The origin of life — A task in molecular engineering

In attempting to understand how life originated, we search for a detailed sequence of experimentally testable physico-chemical steps in an appropriately structured system. This goal is approached in two stages. First we search for the organizational structure of processes leading to systems with the basic features of living organisms. This is an engineering problem: finding a certain construct by taking care of logical requirements and restrictions from physics. Then we face this construct with the chemical and geophysical reality, and this leads to the view that systems with the essential features of early living organisms evolve following a distinct pathway. Energy supply and the presence of a particular structure in space and time are necessary to induce and drive the processes triggered by stochastic events; but if these particular conditions are given, the broad line of the evolutionary processes is determined by logical requirements and by chemical and geophysical constrains and invariants. The genetic machinery considered to evolve in this manner agrees, in its organizational structure and in many details, with the actual genetic machinery of biosystems. A surprising simplicity and transparency is observed in the logic of the basic processes involved in the origin of life.In the present view, the processes leading to the origin of life begin in a very particular, highly structured, small region where the relevant chemistry can be quite different from overall prebiotic chemistry. Energy-rich compounds are present in ample amounts and a succession of physico-chemical processes, which are per se thermodynamically allowed, takes place. This is in contrast to popular views that the origin of life is connected with fundamental thermodynamic questions related to the problem of getting order out of chaos.     

The phenogenetic logic of life

For nearly a century we have understood that life works through genes, and so have had an elegant theory for general evolution. But this did not explain the kinds of traits that characterize organisms, nor how genes produce them. Advances in recent decades have opened the way for an understanding of the phenogenetic logic or relational principles of life, by which a few basic characteristics of genomes produce biological phenotypes through some basic developmental processes. This logic provides a general explanation of the nature and source of organismal design, and a powerful programme for research.     

The basic reproductive ratio of life

Template-directed polymerization of nucleotides is believed to be a pathway for the replication of genetic material in the earliest cells. We assume that activated monomers are produced by prebiotic chemistry. These monomers can undergo spontaneous polymerization, a system that we call “prelife.” Adding template-directed polymerization changes the equilibrium structure of prelife if the rate constants meet certain criteria. In particular, if the basic reproductive ratio of sequences of a certain length exceeds one, then those sequences can attain high abundance. Furthermore, if many sequences replicate, then the longest sequences can reach high abundance even if the basic reproductive ratios of all sequences are less than one. We call this phenomenon “subcritical life.” Subcritical life suggests that sequences long enough to be ribozymes can become abundant even if replication is relatively inefficient. Our work on the evolution of replication has interesting parallels to infection dynamics. Life (replication) can be seen as an infection of prelife.     

Counting on neurons: the neurobiology of numerical competence

Numbers are an integral part of our everyday life - we use them to quantify, rank and identify objects. The verbal number concept allows humans to develop superior mathematical and logic skills that define technologically advanced cultures. However, basic numerical competence is rooted in biological primitives that can be explored in animals, infants and human adults alike. We are now beginning to unravel its anatomical basis and neuronal mechanisms on many levels, down to its single neuron correlate. Neural representations of numerical information can engage extensive cerebral networks, but the posterior parietal cortex and the prefrontal cortex are the key structures in primates.     

An error model for protein quantification

MOTIVATION: Quantitative experimental data is the critical bottleneck in the modeling of dynamic cellular processes in systems biology. Here, we present statistical approaches improving reproducibility of protein quantification by immunoprecipitation and immunoblotting. RESULTS: Based on a large data set with more than 3600 data points, we unravel that the main sources of biological variability and experimental noise are multiplicative and log-normally distributed. Therefore, we suggest a log-transformation of the data to obtain additive normally distributed noise. After this transformation, common statistical procedures can be applied to analyze the data. An error model is introduced to account for technical as well as biological variability. Elimination of these systematic errors decrease variability of measurements and allow for a more precise estimation of underlying dynamics of protein concentrations in cellular signaling. The proposed error model is relevant for simulation studies, parameter estimation and model selection, basic tools of systems biology. AVAILABILITY: Matlab and R code is available from the authors on request. The data can be downloaded from our website www.fdm.uni-freiburg.de/~ckreutz/data.     

Metabolism and the problem of its universalization

Metabolism tends to be conceived either as an operationally closed network of production of components or as an autonomous apparatus of management of energy flows. Taking up some recent ideas that connect the concept of autonomy with thermodynamic requirements, we move further to defend the hypothesis that there must be a deep intertwinement between the relational-constructive logic of a basic biological system and the logic of its thermodynamic implementation. Hence, we propose that metabolism should be universally defined as the recursive self-maintenance of controls upon the energy flows necessary for the physical realization of a component production system operationally closed. Finally, being critical with some claims of the so-called 'strong' artificial life approach, we try to show that present 'computational metabolisms' are necessarily different in their structure and functioning from any real metabolic system, due to the distinct type of causal relations and mechanisms which are respectively established in them.     

