Solving the At-Most-Once Problem with Nearly Optimal Effectiveness

We present and analyze a wait-free deterministic algorithm for solving the at-most-once problem: how m shared-memory fail-prone processes perform asynchronously n jobs at most once. Our algorithmic strategy provides for the first time nearly optimal effectiveness, which is a measure that expresses the total number of jobs completed in the worst case. The effectiveness of our algorithm equals n-2m+2. This is up to an additive factor of m close to the known effectiveness upper bound n-m+1 over all possible algorithms and improves on the previously best known deterministic solutions that have effectiveness only n-log m o(n). We also present an iterative version of our algorithm that for any $m = O\left(\sqrt[3+\epsilon]{n/\log n}\right)$ is both effectiveness-optimal and work-optimal, for any constant $\epsilon > 0$. We then employ this algorithm to provide a new algorithmic solution for the Write-All problem which is work optimal for any $m=O\left(\sqrt[3+\epsilon]{n/\log n}\right)$.Comment: Updated Version. A Brief Announcement was published in PODC 2011. An Extended Abstract was published in the proceeding of ICDCN 2012. A full version was published in Theoretical Computer Science, Volume 496, 22 July 2013, Pages 69 - 8

PAXX and its paralogues synergistically direct DNA polymerase λ activity in DNA repair

PAXX is a recently identified component of the nonhomologous end joining (NHEJ) DNA repair pathway. The molecular mechanisms of PAXX action remain largely unclear. Here we characterise the interactomes of PAXX and its paralogs, XLF and XRCC4, to show that these factors share the ability to interact with DNA polymerase λ (Pol λ), stimulate its activity and are required for recruitment of Pol λ to laser-induced DNA damage sites. Stimulation of Pol λ activity by XRCC4 paralogs requires a direct interaction between the SP/8 kDa domain of Pol λ and their N-terminal head domains to facilitate recognition of the 5′ end of substrate gaps. Furthermore, PAXX and XLF collaborate with Pol λ to promote joining of incompatible DNA ends and are redundant in supporting Pol λ function in vivo. Our findings identify Pol λ as a novel downstream effector of PAXX function and show XRCC4 paralogs act in synergy to regulate polymerase activity in NHEJ.This work was supported by the Medical Research Council (MRC) UK

ZNF281 is recruited on DNA breaks to facilitate DNA repair by non-homologous end joining

Abstract: Efficient repair of DNA double-strand breaks (DSBs) is of critical importance for cell survival. Although non-homologous end joining (NHEJ) is the most used DSBs repair pathway in the cells, how NHEJ factors are sequentially recruited to damaged chromatin remains unclear. Here, we identify a novel role for the zinc-finger protein ZNF281 in participating in the ordered recruitment of the NHEJ repair factor XRCC4 at damage sites. ZNF281 is recruited to DNA lesions within seconds after DNA damage through a mechanism dependent on its DNA binding domain and, at least in part, on poly-ADP ribose polymerase (PARP) activity. ZNF281 binds XRCC4 through its zinc-finger domain and facilitates its recruitment to damaged sites. Consequently, depletion of ZNF281 impairs the efficiency of the NHEJ repair pathway and decreases cell viability upon DNA damage. Survival analyses from datasets of commonly occurring human cancers show that higher levels of ZNF281 correlate with poor prognosis of patients treated with DNA-damaging therapies. Thus, our results define a late ZNF281-dependent regulatory step of NHEJ complex assembly at DNA lesions and suggest additional possibilities for cancer patients’ stratification and for the development of personalised therapeutic strategies

Evidence that Amphotericin B Mediates Reactivation of Latent Epstein-Barr Virus in Hodgkin's Lymphoma Allowing Cytotoxicity by Acyclovir

This brief communication focuses on aspects of a recent case report (Yonsei Med J 2005;46:425-30) on a full and sustained remission of Hodgkin's lymphoma (HL) after a single day of chemotherapy. A septic episode required stopping chemotherapy and starting amphotericin B and acyclovir. Remission evidence was seen within days of starting these. A review of research supporting the notion that amphotericin B can reactivate latent Epstein-Barr virus and thus allow acyclovir to kill infected HL cells is given. Experimental work is required to confirm or refute this possibility. If successful, amphotericin B and acyclovir treatment could be extended to other EBV-driven cancers such as Burkitt's lymphoma, nasopharyngeal carcinoma and the occasional EBV-related epithelial cancer of the breast, colon, prostate, and others

NR4A Nuclear Receptors Target Poly-ADP-Ribosylated DNA-PKcs Protein to Promote DNA Repair.

Although poly-ADP-ribosylation (PARylation) of DNA repair factors had been well documented, its role in the repair of DNA double-strand breaks (DSBs) is poorly understood. NR4A nuclear orphan receptors were previously linked to DSB repair; however, their function in the process remains elusive. Classically, NR4As function as transcription factors using a specialized tandem zinc-finger DNA-binding domain (DBD) for target gene induction. Here, we show that NR4A DBD is bi-functional and can bind poly-ADP-ribose (PAR) through a pocket localized in the second zinc finger. Separation-of-function mutants demonstrate that NR4A PAR binding, while dispensable for transcriptional activity, facilitates repair of radiation-induced DNA double-strand breaks in G1. Moreover, we define DNA-PKcs protein as a prominent target of ionizing radiation-induced PARylation. Mechanistically, NR4As function by directly targeting poly-ADP-ribosylated DNA-PKcs to facilitate its autophosphorylation-promoting DNA-PK kinase assembly at DNA lesions. Selective targeting of the PAR-binding pocket of NR4A presents an opportunity for cancer therapy

Vibrational and vibrational-torsional interactions in the 0–600 cm-1 region of the S1 ← S0 spectrum of p-xylene investigated with resonance-enhanced multiphoton ionization (REMPI) and zero-kinetic-energy (ZEKE) spectroscopy

We assign the 0–600 cm-1 region of the S1 ← S0 transition in p-xylene using resonance-enhanced multiphoton ionization (REMPI) and zero-kinetic-energy (ZEKE) spectroscopy. In the 0–300 cm-1 range, as well as the intense origin band there are a number of torsional and vibration-torsion (vibtor) features. The latter are discussed in more detail in an accompanying paper [Gardner et al. J. Chem. Phys. XXX, xxxxxx (2016)]. Here we focus on the origin and the 300–650 cm-1 region, where vibrational bands and some vibtor activity is observed. From the origin ZEKE spectrum we derive the ionization energy of p-xylene as 68200 ± 5 cm-1. The assignment of the REMPI spectrum is based on the activity observed in the ZEKE spectra coupled with knowledge of the vibrational wavenumbers obtained from quantum chemical calculations. We assign several isolated vibrations, and a complex Fermi resonance that is found to comprise contributions from both vibrations and vibtor levels, and we examine this via a two-dimensional ZEKE (2D-ZEKE) spectrum. A number of the vibrational features in the REMPI and ZEKE spectra of p-xylene that have been reported previously are reassigned and now largely consist of totally-symmetric contributions. We briefly discuss the appearance of non-Franck-Condon allowed transitions. Finally, we find remarkably similar spectral activity to that in the related disubstituted benzenes, para-difluorobenzene and para-fluorotoluene