Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives

We study the origin of robustness of yeast cell cycle cellular network through uncovering its underlying energy landscape. This is realized from the information of the steady-state probabilities by solving a discrete set of kinetic master equations for the network. We discovered that the potential landscape of yeast cell cycle network is funneled toward the global minimum, G1 state. The ratio of the energy gap between G1 and average versus roughness of the landscape termed as robustness ratio ( RR) becomes a quantitative measure of the robustness and stability for the network. The funneled landscape is quite robust against random perturbations from the inherent wiring or connections of the network. There exists a global phase transition between the more sensitive response or less self-degradation phase leading to underlying funneled global landscape with large RR, and insensitive response or more self-degradation phase leading to shallower underlying landscape of the network with small RR. Furthermore, we show that the more robust landscape also leads to less dissipation cost of the network. Least dissipation and robust landscape might be a realization of Darwinian principle of natural selection at cellular network level. It may provide an optimal criterion for network wiring connections and design.

Cure processing modeling and cure cycle simulation of epoxy-terminated poly(phenylene ether ketone). V: Estimation of temperature distribution during cure process

A numerical method to estimate temperature distribution during the cure of epoxy-terminated poly(phenylene ether ketone) (E-PEK)-based composite is suggested. The effect of the temperature distribution on the selection of cure cycle is evaluated using a suggested alternation criterion. The effect of varying heating rate and thickness on the temperature distribution, viscosity distribution and distribution of the extent of cure reaction are discussed based on the combination of the here-established temperature distribution model and the previously established curing kinetics model and chemorheological model. It is found that, for a thin composite (<=10mm) and low heating rate (<=2.5K/min), the effect of temperature distribution on cure cycle and on the processing window for pressure application can be neglected. Low heating rate is of benefit to reduce the temperature gradient. The processing window for pressure application becomes narrower with increasing thicknesses of composite sheets. The validity of the temperature distribution model and the modified processing window is evaluated through the characterization of mechanical and physical properties of E-PEK-based composite fabricated according to different temperature distribution conditions.

Cure processing modeling and cure cycle simulation of epoxy-terminated poly(phenylene ether ketone) .3. Determination of the time of pressure application

The curing temperature, pressure, and curing time have significant influence on finished thermosetting composite products. The time of pressure application is one of the most important processing parameters in the manufacture of a thermosetting composite. The determination of the time of pressure application relies on analysis of the viscosity variation of the polymer, associated with curing temperature and curing time. To determine it, the influence of the time of pressure application on the physical properties of epoxy-terminated poly(phenylene ether ketone) (E-PEK)-based continuous carbon fiber composite was studied. It was found that a stepwise temperature cure cycle is more suitable for manufacture of this composite. There are two viscosity valleys, in the case of the E-PEK system, associated with temperature during a stepwise cure cycle. The analysis on the effects of reinforcement fraction and defect content on the composite sheet quality indicates that the width-adjustable second viscosity valley provides a suitable pressing window. The viscosity, ranging from 400 to 1200 Pa . s at the second viscosity valley, is the optimal viscosity range for applying pressure to ensure appropriate resin flow during curing process, which enables one to get a finished composite with optimal fiber volume fraction and low void content. (C) 1997 John Wiley & Sons, Inc.

Cure processing modeling and cure cycle simulation of epoxy-terminated poly(phenylene ether ketone) .4. Cure cycle simulation

Epoxy-terminated poly(phenylene ether ketone) (E-PEK) developed in this Institute is a candidate matrix resin for polymer composites as structural materials. Cure cycles for this reaction system were simulated according to the previously established processing model. It is found that for the E-PEK system, the curing process is best completed by a stepwise cure cycle comprising two isothermal processes at different temperatures, T-1 and T-2. The cure cycles over a wide range of processing parameters simulated, based on the established processing model, indicate that the processing window is width-adjustable. Analysis of the mechanical properties of the composite sheets showed that the simulated cure cycles are acceptable and reliable. (C) 1997 John Wiley & Sons, Inc.

