Self-assembly of rationally designed peptides under two-dimensional confinement

The rational design of interfacially confined biomolecules offers a unique opportunity to explore the cooperative relationship among self-assembly, nucleation, and growth processes. This article highlights the role of electrostatics in the self-assembly of β-sheet-forming peptides at the air-water interface. We characterize the phase behavior of a periodically sequenced sheet-forming peptide by using Langmuir techniques, Brewster angle microscopy, attenuated total reflection Fourier transform infrared spectroscopy, and circular dichroism spectroscopy. We find that peptides with an alternating binary sequence transition at high pressures from discrete circular domains to fibrous domains. The qualitative behavior is independent of surface pressure but dependent on molecular areas. In addition, thermodynamic models are employed to specifically quantify differences in electrostatics by obtaining parameters for the critical aggregation area, the limiting molecular area, and the dimensionless ratio of line tension/dipole density. Using these parameters, we are able to relate localized charge distribution to phase transitions, which will allow us to apply these molecules to examine how the dynamics of self-assembly can be directly coupled to the formation of composite nanostructures in biology.     

Searching target sites on DNA by proteins: Role of DNA dynamics under confinement

DNA-binding proteins (DBPs) rapidly search and specifically bind to their target sites on genomic DNA in order to trigger many cellular regulatory processes. It has been suggested that the facilitation of search dynamics is achieved by combining 3D diffusion with one-dimensional sliding and hopping dynamics of interacting proteins. Although, recent studies have advanced the knowledge of molecular determinants that affect one-dimensional search efficiency, the role of DNA molecule is poorly understood. In this study, by using coarse-grained simulations, we propose that dynamics of DNA molecule and its degree of confinement due to cellular crowding concertedly regulate its groove geometry and modulate the inter-communication with DBPs. Under weak confinement, DNA dynamics promotes many short, rotation-decoupled sliding events interspersed by hopping dynamics. While this results in faster 1D diffusion, associated probability of missing targets by jumping over them increases. In contrast, strong confinement favours rotation-coupled sliding to locate targets but lacks structural flexibility to achieve desired specificity. By testing under physiological crowding, our study provides a plausible mechanism on how DNA molecule may help in maintaining an optimal balance between fast hopping and rotation-coupled sliding dynamics, to locate target sites rapidly and form specific complexes precisely.     

Improvement of plasma energy confinement in tokamak under radiative cooling of the edge plasma

Improvement of plasma energy confinement in the T-10 tokamak by injection of impurity gases was studied experimentally. Injection of Ne and He in the ohmic and ECR heating regimes allows one to separate the dependences of energy confinement on the plasma density and on the edge plasma cooling rate. It is shown that the well-known dependence of the energy confinement time on the plasma density is, in fact, the dependence on the radiative loss power. This phenomenon can be explained by plasma self-organization. The experiments are described by a thermodynamic model for self-organized plasma in which the transport coefficient depends on the difference between the actual and self-consistent pressure profiles. The reduction in the heat flux at the plasma edge due to radiative cooling leads to a decrease in the transport coefficient in this region and, accordingly, improves energy confinement. Results of approximate model calculations for experiments with Ne injection are presented.     

Dissipative particle dynamics simulation on the meso-scale structure of diblock copolymer under cylindrical confinement

The meso-scale structure of symmetric diblock copolymer under cylindrical confinement is studied by dissipative particle dynamics (DPD). The simulation results show that coiled cylindrical geometry is favored in the presence of larger cylinder radius (R/L ₀>～1.5), and the number of rings depends on the cylinder radius. Because of the cylinder wall's selectivity, each block can form the central core, but only the preferential block forms the outmost layer. An approximately linear relationship exists between structure transition point, which is approximately in proportion to the 3/5 exponential of chain length of copolymer and number of layers. As the cylinder radius is decreased, a helical morphology is found. Lamellae parallel to the underside of the cylinder appear when the cylinder radius is made smaller (R/L ₀ < ～1.1).     

Stability of a quasi-flute mode under the Bernstein-Kadomtsev condition in a toroidal confinement system

It is shown that the growth rate of the MHD instability in toroidal configurations is slower in a situation in which the Bernstein-Kadomtsev condition is satisfied while the Mercier stability criterion is not. Under the Bernstein-Kadomtsev condition, Alfvénic Mercier modes are not excited, but quasi-flute acoustic Mercier modes develop instead. In confinement systems with closed magnetic field lines, the Bernstein-Kadomtsev condition ensures MHD stability; however, a small rotational transform produced by magnetic perturbations can give rise to a quasi-flute acoustic instability whose growth rate is proportional to the perturbation amplitude, in which case the fastest growing oscillations are those with the shortest wavelengths.     

