Simulations and mechanisms of subtropical low-cloud response to climate change

This thesis focuses on improving the simulation skills and the theoretical understanding of the subtropical low cloud response to climate change.

First, an energetically consistent forcing framework is designed and implemented for the large eddy simulation (LES) of the low-cloud response to climate change. The three representative current-day subtropical low cloud regimes of cumulus (Cu), cumulus-over-stratocumulus, and stratocumulus (Sc) are all well simulated with this framework, and results are comparable to the conventional fixed-SST approach. However, the cumulus response to climate warming subject to energetic constraints differs significantly from the conventional approach with fixed SST. Under the energetic constraint, the subtropics warm less than the tropics, since longwave (LW) cooling is more efficient with the drier subtropical free troposphere. The surface latent heat flux (LHF) also increases only weakly subject to the surface energetic constraint. Both factors contribute to an increased estimated inversion strength (EIS), and decreased inversion height. The decreased Cu-depth contributes to a decrease of liquid water path (LWP) and weak positive cloud feedback. The conventional fixed-SST approach instead simulates a strong increase in LHF and deepening of the Cu layer, leading to a weakly negative cloud feedback. This illustrates the importance of energetic constraints to the simulation and understanding of the sign and magnitude of low-cloud feedback.

Second, an extended eddy-diffusivity mass-flux (EDMF) closure for the unified representation of sub-grid scale (SGS) turbulence and convection processes in general circulation models (GCM) is presented. The inclusion of prognostic terms and the elimination of the infinitesimal updraft fraction assumption makes it more flexible for implementation in models across different scales. This framework can be consistently extended to formulate multiple updrafts and downdrafts, as well as variances and covariances. It has been verified with LES in different boundary layer regimes in the current climate, and further development and implementation of this closure may help to improve our simulation skills and understanding of low-cloud feedback through GCMs.

Observation and interpretation of tectonic strain release mechanisms

In four chapters various aspects of earthquake source are studied.

Chapter I

Surface displacements that followed the Parkfield, 1966, earthquakes were measured for two years with six small-scale geodetic networks straddling the fault trace. The logarithmic rate and the periodic nature of the creep displacement recorded on a strain meter made it possible to predict creep episodes on the San Andreas fault. Some individual earthquakes were related directly to surface displacement, while in general, slow creep and aftershock activity were found to occur independently. The Parkfield earthquake is interpreted as a buried dislocation.

Chapter II

The source parameters of earthquakes between magnitude 1 and 6 were studied using field observations, fault plane solutions, and surface wave and S-wave spectral analysis. The seismic moment, M_O, was found to be related to local magnitude, M_L, by log M_O = 1.7 M_L + 15.1. The source length vs magnitude relation for the San Andreas system found to be: M_L = 1.9 log L - 6.7. The surface wave envelope parameter AR gives the moment according to log M_O = log AR₃₀₀ + 30.1, and the stress drop, τ, was found to be related to the magnitude by τ = 0.54 M - 2.58. The relation between surface wave magnitude M_S and M_L is proposed to be M_S = 1.7 M_L - 4.1. It is proposed to estimate the relative stress level (and possibly the strength) of a source-region by the amplitude ratio of high-frequency to low-frequency waves. An apparent stress map for Southern California is presented.

Chapter III

Seismic triggering and seismic shaking are proposed as two closely related mechanisms of strain release which explain observations of the character of the P wave generated by the Alaskan earthquake of 1964, and distant fault slippage observed after the Borrego Mountain, California earthquake of 1968. The Alaska, 1964, earthquake is shown to be adequately described as a series of individual rupture events. The first of these events had a body wave magnitude of 6.6 and is considered to have initiated or triggered the whole sequence. The propagation velocity of the disturbance is estimated to be 3.5 km/sec. On the basis of circumstantial evidence it is proposed that the Borrego Mountain, 1968, earthquake caused release of tectonic strain along three active faults at distances of 45 to 75 km from the epicenter. It is suggested that this mechanism of strain release is best described as "seismic shaking."

Chapter IV

The changes of apparent stress with depth are studied in the South American deep seismic zone. For shallow earthquakes the apparent stress is 20 bars on the average, the same as for earthquakes in the Aleutians and on Oceanic Ridges. At depths between 50 and 150 km the apparent stresses are relatively high, approximately 380 bars, and around 600 km depth they are again near 20 bars. The seismic efficiency is estimated to be 0.1. This suggests that the true stress is obtained by multiplying the apparent stress by ten. The variation of apparent stress with depth is explained in terms of the hypothesis of ocean floor consumption.