Cure processing modeling and cure cycle simulation of epoxy-terminated poly(phenylene ether ketone) .1. DSC characterization of curing reaction

The curing reaction process of epoxy-terminated poly(phenylene ether ketone) (E-PEK) with 4,4'-diaminodiphenyl sulfone (DDS) and hexahydrophthalic acid anhydride (Nadic) as curing agents was investigated using isothermal differential scanning calorimetry (IDSC) and nonisothermal differential scanning calorimetry (DDSC) techniques. It was found that the curing reactions of E-PEK/DDS and E-PEK/Nadic are nth-order reactions but not autoaccelerating. The experimental results revealed that the curing reaction kinetics parameters measured from IDSC and DDSC are not equivalent. This means that, in the curing reaction kinetics model for our E-PEK system, both isothermal and nonisothermal reaction kinetics parameters are needed to describe isothermal and nonisothermal curing processes, The isothermal and nonisothermal curing processes were successfully simulated using this model. A new extrapolation method was suggested. On the basis of this method the maximum extent of the curing reaction (A(ult)) that is able to reach a certain temperature can be predicted. The A(ult) for the E-PEK system estimated by the new method agrees well with the results obtained from another procedure reported in the literature. (C) 1997 John Wiley & Sons, Inc.

Cure processing modeling and cure cycle simulation of epoxy-terminated poly(phenylene ether ketone) .2. Chemorheological modeling

Chemorheology and corresponding models for an epoxy-terminated poly(phenylene ether ketone) (E-PEK) and 4,4'-diaminodiphenyl sulfone (DDS) system were investigated using a differential scanning calorimeter (DSC) and a cone-and-plate rheometer. For this system, the reported four-parameter chemorheological model and modified WLF chemorheological model can only be used in an isothermal or nonisothermal process, respectively. In order to predict the resin viscosity variation during a stepwise temperature cure cycle actually used, a new model based on the combination of the four-parameter model and the modified WLF model was developed. The combined model can predict the resin viscosity variation during a stepwise temperature cure cycle more accurately than the above two models. In order to simplify the establishment of this model, a new five-parameter chemorheological model was then developed. The parameters in this five-parameter model can be determined through very few rheology and DSC experiments. This model is practicable to describe the resin viscosity variation for isothermal, nonisothermal, or stepwise temperature cure cycles accurately. The five-parameter chemorheological model has also successfully been used in the E-PEK systems with two other curing agents, i.e., the diamine curing agent with the addition of a boron trifluride monoethylamine (BF3-MEA) accelerator and an anhydride curing agent (hexahydrophthalic acid anhydride). (C) 1997 John Wiley & Sons, Inc.

Involvement of p90 ribosomal S6 kinase in termination of cell cycle arrest during development of Artemia-encysted embryos

Artemia has evolved a unique developmental pattern of encysted embryos to cope with various environmental threats. Cell divisions totally cease during the preemergence developmental stage from gastrula to prenauplius. The molecular mechanism of this, however, remains unknown. Our study focuses on the involvement of p90 ribosomal S6 kinase (RSK), a family of serine/threonine kinase-mediating signal transduction downstream of mitogen-activated protein kinase cascades, in the termination of cell cycle arrest during the post-embryonic development of Artemia-encysted gastrula. With immunochemistry, morphology, and cell cycle analysis, the identified Artemia RSK was established to be specifically activated during the post-embryonic and early larval developmental stages when arrested cells of encysted embryos resumed mitoses. In vivo knockdown of RSK activity by RNA interference, kinase inhibition, and antibody neutralization consistently induced defective larvae with distinct gaps between the exoskeleton and internal tissues. In these abnormal individuals, mitoses were detected to be largely inhibited in the affected regions. These results display the requirement of RSK activity during Artemia development and suggest its role in termination of cell cycle (G(2)/M phase) arrest and promotion of mitogenesis. Our findings may, thus, provide insights into the regulation of cell division during Artemia post-embryonic development and reveal further aspects of RSK functions.

