Structural basis for activation of calcineurin by calmodulin

The highly conserved phosphatase calcineurin plays vital roles in numerous processes including T-cell activation, development and function of the central nervous system, and cardiac growth. It is activated by the calcium sensor calmodulin. Calmodulin binds to a regulatory domain within calcineurin, causing a conformational change that displaces an autoinhibitory domain from the active site, resulting in activation of the phosphatase. This is the same general mechanism by which calmodulin activates calmodulin-dependent protein kinases. Previously published data has hinted that the regulatory domain of calcineurin is intrinsically disordered. In this work we demonstrate that the regulatory domain is unstructured and that it folds upon binding calmodulin, ousting the autoinhibitory domain from the catalytic site. The regulatory domain is 95 residues long, with the autoinhibitory domain attached to its C-terminal end and the 24 residue calmodulin binding region towards the N-terminal end. This is unlike the calmodulin-dependent protein kinases which have calmodulin binding sites and autoinhibitory domains immediately adjacent in sequence. Our data demonstrate that not only does the calmodulin binding region fold, but that an ~25-30 residue region between it and the autoinhibitory domain also folds, resulting in over half of the regulatory domain adopting α-helical structure. This appears to be the first observation of calmodulin inducing folding of this scale outside of its binding site on a target protein

Graphical representation of the partition function for a 1-D delta-function Bose gas

One-dimensional repulsive delta-function bose system is studied. By only using the Bethe ansatz equation, n-particle partition functions are exactly calculated. From this expression for the n-particle partition function, the n-particle cluster integral is derived. The results completely agree with those of the thermal Bethe ansatz (TBA). This directly proves the validity of the TBA. The theory of partitions and graphs is used to simplify the discussion.Comment: 15 page

Structural Basis for Activation of Calcineurin by Calmodulin

The highly conserved phosphatase calcineurin (CaN) plays vital roles in numerous processes including T-cell activation, development and function of the central nervous system, and cardiac growth. It is activated by the calcium sensor calmodulin (CaM). CaM binds to a regulatory domain (RD) within CaN, causing a conformational change that displaces an autoinhibitory domain (AID) from the active site, resulting in activation of the phosphatase. This is the same general mechanism by which CaM activates CaM-dependent protein kinases. Previously published data have hinted that the RD of CaN is intrinsically disordered. In this work, we demonstrate that the RD is unstructured and that it folds upon binding CaM, ousting the AID from the catalytic site. The RD is 95 residues long, with the AID attached to its C-terminal end and the 24-residue CaM binding region toward the N-terminal end. This is unlike the CaM-dependent protein kinases that have CaM binding sites and AIDs immediately adjacent in sequence. Our data demonstrate that not only does the CaM binding region folds but also an ∼25- to 30-residue region between it and the AID folds, resulting in over half of the RD adopting α-helical structure. This appears to be the first observation of CaM inducing folding of this scale outside of its binding site on a target protein

Partisan Asymmetries in Online Political Activity

We examine partisan differences in the behavior, communication patterns and social interactions of more than 18,000 politically-active Twitter users to produce evidence that points to changing levels of partisan engagement with the American online political landscape. Analysis of a network defined by the communication activity of these users in proximity to the 2010 midterm congressional elections reveals a highly segregated, well clustered partisan community structure. Using cluster membership as a high-fidelity (87% accuracy) proxy for political affiliation, we characterize a wide range of differences in the behavior, communication and social connectivity of left- and right-leaning Twitter users. We find that in contrast to the online political dynamics of the 2008 campaign, right-leaning Twitter users exhibit greater levels of political activity, a more tightly interconnected social structure, and a communication network topology that facilitates the rapid and broad dissemination of political information.Comment: 17 pages, 10 figures, 6 table

Spontaneous symmetry breaking in the non-linear Schrodinger hierarchy with defect

