Reprogramming cell fates: reconciling rarity with robustness

The stunning possibility of “reprogramming” differentiated somatic cells to express a pluripotent stem cell phenotype (iPS, induced pluripotent stem cell) and the “ground state” character of pluripotency reveal fundamental features of cell fate regulation that lie beyond existing paradigms. The rarity of reprogramming events appears to contradict the robustness with which the unfathomably complex phenotype of stem cells can reliably be generated. This apparent paradox, however, is naturally explained by the rugged “epigenetic landscape” with valleys representing “preprogrammed” attractor states that emerge from the dynamical constraints of the gene regulatory network. This article provides a pedagogical primer to the fundamental principles of gene regulatory networks as integrated dynamic systems and reviews recent insights in gene expression noise and fate determination, thereby offering a formal framework that may help us to understand why cell fate reprogramming events are inherently rare and yet so robust.     

Gravity Constraints Drive Biological Systems Toward Specific Organization Patterns

Different cell lineages growing in microgravity undergo a spontaneous transition leading to the emergence of two distinct phenotypes. By returning these populations in a normal gravitational field, the two phenotypes collapse, recovering their original configuration. In this review, we hypothesize that, once the gravitational constraint is removed, the system freely explores its phenotypic space, while, when in a gravitational field, cells are “constrained” to adopt only one favored configuration. We suggest that the genome allows for a wide range of “possibilities” but it is unable per se to choose among them: the emergence of a specific phenotype is enabled by physical constraints that drive the system toward a preferred solution. These findings may help in understanding how cells and tissues behave in both development and cancer.     

Tychastic Viability

Tychastic viability is defined in an uncertain dynamical framework and used for providing a “viability risk eradication measure”, first, by delineating the set of initial conditions from which all evolutions satisfy viability constraints, second, for the other “risky” initial states, by introducing their duration index. This approach provides an alternative to the stochastic representation of chance and these two measures replace the statistical measures (expectation, variance, etc).     

Reconsidering Darwin’s “Several Powers”

Contemporary textbooks often define evolution in terms of the replication, mutation, and selective retention of DNA sequences, ignoring the contribution of the physical processes involved. In the closing line of The Origin of Species, however, Darwin recognized that natural selection depends on prior more basic living functions, which he merely described as life’s “several powers.” For Darwin these involved the organism’s capacity to maintain itself and to reproduce offspring that preserve its critical functional organization. In modern terms we have come to recognize that this involves the continual generation of complex organic molecules in complex configurations accomplished with the aid of persistent far-from-equilibrium chemical self-organizing and self-assembling processes. But reliable persistence and replication of these processes also requires constantly available constraints and boundary conditions. Organism autonomy further requires that these constraints and co-dependent dynamics are reciprocally produced, each by the other. In this paper I argue that the different constraint-amplifying dynamics of two or more self-organizing processes can be coupled so that they reciprocally generate each other’s critical supportive boundary conditions. This coupling is a higher-order constraint (which can be distributed among components or offloaded onto molecular structures) that effectively constitutes a sign vehicle “interpreted” by the synergistic dynamics of these co-dependent self-organizing process so that they reconstitute this same semiotic-dynamic relationship and its self-reconstituting potential in new substrates. This dynamical co-dependence constitutes Darwin’s “several powers” and is the basis of the biosemiosis that enables evolution.     

The effect of Ca-transport inhibitors on the excitability of the pregnant and post partum rabbit uterus

To continue an earlier study, a total of 54 uterine strips were excised from 25 days pregnant and post partum rabbits. These muscles were examined under a variety of experimental conditions to further define functionally their “activator-Ca” (A-Ca) which couples excitation with contraction under these two extreme regulatory states of the uterus. As in earlier studies, increasing the stimulus strength in graded steps from 2 to 80 V/5 cm revealed two distinct “peaks” of excitability, one at ～12 V/5 cm and another at ～60 V/6 cm, separated by a zone of inhibition. Knowing that effective “first peak” stimulation demands intact membrane function and the availability of A-Ca, while the “second peak” stimulation probably bypasses the membrane process and activates the contractile system directly by mobilizing Ca bound to intracellular structures, the effects on the strength-tension curve of normal and Ca-free KRB, excess KCl, Verapamil, Ruthenium-red and MnCl₂ were examined. These studies exposed again the different states of the A-Ca in the uteri of pregnant and post partum rabbits, which partly explain the functional differences of the myometrium under these two extreme regulatory conditions.     

