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X-Ray Spectrometry     Hybrid Journal   (Followers: 9)
Zeitschrift für Naturforschung B : A Journal of Chemical Sciences     Open Access   (Followers: 1)

  First | 1 2 3 4     

Journal Cover Photochemistry and Photobiology
  [SJR: 0.63]   [H-I: 106]   [1 followers]  Follow
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 0031-8655 - ISSN (Online) 1751-1097
   Published by John Wiley and Sons Homepage  [1605 journals]
  • Novel Bi2WO6 coupled Fe3O4 Magnetic Photocatalysts: Preparation,
           Characterization and Photodegradation of Tetracycline Hydrochloride
    • Authors: Tianye Wang; Shuang Zhong, Shuang Zou, Fuhuan Jiang, Limin Feng, Xiaosi Su
      Abstract: Novel Bi2WO6 coupled Fe3O4 magnetic photocatalysts with excellent and stable photocatalytic activity for degrading tetracycline hydrochloride and RhB were successfully synthesized via a facile solvothermal route. Through the characterization of the as-prepared magnetic photocatalysts by XRD, SEM, TEM, XPS, UV-vis diffuse reflectance spectra, it was found that the as-prepared magnetic photocatalysts were synthesized by the coupling of Bi2WO6 and Fe3O4, and introduction of appropriated Fe3O4 can improved nanospheres morphology and visible-light response. Among them, BFe2 (0.16% Fe3O4) exhibited the best photocatalytic activity for degradation of TCH, reaching 81.53% after 90min. Meanwhile, the as-prepared magnetic photocatalysts showed great separation and recycle property. Moreover, the results of EIS demonstrated that the well conductivity of Fe3O4 can promoted photogenerated charge carriers transfer and inhibited recombination of electron-hole pairs, so that Bi2WO6/Fe3O4 exhibited enhanced photocatalytic activity on degradation of TCH and RhB. Hence, this work provides a principle method to synthesize Bi2WO6/Fe3O4 with excellent photocatalytic performance for actual application, in addition, it showed that introduction of Fe3O4 not only can provide magnetism, but also can enhance photocatalytic activity of Bi2WO6/Fe3O4 magnetic photocatalysts.This article is protected by copyright. All rights reserved.
      PubDate: 2017-02-15T16:45:28.60909-05:0
      DOI: 10.1111/php.12739
  • Enhancement of the Efficacy of Photodynamic Inactivation of Candida
           albicans with the Use of Biogenic Gold Nanoparticles
    • Authors: Irena Maliszewska; Barbara Lisiak, Katarzyna Popko, Katarzyna Matczyszyn
      Abstract: This study reports on successful photodynamic inactivation of planktonic and biofilm cells of Candida albicans using Rose Bengal (RB) in combination with biogenic gold nanoparticles synthesized by the cell-free filtrate of Penicillium funiculosum BL1 strain. Monodispersed colloidal gold nanoparticles coated with proteins were characterized by a number of techniques including SEM-EDS, TEM, UV-Vis absorption and fluorescence spectroscopy, as well as Fourier transform infrared spectroscopy to be 24±3 nm spheres coated with proteins. A Xe-lamp (output power of 20mW, delivering intensity of 53 mW cm−2) was used as a light source. The most effective reduction in the number of planktonic cells was found after 30 minutes of Xe lamp light irradiation (95.4 J cm−2) and was 4.89 log10 that is 99.99% kill compared with 2.19 log10 or 99.37% for RB. The biofilm cells were more resistant to photodynamic inactivation and the highest effective reduction in the number of cells was found after 30 minutes of irradiation in the presence of the RB-gold nanoparticles mixture and was 1.53 log10, that is 97.04% kill compared with 0.6 log10 or 74.73% for RB.The probable mechanism of enhancement of RB-mediated photodynamic fungicidal efficacy against Candida albicans in the presence of biogenic gold nanoparticles is discussed leading to the conclusion that this process may have a multifaceted character.This article is protected by copyright. All rights reserved.
      PubDate: 2017-02-12T20:20:28.272401-05:
      DOI: 10.1111/php.12733
  • Antigenotoxic Effect Against Ultraviolet Radiation Induced DNA Damage of
           the Essential Oils from Lippia Species
    • Authors: Nathalia Quintero Ruiz; Yuri Cordoba Campo, Elena E. Stashenko, Jorge Luis Fuentes
      Abstract: The antigenotoxicity against ultraviolet radiation (UV) -induced DNA damage of essential oils (EO) from Lippia species was studied using SOS Chromotest. Based on the minimum concentration that significantly inhibits genotoxicity, the genoprotective potential of EO from highest to lowest was L. alba, citral -rich chemotype (RC) > L. graveolens, thymol-RC ≈ L. origanoides, thymol-RC ≈ L. origanoides, carvacrol-RC > L. micromera, thymol-RC ≈ L. citriodora, citral-RC > L. alba, myrcenone-RC > L. alba, carvone-RC > L. origanoides, p-cymene/phellandrene-RC. EO from L. dulcis, trans-β-caryophyllene-RC did not reduce the DNA damage. A gas chromatography with flame ionization detection analysis (GC-FID) was conducted to evaluate the solubility of the major EO constituents under our experimental conditions. GC-FID analysis showed that, at least partially, major EO constituents were water-soluble and therefore, they were related with the antigenotoxicity detected for EO. Constituents such as p-cymene, geraniol, carvacrol, thymol, citral and 1,8-cineole showed antigenotoxicity. The antioxidant activity of EO constituents was also determined using the oxygen radical antioxidant capacity (ORAC) assay. The results shown that the antigenotoxicity of the EO constituents was unconnected with their antioxidant activity. The antigenotoxicity to different constituent binary mixtures suggest that synergistic effects can occur in some of the studied EO.This article is protected by copyright. All rights reserved.
