The influence of molecular reach and diffusivity on the efficacy of membrane-confined reactions

Signaling by surface receptors often relies on tethered reactions whereby an enzyme bound to the cytoplasmic tail of a receptor catalyzes reactions on substrates within reach. The overall length and stiffness of the receptor tail, the enzyme, and the substrate determine a biophysical parameter termed the molecular reach of the reaction. This parameter determines the probability that the receptor-tethered enzyme will contact the substrate in the volume proximal to the membrane when separated by different distances within the membrane plane. In this work, we develop particle-based stochastic reaction-diffusion models to study the interplay between molecular reach and diffusion. We find that increasing the molecular reach can increase reaction efficacy for slowly diffusing receptors, whereas for rapidly diffusing receptors, increasing molecular reach reduces reaction efficacy. In contrast, if reactions are forced to take place within the two-dimensional plasma membrane instead of the three-dimensional volume proximal to it or if molecules diffuse in three dimensions, increasing molecular reach increases reaction efficacy for all diffusivities. We show results in the context of immune checkpoint receptors (PD-1 dephosphorylating CD28), a standard opposing kinase-phosphatase reaction, and a minimal two-particle model. The work highlights the importance of the three-dimensional nature of many two-dimensional membrane-confined interactions, illustrating a role for molecular reach in control-ling biochemical reactions.Published versio

Biophysical assay for tethered signaling reactions reveals tether-controlled activity for the phosphatase SHP-1

Tethered enzymatic reactions are ubiquitous in signaling networks but are poorly understood. A previously unreported mathematical analysis is established for tethered signaling reactions in surface plasmon resonance (SPR). Applying the method to the phosphatase SHP-1 interacting with a phosphorylated tether corresponding to an immune receptor cytoplasmic tail provides five biophysical/biochemical constants from a single SPR experiment: two binding rates, two catalytic rates, and a reach parameter. Tether binding increases the activity of SHP-1 by 900-fold through a binding-induced allosteric activation (20-fold) and a more significant increase in local substrate concentration (45-fold). The reach parameter indicates that this local substrate concentration is exquisitely sensitive to receptor clustering. We further show that truncation of the tether leads not only to a lower reach but also to lower binding and catalysis. This work establishes a new framework for studying tethered signaling processes and highlights the tether as a control parameter in clustered receptor signaling

Lectin-mediated bacterial modulation by the intestinal nematode Ascaris suum

Ascariasis is a global health problem for humans and animals. Adult Ascaris nematodes are long-lived in the host intestine where they interact with host cells as well as members of the microbiota resulting in chronic infections. Nematode interactions with host cells and the microbial environment are prominently mediated by parasite-secreted proteins and peptides possessing immunomodulatory and antimicrobial activities. Previously, we discovered the C-type lectin protein AsCTL-42 in the secreted products of adult Ascaris worms. Here we tested recombinant AsCTL-42 for its ability to interact with bacterial and host cells. We found that AsCTL-42 lacks bactericidal activity but neutralized bacterial cells without killing them. Treatment of bacterial cells with AsCTL-42 reduced invasion of intestinal epithelial cells by Salmonella. Furthermore, AsCTL-42 interacted with host myeloid C-type lectin receptors. Thus, AsCTL-42 is a parasite protein involved in the triad relationship between Ascaris, host cells, and the microbiota

SUPPLEMENTARY TECHNICAL BASIS FOR ASME SECTION XI CODE CASE N-597-2

ABSTRACT Section XI of the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code provides rules and requirements for maintaining pressure boundary integrity of components, piping, and equipment during the life of a nuclear power plant. Code Case N-597-2 of Section XI, Requirements for Analytical Evaluation of Pipe Wall Thinning, provides evaluation procedures and acceptance criteria to justify continued operation of Class 1, 2 and 3 piping items subjected to wall thinning by a mechanism such as flow-accelerated corrosion. The acceptance criteria ensure that margins equivalent to those of the ASME B&PV Code are maintained. The technical basis for Code Case N-597-2 was previously presented at the 1999 ASME Pressure Vessels and Piping Conference. Since then, the ASME Section XI Working Group on Pipe Flaw Evaluation has identified the need for further explanation of the technical basis for the Code Case, such as the procedures for evaluation of wall thickness less than the Construction Code Design Pressure-based minimum allowable wall thickness, t min . This paper provides an additional description of the Code Case technical basis and validation against experimental and historic wall thinning events. NOMENCLATURE a = depth of an axial flaw A = reinforcement area required for a Class 1 pipe under internal pressure in accordance with rules in Section III of the ASME B&PV Code A i = predicted inside area of the cross-section of the pipe A o = total cross-sectional area of the pipe based on nominal outside diameter A p = predicted metal cross-sectional area of the pipe A rein = reinforcement area required for a Class 2 or 3 pipe under internal pressure in accordance with rules in Section III of the ASME B&PV Code B = parameter used to calculate maximum allowable length of an axial flaw in ANSI/ASME B31G d = distance from the center of a local thinned area defining the limits of reinforcement for Class 2 and 3 piping in accordance with the Construction Code D o = nominal outside diameter of the piping item f = stress range reduction factor for cyclic conditions for Class 2 and 3 piping i = stress intensification factor for Class 2 and 3 piping i 0 = stress intensification factor based on the design-basis geometry of the piping item k = constant used to describe the assumed linear increase in stress intensification factor i L = maximum extent of a local thinned area with t p < t nom L A = distance used to define limits of reinforcement for Class 1 piping in accordance with rules in Section III of the ASME B&PV Code L ax = maximum allowable length of an axial flaw from ANSI/ASME B31G L m = maximum extent of a local thinned area with t p < t min L m(a) = axial extent of a local thinned area with t p < t min L m(t) = transverse (circumferential) extent of a local thinned area with t p < t min M b = bending moment n = number of load cycles N = number of allowable load cycles N' = number of allowable load cycles corresponding to an assumed linear increase in stress intensification factor i N 0 = number of allowable load cycles based on the as-installed geometry of the piping item P = Design Pressure R = mean radius of the piping item based on nominal outside radius and nominal wall thickness R min = mean radius of the piping item based on nominal outside radius and t min s = stress range due to cyclic loading s 0 = stress range due to cyclic loading based on the design basis geometry of the piping item 1 Copyright © 2006 by ASME = predicted distribution of wall thickness at the end of the evaluation period t p,min = minimum predicted wall thickness at the end of the evaluation period y = factor required by the applicable piping Construction Code in the calculation of t min , and is equal to 0.4 Z min = predicted minimum section modulus of the thinned section of pipe δ = nominal distance between the center of the pipe and the neutral axis of the thinned pipe section σ

