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At least 541 records · Page 30Linked to original sources
PubMedDate not supplied

Monitoring cell survival after extraction of a single subcellular organelle using optical trapping and pulsed-nitrogen laser ablation.

This paper characterizes cell viability in three different cell lines--Chinese hamster ovary cells (CHO), neuroblastoma cells fused with glialoma cells (NG108-15) and murine embryonic stem cells (ES-D3)--after N2 laser disruption of the cell membrane and removal, via optical trapping, of a single subcellular organelle. Morphological changes and viability (as determined by live/dead fluorescent stains) of the cell were monitored every half hour over a 4-h period postsurgery. The ability of the cell to survive organelle extraction was found to depend both on the conditions under which surgery was performed and on the cell type. The average viability after surgery for CHO cells was approximately 80%, for NG 108 cells it was approximately 30% and for ES-D3 cells postsurgery viability was approximately 10%. From over 600 surgeries we found the survival of the cell is determined almost exclusively within the first hour postsurgery regardless of cell line. The optimal pulse energy for N2 laser ablation was approximately 0.7 microJ. The N2 pulse produced an approximately 1-3 microm hole in the cell membrane and proved to be the primary source of cell death in those cells that did not survive the procedure.

Animals↗
PubMed1998

Glutamine, exercise and immune function. Links and possible mechanisms.

Glutamine is the most abundant free amino acid in human muscle and plasma and is utilised at high rates by rapidly dividing cells, including leucocytes, to provide energy and optimal conditions for nucleotide biosynthesis. As such, it is considered to be essential for proper immune function. During various catabolic states including surgical trauma, infection, starvation and prolonged exercise, glutamine homeostasis is placed under stress. Falls in the plasma glutamine level (normal range 500 to 750 mumol/L after an overnight fast) have been reported following endurance events and prolonged exercise. These levels remain unchanged or temporarily elevated after short term, high intensity exercise. Plasma glutamine has also been reported to fall in patients with untreated diabetes mellitus, in diet-induced metabolic acidosis and in the recovery period following high intensity intermittent exercise. Common factors among all these stress states are rises in the plasma concentrations of cortisol and glucagon and an increased tissue requirement for glutamine for gluconeogenesis. It is suggested that increased gluconeogenesis and associated increases in hepatic, gut and renal glutamine uptake account for the depletion of plasma glutamine in catabolic stress states, including prolonged exercise. The short term effects of exercise on the plasma glutamine level may be cumulative, since heavy training has been shown to result in low plasma glutamine levels (< 500 mumol/L) requiring long periods of recovery. Furthermore, athletes experiencing discomfort from the overtraining syndrome exhibit lower resting levels of plasma glutamine than active healthy controls. Therefore, physical activity directly affects the availability of glutamine to the leucocytes and thus may influence immune function. The utility of plasma glutamine level as a marker of overtraining has recently been highlighted, but a consensus has not yet been reached concerning the best method of determining the level. Since injury, infection, nutritional status and acute exercise can all influence plasma glutamine level, these factors must be controlled and/or taken into consideration if plasma glutamine is to prove a useful marker of impending overtraining.

Animals↗
PubMed2004

[Evaluation of radiation therapy for keloid using electron beam].

In radiation therapy for keloid, electron beams are delivered to the skin through a lead shield hollowed into the shape of the keloid. The shape of a postoperative keloid scar is linear, causing the irradiation shield to be long and narrow. This lead shield is put on the surface of the skin. Therefore, it is considered that beam data used in general external irradiation are not applicable to irradiation for keloid. Therefore, we used a water equivalent phantom and measured beam data by using chambers or film dosimeters. Experimental conditions were the same as those of actual radiotherapy for keloid. As a result of this procedure, the radiation technique was optimized. Electron energy and thickness of the bolus, thickness of the lead shield, margins such that the planning target volume would receive the necessary dose, and the method of MU calculation all were determined. It was suggested that these experiments were useful to establish the appropriate technique in irradiation for keloid.