      PubDate: 2017-02-08T13:00:41.334056-05:
      DOI: 10.1111/php.12735
  • Photo Co-Carcinogenesis of Topically Applied Retinyl Palmitate in SKH-1
           Hairless Mice
    • Authors: Mary D. Boudreau; Frederick A. Beland, Robert P. Felton, Peter P. Fu, Paul C. Howard, Paul W. Mellick, Brett T. Thorn, Greg R. Olson
      Abstract: Cosmetic products that contain retinyl palmitate are popular as anti-aging skin treatments; however, recent studies suggest a risk for enhanced skin tumor development with topical retinyl palmitate applications and exposure to solar ultraviolet radiation (UVR). In this study, we investigated the potential of retinyl palmitate to enhance UVR-induced photo co-carcinogenesis. Groups of 36 male and 36 female SKH-1 hairless mice were exposed to simulated solar light (SSL) and treated with the control cream or creams containing retinyl palmitate, five days per week for 40 weeks. Other groups of mice were exposed to SSL and received no cream treatment or received cream treatments and were exposed to ultraviolet-A or -B. Mice were monitored for the development of skin tumors, and the incidences and multiplicities of squamous cell neoplasia were determined by histopathology. In both the absence and presence of SSL, mice administered the control cream developed skin tumors earlier and had higher incidences and multiplicities of skin squamous cell neoplasms than mice that received no cream treatment. Compared to the control cream groups, mice exposed to SSL and administered the retinyl palmitate creams demonstrated earlier onsets of skin tumors and had increased incidences and multiplicities of squamous cell skin neoplasms.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-28T02:50:51.17796-05:0
      DOI: 10.1111/php.12730
  • Luciferin Regenerating Enzyme (LRE) Crystal Structure Is Solved but its
           Function Is Still Unclear
    • Authors: Saman Hosseinkhani; Elaheh Emamgholi Zadeh, Fatemeh Sahebazzamani, Farangis Ataei, Roohullah Hemmati
      Abstract: Contribution of Luciferin-Regenerating Enzyme (LRE) for in vitro recycling of D-luciferin has been reported. According to crystal structure of LRE, it is a beta-propeller protein which is a type of all-β protein architecture. In this overview, reinvestigation of the luciferase-based LRE assays and its function is reported. Until now, sequence of LRE genes from 4 different species of firefly has been reported. In spite of previous reports, T-LRE (from Lampyris turkestanicus) was cloned and expressed in E. coli as well as Pichia pastoris in a non-soluble form as inclusion body. According to recent investigations, bioluminescent signal of soluble T-LRE-luciferase-coupled assay increased and then reached an equilibrium state in the presence of D-cysteine. In addition, the results revealed that both D- and L-cysteine in the absence of T-LRE caused a significant increase in bioluminescence intensity of luciferase over a long time. Based on activity measurements and spectroscopic results, D-cysteine increased the activity of luciferase due to its redox potential and induction of conformational changes in structure and kinetics properties. In conclusion, in spite of previous reports on the effect of LRE (at least T-LRE) on luciferase activity, most of the increase of luciferase activity is caused by direct effect of D-cysteine on structure and activity of firefly luciferase. Moreover, bioinformatics analysis cannot support the presence of LRE in peroxisome of photocytes in firefly lanterns.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-25T04:25:44.969409-05:
      DOI: 10.1111/php.12723
  • Silibinin Treatment Inhibits the Growth of Hedgehog Inhibitor Resistant
           Basal Cell Carcinoma Cells via Targeting EGFR-MAPK-Akt and Hedgehog
    • Authors: Arpit Dheeraj; Cynthia M. Rigby, Cindy L. O'Bryant, Chapla Agarwal, Rana P. Singh, Gagan Deep, Rajesh Agarwal
      Abstract: Basal cell carcinoma (BCC) is the most common skin malignancy. Deregulated hedgehog signaling plays a central role in BCC development; therefore hedgehog inhibitors have been approved to treat locally advanced or metastatic BCC. However, the development of resistance to hedgehog inhibitors is the major challenge in effective treatment of this disease. Herein, we evaluated the efficacy of a natural agent silibinin to overcome resistance with hedgehog inhibitors (Sant-1 and GDC-0449) in BCC cells. Silibinin (25-100 μM) treatment for 48 hrs strongly inhibited growth and induced death in ASZ001, Sant-1 resistant (ASZ001-Sant-1) and GDC-0449 resistant (ASZ001-GDC-0449) BCC cells. Furthermore, colony forming ability of ASZ001, ASZ001-Sant-1 and ASZ001-GDC-0449 cells was completely inhibited by silibinin treatment. Molecular analysis showed that silibinin treatment decreased the level of phosphorylated-EGFR (Tyrosine-1173) and total EGFR in ASZ001-Sant-1 cells; key signaling molecules responsible for BCC resistance towards hedgehog inhibitors. Further, silibinin treatment decreased the phosphorylated-Akt (Serine-473), phosphorylated-ERK1/2 (Threonine 202/Tyrosine 204), cyclin D1 and Gli-1 level but increased the SUFU expression in ASZ001-Sant-1 resistant cells. Silibinin treatment of ASZ001-Sant-1 resistant cells also decreased bcl-2 but increased cleaved caspases 3 and PARP cleavage, suggesting induction of apoptosis. Together, these results support silibinin use to target hedgehog inhibitors resistant BCC cells.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-25T02:20:33.15108-05:0
      DOI: 10.1111/php.12727
  • Probing the Electronic Structure of Bacteriochlorophyll Radical Ions – A
           Theoretical Study of the Effect of Substituents on Hyperfine Parameters
    • Authors: Sebastian Sinnecker; Wolfgang Lubitz
      Abstract: In reaction centers (RCs) of photosynthesis a light-induced charge separation takes place creating radical cations and anions of the participating cofactors. In photosynthetic bacteria different bacteriochlorophylls (BChl) are involved in this process. Information about the electronic structure of the BChl radical cations and anions can be obtained by measuring the electron spin density distribution via the electron-nuclear hyperfine interaction using EPR and ENDOR techniques. In this communication we report isotropic hyperfine coupling constants (hfcs) of the BChl b and g radical cations and anions, calculated by density functional theory, and compare them with the more common radical ions of BChl a and with available experimental data. The observed differences in the computed hyperfine data are discussed in view of a possible distinction between these species by EPR/ENDOR methods. In addition, 14N nuclear quadrupole coupling constants (nqcs) computed for BChl a, b, g, and also for Chl a in their charge neutral, radical cation, and radical anion states are presented. These nqcs are compared with experimental values obtained by ESEEM spectroscopy on several different radical ions.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-25T02:10:41.040684-05:
      DOI: 10.1111/php.12724
  • Ultraviolet Radiation Induced Down-regulation of SERCA2 Mediates
           Activation of NLRP3 Inflammasome in Basal Cell Carcinoma
    • Authors: Israr Ahmad; Kashiff M. Muneer, Michelle E. Chang, Hana M. Nasr, Jacqueline M. Clay, Conway C. Huang, Nabiha Yusuf