"Shrink wrapping" lectures: teaching cell and molecular biology within the context of human pathologies

Students are most motivated and learn best when they are immersed in an environment that causes them to realize why they should learn. Perhaps nowhere is this truer than when teaching the biological sciences to engineers. Transitioning from a traditionally mathematics-based to a traditionally knowledge-based pedagogical style can challenge student learning and engagement. To address this, human pathologies were used as a problem-based context for teaching knowledge-based cell biological mechanisms. Lectures were divided into four modules. First, a disease was presented from clinical, economic, and etiological standpoints. Second, fundamental concepts of cell and molecular biology were taught that were directly relevant to that disease. Finally, we discussed the cellular and molecular basis of the disease based on these fundamental concepts, together with current clinical approaches to the disease. The basic science is thus presented within a "shrink wrap" of disease application. Evaluation of this contextual technique suggests that it is very useful in improving undergraduate student focus and motivation, and offers many advantages to the instructor as well.     

Infants' knowledge of their own species

Recognition of individuals at first sight is important for social species and can be achieved by attending to facial or body information. Previous research suggests that infants possess a perceptual template for evolutionarily relevant stimuli, which may include humans, dangerous animals (e.g. snakes), but not non-dangerous animals. To be effective, such a mechanism should result in a systematic preference for attending to humans over non-dangerous animals. Using a preferential looking paradigm, the present studies investigated the nature of infants' early representation of humans. We show that 3.5- and six-month-old infants attend more to human beings than non-human primates (a gorilla or monkey) which are examplars of non-dangerous animals. This occurred when infants were presented with head or body information in isolation, as well as when both are presented simultaneously. This early preference for humans by 3.5 months of age suggests that there is a basic representation for humans, which includes both head and/or body information. However, neonates demonstrated a preference only for human faces over non-human primate faces, not for humans over non-human primates when the stimuli were presented with both head and body simultaneously. The results show that although neonates display a preference for human faces over others, preference for the human body only develops later, in the first few months of life. This suggests that infants have acquired some knowledge about the human body at 3.5 months of age that may have developed from their privileged experience with other humans in the first few months of life, rather than an innate ability to detect humans in their entirety.     

The prion hypothesis: from biological anomaly to basic regulatory mechanism

Prions are unusual proteinaceous infectious agents that are typically associated with a class of fatal degenerative diseases of the mammalian brain. However, the discovery of fungal prions, which are not associated with disease, suggests that we must now consider the effect of these factors on basic cellular physiology in a different light. Fungal prions are epigenetic determinants that can alter a range of cellular processes, including metabolism and gene expression pathways, and these changes can lead to a range of prion-associated phenotypes. The mechanistic similarities between prion propagation in mammals and fungi suggest that prions are not a biological anomaly but instead could be a newly appreciated and perhaps ubiquitous regulatory mechanism.     

Increased burst size in multiply infected cells can alter basic virus dynamics

ABSTRACT: BACKGROUND: The dynamics of viral infections have been studied extensively in a variety of settings, both experimentally and with mathematical models. The majori-ty of mathematical models assumes that only one virus can infect a given cell at a time. It is, however, clear that especially in the context of high viral load, cells can become infected with multiple copies of a virus, a process called coinfection. This has been best demonstrated experimentally for human immunodeficiency virus (HIV), although it is thought to be equally relevant for a number of other viral infections. In a previously explored mathematical model, the viral output from an infected cell does not depend on the number of viruses that reside in the cell, i.e. viral replication is limited by cellular rather than viral factors. In this case, basic virus dynamics properties are not altered by coinfection. Results: Here, we explore the alternative assumption that multiply infected cells are characterized by an increased burst size and find that this can fundamentally alter model predictions. Under this scenario, establishment of infection may not be solely determined by the basic reproductive ratio of the virus, but can depend on the initial virus load. Upon infection, the virus population need not follow straight exponential growth. Instead, the exponential rate of growth can increase over time as virus load becomes larger. Moreover, the model suggests that the ability of anti-viral drugs to suppress the virus population can depend on the virus load upon initiation of therapy. This is because more coinfected cells, which produce more virus, are present at higher virus loads. Hence, the degree of drug resistance is not only determined by the viral genotype, but also by the prevalence of coinfected cells. Conclusions: Our work shows how an increased burst size in multiply infected cells can alter basic infection dynamics. This forms the basis for future experimental testing of model assumptions and predictions that can distinguish between the different scenarios.     

