Relative affinities of protein–cholesterol interactions from equilibrium molecular dynamics simulations

Specific interactions of lipids with membrane proteins contribute to protein stability and function. Multiple lipid interactions surrounding a membrane protein are often identified in molecular dynamics (MD) simulations and are, increasingly, resolved in cryo-electron microscopy (cryo-EM) densities. Determining the relative importance of specific interaction sites is aided by determination of lipid binding affinities using experimental or simulation methods. Here, we develop a method for determining protein–lipid binding affinities from equilibrium coarse-grained MD simulations using binding saturation curves, designed to mimic experimental protocols. We apply this method to directly obtain affinities for cholesterol binding to multiple sites on a range of membrane proteins and compare our results with free energies obtained from density-based equilibrium methods and with potential of mean force calculations, getting good agreement with respect to the ranking of affinities for different sites. Thus, our binding saturation method provides a robust, high-throughput alternative for determining the relative consequence of individual sites seen in, e.g., cryo-EM derived membrane protein structures surrounded by an array of ancillary lipid densities

Natural History of Very Early Onset Inflammatory Bowel Disease in North America: A Retrospective Cohort Study

Background: The incidence of very early onset inflammatory bowel disease (VEOIBD) is increasing, yet the phenotype and natural history of VEOIBD are not well described. Methods: We performed a retrospective cohort study of patients diagnosed with VEOIBD (6 years of age and younger) between 2008 and 2013 at 25 North American centers. Eligible patients at each center were randomly selected for chart review. We abstracted data at diagnosis and at 1, 3, and 5 years after diagnosis. We compared the clinical features and outcomes with VEOIBD diagnosed younger than 3 years of age with children diagnosed with VEOIBD at age 3 to 6 years. Results: The study population included 269 children (105 [39%] Crohn\u27s disease, 106 [39%] ulcerative colitis, and 58 [22%] IBD unclassified). The median age of diagnosis was 4.2 years (interquartile range 2.9-5.2). Most (94%) Crohn\u27s disease patients had inflammatory disease behavior (B1). Isolated colitis (L2) was the most common disease location (70% of children diagnosed younger than 3 years vs 43% of children diagnosed 3 years and older; P = 0.10). By the end of follow-up, stricturing/penetrating occurred in 7 (6.6%) children. The risk of any bowel surgery in Crohn\u27s disease was 3% by 1 year, 12% by 3 years, and 15% by 5 years and did not differ by age at diagnosis. Most ulcerative colitis patients had pancolitis (57% of children diagnosed younger than 3 years vs 45% of children diagnosed 3 years and older; P = 0.18). The risk of colectomy in ulcerative colitis/IBD unclassified was 0% by 1 year, 3% by 3 years, and 14% by 5 years and did not differ by age of diagnosis. Conclusions: Very early onset inflammatory bowel disease has a distinct phenotype with predominantly colonic involvement and infrequent stricturing/penetrating disease. The cumulative risk of bowel surgery in children with VEOIBD was approximately 14%-15% by 5 years. These data can be used to provide anticipatory guidance in this emerging patient population

High energy Yb:YAG active mirror laser system for transform limited pulses bridging the picosecond gap

A diode-pumped Yb:YAG MOPA-System for the unprecedented generation of transform limited pulses with variable pulse duration in the range between 10 ps and 100 ps is presented. First applications relying on unique pulse parameters as modulation free spectrum, tunability and coherence length, namely the direct laser interference patterning (DLIP) and laser cooling of stored relativistic ion beams are highlighted. Pulses are generated by a mode-locked fs-oscillator while the spectral bandwidth is narrowed in the subsequent regenerative amplifier by an intra-cavity grating monochromator. Two alternative booster amplifiers were added to increase the pulse energy to 100 μJ and 10 mJ, respectively

Wetting considerations in capillary rise and imbibition in closed square tubes and open rectangular cross-section channels

