Effects of modeled tropical sea surface temperature variability on coral reef bleaching predictions

Future widespread coral bleaching and subsequent mortality has been projected using sea surface temperature (SST) data derived from global, coupled ocean–atmosphere general circulation models (GCMs). While these models possess fidelity in reproducing many aspects of climate, they vary in their ability to correctly capture such parameters as the tropical ocean seasonal cycle and El Ni?o Southern Oscillation (ENSO) variability. Such weaknesses most likely reduce the accuracy of predicting coral bleaching, but little attention has been paid to the important issue of understanding potential errors and biases, the interaction of these biases with trends, and their propagation in predictions. To analyze the relative importance of various types of model errors and biases in predicting coral bleaching, various intra- and inter-annual frequency bands of observed SSTs were replaced with those frequencies from 24 GCMs 20th century simulations included in the Intergovernmental Panel on Climate Change (IPCC) 4th assessment report. Subsequent thermal stress was calculated and predictions of bleaching were made. These predictions were compared with observations of coral bleaching in the period 1982–2007 to calculate accuracy using an objective measure of forecast quality, the Peirce skill score (PSS). Major findings are that: (1) predictions are most sensitive to the seasonal cycle and inter-annual variability in the ENSO 24–60 months frequency band and (2) because models tend to understate the seasonal cycle at reef locations, they systematically underestimate future bleaching. The methodology we describe can be used to improve the accuracy of bleaching predictions by characterizing the errors and uncertainties involved in the predictions.     

Postural dynamics of walking in humans

The dynamics of postural control in human biped locomotion were studied using(1) a model, and(2) experimentally applied impulsive force disturbances. The model was planar, and contained five rigid segments, articulating at frictionless pin joints. The model was used to identify joint torque combinations which would successfully correct for an impulsive force disturbance applied at different points in the walking cycle. The simulation results suggested that(1) early responses (within 80ms) can be effective in compensating for impulsive disturbances,(2) the same strategies which successfully counteract similar disturbances during quiet standing are also effective in certain phases of the walking cycle,(3) modifications in the response strategies are needed to accomodate differences in the dynamics over the stride cycle, and(4) the swing leg is ineffective in compensating for disturbances in the short term. These model predictions were tested experimentally. Subject responses to an impulsive force disturbance applied during walking were studied. The electromyographic results generally support the model predictions.     

Synergistic effect of aphidicolin and ethanol on the induction of common fragile sites

Summary The effect of ethanol on the frequency of aphidicolin-induced common fragile sites was studied using lymphocyte cultures from two normal women. Aphidicolin was added to the cultures at a final concentration of 0.2 M and ethanol at 0.02%, 0.1%, 0.2%, 0.5%, and 1%, both during the last 26 h of culture. The frequency of common fragile sites increased from 296% in subject 1 and 201% in subject 2 with aphidicolin plus 0.02% ethanol, to 765% and 823%, respectively, with aphidicolin plus 1% ethanol. Ethanol alone added to cultures did not induce common fragile sites. The gaps and breaks induced by aphidicolin plus ethanol were highly nonrandom. Altogether, 35 common fragile sites were identified. The addition of 1% ethanol to aphidicolin increased both random and nonrandom gaps and breaks as compared with that of 0.02% ethanol. Dimethyl sulfoxide added to culture at final concentrations of 0.02% to 1% did not change the frequency of aphidicolin-induced fragile sites. The frequency of fluorodeoxyuridine-induced fragile sites was not affected by the addition of 0.02% to 1% ethanol. It was thus concluded that ethanol enhances the aphidicolin-induced fragile sites, possibly inhibiting the repair mechanism of gaps and breaks induced by aphidicolin.     

