Inter-individual variation in nucleotide excision repair in young adults: effects of age, adiposity, micronutrient supplementation and genotype

Nucleotide excision repair (NER) is responsible for repairing bulky helix-distorting DNA lesions and is essential for the maintenance of genomic integrity. Severe hereditary impairment of NER leads to cancers such as those in xeroderma pigmentosum, and more moderate reductions in NER capacity have been associated with an increased cancer risk. Diet is a proven modifier of cancer risk but few studies have investigated the potential relationships between diet and NER. In the present study, the plasmid-based host cell reactivation assay was used to measure the NER capacity in peripheral blood mononuclear cells from fifty-seven volunteers aged 18–30 years before and after 6 weeks of supplementation with micronutrients (selenium and vitamins A, C and E). As a control, nine individuals remained unsupplemented over the same period. Volunteers were genotyped for the following polymorphisms in NER genes: ERCC5 Asp1104His (rs17655); XPC Lys939Gln (rs2228001); ERCC2 Lys751Gnl (rs13181); XPC PAT (an 83 bp poly A/T insertion–deletion polymorphism in the XPC gene). NER capacity varied 11-fold between individuals and was inversely associated with age and endogenous DNA strand breaks. For the first time, we observed an inverse association between adiposity and NER. No single polymorphism was associated with the NER capacity, although significant gene–gene interactions were observed between XPC Lys939Gln and ERCC5 Asp1104His and XPC Lys939Gln and ERCC2 Lys751Gnl. While there was no detectable effect of micronutrient supplementation on NER capacity, there was evidence that the effect of fruit intake on the NER capacity may be modulated by the ERCC2 Lys751Gnl single nucleotide polymorphism

A semi-automated non-radiactive system for measuring recovery of RNA synthesis and unscheduled DNA synthesis using ethynyluracil derivatives

Nucleotide excision repair (NER) removes the major UV-photolesions from cellular DNA. In humans, compromised NER activity is the cause of several photosensitive diseases, one of which is the skin-cancer predisposition disorder, xeroderma pigmentosum (XP). Two assays commonly used in measurement of NER activity are ‘unscheduled DNA synthesis (UDS)’, and ‘recovery of RNA synthesis (RRS)’, the latter being a specific measure of the transcription-coupled repair sub-pathway of NER. Both assays are key techniques for research in NER as well as in diagnoses of NER-related disorders. Until very recently, reliable methods for these assays involved measurements of incorporation of radio-labeled nucleosides. We have established non-radioactive procedures for determining UDS and RRS levels by incorporation of recently developed alkyne-conjugated nucleoside analogues, 5-ethynyl-2′-deoxyuridine (EdU) and 5-ethynyuridine (EU). EdU and EU are respectively used as alternatives for 3H-thymidine in UDS and for 3H-uridine in RRS. Based on these alkyne-nucleosides and an integrated image analyser, we have developed a semi-automated assay system for NER-activity. We demonstrate the utility of this system for NER-activity assessments of lymphoblastoid samples as well as primary fibroblasts. Potential use of the system for large-scale siRNA-screening for novel NER defects as well as for routine XP diagnosis are also considered

Structural basis of TFIIH activation for nucleotide excision repair.

Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large multisubunit transcription factor IIH (TFIIH). Here we report the cryo-EM structure of an NER intermediate containing TFIIH and the NER factor XPA. Compared to its transcription conformation, the TFIIH structure is rearranged such that its ATPase subunits XPB and XPD bind double- and single-stranded DNA, consistent with their translocase and helicase activities, respectively. XPA releases the inhibitory kinase module of TFIIH, displaces a 'plug' element from the DNA-binding pore in XPD, and together with the NER factor XPG stimulates XPD activity. Our results explain how TFIIH is switched from a transcription to a repair factor, and provide the basis for a mechanistic analysis of the NER pathway

Nonunion Employee Representation in North America: Diversity, Controversy, and Uncertain Future

The diverse conceptual perspectives and practical experiences with nonunion employee representation (NER) in the United States and Canada are reviewed. We first propose a 6 dimensional descriptive schema to categorize observed NER practices. Dimensions of diversity include (1) form, (2) function, (3) subjects, (4) representation characteristics, (5) extent of power, and (6) degree of permanence. We then turn to the NER controversy, which is a tangled skein consisting of many different threads of values and prescriptions. To unbundle the controversy, we develop four "faces" of NER - (1) evolutionary voice, (2) unity of interest; (3) union avoidance, and (4) complementary voice -- so that future research can more consciously test the validity of competing perspectives with hard data. Generalizing about NER is problematic because of these many dimensions of diversity, and because NER is viewed through different ideological and conceptual lenses. We conclude that NER's future trajectory is uncertain due to conflicting trends but in the short-run is most likely to remain a modest-sized phenomenon. Working Paper 06-4

Weakly Supervised Cross-Lingual Named Entity Recognition via Effective Annotation and Representation Projection

The state-of-the-art named entity recognition (NER) systems are supervised machine learning models that require large amounts of manually annotated data to achieve high accuracy. However, annotating NER data by human is expensive and time-consuming, and can be quite difficult for a new language. In this paper, we present two weakly supervised approaches for cross-lingual NER with no human annotation in a target language. The first approach is to create automatically labeled NER data for a target language via annotation projection on comparable corpora, where we develop a heuristic scheme that effectively selects good-quality projection-labeled data from noisy data. The second approach is to project distributed representations of words (word embeddings) from a target language to a source language, so that the source-language NER system can be applied to the target language without re-training. We also design two co-decoding schemes that effectively combine the outputs of the two projection-based approaches. We evaluate the performance of the proposed approaches on both in-house and open NER data for several target languages. The results show that the combined systems outperform three other weakly supervised approaches on the CoNLL data.Comment: 11 pages, The 55th Annual Meeting of the Association for Computational Linguistics (ACL), 201