Rethinking Causation for Data-intensive Biology: Constraints,Cancellations, and Quantized Organisms

Complex organisms thwart the simple rectilinear causality paradigm of “necessary and sufficient,” with its experimental strategy of “knock down and overexpress.” This Essay organizes the eccentricities of biology into four categories that call for new mathematical approaches; recaps for the biologist the philosopher's recent refinements to the causation concept and the mathematician's computational tools that handle some but not all of the biological eccentricities; and describes overlooked insights that make causal properties of physical hierarchies such as emergence and downward causation straightforward. Reviewing and extrapolating from similar situations in physics, it is suggested that new mathematical tools for causation analysis incorporating feedback, signal cancellation, nonlinear dependencies, physical hierarchies, and fixed constraints rather than instigative changes will reveal unconventional biological behaviors. These include “eigenisms,” organisms that are limited to quantized states; trajectories that steer a system such as an evolving species toward optimal states; and medical control via distributed “sheets” rather than single control points.     

Constraints on the Structure of Combinatorial “Chick-a-dee” Calls

“Chick-a-dee” calls of the black-capped chickadee (Parus atricapillus) constitute a combinatorial system of animal communication, apparently the only such system yet described. Four note-types, which may be omitted or repeated a variable number of times, occur in a fixed sequence (A–B–C–D) to constitute calls. Quantitative analyses determining the nature of departures from first-order transitional probabilities between successive notes revealed a variety of results that point consistently to two underlying features of calls. (1) Some constraint operates to limit the length of calls, as manifest in shortening of repetition-strings and omitting of note-types expected to follow. (2) There is an opposing tendency to include at least one or two D-notes at the end of a call, regardless of the overall length. The second feature suggests important semantic properties of D-notes, especially the ratio of D s to other note-types and the flock-specific acoustical structure of D-notes. The constraint on length of call does not appear intimately related to semantic causes, but may instead be determined by the maximum duration of continuous phonation, in parallel with the fundamental breath-group of human speech. In this respect, a “chick-a-dee” call resembles an entire “natural sentence” of spoken human language.     

Why are conversations limited to about four people? A theoretical exploration of the conversation size constraint

It is genuinely difficult to sustain a casual conversation that includes more than four speakers. Add a fifth speaker, and the conversation often quickly fissions into smaller groups. Termed ‘the dinner party problem,’ this four-person conversation size limit is believed to be caused by evolved cognitive constraints on human mentalizing capacities. In this view, people can mentally manage three other minds at any one time, leading to four-person conversations. But whereas existing work has posited and empirically tested alternative accounts of what drives the conversation size constraint, to our knowledge, no work has explored the question of why this capacity is specifically four? In this theoretical paper, we (a) review research demonstrating this cognitive constraint in sociality, (b) review the relevant working memory literature, which has explored the “why four” question at some length, and (c) we begin to pose possible answers to our specific social “why four” question. Using simple mathematical models of small-scale sociality, which we imbue with evolutionarily-relevant content, we present one novel possible explanation for the four-person conversation size constraint.     

The fine structure of the trout blastoderm, Salvelinus fontinalis (Mitchill)

The Speckled Trout blastoderm at the late high blastula stage is characterized by two different cell populations. The “light” blastomeres comprise one cell type while the “dark” and “medium” blastomeres appear to differ from one another only in degree and thus may be considered as the second type. “Dark” and “medium” blastomeres are irregular in shape, are located centrally and deep in the blastoderm, have an abundance of smooth endoplasmic reticulum with associated 520 Å glycogen particles and a single mitochondrial profile. The “light” blastomeres have randomly arranged glycogen particles in minimal quantities in contrast to the “medium” and “dark” blastomeres and in addition exhibit three mitochondrial profiles, which could however represent artifacts. It is postulated that in the Speckled Trout cellular differentiation has commenced by the third day of incubation at 10°C and that this is manifested visually by the appearance of two different cell populations; the more differentiated “dark” and “medium” blastomeres possibly destined to give rise to the hypoblast and the less differentiated “light” blastomeres.     