      Abstract: Basal cell carcinomas (BCCs) account for majority of skin malignancies in the United States. The incidence of BCCs is strongly associated with exposure of ultraviolet (UV) radiation. Nucleotide-binding domain, leucine-rich-repeat-containing family, pyrin domain-containing 3 (NLRP3) inflammasome plays an important role in innate immune responses. Different stimuli such as toxins, microorganisms, and particles released from injured cells activate the NLRP3 inflammasome. Activated NLRP3 results in activation of caspase-1, which cleaves pro-IL-1β to active IL-1β. In the present study, we have shown that NLRP3 is expressed in human basal cell carcinomas. The proximal steps in activation of NLRP3 inflammasome are not well understood. Here, we have attempted to elucidate a critical role for Ca2+ mobilization in activation of the NLRP3 inflammasome by UVB exposure using HaCaT keratinocytes. We have demonstrated that UVB exposure blocks Ca2+ mobilization by downregulating the expression of sarco/endoplasmic reticulum Ca2+-ATPase (SERCA2), a component of store-operated Ca2+ entry (SOCE) that leads to activation of the NLRP3 inflammasome.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-25T02:10:37.800776-05:
      DOI: 10.1111/php.12725
  • Proteomic Analyses of Changes in Synechococcus sp. PCC7942 Following UV-C
    • Authors: Xi Peng; Jie Yang, Yang Gao
      Abstract: UV-C's effects on the physiological and biochemical processes of cyanobacteria have been well characterized. However, the molecular mechanisms of cyanobacteria's tolerance to UV-C still needs further investigation. This research attempts to decode the variation in protein abundances in cyanobacteria after UV-C stress. Different expression levels of proteins in the cytoplasm of Synechococcus sp. PCC7942 under UV-C stress were investigated by using a comparative proteomic approach. Forty-seven UV-C-regulated proteins were identified by MALDI-TOF analysis and classified by Gene Ontology (GO). After studying their pathways, the proteins were mainly enriched in the groups of protein folding, inorganic ion transport, and energy production. By focusing on these areas, this study reveals the correlation between UV-C stress-responsive proteins and the physiological changes of Synechococcus sp. PCC7942 under UV-C radiation. These findings may open up new areas for further exploration in the homeostatic mechanisms associated with cyanobacteria responses to UV-C radiation.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-25T02:10:26.721776-05:
      DOI: 10.1111/php.12726
  • Schoolyard Shade and Sun Exposure: Assessment of Personal Monitoring
           During Children's Physical Activity
    • Authors: Jennifer K. Vanos; Grant R. McKercher, Kylie Naughton, Marc Lochbaum
      Abstract: Childhood exposure to ultraviolet radiation (UVR) is a major risk factor for the development of melanoma later in life. However, it is challenging to accurately determine personal outdoor exposure to UVR, specifically erythemally-weighted UVR (UVEry), due to technological constraints, variable time-activity patterns, and the influence of outdoor environmental design. To address this challenge, the current study utilized mobile and stationary techniques to examine the UVEry exposures of 14 children in a schoolyard in Lubbock, TX in spring 2016. The aims of the study were to examine the influence of artificial shade on personal UVEry exposures and to assess full sun exposure ratios (ERs) within the same playground micro-environment. On average, personal wrist dosimeters measured 18% of the total onsite UVEry measured by a stationary UV pyranometer. Shade was found to significantly reduce the personal UVEry exposures by 55%, UVB280–315nm exposures by 91%, and the overall solar radiation by 84%. Substantial benefits can be garnered through focused design of children's recreational space to utilize shade, both natural and artificial, to reduce UVR exposures during play, and to extend safe outdoor stays. Finally, although the wrist is a practical location, it often underestimates full exposures, particularly during physical activity.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-18T03:22:32.320554-05:
      DOI: 10.1111/php.12721
  • A Comparison of Dose Metrics to Predict Local Tumor Control for
           Photofrin-mediated Photodynamic Therapy
    • Authors: Haixia Qiu; Michele M. Kim, Rozhin Penjweini, Jarod C. Finlay, Theresa M. Busch, Tianhao Wang, Wenshen Guo, Keith A. Cengel, Charles B. Simone, Eli Glatstein, Timothy C. Zhu
      Abstract: This preclinical study examines light fluence, PDT dose, and “apparent reacted singlet oxygen”, [1O2]rx, to predict local control rate (LCR) for Photofrin-mediated photodynamic therapy (PDT) of radiation-induced fibrosarcoma (RIF) tumors. Mice bearing RIF tumors were treated with in-air fluences (50-250 J/cm2) and in-air fluence rates (50-150 mW/cm2) at Photofrin dosages of 5 and 15 mg/kg and a drug-light interval of 24 hours using a 630nm 1-cm diameter collimated laser. A macroscopic model were used to calculate [1O2]rx and PDT dose based on in vivo explicit dosimetry of the drug concentration, light fluence, and tissue optical properties. PDT dose and [1O2]rx were defined as a temporal integral of drug concentration and fluence rate, and singlet oxygen concentration consumed divided by the singlet oxygen lifetime, respectively. LCR was stratified for different dose metrics for 74 mice (66 + 8 control). Complete tumor control at 14 days was observed for [1O2]rx ≥ 1.1 mM or PDT dose ≥ 1200 μMJ/cm2 but cannot be predicted with fluence alone. LCR increases with increasing [1O2]rx and PDT dose but is not well correlated with fluence. Comparing dosimetric quantities, [1O2]rx outperformed both PDT dose and fluence in predicting tumor response and correlating with LCR.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-13T03:20:41.343478-05:
      DOI: 10.1111/php.12719
  • The B6-vitamer Pyridoxal is a Sensitizer of UVA-induced Genotoxic Stress
           in Human Primary Keratinocytes and Reconstructed Epidermis
    • Authors: Rebecca Justiniano; Joshua D. Williams, Jessica Perer, Ahn Hua, Jessica Lesson, Sophia L. Park, Georg T. Wondrak
      Abstract: UVA-driven photooxidative stress in human skin may originate from excitation of specific endogenous chromophores acting as photosensitizers. Previously, we have demonstrated that 3-hydroxypyridine-derived chromophores including B6-vitamers (pyridoxine, pyridoxamine, and pyridoxal) are endogenous photosensitizers that enhance UVA-induced photooxidative stress in human skin cells. Here, we report that the B6-vitamer pyridoxal is a sensitizer of genotoxic stress in human adult primary keratinocytes (HEKa) and reconstructed epidermis. Comparative array analysis indicated that exposure to the combined action of pyridoxal and UVA caused upregulation of heat shock (HSPA6, HSPA1A, HSPA1L, HSPA2), redox (GSTM3, EGR1, MT2A, HMOX1, SOD1), and genotoxic (GADD45A, DDIT3, CDKN1A) stress response gene expression. Together with potentiation of UVA-induced photooxidative stress and glutathione depletion, induction of HEKa cell death occurred only in response to the combined action of pyridoxal and UVA. In addition to activational phosphorylation indicative of genotoxic stress [p53 (Ser15) and γ-H2AX (Ser139)], comet analysis indicated the formation of Fpg-sensitive oxidative DNA lesions, observable only after combined exposure to pyridoxal and UVA. In human reconstructed epidermis, pyridoxal pre-incubation followed by UVA exposure caused genomic oxidative base damage, procaspase 3 cleavage, and TUNEL-positivity, consistent with UVA-driven photooxidative damage that may be relevant to human skin exposed to high concentrations of B6-vitamers.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-13T02:25:40.440983-05:
      DOI: 10.1111/php.12720
  • UVA Light-mediated Ascorbate Oxidation in Human Lenses
    • Authors: Stefan Rakete; Ram H. Nagaraj
