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PubMed1998

Effects of the 120 days of head-down bed rest on cytokine secretion and its in vitro modulation by glucocorticoids.

Antiorthostatic hypokinesia or head-down bed rest (HDBR), is a ground-based model system used to simulate some of the physioloical responses observed during space flight. Several studies involving humans and animals have demonstrated the effects of HDBR on different physioloical systems. HDBR produced a large thoracic fluid shift similar to that reported for space flight. Exposure to the combination of -6 degrees HDBR, emotional stress, and hypergravity led to an elevation of plasma histamine and serotinin and a dramatic decrease in the concentration of prostaglandins E, F2-alpha, and erthropoietin. These responses indicated the HDBR produces significant alterations in the neuroendocrine regulatory pathways. The proliferative response of immune cells in response to activators was significantly enhanced in antiorthostatically suspended mice; plasma corticosterone also was higher but splenic natural killer cell cytotoxicity remained unchanged after suspension. Bone-resporbing activity of supernatatants increased in mitogen-stimulated PBMC cultures of subjects exposed to -5 degrees HDBR for 370 days of HDBR. Proliferative activity of PBMCs had declined at the end of a 320-day HDBR and during the initial days of recovery, but the numbers of active rosette-forming T cells increased. These and other results suggest that most stress-induced immune changes are neuroendocrine modulated, and that corticosteroids play a significant role in this modulation. It is expected that HDBR-induced immune changes could result from similar mechanisms. In this study, we investigated the effect of 120 days of HDBR on Type-1 vs. Type-2 cytokine equilibrium in mitogen-activated PBMC culture, and how these reactions may correlate with changes in the neuroendocrine status.

Adult↗

PubMedDate not supplied

Effect of simulated microgravity on testosterone and sperm motility in mice.

We examined changes in the serum testosterone level and in sperm in the testis and epididymis by using tail-suspended mice, which are a simulation model of the body fluid shift in space, to evaluate the possibility of spermatogenesis failure in space environment. We also studied pathological disorders of the testis in the tail-suspended mice. Tail suspension was imposed with a tail harness to a degree at which the hindlegs of mice did not touch the floor of the housing unit. In control mice, the tail was similarly fixed with a tail harness to impose the same stress, except that a hindleg remained on the floor. Body weight was not significantly different between the 2 groups during 7 days, and testicular weight was significantly different. The testosterone level was significantly lower in the tail-suspended group (0.71 +/- 1.24 ng/mL) than in the control group (2.38 +/- 3.50 ng/mL; P <.05). Microscopy with hematoxylin and eosin (HE) and periodic acid-Schiff (PAS) staining showed a small proportion of seminiferous tubules with impairment of spermatogenic function in the tail-suspended group, and multinucleated giant cells were occasionally noted. Terminal deoxynucleotidyl tranferase-mediated nick end-labeling staining revealed positive cells even in animals in which impairment was considered to be mild based on HE and PAS staining. Many cells showed intense p53 immunostaining compared to the control group, with more intense staining of the nucleus in the tail-suspended group. The proportion of motile sperm was slightly but not significantly reduced in the tail-suspended group. However, the mean movement velocity of the motile spermatozoa was significantly decreased.

Animals↗

PubMed1989

Potential sites for the perception of gravity in the acellular slime mold Physarum polycephalum.

Recently a gravisensitivity of the acellular slime mold Physarum polycephalum, which possesses no specialized gravireceptor, could be established by conducting experiments under simulated and under real near weightlessness. In these experiments macroplasmodia showed a modulation of their contraction rhythm followed by regulation phenomena. Until now the perception mechanism for the gravistimulus is unknown, but several findings indicate the involvement of mitochondria: A) During the impediment of respiration the 0g-reaction is inhibited and the regulation is reduced. B) The response to a light stimulus and the following regulation phenomena strongly resemble the behavior during exposure to 0g, the only difference is that the two reactions are directed into opposite directions. In the blue-light reaction a flavin of the mitochondrial matrix seems to be involved in the light perception. C) The contraction rhythm as well as its modulations are coupled to rhythmic changes in the levels of ATP and calcium ions, involving the mitochondria as sites of energy production and of Ca(++)-storage. So the mitochondria could be the site of the regulation and they possibly are the receptor sites for the light and gravity stimuli. Also the observation of a morphologic polarity of the slime mold's plasmodial strands has to be considered: Cross-sections reveal that the ectoplasmic wall surrounding the streaming endoplasm is much thinner on the physically lower side than on the upper side of the strand--this applies to strands lying on or hanging on a horizontal surface. So, in addition to the mitochondria, also the morphologic polarity may be involved in the perception mechanism of the observed gravisensitivity and of the recently established geotaxis. The potential role of the nuclei and of the contractile elements in the perception of gravity is also discussed.