Electrons↗
PubMed2002

What can be deduced about the structure of Shaker from available data?

Voltage-gated K+ channels are transmembrane proteins that control and regulate the flow of K+ ions across cell membranes in response to changes in membrane potential and are essential for the propagation of action potentials in the nervous system. One of the most studied voltage-gated channels is Shaker. Available experimental results clearly provide specific constraints on the structure of the channel, even though the direct translation of the available information into 3D structures is not trivial. The goal of this work is to develop a computational approach to construct and refine 3D models of Shaker by incorporating and integrating available experimental data. Our approach is based on comparative modelization and global conformational optimization using energy restraints extracted from experimental data.

Amino Acid Sequence↗
PubMed2003

[Effect of laser irradiation on structures of the eye fundus].

Mathematical model of selective laser influence on eye fundus structures is proposed. Mathematical calculations of optimal laser parameters for different eye fundus pathologies are made. They will optimize laser energy influence on retina and chorioida and decrease the risk of possible late side effects.

Choroid↗
PubMed1992

Personal renewal.

After John Gardner's presentation on "Self-Renewal" to THE WESTERN JOURNAL OF MEDICINE Editors' Meeting, (*) Joseph Murphy, MD, Special Editor for Wyoming, asked the former Secretary of Health, Education, and Welfare, "Where are you in your life's cycle?" Dr Gardner, who is 80 years old, answered, "When Chief Justice Oliver Wendell Holmes, Jr, was in his 90s, he was asked a similar question and said, ;I'm like a race horse cantering along after the race is over, cooling down.' Well, I'm nowhere near cantering! I'm still in the race, pushing the world." race, pushing the world."John Gardner, who received his undergraduate degree from Stanford and PhD from the University of California, Berkeley, taught at the college level for several years before he joined the Carnegie Foundation. As president of Carnegie Corporation and Carnegie Foundation for the Advancement of Teaching, he began to "push the world" toward education and in 1964 received the country's highest civilian honor, the Presidential Medal of Freedom. He has also pushed it toward political reform by founding Common Cause, toward grass-roots political action by founding the Urban Coalition, toward leadership training by founding the White House Fellows program, and toward volunteerism by founding the Independent Sector (a coalition of for-profit and not-for-profit organizations and foundations). His books, including Excellence, Self-Renewal, No Easy Victories, and On Leadership, have pushed readers to new understanding of themselves and of organizations to higher levels of creativity and energy to get important work done. His current research focuses on discovering and defining the characteristics of healthy, vital communities. His call to "keep on keeping on," indeed, to push the world, leads to constructive change. Active people become effective people, infused with the energy and optimism that good hard work inspires. I think you will find this paper as invigorating to read as it was to hear.

Aging↗
PubMed2004

Interaction of human fibrinogen receptor (GPIIb-IIIa) with decorsin.

AIM: To build up the structure of human fibrinogen receptor GPIIb-IIIa, subsequently combined with its antagonist decorsin, and to investigate the interaction between decorsin and its receptor GPIIb-IIIa at the molecular level. METHODS: A three-dimensional (3D) molecular model of human fibrinogen receptor GPIIb-IIIa was generated by InsightII, a distance geometry-based homologous modeling package. The structure of human fibrinogen receptor GPIIb-IIIa was built by the InsightII/Homology module using the corresponding of integrin alphaVbeta3 (PDB filecode 1JV2) as the template. Then the primary structures were optimized by energy minimization. Subsequently the structural model was docked with its antagonist decorsin (PDB filecode 1dec). RESULTS: A good substrate-receptor interaction model was achieved. The interaction sites with decorsin converge at domain 8 (betaA domain of beta3 subunit) of GPIIb-IIIa. The direct interatomic contacts were made between 16 GPIIb/IIIa residues and 10 decorsin amino-acid residues. These included van der Waals contacts, electrostatic interaction, hydrogen bond, and salt bridge. Residues in contact were concentrated in four dispersed regions of human GPIIb-IIIa: the RGD reaction motif (118-132 of GPIIIa), the span from 210 to 213 of GPIIIa, Thr182 residue and Asp251 residue of GPIIIa; and they were distributed over five segments of decorsin: Asp10 residue, Asn18 and Lys19 residues, Arg28 residue, RGD motif, and Asp35-Pro36-Tyr37 segment. CONCLUSION: This complex model plays an important role in development and research of some new drugs, especially a new guided fusion-type fibrinogen receptor antagonist.

