Lithium-to-calcium ratios in Modern, Cenozoic, and Paleozoic articulate brachiopod shells

Li/Ca ratios in modern brachiopod shells generally correlate inversely with growth temperature, ranging from ∼20 µmol/mol at 30°C to ∼50 µmol/mol at 0°C with no apparent interspecific offsets. Causes of the temperature effect on Li/Ca ratios are not yet understood. Cenozoic brachiopod Li/Ca ratios average ∼30 µmol/mol, similar to the average observed in modern brachiopods. Relatively constant Li/Ca ratios for Eocene to Pleistocene nonluminescent brachiopod shells, consistent with previous observations of Cenozoic planktonic foraminifera, support the conclusion of little variation in Cenozoic seawater Li/Ca. Nonluminescent portions of Permian and Carboniferous brachiopods have Li/Ca ratios substantially lower (generally <10 µmol/mol) than modern, Cenozoic, or Devonian samples. Mass balance considerations, constrained by δ18O of brachiopods, suggest that low Li concentrations in Permo-Carboniferous seawater could be the result of a lower flux of dissolved Li from the continents and/or a higher flux of Li from seawater to clastic marine sediments. Nonluminescent Devonian brachiopods from a single hand specimen have Li/Ca ratios around 70% of the modern average. These Li/Ca ratios can be explained by either somewhat higher temperature with constant seawater Li/Ca, somewhat lower seawater Li/Ca at constant temperature, or a combination of slightly elevated temperature and slightly lower seawater Li/Ca

Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo

Precise patterning of morphogen molecules and their accurate reading out are of key importance in embryonic development. Recent experiments have visualized distributions of proteins in developing embryos and shown that the gradient of concentration of Bicoid morphogen in Drosophila embryos is established rapidly after fertilization and remains stable through syncytial mitoses. This stable Bicoid gradient is read out in a precise way to distribute Hunchback with small fluctuations in each embryo and in a reproducible way, with small embryo-to-embryo fluctuation. The mechanisms of such stable, precise, and reproducible patterning through noisy cellular processes, however, still remain mysterious. To address these issues, here we develop the one- and three-dimensional stochastic models of the early Drosophila embryo. The simulated results show that the fluctuation in expression of the hunchback gene is dominated by the random arrival of Bicoid at the hunchback enhancer. Slow diffusion of Hunchback protein, however, averages out this intense fluctuation, leading to the precise patterning of distribution of Hunchback without loss of sharpness of the boundary of its distribution. The coordinated rates of diffusion and transport of input Bicoid and output Hunchback play decisive roles in suppressing fluctuations arising from the dynamical structure change in embryos and those arising from the random diffusion of molecules, and give rise to the stable, precise, and reproducible patterning of Bicoid and Hunchback distributions

The Phanerozoic δ88/86Sr Record of Seawater: New Constraints on Past Changes in Oceanic Carbonate Fluxes

The isotopic composition of Phanerozoic marine sediments provides important information about changes in seawater chemistry. In particular, the radiogenic strontium isotope (87Sr/86Sr) system is a powerful tool for constraining plate tectonic processes and their influence on atmospheric CO2 concentrations. However, the 87Sr/86Sr isotope ratio of seawater is not sensitive to temporal changes in the marine strontium (Sr) output flux, which is primarily controlled by the burial of calcium carbonate (CaCO3) at the ocean floor. The Sr budget of the Phanerozoic ocean, including the associated changes in the amount of CaCO3 burial, is therefore only poorly constrained. Here, we present the first stable isotope record of Sr for Phanerozoic skeletal carbonates, and by inference for Phanerozoic seawater (δ88/86Srsw), which we find to be sensitive to imbalances in the Sr input and output fluxes. This δ88/86Srsw record varies from ∼0.25‰ to ∼0.60‰ (vs. SRM987) with a mean of ∼0.37‰. The fractionation factor between modern seawater and skeletal calcite Δ88/86Srcc-sw, based on the analysis of 13 modern brachiopods (mean δ88/86Sr of 0.176±0.016‰, 2 standard deviations (s.d.)), is -0.21‰ and was found to be independent of species, water temperature, and habitat location. Overall, the Phanerozoic δ88/86Srsw record is positively correlated with the Ca isotope record (δ44/40Casw), but not with the radiogenic Sr isotope record ((87Sr/86Sr)sw). A new numerical modeling approach, which considers both δ88/86Srsw and (87Sr/86Sr)sw, yields improved estimates for Phanerozoic fluxes and concentrations for seawater Sr. The oceanic net carbonate flux of Sr (F(Sr)carb) varied between an output of -4.7x1010mol/Myr and an input of +2.3x1010mol/Myr with a mean of -1.6x1010mol/Myr. On time scales in excess of 100Myrs the F(Sr)carb is proposed to have been controlled by the relative importance of calcium carbonate precipitates during the “aragonite” and “calcite” sea episodes. On time scales less than 20Myrs the F(Sr)carb seems to be controlled by variable combinations of carbonate burial rate, shelf carbonate weathering and recrystallization, ocean acidification, and ocean anoxia. In particular, the Permian/Triassic transition is marked by a prominent positive δ88/86Srsw-peak that reflects a significantly enhanced burial flux of Sr and carbonate, likely driven by bacterial sulfate reduction (BSR) and the related alkalinity production in deeper anoxic waters. We also argue that the residence time of Sr in the Phanerozoic ocean ranged from ∼1Myrs to ∼20Myrs

