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Complete genomes, far advanced proteomes, and even 'metabolomes' are available for at least a few organisms, e.g., Escherichia coli. Systematic functional analyses of such complete data sets will produce a wealth of information and promise an understanding of the dynamics of complex biological networks and perhaps even of entire living organisms. Such complete and holistic descriptions of biological systems, however, will increasingly require a quantitative analysis and the help of mathematical models for simulating whole systems. In particular, new procedures are required that allow a meaningful reduction of the information derived from complex systems that will consequently be used in the modeling process. In this review the biological elements of such a modeling procedure will be described. In a first step, complex living systems must be structured into well-defined and clearly delimited functional units, the elements of which have a common physiological goal, belong to a single genetic unit, and respond to the signals of a signal transduction system that senses changes in physiological states of the organism. These functional units occur at each level of complexity and more complex units originate by grouping several lower level elements into a single, more complex unit. To each complexity level corresponds a global regulator that is epistatic over lower level regulators. After its structuring into modules (functional units), a biological system is converted in a second step into mathematical submodels that by progressive combination can also be assembled into more aggregated model structures. Such a simplification of a cell (an organism) reduces its complexity to a level amenable to present modeling capacities. The universal biochemistry, however, promises a set of rules valid for modeling biological systems, from unicellular microorganisms and cells, to multicellular organisms and to populations.

Numerous biological experiments with cells have been conducted in space, and the importance of these experiments and this area of study is continually becoming evident. This contribution is a compilation of available information about spaceflight experiments with cells for the purpose of providing a single source of information for those interested in space gravitational cell biology. Experiments focused on a study of the effects of gravity and its absence on cells, cell function, and basic cellular processes have been included. Experiments include those involving viruses, bacteriophage, unicellular organisms, lower fungi, and animal and plant cell and tissue cultures, but exclude experiments with cells that were carried on a flight as part of a whole organism and later removed for study, and experiments with fertilized eggs. In addition, experiments in biotechnology, in which the microgravity environment is employed to study cell purification, cell fusion, protein crystallization, and similar processes, have not been included. Spaceflight experiments conducted by scientists from the U.S., U.S.S.R., and other countries and flown onboard sounding rockets (TEXUS, MAXUS, Consort), biosatellites (Biosatellite II, Cosmos), and various crewed spacecraft including the space shuttle (STS) and Soyuz, and space stations (Salyut, Mir) have been included, as well as high altitude balloon flights. Balloon flights are not spaceflights but can and are used as controls for the effects of space radiation, since organisms carried on balloons may be exposed to some of the same radiation as those taken into space, yet continue to be exposed to Earth's gravitational force. Parabolic flights on aircraft during which periods of microgravity of less than a minute are achieved have arbitrarily been excluded, because even though numerous experiments have been conducted, few results have been published.

Physiological changes in humans during spaceflight upon return to earth have been attributed to systemic adaptation, response to stress, and lack of normal exercise. Studies from the Skylab, SL-3, and D-1 missions have demonstrated that significant physiological alterations are seen in single cell prokaryotes and eukaryotes, as well as in animal tissues. Basic cellular functions such as electrolyte concentration, cell growth rate, glucose utilization, bone formation, response to growth stimulation, and exocytosis are modified in microgravity. Many of the physiological changes seen in humans, vertebrate and simple organisms in spaceflight may originate from dysfunction of basic biological mechanisms caused by microgravity. Aging humans share many of the symptoms seen in astronauts during spaceflight. These include reduced cardiac function, loss of bone and reduced immune response and orthostatic hypotension. It is possible that some of physiological adaptations seen in aging may share common physiological basis with those changes seen in spaceflight. Since microgravity affects prokaryotic and eukaryotic cell function at a subcellular and molecular level, space offers us an opportunity to learn more about basic biological mechanisms which are essential to life.

Surprising experimental data recently provided could indicate ancestral genes common to mammals and bacteria. The detection of prokaryotic structures and/or mechanisms even in higher eukaryotes shows the extreme conservation of gene structures throughout evolution. The occurrence of common structures in pro- and eukaryotes is in good agreement with the new view concerning the early steps of cellular evolution. Because of the relative paucity of research in this area, further prokaryotic features of transcription and translation process may also be evolutionarily conserved in eukaryotes.

Movable sequences described previously in the bacterial genome as insertion sequences and transposons seem to be present in a wide range of forms in all organisms. Structure, mechanism of transposition and regulatory function of these sequences are discussed.

