Publications by authors named "Crain J"

Mechanisms of anion permeation within ion channels and nanopores remain poorly understood. Recent cryo-electron microscopy structures of the human bestrophin 1 Cl channel (hBest1) provide an opportunity to evaluate ion interactions predicted by molecular dynamics (MD) simulations against experimental observations. Here, we implement the fully polarizable force field AMOEBA in MD simulations on different conformations of hBest1.

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Invasive meningococcal disease (IMD) is a severe illness that can have devastating effects; outbreaks are uncommon in the United States. Vaccination is the preferred control measure for IMD outbreaks when a defined population at risk (e.g.

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a nonlinear peptide topology for the assembly of synthetic virions is reported. The topology is a backbone cyclized amino-acid sequence in which polar l- and hydrophobic d-amino acid residues of the same-type alternate. This arrangement introduces pseudo symmetries of side chains within the same cyclopeptide ring, allowing for the lateral propagation of cyclopeptides into networks with a [3/6, 4]-fold rotational symmetry closing into virus-like shells.

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Nuclear quantum effects such as zero-point energy and hydrogen tunneling play a central role in many biological and chemical processes. The nuclear-electronic orbital (NEO) approach captures these effects by treating selected nuclei quantum mechanically on the same footing as electrons. On classical computers, the resources required for an exact solution of NEO-based models grow exponentially with system size.

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Mechanisms of anion permeation within ion channels and nanopores remain poorly understood. Recent cryo-electron microscopy structures of the human bestrophin 1 Cl- channel (hBest1) provide an opportunity to evaluate ion interactions predicted by molecular dynamics (MD) simulations against experimental observations. Here, we implement the fully polarizable forcefield AMOEBA in MD simulations on different conformations of hBest1.

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Intermediate wheatgrass (IWG, [Host] Barkworth & D. R. Dewey) has been developed as a perennial grain crop to provide ecosystem services, environmental benefits, and human food.

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Article Synopsis
  • COVID-19 transmission has been influenced by new variants, particularly Omicron BA.1 and BA.2, which show higher transmissivity and severity compared to the original strain.
  • Molecular dynamics simulations reveal that glycan interactions at the receptor binding domain (RBD) of the spike protein and the human ACE2 receptor are crucial for enhanced binding in these variants.
  • Structural differences between the Omicron subvariants BA.1 and BA.2 indicate that while both have similar charges, BA.2 exhibits more flexibility, allowing for additional binding interactions with ACE2 that are not seen in BA.1.
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Coupled quantum electron-nuclear dynamics is often associated with the Born-Huang expansion of the molecular wave function and the appearance of nonadiabatic effects as a perturbation. On the other hand, native multicomponent representations of electrons and nuclei also exist, which do not rely on any a priori approximation. However, their implementation is hampered by prohibitive scaling.

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Inhibitor discovery for emerging drug-target proteins is challenging, especially when target structure or active molecules are unknown. Here, we experimentally validate the broad utility of a deep generative framework trained at-scale on protein sequences, small molecules, and their mutual interactions-unbiased toward any specific target. We performed a protein sequence-conditioned sampling on the generative foundation model to design small-molecule inhibitors for two dissimilar targets: the spike protein receptor-binding domain (RBD) and the main protease from SARS-CoV-2.

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Perennial grains have potential to contribute to ecological intensification of food production by enabling the direct harvest of human-edible crops without requiring annual cycles of disturbance and replanting. Studies of prototype perennial grains and other herbaceous perennials point to the ability of agroecosystems including these crops to protect water quality, enhance wildlife habitat, build soil quality, and sequester soil carbon. However, genetic improvement of perennial grain candidates has been hindered by limited investment due to uncertainty about whether the approach is viable.

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  • ACL tears are common injuries in NFL players, with a long recovery time and often associated with other injuries detected through MRI.
  • A study reviewed 191 MRI scans of ACL injuries between 2015-2019, finding that 94.8% had bone bruises, 89% had additional knee injuries (including meniscal tears in 70% of cases), and 71% showed other ligament damage.
  • Most ACL injuries in this study were non-contact (79%), but contact injuries were more likely to involve concurrent injuries like MCL tears.
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Nuclear quantum phenomena beyond the Born-Oppenheimer approximation are known to play an important role in a growing number of chemical and biological processes. While there exists no unique consensus on a rigorous and efficient implementation of coupled electron-nuclear quantum dynamics, it is recognized that these problems scale exponentially with system size on classical processors and, therefore, may benefit from quantum computing implementations. Here, we introduce a methodology for the efficient quantum treatment of the electron-nuclear problem on near-term quantum computers, based upon the Nuclear-Electronic Orbital (NEO) approach.

