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PubMed2004

Role and regulation of sigma S in general resistance conferred by low-shear simulated microgravity in Escherichia coli.

Life on Earth evolved in the presence of gravity, and thus it is of interest from the perspective of space exploration to determine if diminished gravity affects biological processes. Cultivation of Escherichia coli under low-shear simulated microgravity (SMG) conditions resulted in enhanced stress resistance in both exponential- and stationary-phase cells, making the latter superresistant. Given that microgravity of space and SMG also compromise human immune response, this phenomenon constitutes a potential threat to astronauts. As low-shear environments are encountered by pathogens on Earth as well, SMG-conferred resistance is also relevant to controlling infectious disease on this planet. The SMG effect resembles the general stress response on Earth, which makes bacteria resistant to multiple stresses; this response is sigma s dependent, irrespective of the growth phase. However, SMG-induced increased resistance was dependent on sigma s only in stationary phase, being independent of this sigma factor in exponential phase. sigma s concentration was some 30% lower in exponential-phase SMG cells than in normal gravity cells but was twofold higher in stationary-phase SMG cells. While SMG affected sigma s synthesis at all levels of control, the main reasons for the differential effect of this gravity condition on sigma s levels were that it rendered the sigma protein less stable in exponential phase and increased rpoS mRNA translational efficiency. Since sigma s regulatory processes are influenced by mRNA and protein-folding patterns, the data suggest that SMG may affect these configurations.

Bacterial Proteins↗
PubMed1994

Influence of antiorthostatic suspension on resistance to murine Listeria monocytogenes infection.

The present study was designed to evaluate the influence of antiorthostatic suspension, a ground-based modeling system employed to simulate certain aspects of weightlessness that occur during space flight, on the capacity of mice to resist infection with the facultative intracellular bacterial pathogen Listeria monocytogenes. Female BDF1 mice were suspended by the tail in the orthostatic or antiorthostatic position and were infected with a sublethal dose of virulent L. monocytogenes at various times during the suspension. It was found that suspension did not influence the kinetics of bacterial growth in vivo if the infection was started concurrently with the suspension. However, mice that were antiorthostatically suspended 2, 4, or 7 days before the onset of infection exhibited an enhanced capacity to eliminate the challenge infection. Suspending mice on day 2 of the infection did not alter the kinetics of bacterial growth. Finally, the enhancement of resistance to the primary Listeria infection was accompanied by failure of the mice to generate long-term protective immunological memory to the challenge organism. Collectively, these results indicate that the stress of antiorthostatic suspension can influence the capacity of mice to resist bacterial infection.

Animals↗
PubMed2005

Error optimization of a three-dimensional magnetic resonance imaging tagging-based cartilage deformation technique.

Three-dimensional strain fields in articular cartilage subjected to compressive loading can be determined using a recently developed MRI-based cartilage deformation by tag registration technique. The objective of this study was to determine the experimental variables that minimize the technique error, which has not been previously reported. Error (strain bias and precision) was determined using direct experiments and Monte Carlo simulations for four variables: spatial resolution, tag line spacing, applied nominal strain, and number of control points used to describe tag lines in a B-spline model. The important results include the following: (1) bias was not significantly different from zero, (2) precision increased with image resolution and with tag line spacing, (3) precision was independent of applied nominal strain, and (4) error was a minimum (absolute precision = 0.41% strain) for the following values: spatial resolution = 0.05 x 0.05 mm2; tag line spacing = 2.0 mm; control points = 6. With these results the technique can now be used in various applications while minimizing error.

Algorithms↗
PubMed2005

Activation of human T lymphocytes under conditions similar to those that occur during exposure to microgravity: a proteomics study.

