Optical Trapping Nanometry of Hypermethylated CPG-Island DNA.

Cytosine methylation is a key mechanism of epigenetic regulation. CpG-dense loci, called "CpG islands", play a particularly important role in modulating gene expression. Methylation has long been suspected to alter the physical properties of DNA, but the full spectrum of the evoked changes is unknown. Here we measured the methylation-induced nanomechanical changes in a DNA molecule with the sequence of a CpG island. For the molecule under tension, contour length, bending rigidity and intrinsic stiffness decreased in hypermethylated dsDNA, pointing at structural compaction which may facilitate DNA packaging in vivo. Intriguingly, increased forces were required to convert hypermethylated dsDNA into an extended S-form configuration. The reduction of force hysteresis during mechanical relaxation indicated that methylation generates a barrier against strand unpeeling and melting-bubble formation. The high structural stability is likely to have significant consequences on the recognition, replication, transcription, and reparation of hypermethylated genetic regions.

Integrative analysis of yeast colony growth.

Yeast colonies are routinely grown on agar plates in everyday experimental settings to understand basic molecular processes, produce novel drugs, improve health, and so on. Standardized conditions ensure these colonies grow in a reproducible fashion, while in nature microbes are under a constantly changing environment. Here we combine the power of computational simulations and laboratory experiments to investigate the impact of non-standard environmental factors on colony growth. We present the developement and parameterization of a quantitative agent-based model for yeast colony growth to reproduce measurements on colony size and cell number in a colony at non-standard environmental conditions. Specifically, we establish experimental conditions that mimic the effects of humidity changes and nutrient gradients. Our results show how colony growth is affected by moisture changes, nutrient availability, and initial colony inoculation conditions. We show that initial colony spread, not initial cell number have higher impact on the final size and cell number of colonies. Parameters of the model were identified by fitting these experiments and the fitted model gives guidance to establish conditions which enable unlimited growth of yeast colonies.

Dissociative photoionization of X(CH(3))(3) (X = N, P, As, Sb, Bi): mechanism, trends, and accurate energetics.

Threshold photoelectron photoion coincidence spectroscopy is used to study the dissociation of energy-selected X(CH(3))(3)(+) ions (X = As, Sb, Bi) by methyl loss, the only process observed up to 2 eV above the ionization energy. The ion time-of-flight distributions and the breakdown diagrams are analyzed in terms of the statistical RRKM theory to obtain accurate ionic dissociation energies. These experiments complement previous studies on analogous trimethyl compounds of the N group where X = N and P. However, trimethylamine was observed to lose only an H atom, whereas trimethylphosphine was shown to lose methyl radical, H atom, and, to a lesser extent, methane in parallel dissociation reactions. Both kinetic and thermodynamic arguments are needed to explain these trends. The methyl radical loss has two channels: either a H transfer to the central atom, followed by CH(3) loss, or a direct homolytic bond cleavage. However, the H transfer channel is blocked in trimethylamine by an H loss channel with an earlier onset, and, thus, the methyl loss is not observed. Bond energies are defined based on ab initio reaction energies and show that the main thermodynamic reason behind the trends in the energetics is the significantly weakening C=X double bond in the ion in the N --> As direction. The first adiabatic ionization energies of Sb(CH(3))(3) and Bi(CH(3))(3) have also been measured by ultraviolet photoelectron spectroscopy to be 8.02 +/- 0.05 and 8.08 +/- 0.05 eV, respectively.

Prenatal THC exposure produces a hyperdopaminergic phenotype rescued by pregnenolone.

The increased legal availability of cannabis has led to a common misconception that it is a safe natural remedy for, among others, pregnancy-related ailments such as morning sickness. Emerging clinical evidence, however, indicates that prenatal cannabis exposure (PCE) predisposes offspring to various neuropsychiatric disorders linked to aberrant dopaminergic function. Yet, our knowledge of how cannabis exposure affects the maturation of this neuromodulatory system remains limited. Here, we show that male, but not female, offspring of Δ9-tetrahydrocannabinol (THC)-exposed dams, a rat PCE model, exhibit extensive molecular and synaptic changes in dopaminergic neurons of the ventral tegmental area, including altered excitatory-to-inhibitory balance and switched polarity of long-term synaptic plasticity. The resulting hyperdopaminergic state leads to increased behavioral sensitivity to acute THC exposure during pre-adolescence. The neurosteroid pregnenolone, a US Food and Drug Administration (FDA) approved drug, rescues synaptic defects and normalizes dopaminergic activity and behavior in PCE offspring, thus suggesting a therapeutic approach for offspring exposed to cannabis during pregnancy.