Protein particles in Chlamydomonas flagella undergo a transport cycle consisting of four phases

We used an improved procedure to analyze the intraflagellar transport (IFT) of protein particles in Chlamydomonas and found that the frequency of the particles, not only the velocity, changes at each end of the flagella. Thus, particles undergo structural remodeling at both flagellar locations. Therefore, we propose that the IFT consists of a cycle composed of at least four phases: phases II and IV, in which particles undergo anterograde and retrograde transport, respectively, and phases I and III, in which particles are remodeled/exchanged at the proximal and distal end of the flagellum, respectively. In support of our model, we also identified 13 distinct mutants of flagellar assembly (fla), each defective in one or two consecutive phases of the IFT cycle. The phase I-II mutant fla10-1 revealed that cytoplasmic dynein requires the function of kinesin II to participate in the cycle. Phase I and II mutants accumulate complex A, a particle component, near the basal bodies. In contrast, phase III and IV mutants accumulate complex B, a second particle component, in flagellar bulges. Thus, fla mutations affect the function of each complex at different phases of the cycle.     

In vivo measurement of dynamic rectus femoris function at postures representative of early swing phase

Forward dynamic models suggest that muscle-induced joint motions depend on dynamic coupling between body segments. As a result, biarticular muscles may exhibit non-intuitive behavior in which the induced joint motion is opposite to that assumed based on anatomy. Empirical validation of such predictions is important for models to be relied upon to characterize muscle function. In this study, we measured, in vivo, the hip and knee accelerations induced by electrical stimulation of the rectus femoris (RF) and the vastus medialis (VM) at postures representatives of the toe-off and early swing phases of the gait cycle. Seven healthy young subjects were positioned side-lying with their lower limb supported on air bearings while a 90 ms pulse train stimulated each muscle separately or simultaneously. Lower limb kinematics were measured and compared to predictions from a similarly configured dynamic model of the lower limb. We found that both RF and VM, when stimulated independently, accelerated the hip and knee into extension at these postures, consistent with model predictions. Predicted ratios of hip acceleration to knee acceleration were generally within 1 s.d. of average values. In addition, measured responses to simultaneous RF and VM stimulation were within 13% of predictions based on the assumption that joint accelerations induced by activating two muscles simultaneously can be found by adding the joint accelerations induced by activating the same muscles independently. These results provide empirical evidence of the importance of considering dynamic effects when interpreting the role of muscles in generating movement.     

Experession and integration of genes introduced into highly synchronized plant protoplasts

Summary Chimaeric genes containing the chloramphenicol acetyltransferase (CAT) coding sequence were introduced into protoplasts of suspension-cultured tobacco cells using improved conditions of electroporation (Okada et al. 1986). CAT activity became detectable in the protoplasts within 3 h, was maximal during a period of 18–36 h after electroporation, and then declined gradually. Alpha-amanitin added to the medium abolished the transient expression of the CAT gene. The closed circular form of input DNA was as effective as the linear form for the transient expression. The suspension culture was treated with aphidicolin, and S, G₂, M and G₁ phases were identified in the highly synchronized cell cycle obtained by releasing the cells from the inhibition of DNA synthesis. When a chimacric CAT gene was introduced into M phase protoplasts prepared from the synchronized culture, the transient expression of the CAT gene was 3–4 times higher than when it was introduced into protoplasts of other cell cycle phases. The frequency of stable transformation with a chimaeric neomycin phosphotransferase II gene was studied using the same system. G-418-resistant transformants were obtained from M phase protoplasts at frequencies 2–8 times those obtained from protoplasts at other cell cycle phases. The results indicate that the absence of the nuclear membrane in mitotic cells favours delivery to the nucleus of exogenous DNA introduced into the cytoplasm.     

