Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor.

Pioneer transcription factors (pTFs) bind to target sites within compact chromatin, initiating chromatin remodeling and controlling the recruitment of downstream factors. The mechanisms by which pTFs overcome the chromatin barrier are not well understood. Here, we reveal, using single-molecule fluorescence, how the yeast transcription factor Rap1 invades and remodels chromatin. Using a reconstituted chromatin system replicating yeast promoter architecture, we demonstrate that Rap1 can bind nucleosomal DNA within a chromatin fiber but with shortened dwell times compared to naked DNA. Moreover, we show that Rap1 binding opens chromatin fiber structure by inhibiting inter-nucleosome contacts. Finally, we reveal that Rap1 collaborates with the chromatin remodeler RSC to displace promoter nucleosomes, paving the way for long-lived bound states on newly exposed DNA. Together, our results provide a mechanistic view of how Rap1 gains access and opens chromatin, thereby establishing an active promoter architecture and controlling gene expression.

First Pregnancy, Somatic and Psychological Status of a 4-Year-Old Child Born following Annexin V TESA Sperm Separation.

Introduction Sperm DNA integrity is a crucial paternal factor affecting fertilization and pregnancy rates, as well as embryo development. Case The present case report describes the successful pregnancy after testicular sperm aspiration (TESA) combined with intracytoplasmic sperm injection (ICSI) (TESA-ICSI) in a couple where the male presented high sperm DNA fragmentation. In order to sort damaged sperm presenting DNA fragmentation, magnetic activated cell sorting (MACS) with annexin V microbeads (MACS Miltenyi Biotec, Teterow, Germany) was used. Conclusion The authors present the first description of a successful medical case using TESA-ICSI annexin V sperm sorting. Additionally, a follow-up of the child at the age of 4 years old was done.

Intermediate electrostatic field for the elongation method.

A simple way to improve the accuracy of the fragmentation methods is proposed. The formalism was applied to the elongation (ELG) method at restricted open-shell Hartree-Fock (ROHF) level of theory. The α-helix conformer of polyglycine was taken as a model system. The modified ELG method includes a simplified electrostatic field resulting from point-charge distribution of the system's environment. In this way the long-distance polarization is approximately taken into account. The field attenuates during the ELG process to eventually disappear when the final structure is reached. The point-charge distributions for each ELG step are obtained from charge sensitivity analysis (CSA) in force-field atoms resolution. The presence of the intermediate field improves the accuracy of ELG calculations. The errors in total energy and its kinetic and potential contributions are reduced by at least one-order of magnitude. In addition the SCF convergence of ROHF scheme is improved.

Bond detectors for molecular dynamics simulations, Part I: Hydrogen bonds.

Charge sensitivity analysis in AMBER force-field resolution has been used in quest for detectors of hydrogen bonds (HBs). The process of HB formation was investigated on ab initio classical trajectories (B3LYP/6-31G*) of different nucleobase pairs. Several charge sensitivities, namely: electronegativity, hardness, Fukui function (FF), and polarization matrix, were analyzed. The global and constrained equilibria were considered. It was demonstrated that FF indices and polarization matrix elements are good detectors of HB formation.

Charge sensitivity approach to mutual polarization of reactants: molecular mechanics perspective.

Charge sensitivity analysis (CSA) in force-field atoms resolution was applied to describe the mutual polarization of reactants as well as charge-transfer (CT) effects. An inclusion complex of ß-cyclodextrin with salicylic acid was used as a model system. Three CSA models were taken into account and verified on a Born-Oppenheimer molecular dynamics (BOMD) trajectory. The models differed in terms of the equilibrium conditions imposed on the system. It was demonstrated that mutual polarization is an important source of stabilization, in contrast to the results obtained from static charge calculations. The energy lowering induced by CT was small and comparable to the CT stabilization that occurs in hydrogen-bonded systems. All models correctly described the main topological features of the BOMD energy surface. CSA in force-field atoms resolution qualitatively reproduced the charge reorganization accompanying hydrogen-bond formation. It was shown that CSA parameters are very sensitive to the bond formation process, which suggests that they could be applied in reactive force fields as detectors of newly formed chemical bonds.

A minimal bacterial RNase J-based degradosome is associated with translating ribosomes.

Protein complexes directing messenger RNA (mRNA) degradation are present in all kingdoms of life. In Escherichia coli, mRNA degradation is performed by an RNA degradosome organized by the major ribonuclease RNase E. In bacteria lacking RNase E, the existence of a functional RNA degradosome is still an open question. Here, we report that in the bacterial pathogen Helicobacter pylori, RNA degradation is directed by a minimal RNA degradosome consisting of Hp-RNase J and the only DExD-box RNA helicase of H. pylori, RhpA. We show that the protein complex promotes faster degradation of double-stranded RNA in vitro in comparison with Hp-RNase J alone. The ATPase activity of RhpA is stimulated in the presence of Hp-RNase J, demonstrating that the catalytic capacity of both partners is enhanced upon interaction. Remarkably, both proteins are associated with translating ribosomes and not with individual 30S and 50S subunits. Moreover, Hp-RNase J is not recruited to ribosomes to perform rRNA maturation. Together, our findings imply that in H. pylori, the mRNA-degrading machinery is associated with the translation apparatus, a situation till now thought to be restricted to eukaryotes and archaea.

Charge sensitivity analysis in force-field-atom resolution.

Charge sensitivity analysis (CSA) was extended to AMBER force-field resolution. The effective electronegativity and hardness data were found using evolutionary algorithms. Four model hardness matrices based on the classical electrostatic, Mataga-Nishimoto, Ohno, and Louwen-Vogt interpolation formulae were considered. Mulliken population analysis and electrostatically derived charges (CHELPG) were taken into account. It was demonstrated that the Ohno interpolation formula gives the best fit to Mulliken charges. For all molecules from the training set and all model hardness matrices, Mulliken charges were reproduced more accurately than CHELPG charges, indicating their good transferability from system to system. The effective electronegativities and hardnesses obtained were further verified by applying CSA to molecules from a validation set that was different from the training set. The correlation between CSA and Mulliken charges was of the same quality as that obtained for the training set.

[The influence of bacterial toxins on the carcinogenesis]. / Wplyw toksyn bakteryjnych na proces nowotworzenia.

Bacterial infections may constitute an important risk factor of developing cancer disease. Molecular mechanisms by which bacteria contribute to cancer are extremely complex and still remain not fully understood. So far, it is generally accepted that Helicobacter pylori infections are associated with induction of gastric adenocarcinoma and MALT lymphoma. Two H. pylori toxins which modulate many cellular functions are VacA and CagA. So far, CagA is the only one known bacterial oncoprotein. However, many other bacteria produce toxins or effector proteins perturbing host cell homeostasis or/and evoking chronic inflammation. Both processes may be associated with tumour formation. Bacterial toxins which interfere, with various host signal transduction pathways, deregulate processes of cell division, proliferation and differentiation and modulate apoptosis. Some toxins cause even direct DNA damage. This review discuss the potential links between action of bacterial toxins and cancer.