TWO SPECIFIC CAUSES OF CELL MORTALITY IN FREEZE-THAW CYCLE OF YOUNG THALLI OF PORPHYRA YEZOENSIS (BANGIALES, RHODOPHYTA)1

Porphyra yezoensis Ueda is an important marine aquaculture crop with single-layered gametophytic thalli. In this work, the influences of thallus dehydration level, cold-preservation (freezing) time, and thawing temperature on the photosynthetic recovery of young P. yezoensis thalli were investigated employing an imaging pulse-amplitude-modulation (PAM) fluorometer. The results showed that after 40 d of frozen storage when performing thallus thawing under 10 degrees C, the water content of the thalli showed obvious effects on the photosynthetic recovery of the frozen thalli. The thalli with absolute water content (AWC) of 10%-40% manifested obvious superiority compared to the thalli with other AWCs, while the thalli thawed at 20 degrees C showed very high survival rate (93.10%) and no obvious correlation between thallus AWCs and thallus viabilities. These results indicated that inappropriate thallus water content contributed to the cell damage during the freeze-thaw cycle and that proper thawing temperature is very crucial. Therefore, AWC between 10% and 40% is the suitable thallus water content range for frozen storage, and the thawing process should be as short as possible. However, it is also shown that for short-term cold storage the Porphyra thallus water content also showed no obvious effect on the photosynthetic recovery of the thalli, and the survival rate was extremely high (100%). These results indicated that freezing time is also a paramount contributor of the cell damage during the freeze-thaw cycle. Therefore, the frozen nets should be used as soon as time permits.

Effects of hydrostatic pressure on microtubule organization and cell cycle in gynogenetically activated eggs of olive flounder (Paralichthys olivaceus)

Indirect immunofluorescence staining was used to detect cytological changes of isolated blastodisks during mitosis of flounder haploid eggs treated with hydrostatic pressure. Changes in microtubule structure and expected cleavage suppression were observed from blastodisk formation to the third cell cycle, with obvious differences between treated and control eggs. In most eggs, microtubules were disassembled and the nucleation capacity of the centrosome was temporarily inhibited after pressure treatment. Within 15-20 min after treatment, the nucleation capacity of the centrosome began to gradually recover, with slow regeneration of microtubules; approximately 25 min after treatment, the nucleation capacity of the centrosome recovered completely, regenerated distinct bipolar spindles, and the first mitosis ensued. During the second cell cycle, approximately 61% of the embryos were at the two-cell stage, with a monopolar spindle in each blastomere; that treatment was effective was based on second cleavage blockage. Approximately 15% of the eggs still remained at the one-cell stage and had a monopolar spindle (treatment was effective, according to the general model of first cleavage blockage). However, treatment was ineffective in approximately 15% of the embryos (bipolar spindle in each blastomeres) and in another 8% (bipolar spindle in one of the two blastomeres and a monopolar spindle in the other; both mechanisms operating in different parts of the embryo). This is the first report elucidating mitotic gynogenetic diploid induction by hydrostatic pressure in marine fishes and provides a cytological basis for developing an efficient method of inducing mitotic gynogenesis in olive flounder. (C) 2007 Elsevier Inc. All rights reserved.

