Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics.

RNA-binding proteins shape biology through their widespread functions in RNA biochemistry. Their function requires the recognition of specific RNA motifs for targeted binding. These RNA binding elements can be composed of both unmodified and chemically modified RNAs, of which over 170 chemical modifications have been identified in biology.

Differential Sources of Resistance from Against Three Races of pathovar (Brown, 1918) Morinière et al. 2020 Causing Bacterial Leaf Spot of Lettuce.

Bacterial leaf spot (BLS) of lettuce ( L.) is caused by the bacterium pv. which is hypothesized to have at least three races of the pathogen present in North America as defined by their differential resistance phenotypes in lettuce cultivars/accessions.

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published.

How to Sample Dozens of Substitutions per Site with λ Dynamics.

Alchemical free energy methods are useful in computer-aided drug design and computational protein design because they provide rigorous statistical mechanics-based estimates of free energy differences from molecular dynamics simulations. λ dynamics is a free energy method with the ability to characterize combinatorial chemical spaces spanning thousands of related systems within a single simulation, which gives it a distinct advantage over other alchemical free energy methods that are mostly limited to pairwise comparisons. Recently developed methods have improved the scalability of λ dynamics to perturbations at many sites; however, the size of chemical space that can be explored at each individual site has previously been limited to fewer than ten substituents.

Pooled DNA sequencing in hairy vetch ( Roth) reveals QTL for seed dormancy but not pod dehiscence.

Introduction: Hairy vetch () is a promising legume cover crop, but its use is limited by high rates of pod dehiscence and seed dormancy.

Methods: We used phenotypically contrasting pooled DNA samples (n=24 with 29-74 individuals per sample) from an ongoing cover crop breeding program across four environments (site-year combinations: Maryland 2020, Maryland 2022, Wisconsin 2021, Wisconsin 2022) to find genetic associations and genomic prediction accuracies for pod dehiscence and seed dormancy. We also combined pooled DNA sample genetic association results with the results of a prior genome-wide association study.

Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design.

Understanding natural protein evolution and designing novel proteins are motivating interest in development of high-throughput methods to explore large sequence spaces. In this work, we demonstrate the application of multisite λ dynamics (MSλD), a rigorous free energy simulation method, and chemical denaturation experiments to quantify evolutionary selection pressure from sequence-stability relationships and to address questions of design. This study examines a mesophilic phylogenetic clade of ribonuclease H (RNase H), furthering its extensive characterization in earlier studies, focusing on RNase H (ecRNH) and a more stable consensus sequence (AncCcons) differing at 15 positions.

Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling.

Relative binding free energy calculations have become an integral computational tool for lead optimization in structure-based drug design. Classical alchemical methods, including free energy perturbation or thermodynamic integration, compute relative free energy differences by transforming one molecule into another. However, these methods have high operational costs due to the need to perform many pairwise perturbations independently.

Genome-wide association mapping in hairy vetch () discovers a large effect locus controlling seed dormancy.

Hairy vetch ( Roth), a winter-hardy annual legume, is a promising cover crop. To fully leverage its potential, seed production and field performance of must be improved to facilitate producer adoption. Two classic domestication traits, seed dormancy (hard seed) and dehiscence (pod shatter), are selection targets in an ongoing breeding program.

Three cases of black pleural effusion.

Black pleural effusions (BPE) are rare, exudative pleural effusions that produce a black fluid on thoracentesis. While the name and definition of this pathology is undeniably simple, the etiologies, outcomes, and treatments for BPE are incredibly complex. Currently, BPE is not well-demonstrated in the literature.

A Systematic Review of Echocardiographic Parameters for the Screening of Pulmonary Hypertension: What Are the Odds?

Pulmonary hypertension (PH) is an insidious disease that often presents in late stages due to nonspecific signs and symptoms. Right heart catheterization (RHC) is the gold standard diagnostic test, and echocardiogram (ECHO) is the best screening tool. However, the strength of evidence and diagnostic utility of various echocardiographic parameters to screen for is not well elucidated.

Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization.

With the ability to sample combinations of alchemical perturbations at multiple sites off a small molecule core, multisite λ-dynamics (MSλD) has become an attractive alternative to conventional alchemical free energy methods for exploring large combinatorial chemical spaces. However, current software implementations dictate that combinatorial sampling with MSλD must be performed with a multiple topology model (MTM), which is nontrivial to create by hand, especially for a series of ligand analogues which may have diverse functional groups attached. This work introduces an automated workflow, referred to as , to assist in the creation of a MTM for use with MSλD.

COVID-19 Vaccine Provider Access and Vaccination Coverage Among Children Aged 5-11 Years - United States, November 2021-January 2022.

On October 29, 2021, the Pfizer-BioNTech pediatric COVID-19 vaccine received Emergency Use Authorization for children aged 5-11 years in the United States. For a successful immunization program, both access to and uptake of the vaccine are needed. Fifteen million doses were initially made available to pediatric providers to ensure the broadest possible access for the estimated 28 million eligible children aged 5-11 years, especially those in high social vulnerability index (SVI) communities.

Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods.

Alchemical free energy methods are playing a growing role in molecular design, both for computer-aided drug design of small molecules and for computational protein design. Multisite λ dynamics (MSλD) is a uniquely scalable alchemical free energy method that enables more efficient exploration of combinatorial alchemical spaces encountered in molecular design, but simulations have typically been limited to a few hundred ligands or sequences. Here, we focus on coupling between sites to enable scaling to larger alchemical spaces.

BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations.

There is an accelerating interest in practical applications of alchemical free energy methods to problems in protein design, constant pH simulations, and especially computer-aided drug design. In the present paper, we describe a basic lambda dynamics engine (BLaDE) that enables alchemical free energy simulations, including multisite λ dynamics (MSλD) simulations, on graphical processor units (GPUs). We find that BLaDE is 5 to 8 times faster than the current GPU implementation of MSλD-based free energy calculations in CHARMM.

Mapping and identification of genetic loci affecting earliness of bolting and flowering in lettuce.

Photoperiod and temperature conditions elicit different genetic regulation over lettuce bolting and flowering. This study identifies environment-specific QTLs and putative genes and provides information for genetic marker assay. Bolting, defined as stem elongation, marks the plant life cycle transition from vegetative to reproductive stage.

Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands.

In this work, the discrete λ variant of the Gibbs sampler-based λ-dynamics (-GSλD) method is developed to enable multiple functional group perturbations to be investigated at one or more sites of substitution off a common ligand core. The theoretical framework and special considerations for constructing discrete λ states for multisite -GSλD are presented. The precision and accuracy of the -GSλD method is evaluated with three test cases of increasing complexity.

A strategy for proline and glycine mutations to proteins with alchemical free energy calculations.

Computation of the thermodynamic consequences of protein mutations holds great promise in protein biophysics and design. Alchemical free energy methods can give improved estimates of mutational free energies, and are already widely used in calculations of relative and absolute binding free energies in small molecule design problems. In principle, alchemical methods can address any amino acid mutation with an appropriate alchemical pathway, but identifying a strategy that produces such a path for proline and glycine mutations is an ongoing challenge.

Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free-Energy Calculations Using Lambda Dynamics.

Accurate predictions of changes to protein-ligand binding affinity in response to chemical modifications are of utility in small-molecule lead optimization. Relative free-energy perturbation (FEP) approaches are one of the most widely utilized for this goal but involve significant computational cost, thus limiting their application to small sets of compounds. Lambda dynamics, also rigorously based on the principles of statistical mechanics, provides a more efficient alternative.

Genetics of Partial Resistance Against Race 2 in Wild and Cultivated Lettuce.

Lettuce () is one of the most economically important vegetables in the United States, with approximately 50% of the domestic production concentrated in the Salinas Valley of California. Verticillium wilt, caused by races 1 and 2 of the fungal pathogen , poses a major threat to lettuce production in this area. Although resistance governed by a single dominant gene against race 1 has previously been identified and is currently being incorporated into commercial cultivars, identification of resistance against race 2 has been challenging and no lines with complete resistance have been identified.

Evaluation of an Occupational Exercise Training Program for Firefighters: Mixed Methods Pilot Study.

Background: Occupational exercise training programs can improve overall health and fitness in firefighters, but evidence beyond clinical and performance outcomes is needed before fire departments invest in and successfully adopt health promotion programs.

Objective: This mixed methods pilot study sought to pair clinical and performance outcomes with participants' qualitative feedback (eg, participants' enjoyment, lifestyle behavior changes, and team structure) with the goal of informing recommendations for future programs.

Methods: Professional firefighters participated in a 14-week occupational exercise training program with assessments conducted pre- and posttraining.

Exploring pH Dependent Host/Guest Binding Affinities.

When the electrostatic environment surrounding binding partners changes between unbound and bound states, the net uptake or release of a proton is possible by either binding partner. This process is pH-dependent in that the free energy required to uptake or release the proton varies with pH. This pH-dependence is typically not considered in conventional free energy methods where the use of fixed protonation states is the norm.

Genome-wide association mapping reveals loci for shelf life and developmental rate of lettuce.

Two major QTL, one for shelf life that corresponds to qSL4 and one, qDEV7, for developmental rate, were identified. Associated markers will be useful in breeding for improved fresh-cut lettuce. Fresh-cut lettuce in packaged salad can have short shelf life, and visible deterioration may start within a week after processing.

Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1.

Alchemical free energy calculations have made a dramatic impact upon the field of structure-based drug design by allowing functional group modifications to be explored computationally prior to experimental synthesis and assay evaluation, thereby informing and directing synthetic strategies. In furthering the advancement of this area, a series of 21 β-secretase 1 (BACE1) inhibitors developed by Janssen Pharmaceuticals were examined to evaluate the ability to explore large substituent perturbations, some of which contain scaffold modifications, with multisite λ-dynamics (MSλD), an innovative alchemical free energy framework. Our findings indicate that MSλD is able to efficiently explore all structurally diverse ligand end-states within a MD simulation with a high degree of precision and with reduced computational costs compared to the widely used approach TI/MBAR.

The genetics of resistance to lettuce drop (Sclerotinia spp.) in lettuce in a recombinant inbred line population from Reine des Glaces × Eruption.

Two QTLs for resistance to lettuce drop, qLDR1.1 and qLDR5.1, were identified.

Harvest of Lettuce from Verticillium-Infested Fields Has Little Impact on Postharvest Quality.

Verticillium wilt of lettuce, caused by the soilborne pathogen Verticillium dahliae, poses a serious threat to the California lettuce industry. Knowledge of disease development and its impact on postharvest marketability would facilitate better management of the affected fields. This study investigated postharvest marketability of 22 lettuce varieties harvested from two Verticillium-infested commercial lettuce fields in Salinas and Watsonville, CA, in 2005 using a randomized complete block design.