple model of suppressive idiotypic immune networks and showed that idiotypic interactions are stabilizing. He concluded that immune networks provide a counterexample to the general analysis of large dynamic systems (Gardner and Ashby, 1970; May, 1972). The latter is often verbalized as: an increase in size and/or connectivity decreases the system stability. We here analyse this apparent contradiction by extending the Hoffmann model (with a decay term), and comparing it to an ecological model that was used as a paradigm in the general analysis. Our analysis confirms that the neighbourhood stability of such idiotypic networks increases with connectivity and/or size. However, the contradiction is one of interpretation, and is not due to exceptional properties of immune networks. The contradiction is caused by the awkward normalization used in the general analysis.

Animals

Memory but no suppression in low-dimensional symmetric idiotypic networks.

We present a new symmetric model of the idiotypic immune network. The model specifies clones of B-lymphocytes and incorporates: (1) influx and decay of cells; (2) symmetric stimulatory and inhibitory idiotypic interactions; (3) an explicit affinity parameter (matrix); (4) external (i.e. non-idiotypic) antigens. Suppression is the dominant interaction, i.e. strong idiotypic interactions are always suppressive. This precludes reciprocal stimulation of large clones and thus infinite proliferation. Idiotypic interactions first evoke proliferation, this enlarges the clones, and may in turn evoke suppression. We investigate the effect of idiotypic interactions on normal proliferative immune responses to antigens (e.g. viruses). A 2-D, i.e. two clone, network has a maximum of three stable equilibria: the virgin state and two asymmetric immune states. The immune states only exist if the affinity of the idiotypic interaction is high enough. Stimulation with antigen leads to a switch from the virgin state to the corresponding immune state. The network therefore remembers antigens, i.e. it accounts for immunity/memory by switching between multiple stable states. 3-D systems have, depending on the affinities, 9 qualitatively different states. Most of these also account for memory by state switching. Our idiotypic network however fails to account for the control of proliferation, e.g. suppression of excessive proliferation. In symmetric networks, the proliferating clones suppress their anti-idiotypic suppressors long before the latter can suppress the former. The absence of proliferation control violates the general assumption that idiotypic interactions play an important role in immune regulation. We therefore test the robustness of these results by abandoning our assumption that proliferation occurs before suppression. We thus define an "escape from suppression" model, i.e. in the "virgin" state idiotypic interactions are now suppressive. This system erratically accounts for memory and never for suppression. We conclude that our "absence of suppression from idiotypic interactions" does not hinge upon our "proliferation before suppression" assumption.

Animals

Local T-T cell and T-B cell interactions: a cellular automaton approach.

In this paper we use cellular automata to study growth factor (IL-2) dependent proliferation of helper T cell (Th) and B cell clones at the level of individual cells. We argue that such a spatially- and individual-oriented approach can provide important insights, not obtainable by more conventional modelling approaches in which the immune system is modelled as a well mixed collection of clones. Two questions are examined: (1) under which conditions can a cell which produces its own growth factor (i.e. Th cells) be regulated by it; and (2) if a growth factor is effective only locally, and if both Th and B cells depend on growth factors excreted by Th cells, how can the spatial segregation of T cells and B cells in lymphoid organs and/or at acute infection sites be explained? The results show that, firstly, autocrine regulation can indeed occur in two ways: it can ensure (a) that the cell reacts only on its growth factor when packed inside tissue of arbitrary cells or (b), that the cell reacts only when close to other growth factor producing cells; and secondly, segregation of T cells and B cells results automatically from simple assumptions about the interaction and proliferation of the cells, notwithstanding the fact that proliferation is slowed down by this segregation.

Animals

Simplicity and complexity in MIRROR universes.

The scientific simplicity principle (OCCAM's razor) has always been strongly enforced by the available modelling tools. Moreover, the concept of simplicity itself is shaped by these (classical) tools. Computer models are less subject to simplicity constraints than other models are. It may be argued that complexity is the preeminent property for biological systems to study. In this paper we discuss our MIRROR modelling methodology in which (a concept of) simplicity is reconciled with biological complexity. Simplicity resides in the simple "TODO" ("do what there is to do") of the "individuals" (molecules, cells, organisms) which inhabit the model universe. The complexity appears in the multiple (levels of) individuals and the multiple levels of observable behavior of the universe. Examples are given of the development of complex, self-regulating social structures by simple interactions of individuals, and the adaptability of TODO based entities is compared to that of evolving entities. On the basis of these examples we sketch a slightly unconventional image of the evolution of complexity in biotic systems and discuss observations on the molecular record of biotic evolution which seem to fit this image.

