Redox-Based Defect Detection in Packed DNA: Insights from Hybrid Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations.

The impact of an 8-oxoguanine (8oxoG) defect on the redox properties of DNA within the nucleosome core particle (NCP) was investigated employing hybrid quantum mechanical/molecular mechanics (QM/MM) molecular dynamics simulations of native and 8oxoG-containing NCP systems with an explicit representation of a biologically relevant environment. Two distinct NCP positions with varying solvent accessibility were considered for 8oxoG insertion. In both cases, it is found that the presence of 8oxoG drastically decreases the redox free energy of oxidation by roughly 1 eV, which is very similar to what was recently reported for free native and 8oxoG-containing DNA. In contrast, the effect of 8oxoG on the reorganization free energy is even smaller for packed DNA (decrease of 0.13 and 0.01 eV for defect-free and defect-containing systems, respectively) compared to the one for free DNA (0.25 eV), consistent with the increased rigidity of the NCP as compared to free DNA. Furthermore, the presence of an 8oxoG defect does not yield any significant changes in the packed DNA structure. Such a conclusion favors the idea that in the case of chromatin, defect-induced changes in DNA redox chemistry can also be exploited to detect damaged bases via DNA-mediated hole transfer.

MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations.

MiMiC is a highly flexible, extremely scalable multiscale modeling framework. It couples the CPMD (quantum mechanics, QM) and GROMACS (molecular mechanics, MM) codes. The code requires preparing separate input files for the two programs with a selection of the QM region. This can be a tedious procedure prone to human error, especially when dealing with large QM regions. Here, we present MiMiCPy, a user-friendly tool that automatizes the preparation of MiMiC input files. It is written in Python 3 with an object-oriented approach. The main subcommand PrepQM can be used to generate MiMiC inputs directly from the command line or through a PyMOL/VMD plugin for visually selecting the QM region. Many other subcommands are also provided for debugging and fixing MiMiC input files. MiMiCPy is designed with a modular structure that allows seamless extensions to new program formats depending on the requirements of MiMiC.

Computational investigation of functionalized carbenes on dinitrogen activation.

Activation of the dinitrogen triple bond is a crucial step in the overall fixation of atmospheric nitrogen into usable forms for industrial and biological applications. Current synthetic catalysts incorporate metal ions to facilitate the activation and cleavage of dinitrogen. The high price of metal-based catalysts and the challenge of catalyst recovery during industrial catalytic processes has led to increasing interest in metal-free catalysts. One step toward metal-free catalysis is the use of frustrated Lewis pairs (FLPs). In this study, we have examined 18 functionalized carbenes as FLPs to elucidate the influence of steric and electronic effects on the activation of dinitrogen. To test the effects of functionalization on dinitrogen activation, we have performed density functional theory (DFT), multireference, non and extended transition state-natural orbital for chemical valence (ETS-NOCV) calculations. Our results suggest that functional groups which introduce strong electron-withdrawing effects and/or engage in extended π/π* systems lead to the lowering of the dissociation energy of the dinitrogen bond, which further contributes to greater nitrogen activation. We conjecture that these effects are due to enhanced back-bonding capability of the p orbital of the carbene carbon atoms to the adjacent nitrogen atoms (increasing Lewis basicity of the carbene carbon atom) and enhanced stability of dissociated products. Our concluding remarks include opportunities to extend this activation study to explore the entire catalytic cycle with promising functionalized carbenes for experimental evaluation.

Impact of tissue processing on microbiological colonization in the context of placentophagy.

A mother's postpartum ingestion of raw or processed placental tissue-referred to as human maternal placentophagy-is an emerging health trend observed in industrialized nations. Placenta is commonly consumed as small pieces of raw tissue, or as raw or steamed dehydrated pulverized and encapsulated tissue. To investigate the potential neonatal health risks of this behavior, the present study focused on microbial colonization of processed placenta preparations with potentially pathogenic bacteria Streptococcus agalactiae (Group-B-Streptococci; GBS) and Escherichia coli (E. coli). In the clinical approach placentas from 24 mothers were analyzed. Two placentas, from 13 mothers with confirmed positive maternal GBS status, showed GBS-growth on their surface (2/13; 15.4%) independent from delivery mode or antibiotic treatment. All processed samples (n = 24) were free from GBS. In the experimental approach, a standardized inoculation protocol was introduced to resemble ascending vaginal and hematogenous colonization. Six placentas from elective term C-sections of GBS negative mothers were collected and artificially inoculated with highly concentrated suspensions of GBS and E. coli. Heat processing significantly reduced the number of colony forming units (CFU) for GBS and E. coli. Our results suggest placentophagy of processed tissue is an unlikely source of clinical infection.

Placenta - Worth Trying? Human Maternal Placentophagia: Possible Benefit and Potential Risks.

The use of placenta preparations as an individual puerperal remedy can be traced back to historical, traditional practices in Western and Asian medicine. To evaluate the ingestion of processed placenta as a puerperal remedy, the potential risks (trace elements, microorganisms) and possible benefit (hormones in the placental tissue) of such a practice are discussed in this article based on a literature review.

Human placentophagy: Effects of dehydration and steaming on hormones, metals and bacteria in placental tissue.

INTRODUCTION: Human maternal placentophagy, the behavior of ingesting the own raw or processed placenta postpartum, is a growing trend by women of western societies. This study aims to identify the impact of dehydration and steaming on hormone and trace element concentration as well as microbial contamination of placental tissue. METHODS: A total of nine placentas have been processed: six were studied for hormone and trace element concentrations; eight were studied for microbial contamination. The concentrations of CRH, hPL, oxytocin and ACTH in samples of raw, steamed dehydrated and raw dehydrated placental tissue were detected using ELISA. A yeast bioassay was performed in order to detect estrogen equivalent (EEQ) and gestagen equivalent (PEQ) active substances. Elements (As, Cd, Fe, Pb, Se, Hg) were analyzed using ICP-MS. Isolated colonies from tissue and placenta swab samples were identified using Vitek MS. RESULTS: Following mean hormone concentrations were detected in raw placental tissue: CRH (177.88 ng/g), hPL (17.99 mg/g), oxytocin (85.10 pg/g), ACTH (2.07 ng/g), estrogen equivalent active substances (46.95 ng/g) and gestagen equivalent active substances (2.12 µg/g). All hormones were sensitive to processing with a significant concentration reduction through steaming and dehydration. Microorganisms mainly from the vaginal flora were detected on placenta swab samples and samples from raw, steamed, dehydrated and steamed dehydrated tissue and mostly disappeared after dehydration. According to regulations of the European Union the concentrations of potentially toxic elements (As, Cd, Hg, Pb) were below the toxicity threshold for foodstuffs. CONCLUSION: The commonly used protocols for preparation of placenta for its individual oral ingestion reduce hormone concentrations and bacterial contamination.