      Abstract: Whether ascorbate oxidation is promoted by UVA light in human lenses and whether this process is influenced by age and GSH levels are not known. In this study, we used paired lenses from human donors. One lens of each pair was exposed to UVA light whereas the other lens was kept in the dark for the same period of time as the control. Using LC-MS/MS analyses, we found that older lenses (41 to 73 years) were more susceptible to UVA-induced ascorbate oxidation than younger lenses (18 to 40 years). Approximately 36% of the ascorbate (relative to control) was oxidized in older lenses compared to ~16% in younger lenses. Furthermore, lenses with higher levels of GSH were less susceptible to UVA-induced ascorbate oxidation compared to those with lower levels, and this effect was not dependent on age. The oxidation of ascorbate led to elevated levels of reactive α-dicarbonyl compounds. In summary, our study showed that UVA light exposure leads to ascorbate oxidation in human lenses and that such oxidation is more pronounced in aged lenses and is inversely related to GSH levels. Our findings suggest that UVA light exposure could lead to protein aggregation through ASC oxidation in human lenses.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-13T02:06:07.964104-05:
      DOI: 10.1111/php.12717
  • Bioluminescence Imaging of Spheroids for High-throughput Longitudinal
           Studies on 3D Cell Culture Models
    • Authors: Luca Cevenini; Maria M. Calabretta, Antonia Lopreside, Bruce R. Branchini, Tara L. Southworth, Elisa Michelini, Aldo Roda
      Abstract: Bioluminescent (BL) cell-based assays based on two-dimensional (2D) monolayer cell cultures represent well-established bioanalytical tools for pre-clinical screening of drugs. However, cells in 2D cultures do not often reflect the morphology and functionality of living organisms, thus limiting the predictive value of 2D cell-based assays. Conversely, 3D cell models have the capability to generate the extracellular matrix and restore cell-to-cell communications; thus, they are the most suitable model to mimic in vivo physiology. In this work we developed a non-destructive real time BL imaging assay of spheroids for longitudinal studies on 3D cell models. A high-throughput BL 3D cell-based assay in micro-patterned 96 multi-well plate format is reported. The assay performance was assessed using the transcriptional regulation of nuclear factor K beta response element in human embryonic kidney (Hek293) cells. We compared concentration-response curves for tumor necrosis factor α with those obtained using conventional 2D cell cultures. One of the main advantages of this approach is the non-lysing nature of the assay, which allows for repetitive measurements on the same sample. The assay can be implemented in any laboratory equipped with basic cell culture facilities and paves the way to the development of new 3D bioluminescent cell-based assays.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-13T02:06:03.66227-05:0
      DOI: 10.1111/php.12718
  • Type I and II Photosensitized Oxidation Reactions: Guidelines and
           Mechanistic Pathways
    • Authors: Maurício da Silva Baptista; Jean Cadet, Paolo Di Mascio, Ashwini A. Ghogare, Alexander Greer, Michael R. Hamblin, Carolina Lorente, Silvia Cristina Nunez, Martha Simões Ribeiro, Andrés H. Thomas, Mariana Vignoni, Tania Mateus Yoshimura
      Abstract: Here, ten guidelines are presented for a standardized definition of type I and II photosensitized oxidation reactions. Because of varied notions of reactions mediated by photosensitizers, a checklist of recommendations is provided for their definitions. Type I and type II photoreactions are oxygen-dependent and involve unstable species such as the initial formation of radical cation or neutral radicals from the substrates and/or singlet oxygen (1O2 1∆g) by energy transfer to molecular oxygen. In addition, superoxide anion radical (O2•-) can be generated by a charge transfer reaction involving O2 or more likely indirectly as the result of O2-mediated oxidation of the radical anion of type I photosensitizers. In subsequent reactions, O2•- may add and/or reduce a few highly oxidizing radicals that arise from the deprotonation of the radical cations of key biological targets. O2•- can also undergo dismutation into H2O2, the precursor of the highly reactive hydroxyl radical (•OH) that may induce delayed oxidation reactions in cells. In the second part several examples of type I and type II photosensitized oxidation reactions are provided to illustrate the complexity and the diversity of the degradation pathways of mostly relevant biomolecules upon one-electron oxidation and singlet oxygen reactions.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-13T01:55:29.576825-05:
      DOI: 10.1111/php.12716
  • Bioluminescence in Dinoflagellates: Evidence that the Adaptive Value of
           Bioluminescence in Dinoflagellates is Concentration Dependent
    • Authors: Karen A. Hanley; Edith A. Widder
      Abstract: Three major hypotheses have been proposed to explain why dinoflagellate bioluminescence deters copepod grazing: startle response, aposematic warning, and burglar alarm. These hypotheses propose dinoflagellate bioluminescence (A) startles predatory copepods, (B) warns potential predators of toxicity, and (C) draws the attention of higher-order visual predators to the copepod's location. While the burglar alarm is the most commonly accepted hypothesis, it requires a high concentration of bioluminescent dinoflagellates to be effective, meaning the bioluminescence selective advantage at lower, more commonly observed, dinoflagellate concentrations may result from another function (e.g. startle response or aposematic warning). Therefore, a series of experiments was conducted to evaluate copepod grazing (Acartia tonsa) on bioluminescent dinoflagellates (during bioluminescent and non-bioluminescent phases, corresponding to night and day, respectively) at different concentrations (10, 1000, and 3000 cells ml−1), on toxic (Pyrodinium bahamense var. bahamense) and non-toxic (Lingulodinium polyedrum) bioluminescent dinoflagellates, and in the presence of non-luminescent diatoms (Thalassiosira eccentrica). Changes in copepod ingestion rates, clearance rates, and feeding preferences as a result of these experimental factors, particularly during the mixed trails with non-luminescent diatoms, indicate there is a concentration threshold at which the burglar alarm becomes effective and below which dinoflagellate bioluminescence functions as an aposematic warning.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-07T02:30:28.904989-05:
      DOI: 10.1111/php.12713
  • Mutants of Ca2+-regulated Photoprotein Obelin for Site-specific
    • Authors: Vasilisa V. Krasitskaya; Ludmila P. Burakova, Anastasia A. Komarova, Eugenia E. Bashmakova, Ludmila A. Frank
      Abstract: Color variants of Ca2+-regulated photoprotein obelin were shown to be an important tool for dual-analyte binding assay. To provide site-directed conjugation with biospecific molecules, several obelin color mutants carrying unique cysteine residues were obtained and characterized for their novel properties.A pair of obelins Y138F,A5C and W92F,H22E,D12C was found to be most suitable (in terms of high bioluminescent activity and stability) as reporters in simultaneous assay of two targets in a sample. Availability of SH-groups, accessible for chemical modification essentially simplifies the synthesis of biospecific conjugates, increases their yield and conserves obelins’ bioluminescence activity. Conjugates with immunoglobulin and oligonucleotide were produced and successfully applied in single nucleotide polymorphism genotyping.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-07T02:30:22.349355-05:
      DOI: 10.1111/php.12712
  • Changes in Time Spent Outdoors During the Daytime in Rural Populations in
           Four Geographically Distinct Regions in China: A Retrospective Study
