Computational Evaluation of Nucleotide Insertion Opposite Expanded and Widened DNA by the Translesion Synthesis Polymerase Dpo4.

Expanded (x) and widened (y) deoxyribose nucleic acids (DNA) have an extra benzene ring incorporated either horizontally (xDNA) or vertically (yDNA) between a natural pyrimidine base and the deoxyribose, or between the 5- and 6-membered rings of a natural purine. Far-reaching applications for (x,y)DNA include nucleic acid probes and extending the natural genetic code. Since modified nucleobases must encode information that can be passed to the next generation in order to be a useful extension of the genetic code, the ability of translesion (bypass) polymerases to replicate modified bases is an active area of research. The common model bypass polymerase DNA polymerase IV (Dpo4) has been previously shown to successfully replicate and extend past a single modified nucleobase on a template DNA strand. In the current study, molecular dynamics (MD) simulations are used to evaluate the accommodation of expanded/widened nucleobases in the Dpo4 active site, providing the first structural information on the replication of (x,y)DNA. Our results indicate that the Dpo4 catalytic (palm) domain is not significantly impacted by the (x,y)DNA bases. Instead, the template strand is displaced to accommodate the increased C1'-C1' base-pair distance. The structural insights unveiled in the present work not only increase our fundamental understanding of Dpo4 replication, but also reveal the process by which Dpo4 replicates (x,y)DNA, and thereby will contribute to the optimization of high fidelity and efficient polymerases for the replication of modified nucleobases.

Changing weak halogen bonds into strong ones through cooperativity with beryllium bonds.

The mutual interaction between beryllium bonds and halogen bonds within H2Be···FCl···Base complexes, where Base includes a wide set of N- and O-containing Lewis bases, has been studied at the M06-2X/6-31+G(d,p) level of theory. The reliability of this theoretical model was assessed by comparison with ab initio CCSD/aug-cc-pVTZ reference calculations. Cooperative effects were investigated within the framework of the atoms in molecules theory (AIM) by analyzing the topology of the electron density and the changes in the atomic energy components. The decomposition of the total stabilization energy into atomic components is found to be a very reliable tool to describe halogen bond interactions. Both the topological analysis of the electron density and the changes in the atomic energy components of the binding energy show the existence of strong cooperative effects between beryllium and halogen bonds, which are in some cases very intense. In general, there is a correlation between the intrinsic basicity of the Lewis base participating in the halogen bond and the resulting cooperativity in the sense that the stronger the base, the larger the cooperative effects.

Hydrogen bond cooperativity in water hexamers: atomic energy perspective of local stabilities.

Atomic energies are used to describe local stability in eight low-lying water hexamers: prism, cage, boat 1, boat 2, bag, chair, book 1, and book 2. The energies are evaluated using the quantum theory of atoms in molecules (QTAIM) at MP2/aug-cc-pVTZ geometries. It is found that the simple, stabilizing cooperativity observed in linear hydrogen-bonded water systems is diminished as clusters move from nearly planar to three-dimensional structures. The prism, cage, and bag clusters can have local water stabilities differing up to 5 kcal mol(-1) as a result of mixed cooperative and anticooperative interactions. At the atomic level, in many cases a water may have a largely stabilized oxygen atom but the net water stability will be diminished due to strong destabilization of the water's hydrogen atoms. Analysis of bond critical point (BCP) electron densities shows that the reduced cooperativity results in a decrease in hydrogen bond strength and an increase in covalent bond strength, most evident in the prism. The chair, with the greatest cooperativity, has the largest average electron density at the BCP per hydrogen bond, whereas the cage has the largest total value for BCP density at all hydrogen bonds. The cage also has the second largest value (after the prism) for covalent bond critical point densities and an oxygen-oxygen BCP which may factor into the experimentally observed stability of the structure.

Investigating the impact of environmental factors on West Nile virus human case prediction in Ontario, Canada.

West Nile virus is the most common mosquito borne disease in North America and the leading cause of viral encephalitis. West Nile virus is primarily transmitted between birds and mosquitoes while humans are incidental, dead-end hosts. Climate change may increase the risk of human infections as climatic variables have been shown to affect the mosquito life cycle, biting rate, incubation period of the disease in mosquitoes, and bird migration patterns. We develop a zero-inflated Poisson model to investigate how human West Nile virus case counts vary with respect to mosquito abundance and infection rates, bird abundance, and other environmental covariates. We use a Bayesian paradigm to fit our model to data from 2010-2019 in Ontario, Canada. Our results show mosquito infection rate, temperature, precipitation, and crow abundance are positively correlated with human cases while NDVI and robin abundance are negatively correlated with human cases. We find the inclusion of spatial random effects allows for more accurate predictions, particularly in years where cases are higher. Our model is able to accurately predict the magnitude and timing of yearly West Nile virus outbreaks and could be a valuable tool for public health officials to implement prevention strategies to mitigate these outbreaks.

Data-driven evaluation of the Boston marathon qualifying times.

The Boston Marathon is one of the most prestigious running races in the world. From its inception in 1897, popularity grew to a point in 1970 where qualifying times were implemented to cap the number of participants. Currently, women's qualifying times in each age group are thirty minutes slower than the men's qualifying times equating to a 16.7% adjustment for the 18-34 age group, decreasing with age to a 10.4% adjustment for the 80+ age group. This setup somewhat counter-intuitively implies that women become faster with age relative to men. We present a data-driven approach to determine qualifying standards that lead to an equal proportion of qualifiers in each age category and gender. We had to exclude the 75-79 and 80+ age groups from analysis due to limited data. When minimizing the difference in proportion of men and women qualifying, the women's times for the 65-69 and 70-74 age groups are 4-5 minutes slower than the current qualifying standard, while they are 0 to 3 minutes faster for all other age groups.