Heat confinement in spheromaks

Calculations are presented showing the temperatures expected in a spheromak sustained by continuous injection of helicity, based on a model previously shown to agree with temperatures achieved in spheromak experiments carried out in the 1980's. New experiments with Thomson scattering measurements of electron temperature will provide an experimental test.     

Asymmetric perception of twilight affecting diapause induction by the fall webworm Hyphantria cunea

In order to assess the natural photophase effective for controlling the pupal diapause of Hyphantria cunea, larvae were exposed in the long-day season to natural conditions of light (through a window) for a period of 14 hr, 50 min. This photophase included different portions of either the dawn or dusk twilight period. Since the critical photophase was found to be 14 hr 35 min under natural daylight as well as under conditions of artificial light, 50% diapause was expected when the twilight intensity reached the threshold level 15 min after the onset (dawn) or before the end (dusk) of the exposure. The threshold intensities of twilight thus determined showed a significant asymmetry, being about 1 and 10 lux at dawn and dusk, respectively. From this, it was inferred that the photophase under natural conditions would begin about 40 min before sunrise and end about 20 min after sunset. This asymmetry in sensitivity seems to be caused by the conditions (light or dark) to which the larval photo-receptive system has been exposed. The larvae that had been kept under artificial light of 180–200 lux for 14 hr were sensitive to a subsequent 1 hr exposure to 0.5 lux or greater and averted diapause, whereas those held under 9,000 lux failed to avert diapause even when the photophase was supplemented by light of 7.5 lux for 1 hr

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Résumé De facon à évaluer la photophase naturelle efficace pour maîtriser la diapause nymphale de Hyphantria cunea, les chenilles ont été exposées pendant la saison aux jours longs aux conditions naturelles d'éclairement (à travers une fenêtre) pendant une période de 14 h 50 min. Puisqu'il a été établi que la photophase critique est de 14 h 35 min sous éclairement naturel aussi bien qu'artificiel, 50% de diapause était prévu quand l'intensité crépusculaire atteignait le seuil 15 min après le début (aube) ou avant la fin (crépuscule) de l'exposition. Les intensités-seuil crépusculaires ainsi déterminées ont présenté une asymétrie significative, étant respectivement de 1 à 10 lux à l'aube et au crépuscule. Il a été déduit de ces observations que la photophase en conditions naturelles commencerait environ 40 min avant le lever du soleil et se terminerait environ 20 min après son coucher. L'asymétrie de cette sensibilité semble être due aux conditions (lumière ou obscurité) auxquelles le système photo-récepteur des chenilles a été exposé. Les chenilles qui ont été maintenues pendant 14 h sous éclairage artificiel de 180–200 lux sont sensibles à une exposition ultérieure de 0,5 lux ou plus et évitent la diapause, tandis que celles maintenues à 9000 lux ou plus n'évitent pas la diapause quand la photophase est prolongée par un éclairement de 7,5 lux pendant une heure.

     

Engineering productive enzyme confinement

Natural enzymes were selected to function inside the cell, not in the test tube; therefore, their performance is optimized for the crowded conditions encountered in vivo. Most man-made matrices for enzyme confinement lead to suboptimal catalytic activity. Ackerman and colleagues showed that an entrapping environment consisting of functionalized mesoporous silica actually enhances enzyme activity beyond the test-tube levels of free enzymes in solution. These findings provide an approach for dissecting the effect of various contributors to enzyme activity and thereby provide a means for fine-tuning the entrapping matrices to optimize enzyme performance in a rational way.     

Human immunity system under conditions of 105-day isolation and confinement in an artificial environment

The study of the adaptive immunity system of six test subjects volunteered for a 105-day isolation and confinement in an artificial environment showed activation of the immune system and overstrain and depletion of its functional reserve. Significant differences in the adaptability of the immune system of the test subjects indicate individual susceptibility to disorders in immunological reactivity.     

Cells as Active Particles in Asymmetric Potentials: Motility under External Gradients

Cell migration is a crucial event during development and in disease. Mechanical constraints and chemical gradients can contribute to the establishment of cell direction, but their respective roles remain poorly understood. Using a microfabricated topographical ratchet, we show that the nucleus dictates the direction of cell movement through mechanical guidance by its environment. We demonstrate that this direction can be tuned by combining the topographical ratchet with a biochemical gradient of fibronectin adhesion. We report competition and cooperation between the two external cues. We also quantitatively compare the measurements associated with the trajectory of a model that treats cells as fluctuating particles trapped in a periodic asymmetric potential. We show that the cell nucleus contributes to the strength of the trap, whereas cell protrusions guided by the adhesive gradients add a constant tunable bias to the direction of cell motion.     

