BACKGROUND Telomeres are required to prevent end-to-end chromosome fusions. End-to-end fusions of metaphase chromosomes are observed in mammalian cells with dysfunctional telomeres due to diminished function of telomere-associated proteins and in cells experiencing extensive attrition of telomeric DNA. However, the molecular nature of these fusions and the mechanism by which they occur have not...

Toxoplasma gondii is a parasitic protozoan that causes disseminated toxoplasmosis, a disease that afflicts roughly a third of the worlds population. Its virulence is predicated on its motility and ability to enter and exit nucleated cells; therefore, studies elucidating its mechanism of motility and in particular, its motility patterns in the context of its lytic cycle, are critical to the even...

We introduce a model of thermalized conformations in space of RNA -or single stranded DNAmolecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the study of one element of the ternary structure, namely the end-to-end distance. The computed force-elongation characteristics is in good agreemement with some r...

In mammalian cells, nonhomologous end-joining (NHEJ) repairs DNA double-strand breaks created by ionizing radiation and V(D)J recombination. We have developed a cell-free system capable of processing and joining noncompatible DNA ends. The system had key features of NHEJ in vivo, including dependence on Ku, DNA-PKcs, and XRCC4/Ligase4. The NHEJ reaction had striking properties. Processing of no...

Telomeres are protected from nonhomologous end-joining (NHEJ) to avoid deleterious chromosome fusions, yet they associate with the Ku heterodimer that is principal in the classical NHEJ (c-NHEJ) pathway. T-loops have been proposed to inhibit Ku's association with telomeric ends, thus inhibiting c-NHEJ; however, deficiencies in the t-loop model suggest additional mechanisms are in effect. We dem...

Nonhomologous end joining (NHEJ) refers to a set of genome maintenance pathways in which two DNA double-strand break (DSB) ends are (re)joined by apposition, processing, and ligation without the use of extended homology to guide repair. Canonical NHEJ (c-NHEJ) is a well-defined pathway with clear roles in protecting the integrity of chromosomes when DSBs arise. Recent advances have revealed muc...

The repair of DNA double-strand breaks (DSBs) is essential to maintain genomic integrity. In higher eukaryotes, DNA DSBs are predominantly repaired by non-homologous end joining (NHEJ), but DNA ends can also be joined by an alternative error-prone mechanism termed microhomology-mediated end joining (MMEJ). In MMEJ, the repair of DNA breaks is mediated by annealing at regions of microhomology an...

In this paper, we propose a hybrid representation, which leverages the great discriminative capacity of CNNs and the efficiency of descriptor encoding scheme scene recognition. We make three main contributions. First, we train an end-to-end PatchNet in a weakly supervised manner, in order to extract the discriminative deep descriptors of local patches. Second, we design a novel VSAD encoding ap...