Biology subjects

Chen, L. Y.

Publications and source records attributed to Chen, L. Y..

17 recordsLinked to original sources

bioRxiv2025

Solriamfetol enhances alertness and cognitive performance in mice

Solriamfetol [(R)-2-amino-3-phenylpropylcarbamate hydrochloride], a phenylalanine derivative initially developed as potential antidepressant, was shown by our group in 2009 to have potent, dose-dependent wake-promoting activity in mice. Solriamfetol (Sunosi(R)) is used since 2019 to counteract excessive daytime sleepiness (EDS) in patients with narcolepsy and obstructive sleep apnea (OSA). It has several advantages over other stimulants, notably that it is not associated with strong psychomotor activity, does not induce behavioral stereotypies and anxiety-related behaviors, in contrast to amphetamines and modafinil. Its mode-of-action remains incompletely solved. It was reported to act as dual dopamine-and-noradrenaline-reuptake-inhibitor (DNRI), and more recently, to have TAAR1 agonist activity. In our early mouse study, we showed that, at 150 mg/kg, Solriamfetol induces a state of wakefulness featuring a dramatic upregulation of EEG gamma activity, a cognitive biomarker, and the expression of genes implicated in neural plasticity, learning and memory. Besides being prescribed to treat EDS, central nervous system stimulants are commonly used as smart drugs to enhance cognition in normal individuals. Therefore, based on Solriamfetols ability to potently induce wakefulness, EEG and molecular markers of learning and memory, we aimed to determine whether it could improve the cognitive performance of wild-type mice. Because at doses of 50-150 mg/kg, Solriamfetol induced an alert waking state associated with low mobility, thus precluding behavioral testing, we used lower doses (1-3 mg/kg) to assess cognition in a battery of tests evaluating short- or long-term memory and spatial navigation. We found that compared to saline, Solriamfetol 3 mg/kg consistently improves sustained attention for a novel object, as well as spatial memory. Next, to determine the brain activity correlates of enhanced cognition, we performed EEG/EMG recording while the mice performed the novel object recognition (NOR) task. Power spectral density (PSD) analysis revealed that 3 mg/kg Solriamfetol reduced EEG delta (an index of sleepiness) during exposure to a novel context, and enhanced EEG fast-gamma (an index of mental concentration) during execution of the NOR task. Taken together, our data demonstrate that low-dose Solriamfetol improves memory and attentional performance in wild-type mice.

animal behavior and cognition↗

bioRxiv2024

The VGCC auxiliary subunit α2δ1 is an extracellular GluA1 interactor and regulates LTP, spatial memory, and seizure susceptibility

Activity-dependent synaptic accumulation of AMPA receptors (AMPARs) and subsequent long-term synaptic strengthening underlie different forms of learning and memory. The AMPAR subunit GluA1 amino-terminal domain is essential for synaptic docking of AMPAR during LTP, but the precise mechanisms involved are not fully understood. Using unbiased proteomics, we identified the epilepsy and intellectual disability-associated VGCC auxiliary subunit 2{delta}1 as a candidate extracellular AMPAR slot. Presynaptic 2{delta}1 deletion in CA3 affects synaptic AMPAR incorporation during long-term potentiation, but not basal synaptic transmission, at CA1 synapses. Consistently, mice lacking 2{delta}1 in CA3 display a specific impairment in CA1-dependent spatial memory, but not in memory tests involving other cortical regions. Decreased seizure susceptibility in mice lacking 2{delta}1 in CA3 suggests a regulation of circuit excitability by 2{delta}1/AMPAR interactions. Our study sheds light on the regulation of activity-dependent AMPAR trafficking, and highlights the synaptic organizing roles of 2{delta}1. Significance statementActivity-dependent accumulation of AMPA receptors (AMPARs) at excitatory synapses and subsequent synaptic strengthening underlies long-term potentiation (LTP), forms of learning and memory, and some epilepsies. The "slot model" posits that postsynaptic scaffolding contain "slots" for AMPAR complexes, and that increased synaptic activity augments the availability of slots to accommodate more receptors, thereby strengthening synapses and enabling LTP. The presence of the GluA1 AMPAR subunit amino-terminal domain (ATD) has recently emerged as an additional requirement for LTP. Here we identify the auxiliary voltage-gated calcium channel subunit 2{delta}1 as a GluA1 ATD interacting protein and provide evidence supporting a role for 2{delta}1 as an extracellular AMPAR slot regulating activity dependent synaptic AMPAR clustering, excitability, and cognitive function.

