Acute and chronic toxicity of cationic polyquaterniums of varying charge density and molecular weight to Daphnia magna and Ceriodaphnia dubia.

Cationic polymers have the unique ability to neutralize negative charge with practical applications in personal care products, such as shampoos, conditioners, contact lens solutions, and as flocculants in wastewater treatment processes. Cationic polymers are a diverse class of materials varying in structural composition, cationic charge density (CD), and molecular weight (MW). In this study, we investigated three classes of polyquaternium cationic polymers (PQ-6, PQ-10, PQ-16) of varying CD and MW to characterize their toxicity to aquatic invertebrates.

Divergent folding-mediated epistasis among unstable membrane protein variants.

Many membrane proteins are prone to misfolding, which compromises their functional expression at the plasma membrane. This is particularly true for the mammalian gonadotropin-releasing hormone receptor GPCRs (GnRHR). We recently demonstrated that evolutionary GnRHR modifications appear to have coincided with adaptive changes in cotranslational folding efficiency.

Modeling membrane geometries implicitly in Rosetta.

Interactions between membrane proteins (MPs) and lipid bilayers are critical for many cellular functions. In the Rosetta molecular modeling suite, the implicit membrane energy function is based on a "slab" model, which represent the membrane as a flat bilayer. However, in nature membranes often have a curvature that is important for function and/or stability.

Divergent Folding-Mediated Epistasis Among Unstable Membrane Protein Variants.

Many membrane proteins are prone to misfolding, which compromises their functional expression at the plasma membrane. This is particularly true for the mammalian gonadotropin-releasing hormone receptor GPCRs (GnRHR). We recently demonstrated that evolutionary GnRHR modifications appear to have coincided with adaptive changes in cotranslational folding efficiency.

Computational modeling and prediction of deletion mutants.

In-frame deletion mutations can result in disease. The impact of these mutations on protein structure and subsequent functional changes remain understudied, partially due to the lack of comprehensive datasets including a structural readout. In addition, the recent breakthrough in structure prediction through deep learning demands an update of computational deletion mutation prediction.

A novel task of canine olfaction for use in adult and senior pet dogs.

While much work has been done in the field of canine olfaction, there has been little exploration of hyposmia or anosmia. This is partly due to difficulties in reducing confounds like training history and environmental distraction. The current study describes a novel olfaction test using spontaneous search behavior in dogs to find a hidden food treat in a three-choice task with both light-phase and dark-phase conditions.

Relationship between engagement with the impossible task, cognitive testing, and cognitive questionnaires in a population of aging dogs.

Introduction: The aim of this study was to evaluate the engagement of aging dogs with a cognitively challenging and potentially frustrating task (the impossible task). Based on previous observations, we predicted that dogs showing signs of cognitive impairment in other cognitive tests and owner-completed questionnaires would show reduced engagement with the task.

Methods: In this task, dogs were shown a piece of food in a clear container that they could not open; time spent interacting with the container and the experimenter was measured.

Molecular basis for variations in the sensitivity of pathogenic rhodopsin variants to 9-cis-retinal.

Over 100 mutations in the rhodopsin gene have been linked to a spectrum of retinopathies that include retinitis pigmentosa and congenital stationary night blindness. Though most of these variants exhibit a loss of function, the molecular defects caused by these underlying mutations vary considerably. In this work, we utilize deep mutational scanning to quantitatively compare the plasma membrane expression of 123 known pathogenic rhodopsin variants in the presence and absence of the stabilizing cofactor 9-cis-retinal.

Towards generalizable predictions for G protein-coupled receptor variant expression.

Missense mutations that compromise the plasma membrane expression (PME) of integral membrane proteins are the root cause of numerous genetic diseases. Differentiation of this class of mutations from those that specifically modify the activity of the folded protein has proven useful for the development and targeting of precision therapeutics. Nevertheless, it remains challenging to predict the effects of mutations on the stability and/ or expression of membrane proteins.

Structural Comparative Modeling of Multi-Domain F508del CFTR.

Cystic fibrosis (CF) is a rare genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an epithelial anion channel expressed in several vital organs. Absence of functional CFTR results in imbalanced osmotic equilibrium and subsequent mucus build up in the lungs-which increases the risk of infection and eventually causes death. CFTR is an ATP-binding cassette (ABC) transporter family protein composed of two transmembrane domains (TMDs), two nucleotide binding domains (NBDs), and an unstructured regulatory domain.

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.

Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met.

Systematic profiling of temperature- and retinal-sensitive rhodopsin variants by deep mutational scanning.

Membrane protein variants with diminished conformational stability often exhibit enhanced cellular expression at reduced growth temperatures. The expression of "temperature-sensitive" variants is also typically sensitive to corrector molecules that bind and stabilize the native conformation. There are many examples of temperature-sensitive rhodopsin variants, the misfolding of which is associated with the molecular basis of retinitis pigmentosa.

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.

Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design. Constant improvements in performance within the Rosetta software suite for biomolecular modeling have given rise to a greater breadth of structure prediction, including docking and design application cases for antibody and antigen modeling. Here, we present an overview of current protocols for antibody and antigen modeling using Rosetta and exemplify those by detailed tutorials originally developed for a Rosetta workshop at Vanderbilt University.

A functional linear modeling approach to sleep-wake cycles in dogs.

The study of companion (pet) dogs is an area of great translational potential, as they share a risk for many conditions that afflict humans. Among these are conditions that affect sleep, including chronic pain and cognitive dysfunction. Significant advancements have occurred in the ability to study sleep in dogs, including development of non-invasive polysomnography; however, basic understanding of dog sleep patterns remains poorly characterized.

Allosteric mechanism for KCNE1 modulation of KCNQ1 potassium channel activation.

The function of the voltage-gated KCNQ1 potassium channel is regulated by co-assembly with KCNE auxiliary subunits. KCNQ1-KCNE1 channels generate the slow delayed rectifier current, I, which contributes to the repolarization phase of the cardiac action potential. A three amino acid motif (F57-T58-L59, FTL) in KCNE1 is essential for slow activation of KCNQ1-KCNE1 channels.

Probing biophysical sequence constraints within the transmembrane domains of rhodopsin by deep mutational scanning.

Membrane proteins must balance the sequence constraints associated with folding and function against the hydrophobicity required for solvation within the bilayer. We recently found the expression and maturation of rhodopsin are limited by the hydrophobicity of its seventh transmembrane domain (TM7), which contains polar residues that are essential for function. On the basis of these observations, we hypothesized that rhodopsin's expression should be less tolerant of mutations in TM7 relative to those within hydrophobic TM domains.

Upgraded molecular models of the human KCNQ1 potassium channel.

The voltage-gated potassium channel KCNQ1 (KV7.1) assembles with the KCNE1 accessory protein to generate the slow delayed rectifier current, IKS, which is critical for membrane repolarization as part of the cardiac action potential. Loss-of-function (LOF) mutations in KCNQ1 are the most common cause of congenital long QT syndrome (LQTS), type 1 LQTS, an inherited genetic predisposition to cardiac arrhythmia and sudden cardiac death.