Changes in the content of phenolic substances during the growth ofNicotiana tabacum cell suspension culture

The dynamics of changes in the content of four groups of phenolic substances was investigated during the growth cycle of the cell suspension culture ofNicotiana tábacum by means of fractionation. The relative contents of free phenolic acids, their esters, phenolic glycosides, and phenole acids non-extractable with methanol changed in dependence on the growth phase of the culture. A sharp increase, especially in the content of ester- and glycoside-bound phenolics and to a lesser extent also of phenolics belonging to the other two groups, occurred at the end of the lag phase. Then, after a temporary decrease at the early linear phase, the level of phenolics in the three fractions representing bound forms considerably increased again at the late linear and early stationary phases. The synthesized phenolic substances were partially released from the cells into the cultivation medium, which contained 15 to 30 % of the total content of the phenolics in the culture at different phases of the growth cycle. Likely causes of these changes are discussed.     

正常猫膈神经单纤维电活动特征

在麻醉猫和麻痹的切断迷走神经的清醒猫,观察了膈神经单纤维电活动特征。1.电活动类型:按膈神经单纤维放电与其总干放电的相位关系分为三种类型。(1)完全同步型,即单纤维放电与总干放电同时开始并同时停止,占76.9％。(2)部分同步型占15.4％,其中早期同步,即单纤维放电与总干放电同时开始,但提前终止,占1.9％,中期同步,即单纤维放电较总干放电开始晚,又提前终止,占5.8％,晚期同步,即单纤维放电较总干放电开始晚,但两者同时终止,占7.7％。(8)非同步型,即吸气相和呼气相都有放电,但呼气相时冲动频率较低,占7.7％。前两型为单纯的吸气性放电,共占92.3％。2.单纤维放电平均参数值:麻醉猫每次吸气发放11个冲动,其频率为21次/秒,清醒猫每次吸气发放18个冲动,其频率为34次/秒。结果表明:猫膈神经单纤维放电类型和文献上报导的直接记录膈神经运动神经元放电一致,即以单纯的吸气性放电为最多。     

Quantifying the Adaptive Cycle

The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994–2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and adaptation provides opportunities to cope with the intricacies and uncertainties associated with fast ecological change, driven by shifting system controls. Ultimately, combining traditional ecological paradigms with heuristics of complex system dynamics using quantitative approaches may help refine ecological theory and improve our understanding of the resilience of ecosystems.     

An Investigation of Assessment Games During Fallow Deer Fights

An improved understanding of the decision rules used by competing animals can be achieved by examining both the temporal structure and display rate of competitors during a contest. Current models of animal competition make different predictions regarding the behaviour of competing animals and the present study evaluates the predictions of three such models, the energetic war of attrition (eWOA), the sequential assessment game (SAG) and the cumulative assessment model (CAM) by applying them to the fighting behaviour of male fallow deer (Dama dama L.). There was no difference in rate at which the jump clash and backward push were recorded over fight duration; therefore, in terms of the temporal distribution of behavioural acts within fights, the jump clash and backward push conformed to the predictions of the SAG. There was a difference between winners and losers of fights for the frequency that the jump clash and backward push were recorded consistent with both the SAG and CAM. Analysis of bout duration showed that there was a decrease in the duration of subsequent bouts of fighting; this is only permitted under eWOA. In so far as current assessment models permit interpretation of the data, our results meet only a limited number of predictions of any one model. Given the difficulty in interpreting our data within the context of current assessment models, recommendations for the development of more complex models are presented.     

Synchronized mammalian cell culture: Part II—population ensemble modeling and analysis for development of reproducible processes