neuroscience↗

bioRxiv2022

Stress-induced plasticity of a novel CRH GABA projection disrupts reward behaviors

Disrupted operations of the reward circuit are thought to underlie major emotional disorders including depression and drug abuse1-3. These disorders commonly arise following early life stress4,5; however, how stress early in life enduringly impacts reward circuit functions to promote disease remains unclear. Here, we discover and characterize a novel stress-sensitive reward-circuit projection connecting the basolateral amygdala (BLA) and nucleus accumbens (NAc) that co-expresses GABA and the stress-reactive neuropeptide corticotropin-releasing hormone (CRH). We then identify a crucial role for this projection in executing the disrupted reward behaviors provoked by early-life adversity (ELA): Chemogenetic and optogenetic stimulations of the CRHGABA BLA[->]NAc projection in typically reared mice suppressed several reward seeking behaviors, recapitulating deficits resulting from ELA and demonstrating a key contribution of this pathway in the normal operations of the reward circuit. Next, inhibition of the CRHGABA BLA[->]NAc projection in adult mice that experienced ELA restored typical reward behaviors in these mice, and, in contrast, had little effect in typically reared mice, indicating a selective ELA-induced maladaptive plasticity of this reward-circuit projection. We discover a novel, stress-sensitive, reward inhibiting projection from the BLA[->]NAc with unique molecular features, which may provide targets for intervention in disabling mental illnesses.

neuroscience↗

bioRxiv2021

Aquaglyceroporin AQP7's affinity for its substrate glycerol

AQP7 is one of the four human aquaglyceroporins that facilitate glycerol transport across the cell membrane, a biophysical process that is essential in human physiology. Therefore, it is interesting to compute AQP7s affinity for its substrate (glycerol) with reasonable certainty to compare with the experimental data suggesting high affinity in contrast with most computational studies predicting low affinity. In this study aimed at computing the AQP7-glycerol affinity with high confidence, we implemented a direct computation of the affinity from unbiased equilibrium molecular dynamics (MD) simulations of three all-atom systems constituted with 0.16M, 4.32M, and 10.23M atoms, respectively. These three sets of simulations manifested a fundamental physics law that the intrinsic fluctuations of pressure in a system are inversely proportional to the system size (the number of atoms in it). These simulations showed that the computed values of glycerol-AQP7 affinity are dependent upon the system size (the inverse affinity estimations were, respectively, 47.3 mM, 1.6 mM, and 0.92 mM for the three model systems). In this, we obtained a lower bound for the AQP7-glycerol affinity (an upper bound for the dissociation constant). Namely, the AQP7-glycerol affinity is stronger than 1087/M (the dissociation constant is less than 0.92 mM). Additionally, we conducted hyper steered MD (hSMD) simulations to map out the Gibbs free-energy profile. From the free-energy profile, we produced an independent computation of the AQP7-glycerol dissociation constant being approximately 0.18 mM. Table of contents entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/469753v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@420c90org.highwire.dtl.DTLVardef@46d27borg.highwire.dtl.DTLVardef@1a4b269org.highwire.dtl.DTLVardef@1bd3979_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2021

Neurexins Regulate GABA Co-release by Dopamine Neurons

Midbrain dopamine (DA) neurons are key regulators of basal ganglia functions. The axonal domain of these neurons is highly complex, with a large subset of non-synaptic release sites and a smaller subset of synaptic terminals from which glutamate or GABA are released. The molecular mechanisms regulating the connectivity of DA neurons and their neurochemical identity are unknown. Here we tested the hypothesis that the trans-synaptic cell adhesion molecules neurexins (Nrxns) regulate DA neuron neurotransmission. Conditional deletion of all Nrxns in DA neurons (DAT::Nrxns KO) showed that loss of Nrxns does not impair the basic development and ultrastructural characteristics of DA neuron terminals. However, loss of Nrxns caused an impairment of DA transmission revealed as a reduced rate of DA reuptake following activity-dependent DA release, decreased DA transporter levels, increased vesicular monoamine transporter expression, and impaired amphetamine-induced locomotor activity. Strikingly, electrophysiological recording revealed an increase of GABA co-release from DA neuron axons in the striatum of the KO mice. These findings suggest that Nrxns act as key regulators of DA neuron connectivity and DA-mediated functions. HighlightsO_LIThe study provides the first direct evidence of the role of neurexins in dopaminergic neurons. C_LIO_LIThe synaptic adhesion molecules, neurexins, are not required for maintaining the structure of dopamine neuron terminals. C_LIO_LINeurexins regulate dopaminergic neurotransmission through regulation of dopamine reuptake, impacting amphetamine-induced locomotion. C_LIO_LIDeletion of Nrxns in DA neurons causes a region-specific increase of GABA release by DA neurons. C_LI

neuroscience↗

bioRxiv2020

Quantitative study of unsaturated transport of glycerol through aquaglyceroporin that has high affinity for glycerol

Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=37 SRC="FIGDIR/small/152512v1_ufig1.gif" ALT="Figure 1"> View larger version (9K): org.highwire.dtl.DTLVardef@19dcc7forg.highwire.dtl.DTLVardef@dce74dorg.highwire.dtl.DTLVardef@d599b4org.highwire.dtl.DTLVardef@15e24f5_HPS_FORMAT_FIGEXP M_FIG C_FIG ABSTRACTThe structures of several aquaglyceroporins have been resolved to atomic resolution showing two or more glycerols bound inside a channel and confirming a glycerol-facilitators affinity for its substrate glycerol. However, the kinetics data of glycerol transport experiments all point to unsaturated transport that is characteristic of low substrate affinity in terms of the Michaelis-Menten kinetics. In this article, we present an in silico-in vitro research focused on AQP3, one of the human aquaglyceroporins that is natively expressed in the abundantly available erythrocytes. We conducted 2.1 s in silico simulations of AQP3 embedded in a model erythrocyte membrane with intracellular-extracellular asymmetries in leaflet lipid compositions and compartment salt ions. From the equilibrium molecular dynamics (MD), we elucidated the mechanism of glycerol transport at high substrate concentrations. From the steered MD simulations, we computed the Gibbs free-energy profile throughout the AQP3 channel. From the free-energy profile, we quantified the kinetics of glycerol transport that is unsaturated due to glycerol-glycerol interaction mediated by AQP3 resulting in the concerted movement of two glycerol molecules for the transport of one glycerol molecule across the cell membrane. We conducted in vitro experiments on glycerol uptake into human erythrocytes for a wide range of substrate concentrations and various temperatures. The experimental data quantitatively validated our theoretical-computational conclusions on the unsaturated glycerol transport through AQP3 that has high affinity for glycerol.

biophysics↗

bioRxiv2020

In silico simulations of erythrocyte aquaporins with quantitative in vitro validation

Modelling water and membrane lipids is an essential element in the computational research of biophysical/biochemical processes such as water transport across the cell membrane. In this study, we examined the accuracies of two popular water models, TIP3P and TIP4P, in the molecular dynamics simulations of erythrocyte aquaporins (AQP1 and AQP3). We modelled the erythrocyte membrane as an asymmetric lipid bilayer with appropriate lipid compositions of its inner and outer leaflet, in comparison with a symmetric lipid bilayer of a single lipid type. We computed the AQP1/3 permeabilities with the transition state theory with full correction for recrossing events. We also conducted cell swelling assays for water transport across the erythrocyte membrane. The experimental results agree with the TIP3P water-erythrocyte membrane model, in confirmation of the expected accuracy of the erythrocyte membrane model, the TIP3P water model, and the CHARMM parameters for water-protein interactions.

biophysics↗

bioRxiv2019

Quantitative characterization of the path of glucose diffusion facilitated by human glucose transporter 1

Glucose transporter GLUT1 is ubiquitously expressed in the human body from the red cells to the blood-brain barrier to the skeletal muscles. It is physiologically relevant to understand how GLUT1 facilitates diffusion of glucose across the cell membrane. It is also pathologically relevant because GLUT1 deficiency causes neurological disorders and anemia and because GLUT1 overexpression fuels the abnormal growth of cancer cells. This article presents a quantitative investigation of GLUT1 based on all-atom molecular-dynamics (MD) simulations of the transporter embedded in lipid bilayers of asymmetric inner-and-outer-leaflet lipid compositions, subject to asymmetric intra-and-extra-cellular environments. This is in contrast with the current literature of MD studies that have not considered both of the aforementioned asymmetries of the cell membrane. The equilibrium (unbiased) dynamics of GLUT1 shows that it can facilitate glucose diffusion across the cell membrane without undergoing large-scale conformational motions. The Gibbs free-energy profile, which is still lacking in the current literature of GLUT1, quantitatively characterizes the diffusion path of glucose from the periplasm, through an extracellular gate of GLUT1, on to the binding site, and off to the cytoplasm. This transport mechanism is validated by the experimental data that GLUT1 has low water-permeability, uptake-efflux symmetry, and 10 kcal/mol Arrhenius activation barrier around 37{degrees}C. GRAPHICAL ABSTRACT (or TABLE OF CONTENTS ENTRY) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/787259v2_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@287ab0org.highwire.dtl.DTLVardef@18ecd68org.highwire.dtl.DTLVardef@4fa531org.highwire.dtl.DTLVardef@e63b4e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2019