Amino Acid Sequence↗
PubMed2005

[Definition of therapeutic effect of mildronate in patients with chronic heart failure].

In developed countries chronic heart failure (CHF) is one of the main reasons of death and physical disability. CHF affects approximately 1-2% of the population and its prevalence is still increasing. Today ACE inhibitors, beta-blockers, diuretics are the first line drugs in treatment of CHF. Mildronate is a new drug optimizing cardiac energy metabolism and could be an effective approach in CHF patients' management. The aim of the study was to investigate the efficacy and safety of mildronate in treatment of CHF (NYHA III-IV funct. class) patients. 110 patients with CHF, stable on conventional treatment (diuretics, ACE inhibitors, beta-blokers, digoxin), were treated additionally with mildronate. Assessment was performed with clinical data, FC change, ECO-cardiography, 6-minute walk test. Mildronate showed to be an effective drug in complex treatment of chronic heart failure.

Cardiac Output, Low↗
PubMedDate not supplied

Trimetazidine increases [3H]glucose uptake in rat brain.

Trimetazidine, a clinically effective antianginal agent with no negative inotropic or vascular properties, acts by optimizing cardiac energy metabolism through inhibition of free fatty acid oxidation, shifting substrate utilization from fatty acids to glucose. Up to now there has been no study associating trimetazidine's effect on metabolic processes with glucose utilization in the mammalian brain. The objective of the present study was to determine if trimetazidine altered [(3)H]glucose uptake in rat brain. Adult male Wistar rats were administered trimetazidine (Metazydyna, Polfa) either as a single dose (10.0 mg/kg po) or for 14 consecutive days (5.0 mg/kg po per day) or vehicle saline (2.0 ml/kg po). Sixty minutes after the single dose or 14th dose of trimetazidine, and 15 min before experiment termination and brain dissection, 6-[(3)H]D-glucose (500 Ci/kg ip; Amersham) was administered. Using liquid scintillation counting, trimetazidine, either in a single or multiple dose regimen, was found to increase [(3)H]glucose uptake (DPM/100 mg of wet tissue) in all dissected regions of the brain (i.e., striatum, hippocampus, frontal cortex, thalamus with hypothalamus, pons with medulla oblongata, and cerebellum). Therefore, central effects need to be taken into consideration as possibly adding to known beneficial cardiac effects of trimetazidine.

Animals↗
PubMed1990

[Model of protease I from the crab Uca pugilator].

Collagenolytic protease I from the fiddler crab Uca pugilator is one of the serine proteases of the trypsin family. A graphic molecular model was built on the basis of the sequences and crystalline structures of four homologous proteins which were superimposed in order to identify structurally conserved regions. The sequence of protease I was matched to sequences of the reference proteins, without allowing any deletions or insertions in these regions. For structurally variable regions, the most similar sequences of the four reference proteins were selected. Intramolecular steric clumping due to replacement of reference side-chains by protease I side-chains were corrected by adjusting side-chain conformations. The model was optimized by energy minimization. The conformation of the primary specificity pocket for protease I predicted by the model indicated a preference for P1 hydrophobic or positively charged substrates. This prediction is consistent with biochemical findings. Because soya bean trypsin inhibitor (STI) has been shown to inhibit protease I, a tentative model of the complex was constructed and possible protease I-STI interactions were analyzed.

Animals↗
PubMedDate not supplied

[Seasonal rhythms in the functioning of the hypophyseo-thyroid system of the suslik Citellus parryi].

