DeWitt Wallace Library Biennial Report 2011-2013

Summary of library activities for 2011-201

Repair of oxidative DNA base damage in the host genome influences the HIV integration site sequence preference

Host base excision repair (BER) proteins that repair oxidative damage enhance HIV infection. These proteins include the oxidative DNA damage glycosylases 8-oxo-guanine DNA glycosylase (OGG1) and mutY homolog (MYH) as well as DNA polymerase beta (Polβ). While deletion of oxidative BER genes leads to decreased HIV infection and integration efficiency, the mechanism remains unknown. One hypothesis is that BER proteins repair the DNA gapped integration intermediate. An alternative hypothesis considers that the most common oxidative DNA base damages occur on guanines. The subtle consensus sequence preference at HIV integration sites includes multiple G:C base pairs surrounding the points of joining. These observations suggest a role for oxidative BER during integration targeting at the nucleotide level. We examined the hypothesis that BER repairs a gapped integration intermediate by measuring HIV infection efficiency in Polβ null cell lines complemented with active site point mutants of Polβ. A DNA synthesis defective mutant, but not a 59dRP lyase mutant, rescued HIV infection efficiency to wild type levels; this suggeted Polβ DNA synthesis activity is not necessary while 59dRP lyase activity is required for efficient HIV infection. An alternate hypothesis that BER events in the host genome influence HIV integration site selection was examined by sequencing integration sites in OGG1 and MYH null cells. In the absence of these 8-oxo-guanine specific glycosylases the chromatin elements of HIV integration site selection remain the same as in wild type cells. However, the HIV integration site sequence preference at G:C base pairs is altered at several positions in OGG1 and MYH null cells. Inefficient HIV infection in the absence of oxidative BER proteins does not appear related to repair of the gapped integration intermediate; instead oxidative damage repair may participate in HIV integration site preference at the sequence level. © 2014 Bennett et al

Machine translation for subtitling: a large-scale evaluation

This article describes a large-scale evaluation of the use of Statistical Machine Translation for professional subtitling. The work was carried out within the FP7 EU-funded project SUMAT and involved two rounds of evaluation: a quality evaluation and a measure of productivity gain/loss. We present the SMT systems built for the project and the corpora they were trained on, which combine professionally created and crowd-sourced data. Evaluation goals, methodology and results are presented for the eleven translation pairs that were evaluated by professional subtitlers. Overall, a majority of the machine translated subtitles received good quality ratings. The results were also positive in terms of productivity, with a global gain approaching 40%. We also evaluated the impact of applying quality estimation and filtering of poor MT output, which resulted in higher productivity gains for filtered files as opposed to fully machine-translated files. Finally, we present and discuss feedback from the subtitlers who participated in the evaluation, a key aspect for any eventual adoption of machine translation technology in professional subtitlin

Phosphorylation of histone H3(T118) alters nucleosome dynamics and remodeling

Nucleosomes, the fundamental units of chromatin structure, are regulators and barriers to transcription, replication and repair. Post-translational modifications (PTMs) of the histone proteins within nucleosomes regulate these DNA processes. Histone H3(T118) is a site of phosphorylation [H3(T118ph)] and is implicated in regulation of transcription and DNA repair. We prepared H3(T118ph) by expressed protein ligation and determined its influence on nucleosome dynamics. We find H3(T118ph) reduces DNA–histone binding by 2 kcal/mol, increases nucleosome mobility by 28-fold and increases DNA accessibility near the dyad region by 6-fold. Moreover, H3(T118ph) increases the rate of hMSH2–hMSH6 nucleosome disassembly and enables nucleosome disassembly by the SWI/SNF chromatin remodeler. These studies suggest that H3(T118ph) directly enhances and may reprogram chromatin remodeling reactions

Healthcare Utilization and Quality of Life Improvement after Ablation for Paroxysmal AF in Younger and Older Patients