Use of correlation matrices in lattice quantum chromodynamics

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Physics, 2004.Includes bibliographical references (p. 117).This thesis explores the use of correlation matrices in analyzing Monte Carlo calculations from lattice quantum chromodynamics. Correlation matrices are a powerful tool for examining many problems in which significant correlations exist, and thus offer potential advantages for lattice QCD. Several models were used to study the relative advantages of correlated and uncorrelated analyses. However, when applied to actual lattice data at current statistics, the method appears to be undesirably biased.by David Lepzelter.S.B

Clustered Diffusion of Integrins

We discuss the diffusion of clusters of integrins (and other similar membrane proteins) on a cell membrane with a cortical cytoskeleton. We argue that protein clusters—in contrast with normal oligomers, which are forced to pass through cytoskeletal barriers all at once—should be treated essentially as many-legged random walkers that can pass through a cytoskeletal barrier by putting one leg at a time through the fence. We present the mathematics that should describe the phenomenon, which result in a two-parameter model of diffusion that should apply to any cluster size. We also perform and discuss numerical simulations of the effect in the erythrocyte model system

Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction

We develop a probabilistic method for analyzing global features of a cellular network under intrinsic statistical fluctuations, which is important when there are finite numbers of molecules. By making a self-consistent mean field approximation of splitting the variables in order to reduce the large number of degrees of freedom, which is reasonable for a not very strongly interacting network, we discovered that the underlying energy landscape of the mitogen-activated protein kinases (MAPKs) signal transduction network (with experimentally measured or inferred parameters such as chemical reaction rate coefficients in the network) is funneled toward a global minimum characterized by the nonequilibrium steady-state fixed point of the system at the end of the signal transduction process. For this system, we also show that the energy landscape is robust against intrinsic fluctuations and random perturbation to the inherent chemical reaction rates. The ratio of the slope versus the roughness of the energy landscape becomes a quantitative measure of robustness and stability of the network. Furthermore, we quantify the dissipation cost of this nonequilibrium system through entropy production, caused by the nonequilibrium flux in the system. We found that a lower dissipation cost corresponds to a more robust network. This least dissipation property might provide a design principle for robust and functional networks. Finally, we find the possibility of bistable and oscillatory-like solutions, which are important for cell fate decisions, upon perturbations. The method described here can be used in a variety of biological networks

Precision of Sensing Cell Length via Concentration Gradients

Unicellular organisms are typically found to have a characteristic cell size. To achieve a homeostatic distribution of cell sizes over many generations requires that cell length is actively sensed and regulated. However, the mechanisms by which cell size is controlled remain poorly understood. Recent experiments in fission yeast have shown that cell length is controlled in part by polar gradients of the protein Pom1 together with localized measurement of concentration at midcell. Dilution as the cell grows leads to a reduction in the midcell protein concentration, which lifts a block on mitosis. Here we analyze the precision of this mechanism for length sensing in the presence of inevitable intrinsic noise in the processes leading to formation and measurement of this gradient. We find that the use of concentration gradients allows for more robust length sensing than a comparable spatially uniform system, and allows for reliable length determination even if the average protein concentration throughout the cell remains constant as the cell grows. Optimal values for the gradient decay length and receptor dissociation constant emerge from maximizing sensitivity while minimizing the impact of density fluctuations