In experiments on the Arctic ground squirrel Citellus parryi, radioimmune assay of the content of thyrotropin of the hypophysis and thyroxine and triiodothyronine of the thyroid in the peripheral blood has been made at monthly intervals from July until May. It was found that during hibernation period, thyroxine and triiodothyronine concentrations in the blood of sleeping animals are high as compared with those during pre-hibernation period in autumn and active period in May. Thyrotropin content of the blood increases from October to May, being the lowest however during the season of the deepest hibernation from December to February. It is suggested that activation of the hypophysial--thyroid system after resting period in summer and autumn begins in October. During deep sleeping, it is depressed, being recovered in March. High levels of the thyroid hormones during hibernation period may be explained by metabolic strategy of the organism in hibernating animals which is directed to optimization of energy supply of hibernation.

Animals↗
PubMed1987

[Electron microscopy studies of ciliated cells in the larval epidermis of Rana t. temporaria (L.) (Amphibia, Anura)].

Examination of the epidermis of Rana temporaria in various stages of development revealed the presence of densely ciliated cells from the late neurula until shortly before metamorphosis. Unlike the other epidermal cells, these ciliated cells do not divide; once formed, they are constant in number until they disappear. In shape, size, and structure, however, they vary depending on stage of development and on their position in the body. In older larval stages and young tadpoles they are fully differentiated and strongly basophilic. Their function is to improve the hydrodynamic properties of the larval body, and hence ultimately to optimize the energy balance during locomotion.

Animals↗
PubMed1986

Brief survey of scope and limitations of quantum and statistical mechanical methods.

An attempt is made to delineate the scope and limitations, and future perspectives, of the theoretical methods being applied increasingly to various aspects of drug design and associated problems. The two methods of approach, quantum mechanics and statistical physics (Monte Carlo, Molecular Dynamics), are used to evaluate such properties as electron density distribution, structure and conformation, intermolecular interactions, etc. for isolated molecules and their autoassociates, and for interactions with the environment (e.g., solvent, receptor molecules). The validity of such calculations, dependent on factors such as geometrical optimalization, correlation energy and differing approximations of the form of the wave function, is illustrated in the case of enol-keto tautomerism of nitrogen heterocycles, relevant to the biological (including chemotherapeutic) activities of some nucleoside analogues. Intermolecular interactions, including the role of solvent, are assessed for purine and pyrimidines. The scope of the Molecular Dynamics methods is exemplified by its application to the mode of action of lysozyme.

Drug Compounding↗
PubMed1981

A self-consistent field molecular orbital study of hydroxyguanidine.

Theoretical self-consistent field molecular orbital calculations indicate that the hydroxyguanidinium ion can dissociate in alkaline or neutral medium by the loss of the hydroxyl proton, leading to the formation of a strong nucleophilic agent which can attack a positive receptor in enzymes, acting in this way as an antitumor and an antiviral agent. Geometry optimization, total energies, and net atomic charges are calculated using a Gaussian basis set for the hydroxyguanidinium ion and its conjugate bases.

Antineoplastic Agents↗
PubMed2005

Longitudinal cooling of non-neutral plasma by energy exchange.

The optimal values of Q and Deltaomega (Deltaomega identical withomega-Omega) for cooling a pure electron plasma with a microwave bath have been calculated. An electron plasma, which has no internal degree of freedom, cannot be cooled below the temperature of a heat bath. However, longitudinal cooling can be achieved by energy transfer from the poorly cooled longitudinal degree of freedom to the well-cooled (by synchrotron radiation) transverse degree of freedom. To do this, a microwave bath is introduced to the electron plasma. A microwave tuned to a frequency below the gyrofrequency forces electrons moving towards the microwave to absorb a microwave photon. The electrons move up one in Landau state and then lose their longitudinal momenta. In this process, the longitudinal temperature of the electron plasma decreases. On the basis that the perpendicular temperature is below the Landau temperature of the plasma, we set up two level transition equations and then derive a Fokker-Planck equation from them. With the aid of a finite element method (FEM) code for the equation, the cooling times for several values of the magnetic field, the microwave cavity (Q), and the relative detuning frequency from the gyrofrequency (Deltaomega) are calculated. Thus optimal values of the microwave cavity and the detuning frequency for longitudinal cooling of a strongly magnetized electron plasma with a microwave bath have been found. By applying these optimal values with an appropriate microwave intensity, the best cooling can be obtained. For an electron plasma magnetized to 10 T, the cooling time to the solid state is approximately two hours.