A number of experiments, conducted under microgravity conditions, i.e. in space shuttle biolaboratories or in ground based systems simulating the conditions occurring in microgravity, show that in hypogravity, in vitro human lymphocyte activation is severely impaired. However, very early stimulation steps of T lymphocytes are not compromised, since CD69 receptor, the earliest membrane activation marker, is expressed by T cells at a level comparable to that observed on 1 g activated lymphocytes. Since CD69 engagement, together with submitogenic doses of phorbol esters, transduces an activation signal to T lymphocytes, we undertook a comparative study on the stimulation mediated through this receptor on human CD3+ cells cultured under conditions similar to those which occur during exposure to microgravity, i.e. in clinorotation, or at 1 g. During the early hours of activation, increased levels of intracellular calcium and increased mitochondrial membrane potential were detectable in clinorotating as well as in 1 g cells. However, after 48 hours clinorotation, interleukin 2 production by T lymphocytes was significantly reduced and cell proliferation was greatly decreased. By means of a differential proteomics approach on T cells activated in clinorotation or at 1 g for 48 hours, we were able to detect statistically significant quantitative protein alterations. Seven proteins with modified expression values were identified; they are involved in nucleic acids processing, proteasome regulation and cytoskeleton structure.

Antigens, CD↗
PubMed1995

Conservative and nonconservative mutations in proteins: anomalous mutations in a transport receptor analyzed by free energy and quantum chemical calculations.

Experimental studies on a bacterial sulfate receptor have indicated anomalous relative binding affinities for the mutations Ser130-->Cys,Ser130-->Gly, and Ser130-->Ala. The loss of affinity for sulfate in the former mutation was previously attributed to a greater steric effect on the part of the Cys side chain relative to the Ser side chain, whereas the relatively small loss of binding affinity for the latter two mutations was attributed to the loss of a single hydrogen bond. In this report we present quantum chemical and statistical thermodynamic studies of these mutations. Qualitative results from these studies indicate that for the Ser130-->Cys mutation the large decrease in binding affinity is in part caused by steric effects, but also significantly by the differential work required to polarize the Cys thiol group relative to the Ser hydroxyl group. The Gly mutant cobinds a water molecule in the same location as the Ser side chain resulting in a relatively small decrease in binding affinity. Results for the Ala mutant are in disagreement with experimental results but are likely to be limited by insufficient sampling of configuration space due to physical constraints applied during the simulation.

Bacterial Proteins↗
PubMed2003

Generalized monotonic regression using random change points.

We introduce a procedure for generalized monotonic curve fitting that is based on a Bayesian analysis of the isotonic regression model. Conventional isotonic regression fits monotonically increasing step functions to data. In our approach we treat the number and location of the steps as random. For each step level we adopt the conjugate prior to the sampling distribution of the data as if the curve was unconstrained. We then propose to use Markov chain Monte Carlo simulation to draw samples from the unconstrained model space and retain only those samples for which the monotonic constraint holds. The proportion of the samples collected for which the constraint holds can be used to provide a value for the weight of evidence in terms of Bayes factors for monotonicity given the data. Using the samples, probability statements can be made about other quantities of interest such as the number of change points in the data and posterior distributions on the location of the change points can be provided. The method is illustrated throughout by a reanalysis of the leukaemia data studied by Schell and Singh.

Bayes Theorem↗
PubMed1994

The origins of protein secondary structure. Effects of packing density and hydrogen bonding studied by a fast conformational search.

Globular proteins fold to create compact structures rich in alpha-helices and beta-sheets. While studies of cubic lattice models of simplified polypeptide chains have concluded that secondary structure is a necessary consequence of chain compactness, different conclusions have been reached from studies of off-lattice models of simplified chains. In an attempt to resolve this controversy, we study an all-atom off-lattice model of a protein subject to a variety of simplified energy functions. A Monte Carlo simulated annealing algorithm is used to search conformational space quickly. The algorithm uses pivot-type moves in which a residue is selected at random and the values of its main-chain dihedral angles are changed. The energy function used to accept or reject moves is taken to be either a term proportional to the volume occupied by a structure (to mimic the hydrophobic effect), a term proportional to the energy of main-chain hydrogen bonding, or a combination of these two terms. Secondary structure content is evaluated using several different definitions. For all the definitions used, compactness alone produces a 10% increase in secondary structure content. However, this is a small fraction of the secondary structure observed in native protein structures. Structures produced by minimizing the hydrogen bond energy have extensive secondary structure but are not densely packed. Structures having both the high density of native structures and extensive secondary structure are produced by minimizing combinations of the volume and hydrogen bond energy terms. Our results emphasize the close relationship between secondary structure and the geometry of main-chain hydrogen bonding. The results are consistent with a description of protein folding in which the hydrophobic effect favors dense packing while hydrogen bonding determines the specific local geometry which generates secondary structure. To make an analogy with lattice studies of packing density and secondary structure, it seems that hydrophobicity provides the packing density while hydrogen bonding provides the lattice.