Background Atrial fibrillation (AF) prevalence increases significantly with age. Little is known about the effect of AF ablation on quality of life and healthcare utilization in the elderly. The objective of this study was to quantify the healthcare utilization and quality of life benefits of catheter ablation for AF, for patients ≥65 years compared to patients <65 years. Methods Two multicenter U.S. registry studies enrolled patients with paroxysmal AF. Baseline characteristics and acute outcomes were collected for 736 patients receiving catheter ablation with the Navistar® ThermoCool® SF Catheter (Biosense Webster, Inc., Diamond Bar, CA, USA). Healthcare utilization and quality of life outcomes were collected through 1 year postablation for 508 patients. Results The rates of acute pulmonary vein isolation were high and similar between patients ≥65 years and <65 years (97.5% vs 95.8%, P = 0.2130). Length of stay for the index procedure was similar between age groups with 82.2% of the older group and 83.2% of the younger group having one-day hospitalization. Disease-specific quality of life instrument scores improved significantly and similarly for older and younger patients at 1 year postablation, compared to baseline. AF-related hospitalizations and emergency department visits were similar or lower in older patients compared to younger patients, as reported at 1 year postablation. Conclusion For older patients undergoing catheter ablation for paroxysmal AF, healthcare utilization parameters were lower or not significantly different than for younger patients, and quality of life outcomes were similarly improved. These findings support the use of catheter ablation as a treatment option in older patients with paroxysmal AF

Anti-tumor activity and mechanistic characterization of APE1/Ref-1 inhibitors in bladder cancer

Bladder cancer is the ninth most common cause of cancer-related deaths worldwide. Although cisplatin is used routinely in treating bladder cancer, refractory disease remains lethal for many patients. The recent addition of immunotherapy has improved patient outcomes; however, a large cohort of patients does not respond to these treatments. Therefore, identification of innovative molecular targets for bladder cancer is crucial. Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/Ref-1) is a multifunctional protein involved in both DNA repair and activation of transcription factors through reduction-oxidation (redox) regulation. High APE1/Ref-1 expression is associated with shorter patient survival time in many cancer types. In this study, we found high APE1/Ref-1 expression in human bladder cancer tissue relative to benign urothelium. Inhibition of APE1/Ref-1 redox signaling using APE1/Ref-1-specific inhibitors attenuates bladder cancer cell proliferation in monolayer, in three-dimensional cultures, and in vivo. This inhibition corresponds with an increase in apoptosis and decreased transcriptional activity of NF-κB and STAT3, transcription factors known to be regulated by APE1/Ref-1, resulting in decreased expression of downstream effectors survivin and Cyclin D1 in vitro and in vivo. We also demonstrate that in vitro treatment of bladder cancer cells with APE1/Ref-1 redox inhibitors in combination with standard-of-care chemotherapy cisplatin is more effective than cisplatin alone at inhibiting cell proliferation. Collectively, our data demonstrate that APE1/Ref-1 is a viable drug target for the treatment of bladder cancer, provide a mechanism of APE1/Ref-1 action in bladder cancer cells, and support the use of novel redox-selective APE1/Ref-1 inhibitors in clinical studies. SIGNIFICANCE: This work identifies a critical mechanism for APE1/Ref-1 in bladder cancer growth and provides compelling preclinical data using selective redox activity inhibitors of APE1/Ref-1 in vitro and in vivo

Retroviral intasomes search for a target DNA by 1D diffusion which rarely results in integration

Retroviruses must integrate their linear viral cDNA into the host genome for a productive infection. Integration is catalysed by the retrovirus-encoded integrase (IN), which forms a tetramer or octamer complex with the viral cDNA long terminal repeat (LTR) ends termed an intasome. IN removes two 3&apos;-nucleotides from both LTR ends and catalyses strand transfer of the recessed 3&apos;-hydroxyls into the target DNA separated by 4-6 bp. Host DNA repair restores the resulting 5&apos;-Flap and single-stranded DNA (ssDNA) gap. Here we have used multiple single molecule imaging tools to determine that the prototype foamy virus (PFV) retroviral intasome searches for an integration site by one-dimensional (1D) rotation-coupled diffusion along DNA. Once a target site is identified, the time between PFV strand transfer events is 470 ms. The majority of PFV intasome search events were non-productive. These observations identify new dynamic IN functions and suggest that target site-selection limits retroviral integration.open1196sciescopu