    • Authors: Qian Gao; Fang Wang, Liwen Hu, Jiaming Yu, Rong Liu, Yang Wang, Yang Liu
      Abstract: Changes in time-activity patterns may influence personal exposure to various environmental factors and affect individual health. However, few studies have investigated the changes in patterns of time spent outdoors. To investigate the trends in outdoor activity in recent decades in China, a retrospective questionnaire was used to examine the amount and pattern of time spent outdoors during the day by 2076 subjects in four geographically distinct rural regions of China. Rural Chinese people spent less time outdoors than they used to because of the economic development, increase in education, and changes in working conditions that occurred over time. Outdoor time was the shortest during the school stage of life (Sanya: 3.24-3.61; Shaoxing: 3.35-3.68; Lhasa: 4.37-4.54; Xiuyan: 2.94-3.26 hours per day). Subjects in wealthy regions spent less time outdoors during their working stage of life. In the four regions in this study, the average daily times spent outdoors were 3%–13% lower for subjects aged 40 to 59 years and 20%–38% lower for those under 40 years compared to subjects aged 60 years and over. Certain health-related issues, such as vitamin D deficiency, will become more prominent in China if this trend continues.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-07T02:30:20.063399-05:
      DOI: 10.1111/php.12714
  • Progress in the Study of Bioluminescent Earthworms
    • Authors: Natalja S. Rodionova; Emilia Rota, Aleksandra S. Tsarkova, Valentin N. Petushkov
      Abstract: Even though bioluminescent oligochaetes rarely catch people's eyes due to their secretive lifestyle, glowing earthworms sighting reports have come from different areas on all continents except Antarctica. A major breakthrough in the research of earthworm bioluminescence occurred in the 1960s with the studies of the North American Diplocardia longa. Comparative studies conducted on 13 earthworm species belonging to six genera showed that N-isovaleryl-3-aminopropanal (Diplocardia luciferin) is the common substrate for bioluminescence in all examined species, while luciferases appeared to be responsible for the color of bioluminescence. The second momentous change in the situation has occurred with the discovery in Siberia (Russia) of two unknown luminous enchytraeids. The two bioluminescent systems belong to different types, have different spectral characteristics and localization, and different temperature and pH optima. They are unique, and this fact is confirmed by the negative results of all possible cross-reactions. The bioluminescent system of Henlea sp. comprises four essential components: luciferase, luciferin, oxygen and calcium ion. For F. heliota the luminescent reaction requires five components: luciferase, luciferin, ATP, magnesium ion and oxygen. Along with luciferin more than a dozen analogs were isolated from earthworm biomass. These novel peptide-like natural compounds represent an unprecedented chemistry found in terrestrial organisms.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-07T02:25:26.127988-05:
      DOI: 10.1111/php.12709
  • Phytochemicals for the Prevention of Photocarcinogenesis
    • Authors: Mary Katherine Montes de Oca; Ross L. Pearlman, Sarah F. McClees, Rebecca Strickland, Farrukh Afaq
      Abstract: Ultraviolet (UV) exposure has an array of damaging effects and is the main cause of skin cancer in humans. Non-melanoma skin cancer (NMSC), including basal cell carcinoma and squamous cell carcinoma, is the most common type of cancer. Incidence of NMSC has increased due to greater UV radiation, increased life expectancy, and other changes in lifestyle; the annual cost of skin cancer treatment in the United States has increased concurrently to around eight billion dollars. Because of these trends, novel approaches to skin cancer prevention have become an important area of research to decrease skin cancer morbidity and defray the costs associated with treatment. Chemoprevention aims to prevent or delay the development of skin cancer through the use of phytochemicals. Use of phytochemicals as chemopreventive agents has gained attention due to their low toxicity and anti-carcinogenic properties. Phytochemicals also exhibit antioxidant, anti-inflammatory, and anti-proliferative effects which support their use as chemopreventive agents, particularly for skin cancer. Preclinical and human studies have shown that phytochemicals decrease UV-induced skin damage and photocarcinogenesis. In this review article, we discuss the selected phytochemicals that may prevent or delay UV-induced carcinogenesis and highlights their potential use for skin protection.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-07T02:25:24.45797-05:0
      DOI: 10.1111/php.12711
  • FRET in a Synthetic Flavin- and Bilin-binding Protein
    • Authors: Julian Simon; Aba Losi, Kai-Hong Zhao, Wolfgang Gärtner
      Abstract: The last decade has seen development and application of a large number of novel fluorescence-based techniques that have revolutionized fluorescence microscopy in life sciences. Preferred tags for such applications are genetically encoded fluorescent proteins (FP), mostly derivatives of the green fluorescent protein (GFP). Combinations of FPs with wavelength-separated absorption/fluorescence properties serve as excellent tools for molecular interaction studies, e.g., protein-protein complexes or enzyme-substrate complexes, based on the FRET phenomenon (Förster resonance energy transfer). However, alternatives are requested for experimental conditions where FP proteins or FP couples are not or less efficiently applicable. We here report as a ‘proof of principle’ a specially designed, non-naturally occurring protein (LG1) carrying a combination of a flavin- binding LOV- and a photochromic bilin-binding GAF-domain and demonstrate a FRET process between both chromophores.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-05T09:50:47.921404-05:
      DOI: 10.1111/php.12707
  • Computed Regioselectivity and Conjectured Biological Activity of Ene
           Reactions of Singlet Oxygen with the Prenylnatural Product Hyperforin
    • Authors: Inna Abramova; Benjamin Rudshteyn, Joel F. Liebman, Alexander Greer
      Abstract: Hyperforin is a constituent of St. John's wort and coexists with the singlet oxygen sensitizer hypericin. Density functional theory, molecular mechanics and Connolly surface calculations show that accessibility in the singlet oxygen ‘ene’ reaction favors the hyperforin “southwest” and “southeast” prenyl (2-methyl-2-butenyl) groups over the northern prenyl groups. While the southern part of hyperforin is initially more susceptible to oxidation, up to 4 ‘ene’ reactions of singlet oxygen can take place. Computational results assist in predicting the fate of adjacent hydroperoxides in hyperforin, where the loss of hydrogen atoms may lead to the formation of a hydrotrioxide and a carbonyl instead of a Russell reaction.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-04T03:19:37.387279-05:
      DOI: 10.1111/php.12706
  • The Properties and Activity of TiO2/beta-SiC Nanocomposites in Organic
           Dyes Photodegradation
    • Authors: Katarzyna Pstrowska; Bartłomiej Maciej Szyja, Hanna Czapor-Irzabek, Adam Kiersnowski, Jerzy Walendziewski