Mechanisms of E2F2-mediated transcriptional repression

In this work we wanted to study the mechanism of E2F2-mediated repression. Our hypothesis is that E2F2 activates the expression of one or more E2F members of the “repressor” subset of the family through the E2F motifs present in their promoters, and those repressor E2F(s) would subsequently repress the target promoters. To address this hypothesis, we focused on E2F7. E2F7 is a repressor that lacks the Rb binding domain, and associates with DNA through E2F binding sites (de Bruin et al., 2003). Furthermore, E2F7 itself is also regulated by E2F motifs on its own promoter, and it has been shown to repress DNA metabolism and replication genes in late S-phase (de Bruin et al., 2003; Westendorp et al., 2012). E2F7, together with E2F8 has been found to form heterodimers, being critical on cell proliferation and development, and both seem to have similar functions (Li et al., 2008). Preliminary results from Zubiaga’s group have indicated that E2F2 activates E2F7 transcription in U2OS cells, suggesting that E2F2’s repressor function could be mediated by E2F7. For this purpose, we focused on studying E2F7’s role on the target genes previously known to be repressed by E2F2: Chk1 and Mcm5. The specific aims for this work were the following: - Confirm that E2F2 induces E2F7 in HEK-293T cells - Assess whether E2F7 acts as a transcriptional repressor on E2F sites - Evaluate the role of E2F7 on E2F2-mediated transcriptional repression of Chk1 and Mcm5.

Part I. Coenzyme B12 as a hydroformylation-type catalyst. Part II. Mechanisms of hydrogen transfer in the methylmalonyl coenzyme a mutase reaction

Part I

The mechanism of the hydroformylation reaction was studied. Using cobalt deuterotetracarbonyl and 1-pentene as substrates, the first step in the reaction, addition of cobalt tetracarbonyl to an olefin, was shown to be reversible.

Part II

The role of coenzyme B₁₂ in the isomerization of methylmalonyl coenzyme A to succinyl coenzyme A by methylmalonyl coenzyme A mutase was studied. The reaction was allowed to proceed to partial completion using a mixture of methylmalonyl coenzyme A and 4, 4, 4-tri-²H-methylmalonyl coenzyme A as substrate. The deuterium distribution in the product, succinyl coenzyme A, was shown to best fit a model in which hydrogen is transferred from C-4 of methylmalonyl coenzyme A to C-5’ of the adenosyl moiety of coenzyme B₁₂ in the rate determining step. The three hydrogens at the 5’-adenosyl position of the coenzyme B₁₂ intermediate are then able to become enzymatically equivalent before hydrogen is transferred from the coenzyme B₁₂ intermediate to form succinyl coenzyme A.

Phytoplankton periodicity: its motivation, mechanisms and manipulation

This review summarizes some recent work to find a generalized explanation of phytoplankton periodicity in lakes. Much of the observational and experimental evidence is drawn from work centred on the large enclosures (Lund Tubes) installed in Blelham Tarn, English Lake District. Observations on the phytoplankton in the tubes are related to the periodic changes that occur in natural lakes and it is suggested that such changes have common patterns, that they are due to common causes, that they are affected by similar processes and that they are therefore predictable and, potentially, manipulable.

Control mechanisms in the human binocular oculomotor system

A study of human eye movements was made in order to elucidate the nature of the control mechanism in the binocular oculomotor system.

We first examined spontaneous eye movements during monocular and binocular fixation in order to determine the corrective roles of flicks and drifts. It was found that both types of motion correct fixational errors, although flicks are somewhat more active in this respect. Vergence error is a stimulus for correction by drifts but not by flicks, while binocular vertical discrepancy of the visual axes does not trigger corrective movements.

Second, we investigated the non-linearities of the oculomotor system by examining the eye movement responses to point targets moving in two dimensions in a subjectively unpredictable manner. Such motions consisted of hand-limited Gaussian random motion and also of the sum of several non-integrally related sinusoids. We found that there is no direct relationship between the phase and the gain of the oculomotor system. Delay of eye movements relative to target motion is determined by the necessity of generating a minimum afferent (input) signal at the retina in order to trigger corrective eye movements. The amplitude of the response is a function of the biological constraints of the efferent (output) portion of the system: for target motions of narrow bandwidth, the system responds preferentially to the highest frequency; for large bandwidth motions, the system distributes the available energy equally over all frequencies. Third, the power spectra of spontaneous eye movements were compared with the spectra of tracking eye movements for Gaussian random target motions of varying bandwidths. It was found that there is essentially no difference among the various curves. The oculomotor system tracks a target, not by increasing the mean rate of impulses along the motoneurons of the extra-ocular muscles, but rather by coordinating those spontaneous impulses which propagate along the motoneurons during stationary fixation. Thus, the system operates at full output at all times.

Fourth, we examined the relative magnitude and phase of motions of the left and the right visual axes during monocular and binocular viewing. We found that the two visual axes move vertically in perfect synchronization at all frequencies for any viewing condition. This is not true for horizontal motions: the amount of vergence noise is highest for stationary fixation and diminishes for tracking tasks as the bandwidth of the target motion increases. Furthermore, movements of the occluded eye are larger than those of the seeing eye in monocular viewing. This effect is more pronounced for horizontal motions, for stationary fixation, and for lower frequencies.