Journal Article↗
PubMed2000

Modeling of loops in protein structures.

Comparative protein structure prediction is limited mostly by the errors in alignment and loop modeling. We describe here a new automated modeling technique that significantly improves the accuracy of loop predictions in protein structures. The positions of all nonhydrogen atoms of the loop are optimized in a fixed environment with respect to a pseudo energy function. The energy is a sum of many spatial restraints that include the bond length, bond angle, and improper dihedral angle terms from the CHARMM-22 force field, statistical preferences for the main-chain and side-chain dihedral angles, and statistical preferences for nonbonded atomic contacts that depend on the two atom types, their distance through space, and separation in sequence. The energy function is optimized with the method of conjugate gradients combined with molecular dynamics and simulated annealing. Typically, the predicted loop conformation corresponds to the lowest energy conformation among 500 independent optimizations. Predictions were made for 40 loops of known structure at each length from 1 to 14 residues. The accuracy of loop predictions is evaluated as a function of thoroughness of conformational sampling, loop length, and structural properties of native loops. When accuracy is measured by local superposition of the model on the native loop, 100, 90, and 30% of 4-, 8-, and 12-residue loop predictions, respectively, had <2 A RMSD error for the mainchain N, C(alpha), C, and O atoms; the average accuracies were 0.59 +/- 0.05, 1.16 +/- 0.10, and 2.61 +/- 0.16 A, respectively. To simulate real comparative modeling problems, the method was also evaluated by predicting loops of known structure in only approximately correct environments with errors typical of comparative modeling without misalignment. When the RMSD distortion of the main-chain stem atoms is 2.5 A, the average loop prediction error increased by 180, 25, and 3% for 4-, 8-, and 12-residue loops, respectively. The accuracy of the lowest energy prediction for a given loop can be estimated from the structural variability among a number of low energy predictions. The relative value of the present method is gauged by (1) comparing it with one of the most successful previously described methods, and (2) describing its accuracy in recent blind predictions of protein structure. Finally, it is shown that the average accuracy of prediction is limited primarily by the accuracy of the energy function rather than by the extent of conformational sampling.

Models, Molecular↗
PubMed2004

Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.

The treatment of hydration effects in protein dynamics simulations varies in model complexity and spans the range from the computationally intensive microscopic evaluation to simple dielectric screening of charge-charge interactions. This paper compares different solvent models applied to the problem of estimating the free-energy difference between two loop conformations in acetylcholinesterase. Molecular dynamics (MD) simulations were used to sample potential energy surfaces of the two basins with solvent treated by means of explicit and implicit methods. Implicit solvent methods studied include the generalized Born (GB) model, atomic solvation potential (ASP), and the distance-dependent dieletric constant. By using the linear response approximation (LRA), the explicit solvent calculations determined a free-energy difference that is in excellent agreement with the experimental estimate, while rescoring the protein conformations with GB or the Poisson equation showed inconsistent and inferior results. While the approach of rescoring conformations from explicit water simulations with implicit solvent models is popular among many applications, it perturbs the energy landscape by changing the solvent contribution to microstates without conformational relaxation, thus leading to non-optimal solvation free energies. Calculations applying MD with a GB solvent model produced results of comparable accuracy as observed with LRA, yet the electrostatic free-energy terms were significantly different due to optimization on a potential energy surface favored by an implicit solvent reaction field. The simpler methods of ASP and the distance-dependent scaling of the dielectric constant both produced considerable distortions in the protein internal free-energy terms and are consequently unreliable.

Acetylcholinesterase↗