Maternal exposure to paternal antigens can modulate the foetus immune system and is associated with reduced atopy in the childhood

The influence of the maternal immune system on pregnancy and on the foetus immune system have given rise to a variety of observations and interesting hypotheses. For example, the higher prevalence of atopy in first-born children as compared to their brotherhood is known as the “birth order effect”. The “hygienic hypothesis” states that more hygienic live conditions, and consequently reduced exposure to pathogens in young age (included the period of foetal development), increases the risk of atopy. Here we review the ideas concerning maternal exposure to paternal antigens and immunomodulation. In particularly, we discuss the idea that this phenomenon may induce a regulatory environment in women that interfere with the developing foetal immune system. This regulatory environment could be responsible for protecting children to the development of atopy during adulthood. We propose that maternal exposure to paternal antigens through different situations, such as pregnancy, repeated exposure to sperm or Paternal Leukocyte Immunization (PLI) would combine the “birth order effect” and the “hygienic hypothesis” and thus lower the risk to atopy in children through the transference of a regulatory environment to the foetus.     

Depression, Constraint, and the Liver: (Dis)assembling the Treatment of Emotion-Related Disorders in Chinese Medicine

Traditional Chinese medicine (TCM) is today practiced worldwide, rivaling biomedicine in terms of its globalization. One of the most common TCM diagnoses is “Liver qi constraint,” which, in turn, is commonly treated by an herbal formula dating back to the 10th century. In everyday TCM practice, biomedical disease categories such as depression or anxiety and popular disease categories such as stress are often conflated with the Chinese medical notion of constraint. Medical anthropologists, meanwhile, argue that constraint reveals to us a distinctive aesthetics of constructing body/persons in Chinese culture, while psychologists seek to define constraint as a distinctive psychiatric disorder distinctive from depression and anxiety. All of these actors agree in defining constraint as a concept dating back two thousand years to the very origins of Chinese medicine. This article disassembles the articulations by means of which these different facts about constraint are constructed. It shows how ideas about constraint as a disorder caused by the penetration of external pathogens into the body were gradually transformed from the eleventh century onward into constraint as an emotion-related disorder, while treatment strategies were adjusted to match perceptions about body/self that developed among the gentry elite of southeast China in late imperial China.     

Between Europe and the Balkans: Mapping Slovenia and Croatia's “Return to Europe” in the 1990s

This essay traces the ongoing discursive processes through which two former Yugoslav states — Croatia and Slovenia — framed their so-called “exit from the Balkans” and “return to Europe” throughout the 1990s. Applying Maria Todorova's framework of “Balkanism” to these two cases, the essay examines how leaders sought recognition as belonging to Europe, or Central Europe, by defining their respective national identities in opposition to Balkan or Yugoslav ones. What distinguishes Balkanism from other critical traditions such as Orientalism is that the Balkans are located in a distinctively liminal position: at the same time part of Europe as well as its antithetical periphery, the “other” within. This in-between position can often lead to contradictory identity constructions, whereby an insistence on concretizing one's Europeanness coincides with a certain awareness that this European status is never ontologically secure. The essay concludes by considering ways in which the Balkans can be re-imagined, reassembling diverse fragments of Balkan identity into a site for positive engagement and critique.     

Controlled Enzymatic Hydrolysis: A New Strategy for the Discovery of Antimicrobial Peptides

The use of antimicrobial peptides (AMPs) is an alternative to traditional antibiotics. AMPs are obtained using different methods such as bacterial synthesis, chemical synthesis and controlled enzymatic hydrolysis. The later is an interesting approach that deserves our attention because of the yields gathered and peptides engineered. Usually, activities of AMPs obtained in such a way are tightly dependent on the hydrolysis mechanism used. This paper deals with the hydrolysis of hemoglobin mechanism as a potential source of AMPs. Production of AMPs from hemoglobin using enzymatic controlled system is linked to hemoglobin structure. Further, we show that bovine hemoglobin, which is sensitive to peptic hydrolysis, results upon enzymatic digestion as a great source of AMPs. The hemoglobin in native and denatured states was hydrolyzed by “one-by-one” and “zipper” mechanisms, respectively. Nevertheless, a new mechanism named “semi-zipper” mechanism is obtained when protein is in molten globule structural state, constituting an original strategy for AMPs production. Seventy seven percentage of the peptides obtained by this new strategy showed antibacterial activity against nine strains.     

