Ubiquitylation, neddylation and the DNA damage response.

Failure of accurate DNA damage sensing and repair mechanisms manifests as a variety of human diseases, including neurodegenerative disorders, immunodeficiency, infertility and cancer. The accuracy and efficiency of DNA damage detection and repair, collectively termed the DNA damage response (DDR), requires the recruitment and subsequent post-translational modification (PTM) of a complex network of proteins. Ubiquitin and the ubiquitin-like protein (UBL) SUMO have established roles in regulating the cellular response to DNA double-strand breaks (DSBs). A role for other UBLs, such as NEDD8, is also now emerging. This article provides an overview of the DDR, discusses our current understanding of the process and function of PTM by ubiquitin and NEDD8, and reviews the literature surrounding the role of ubiquitylation and neddylation in DNA repair processes, focusing particularly on DNA DSB repair.J.S.B. is funded by the Wellcome Trust Clinical Fellowship (grant no. 094794/Z/10/Z). Research in the Jackson laboratory is funded by Cancer Research UK programme grant C6/A11224, the European Research Council and the European Community Seventh Framework Programme grant agreement no. HEALTH-F2-2010-259893 (DDResponse). Core funding is provided by CRUK (C6946/A14492) and the Wellcome Trust (WT092096). S.P.J. receives his salary from the University of Cambridge UK, supplemented by CRUK.This is the final published version. It first appeared at http://rsob.royalsocietypublishing.org/content/5/4/150018

RP-1 and JP-8 Thermal Stability Experiments

This work experimentally investigates the effect of fuel composition changes on jet and rocket fuel thermal stability. A High Reynolds Number Thermal Stability test device evaluated JP-8 and RP-1 fuels. The experiment consisted of an electrically heated, stainless steel capillary tube with a controlled fuel outlet temperature. An optical pyrometer monitored the increasing external temperature profiles of the capillary tube as deposits build inside during each test. Multiple runs of each fuel composition provided results on measurement repeatability. Testing a t two different facilities provided data on measurement reproducibility. The technique is able to distinguish between thermally stable and unstable compositions of JP-8 and intermediate blends made by combining each composition. The technique is also able to distinguish among standard RP-1 rocket fuels and those having reduced sulfur levels. Carbon burn off analysis of residue in the capillary tubes on the RP-1 fuels correlates with the external temperature results

Flicker fusion thresholds as a clinical identifier of a magnocellular-deficit dyslexic subgroup.

The magnocellular-dorsal system is well isolated by high temporal frequency. However, temporal processing thresholds have seldom been explored in developmental dyslexia nor its subtypes. Hence, performances on two, four-alternative forced-choice achromatic flicker fusion threshold tasks modulated at low (5%) and high (75%) temporal contrast were compared in dyslexic and neurotypical children individually matched for age and intelligence (8-12 years, n = 54 per group). As expected, the higher modulation resulted in higher flicker fusion thresholds in both groups. Compared to neurotypicals, the dyslexic group displayed significantly lower ability to detect flicker at high temporal frequencies, both at low and high temporal contrast. Yet, discriminant analysis did not adequately distinguish the dyslexics from neurotypicals, on the basis of flicker thresholds alone. Rather, two distinct dyslexic subgroups were identified by cluster analysis - one characterised by significantly lower temporal frequency thresholds than neurotypicals (referred to as 'Magnocellular-Deficit' dyslexics; 53.7%), while the other group ('Magnocellular-Typical' dyslexics; 46.3%) had comparable thresholds to neurotypicals. The two dyslexic subgroups were not differentially associated with phonological or naming speed subtypes and showed comparable mean reading rate impairments. However, correlations between low modulation flicker fusion threshold and reading rate for the two subgroups were significantly different (p = .0009). Flicker fusion threshold performances also showed strong classification accuracy (79.3%) in dissociating the Magnocellular-Deficit dyslexics and neurotypicals. We propose that temporal visual processing impairments characterize a previously unidentified subgroup of dyslexia and suggest that measurement of flicker fusion thresholds could be used clinically to assist early diagnosis and appropriate treatment recommendations for dyslexia

Flicker fusion thresholds as a clinical identifier of a magnocellular-deficit dyslexic subgroup.