Artificial Intelligence

Differential premature termination of transcription as a proposed mechanism for the regulation of coronavirus gene expression.

We propose that the different subgenomic mRNA levels of coronaviruses are controlled through differential premature termination of transcription, and are modulated by the relative strength of transcriptional initiation/blockage events. We present the complete set of sequences covering the leader encoding and intergenic regions of the MHV-A59 strain. A computer-assisted analysis of the two now complete sets of these sequences of strain IBV-M42 and MHV-A59 shows that, in contrast to the previous theory, differences amongst stabilities of intermolecular base-pairings between the leader and the intergenic regions are not sufficient to determine the mRNA gradients in both MHV and IBV infected cells. Neither can the accessibility of the interacting regions on the leader and the negative stranded genome, as revealed by secondary structure analysis, explain the mRNA levels. The nested gene organisation itself, on the other hand, could be responsible for observed mRNA levels gradually increasing with gene order. Relatively slow new initiation events at intergenic regions are proposed to block elongation of passing transcripts which, via temporary pausing, can cause premature termination of transcription. This effects longer transcripts more than shorter ones.

Base Composition

Minimal energy foldings of eukaryotic mRNAs form a separate leader domain.

We have investigated the minimal energy foldings of 38 mature mRNAs, including the globin family, the insulins, the growth hormones and interleukin-2, and have compared these foldings with those of fully and partly randomised sequences. The mRNAs differ from the random sequences in that they form a separate leader hairpin of 40-60 nucleotides, with the initiation codon typically located downstream of this hairpin, followed by a main fold in which a region flanking the initiation codon is basepaired with the trailer: resulting in a close proximity of the 5' and 3' end of the mRNA. The formation of this conformation depends not only--or primarily--on the structure of the leader, but on both the leader and trailer sequence and their interaction with the coding sequence. Thus if, as the frequent occurrence of this pattern suggests, the secondary structure of the leader regions plays a role in the initiation of translation, possibly accounting for the specificity of initiation and the different translational efficiencies of various mRNAs, we expect that these features may be influenced both by leader and trailer mutants.

Adenoviridae

Immunological discrimination between self and non-self by precursor depletion and memory accumulation.

We study processes by which T-lymphocytes "learn" to discriminate "self" from "non-self". We show that intrinsic features of the T cell activation and proliferation process are sufficient to tolerize (self) reactive T-lymphocyte clones. Self vs non-self discrimination therefore develops without any down-regulatory (e.g. suppressive) interactions. T-lymphocyte clones will expand by proliferation only if the IL2 concentration is high enough to induce a proliferation rate larger than the rate of cell decay. This concentration is the proliferation threshold. Because effector T cells are short-lived the proliferation threshold must be quite high. Such high numbers of cells producing IL2 are achieved only when sufficient (memory) precursors are activated. Self and non-self antigens differ with respect the number of (memory) precursor cells they accumulate, as a result of two processes, i.e. precursor depletion and memory accumulation, and can thus be discriminated. Precursor depletion: the dynamics of long-lived precursors can cause tolerization. In neonatal circumstances precursor influx is still low, newborn cells reacting with self antigens are immediately activated, generating (few), i.e. fewer than the proliferation threshold, effectors that decay rapidly. Thus total lymphocyte numbers remain low, yielding self tolerance. Conversely, large doses of similar antigens introduced in mature systems push "their" lymphocyte clone over the proliferation threshold because a large (accumulated) precursor population is rapidly activated. Small doses are however low zone tolerized. Memory accumulation: peripheral T-lymphocyte populations in fact consist of a mixture of virgin precursors and memory cells. If the formation process of (long-lived) memory cells is taken into account and virgin precursors are made short-lived, the proliferation threshold again accounts for self non-self discrimination. Memory cells accumulate when antigenic restimulation is low; it is low when the antigen concentration and/or the antigen affinity is low. Therefore self antigens, which are present in relatively high concentrations, fail to accumulate high affinity memory cells, and are hence tolerated. Memory cells crossreacting to self antigens with low affinity, however accumulate neonatally, pushing those clones over the proliferation threshold whenever "their" high affinity antigen enters the immune system. Thus the model generates differences in the antigenicity (i.e. memory precursor frequency) of self and non-self.(ABSTRACT TRUNCATED AT 400 WORDS)

Antigens

Evolution of the primary and secondary structures of the E1a mRNAs of the adenovirus.