Cooperativity between hydrogen bonds and beryllium bonds in (H2O)(n)BeX2 (n = 1-3, X = H, F) complexes. A new perspective.

The interaction of BeX(2) (X = H, F) with water molecules has been analyzed at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. The formation of strong beryllium bonds between water molecules and the BeX(2) derivative triggers significant electron density redistribution within the whole system, resulting in significant changes in the proton donor and proton acceptor capacity of the water molecules involved. Hence, significant cooperative and anti-cooperative effects are present, explaining why there is no case in which the global minimum corresponds to a tetracoordinated beryllium atom. In fact, the most stable clusters can be viewed as the result of the attachment of BeX(2) to the water trimer and the water dimer, respectively, and not as the result of the solvation of the BeX(2) molecule. We have also shown that the decomposition of the interaction energy into atomic components is a reliable quantitative tool to describe all the closed-shell interactions present in the clusters investigated herein, namely hydrogen bonds, beryllium bonds and dihydrogen bonds. Indeed, we have shown that the changes in the atomic energy components are correlated with the changes in the strength of these interactions, and they provide a quantitative measure of cooperative effects directly in terms of energies.

Visualizing internal stabilization in weakly bound systems using atomic energies: hydrogen bonding in small water clusters.

Atomic energies are used to visualize the local stabilizing and destabilizing energy changes in water clusters. Small clusters, (H(2)O)(n), from n = 2-5, at MP2/aug-cc-pVTZ geometries are evaluated using energies defined by the quantum theory of atoms in molecules (QTAIM). The atomic energies reproduce MP2 total energies to within 0.005 kcal mol(-1). Oxygen atoms are stabilized for all systems and hydrogen atoms are destabilized. The increased stability of the water clusters due to hydrogen bond cooperativity is demonstrated at an atomic level. Variations in atomic energies within the clusters are correlated to the geometry of the waters and reveal variations in the hydrogen bond strengths. The method of visualization of the energy changes applied here is especially suited for application to large biomolecules.

Serum fibroblast growth factor 21 levels after out of hospital cardiac arrest are associated with neurological outcome.

Fibroblast growth factor (FGF) 21 is a marker associated with mitochondrial and cellular stress. Cardiac arrest causes mitochondrial stress, and we tested if FGF 21 would reflect the severity of hypoxia-reperfusion injury after cardiac arrest. We measured serum concentrations of FGF 21 in 112 patients on ICU admission and 24, 48 and 72 h after out-of-hospital cardiac arrest with shockable initial rhythm included in the COMACARE study (NCT02698917). All patients received targeted temperature management for 24 h. We defined 6-month cerebral performance category 1-2 as good and 3-5 as poor neurological outcome. We used samples from 40 non-critically ill emergency room patients as controls. We assessed group differences with the Mann Whitney U test and temporal differences with linear modeling with restricted maximum likelihood estimation. We used multivariate logistic regression to assess the independent predictive value of FGF 21 concentration for neurologic outcome. The median (inter-quartile range, IQR) FGF 21 concentration was 0.25 (0.094-0.91) ng/ml in controls, 0.79 (0.37-1.6) ng/ml in patients at ICU admission (P < 0.001 compared to controls) and peaked at 48 h [1.2 (0.46-2.5) ng/ml]. We found no association between arterial blood oxygen partial pressure and FGF 21 concentrations. We observed with linear modeling an effect of sample timepoint (F 5.6, P < 0.01), poor neurological outcome (F 6.1, P = 0.01), and their interaction (F 3.0, P = 0.03), on FGF 21 concentration. In multivariate logistic regression analysis, adjusting for relevant clinical covariates, higher average FGF 21 concentration during the first 72 h was independently associated with poor neurological outcome (odds ratio 1.60, 95% confidence interval 1.10-2.32). We conclude that post cardiac arrest patients experience cellular and mitochondrial stress, reflected as a systemic FGF 21 response. This response is higher with a more severe hypoxic injury but it is not exacerbated by hyperoxia.

Effect of counterions on the protonation state in a poly(G)-poly(C) radical cation.

The proton transfer process from a guanine to its complementary cytosine in a B-form d[GG] radical cation is investigated theoretically. The d[GG] radical cation is optimized by the ONIOM + PCM method. In this two-layer ONIOM method, the high layer consists of the π-stacked complementary base pairs with a hole charge, which is treated at the B97D/6-31G(d) level. The low layer includes the sugar-phosphate backbone and sodium ions, which is treated with the Amber99SB/Parmbsc0 force field. Our calculations reveal that the stabilization of the deprotonated state in d[GG] oligomers is related to the location of sodium ions. When sodium ions are located near phosphate groups, the proton prefers bonding with the guanine, and 80% of the hole charge is delocalized on the guanine residues. When sodium ions are placed in the major groove, the deprotonated state is favorable, and 70% of the hole charge localizes on the corresponding guanine-cytosine pair. According to the natural bond orbital analysis, the N-H···N hydrogen bond between the guanine-cytosine pair provides an important contribution to the stabilization of the deprotonated state. Stabilization of this hydrogen bond is very sensitive to the d[GG] oligomer configuration. In summary, the proton transfer process in a guanine-cytosine pair of poly(G)-poly(C) radical cations is largely affected by the arrangement of counterions.