Asymmetric induction in steriod synthesis: synthesis of D-homoestrone methyl ether using a novel annulation reaction.

Asymmetric synthesis of D-homoestrone methyl ether was achieved by a new annalation reaction.     

Biodegradation of polyphenols with immobilized Candida tropicalis under metabolic induction

During olive oil production, large quantities of olive mill wastewater (OMW) are produced. This wastewater material, containing a high level of phenolic compounds, poses a serious environmental problem in almost all Mediterranean countries. Candida tropicalis YMEC14 was used as an extremophile strain to design an aerobic biotreatment process to detoxify OMW and reduce its polluting organic load. The process was enhanced by directing yeast metabolism towards biodegradation pathways using hexadecane as co-metabolite and by immobilizing yeast cells in calcium alginate beads. Under immobilization conditions, C. tropicalis YMEC14 grown at 40 degrees C in OMW supplemented with hexadecane resulted in 69.7%, 69.2% and 55.3% reduction of chemical oxygen demand, monophenols and polyphenols, respectively, after a 24-h fermentation cycle.     

Chaperonin function--effects of crowding and confinement

Chaperonins assist in the acquisition of native protein structure in the cell by providing a shielded environment for a folding polypeptide chain, generated by the interior surface of their cylindrical structure. The folding chain is isolated from the highly crowded cytoplasm, but at the same time confined within the chaperonin folding cage. Both confinement and macromolecular crowding can affect folding kinetics and yields, the modus operandi of chaperonins and their interaction with their protegés. Recent experimental data, as well as computer simulations, provide increasing evidence that the particular physico-chemical conditions prevailing in the cellular interior have to be taken into account when trying to unravel the processes of cellular protein folding.     

UV light induction of proteins in Bacteroides fragilis under anaerobic conditions

Far-UV irradiation of Bacteroides fragilis cells under anaerobic conditions resulted in the induction of a new 95,000-molecular-weight protein and the increased synthesis of two proteins with molecular weights of 90,000 and 70,000. The latter two proteins were synthesized in small amounts in unirradiated cells. The induction of a 37,000- to 40,000-molecular-weight protein was not observed in irradiated B. fragilis cells. Caffeine, which affected the survival of irradiated B. fragilis cells and reduced host cell-mediated UV reactivation, specifically inhibited the induction of the 95,000-, 90,000-, and 70,000-molecular-weight proteins. Sodium arsenite did not affect the induction of the three inducible proteins or the survival of irradiated B. fragilis cells.     

Basal autophagy induction without AMP-activated protein kinase under low glucose conditions

When ATP levels in a cell decrease, various homeostatic intracellular mechanisms initiate attempts to restore ATP levels. As a prominent energy sensor, AMP-activated protein kinase (AMPK) represents one molecular gauge that links energy levels to regulation of anabolic and catabolic processes to restore energy balance. Although pharmacological studies have suggested that an AMPK activator, AICAR (5-aminoimidazole-4-carboxamide ribonucleoside) may link AMPK activation to autophagy, a process that can provide short-term energy within the cell, AICAR can have AMPK-independent effects. Therefore, using a genetic-based approach we investigated the role of AMPK in cellular energy balance. We demonstrate that genetically altered cells, mouse embryonic fibroblasts (MEFs), lacking functional AMPK display altered energy balance under basal conditions and die prematurely under low glucose-serum starvation challenge. These AMPK mutant cells appear to be abnormally reliant on autophagy under low glucose basal conditions, and therefore cannot rely further on autophagy like wildtype cells during further energetic stress and instead undergo apoptosis. This data suggests that AMPK helps regulate basal energy levels under low glucose. Further, AMPK mutant cells show increased basal phosphorylation of p53 at serine 15, a residue phosphorylated under glucose deprivation. We propose that cells lacking AMPK function have altered p53 activity that may help sensitize these cells to apoptosis under energetic stress.     

Asymmetric induction in catalyzed synthesis of organic compounds as an important stage in the evolution of life on earth

It is shown that natural chiral catalysts, which could be formed e.g., from optically active amino acids on basic natural minerals, could lead, at early stages of evolution, to the formation of rather complex optically active products from starting achiral compounds. Using biomimetic combinations of vanadium ion complexes and chiral ligands synthesized from widely occurring natural compounds, we created novel catalytic systems, permitting the transfer of optical activity in the course of catalytic chemical transformations of achiral compounds. We found that in the presence of natural clay, optically active terpenoids from the pinane series undergo multistage transformations, forming unexpected new products with preservation of optical purity.