Accuracy and response-time distributions for decision-making: linear perfect integrators versus nonlinear attractor-based neural circuits

Animals choose actions based on imperfect, ambiguous data. “Noise” inherent in neural processing adds further variability to this already-noisy input signal. Mathematical analysis has suggested that the optimal apparatus (in terms of the speed/accuracy trade-off) for reaching decisions about such noisy inputs is perfect accumulation of the inputs by a temporal integrator. Thus, most highly cited models of neural circuitry underlying decision-making have been instantiations of a perfect integrator. Here, in accordance with a growing mathematical and empirical literature, we describe circumstances in which perfect integration is rendered suboptimal. In particular we highlight the impact of three biological constraints: (1) significant noise arising within the decision-making circuitry itself; (2) bounding of integration by maximal neural firing rates; and (3) time limitations on making a decision. Under conditions (1) and (2), an attractor system with stable attractor states can easily best an integrator when accuracy is more important than speed. Moreover, under conditions in which such stable attractor networks do not best the perfect integrator, a system with unstable initial states can do so if readout of the system’s final state is imperfect. Ubiquitously, an attractor system with a nonselective time-dependent input current is both more accurate and more robust to imprecise tuning of parameters than an integrator with such input. Given that neural responses that switch stochastically between discrete states can “masquerade” as integration in single-neuron and trial-averaged data, our results suggest that such networks should be considered as plausible alternatives to the integrator model.     

Qualitative dynamics of a network model of regulation of the immune system: A rationale for the IgM to IgG switch

A mathematical model has been developed that simulates some of the main features of a network theory of regulation of the immune system. According to the network viewpoint, the V regions (idiotypes) on antibodies and lymphocytes are self-antigens, to which other lymphocytes of the system can respond specifically, just as they respond to foreign antigens. The resultant couplings between the lymphocytes are considered to be basic for the regulation of the system.The present mathematical model simulates the interactions between cells that recognize the antigen (“positive cells”), and “negative cells” that have receptors that specifically recognize the V regions of the positive cells. The mathematical model incorporates only the interactions that are postulated to be important in the four steady states of the theory, and includes neither the antigen nor any accessory (“A”) cells. The effects of both antigen-specific and anti-idiotypic T and B cells are included, as well as antigen-specific and anti-idiotypic T cell factors, and the two main classes of antibodies. The model is a first order autonomous ordinary differential equation in two variables. We describe a geometric technique that gives strong information on the model, without explicitly solving the ordinary differential equation. This technique proves to be powerful in permitting us to systematically scan the parameter space of the model. The detailed analysis leads to support for the idea that the model provides a rationale for the switch observed in the immune system from the production of one major class of antibody (IgM) to the other major class (IgG). The analysis also leads to a new, previously unsuspected possibility for the nature of the suppressed state within the context of the postulates of the symmetrical network theory.     

Logical-Semantic Analysis and the Development of L.S. Vygotsky's Ideas About “Units” and “Elements” of Psychological Systems

Based on an analysis of L.S. Vygotsky's concepts of “units” and “elements” of psychological systems, this article highlights five of their attributes. It shows that these attributes are logically symmetrical, since in their wording they can be converted into one another by negation or by replacing some words with their opposites. This suggests that the concepts of the “unit” and “element” of a system are different poles of one theoretical construct of the activity of human psychology. Thus methods for the study of psychological systems by breaking them down into elements or by separating them into units can be seen as complementary. The article describes differences among the concepts of “unit,” “minimal unit,” and “cell” of a psychological system. It reviews several problems that are solvable using the “method of units,” as well as some concepts of the theory of psychological systems that are understood as holistic, conceptual, and active processes and/or results of human interaction with the world. Among the examples of such systems are “systems of psychological functions” (according to Vygotsky), as well as separate activities (according to A.N. Leontiev), human actions and operations (interactions with the world on the level of objects and mental or physical means). The “component” of a psychological system is defined as any “something” that in some sense belongs to or is included in human interaction with the world. A component that belongs to the system is called an “element” of it, but a component that is included in the functioning and development of the system is called a “part” of it. The article presents the mathematical and psychological foundation of these definitions. It identifies and discusses the substantial (independently existing) components of psychological systems and their attributes (properties and conditions). It describes the relationships between them using the bipolar theoretical constructs “part-element” and “substantial-attributive” component of a system.     