Algorithms↗
PubMed1998

A multiscale model of plant topological structures

In applications dealing with plant growth modeling, increasing attention is being devoted to the topological structure of plants. Different models, based on tree-graphs, have been introduced to represent plants. These models assume that the scale of description is fixed. However, this hypothesis is too restrictive for new modeling applications that aim to tackle analysis or simulation of plant growth at different time and space scales. In order to make such multiscale descriptions available to computer applications, we have defined a general methodology for measuring and representing multiscale plant topological structures. This paper discusses the design of a model of plant topological structures and sketches out its general formal properties. The model supports multiscale, attributed and time-varying descriptions of plants. It is intended to be used for plant analysis methodologies and plant growth simulations.Copyright 1998 Academic Press Limited

Journal Article↗
PubMed2001

Increased coupling between subpopulations in a spatially structured environment can lead to population outbreaks.

Destruction and fragmentation of habitats is widely considered as a major threat to biological diversity. A theoretical framework aimed at understanding and predicting species responses to these destructive processes is still lacking, however. In this paper, the species dynamics in a spatially structured, two-habitat, patchy environment is considered subject to changes in individual migration intensity, i.e. coupling between the habitats. The subpopulation dynamics inside each habitat is assumed to be bistable but with different parameter values. By using space-discrete/continuous metapopulation dynamic models and computer simulations, we show that there can be two principally different regimes of metapopulation dynamics. With increasing intensity in the interplay between subpopulations, the total abundance can either gradually decrease or experience a sudden burst-like increase. This result is shown to be robust to the choice of mathematical models (discrete or continuous). Particularly, both the "self-excitation" and "self-inhibition" regimes of the metapopulation system are robust to variation in habitat size; however, when one of the habitats is much smaller than the other, the "self-excitation" regime can give way to the "self-inhibition" regime and vice versa.

Animals↗
PubMed1990

An algorithmic approach to modelling the retinal receptor topography.

Based on published research results on the structure of the human retina and the initial assumption of tight hexagonal packing of cones, the mean cone-distance function is derived. Disorder in the cone lattice is explained as the superposition of increasing topological distortion in the hexagonal lattice (providing a possible explanation for observed systematic lattice distortions) and local jitter of neighbor-to-neighbor distances, for which a simple statistical model is provided. These individual results are incorporated into a proposed algorithm for simulating the cone receptors' topography in 3D-space. Finally, possible software and hardware applications of the algorithmically defined retina model are briefly touched.

Algorithms↗
PubMed1996

Calbindins decreased after space flight.

Exposure of the body to microgravity during space flight causes a series of well-documented changes in Ca2+ metabolism, yet the cellular and molecular mechanisms leading to these changes are poorly understood. Calbindins, vitamin D-dependent Ca2+ binding proteins, are believed to have a significant role in maintaining cellular Ca2+ homeostasis. In this study, we used biochemical and immunocytochemical approaches to analyze the expression of calbindin-D28k and calbindin-D9k in kidneys, small intestine, and pancreas of rats flown for 9 d aboard the space shuttle. The effects of microgravity on calbindins in rats from space were compared with synchronous Animal Enclosure Module controls, modeled weightlessness animals (tail suspension), and their controls. Exposure to microgravity resulted in a significant and sustained decrease in calbindin-D28k content in the kidney and calbindin-D9k in the small intestine of flight animals, as measured by enzyme-linked immunosorbent assay (ELISA). Modeled weightlessness animals exhibited a similar decrease in calbindins by ELISA. Immunocytochemistry (ICC) in combination with quantitative computer image analysis was used to measure in situ the expression of calbindins in the kidney and the small intestine, and the expression of insulin in pancreas. There was a large decrease of immunoreactivity in renal distal tubular cell-associated calbindin-D28k and in intestinal absorptive cell-associated calbindin-D9k of space flight and modeled weightlessness animals compared with matched controls. No consistent difference in pancreatic insulin immunoreactivity between space flight, modeled weightlessness, and controls was observed. Regression analysis of results obtained by quantitative ICC and ELISA for space flight, modeled weightlessness animals, and their controls demonstrated a significant correlation. These findings after a short-term exposure to microgravity or modeled weightlessness suggest that a decreased expression of calbindins may contribute to the disorders of Ca2+ metabolism induced by space flight.