Unsupervised logic-based mechanism inference for network-driven biological processes

Modern analytical techniques enable researchers to collect data about cellular states, before and after perturbations. These states can be characterized using analytical techniques, but the inference of regulatory interactions that explain and predict changes in these states remains a challenge. Here we present a generalizable, unsupervised approach to generate parameter-free, logic-based models of cellular processes, described by multiple discrete states. Our algorithm employs a Hamming-distance based approach to formulate, test, and identify optimized logic rules that link two states. Our approach comprises two steps. First, a model with no prior knowledge except for the mapping between initial and attractor states is built. We then employ biological constraints to improve model fidelity. Our algorithm automatically recovers the relevant dynamics for the explored models and recapitulates key aspects of the biochemical species concentration dynamics in the original model. We present the advantages and limitations of our work and discuss how our approach could be used to infer logic-based mechanisms of signaling, gene-regulatory, or other input-output processes describable by the Boolean formalism.     

The Croonian lecture 2006. Structure of the living cell

The smallest viable unit of life is a single cell. To understand life, we need to visualize the structure of the cell as well as all cellular components and their complexes. This is a formidable task that requires sophisticated tools. These have developed from the rudimentary early microscopes of 350 years ago to a toolbox that includes electron microscopes, synchrotrons, high magnetic fields and vast computing power. This lecture briefly reviews the development of biophysical tools and illustrates how they begin to unravel the 'molecular logic of the living state'.     

Ready player one? Autophagy shapes resistance to photodynamic therapy in cancers

Photodynamic therapy (PDT) is a procedure used in cancer therapy that has been shown to be useful for certain indications. Considerable evidence suggests that PDT might be superior to conventional modalities for some indications. In this report, we examine the relationship between PDT responsiveness and autophagy, which can exert a cytoprotective effect. Autophagy is an essential physiological process that maintains cellular homeostasis by degrading dysfunctional or impaired cellular components and organelles via a lysosome-based pathway. Autophagy, which includes macroautophagy and microautophagy, can be a factor that decreases or abolishes responses to various therapeutic protocols. We systematically discuss the mechanisms underlying cell-fate decisions elicited by PDT; analyse the principles of PDT-induced autophagy, macroautophagy and microautophagy; and present evidence to support the notion that autophagy is a critical mechanism in resistance to PDT. A combined strategy involving autophagy inhibitors may be able to further enhance PDT efficacy. Finally, we provide suggestions for future studies, note where our understanding of the relevant molecular regulators is deficient, and discuss the correlations among PDT-induced resistance and autophagy, especially microautophagy.     

Role of amphiphilic compounds in the evolution of membrane structure on the early earth

A variety of amphiphilic compounds have the capacity to self-assemble into membranous structures in the form of bilayers. The earliest cellular organisms must have incorporated such compounds into boundary membranes, and this review discusses amphiphilic components of the prebiotic environment which would be candidates. One possible source is organic material carried to the earth's surface by meteoritic infall. To test this, we have extracted and analysed non-polar substances from the Murchison carbonaceous chondrite, and found that at least some of the components can produce boundary structures which resemble membranes. This observation suggests that membranous boundary structures were present on the early earth, and available to participate in the origin and evolution of the first cellular forms of life.     

Assessment of the Immunomodulatory Properties of Human Mesenchymal Stem Cells (MSCs)

The immunomodulatory properties of multilineage human mesenchymal stem cells (MSCs) appear to be highly relevant for clinical use towards a wide-range of immune-related diseases. Mechanisms involved are increasingly being elucidated and in this article, we describe the basic experiment to assess MSC immunomodulation by assaying for suppression of effector leukocyte proliferation. Representing activation, leukocyte proliferation can be assessed by a number of techniques, and we describe in this protocol the use of the fluorescent cellular dye carboxyfluorescein succinimidyl ester (CFSE) to label leukocytes with subsequent flow cytometric analyses. This technique can not only assess proliferation without radioactivity, but also the number of cell divisions that have occurred as well as allowing for identification of the specific population of proliferating cells and intracellular cytokine/factor expression. Moreover, the assay can be tailored to evaluate specific populations of effector leukocytes by magnetic bead surface marker selection of single peripheral blood mononuclear cell populations prior to co-culture with MSCs. The flexibility of this co-culture assay is useful for investigating cellular interactions between MSCs and leukocytes.