Finally, we have related our findings to previously known facts about the pertinent nerve pathways in order to postulate a model for the neurological binocular control of the visual axes.

The ecological impact of different mechanisms of chronic sub-lethal toxicity on feeding and respiratory physiology

Sub-lethal toxicity tests, such as the scope-for-growth test, reveal simple relationships between measures of contaminant concentration and effect on respiratory and feeding physiology. Simple models are presented to investigate the potential impact of different mechanisms of chronic sub-lethal toxicity on these physiological processes. Since environmental quality is variable, even in unimpacted environments, toxicants may have differentially greater impacts in poor compared to higher quality environments. The models illustrate the implications of different degrees and mechanisms of toxicity in response to variability in the quality of the feeding environment, and variability in standard metabolic rate. The models suggest that the relationships between measured degrees of toxic stress, and the maintenance ration required to maintain zero scope-for-growth, may be highly nonlinear. In addition it may be possible to define critical levels of sub-lethal toxic effect above which no environment is of sufficient quality to permit prolonged survival.

Resveratrol: Anti-Obesity Mechanisms of Action

Resveratrol is a non-flavonoid polyphenol which belongs to the stilbenes group and is produced naturally in several plants in response to injury or fungal attack. Resveratrol has been recently reported as preventing obesity. The present review aims to compile the evidence concerning the potential mechanisms of action which underlie the anti-obesity effects of resveratrol, obtained either in cultured cells lines and animal models. Published studies demonstrate that resveratrol has an anti-adipogenic effect. A good consensus concerning the involvement of a down-regulation of C/EBPa and PPAR. in this effect has been reached. Also, in vitro studies have demonstrated that resveratrol can increase apoptosis in mature adipocytes. Furthermore, different metabolic pathways involved in triacylglycerol metabolism in white adipose tissue have been shown to be targets for resveratrol. Both the inhibition of de novo lipogenesis and adipose tissue fatty acid uptake mediated by lipoprotein lipase play a role in explaining the reduction in body fat which resveratrol induces. As far as lipolysis is concerned, although this compound per se seems to be unable to induce lipolysis, it increases lipid mobilization stimulated by beta-adrenergic agents. The increase in brown adipose tissue thermogenesis, and consequently the associated energy dissipation, can contribute to explaining the body-fat lowering effect of resveratrol. In addition to its effects on adipose tissue, resveratrol can also acts on other organs and tissues. Thus, it increases mitochondriogenesis and consequently fatty acid oxidation in skeletal muscle and liver. This effect can also contribute to the body-fat lowering effect of this molecule.

Mechanisms involved in Escherichia coli and Serratia marcescens removal during activated sludge wastewater treatment

Wastewater treatment reduces environmental contamination by removing gross solids and mitigating the effects of pollution. Treatment also reduces the number of indicator organisms and pathogens. In this work, the fates of two coliform bacteria, Escherichia coli and Serratia marcescens, were analyzed in an activated sludge process to determine the main mechanisms involved in the reduction of pathogenic microorganisms during wastewater treatment. These bacteria, modified to express green fluorescent protein, were inoculated in an activated sludge unit and in batch systems containing wastewater. The results suggested that, among the different biological factors implied in bacterial removal, bacterivorous protozoa play a key role. Moreover, a representative number of bacteria persisted in the system as free-living or embedded cells, but their distribution into liquid or solid fractions varied depending on the bacterium tested, questioning the real value of bacterial indicators for the control of wastewater treatment process. Additionally, viable but nonculturable cells constituted an important part of the bacterial population adhered to solid fractions, what can be derived from the competition relationships with native bacteria, present in high densities in this environment. These facts, taken together, emphasize the need for reliable quantitative and qualitative analysis tools for the evaluation of pathogenic microbial composition in sludge, which could represent an undefined risk to public health and ecosystem functions when considering its recycling.

Mechanisms of Yb3+ sensitization to Tm3+ for blue upconversion luminescence in fluorophosphate glass

The sensitization mechanisms of Yb3+ to Tm3+ for the blue upconversion luminescence in fluorophosphate glass were studied. Two different mechanisms exist in the sensitization. One is the sequential sensitization that Tm3+ is excited from H-3(6) to (1)G(4) through absorbing three photons transferred from Yb3+ one by one. Another is the cooperative sensitization that two Yb3+ ions form a couple cluster firstly, and then the couple cluster Yb3+ ions transfer their energy to Tm3+ and excite it to (1)G(4). With the increment of the concentration of Yb3+ ions, the sequential sensitization becomes weak and the cooperative sensitization becomes intense, and the transformation trend of sensitization mechanism with the increment of Yb3+ concentration can be clarified by the introduction of Th3+ ions in the glass. (c) 2006 Elsevier B.V. All rights reserved.