A bifurcation model for developmental processes

I have constructed, for developmental processes, a qualitative model similar to the compartment hypothesis in Drosophila, and examined its relevance to vertebrate systems. In this model a polarized “cluster” of interacting cells will be the unit for “bifurcation” of the developmental pathway into two alternative states of “locon” which is the genetic unit controlling this process. The minimum size of the cluster critical for bifurcation and the size of the emerging subclusters will be dictated by the cognate locon. This will obviate the need for an extrinsically imposed threshold of some state variable for the boundary of the two subclusters. However, the orientation of bifurcation will be determined by the polarity of the cluster. A physiological factor of competence will impose a temporal constraint to bifurcation.Thus, combinatorial binary codes for a set of locons, like those originally devised by Kauffman (1973), can be assigned to developmental pathways. One of the clusters emerging from a sequence of bifurcations will have the same code as the mother cluster. It will represent the “developmental sink”, and will not recycle through the bifurcation series originating from the initial mother cluster, because of the difference in spatio-temporal factors incorporated in the size and competence of the individual clusters. If bifurcations are prevented, the mother cluster will be forced along the pathway of the developmental sink.I have applied the model to cases in vertebrate development where commitments to developmental pathways for aperiodic or periodic segmentations may follow a linear temporal sequence, producing, in turn, subclusters of uncommitted, or stem, cells towards the more intensely polarized end of the mother cluster. Such cases include limb, somite and tail formation and several stem cell systems with a finite lifespan. I have discussed some possible experimentation which emerges from the model.     

Spatiotemporal analysis of simultaneous single-unit activity in the dragonfly

Continuous neural spiking records were obtained from the mesothoracic ganglion of the dragonfly. For analysis the 12 s records of all 58 discriminated cells were “tracked” across three continuous behavioral states: pre-flight, flight and post-flight. The recorded spike amplitudes and angles (widths) for each cell were used to construct a simple map of individual cell positions relative to each other within the ganglion. Individual cell activity patterns were then characterized both with respect to neighboring cell locations and patterns of cell spiking observed across three behavioral states. The results indicated that this technique for constructing a “neighboring cell map” effectively reflects the known histological features of the ganglionic cell architecture. The gross firing histories of individual cells were found to correspond to the overall spike patterns of neighboring ganglionic cells as opposed to more distal cells. Such relationships suggest that the physical layout of this ganglionic network may help to determine or bias individual cell firing histories that occur during different behavioral states in the dragonfly.     

The field-dependence of the solid-state photo-CIDNP effect in two states of heliobacterial reaction centers

The solid-state photo-CIDNP (photochemically induced dynamic nuclear polarization) effect is studied in photosynthetic reaction centers of Heliobacillus mobilis at different magnetic fields by ¹³C MAS (magic-angle spinning) NMR spectroscopy. Two active states of heliobacterial reaction centers are probed: an anaerobic preparation of heliochromatophores (“Braunstoff”, German for “brown substance”) as well as a preparation of cells after exposure to oxygen (“Grünstoff”, “green substance”). Braunstoff shows significant increase of enhanced absorptive (positive) signals toward lower magnetic fields, which is interpreted in terms of an enhanced differential relaxation (DR) mechanism. In Grünstoff, the signals remain emissive (negative) at two fields, confirming that the influence of the DR mechanism is comparably low.     

A model of binocular stereopsis including a global consistency constraint

 The binocular correspondence problem was solved by implementing the uniqueness constraint and the continuity constraint, as proposed by Marr and Poggio [Marr D, PoggioT (1976) Science 194: 283–287]. However, these constraints are not sufficient to define the proper correspondence uniquely. With these constraints, random-dot stereograms (RDSs), consisting of the periodic textures in each image, are treated as a correspondence of surfaces composed of patches of alternating values of disparity. This is quite different from the surface we perceive through the RDSs, that is a surface characterized by a single depth. Because these constraints are local, they cannot produce the global optimum of correspondence. To obtain the global optimum of correspondence, we propose a model of binocular stereopsis in which a global measure of correspondence is explicitly employed. The model consists of two hierarchical systems. First, the lower system processes various correspondences based on the uniqueness constraint. Second, the higher system provides a global measure of correspondence for the disparity in question. The higher system uniquely determines the global optimum of correspondence in the lower system through the recurrent loop between hierarchical systems. The convergence of the recurrent loop is determined by the consistency between the hierarchical systems. The condition is termed the `global consistency constraint. Received: 27 August 1998 / Accepted in revised form: 8 November 1999