Animals↗
PubMed2004

Solution structure of T4moC, the Rieske ferredoxin component of the toluene 4-monooxygenase complex.

Toluene 4-monooxygenase, a four-protein complex from Pseudomonas mendocina KR1, catalyzes the NADH- and O(2)-dependent hydroxylation of toluene to form p-cresol. The solution structure of the 112-amino-acid Rieske ferredoxin component, T4moC, was determined from 2D and 3D (1)H, (13)C, and (15)N NMR data. The structural model was refined through simulated annealing by molecular dynamics in torsion angle space with input from 1650 experimental restraints, including 1264 inter-proton distance restraints obtained from NOEs, 247 non-redundant intra-residue NOEs, 26 hydrogen bond restraints, and 113 dihedral angle ( phi, psi) restraints. The 20 calculated conformers that best satisfied the input restraints were submitted to refinement in explicit solvent to improve the stereochemical quality. With exclusion of ill-defined N- and C-terminal segments (Ser2; His111-Ser112) and residues near to the [2Fe-2S] cluster, the atomic root mean square deviation for the 20 conformers with respect to the mean coordinates was 1.09 A for the backbone and 1.60 A for all non-hydrogen atoms. The T4moC structure consists of 10 beta-strands arranged in the three anti-parallel beta-sheet topology observed in all Rieske [2Fe-2S] domain proteins. The S(gamma) of Cys45 and Cys64 and the N(delta1) of His47 and His67 provide the ligands to the [2Fe-2S] cluster of T4moC. (1)H-(15)N HSQC measurements show that both His47-N(epsilon2) and His67-N(epsilon2) are protonated at the pH of the NMR experiments. Comparisons are made between the present NMR structure, previous paramagnetic NMR studies of T4moC, and the X-ray structures of other members of the Rieske protein family.

Catalysis↗
PubMed1991

The involvement of cerebrovascular reactivity in pathogenesis of space motion sickness.

The aim of the presented work is to investigate the mechanisms of involvement of cerebral circulation in pathogenesis of space motion sickness. In experiments on chronic rabbits the 2-hours rocking and antiorthostasis served as a model of influences of the zero-gravity conditions intracranial hemo- and liquorodynamics. Cerebravascular reactivity was evaluated as a response of cerebral blood flow and intracerebral rheoencephalography to functional loads (photostimulation, CO2-inhalation, Stookey test). Shifts of water balance in the brain tissue has been assessed by means of three-frequency brain electrical impedance. Rocking plus aniorthostatis resulted in decrease of the cerebrovascular reactivity and hyperhydration. The data obtained show a significant decrease of compensatory abilities of the cerebrovascular system under the zero-gravity conditions.

Animals↗
PubMedDate not supplied

Choroidal responses in microgravity. (SLS-1, SLS-2 and hindlimb-suspension experiments).

