Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome.

Dolosigranulum pigrum-a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the design and validation of a novel PCR assay targeting D. pigrum that is both sensitive and specific. We designed a PCR assay targeting murJ, a single-copy core species gene identified through the analysis of 21 D. pigrum whole genome sequences. The assay achieved 100% sensitivity and 100% specificity against D. pigrum and diverse bacterial isolates and an overall 91.1% sensitivity and 100% specificity using nasal swabs, detecting D. pigrum at a threshold of 1.0 × 104 D. pigrum 16S rRNA gene copies per swab. This assay adds a reliable and rapid D. pigrum detection tool to the microbiome researcher toolkit investigating the role of generalist and specialist bacteria in the nasal environment.

A High-Fidelity Percutaneous Model Used to Demonstrate ECMO Cannulation.

Medical simulation provides a realistic environment for practitioners to experience a planned clinical event in a controlled educational setting. We established a simulation model composed of synthetic ballistic gelatin that provided an inexpensive high-fidelity model for our extracorporeal membrane oxygenation (ECMO) team members to develop, master, and maintain clinical skills necessary for percutaneous cervical or femoral cannulation. The simulation component includes a cervical torso or femoral percutaneous synthetic gelatin model that is attached to either a static fluid model or to the high-fidelity perfusion simulator. Either model can be accessed with ultrasound guidance, cannulated with appropriately sized cannula, and connected to an in situ ECMO circuit. This article explains how the model is made and connected to the simulator with the purpose of re-creating this high-fidelity experience at any institution.

Structural analysis of α-fetoprotein (AFP)-like peptides with anti-breast-cancer properties.

The abundance of α-fetoprotein (AFP), a natural protein produced by the fetal yolk sac during pregnancy, correlates with lower incidence of estrogen receptor positive (ER+) breast cancer. The pharmacophore region of AFP has been narrowed down to a four amino acid (AA) region in the third domain of the 591 AA peptide. Our computational study focuses on a 4-mer segment consisting of the amino acids threonine-proline-valine-asparagine (TPVN). We have run replica exchange molecular dynamics (REMD) simulations and used 120 configurational snapshots from the total trajectory as starting configurations for quantum chemical calculations. We optimized structures using semiempirical (PM3, PM6, PM6-D2, PM6-H2, PM6-DH+, PM6-DH2) and density functional methods (TPSS, PBE0, M06-2X). By comparing the accuracy of these methods against RI-MP2 benchmarks, we devised a protocol for calculating the lowest energy conformers of these peptides accurately and efficiently. This protocol screens out high-energy conformers using lower levels of theory and outlines a general method for predicting small peptide structures.