We introduce and solve the one-dimensional quantum non-linear Schrodinger (NLS) equation for an N-component field defined on the real line with a defect sitting at the origin. The quantum solution is constructed using the quantum inverse scattering method based on the concept of Reflection-Transmission (RT) algebras recently introduced. The symmetry of the model is generated by the reflection and transmission defect generators defining a defect subalgebra. We classify all the corresponding reflection and transmission matrices. This provides the possible boundary conditions obeyed by the canonical field and we compute these boundary conditions explicitly. Finally, we exhibit a phenomenon of spontaneous symmetry breaking induced by the defect and identify the unbroken generators as well as the exact remaining symmetry.Comment: discussion on symmetry breaking has been improved and examples adde

The quantum non-linear Schrodinger model with point-like defect

We establish a family of point-like impurities which preserve the quantum integrability of the non-linear Schrodinger model in 1+1 space-time dimensions. We briefly describe the construction of the exact second quantized solution of this model in terms of an appropriate reflection-transmission algebra. The basic physical properties of the solution, including the space-time symmetry of the bulk scattering matrix, are also discussed.Comment: Comments on the integrability and the impurity free limit adde

Local correlations in a strongly interacting 1D Bose gas

We develop an analytical method for calculating local correlations in strongly interacting 1D Bose gases, based on the exactly solvable Lieb-Liniger model. The results are obtained at zero and finite temperatures. They describe the interaction-induced reduction of local many-body correlation functions and can be used for achieving and identifying the strong-coupling Tonks-Girardeau regime in experiments with cold Bose gases in the 1D regime.Comment: 8 pages, REVTeX4, published in the New Journal of Physic

Technical report: Modeling nitrate leaching risk from specialty crop fields during on-farm managed floodwater recharge in the Kings Groundwater Basin and the potential for its management

This project has focused on better understanding the potential impact of On-Farm Flood Capture and Recharge (OFFCR) on groundwater quality pertaining to salts and nitrate and on assessing potential management opportunities. To achieve these goals, we used a combination of field and modeling studies. For the field study, soil cores were taken to a depth of 30 feet in replicate across fields with three different specialty crops identified as important to the San Joaquin Valley (tomatoes, almonds, vineyards) and with potential suitability for OFFCR. A prime goal of the field study was to provide data for parameterizing two models developed to assess nitrate, salt and water transport through the vadose zone, prior to percolating into the groundwater aquifer. However, the field study also resulted in key findings that show its value as a stand-alone study: 1) Nitrate concentrations are highest in the upper vadose zone and affected by texture. Those effects are not evident in the deeper vadose zone. 2) Vadose zone nitrate concentrations are affected by the crop grown. These results suggest an opportunity for lower legacy mass transport for grapes and higher legacy mass transport for both tomatoes and almonds. 3) Variability in individual farmers’ past and present fertilizer and water management practices contributes to different legacy salt and nitrate loads in the vadose zone. Data from the field study and other related and concurrent OFFCR field efforts were used during model development. The overall modeling approach was designed to model nitrate and salt transport for lands under OFFCR operation for different crop types, vadose zone characteristics and groundwater characteristics. The defined goals of this design and modeling approach were to: 1) model nitrate and salt movement through the vadose zone and into groundwater; 2) test the model against scenarios that consider different recharge rates, cultural practices, soil types, and depths to groundwater, assessing the timing and magnitude of loading through the vadose zone and the effects on underlying groundwater; and 3) recommend management practices to mitigate potential groundwater impacts. To achieve these goals, two models were integrated to simulate nitrate and salt transport through the vadose zone to groundwater under different scenarios: a 1D Hydrus model and an analytical groundwater model (AGM)

Universal correlations of trapped one-dimensional impenetrable bosons

We calculate the asymptotic behaviour of the one body density matrix of one-dimensional impenetrable bosons in finite size geometries. Our approach is based on a modification of the Replica Method from the theory of disordered systems. We obtain explicit expressions for oscillating terms, similar to fermionic Friedel oscillations. These terms are universal and originate from the strong short-range correlations between bosons in one dimension.Comment: 18 pages, 3 figures. Published versio