Circulating electrolytes and the prevalence of atrial fibrillation and supraventricular ectopy: the Atherosclerosis Risk in Communities (ARIC) Study

BackgroundEvaluating associations of circulating electrolytes with atrial fibrillation (AF) and burden of supraventricular arrhythmias can give insights into arrhythmia pathogenesis.\n\nMethodsWe conducted a cross-sectional analysis of 6,398 participants of the Atherosclerosis Risk in Communities (ARIC) study, ages 71-90, with data on serum electrolytes (magnesium, calcium, potassium, phosphorus, chloride, sodium). Prevalence of AF was determined from study 12-lead electrocardiograms and prior history of AF-related hospitalizations. A subset of 317 participants also underwent electrocardiographic recordings for up to 14 days using the Zio(R) patch. Burden of other supraventricular arrhythmias [premature atrial contractions (PACs), supraventricular tachycardia] was determined with the Zio(R) patch. We used multivariable logistic and linear regression adjusting for potential confounders to determine associations of electrolytes with arrhythmia prevalence and burden.\n\nResultsAmong 6,394 eligible participants, 614 (10%) had prevalent AF. Participants in the top quintiles of magnesium [odds ratio (OR) 0.82, 95% confidence interval (CI) 0.62, 1.08], potassium (OR 0.82, 95%CI 0.68, 1.00), and phosphorus (OR 0.73, 95%CI 0.59, 0.89) had lower prevalence of AF compared to those in the bottom quintiles. No clear association was found for circulating chloride, calcium or sodium. Higher concentrations of circulating calcium were associated with lower prevalence of PACs using a standard 12-lead electrocardiogram, while higher concentrations of potassium, chloride and sodium were associated with higher PAC prevalence. Circulating electrolytes were not significantly associated with the burden of PACs or supraventricular tachycardia among a subset of 317 participants with extended electrocardiographic monitoring.\n\nConclusionConcentrations of circulating electrolytes present complex associations with selected supraventricular arrhythmias. Future studies should evaluate underlying mechanisms.

epidemiology↗

bioRxiv2019

Association and impact of hypertension defined using the 2017 AHA/ACC guidelines on the risk of atrial fibrillation in the Atherosclerosis Risk in Communities Study

Hypertension is an established risk factor for the development of atrial fibrillation (AF). We evaluated the association and population impact of hypertension, defined using the new 2017 guidelines, on risk of AF. In this analysis, we included 9,207 participants in the Atherosclerosis Risk in Communities study without history of cardiovascular disease or diabetes. Participants underwent blood pressure measurements at baseline and their antihypertensive medication use was assessed. AF was ascertained from study electrocardiograms, hospital records and death certificates. Cox proportional models were used to estimate hazard ratios (HR) and 95% confidence intervals (CI) of AF among individuals with hypertension based on the JNC7 and 2017 ACC/AHA guidelines. Poisson models were used to obtain risk ratios and calculate population-attributable fractions (PAFs). We identified 1,573 cases of incident AF during 22.1 years of mean follow-up. Prevalence of hypertension was 29% and 43% under the JNC7 and 2017 ACC/AHA definitions, respectively. HRs (95%CI) of AF in hypertensives versus non-hypertensives were 1.54 (1.39, 1.72) and 1.45 (1.31, 1.61) after multivariable adjustment under the old and new guidelines, respectively. The corresponding PAF (95%CI) using the old and new guidelines were 12% (9%, 14%) and 14% (10%, 18%), respectively. Overall, our analysis shows that even though the prevalence of hypertension using the new criteria is 50% higher than with the old criteria, this does not translate into meaningful increases in AF attributable to hypertension. These results suggest that prevention or treatment of hypertension based on the new (versus old) guidelines may have limited impact on AF incidence.