The consideration of inherent population inhomogeneities of mammalian cell cultures becomes increasingly important for systems biology study and for developing more stable and efficient processes. However, variations of cellular properties belonging to different sub‐populations and their potential effects on cellular physiology and kinetics of culture productivity under bioproduction conditions have not yet been much in the focus of research. Culture heterogeneity is strongly determined by the advance of the cell cycle. The assignment of cell‐cycle specific cellular variations to large‐scale process conditions can be optimally determined based on the combination of (partially) synchronized cultivation under otherwise physiological conditions and subsequent population‐resolved model adaptation. The first step has been achieved using the physical selection method of countercurrent flow centrifugal elutriation, recently established in our group for different mammalian cell lines which is presented in Part I of this paper series. In this second part, we demonstrate the successful adaptation and application of a cell‐cycle dependent population balance ensemble model to describe and understand synchronized bioreactor cultivations performed with two model mammalian cell lines, AGE1.HN_AAT and CHO‐K1. Numerical adaptation of the model to experimental data allows for detection of phase‐specific parameters and for determination of significant variations between different phases and different cell lines. It shows that special care must be taken with regard to the sampling frequency in such oscillation cultures to minimize phase shift (jitter) artifacts. Based on predictions of long‐term oscillation behavior of a culture depending on its start conditions, optimal elutriation setup trade‐offs between high cell yields and high synchronization efficiency are proposed. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:175–185, 2015     

Familial and individual variation in chromosome fragility

An extremely high frequency of fra 6q26 (25%) was detected during a routine cytogenetic investigation of a 9-year-old girl. This prompted us to perform an extensive study of fragile site expression in her cells and those of her parents and sister. The very high frequency of fragility at 6q26 which had been discovered initially in the proband was not detected in the first repeat culture under the same experimental conditions. However, in the second repeat culture fragility at 6q26 was clearly present again. In the 4 members of this family fragile site expression was found to vary significantly between repeat samples from the same person. Also, a specific order of individual fragile site expression appeared to be present. This order was the same for the different culture conditions used.     

Dynamic instability of individual microtubules analyzed by video light microscopy: rate constants and transition frequencies

We have developed video microscopy methods to visualize the assembly and disassembly of individual microtubules at 33-ms intervals. Porcine brain tubulin, free of microtubule-associated proteins, was assembled onto axoneme fragments at 37 degrees C, and the dynamic behavior of the plus and minus ends of microtubules was analyzed for tubulin concentrations between 7 and 15.5 microM. Elongation and rapid shortening were distinctly different phases. At each end, the elongation phase was characterized by a second order association and a substantial first order dissociation reaction. Association rate constants were 8.9 and 4.3 microM-1 s-1 for the plus and minus ends, respectively; and the corresponding dissociation rate constants were 44 and 23 s-1. For both ends, the rate of tubulin dissociation equaled the rate of tubulin association at 5 microM. The rate of rapid shortening was similar at the two ends (plus = 733 s-1; minus = 915 s-1), and did not vary with tubulin concentration. Transitions between phases were abrupt and stochastic. As the tubulin concentration was increased, catastrophe frequency decreased at both ends, and rescue frequency increased dramatically at the minus end. This resulted in fewer rapid shortening phases at higher tubulin concentrations for both ends and shorter rapid shortening phases at the minus end. At each concentration, the frequency of catastrophe was slightly greater at the plus end, and the frequency of rescue was greater at the minus end. Our data demonstrate that microtubules assembled from pure tubulin undergo dynamic instability over a twofold range of tubulin concentrations, and that the dynamic instability of the plus and minus ends of microtubules can be significantly different. Our analysis indicates that this difference could produce treadmilling, and establishes general limits on the effectiveness of length redistribution as a measure of dynamic instability. Our results are consistent with the existence of a GTP cap during elongation, but are not consistent with existing GTP cap models.     

Neural network modeling of the light profile in a novel photobioreactor

An artificial neural network (ANN) was implemented to model the light profile pattern inside a photobioreactor (PBR) that uses a toroidal light arrangement. The PBR uses Tequila vinasses as culture medium and purple non-sulfur bacteria Rhodopseudomonas palustris as biocatalyzer. The performance of the ANN was tested for a number of conditions and compared to those obtained by using deterministic models. Both ANN and deterministic models were validated experimentally. In all cases, at low biomass concentration, model predictions yielded determination coefficients greater than 0.9. Nevertheless, ANN yielded the more accurate predictions of the light pattern, at both low and high biomass concentration, when the bioreactor radius, the depth, the rotational speed of the stirrer and the biomass concentration were incorporated in the ANN structure. In comparison, most of the deterministic models failed to correlate the empirical data at high biomass concentration. These results show the usefulness of ANNs in the modeling of the light profile pattern in photobioreactors.     

