The integrity of the genome is threatened by DNA damage that blocks the progression of replication forks. Little is known about the genomic locations of replication fork stalling, and its determinants and consequences in vivo. Here we show that bulky DNA damaging agents induce localized fork stalling at yeast replication origins, and that localized stalling is dependent on proximal origin activ...

We investigate the issue of stalling in the LogP model. In particular, we introduce a novel quantitative characterization of stalling, referred to as δ-stalling, which intuitively captures the realistic assumption that once the network’s capacity constraint is violated, it takes some time (at most δ) for this information to propagate to the processors involved. We prove a lower bound that shows...

We investigate the issue of stalling in the LogP model. In particular, we introduce a novel quantitative characterization of stalling, referred to as -stalling, which intuitively captures the realistic assumption that once the network’s capacity constraint is violated, it takes some time (at most ) for this information to propagate to the processors involved. We prove a lower bound that shows t...

The prevailing "plug-in-the-bottle" model suggests that macrolide antibiotics inhibit translation by binding inside the ribosome tunnel and indiscriminately arresting the elongation of every nascent polypeptide after the synthesis of six to eight amino acids. To test this model, we performed a genome-wide analysis of translation in azithromycin-treated Staphylococcus aureus. In contrast to earl...

Replication, transcription, and translation stress all lead to stalling of their respective polymerases (DNA polymerase, RNA polymerase, and the ribosome), and the cell must respond to these events in order to preserve macromolecular integrity. In response to replication stress such as DNA damage, the cell activates a checkpoint and promotes repair or bypass at the lesion. Transcriptional stres...

Ribosomal stalling is used to regulate gene expression and can occur in a species-specific manner. Stalling during translation of the MifM leader peptide regulates expression of the downstream membrane protein biogenesis factor YidC2 (YqjG) in Bacillus subtilis, but not in Escherichia coli. In the absence of structures of Gram-positive bacterial ribosomes, a molecular basis for species-specific...

background and objective: the quality of flat breads depends in part on the textural and structural properties of breads during storage. these properties are largely affected by flour quality. this research aimed at evaluating textural and structural properties of lavash bread types during storage by different techniques, comparing these methods and determination of correlation between their re...