Living nanovesicles--chemical and physical survival strategies of primordial biosystems

Life on Earth and Mars could have started with self-assembled nanovesicles similar to the present nanobacteria (NB). To resist extreme environmental stress situations and periods of nutritional deprivation, nanovesicles would have had a chemical composition protected by a closed mineralized compartment, facilitating their development in a primordial soup, or other early wet environment. Their survivability would have been enhanced if they had mechanisms for metabolic communication, and an ability to collect primordially available energy forms. Here, we establish an irreducible model system for life formation starting with NB.     

Use of 1H NMR to study transport processes in porous biosystems

The operation of bioreactors and the metabolism of microorganisms in biofilms or soil/sediment systems are strongly dictated by the transport processes therein. Nuclear magnetic resonance (NMR) spectroscopy or magnetic resonance imaging (MRI) allow nondestructive and noninvasive quantification and visualisation (in case of MRI) of both static and dynamic water transport phenomena. Flow, mass transfer and transport processes can be measured by mapping the (proton) displacement in a defined time interval directly in a so-called pulsed field gradient (PFG) experiment. Other methods follow the local intensity in time-controlled sequential images of water or labelled molecules, or map the effect of contrast agents. Combining transport measurements with relaxation-time information allows the discrimination of transport processes in different environments or of different fluids, even within a single picture element in an image of the porous biosystem under study. By proper choice of the applied NMR method, a time window ranging from milliseconds to weeks (or longer) can be covered. In this paper, we present an overview of the principles of NMR and MRI techniques to visualise and unravel complex, heterogeneous transport processes in porous biological systems. Applications and limitations will be discussed, based on results obtained in (model) biofilms, bioreactors, microbial mats and sediments. Journal of Industrial Microbiology & Biotechnology (2001) 26, 43–52. Received 20 April 2000/ Accepted in revised form 14 August 2000     

Pink-noise behaviour of biosystems

Pink (1/f) noise is one of the most common behaviours of biosystems. Our present paper is devoted to clarify the origin of this interesting phenomenon. It is shown that the stationary random stochastic processes under self-similar conditions (as we have in living objects) generate pink noise independently of the kind and number of variables.     

Biomanufacturing by in vitro biosystems containing complex enzyme mixtures

Microbial fermentation is the current predominant biomanufacturing platform. However, it suffers from low production yields, slow reaction rates, and scaling-up challenges. In vitro enzymatic biosystems are emerging to expand the traditional biotechnological mode by utilizing more than three enzymes for manufacturing the desired product from cheap substrate. In the past few years, numerous proofs of the concept of in vitro biosystems containing complex enzyme mixtures from different groups worldwide have inspired the development of these platforms for biomanufacturing, these biosystems show advantages such as near-theoretical product yields, faster reaction rates, reduced interference from toxic compounds, and unprecedented level of engineering. In this review, several examples of in vitro systems are presented to illustrate these advantages and possible solutions to overcome the remaining challenges are discussed. The continuing decrease in enzyme cost and improvements in enzyme engineering techniques will make in vitro biosystems a comparable biomanufacturing platform for microbial fermentation in the near future.     

Modelling the dynamics of biosystems

The need for a more formal handling of biological information processing with stochastic and mobile process algebras is addressed. Biology can benefit this approach, yielding a better understanding of behavioural properties of cells, and computer science can benefit this approach, obtaining new computational models inspired by nature.     

Reliability of autoregulatory mechanisms of biosystems as affected by ionizing radiation

Reliability of biosystems in processes of adaptation and homeostasis after whole-body irradiation of rats with different doses was determined in terms of the stochastic process theory developed for the autoregulatory systems with random parameters. Fluctuations in the rate of spontaneous chemiluminescence of blood serum and accumulation of lipid peroxidation products by erythrocyte membranes of rat blood were taken as the initial material. The analysis of fluctuations of peculiar parameters permitted to predict the adaptability of the system and to make timely corrections.     

On the unlikelihood of non-aqueous biosystems

Theunique ability of the solvent liquid water to form polymorphic, 3-dimensional, H-bonded aggregates and solvation envelopes of widely different character (hydrophilic or coulombic hydration and hydrophobic hydration) is anecessary condition for the realization of the levels of order in form and complexity in function required by carbonaceous biotic systems.Woods Hole Oceanographic Institution Contribution No. 2572.     

Generation of oxy radicals in biosystems

Many recent lines of evidence indicate that endogenous free radicals contribute to spontaneous mutagenesis through the direct induction of DNA damage. However, the mechanisms underlying this process are not yet fully understood. A brief overview of the knowledge that is currently available is provided here, with emphasis on the generation of oxy radicals in biosystems, the reactions of those radicals with biomolecules, and the induction of oxidative DNA base damage that might lead to mutation.     

Bond graph models for plant biosystems

Computable dynamic models for plant biosystems permit the study of effects of environmental variables on plant growth and productivity. Using bond graphs, a comprehensive phenomenological model of a plant biosystem may be developed and used in computer simulations. Elements of a model studied in this paper include a gas diffusion network between the atmosphere and leaf cytoplasm, intracellular chemistry, and the translocation networks of the phloem. Bond graphs are shown to provide a conceptual basis for the development of biological subsystem and system models and lead to computable representations.     

Synthetic biology, inspired by synthetic chemistry

The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell.     

Model of active peristaltic transport in biosystems

A nonlinear distributed mathematical model of a soft vessel with a nonmonotonic static characteristic is proposed and considered. The model describes space-time dynamics of the vascular lumen. Wave phenomena in vessels of different nature and the possibility of peristaltic fluid pumping are discussed and analyzed. The model is quite general in character and represents a broad class of transport phenomena. Lymphatic vessels are considered as an example.     

Nonlinear mechanism for weak photon emission from biosystems

The nonlinear mechanism for the origin of the weak biophoton emission from biological systems is suggested. The mechanism is based on the properties of solitons that provide energy transfer and charge transport in metabolic processes. Such soliton states are formed in alpha-helical proteins. Account of the electron-phonon interaction in macromolecules results in the self-trapping of electrons in a localized soliton-like state, known as Davydov's solitons. The important role of the helical symmetry of macromolecules is elucidated for the formation, stability and dynamical properties of solitons. It is shown that the soliton with the lowest energy has an inner structure with the many-hump envelope. The total probability of the excitation in the helix is characterized by interspine oscillations with the frequency of oscillations, proportional to the soliton velocity. The radiative life-time of a soliton is calculated and shown to exceed the life-time of an excitation on an isolated peptide group by several orders of magnitude.     

Skeletal myogenesis by human primordial germ cell-derived progenitors

We have isolated and cultured human primordial germ cells (PGCs) from early embryos. The PGCs expressed embryonic germ (EG) cell-specific surface markers, including Oct4 and Nanos. We derived a cell population from these PGCs that we termed embryoid body-derived (EBD) cells. EBD cells can be extensively expanded in vitro for more than 50 passages and express lineage markers from all three primary germ layers. The myogenic potential of the EBD cells was examined both in vitro and in vivo.In vitro, the EBD cells can be induced to form multinucleated myotubes, which express late skeletal muscle-specific markers, including MHC and dystrophin, when exposed to human galectin-1. In vivo, the EBD cells gave rise to all the myogenic lineages, including the skeletal muscle stem cells known as satellite cells. Strikingly, these cells were able to partially restore degenerated muscles in the SCID/mdx mouse, an animal model of the Duchenne’s muscular dystrophy. These results indicate the EBD cells may be a promising source of myogenic stem cells for cell-based therapies for muscle degenerative disorders.