晋陕宁黄土丘陵区生态修复与农林牧业持续发展仿真研究

晋陕宁黄土丘陵区土壤侵蚀严重,生态环境脆弱,不合理利用土地是其主要原因,生态修复与环境重建是该区生态与经济持续发展的重要战略措施。应用系统动力学（System Dynamic,简称SD）和“反馈控制（Feedback control）理论建立了该区生态修复和环境重建的SD模型,它分为人口、农业、林业、牧业、农村经济、土壤侵蚀和生态环境6个模块,仿真时间1990～2080年,步长1a。经检验该SD模型的有效性为93．5％,可用于未来仿真预测。根据该区的生态环境特点和农牧业发展现状,选择生态环境恢复重建的3种典型模式——同步发展模式（A模式）、逐步调整模式（B模式）和现状发展模式（C模式）进行仿真研究,预测3种模式2000～2080年的土壤侵蚀、土地利用的发展动态以及农林牧业和生态环境演化趋势。仿真结果表明：土地利用与农、林、牧业持续发展密切相关,坡耕地和草场退化是制约农林牧业发展的主要因素。合理调整土地利用结构和加速治理侵蚀,可促进生态环境逐步恢复和农林牧业持续发展。同步发展模式（A模式）是该区生态修复和环境重建的3个仿真模式中的最优策略,它可促进农林牧协调发展和生态一经济趋向良性循环,并提出该区生态修复与环境重建的对策措施。该SD模型结构合理,运行功能良好,能较真实的模拟具有多变量、非线性变量的复杂生态系统的动态行为,为生态修复研究提供一种有效工具。     

STUDIES ON THE DIVISION CYCLE OF MAMMALIAN CELLS : V. Modifications of Time Parameters by Different Steady-State Culture Conditions

In cultures of murine neoplastic mast cells, the duration of different phases of the division cycle (G₁, S, G₂, and mitosis [M]) was determined under optimal and several well-defined suboptimal growth conditions. Two methods of evaluation were applied to the same culture system: first, the relative number of G₁, S, G₂, and M cells was determined by pulse labeling of samples with thymidine-³H and subsequent radioautography in conjunction with a microfluorometric technique permitting rapid measurements of cellular DNA content; second, after pulse labeling with thymidine-³H, the variations with time of the mitotic labeling index were analyzed. Suboptimal culture conditions were obtained by reducing the concentration of single essential medium components (leucine, glucose, or serum) or by the addition of specific metabolic inhibitors (actinomycin D, amethopterin). Growth-limiting culture conditions resulted in increased generation times. Even under control conditions, the cell number doubling time exceeded the generation time, and this difference was more pronounced in suboptimal media. Under most of the suboptimal conditions tested, the increase in generation time was attributable primarily to an extended duration of the G₁ phase. Under certain growth-limiting conditions, however, other phases were also prolonged. In addition, the variabilities of the generation time and of certain cell cycle phases were increased under suboptimal culture conditions. Results obtained by the two methods of evaluation were, in general, in good agreement with each other. Some differences were, however, observed and interpreted in terms of cell death and/or asymmetric frequency distributions of cell cycle parameters.     

The expression of fragile X chromosomes in members of the same family at different times of examination

Summary Three brothers with fragile X chromosomes were repeatedly examined using the same culture and preparation techniques. It was observed that a given individual showed a very constant frequency of fragile sites at his X chromosomes, whereas large differences in the the fragile X counts occurred between the three brothers.     

