Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.     

Anion binding to monotopic and ditopic macrocyclic amides

[Structure: see text] Binding of fluoride anion as well as carboxylic acid tetraalkylammonium salts by macrocyclic compounds of different size was studied by NMR in DMSO-d6. It has been found that at least a 15-membered ring is necessary for successful recognition of fluoride. Larger macrocycles obtained in a [2+2] cyclization were shown to bind dicarboxylic acid salts. Effects of binding topicity are discussed.     

How do women decide? Accepting or declining BRCA1/2 testing in a nationwide clinical sample in the United States

OBJECTIVE: To examine the role of the practitioner, informed consent, and genetic counseling in genetic testing decisions and to assess their relative influence on women's decision to have clinical BRCA1/2 testing. METHODS: Qualitative study using in-depth open-ended interviews with 68 women who had considered clinical BRCA1/2 testing. RESULTS: Slightly less than half of the women who had considered BRCA1/2 testing were found to have had a clear and preexisting desire to test or not to test, irrespective of practitioner attitude or advice. CONCLUSION: The decision to accept or decline genetic testing is the result of a complex process that goes beyond interactions between health care providers and patients, indicating a caution against exclusive reliance on informed consent or counseling encounters.     

Purification and characterization of a biosurfactant produced by Pseudomonas sp. G11 by asymmetrical flow field-flow fractionation (AsFlFFF)

Three hundred and thirty two bacterial colonies were isolated from soil contaminated by an oil spill. All the bacteria were cultured in a liquid medium individually, and the surface tensions of the media were compared. The bacterium whose culture medium had the lowest surface tension was identified as Pseudomonas sp. G11. A biosurfactant was produced by cultivation of the Pseudomonas sp. G11 in the LB media. For extraction of the biosurfactant, two solvent systems were used (n-hexane and a 2:1 (v/v) mixture of chloroform/MeOH), and the results were compared. Various experimental conditions (solvent composition, flow rate, etc.) were tested to optimize the analysis of the biosurfactant by asymmetrical flow field-flow fractionation (AsFlFFF). The biosurfactant was successfully separated from the culture medium by AsFlFFF when pure water was used as the carrier. From the retention data, the hydrodynamic diameter (d _H) and molecular weight (M) of the biosurfactant were determined by AsFlFFF. The molecular weight was determined by using pullulans as the calibration standards. The d _H and M were 49 nm and 2.3 × 10⁵ Da when extracted with n-hexane, and 39 nm and 1.13 × 10⁵ Da when extracted with the 2:1 mixture of chloroform/MeOH, respectively. Figure Separation of biosurfactant from its culture medium by flow FFF     

Regulation of mesenchymal stem cell adhesion and orientation in 3D collagen scaffold by electrical stimulus

Cell adhesion and orientation are important for both natural and engineered tissues to fully achieve physiologic functions. Based on diverse cellular responses induced by electrical stimulus on 2D substrate, we applied non-invasive electrical stimulus to regulate cell adhesion and orientation of bone marrow-derived mesenchymal stem cells (MSCs) and fibroblasts in a reconstituted 3D collagen-based scaffold. While fibroblasts were induced to reorient perpendicularly in response to direct current electrical stimulus, rat MSCs showed only slight changes in cell reorientation. Multiphoton microscopy revealed that rat MSCs exhibited much stronger 3D adhesion, which appears to resist cell reorientation. Only in response to a large electrical stimulus (e.g., 10 V/cm), collagen fibers around rat MSCs became disconnected and loosely reorganized. In contrast, the collagen fibers surrounding the fibroblasts were entangled in a random network and became preferentially aligned in the direction of the electrical stimulus. When incubated with integrin antibodies, both fibroblasts and rat MSCs failed to respond to electrical stimulus, providing evidence that integrin-dependent molecular mechanisms are involved in 3D cell adhesion and orientation. Elucidation of physical regulation of 3D cell adhesion and orientation may offer a novel approach in controlling cell growth and differentiation and could be useful for stem cell-based therapeutic application and engineering tissue constructs.     

Weighted estimates of solutions to second order parabolic equations

We evaluate the rate of decay for solutions to second order parabolic equations, which vanish on the boundary, while the right-hand side is allowed to be unbounded. Our approach is based on a special growth lemma, and it works for both divergence and non-divergence equations, in domains satisfying a general “exterior measure condition” (A). The result for elliptic case is published in Cho and Safonov (2007) [2].     

Classification of α-Ricci flat graphs with girth at least five

Lin, Lu and Yau classified Ricci flat graphs with girth at least 5 in Lin et al., 2014 [7] and Cushing et al., 2018 [4,5]. In Lin et al., 2014, they defined $\alpha$-Ricci curvature for the definition of Ricci curvature. We will classify $\alpha$-Ricci flat graphs with girth at least 5 for all $\alpha \in (0,1)$.     

Finite group action and Gromov-Witten invariants in symplectic four-manifolds

Let a finite group act semi-freely on a closed symplectic four-manifold with a 2-dimensional fixed point set. Then we show that the relative Gromov-Witten invariants are the same as the invariants on the quotient set-up with respect to the fixed point set.     

Operator-valued Feynman integral via conditional Feynman integrals on a function space

Let C ₀ ^r [0; t] denote the analogue of the r-dimensional Wiener space, define X _t : C ^r [0; t] → ?^2r by X _t (x) = (x(0); x(t)). In this paper, we introduce a simple formula for the conditional expectations with the conditioning function X _t . Using this formula, we evaluate the conditional analytic Feynman integral for the functional $$ \Gamma _t \left( x \right) = exp \left\{ {\int_0^t {\theta \left( {s,x\left( s \right)} \right)d\eta \left( s \right)} } \right\}\varphi \left( {x\left( t \right)} \right) x \in C^r \left[ {0,t} \right] $$ , where η is a complex Borel measure on [0, t], and θ(s, ·) and φ are the Fourier-Stieltjes transforms of the complex Borel measures on ? ^r . We then introduce an integral transform as an analytic operator-valued Feynman integral over C ^r [0, t], and evaluate the integral transform for the function Γ _t via the conditional analytic Feynman integral as a kernel.