The magnocellular-dorsal system is well isolated by high temporal frequency. However, temporal processing thresholds have seldom been explored in developmental dyslexia nor its subtypes. Hence, performances on two, four-alternative forced-choice achromatic flicker fusion threshold tasks modulated at low (5%) and high (75%) temporal contrast were compared in dyslexic and neurotypical children individually matched for age and intelligence (8-12 years, n = 54 per group). As expected, the higher modulation resulted in higher flicker fusion thresholds in both groups. Compared to neurotypicals, the dyslexic group displayed significantly lower ability to detect flicker at high temporal frequencies, both at low and high temporal contrast. Yet, discriminant analysis did not adequately distinguish the dyslexics from neurotypicals, on the basis of flicker thresholds alone. Rather, two distinct dyslexic subgroups were identified by cluster analysis - one characterised by significantly lower temporal frequency thresholds than neurotypicals (referred to as 'Magnocellular-Deficit' dyslexics; 53.7%), while the other group ('Magnocellular-Typical' dyslexics; 46.3%) had comparable thresholds to neurotypicals. The two dyslexic subgroups were not differentially associated with phonological or naming speed subtypes and showed comparable mean reading rate impairments. However, correlations between low modulation flicker fusion threshold and reading rate for the two subgroups were significantly different (p = .0009). Flicker fusion threshold performances also showed strong classification accuracy (79.3%) in dissociating the Magnocellular-Deficit dyslexics and neurotypicals. We propose that temporal visual processing impairments characterize a previously unidentified subgroup of dyslexia and suggest that measurement of flicker fusion thresholds could be used clinically to assist early diagnosis and appropriate treatment recommendations for dyslexia

Hiding in plain sight: the globally distributed bacterial candidate phylum PAUC34f

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chen, M. L., Becraft, E. D., Pachiadaki, M., Brown, J. M., Jarett, J. K., Gasol, J. M., Ravin, N. V., Moser, D. P., Nunoura, T., Herndl, G. J., Woyke, T., & Stepanauskas, R. Hiding in plain sight: the globally distributed bacterial candidate phylum PAUC34f. Frontiers in Microbiology, 11, (2020): 376, doi: 10.3389/fmicb.2020.00376.Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.This work was funded by the United States National Science Foundation grants 1460861 (REU site at Bigelow Laboratory for Ocean Sciences), 1441717, 1335810, and 1232982 to RS, and the Simons Foundation (Life Sciences Project Award ID 510023) to RS. NR was supported by the Ministry of Science and Higher Education of Russia. GH was supported by the Austrian Science Fund (FWF) project ARTEMIS (P28781-B21) and the European Research Council under the European Community’s Seventh Framework Program (FP7/2007-2013)/ERC (Grant Agreement No. 268595). JG was supported by Spanish project RTI2018-101025-B-I00. TW and JJ were funded by the U.S. Department of Energy, Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231

Lethal Mutagenesis of Picornaviruses with N-6-Modified Purine Nucleoside Analogues

RNA viruses exhibit extraordinarily high mutation rates during genome replication. Nonnatural ribonucleosides that can increase the mutation rate of RNA viruses by acting as ambiguous substrates during replication have been explored as antiviral agents acting through lethal mutagenesis. We have synthesized novel N-6-substituted purine analogues with ambiguous incorporation characteristics due to tautomerization of the nucleobase. The most potent of these analogues reduced the titer of poliovirus (PV) and coxsackievirus (CVB3) over 1,000-fold during a single passage in HeLa cell culture, with an increase in transition mutation frequency up to 65-fold. Kinetic analysis of incorporation by the PV polymerase indicated that these analogues were templated ambiguously with increased efficiency compared to the known mutagenic nucleoside ribavirin. Notably, these nucleosides were not efficient substrates for cellular ribonucleotide reductase in vitro, suggesting that conversion to the deoxyriboucleoside may be hindered, potentially limiting genetic damage to the host cell. Furthermore, a high-fidelity PV variant (G64S) displayed resistance to the antiviral effect and mutagenic potential of these analogues. These purine nucleoside analogues represent promising lead compounds in the development of clinically useful antiviral therapies based on the strategy of lethal mutagenesis

Recurrence of cervical intraepithelial lesions after thermo-coagulation in HIV-positive and HIV-negative Nigerian women

Background: The burden of cervical cancer remains huge globally, more so in sub-Saharan Africa. Effectiveness of screening, rates of recurrence following treatment and factors driving these in Africans have not been sufficiently studied. The purpose of this study therefore was to investigate factors associated with recurrence of cervical intraepithelial lesions following thermo-coagulation in HIV-positive and HIV-negative Nigerian women using Visual Inspection with Acetic Acid (VIA) or Lugol’s Iodine (VILI) for diagnosis. Methods: A retrospective cohort study was conducted, recruiting participants from the cervical cancer “see and treat” program of IHVN. Data from 6 sites collected over a 4-year period was used. Inclusion criteria were: age ≥18 years, baseline HIV status known, VIA or VILI positive and thermo-coagulation done. Logistic regression was performed to examine the proportion of women with recurrence and to examine factors associated with recurrence. Results: Out of 177 women included in study, 67.8 % (120/177) were HIV-positive and 32.2 % (57/177) were HIV-negative. Recurrence occurred in 16.4 % (29/177) of participants; this was 18.3 % (22/120) in HIV-positive women compared to 12.3 % (7/57) in HIV-negative women but this difference was not statistically significant (p-value 0.31). Women aged ≥30 years were much less likely to develop recurrence, adjusted OR = 0.34 (95 % CI = 0.13, 0.92). Among HIV-positive women, CD4 count <200cells/mm3 was associated with recurrence, adjusted OR = 5.47 (95 % CI = 1.24, 24.18). Conclusion: Recurrence of VIA or VILI positive lesions after thermo-coagulation occurs in a significant proportion of women. HIV-positive women with low CD4 counts are at increased risk of recurrent lesions and may be related to immunosuppression

Neddylation promotes ubiquitylation and release of Ku from DNA-damage sites.