A hypothesis for the origin of introns in eukaryotic genes is developed. By computer simulation it was found that the reading-frame lengths in a random nucleotide sequence are distributed in a negative exponential manner and that there exists an upper limit of about 200 codons in the length of the reading frames (RFs). These characteristics suggest that, if primordial DNA contained a random nucleotide sequence, the most primitive cells would have been under selective pressure to eliminate interfering stop codons in order to increase the length of RFs. Further, they indicate that the only possible way that a coding sequence that is considerably longer than 600 nucleotides could be derived from the short coding sequences occurring in a random sequence would be to splice the short coding sequences and to eliminate the stretches of sequences containing clusters of inframe stop codons. Thus, introns are suggested to be those stretches of sequences containing interfering stop codons that were originally earmarked in the first primitive cells to be eliminated in order to enable the coding for long polypeptides. Because the statistical characteristics of codon distributions in today's eukaryotic DNA sequences resemble closely those of a random sequence and because the upper limit in the length of RFs (200 codons) in a random sequence corresponds precisely to the observed maximum length of exons in today's eukaryotic genes (600 nucleotides), it is suggested that introns originated in the most primitive unicellular eukaryotes when they evolved from primordial sequences. The data from the prokaryotic gene sequences indicate that prokaryotic genes may have been derived originally from primitive unicellular eukaryotic genes by losing introns from them.

Organisms as diverse as bacteria and man contain genes that show transcriptional induction when the intracellular concentration of cAMP is increased. This regulated transcriptional response is mediated through specific promoter elements located, in general, upstream from the transcription start site. In Escherichia coli the element responsible for cAMP-mediated transcriptional induction is the binding site for the cAMP-receptor protein (CAP). In mammalian cells the cAMP regulatory element is composed of one or more binding sites for various transcription factors. In many instances the cAMP regulatory element contains binding sites for a family of proteins referred to as ATF. Here we provide evidence that some prokaryotic and mammalian cAMP-response elements are functionally related. First, we show that mammalian ATF binds specifically to some E. coli CAP sites, and conversely E. coli CAP binds specifically to some mammalian ATF sites. Second, we demonstrate that an E. coli CAP binding site can confer cAMP-inducibility onto a mammalian gene when assayed in transfected mammalian cells.

In overlapping reading frames of prokaryotic mRNA, the ribosome-binding site (RBS) of the downstream cistron is part of the coding sequence of the upstream message. We have examined whether the rate of translation in Escherichia coli can be sufficiently high to preclude the use of an RBS in initiation of protein synthesis when it is part of an actively decoded reading frame. The two sets of gene overlap present in the RNA phage MS2 are used as a model system. We find that translation of an upstream cistron can fully block initiation of protein synthesis at the overlapping RBS of the downstream cistron. Nonsense mutations in the upstream gene restore the translation of the downstream gene.

The archaebacteria are a group of prokaryotes which seem as distinct from the true bacteria (eubacteria) as they are from eukaryotes. The evidence on which this conclusion rests is of two types: genotypic (quantitative)--that is, comparative sequence studies, and phenotypic (qualitative)--that is, differences in various organismal characteristics. The differences between archaebacteria and true bacteria are so great, both quantitatively and qualitatively, that the two bacterial groups should be considered as representing separate primary lines of descent, each tracing directly back to the universal ancestor. Furthermore, this ancestor itself seems not to be a prokaryote; rather it was a far simpler type of organism, one properly called a progenote. If this is true, the discovery of archaebacteria marks a major advance in the biologist's attempts to understand the basis for the evolution of the cell.

Learning processes are applied to the recognition of protein coding regions in prokaryotes. Non-contradictory, statistical rules are deduced from a set of known examples of coding regions. These rules allow us to build characteristic patterns on the m-RNA upstream the initiating codon. These rules are applied to recognize more than 180 coding sequences.

The in vivo activity of ribozymes designed against mRNA coding for E. coli beta-galactosidase was tested both in intramolecular and in intermolecular conditions. When recombinant M13 phage DNA carrying on the same molecule the information for both the ribozyme and the target was transfected into bacterial cells, ribozyme activity was observed. Conversely, a ribozyme coded by a recombinant M13 vector, but targeted against an mRNA transcribed from the F episome including the remaining part of the beta-galactosidase gene, was inefficient.

The published translation termination sequences have been compiled and analysed to aid the interpretation of experiments on termination codon usage in the Xenopus oocyte (Bienz et al. 1981). There are significant differences between prokaryotes and eukaryotes concerning the usage of the three termination codons and of tandem stops. In addition viruses show termination strategies that differ from those of their hosts. Preferred context sequences flanking termination codons are described. Contexts vary within the last codon according to the nature of the termination codon, but are uniform within the first triplet following the terminators.

Germfree rats and mice were given by gavage samples of ileal homogenates prepared from conventional rats and mice. Filamentous, segmented procaryotes adhered to the small bowel epithelium in the ex-germfree mice only when the homogenate was made from mouse bowel and in the ex-germfree rats only when the inoculum came from rats. Thus, the filamentous microorganisms are host animal specific.