Population-based analysis of POT1 variants in a cutaneous melanoma case-control cohort.

Pathogenic germline variants in the protection of telomeres 1 gene (POT1) have been associated with predisposition to a range of tumour types, including melanoma, glioma, leukaemia and cardiac angiosarcoma. We sequenced all coding exons of the POT1 gene in 2928 European-descent melanoma cases and 3298 controls, identifying 43 protein-changing genetic variants. We performed POT1-telomere binding assays for all missense and stop-gained variants, finding nine variants that impair or disrupt protein-telomere complex formation, and we further define the role of variants in the regulation of telomere length and complex formation through molecular dynamics simulations. We determine that POT1 coding variants are a minor contributor to melanoma burden in the general population, with only about 0.5% of melanoma cases carrying germline pathogenic variants in this gene, but should be screened in individuals with a strong family history of melanoma and/or multiple malignancies.

Metabolic Reprogramming in SARS-CoV-2 Infection Impacts the Outcome of COVID-19 Patients.

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection triggers inflammatory clinical stages that affect the outcome of patients with coronavirus disease 2019 (COVID-19). Disease severity may be associated with a metabolic imbalance related to amino acids, lipids, and energy-generating pathways. The aim of this study was to characterize the profile of amino acids and acylcarnitines in COVID-19 patients. A multicenter, cross-sectional study was carried out. A total of 453 individuals were classified by disease severity. Levels of 11 amino acids, 31 acylcarnitines, and succinylacetone in serum samples were analyzed by electrospray ionization-triple quadrupole tandem mass spectrometry. Different clusters were observed in partial least squares discriminant analysis, with phenylalanine, alanine, citrulline, proline, and succinylacetone providing the major contribution to the variability in each cluster (variable importance in the projection >1.5). In logistic models adjusted by age, sex, type 2 diabetes mellitus, hypertension, and nutritional status, phenylalanine was associated with critical outcomes (odds ratio=5.3 (95% CI 3.16-9.2) in the severe vs. critical model, with an area under the curve of 0.84 (95% CI 0.77-0.90). In conclusion the metabolic imbalance in COVID-19 patients might affect disease progression. This work shows an association of phenylalanine with critical outcomes in COVID-19 patients, highlighting phenylalanine as a potential metabolic biomarker of disease severity.

A Many-Body, Fully Polarizable Approach to QM/MM Simulations.

We present a new development in quantum mechanics/molecular mechanics (QM/MM) methods by replacing conventional MM models with data-driven many-body (MB) representations rigorously derived from high-level QM calculations. The new QM/MM approach builds on top of mutually polarizable QM/MM schemes developed for polarizable force fields with inducible dipoles and uses permutationally invariant polynomials to effectively account for quantum-mechanical contributions (e.g., exchange-repulsion and charge transfer and penetration) that are difficult to describe by classical expressions adopted by conventional MM models. Using the many-body MB-pol and MB-DFT potential energy functions for water, which include explicit two-body and three-body terms fitted to reproduce the corresponding CCSD(T) and PBE0 two-body and three-body energies for water, we demonstrate a smooth energetic transition as molecules are transferred between QM and MM regions, without the need of a transition layer. By effectively elevating the accuracy of both the MM region and the QM/MM interface to that of the QM region, the new QM/MB-MM approach achieves an accuracy comparable to that obtained with a fully QM treatment of the entire system.

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings.

In this work, we present a general route to hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Molecular Dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the AMOEBA polarizable force field to treat large (bio)systems where the QM and the MM subsystems are covalently bound, adopting pseudopotentials at the boundaries between the two regions. We discuss in detail the implementation and demonstrate the global energy conservation of our QM/MM Born-Oppenheimer molecular dynamics approach using Density Functional Theory. Finally, the approach is assessed on the electronic absorption properties of a 16 500 atom complex encompassing an organic dye embedded in a DNA matrix in solution, extending the hybrid method to a time-dependent Density Functional Theory approach. The results obtained comparing different partitions between the quantum and the classical subsystems also suggest that large QM portions are not necessary if accurate polarizable force fields are used in a variational formulation of the embedding, properly including the QM/MM mutual polarization.

ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding.

The search for prostate cancer biomarkers has received increased attention and several DNA repair related enzymes have been linked to this dysfunction. Here we report a targeted search for single nucleotide polymorphisms (SNPs) and functional impact characterization of human ALKBH family dioxygenases related to prostate cancer. Our results uncovered a SNP of ALKBH7, rs7540, which is associated with prostate cancer disease in a statistically significantly manner in two separate cohorts, and maintained in African American men. Comparisons of molecular dynamics (MD) simulations on the wild-type and variant protein structures indicate that the resulting alteration in the enzyme induces a significant structural change that reduces ALKBH7's ability to bind its cosubstrate. Experimental spectroscopy studies with purified proteins validate our MD predictions and corroborate the conclusion that this cancer-associated mutation affects productive cosubstrate binding in ALKBH7.

Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.

Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.

Pattern formation by two precipitated species during solvent evaporation.

We investigate the pattern formation produced by precipitated species during solvent evaporation through the numerical solution of a set of partial differential equations that account for the mechanisms of evaporation, diffusion, and precipitation. A pattern is formed because solvent evaporation provokes precipitation of species near the border of the system producing ringlike depositions from the edge to the center. Solvent evaporation is modeled as occurs with a liquid drop on a surface. The spacing between rings and its width are constant and roughly constant, respectively. Pattern formation follows the evaporation process inducing trends on pattern formation that are different to those produced by the precipitation of two species in a diffusive front (Liesegang rings). The spatial structure of rings under solvent evaporation is similar to those observed during solvent evaporation on two oppositely charged colloids and is attributable to the competition between precipitation and evaporation processes.

One-day quadruple therapy compared with 7-day triple therapy for Helicobacter pylori infection.

BACKGROUND: Eradication of Helicobacter pylori infection has had an impact on the treatment and recurrence rates of peptic ulcer disease and malignancies such as mucosa-associated lymphoid tissue lymphoma. Treatment options are cumbersome, expensive, and associated with side effects. METHODS: Randomized, prospective, open-labeled equivalence trial with a parallel-group design to compare eradication rates of H pylori with a 1-day, 4-drug regimen with a 7-day, 3-drug regimen. A total of 160 patients with dyspepsia and a Glasgow Dyspepsia Severity Score of at least 3 had a urea breath test labeled with carbon 14. Patients who tested positive were randomized to 1 of the 2 study groups. The study was designed to test the therapeutic equivalence of 1-day and 7-day regimens based on the percentage of H pylori eradication in each group at 5 weeks. RESULTS: The 1-day treatment group (n = 80) had a slightly higher eradication percentage (95%) than the 7-day group (90%). The possible inferiority of the 1-day treatment relative to the 7-day treatment, a 15% difference in the number of patients whose infection was not eradicated at 5 weeks, was rejected (P<.001; 90% confidence interval, 2.7%-11%). Both groups demonstrated a mean decrease of 7.5 points in the Glasgow Dyspepsia Severity Score. The 2 groups showed no significant differences in side effects. Patients whose treatment failed (4 in the 1-day treatment group and 7 in the 7-day treatment group) were re-treated for 10 days. One patient from the 7-day treatment group still tested positive after the second treatment. CONCLUSIONS: The 1-day treatment proved to be statistically similar to the 7-day treatment for the eradication of H pylori in patients with dyspepsia and a positive urea breath test. Further evaluation will be necessary to determine whether the 1-day regimen is adequate for patients with peptic ulcer disease, mucosa-associated lymphoid tissue lymphoma, or gastric adenocarcinoma.