Adenosine Triphosphate↗

PubMed2002

Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model.

A theoretical and computational approach to ab initio structure prediction for polypeptides in water is described and applied to selected amino acid sequences for testing and preliminary validation. The method builds systematically on the extensive efforts applied to parameterization of molecular dynamics (MD) force fields, employs an empirically well-validated continuum dielectric model for solvation, and an eminently parallelizable approach to conformational search. The effective free energy of polypeptide chains is estimated from AMBER united atom potential functions, with internal degrees of freedom for both backbone and amino acid side chains explicitly treated. The hydration free energy of each structure is determined using the Generalized Born/Solvent Accessibility (GBSA) method, modified and reparameterized to include atom types consistent with the AMBER force field. The conformational search procedure employs a multiple copy, Monte Carlo simulated annealing (MCSA) protocol in full torsion angle space, applied iteratively on sets of structures of progressively lower free energy until a prediction of a structure with lowest effective free energy is obtained. Calibration tests for the effective energy function and search algorithm are performed on the alanine dipeptide, selected protein crystal structures, and united atom decoys on barnase, crambin, and six examples from the Rosetta set. Specific demonstration cases of the method are provided for the 8-mer sequence of Ala residues, a 12-residue peptide with longer side chains QLLKKLLQQLKQ, a de novo designed 16 residue peptide of sequence (AAQAA)3Y, a 15-residue sequence with a beta sheet motif, GEWTWDATKTFTVTE, and a 36 residue small protein, Villin headpiece. The Ala 8-mer readily formed an alpha-helix. An alpha-helix structure was predicted for the 16-mer, consistent with observed results from IR and CD spectroscopy and with the pattern in psi/straight phi angles of known protein structures. The predicted structure for the 12-mer, composed of a mix of helix and less regular elements of secondary structure, lies 2.65 A RMS from the observed crystal structure. Structure prediction for the 8-mer beta-motif resulted in form 4.50 A RMS from the crystal geometry. For Villin, the predicted native form is very close to the crystal structure, RMS values of 3.5 A (including sidechains), and 1.01 A (main chain only). The methodology permits a detailed analysis of the molecular forces which dominate various segments of the predicted folding trajectory. Analysis of the results in terms of internal torsional, electrostatic and van der Waals and the electrostatic and non-electrostatic contributions to hydration, including the hydrophobic effect, is presented.

Alanine↗

PubMed2006

Active mechanical stabilization of the viscoplastic intracellular space of Dictyostelia cells by microtubule-actin crosstalk.

The micro-viscoelasticity of the intracellular space of Dictyostelium discoideum cells is studied by evaluating the intracellular transport of magnetic force probes and their viscoelastic responses to force pulses of 20-700 pN. The role of the actin cortex, the microtubule (MT) aster and their crosstalk is explored by comparing the behaviour of wild-type cells, myosin II null mutants, latrunculin A and benomyl treated cells. The MT coupled beads perform irregular local and long range directed motions which are characterized by measuring their velocity distributions (P(v)). The correlated motion of the MT and the centrosome are evaluated by microfluorescence of GFP-labelled MTs. P(v) can be represented by log-normal distributions with long tails and it is determined by random sweeping motions (v approximately 0.5 microm/s) of the MTs (caused by tangential forces on the filament ends coupled to the actin cortex) and by intermittent bead transports parallel to the MTs (v(max) approximately 1.5 microm/s). The tails are due to spontaneous filament deflections (with speeds up to 10 microm/s) attributed to pre-stressing of the MT by local cortical tensions, generated by dynactin motors generating plus-end directed forces in the MTs. The viscoelastic responses are strongly non-linear and are mostly directed opposite or perpendicular to the force, showing that the cytoplasm behaves as an active viscoplastic body with time and force dependent drag coefficients. Nano-Newton loads exerted on the soft MT are balanced by traction forces arising at the MT ends coupled to the actin cortex and the centrosome, respectively. The mechanical coupling between the soft microtubules and the viscoelastic actin cortex provides cells with high mechanical stability despite the softness of the cytoplasm.