A Fast Scan Submillimeter Spectroscopic Technique

A new fast scan submillimeter spectroscopic technique (FASSST) has been developed which uses a voltage tunable backward wave oscillator (BWO) as a primary source of radiation, but which uses fast scan (~105 Doppler limited resolution elements/s) and optical calibration methods rather than the more traditional phase or frequency lock techniques. Among its attributes are (1) absolute frequency calibration to ~1/10 of a Doppler limited gaseous absorption linewidth (\u3c0.1 MHz, 0.000 003 cm-1), (2) high sensitivity, and (3) the ability to measure many thousands of lines/s. Key elements which make this system possible include the excellent short term spectral purity of the broadly (~100 GHz) tunable BWO; a very low noise, rapidly scannable high voltage power supply; fast data acquisition; and software capable of automated calibration and spectral line measurement. In addition to the unique spectroscopic power of the FASSST system, its implementation is simple enough that it has the prospect of impacting a wide range of scientific problems

Drivers of phytoplankton responses to summer wind events in a stratified lake: A modeling study

Extreme wind events affect lake phytoplankton by deepening the mixed layer and increasing internal nutrient loading. Both increases and decreases in phytoplankton concentration after strong wind events have been observed, but the precise mechanisms driving these responses remain poorly understood or quantified. We coupled a one-dimensional physical model to a biogeochemical model to investigate the factors regulating short-term phytoplankton responses to summer wind events, now and under expected warmer future conditions. We simulated physical, chemical, and biological dynamics in Lake Erken, Sweden, and found that strong wind could increase or decrease the phytoplankton concentration in the euphotic zone 1 week after the event, depending on antecedent lake physical and chemical conditions. Wind had little effect on phytoplankton concentration if the mixed layer was deep prior to wind exposure. Higher incoming shortwave radiation and hypolimnetic nutrient concentration boosted phytoplankton concentration, whereas higher surface water temperatures decreased concentrations after wind events. Medium-intensity wind events resulted in more phytoplankton than high-intensity wind. Simulations under a future climate scenario did not show marked differences in the way wind events affect phytoplankton concentration. These findings help to better understand how wind impacts vary as a function of local environmental conditions and how climate warming and changing extreme weather dynamics will affect lake ecosystems

Performance of one-dimensional hydrodynamic lake models during short-term extreme weather events

Numerical lake models are useful tools to study hydrodynamics in lakes, and are increasingly applied to extreme weather events. However, little is known about the accuracy of such models during these short-term events. We used high-frequency data from three lakes to test the performance of three one-dimensional (1D) hydrodynamic models (Simstrat, GOTM, GLM) during storms and heatwaves. Models reproduced the overall direction and magnitude of changes during the extreme events, with accurate timing and little bias. Changes in volume-averaged and surface temperatures and Schmidt stability were simulated more accurately than changes in bottom temperature, maximum buoyancy frequency, or mixed layer depth. However, in most cases the model error was higher (30-100%) during extreme events compared to reference periods. As a consequence, while 1D lake models can be used to study effects of extreme weather events, the increased uncertainty in the simulations should be taken into account when interpreting results

Drivers of phytoplankton responses to summer wind events in a stratified lake: A modeling study

Extreme wind events affect lake phytoplankton by deepening the mixed layer and increasing internal nutrient loading. Both increases and decreases in phytoplankton concentration after strong wind events have been observed, but the precise mechanisms driving these responses remain poorly understood or quantified. We coupled a one-dimensional physical model to a biogeochemical model to investigate the factors regulating short-term phytoplankton responses to summer wind events, now and under expected warmer future conditions. We simulated physical, chemical, and biological dynamics in Lake Erken, Sweden, and found that strong wind could increase or decrease the phytoplankton concentration in the euphotic zone 1 week after the event, depending on antecedent lake physical and chemical conditions. Wind had little effect on phytoplankton concentration if the mixed layer was deep prior to wind exposure. Higher incoming shortwave radiation and hypolimnetic nutrient concentration boosted phytoplankton concentration, whereas higher surface water temperatures decreased concentrations after wind events. Medium-intensity wind events resulted in more phytoplankton than high-intensity wind. Simulations under a future climate scenario did not show marked differences in the way wind events affect phytoplankton concentration. These findings help to better understand how wind impacts vary as a function of local environmental conditions and how climate warming and changing extreme weather dynamics will affect lake ecosystems