epidemiology↗

bioRxiv2019

Sex and racial differences in cardiovascular disease risk in patients with atrial fibrillation

BackgroundOutcomes among atrial fibrillation (AF) patients may differ according to race/ethnicity and sex due to differences in biology, the prevalence of cardiovascular risk factors, and the use and effectiveness of AF treatments. We aimed to characterize patterns of cardiovascular risk across subgroups of AF patients by sex and race/ethnicity, since doing so may provide opportunities to identify interventions. We also evaluated whether these patterns changed over time.\n\nMethodsWe utilized administrative claims data from the Optum Clinformatics(R) Datamart database from 2009 to 2015. Patients with AF with [≥]6 months of enrollment prior to the first non-valvular AF diagnosis were included in the analysis. Final analysis utilized Cox proportional hazard models to estimate adjusted hazard ratios (HR) and 95% confidence intervals (CI) for cardiovascular outcomes stratified by sex and race/ethnicity. An additional analysis stratified outcomes by calendar year of AF diagnosis to evaluate changes in outcomes over time.\n\nResultsIn a cohort of 380,636 AF patients, women had a higher risk of ischemic stroke [HR (95% CI):1.25 (1.19, 1.31)] and lower risk of heart failure and myocardial infarction [HR (95% CI): 0.91 (0.88, 0.94) and 0.81 (0.77, 0.86), respectively)] compared to men. Black patients had elevated risk across all endpoints compared to whites, while Hispanics and Asian Americans showed no significant differences in any outcome compared to white patients. These sex and race/ethnic differences did not change over time.\n\nConclusionsWe found sex and race/ethnic disparities in risk of cardiovascular outcomes among AF patients, without evidence of improvement over time.

epidemiology↗

bioRxiv2018

Plasma metabolomics and incidence of atrial fibrillation: the Atherosclerosis Risk in Communities (ARIC) Study

We have previously identified associations of two circulating secondary bile acids (glycocholenate and glycolithocolate sulfate) with atrial fibrillation (AF) risk among blacks. We aimed to replicate these findings in an independent sample including both whites and blacks, and performed a new metabolomic analysis in the combined sample. We studied 3,922 participants from the ARIC cohort followed between 1987 and 2013. Of these, 1,919 had been included in the prior analysis and 2,003 were new samples. Metabolomic profiling was done in baseline serum samples using gas and liquid chromatography mass spectrometry. AF was ascertained from electrocardiograms, hospitalizations, and death certificates. We used multivariable Cox regression to estimate hazard ratios (HR) and 95% confidence intervals (95%CI) of AF by one standard deviation difference of metabolite levels. Over a mean follow-up of 20 years, 608 participants developed AF. Glycocholenate sulfate was associated with AF in the replication and combined samples (HR 1.10, 95%CI 1.00, 1.21 and HR 1.13, 95%CI 1.04, 1.22, respectively). Glycolithocolate sulfate was not related to AF risk in the replication sample (HR 1.02, 95%CI 0.92, 1.13). An analysis of 245 metabolites in the combined cohort identified three additional metabolites associated with AF after multiple-comparison correction: pseudouridine (HR 1.18, 95%CI 1.10, 1.28), uridine (HR 0.86, 95%CI 0.79, 0.93) and acisoga (HR 1.17, 95%CI 1.09, 1.26). To conclude, we replicated a prospective association between a previously identified secondary bile acid, glycocholenate sulfate, and AF incidence, and identified new metabolites involved in nucleoside and polyamine metabolism as markers of AF risk.

epidemiology↗

bioRxiv2017

A Pilot Randomized Trial of Oral Magnesium Supplementation on Supraventricular Arrhythmias