Effects of cold shock on microtubule organization and cell cycle in gynogenetically activated eggs of olive flounder (Paralichthys olivaceus)

Cytological changes and subsequent mitotic processes were studied in gynogenetically activated eggs of olive flounder subjected to cold-shock treatment using indirect immunofluorescence staining of isolated blastodisks. Obvious differences between controls and treated eggs were detected during early cell division. The developmental process of haploid control was similar to that of the diploid control except several minutes delayed. Spindles disassembled by the cold-shock treatment regenerated soon after treatment, resulting in the occurrence of the first mitosis. The immature daughter centriole was easily depolymerized by cold-shock treatment, leading to the formation of the bipolar spindle in the first cell cycle and the formation of the monopolar spindle in the second cell cycle, resulting in chromosome set doubling. Some two-cell stage eggs had a monopolar spindle in one blastomere and a bipolar spindle in another during the second mitosis. These eggs had a high potency developing into haploid-diploid mosaics. To the best of our knowledge, this study is the first to clarify the mechanism of chromosome set doubling in marine fishes and provides a preliminary cytological basis for developing a reliable and efficient protocol for mitotic gynogenesis induction by cold-shock treatment in olive flounder.

Carbonate cycle and its control factors in Kuroshio source region during the last 190ka BP

Two deep sea cores (Ph05-5, 16.05 degrees N, 124.34 degrees E, water depth 3382m and WP3: 22.15 degrees N, 122.95 degrees E, water depth 2700m) retrieved from the Kuroshio source region of the western Philippine Sea were selected to carry out the CaCO3 and calcareous nannofossil faunas study. Based on AMS(14)C data and comparing tire oxygen isotope curve with SPECMAP delta O-18 (Martinson et al., 1987) a stratigraphy was established. And, combining the changes of primary productivity and dissolution index of carbonate, the carbonate cycle and its control factors were analyzed in this region during the last 190ka BP. The carbonate contents showed higher values in the glacial periods and lower values during the interglacial and Holocene periods, which characteristics was similar to the tendency of "Pacific Type" carbonate cycle. However, there were high carbonate contents in the warm period and low values during the cold interval, which displayed the same tendency with the "Atlantic Type" carbonate cycle during the last glacial period (MIS4-2) in the east of Phillipines. The variations of primary productivity and carbonate dissolution index indicated that the carbonate dissolution was a major factor controlling the carbonate content in tire cast of Philippines, and the variations in carbonate contents were mainly affected by the productivity of calcareous organism in the Southeast of Taiwan. The "Atlantic Type" carbonate cycle in the cast of Phillipines during the last glacial period (MIS4-2) was an effect of the process of dissolution combined with the change of primary productivity.

Sea surface temperature reconstruction for the middle Okinawa Trough during the last glacial-interglacial cycle using C-37 unsaturated alkenones

C-37 unsaturated alkenones were analyzed on a core retrieved from the middle Okinawa Trough. The calculated U-37(K') displays a trend generally parallel with those of the oxygen isotopic compositions of two planktonic foraminiferal species, Neogloboquadrina dutertrei and Globigerinoides sacculifer, suggesting that in this region, SST has varied in phase with global ice volume change since the last glacial -interglacial cycle. The U-37(K')-derived SST ranged from ca. 24.0 to 27.5 degrees C, with the highest value 27.5 degrees C occurring in marine isotope stage 5 and the lowest similar to 24.0 degrees C in marine isotope stage 2. This trend is consistent with the continental records from the East Asian monsoon domain and the marine records from the Equatorial Pacific. The deglacial increase of the U-37(K')-derived SST is similar to 2.4 degrees C from the Last Glacial Maximum to the Holocene. (c) 2007 Elsevier B.V. All rights reserved.