Actins↗

PubMed2004

Simulation of size-exclusion chromatography distribution coefficients of comb-shaped molecules in spherical pores comparison of simulation and experiment.

Simulations of the distribution coefficients of linear polymers and regular combs with various spacings between the arms have been performed. The distribution coefficients were plotted as a function of the number of segments in order to compare the size exclusion chromatography (SEC)-elution behavior of combs relative to linear molecules. By comparing the simulated SEC-calibration curves it is possible to predict the elution behavior of comb-shaped polymers relative to linear ones. In order to compare the results obtained by computer simulations with experimental data, a variety of comb-shaped polymers varying in side chain length, spacing between the side chains and molecular weights of the backbone were analyzed by SEC with light-scattering detection. It was found that the computer simulations could predict the molecular weights of linear molecules having the same retention volume with an accuracy of about 10%, i.e. the error in the molecular weight obtained by calculating the molecular weight of the comb-polymer based on a calibration curve constructed using linear standards and the results of the computer simulations are of the same magnitude as the experimental error of absolute molecular weight determination.

Algorithms↗

PubMed2001

On the radiosensitivity of man in space.

Astronauts' radiation exposure limits are based on experimental and epidemiological data obtained on Earth. It is assumed that radiation sensitivity remains the same in the extraterrestrial space. However, human radiosensitivity is dependent upon the response of the hematopoietic tissue to the radiation insult. It is well known that the immune system is affected by microgravity. We have developed a mathematical model of radiation-induced myelopoiesis which includes the effect of microgravity on bone marrow kinetics. It is assumed that cellular radiosensitivity is not modified by the space environment, but repopulation rates of stem and stromal cells are reduced as a function of time in weightlessness. A realistic model of the space radiation environment, including the HZE component, is used to simulate the radiation damage. A dedicated computer code was written and applied to solar particle events and to the mission to Mars. The results suggest that altered myelopoiesis and lymphopoiesis in microgravity might increase human radiosensitivity in space.

Aerospace Medicine↗

PubMed2001

A model of radiation-induced myelopoiesis in space.

Cell Survival↗

PubMed2006

Fast, flexible algorithm for calculating photon correlations.

We introduce a new algorithm for computing correlations of photon arrival time data acquired in single-molecule fluorescence spectroscopy and fluorescence correlation spectroscopy (FCS). The algorithm is based on rewriting the correlation as a counting operation on photon pairs and can be used with arbitrary bin widths and spacing. The flexibility of the algorithm is demonstrated by use of FCS simulations and single-molecule photon antibunching experiments. Execution speed is comparable to the commonly used multiple-tau correlation technique. Wide bin spacings are possible that allow for real-time software calculation of correlations, even for high count rates.

Algorithms↗

PubMedDate not supplied

Human productivity in space and systems costs.

Human productivity during assembly operations in-orbit is dependent on limits set by fatigue, metabolic rates, learning, and assembly techniques. In order to quantify these effects, tests were conducted in the NASA MSFC Neutral Buoyancy Simulator, in the NASA KC-135 in parabolic flight, and in space with the EASE program during the Shuttle Atlantis mission 61-B . A separate program attempted to relate productivity to system costs. Because of the surprisingly high productivity which had been demonstrated in orbit, it was shown that assembly operations would have only a small effect on system costs at the present level of launch costs. The results of these continuing studies have been reported in a recent paper. They will be briefly summarized here and the results updated to include additional cost elements and to examine the effects of reductions in transportation costs, resulting from advances in technology and from increased demand, on system costs. It is shown that, as launch costs are reduced, the assembly costs could become an increasingly important component of the total system costs.