BackgroundMagnesium is believed to have a physiologic role in cardiac contractility, and evidence from epidemiologic and clinical studies has suggested that low serum concentrations of magnesium may be associated with increased risk of atrial fibrillation (AF).\n\nObjectiveAs part of the planning effort for a large randomized trial to prevent AF with magnesium supplementation, we conducted a 12-week pilot study to assess adherence to oral magnesium supplementation and matching placebo, estimate the effect on circulating magnesium concentrations, and evaluate the feasibility of using an ambulatory monitoring device (ZioPatch) for assessing premature atrial contractions (PACs), a predictor of AF.\n\nDesignDouble-blind randomized pilot clinical trial comparing supplementation with 400 mg magnesium oxide daily (versus placebo) over 12 weeks of follow-up. The ZioPatch was applied for 14 days at baseline and the end of follow-up. Adherence to the assigned treatment, and changes in PACs, serum magnesium concentration, glucose and blood pressure were assessed.\n\nResultsA total of 59 participants, 73% women and average age 62 years, were randomized. 98% of participants completed follow-up. Those assigned to the magnesium supplement took 75% of tablets as compared to 83% for those in the placebo group. Change in magnesium concentrations was significantly greater for those given magnesium supplement compared to placebo (0.07; 95% confidence interval (CI): 0.03, 0.12 mEq/L; p = 0.002). ZioPatch was worn for an average of 13.0 of the requested 14 days at baseline; at the end of follow-up, the average number of days of monitoring was 13.0 days for the magnesium supplement group and 12.7 days for the placebo group. For log PAC burden (episodes per hour), the average change from baseline was -0.05 (95% CI: -0.31, 0.20) for those randomized to magnesium supplement and 0.04 (95% CI: -0.24, 0.31) for those randomized to placebo (p=0.79 for difference). Gastrointestinal problems were reported by 50% of participants in the magnesium supplement group and 7% in the placebo group. Only one person in the magnesium supplement group and none in the placebo group experienced adverse events which led to treatment discontinuation.\n\nConclusionsIn this pilot randomized clinic trial, although gastrointestinal side effects to the magnesium supplement were common, adherence, measured by pill counts, was very good and, as a consequence, magnesium concentrations were greater for those randomly assigned to the magnesium supplement compared to placebo. Participant acceptance of the planned monitoring with ZioPatch was also very good. While the difference in the change in PACs was not significant, this pilot study was small, short-term, and did not include participants at high risk of AF. Thus, we could not reliably evaluate the effect of magnesium supplementation on PACs.\n\nClinicaltrials.gov registrationNCT02837328

clinical trials↗

bioRxiv2017

Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions

Thermodynamic integration (TI), a powerful formalism for computing the Gibbs free energy, has been implemented for many biophysical processes characterized by one-dimensional order parameters with alchemical schemes that require delicate human efforts to choose/design biasing potentials for sampling the desired biophysical events and to remove their artifactitious consequences afterwards. Theoretically, an alchemical scheme is exact but practically, it causes error amplification. Small relative errors in the interaction parameters can be amplified many times in their propagation into the computed free energy [due to subtraction of similar numbers such as (105 {+/-} 5) - (100 {+/-} 5) = 5 {+/-} 7], which would render the results significantly less accurate than the input interaction parameters. In this paper, we present an unsophisticated implementation of TI in 3n dimensions (3nD) (n=1,2,3...) without alchemy or biasing potentials. In TI3nD, the errors in the interaction parameters will not be amplified and human efforts are not required to design biasing potentials that generate unphysical consequences. Using TI3nD, we computed the standard free energies of three protein complexes: trometamol in Salmonella effector SpvD (n=1), biotin in avidin (n=2), and Colicin E9 endonuclease with cognate immunity protein Im9 (n=3) and the hydration energies of ten biologically relevant compounds (n=1 for water, acetamide, urea, glycerol, trometamol, ammonium and n=2 for erythritol, 1,3-propanediol, xylitol, biotin). The computed results all agree with available experimental data. Each of the 13 computations is accomplishable within two (for a hydration problem) to ten (for the protein-recognition problem) days on an inexpensive workstation (two Xeon E5-2665 2.4GHz CPUs and one nVidia P5000 GPU).

biophysics↗

bioRxiv2017

Biologics-associated Risks for Incident Skin and Soft Tissue Infections in Psoriasis Patients: Results from Propensity Score-Stratified Survival Analysis