The spontaneous capillary-driven filling of microchannels is important for a wide range of applications. These channels are often rectangular in cross-section, can be closed or open, and horizontal or vertically orientated. In this work, we develop the theory for capillary imbibition and rise in channels of rectangular cross-section, taking into account rigidified and non-rigidified boundary conditions for the liquid–air interfaces and the effects of surface topography assuming Wenzel or Cassie-Baxter states. We provide simple interpolation formulae for the viscous friction associated with flow through rectangular cross-section channels as a function of aspect ratio. We derive a dimensionless cross-over time, Tc, below which the exact numerical solution can be approximated by the Bousanquet solution and above which by the visco-gravitational solution. For capillary rise heights significantly below the equilibrium height, this cross-over time is Tc ≈ (3Xe/2)^(2/3) and has an associated dimensionless cross-over rise height Xc ≈ (3Xe/2)^(1/3), where Xe = 1/G is the dimensionless equilibrium rise height and G is a dimensionless form of the acceleration due to gravity. We also show from wetting considerations that for rectangular channels, fingers of a wetting liquid can be expected to imbibe in advance of the main meniscus along the corners of the channel walls. We test the theory via capillary rise experiments using polydimethylsiloxane oils of viscosity 96.0, 48.0, 19.2 and 4.8 mPa s within a range of closed square tubes and open rectangular cross-section channels with SU-8 walls. We show that the capillary rise heights can be fitted using the exact numerical solution and that these are similar to fits using the analytical visco-gravitational solution. The viscous friction contribution was found to be slightly higher than predicted by theory assuming a non-rigidified liquid–air boundary, but far below that for a rigidified boundary, which was recently reported for imbibition into horizontally mounted open microchannels. In these experiments we also observed fingers of liquid spreading along the internal edges of the channels in advance of the main body of liquid consistent with wetting expectations. We briefly discuss the implications of these observations for the design of microfluidic systems

Natural History of Very Early Onset Inflammatory Bowel Disease in North America: A Retrospective Cohort Study

BACKGROUND: The incidence of very early onset inflammatory bowel disease (VEOIBD) is increasing, yet the phenotype and natural history of VEOIBD are not well described. METHODS: We performed a retrospective cohort study of patients diagnosed with VEOIBD (6 years of age and younger) between 2008 and 2013 at 25 North American centers. Eligible patients at each center were randomly selected for chart review. We abstracted data at diagnosis and at 1, 3, and 5 years after diagnosis. We compared the clinical features and outcomes with VEOIBD diagnosed younger than 3 years of age with children diagnosed with VEOIBD at age 3 to 6 years. RESULTS: The study population included 269 children (105 [39%] Crohn's disease, 106 [39%] ulcerative colitis, and 58 [22%] IBD unclassified). The median age of diagnosis was 4.2 years (interquartile range 2.9-5.2). Most (94%) Crohn's disease patients had inflammatory disease behavior (B1). Isolated colitis (L2) was the most common disease location (70% of children diagnosed younger than 3 years vs 43% of children diagnosed 3 years and older; P = 0.10). By the end of follow-up, stricturing/penetrating occurred in 7 (6.6%) children. The risk of any bowel surgery in Crohn's disease was 3% by 1 year, 12% by 3 years, and 15% by 5 years and did not differ by age at diagnosis. Most ulcerative colitis patients had pancolitis (57% of children diagnosed younger than 3 years vs 45% of children diagnosed 3 years and older; P = 0.18). The risk of colectomy in ulcerative colitis/IBD unclassified was 0% by 1 year, 3% by 3 years, and 14% by 5 years and did not differ by age of diagnosis. CONCLUSIONS: Very early onset inflammatory bowel disease has a distinct phenotype with predominantly colonic involvement and infrequent stricturing/penetrating disease. The cumulative risk of bowel surgery in children with VEOIBD was approximately 14%-15% by 5 years. These data can be used to provide anticipatory guidance in this emerging patient population