Cost Allocation↗

PubMed2003

Constructing linkage maps in autotetraploid species using simulated annealing.

In this paper we demonstrate how molecular markers segregating in a full-sib autotetraploid mapping population can be ordered to form a linkage map using simulated annealing. This approach facilitates the examination of orders close to the optimum to see which marker placings are fixed and identify the markers whose position is less certain. A simulation study investigates the effects of population size, marker spacing, ratio of dominant to codominant markers, typing errors and missing values. The method is applied to map 30 amplified fragment length polymorphism and microsatellite markers on linkage group IV of potato.

Chromosome Mapping↗

PubMed1990

How effectively does a clinostat mimic the ultrastructural effects of microgravity on plant cells?

Columella cells of seedlings of Zea mays L. cv. Bear Hybrid grown in the microgravity of orbital flight allocate significantly larger relative-volumes to hyaloplasm and lipid bodies, and significantly smaller relative-volumes to dictyosomes, plastids, and starch than do columella cells of seedlings grown at 1 g. The ultrastructure of columella cells of seedlings grown at 1 g and on a rotating clinostat is not significantly different. However, the ultrastructure of cells exposed to these treatments differs significantly from that of seedlings grown in microgravity. These results indicate that the actions of a rotating clinostat do not mimic the ultrastructural effects of microgravity in columella cells of Z. mays.

Cell Compartmentation↗

PubMed1986

Computer simulations of cyclic enkephalin analogues.

Molecular dynamics simulations and energy minimization studies of cyclic enkephalin analogues incorporating retro-inverso modifications have been carried out. The dynamic trajectories are analyzed in terms of the relative mobility of the 14-membered rings, conformational transitions among equilibrium states, and hydrogen-bonding patterns. The cyclization of the molecules reduces the motion of the ring structures substantially. Time-correlated conformational transitions resulting in the reorientation of peptide units are observed. Hydrogen bonds form principally C7 structures. Because of the incorporation of retro-inverso residues, C6 and C8 structures are also formed. Starting conformations for energy minimizations were obtained from the molecular dynamics simulations and from a systematic search of the conformational space available to the molecules. Several minimum energy backbone and side-chain conformations were found for each analogue. The effect of retro-inverso residues on hydrogen-bonding patterns and backbone conformations is discussed.

Amino Acid Sequence↗

PubMed2005

Power and type I error rate of false discovery rate approaches in genome-wide association studies.

In genome-wide genetic studies with a large number of markers, balancing the type I error rate and power is a challenging issue. Recently proposed false discovery rate (FDR) approaches are promising solutions to this problem. Using the 100 simulated datasets of a genome-wide marker map spaced about 3 cM and phenotypes from the Genetic Analysis Workshop 14, we studied the type I error rate and power of Storey's FDR approach, and compared it to the traditional Bonferroni procedure. We confirmed that Storey's FDR approach had a strong control of FDR. We found that Storey's FDR approach only provided weak control of family-wise error rate (FWER). For these simulated datasets, Storey's FDR approach only had slightly higher power than the Bonferroni procedure. In conclusion, Storey's FDR approach is more powerful than the Bonferroni procedure if strong control of FDR or weak control of FWER is desired. Storey's FDR approach has little power advantage over the Bonferroni procedure if there is low linkage disequilibrium among the markers. Further evaluation of the type I error rate and power of the FDR approaches for higher linkage disequilibrium and for haplotype analyses is warranted.

False Positive Reactions↗

PubMed2002

Folded conformation of an immunostimulating tetrapeptide rigin: high temperature molecular dynamics simulation study.

