748 research outputs found
Kinetics of Fast Changing Intramolecular Distance Distributions Obtained by Combined Analysis of FRET Efficiency Kinetics and Time-Resolved FRET Equilibrium Measurements
AbstractDetailed studies of the mechanisms of macromolecular conformational transitions such as protein folding are enhanced by analysis of changes of distributions for intramolecular distances during the transitions. Time-resolved Förster resonance energy transfer (FRET) measurements yield such data, but the more readily available kinetics of mean FRET efficiency changes cannot be analyzed in terms of changes in distances because of the sixth-power dependence on the mean distance. To enhance the information obtained from mean FRET efficiency kinetics, we combined the analyses of FRET efficiency kinetics and equilibrium trFRET experiments. The joint analysis enabled determination of transient distance distributions along the folding reaction both in cases where a two-state transition is valid and in some cases consisting of a three-state scenario. The procedure and its limits were tested by simulations. Experimental data obtained from stopped-flow measurements of the refolding of Escherichia coli adenylate kinase were analyzed. The distance distributions between three double-labeled mutants, in the collapsed transient state, were determined and compared to those obtained experimentally using the double-kinetics technique. The proposed method effectively provides information on distance distributions of kinetically accessed intermediates of fast conformational transitions induced by common relaxation methods
Quantitative Theory of a Relaxation Function in a Glass-Forming System
We present a quantitative theory for a relaxation function in a simple
glass-forming model (binary mixture of particles with different interaction
parameters). It is shown that the slowing down is caused by the competition
between locally favored regions (clusters) which are long lived but each of
which relaxes as a simple function of time. Without the clusters the relaxation
of the background is simply determined by one typical length which we deduce
from an elementary statistical mechanical argument. The total relaxation
function (which depends on time in a nontrivial manner) is quantitatively
determined as a weighted sum over the clusters and the background. The
`fragility' in this system can be understood quantitatively since it is
determined by the temperature dependence of the number fractions of the locally
favored regions.Comment: 4 pages, 5 figure
Tumour-derived leukaemia inhibitory factor is a major driver of cancer cachexia and morbidity in C26 tumour-bearing mice
BACKGROUND: Cancer cachexia is a metabolic wasting syndrome that is strongly associated with a poor prognosis. The initiating factors causing fat and muscle loss are largely unknown. Previously, we found that leukaemia inhibitory factor (LIF) secreted by C26 colon carcinoma cells was responsible for atrophy in treated myotubes. In the present study, we tested whether C26 tumourâderived LIF is required for cancer cachexia in mice by knockout of Lif in C26 cells.
METHODS: A C26 Lif null tumour cell line was made using CRISPRâCas9. Measurements of cachexia were compared in mice inoculated with C26 vs. C26^Lifâ/â tumour cells, and atrophy was compared in myotubes treated with medium from C26 vs. C26^Lifâ/â tumour cells. Levels of 25 cytokines/chemokines were compared in serum of mice bearing C26 vs. C26^Lifâ/â tumours and in the medium from these tumour cell lines.
RESULTS: At study endpoint, C26 mice showed outward signs of sickness while mice with C26^Lifâ/â tumours appeared healthy. Mice with C26^Lifâ/â tumours showed a 55â75% amelioration of body weight loss, muscle loss, fat loss, and splenomegaly compared with mice with C26 tumours (P < 0.05). The heart was not affected by LIF levels because the loss of cardiac mass was the same in C26 and C^26Lifâ/â tumourâbearing mice. LIF levels in mouse serum was entirely dependent on secretion from the tumour cells. Serum levels of interleukinâ6 and GâCSF were increased by 79âfold and 68âfold, respectively, in C26 mice but only by fiveâfold and twoâfold, respectively, in C26^Lifâ/â mice, suggesting that interleukinâ6 and GâCSF increases are dependent on tumourâderived LIF.
CONCLUSIONS: This study shows the first use of CRISPRâCas9 knockout of a candidate cachexia factor in tumour cells. The results provide direct evidence for LIF as a major cachexia initiating factor for the C26 tumour in vivo. Tumourâderived LIF was also a regulator of multiple cytokines in C26 tumour cells and in C26 tumourâbearing mice. The identification of tumourâderived factors such as LIF that initiate the cachectic process is immediately applicable to the development of therapeutics to treat cachexia. This is a proof of principle for studies that when carried out in human cells, will make possible an understanding of the factors causing cachexia in a patientâspecific manner.This work was supported by NIAMS R01AR060217 to S. C. K. and R. W. J. and NIAMS R01 R01AR060209 to A. R. J., and by the Dudley Allen Sargent Research Fund. The authors certify that they comply with the ethical guidelines for publishing in the Journal of Cachexia, Sarcopenia and Muscle: update 2017.40 (R01AR060217 - NIAMS; R01 R01AR060209 - NIAMS; Dudley Allen Sargent Research Fund)Published versio
Strain localization and anisotropic correlations in a mesoscopic model of amorphous plasticity
A mesoscopic model for shear plasticity of amorphous materials in two
dimensions is introduced, and studied through numerical simulations in order to
elucidate the macroscopic (large scale) mechanical behavior. Plastic
deformation is assumed to occur through a series of local reorganizations.
Using a discretization of the mechanical fields on a discrete lattice, local
reorganizations are modeled as local slip events. Local yield stresses are
randomly distributed in space and invariant in time. Each plastic slip event
induces a long-ranged elastic stress redistribution. Rate and thermal effects
are not discussed in the present study. Extremal dynamics allows for recovering
many of the complex features of amorphous plasticity observed experimentally
and in numerical atomistic simulations in the quasi-static regime. In
particular, a quantitative picture of localization, and of the anisotropic
strain correlation both in the initial transient regime, and in the steady
state are provided. In addition, the preparation of the amorphous sample is
shown to have a crucial effect of on the localization behavior
Managed Aquifer Recharge as a Tool to Enhance Sustainable Groundwater Management in California
A growing population and an increased demand for water resources have resulted in a global trend of groundwater depletion. Arid and semi-arid climates are particularly susceptible, often relying on groundwater to support large population centers or irrigated agriculture in the absence of sufficient surface water resources. In an effort to increase the security of groundwater resources, managed aquifer recharge (MAR) programs have been developed and implemented globally. MAR is the approach of intentionally harvesting and infiltrating water to recharge depleted aquifer storage. California is a prime example of this growing problem, with three cities that have over a million residents and an agricultural industry that was valued at 47 billion dollars in 2015. The present-day groundwater overdraft of over 100 km3 (since 1962) indicates a clear disparity between surface water supply and water demand within the state. In the face of groundwater overdraft and the anticipated effects of climate change, many new MAR projects are being constructed or investigated throughout California, adding to those that have existed for decades. Some common MAR types utilized in California include injection wells, infiltration basins (also known as spreading basins, percolation basins, or recharge basins), and low-impact development. An emerging MAR type that is actively being investigated is the winter flooding of agricultural fields using existing irrigation infrastructure and excess surface water resources, known as agricultural MAR. California therefore provides an excellent case study to look at the historical use and performance of MAR, ongoing and emerging challenges, novel MAR applications, and the potential for expansion of MAR. Effective MAR projects are an essential tool for increasing groundwater security, both in California and on a global scale. This chapter aims to provide an overview of the most common MAR types and applications within the State of California and neighboring semi-arid regions
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