      Abstract: The TiO2/beta-SiC nanocomposites containing 0-25 wt. % of beta-SiC were synthesized by the sol-gel method and tested in the photodegradation of methylene blue and methyl orange water solutions. With the increase of SiC content, only a slight decrease in energy band gap was observed (3.19-3.12 eV), together with significant increase of the surface area of the catalysts (42.7-80.4 m2/g). In the synthesized material the anatase phase of TiO2 was present in the form of small agglomerates resulting from the mechanical mixing process. In the process conditions (catalyst concentration 0.5 g/L, initial dye concentration 100 ppm, light source 100 W UV-Vis lamp) we have observed no signs of catalyst deactivation. The significantly higher photodegradation activity of methylene blue than methyl orange can be attributed to the preferable pH of the solution compared to pHPZC and the cationic character of the first dye. In case of methyl orange, pH process conditions substantially limit the contact of the catalyst with the dye, since negatively charged surface of the catalysts repels the dissociated anionic dye molecules.This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-04T03:00:38.450521-05:
      DOI: 10.1111/php.12705
  • Issue Information
    • Pages: 1 - 2
      PubDate: 2017-02-17T02:27:48.827049-05:
      DOI: 10.1111/php.12629
  • Editorial
    • Authors: Jean Cadet
      Pages: 3 - 3
      PubDate: 2017-02-17T02:27:54.76172-05:0
      DOI: 10.1111/php.12715
  • Introduction
    • Authors: Dongping Zhong; Jean Cadet
      Pages: 5 - 6
      PubDate: 2017-02-17T02:27:59.129738-05:
      DOI: 10.1111/php.12722
  • Biography
    • Authors: Aziz Sancar
      Pages: 7 - 14
      PubDate: 2017-02-17T02:27:50.286045-05:
      DOI: 10.1111/php.12731
  • In-Planta Expression: Searching for the Genuine Chromophores of
           Cryptochrome-3 from Arabidopsis thaliana
    • Authors: Wolfgang Gärtner
      Pages: 382 - 384
      Abstract: Göbel et al. present in this issue an exemplary study of identification of chromophores from Arabidopsis thaliana cryptochrome-3. Usually taken for granted, proteins and cofactors, respective chromophores, from heterologous expression are considered identical to material isolated from their genuine host. Cryptochromes carry two chromophores, an antenna cofactor and a functional flavin chromophore, both noncovalently embedded into the protein. In particular the antenna chromophore is loosely bound and often lost during protein purification. The authors identify from plant-extracted Cry3 unambiguously N5,N10-methenyltetrahydrofolate as antenna chromophore and flavin adenine dinucleotide as the functional chromophore.Flavin-binding, blue light-sensing cryptochromes regulate a wide variety of photomorphogenic processes in plants such as cotyledon opening or hypocotyl lengthening (figure, wild-type plant, left, cryptochrome knockout mutant, right). This editorial praises an article by Göbel et al. published in issue 93(1) that identifies the genuine chromophores of cry3 from Arabidopsis thaliana by in-planta expression of the protein.
      PubDate: 2017-02-17T02:27:45.467723-05:
      DOI: 10.1111/php.12693
  • UVB-generated Microvesicle Particles: A Novel Pathway by Which a
           Skin-specific Stimulus Could Exert Systemic Effects
    • Authors: Katherine Fahy; Langni Liu, Christine M. Rapp, Christina Borchers, Ji C. Bihl, Yanfang Chen, Richard Simman, Jeffrey B. Travers
      Abstract: Ultraviolet B radiation (UVB) exerts profound effects on human skin. Much is known regarding the ability of UVB to generate a plethora of bioactive agents ranging from cytokines and other bioactive proteins, lipid mediators and micro-RNAs. It is presumed that these agents are in large part responsible for the effects of UVB, which only is absorbed appreciably in the epidermis. However, the exact mechanism by which these bioactive agents can leave the epidermis are as yet unclear. This review addresses the potential role of microvesicle particles (MVP) as UVB signaling agents through transmitting biologic mediators. New data is provided that UVB treatment of human skin explants also generates MVP production. We hypothesize that UVB production of MVPs (UVB-MVP) could serve this important function of transmitting keratinocyte-derived bioactive agents. Moreover, we propose that UVB-MVP formation involves the lipid mediator Platelet-activating factor. This novel pathway has the potential to be exploited pharmacologically to modulate UVB effects.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-31T06:00:30.991563-05:
      DOI: 10.1111/php.12703
  • Selected Least Studied but not Forgotten Bioluminescent Systems
    • Authors: Yuichi Oba; Cassius V. Stevani, Anderson G. Oliveira, Aleksandra S. Tsarkova, Tatiana V. Chepurnykh, Ilia V. Yampolsky
      Abstract: Bioluminescence is a form of chemiluminescence generated by luminous organisms. Luminous taxa have currently been reported from about 800 genera and probably over 10,000 species in the world. On the other hand, their bioluminescent systems, including chemical structures of luciferins/chromophores and the genes encoding luciferases/photoproteins, have been elucidated from only a few taxonomic groups; e.g. beetles, bacteria, dinoflagellates, ostracods, and some cnidarians. Research efforts to understand unknown bioluminescence systems are being conducted around the world, and recently, for example, novel luciferin structures of luminous enchytraeid potworms and fungi were identified by the authors. In this paper, we review the current status and perspectives, in the context of post-genomic era, of most-likely novel but less-revealed bioluminescence systems of ten selected organisms; earthworm, parchment tubeworm, fireworm, scaleworm, limpet, millipede, brittle star, acorn worms, tunicate, and shark, which indeed are the next focus of our international collaboration.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-31T06:00:28.606469-05:
      DOI: 10.1111/php.12704
  • DNA Repair by the Radical SAM Enzyme Spore Photoproduct Lyase: From
           Biochemistry to Structural Investigations
    • Authors: Olivier Berteau; Alhosna Benjdia
      Abstract: Radical S-adenosyl-L-methionine (SAM) enzymes have emerged as one of the last superfamilies of enzymes discovered to date. Arguably, it is the most versatile group of enzymes involved in at least 85 biochemical transformations. One of the founding members of this enzyme superfamily is the Spore Photoproduct (SP) lyase, a DNA repair enzyme catalyzing the direct reversal repair of a unique DNA lesion, the so-called spore photoproduct, back into two thymidine residues. Discovered more than 20 years ago in the bacterium Bacillus subtilis, SP lyase has been shown to be widespread in the endospore-forming Firmicutes from the Bacilli and Clostridia classes and to use radical-based chemistry to perform C-C bond breakage, a chemically challenging reaction. This review describes how the work on SP lyase has illuminated a unique strategy for DNA repair and provided major advances in our understanding of the emerging radical SAM superfamily of enzymes, from a biochemical and structural perspective.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-27T12:20:31.574807-05:
      DOI: 10.1111/php.12702
  • In vivo Confocal Raman Spectroscopic Analysis of the Effects of IR
           Radiation in the Human Skin Dermis
    • Authors: Monica Bergamo Lopes; Ramu Rajasekaran, Ana Clara Figueira Lopes Cançado, Airton Abrahão Martin