Fluid and electrolyte shifts occurring during human spaceflight have been reported and investigated at the level of blood, cardiovascular and renal responses. Very few data were available concerning the cerebral fluid and electrolyte adaptation to microgravity, even in animal models. It is the reason why we developed several studies focused on the effects of spaceflight (SLS-1 and SLS-2 programs, carried on NASA STS 40 and 56 missions, which were 9- and 14-day flights, respectively), on structural and functional features of choroid plexuses, organs which secrete 70-90% of cerebrospinal fluid (CSF) and which are involved in brain homeostasis. Rats flown aboard space shuttles were sacrificed either in space (SLS-2 experiment, on flight day 13) or 4-8 hours after landing (SLS-1 and SLS-2 experiments). Quantitative autoradiography performed by microdensitometry and image analysis, showed that lateral and third ventricle choroid plexuses from rats flown for SLS-1 experiment demonstrated an increased number (about x 2) of binding sites to natriuretic peptides (which are known to be involved in mechanisms regulating CSF production). Using electron microscopy and immunocytochemistry, we studied the cellular response of choroid plexuses, which produce cerebrospinal fluid (CSF) in brain lateral, third and fourth ventricles. We demonstrated that spaceflight (SLS-2 experiment, inflight samples) induces changes in the choroidal cell structure (apical microvilli, kinocilia organization, vesicle accumulation) and protein distribution or expression (carbonic anhydrase II, water channels,...). These observations suggested a loss of choroidal cell polarity and a decrease in CSF secretion. Hindlimb-suspended rats displayed similar choroidal changes. All together, these results support the hypothesis of a modified CSF production in rats during long-term (9, 13 or 14 days) adaptations to microgravity.

Adaptation, Physiological↗
PubMed1985

Intramitochondrial localization of fumarate reductase, NADPH----NAD transhydrogenase, 'malic' enzyme and fumarase in adult Hymenolepis diminuta.

The intramitochondrial localization of the fumarate reductase, NADPH----NAD transhydrogenase, 'malic' enzyme and fumarase was determined in adult Hymenolepis diminuta. The distribution of marker enzymes for the inner membrane, matrix, intermembrane space and outer membrane of H. diminuta mitochondria simulated that of the corresponding ascarid and mammalian organelles. The electron transport-coupled fumarate reductase and the NADPH----NAD transhydrogenase were components of the inner membrane whereas the 'malic' enzyme and fumarase were in the matrix soluble compartment. Assessments of NADH utilization, malate-dependent NADP reduction and NADPH----NAD transhydrogenation by presumedly intact and disrupted mitochondria supported the localization data. The findings presented indicate that in H. diminuta mitochondria (a) NADPH and fumarate are accumulated within the matrix compartment; (b) transhydrogenation between NADPH and NAD is an event associated with the matrix side of the inner membrane; and (c) electron transport-dependent NADH oxidation and fumarate reduction occur at sites on the matrix side of the inner membrane.

Animals↗
PubMed1989

Formation and growth of callus tissue of Arabidopsis under changed gravity.

The changed gravity conditions do not prevent the process of cell dedifferentiation and formation of callus. Yet, callus grown on the clinostat and in space differs from the control one: its consistence is denser, occurence of meristematic centres is less frequent and it shows a reduced proliferative activity of cells. Average size of cell and nuclei area in the test variants is lower than in the control.

Arabidopsis↗
PubMed1992

Ultrastructural analysis of organization of roots obtained from cell cultures at clinostating and under microgravity.

Data are presented of a comparative analysis on rhizogenesis in the Arabidopsis thaliana tissue culture growing in a solid nutrient medium under stationary conditions, clinostatic conditions and microgravity. Tissue samples weighing 100 mg. were set in the Petri dishes and placed in a horizontal slow clinostat /2 revs/min/. After 14 days of growth they were analyzed. On clinostating the number of roots formed from the callus cells was approximately one half the control. The formed root cap manifested no essential differences, in comparison with the stationary control, in the number of layers and cell sizes in its layers. In callusogenic roots, formed from clinostated cells, differentiation including root cap cells, proceeds without noticeable deviations from the norm. At the same time, gravireceptor cells do not function under these conditions. This is clearly displayed at a structural level in the location of amyloplasts-statoliths throughout the cytoplasm. The callus cell cultures experienced microgravity for 8 days. The number of formed roots under the influence of this factor was 36% relative to the stationary control. Root cap formation was abnormal. Gravireceptor cells did not formed under microgravity.

Arabidopsis↗