BackgroundHow biologics affect psoriasis patients risks for SSTIs in a pragmatic clinical setting remains unclear.\n\nMethodsIn a cohort of adult psoriasis outpatients (aged 20 years or older) who visited the Dermatology Clinic in 2010-2015, we compared incident SSTI risks between patients using biologics (users) versus nonbiologics (nonusers). We also estimated SSTI risks in biologics-associated time-periods relative to nonbiologics only in users. We applied random effects Cox proportional hazard models with propensity score-stratification to account for differential baseline hazards.\n\nResultsOver a median follow-up of 2.8 years (interquartile range: 1.5, 4.3), 172 of 922 patients ever received biologics (18.7%); 233 SSTI incidents occurred during 2518.3 person-years, with an overall incidence of 9.3/100 person-years (95% confidence interval [CI]: 8.1, 10.6). In univariate analysis, users showed an 89% lower risk for SSTIs than nonusers (hazard ratio [HR]: 0.11, 95%CI: 0.05, 0.26); the association persisted in a multivariable model (adjusted HR: 0.26, 95%CI: 0.12, 0.58). Among biologics users, biologics-exposed time-periods were associated with a nonsignificant 21% increased risk (adjusted HR: 1.21, 95%CI: 0.41, 3.59).\n\nConclusionsDespite of adjusting for the underlying risk profiles, risk comparisons between biologics users and nonusers remained confounded by treatment selection. By comparing time-periods being exposed versus unexposed to biologics among users, the current analysis did not find evidence for an increased SSTI risk that was associated with biologics use in psoriasis patients.

epidemiology↗

bioRxiv2017

Mupirocin-associated temporal changes in the nasal microbiota and host’s antimicrobial responses: A pilot study in healthy staphylococcal carriers

BackgroundHow mupirocin affects the human nasal microbiota over time remains uncharacterized.\n\nMethodsWe repeatedly sampled the anterior nares of four healthy staphylococcal carriers before and after mupirocin use. By sequencing bacterial 16S ribosomal cDNA, we characterized sequential changes in the carriage status, the nasal microbiota, and the hosts antimicrobial peptide expression up to 90 days after decolonization.\n\nResultsBefore mupirocin use, the nasal microbiota differed by the initial, culture-based staphylococcal carriage status, with Firmicutes (54.1%) being the most predominant in carriers and Proteobacteria (75.8%) in the only noncarrier. The nasal microbiota became less diverse (Shannon diversity: 1.33, 95% confidence interval [CI]: 1.06-1.54) immediately after decolonisation than that before decolonisation (1.78, 95%CI: 0.58-1.93). Based on results of differential abundance analysis, Firmicutes were significantly enriched (log2 fold changes [≥] 4, Benjamini-Hochberg adjusted P < .01) while Actinobacteria, particularly Corynbebacterium, were relatively depleted in samples from staphylococcal carriers. Results of nonmetric multidimensional scaling (NMDS) and constrained correspondence analysis (CCA) also suggested that the initial staphylococcal carriage status, human neutrophil peptide 1 levels, and sampling times were major contributors to the between-community dissimilarities (P for marginal permutation test: .014) though the significance attenuated when within-group correlation was considered (P for blocked permutation test: .047).\n\nConclusionThese findings suggest that large-scale investigations on antibiotic effects on the human nasal microbiota are warranted.

microbiology↗

bioRxiv2017

Computing Osmotic Permeabilities of Aquaporins AQP4, AQP5, and GlpF from Near-Equilibrium Simulations

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC=\"FIGDIR/small/102343_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@c57ff0org.highwire.dtl.DTLVardef@527a79org.highwire.dtl.DTLVardef@e6bde6org.highwire.dtl.DTLVardef@bd53cf_HPS_FORMAT_FIGEXP M_FIG C_FIG Measuring or computing the single-channel permeability of aquaporins/aquaglyceroporins (AQPs) has long been a challenge. The measured values scatter over an order of magnitude but the corresponding Arrhenius activation energies converge in the current literature. Osmotic flux through an AQP was simulated as water current forced through the channel by kilobar hydraulic pressure or theoretically approximated as single-file diffusion. In this paper, we report large scale simulations of osmotic current under sub M gradient through three water channels (the water-specific AQP4 and AQP5 along with aquaglyceroporin GlpF) using the mature particle mesh Ewald technique (PME) for which the established force fields have been optimized with known accuracy. These simulations were implemented with hybrid periodic boundary conditions devised to avoid the artifactitious mixing across the membrane in a regular PME simulation. The computed single-channel permeabilities at 5{degrees}C and 25{degrees}C are in agreement with recently refined experiments on GlpF. The Arrhenius activation energies extracted from our simulations for all the three AQPs agree with the in vitro measurements. The single-file diffusion approximations from our large-scale simulations are consistent with the current literature on smaller systems. From these unambiguous agreements among the in vitro and in silico studies, we observe the quantitative accuracy of the all-atom force fields of the current literature for water-channel biology. We also observe that AQP4, that is particularly rich in the central nervous system, is more efficient in water conduction and more temperature-sensitive than other water-specific channel proteins.

biophysics↗