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  • The study investigates how chloride ions interact with a rhodopsin protein using different molecular dynamics simulations to understand the role of electronic polarization in binding.
  • It compares three force fields: a fixed-charge force field that doesn't account for polarization, one that includes polarization implicitly, and one that includes it explicitly.
  • Findings suggest that incorporating polarization leads to stronger ion binding, longer binding durations, and a second binding site, highlighting its significance in understanding anion behavior in protein interactions.
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, and are important conifer species native to Mediterranean regions that are cultivated in the southwestern United States for landscaping (Phillips and Gladfelter, 1991; Chambel et al., 2013). Among them, Monterey pine () is native to restricted areas of California and Mexico, but it is extensively grown for timber production in other countries, especially in the Southern Hemisphere (Rogers, 2004).

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The development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples.

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Monkeypox is a viral zoonotic disease endemic in Central and West Africa. In May 2022, dozens of non-endemic countries reported hundreds of monkeypox cases, most with no epidemiological link to Africa. We identified two lineages of monkeypox virus (MPXV) among two 2021 and seven 2022 US monkeypox cases: the major 2022 outbreak variant called B.

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  • An injury prevention program called Prep-to-Play was developed for women's Australian Football to reduce ACL injuries and concussions, involving input from players, coaches, and the Australian Football League.
  • The study will involve over 140 teams in a cluster randomised controlled trial, where teams will start in a control group and gradually transition to the Prep-to-Play intervention with support from physiotherapists.
  • The main goal is to measure how well teams use the program and to track any changes in injury rates during the 2021 and 2022 seasons.
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Effective native plant materials are critical to restoring the structure and function of extensively modified ecosystems, such as the sagebrush steppe of North America's Intermountain West. The reestablishment of native bunchgrasses, e.g.

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Analysis of multi-year breeding program data revealed that the genetic architecture of an intermediate wheatgrass population was highly polygenic for both domestication and agronomic traits, supporting the use of genomic selection for new crop domestication. Perennial grains have the potential to provide food for humans and decrease the negative impacts of annual agriculture. Intermediate wheatgrass (IWG, Thinopyrum intermedium, Kernza®) is a promising perennial grain candidate that The Land Institute has been breeding since 2003.

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Interactions between ions and water at hydrophobic interfaces within ion channels and nanopores are suggested to play a key role in the movement of ions across biological membranes. Previous molecular-dynamics simulations have shown that anion affinity for aqueous/hydrophobic interfaces can be markedly influenced by including polarization effects through an electronic continuum correction. Here, we designed a model biomimetic nanopore to imitate the polar pore openings and hydrophobic gating regions found in pentameric ligand-gated ion channels.

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Barley yellow dwarf is one of the major viral diseases of cereals. Phenotyping barley yellow dwarf in wheat is extremely challenging due to similarities to other biotic and abiotic stresses. Breeding for resistance is additionally challenging as the wheat primary germplasm pool lacks genetic resistance, with most of the few resistance genes named to date originating from a wild relative species.

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Point-of-care testing (POCT) is an emerging technology that provides crucial assistance in delivering healthcare. The COVID-19 pandemic led to the accelerated importance of POCT technology due to its in-home accessibility. While POCT use and implementation has increased, little research has been published about how healthcare professionals perceive these technologies.

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The skin-associated microbiome plays an important role in general well-being and in a variety of treatable skin conditions. In this regard, endogenous antimicrobial peptides have both a direct and indirect role in determining the composition of the microbiota. We demonstrate here that certain small molecular species can amplify the antimicrobial potency of naturally occurring antimicrobial peptides.

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The prevalence of inflammatory bowel diseases (IBD), Crohn's disease and ulcerative colitis, in Canada, is over 0.75% in 2021. Many individuals with IBD are immunocompromised.

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