Employing high temperature quenched molecular dynamics (QMD) stimulations the conformational energy space of an immunostimulating tetrapeptide rigin: H-Gly341-Gln-Pro-Arg344-OH, is explored. Using distance dependent dielectric (epsilon =r(ij)) 31 different low energy starting structures with identical sequence were computed for their conformational preferences. According to the hypothesis of O'Connors et al. [J. Med. Chem. 35 (1992), 2870], 83 low-energy conformers resulted from unrestrained molecular dynamics (MD) simulations, could be classified into two energy minimized families: A and B, comprised of 64 (Pro C(gamma)-endo orientation) and 19 (Pro C(gamma)-exo orientation) structures, respectively. An examination of these families revealed the existence of a remarkably similar folded backbone conformation: torsion angles being phi(i+1) approximately -65 degrees, psi(i+1) approximately -65 degrees, phi(i+2) approximately -65 degrees, psi(i+2) approximately -60 degrees, characterizing a distorted type III beta-turn structure across the central Gln-Pro segment. The folded conformation of rigin is devoid of a classical 1 <-- 4 intra-molecular hydrogen bond nevertheless, the conformation is stabilized by an effective 'salt-bridge', i.e., Gly H(3)N(+)...C(alpha)OO(-) Arg interaction. Surprisingly, in both the families the unusual folded side-chain dispositions of the Gln residue favor the formation of a unique intra-residue 'main-chain to side-chain' H-bond, i.e., N(alpha)-H...N(epsilon) interaction, encompassing a seven-membered ring motif. The conformational attributes may be valuable in de novo construction of structure-based drug candidates having sufficient stimulating activity.

Adjuvants, Immunologic↗

PubMed1996

A neural model for generating and learning a rapid movement sequence.

In this article, a neural model for generating and learning a rapid ballistic movement sequence in two-dimensional (2D) space is presented and evaluated in the light of some considerations about handwriting generation. The model is based on a central nucleus (called a planning space) consisting of a fully connected grid of leaky integrators simulating neurons, and reading an input vector [symbol: see text] (t) which represents the external movement of the end effector. The movement sequencing results in a succession of motor strokes whose instantiation is controlled by the global activation of the planning space as defined by a competitive interaction between the neurons of the grid. Constraints such as spatial accuracy and movement time are exploited for the correct synchronization of the impulse commands. These commands are then fed into a neuromuscular synergy whose output is governed by a delta lognormal equation. Each movement sequence is memorized originally as a symbolic engram representing the sequence of the principal reference points of the 2D movement. These points, called virtual targets, correspond to the targets of each single rapid motor stroke composing the movement sequence. The task during the learning phase is to detect the engram corresponding to a new observed movement; the process is controlled by the dynamics of the neural grid.

Computer Simulation↗

PubMed2003

[Osteoporosis and genes in space environment].

Based on observations of extreme and accelerated loss of bone density in astronauts flying on longer space missions, scientists coordinated by the European Space Agency, ESA, have since the mid 1990'ies been focusing on potential causes for this alarming finding. The experimental conditions on board space craft are however very restrictive, for which reason research into human physiology in the space environment has gone its own ways regarding how to create solid and statistically significant data. Space observations can profit markedly from ground-based simulations studies, and some interesting data on countermeasures against loss of bone matter, that have been tested in the recently completed 90-days bed rest study, are reported here. Paired with information on different phenotypes observed in such studies, the data reported looks very promising. This bed rest study has generated a set of extremely interesting data, which in terms of resolution and quality allows the researchers to consider this study as a significant step ahead, and as a crucial steppingstone in defining the next round of space based studies of bone metabolism. In addition the findings in the bed rest study are directly applicable to long-term bed ridden patients in terms of the need to maintain activity as a means to improve the recovery prognosis.

Adaptation, Physiological↗

PubMed2002

Calculation of the Coulomb energy in quasi-two-dimensional systems.

In this paper we obtain expressions for the Coulomb energy in infinite quasi-two-dimensional systems in the form of fast converging Ewald sums in the three-dimensional coordinate and two-dimensional inverse space needed for accurate formulation of periodic boundary conditions in computer simulations. Numerical tests evidence that the acceptable accuracy in the total energy is achieved by taking into account rather small number of terms in the sum for the inverse space responsible for the long-range part of interaction.

Journal Article↗