Molecular parameters of genome instability: roles of fragile genes at common fragile sites

Common chromosome fragile sites occur at specific sequences within mammalian genomes that exhibit apparent single-stranded regions in mitotic chromosomes on exposure of cells to replication stress. Recent progress in the characterization of sequences, and more precise mapping of common fragile sites in mammalian and yeast genomes, has led to the exact placement of large common fragile regions straddling the borders of chromosomal G and R bands, with early and late replicating genomic regions, respectively, and could lead to breakthroughs in understanding the function of these evolutionarily conserved but highly recombinogenic chromosome elements. Deficiency of genes involved in DNA damage checkpoint responses, such as ATR, CHK1, HUS1 leads to increased frequency of fragile site instability. Some of these fragile sites, particularly FRA3B, encode genes that are themselves involved in the protection of cells from DNA damage through various mechanisms. Protection of mammalian genomes from accumulation of DNA damage in somatic cells is critical during development, puberty and during the reproductive lifespan, and occurs through mechanisms involving surveillance of the genome for damage, signals to the cell cycle machinery to stop cell cycle progression, signals to repair machinery to repair damage, signals to resume cycling or initiate apoptotic programs, depending on the extent of damage and repair. When genes involved in these processes are altered or deleted, cancer can occur. The tumor suppressor gene, FHIT at the FRA3B locus, and possibly other fragile genes, is a common target of damage and paradoxically encodes a protein with roles in protection from DNA damage.     

Increased common fragile site expression, cell proliferation defects, and apoptosis following conditional inactivation of mouse Hus1 in primary cultured cells

Targeted disruption of the mouse Hus1 cell cycle checkpoint gene results in embryonic lethality and proliferative arrest in cultured cells. To investigate the essential functions of Hus1, we developed a system for the regulated inactivation of mouse Hus1 in primary fibroblasts. Inactivation of a loxP site-flanked conditional Hus1 allele by using a cre-expressing adenovirus resulted in reduced cell doubling, cell cycle alterations, and increased apoptosis. These phenotypes were associated with a significantly increased frequency of gross chromosomal abnormalities and an S-phase-specific accumulation of phosphorylated histone H2AX, an indicator of double-stranded DNA breaks. To determine whether these chromosomal abnormalities occurred randomly or at specific genomic regions, we assessed the stability of common fragile sites, chromosomal loci that are prone to breakage in cells undergoing replication stress. Hus1 was found to be essential for fragile site stability, because spontaneous chromosomal abnormalities occurred preferentially at common fragile sites upon conditional Hus1 inactivation. Although p53 levels increased after Hus1 loss, deletion of p53 failed to rescue the cell-doubling defect or increased apoptosis in conditional Hus1 knockout cells. In summary, we propose that Hus1 loss leads to chromosomal instability during DNA replication, triggering increased apoptosis and impaired proliferation through p53-independent mechanisms.     

Sensitivity of a human hybrid cell line (HeLa X skin fibroblast) to radiation-induced neoplastic transformation in G2, M, and mid-G1 phases of the cell cycle

The dependence of gamma-radiation-induced neoplastic transformation frequency on position in the cell cycle was measured for a human hybrid cell line (HeLa X skin fibroblast). The end point used was the induction of a tumor-associated antigen which in these cells correlates with tumorigenicity. Induction was measured in cells at G2, M, and mid-G1 phases and compared with the frequency induced in asynchronous cells. For studies of cells in G2 phase, the cells of an asynchronous population were collected for 3 h post-irradiation using the mitotic shake-off technique. For studies of cells in M and mid-G1 phases, cells were collected by mitotic harvest and then treated at the appropriate time. The data show that cells in G2 and M phase are very radiosensitive in terms of both cell killing and induction of neoplastic transformation compared to cells in mid-G1 or asynchronous populations. At a dose of 1 Gy, the transformation frequency was 10- to 20-fold higher for cells in M and G2 phase than for cells in mid-G1 or for asynchronous cells. However, the data indicate that the transformation frequencies were similar in the different phases of the cell cycle when correlated with surviving fraction. The results indicate that transformation frequency is more sensitive to changes in dose than is cell survival.