Annual cycle of carbon, nitrogen and phosphorus in the Bohai Sea: A model study

The annual cycle of nutrient-phytoplankton dynamics in Bohai Sea (BS) is simulated using a coupled physical-biological model in this study. By comparison, the modeled seasonal variations of nutrients and primary productivity agree with observations rather well. Although the annual cycles of chlorophyll a and primary production are both characterized by a double-peak configuration, a structural difference is still apparent: the phytoplankton biomass reaches the highest value in spring while summer is characterized by the most productivity in the BS, which can be ascribed to the combined impact of seawater temperature and zooplankton-grazing pressure on the growth of algae. Based on the validated simulations, the annual budgets of carbon, nitrogen and phosphorus are estimated, and are about 0.82 mt C surplus, 39 kt N deficit and 12kt P surplus, respectively, implying that the BS ecosystem is somewhat nitrogen limited. The contribution of two external nutrient sources, namely river discharges and resuspended sediments, to the growth of algae is also examined numerically, and it is found that the influence of river-borne nutrients mainly concentrates in estuaries, whereas the reduction of sediment-borne nutrients may significantly inhibit the onset of algae bloom in the whole BS. (c) 2007 Elsevier Ltd. All rights reserved.

Annual cycle of stratification and tidal fronts in the Bohai Sea: A model study

In general, competition between buoyancy mechanisms and mixing dynamics largely determines the water column structure in a shelf sea. A three dimensional baroclinic ocean model forced by surface heat fluxes and the 2.5 order Mellor-Yamada turbulence scheme is used to simulate the annual cycle of the temperature in the Bohai Sea. The difference between the sea surface temperature (SST) and sea bottom temperature (SBT) is used to examine the evolution of its vertical stratification. It is found that the water column is well-mixed from October to March and that the seasonal thermocline appears in April, peaks in July and then weakens afterwards, closely following the heat budget. In addition, the Loder parameter based on the topography and tidal current amplitude is also computed in order to examine tidal fronts in the BS, which are evident in summer months when the wind stirring mechanism is weak.

Mixed-layer water oscillations in tropical Pacific for ENSO cycle

The main modes of interannal variabilities of thermocline and sea surface wind stress in the tropical Pacific and their interactions are investigated, which show the following results. (1) The thermocline anomalies in the tropical Pacific have a zonal dipole pattern with 160 W as its axis and a meridional seesaw pattern with 6-8 degrees N as its transverse axis. The meridional oscillation has a phase lag of about 90 to the zonal oscillation, both oscillations get together to form the El Nino/La Nina cycle, which behaves as a mixed layer water oscillates anticlockwise within the tropical Pacific basin between equator and 12 degrees N. (2) There are two main patterns of wind stress anomalies in the tropical Pacific, of which the first component caused by trade wind anomaly is characterized by the zonal wind stress anomalies and its corresponding divergences field in the equatorial Pacific, and the abnormal cross- equatorial flow wind stress and its corresponding divergence field, which has a sign opposite to that of the equatorial region, in the off-equator of the tropical North Pacific, and the second component represents the wind stress anomalies and corresponding divergences caused by the ITCZ anomaly. (3) The trade winds anomaly plays a decisive role in the strength and phase transition of the ENSO cycle, which results in the sea level tilting, provides an initial potential energy to the mixed layer water oscillation, and causes the opposite thermocline displacement between the west side and east side of the equator and also between the equator and 12 degrees N of the North Pacific basin, therefore determines the amplitude and route for ENSO cycle. The ITCZ anomaly has some effects on the phase transition. (4) The thermal anomaly of the tropical western Pacific causes the wind stress anomaly and extends eastward along the equator accompanied with the mixed layer water oscillation in the equatorial Pacific, which causes the trade winds anomaly and produces the anomalous wind stress and the corresponding divergence in favor to conduce the oscillation, which in turn intensifies the oscillation. The coupled system of ocean-atmosphere interactions and the inertia gravity of the mixed layer water oscillation provide together a phase-switching mechanism and interannual memory for the ENSO cycle. In conclusion, the ENSO cycle essentially is an inertial oscillation of the mixed layer water induced by both the trade winds anomaly and the coupled ocean-atmosphere interaction in the tropical Pacific basin between the equator and 12 degrees N. When the force produced by the coupled ocean-atmosphere interaction is larger than or equal to the resistance caused by the mixed layer water oscillation, the oscillation will be stronger or maintain as it is, while when the force is less than the resistance, the oscillation will be weaker, even break.