In this paper we investigate and compare (evolutionary) patterns in the primary and secondary structure of four homologous E1a mRNAs of the adenovirus. Our main results are as follows: (1) The similarity of the coding regions of the mRNA sequences reflects both similarity in function (i.e., oncogenicity) and evolutionary divergence. (2) The similarity of the leader and the trailer regions reflects host specificity (i.e., human or simian) and must therefore arise from convergence. (3) Minimal energy foldings of the mRNAs show similar secondary structures (in particular around the splice sites). The conservation of pre-mRNA secondary structure shows that mRNAs are subject to selection constraints in addition to those associated with proteins. (4) The conserved secondary (helical) structures consist of nonhomologous subsequences, i.e., shifts have occurred. The observed shifts near the splice sites seem to be the simplest way of dealing with the dual constraints.

Adenoviridae

Interactions between macrophages and T-lymphocytes: tumor sneaking through intrinsic to helper T cell dynamics.

In a mathematical model of the cellular immune response we investigate immune reactions to tumors that are introduced in various doses. The model represents macrophage T-lymphocyte interactions that generate cytotoxic macrophages and cytotoxic T-lymphocytes. In this model antigens (tumors) can induce infinitely large T-lymphocyte effector populations because effector T-lymphocytes are capable of repeated proliferation and we have omitted immunosuppression. In this (proliferative) model small doses of weakly antigenic tumors grow infinitely large (i.e. sneak through) eliciting an immune response of limited magnitude. Intermediate doses of the same tumor induce larger immune responses and are hence rejected. Large doses of the tumor break through, but their progressive growth is accompanied by a strong immune response involving extensive lymphocyte proliferation. Similarly a more antigenic tumor is rejected in intermediate doses and breaks through in large doses. Initially small doses however lead to tumor dormancy. Thus although the model is devoid of explicit regulatory mechanisms that limit the magnitude of its response (immunosuppression is such a mechanism), the immune response to large increasing tumors may either be a stable reaction of limited magnitude (experimentally known as tolerance or unresponsiveness) or a strong and ever increasing reaction. Unresponsiveness can evolve because in this model net T-lymphocyte proliferation requires the presence of a minimum number of helper T cells (i.e. a proliferation threshold). Unresponsiveness is caused by depletion of helper T cell precursors.

Aging

Concomitant immunization by the fully antigenic counterparts prevents modulated tumor cells from escaping cellular immune elimination.

In a mathematical model of the cellular antitumor immune response, we studied the possible role of antigenic modulation as a tumor escape mechanism. Modulated tumor cells arise from normal (fully antigenic) tumor cells when the latter interact with antibodies. Modulated tumor cells demodulate when antibody concentrations are sufficiently low. Through modulation, tumor cells become less sensitive to cytotoxic macrophages (cell lysis) and contribute less to the stimulation of the immune system. These experimental data are incorporated in a model which we have analyzed previously. The model incorporates interactions between macrophages and T lymphocytes, which lead to cellular antitumor immune reactions (i.e., to cytotoxic macrophages). Parameters were derived from the immune resistance of DBA/2 mice to the SL2 tumor. Although all parameters were chosen deliberately to favor the modulation process (i.e., modulation proceeds fast, demodulation slowly, and the killing rate is reduced 50-fold), modulation is found to be a poor tumor escape mechanism. Heterogeneous populations of modulated and normal tumor cells are easily rejected. Homogeneous populations of modulated cells do escape, however. We conclude that the impact of modulation as an escape mechanism remains small because modulated tumor cells do not appear until the immune system has been stimulated (immunized) by the fully antigenic tumor cells. Thus, the elimination of modulated tumor cells generally occurs merely as a side effect of the immune response which is directed primarily against the fully antigenic tumor cells. Parameter sensitivity analysis shows that this conclusion holds true only for cellular immunity. Conversely, the parameter analysis suggests that antigenic modulation plays a deleterious role in cytotoxic antibody responses (e.g., monoclonal antibody therapy).

Animals

Tumor escape from immune elimination: simplified precursor bound cytotoxicity models.

In this paper we present a series of models on cytotoxic T-cell activation derived, by successive simplifications, from the model for Tumor Escape from Immune Elimination of Grossman & Berke (1980). In their model Grossman & Berke (1980) investigate the "sneaking through" phenomenon, by which they mean that small tumors grow progressively, medium-sized tumors are rejected and large ones break through again. We define precursor bound cytotoxicity models as systems incapable of infinite proliferation. We show that sneaking through can occur in a broad class of very simple precursor bound cytotoxicity models due to the depletion of the precursor cells. The simplest process by which precursors can be depleted is long-lasting antigenic stimulation. We conclude that in precursor bound cytotoxicity models sneaking through does not need the rather intricate combination of counteracting feedback loops, memory and blocking described by Grossman & Berke (1980).

Antigens, Neoplasm