The activities of many DNA-repair proteins are controlled through reversible covalent modification by ubiquitin and ubiquitin-like molecules. Nonhomologous end-joining (NHEJ) is the predominant DNA double-strand break (DSB) repair pathway in mammalian cells and is initiated by DSB ends being recognized by the Ku70/Ku80 (Ku) heterodimer. By using MLN4924, an anti-cancer drug in clinical trials that specifically inhibits conjugation of the ubiquitin-like protein, NEDD8, to target proteins, we demonstrate that NEDD8 accumulation at DNA-damage sites is a highly dynamic process. In addition, we show that depleting cells of the NEDD8 E2-conjugating enzyme, UBE2M, yields ionizing radiation hypersensitivity and reduced cell survival following NHEJ. Finally, we demonstrate that neddylation promotes Ku ubiquitylation after DNA damage and release of Ku and Ku-associated proteins from damage sites following repair. These studies provide insights into how the NHEJ core complex dissociates from repair sites and highlight its importance for cell survival following DSB induction.We thank Thimo Kurz (University of Dundee, UK) for providing MLN4924 and Kate Dry, Rimma Berlotserkovskaya (S.P.J.’s laboratory), and Eric Lightcap (Takeda Pharmaceuticals) for critical reading of the manuscript. We thank Sylvie Urbe and Michael Clague (University of Liverpool, UK) for providing the GFP-CSN5 plasmid, the Division of Signal Transduction Therapy (University of Dundee, UK) for providing UBE2M and UBE2F plasmids, Matthew Petroski (Sanford-Burnham Medical Research Institute, US) for providing FLAG-UBA3 wild-type (WT) and FLAG-UBA3-A171T constructs, and Nico Dantuma (Karolinska Institute, Sweden) and Changshun Shao (Rutgers University) for providing CUL4A and CUL4B plasmids, respectively. We also thank Nicola Lawrence, Alex Sossick, and Richard Butler (Gurdon Institute, Cambridge, UK) for help with microscopy, Volocity, and Fiji. Research in the S.P.J.’s laboratory is funded by Cancer Research UK programme grant C6/A11224, the European Research Council, and the European Community Seventh Framework Programme grant agreement no. HEALTH-F2-2010-259893 (DDResponse). Core funding is provided by CRUK (C6946/A14492) and the Wellcome Trust (WT092096). S.P.J. receives his salary from the University of Cambridge, UK, supplemented by CRUK. N.L. is funded by CRUK programme grant C6/A11224, J.S.B. is funded by a Wellcome Trust Clinical Fellowship (WT083416), and Y.G. and M.S.-C. are funded by European Research Council grant DDREAM. S.B. was funded by an EMBO long-term fellowship ALTF 93-2010, Cancer Research UK, and a post-doctoral grant from Ligue Nationale Contre le Cancer. P.B. is supported by the Emmy Noether Programme of the German Research Foundation (DFG, BE 5342/1-1).This is the final published version. It first appeared at http://www.sciencedirect.com/science/article/pii/S2211124715003496

Multiple Method Contraception Use among African American Adolescents in Four US Cities

We report on African American adolescents' (N = 850; M age = 15.4) contraceptive practices and type of contraception utilized during their last sexual encounter. Respondents completed measures of demographics, contraceptive use, sexual partner type, and ability to select “safe” sexual partners. 40% endorsed use of dual or multiple contraceptive methods; a total of 35 different contraceptive combinations were reported. Perceived ability to select “safe” partners was associated with not using contraception (OR = 1.25), using less effective contraceptive methods (OR = 1.23), or hormonal birth control (OR = 1.50). Female gender predicted hormonal birth control use (OR = 2.33), use of less effective contraceptive methods (e.g., withdrawal; OR = 2.47), and using no contraception (OR = 2.37). Respondents' age and partner type did not predict contraception use. Adolescents used contraceptive methods with limited ability to prevent both unintended pregnancies and STD/HIV. Adolescents who believed their partners posed low risk were more likely to use contraceptive practices other than condoms or no contraception. Reproductive health practitioners are encouraged to help youth negotiate contraceptive use with partners, regardless of the partner's perceived riskiness