      Abstract: Human skin is the outer covering of the body and its composition changes with over exposure to environmental pollution and solar radiation. IR radiation is capable of penetrating more deeply into the skin producing free radicals causing irreversible damage. Confocal Raman spectroscopy was considered as a potential tool for the in vivo analysis of the different metabolic conditions with respect to different depths of the skin. In this regard, this work verifies the influence of infrared radiation on the skin dermis after having been exposed to 432 J/cm2 which corresponds to the dose received in a day in the summer time in a tropical region. The present study was performed with 17 female volunteers who were divided into two groups. The marked skin area was exposed twice to IR radiation for a duration of 30 minutes each with an interval of 30 minutes. The spectral signatures were collected in the fingerprint region before (T0) and after 60 min (T60) of IR irradiation. The analysis shows that, on average, no significant variations occurred in group I and decreased collagen was observed in group II. However, when considering the effect seen in each individual, collagen degradation was detected in 60% of volunteers.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-27T12:20:29.313804-05:
      DOI: 10.1111/php.12701
  • Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA
           Repair Activity
    • Authors: Fan Zhang; Hongju Ma, Kalinga Bowatte, Dennis Kwiatkowski, Esther Mittmann, Heba Qasem, Norbert Krauss, Xiaoli Zeng, Zhong Ren, Patrick Scheerer, Xiaojing Yang, Tilman Lamparter
      Abstract: PhrB from Agrobacterium fabrum is the first prokaryotic photolyase which repairs (6-4) UV DNA-photoproducts. The protein harbors three cofactors, the enzymatically active FAD chromophore, a second chromophore, 6,7-dimethyl-8-ribityllumazine (DMRL) and a cubane-type Fe-S cluster. Tyr424 of PhrB is part of the DNA binding site and could provide an electron link to the Fe-S cluster. The PhrBY424F mutant showed reduced binding of lesion DNA and loss of DNA repair. The mutant PhrBI51W, is characterized by the loss of the DMRL chromophore, reduced photoreduction and reduced DNA repair capacity. We have determined the crystal structures of both mutants and found that both mutations only affect local protein environments whereas the overall fold remained unchanged. The crystal structure of PhrBY424F revealed a water network extending to His366 which are part of the lesion binding site. The crystal structure of PhrBI51W shows how the bulky Trp leads to structural rearrangements in the DMRL chromophore pocket. Spectral characterizations of PhrBI51W suggest that DMRL serves as an antenna chromophore for photoreduction and DNA repair in the wild type. The energy transfer from DMRL to FAD could represent a phylogenetically ancient process.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-19T16:30:20.741768-05:
      DOI: 10.1111/php.12699
  • Divalent Cations Increase DNA Repair Activities of Bacterial (6-4)
    • Authors: Hongju Ma; Fan Zhang, Elisabeth Ignatz, Martin Suehnel, Peng Xue, Patrick Scheerer, LarsOliver Essen, Norbert Krauß, Tilman Lamparter
      Abstract: The (6-4) photolyases of the FeS-BCP group can be considered as the most ancient type among the large family of cryptochrome and photolyase flavoproteins. In contrast to other photolyases they contain an Fe-S cluster of unknown function, a DMRL chromophore, an interdomain loop which could interact with DNA, and a long C-terminal extension. We compared DNA repair and photoreduction of two members of the FeS-BCP family, Agrobacterium fabrum PhrB and Rhodobacter sphaeroides RsCryB, with a eukaryotic (6-4) photolyase from Ostreococcus, OsCPF, and a member of the class III CPD photolyases, PhrA from A. fabrum. We found that the low DNA repair effectivity of FeS-BCP proteins is largely stimulated by Mg2+ and other divalent cations, whereas no effect of divalent cations was observed in OsCPF and PhrA. The (6-4) repair activity in the presence of Mg2+ is comparable with the repair activities of the other two photolyases. The photoreduction, on the other hand, is negatively affected by Mg2+ in PhrB, but stimulated by Mg2+ in PhrA. A clear relationship of Mg2+ dependency on DNA repair with the evolutionary position conflicts with Mg2+ dependency of photoreduction. We discuss the Mg2+ effect in the context of structural data and DNA binding.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-19T16:25:20.742124-05:
      DOI: 10.1111/php.12698
  • Kinetic Isotope Effects and Hydrogen/Deuterium Exchange Reveal Large
           Conformational Changes During the Catalysis of the Clostridium
           acetobutylicum Spore Photoproduct Lyase
    • Authors: Linlin Yang; Jagat Adhikari, Michael L. Gross, Lei Li
      Abstract: Spore photoproduct lyase (SPL) catalyzes the direct reversal of a thymine dimer 5-thyminyl-5,6-dihydrothymine (i.e., the spore photoproduct (SP)) to two thymine residues in germinating endospores. Previous studies suggest that SPL from the bacterium Bacillus subtilis (Bs) harbors an unprecedented radical transfer pathway starting with cysteine 141 proceeding through tyrosine 99. However, in SPL from the bacterium C. acetobutylicum (Ca), the cysteine (at position 74) and tyrosine are located on the opposite sides of a substrate binding pocket that has to collapse to bring the two residues into proximity, enabling the CY radical passage as implied in SPL(Bs). To test this hypothesis, we adopted hydrogen/deuterium exchange mass spectrometry (HDX MS) to show that C74(Ca) is located at a highly flexible region. The repair of dinucleotide SP TpT by SPL(Ca) is 8-10-fold slower than that by SPL(Bs); the process also generates a large portion of the aborted product TpTSO2–. SPL(Ca) exhibits apparent (DV) kinetic isotope effects (KIEs) of ~ 6 and abnormally large competitive (DV/K) KIEs (~ 20), both of which are much larger than the KIEs observed in SPL(Bs). All these observations indicate that SPL(Ca) possesses a flexible active site and readily undergoes conformational changes during catalysis.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-19T15:30:22.459702-05:
      DOI: 10.1111/php.12697
  • Repair of (6-4) Lesions in DNA by (6-4) Photolyase: 20 Years of Quest for
           the Photoreaction Mechanism
    • Authors: Junpei Yamamoto; Pascal Plaza, Klaus Brettel
      Abstract: Exposure of DNA to ultraviolet (UV) light from the Sun or from other sources causes formation of harmful and carcinogenic crosslinks between adjacent pyrimidine nucleobases, namely cyclobutane pyrimidine dimers and pyrimidine(6–4)pyrimidone photoproducts. Nature has developed unique flavoenzymes, called DNA photolyases, that utilize blue light, i.e. photons of lower energy than those of the damaging light, to repair these lesions. In this review, we focus on the chemically challenging repair of the (6–4) photoproducts by (6–4) photolyase and describe the major events along the quest for the reaction mechanisms, over the 20 years since the discovery of (6-4) photolyase.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-19T15:25:22.399861-05:
      DOI: 10.1111/php.12696
  • Photolyase: Dynamics and Mechanisms of Repair of Sun-Induced DNA Damage
    • Authors: Meng Zhang; Lijuan Wang, Dongping Zhong
      Abstract: Photolyase, a photomachine discovered half a century ago for repair of sun-induced DNA damage of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs), has been characterized extensively in biochemistry (function), structure and dynamics since 1980s. The molecular mechanism and repair photocycle have been revealed at the most fundamental level. Using femtosecond spectroscopy, we have mapped out the entire dynamical evolution and determined all actual timescales of the catalytic processes. Here, we review our recent efforts in studies of the dynamics of DNA repair by photolyases. The repair of CPDs in three life kingdoms includes seven electron-transfer (ET) reactions among ten elementary steps through initial bifurcating ET pathways, a direct tunneling route and a two-step hopping path both through an intervening adenine from the cofactor to CPD, with a conserved folded structure at the active site. The repair of 6-4PPs is challenging and requires similar ET reactions and a new cyclic proton transfer with a conserved histidine residue at the active site of (6-4) photolyases. Finally, we also summarize our efforts on multiple intraprotein ET of photolyases in different redox states and such mechanistic studies are critical to the functional mechanism of homologous cryptochromes of blue-light photoreceptors.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-19T06:56:55.158175-05:
      DOI: 10.1111/php.12695
  • Tyr72 and Tyr80 Are Involved in the Formation of an Active Site of a
           Luciferase of Copepod Metridia longa
    • Authors: Marina D. Larionova; Svetlana V. Markova, Eugene S. Vysotski
      Abstract: Luciferase of copepod Metridia longa (MLuc) is a naturally secreted enzyme catalyzing the oxidative decarboxylation of coelenterazine with the emission of light. To date, 3 non-allelic isoforms of different length (17-24 kDa) for M. longa luciferase have been cloned. All the isoforms are single-chain proteins consisting of a 17-residue signal peptide for secretion, variable N-terminal part, and conservative C-terminus responsible for luciferase activity. In contrast to other bioluminescent proteins containing a lot of aromatic residues which are frequently involved in light emission reaction, the C-terminal part of MLuc contains only four Phe, two Tyr, one Trp, and two His residues. To figure out whether Tyr residues influence bioluminescence we constructed the mutants with substitution of Tyr to Phe (Y72F and Y80F). Tyrosine substitutions do not eliminate the ability of luciferase to bioluminescence albeit significantly reduce relative specific activity and change bioluminescence kinetics. In addition, the Tyr replacements have no effect on bioluminescence spectrum, thereby indicating that tyrosines are not involved in the emitter formation. However, since it was found that the intrinsic fluorescence caused by Tyr residues is quenched by a reaction substrate, coelenterazine, in concentration-dependent manner, we infer that both tyrosine residues are located in the luciferase substrate-binding cavity.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-14T08:30:32.745715-05:
      DOI: 10.1111/php.12694
  • The Anthocyanins, Oenin and Callistephin, Protect RPE Cells Against
           Oxidative Stress
    • Authors: Sally M. Yacout; Elizabeth R. Gaillard
      Abstract: The retinal pigment epithelium (RPE) is a highly metabolic layer of post-mitotic cells lining the Bruch's membrane in the retina. While these cells contain endogenous photosensitizers that mediate blue light induced damage, it has also been shown that blue light exposure damages mitochondrial DNA in RPE cells resulting in mitochondrial dysfunction and unregulated generation of reactive oxygen species. As RPE cells are post-mitotic, it is imperative to decrease oxidative stress to these cells and preserve function. Dietary plant-derived antioxidants such as anthocyanins offer a simple and accessible solution for decreasing oxidative stress. Anthocyanins malvidin-3-O-glucoside (oenin) and pelargonidin-3-O-glucoside (callistephin) were tested for their ability and efficacy in decreasing ROS generation and preserving mitochondrial redox activity in blue-light irradiated ARPE-19 cells. A significant decrease in intracellular ROS with concurrent increase in mitochondrial redox activity was observed for tested concentrations of oenin, while callistephin was beneficial to stressed cells at higher concentrations. These findings suggest anthocyanins are effective antioxidants in blue-light stressed RPE cells in vitro. Additionally, oxidation products of these anthocyanins were examined using LC/MS and findings suggest the possibility of multiple oxidation sites for these compounds.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-09T07:36:47.638581-05:
      DOI: 10.1111/php.12683
  • Chemiluminescence of Cigarette Smoke: Salient Features of the Phenomenon
    • Authors: Galina F. Fedorova; Valery A. Menshov, Aleksei V. Trofimov, Yury B. Tsaplev, Rostislav F. Vasil'ev, Olga I. Yablonskaya
      Abstract: The study disclosed herein provides for the first time a detailed experimental support for the general mechanism of the cigarette-smoke-derived chemiluminescence, as an example par excellence of the excited-state generation in a chemically complex aerosol medium. The mechanism involves chemiexcitation in a unimolecular transformation of the smoke-borne free-radical species. However, the concentration of these radicals, [r.], obeys a bimolecular (second-order) kinetics and depends on a particulate-phase content (total particulate matter, TPM) of the cigarette smoke. The decrease of [r.] with increasing the TPM amount manifests radical-scavenging propensity of the smoke particulate phase. Astonishingly, no energy transfer takes place from the primary excited light-emitting species to luminophoric molecules abundant in the smoke. The reported results build up fundamentals of a facile chemiluminescence assay for free-radical properties of the smoke. The experimental approaches developed for the current study are of general scope and may be used for mechanistic elucidation of the excited-state generation in chemical systems and environments of an arbitrary complexity.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-09T07:36:46.387821-05:
      DOI: 10.1111/php.12689
  • Crosstalk Among UV-Induced Inflammatory Mediators, DNA Damage and
           Epigenetic Regulators Facilitates Suppression of the Immune System
    • Authors: Ram Prasad; Santosh K. Katiyar
      Abstract: The suppression of the immune system by overexposure to ultraviolet (UV) radiation has been implicated in the initiation and progression of photocarcinogenesis. Numerous changes occur in the skin on UVB exposure, including the generation of inflammatory mediators, DNA damage, epigenetic modifications, and migration and functional alterations in the antigen-presenting dendritic cells. Although each of these alterations can elicit a cascade of events that have the potential to modulate immune sensitivity alone, there is emerging evidence that there is considerable crosstalk between these cascades. The development of an understanding of UV-induced changes in the skin that culminate in UV-induced immunosuppression, which has been implicated in the risk of non-melanoma skin cancer, as a network of events has implications for the development of more effective chemopreventive strategies. In the current review article, we discuss the evidence of interactions between the various molecular targets and signaling mechanisms associated with UV-induced immunosuppression.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-09T07:34:56.266829-05:
      DOI: 10.1111/php.12687
  • Insight in DNA Repair of UV-induced Pyrimidine Dimers by Chromatographic
    • Authors: Thierry Douki; Anne Koschembahr, Jean Cadet
      Abstract: UV-induced formation of pyrimidine dimers in DNA is a major deleterious event in both eukaryotic and prokaryotic cells. Accumulation of cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts can lead to cell death or be at the origin of mutations. In skin, UV-induction of DNA damage is a major initiating event in tumorigenesis. To counteract these deleterious effects, all cell types possess DNA repair machinery, such as nucleotide excision repair and, in some cell types, direct reversion. Different analytical approaches were used to assess the efficiency of repair and decipher the enzymatic mechanisms. We presently review the information provided by chromatographic methods, which are complementary to biochemical assays, such as immunological detection and electrophoresis-based techniques. Chromatographic assays are interesting in their ability to provide quantitative data on a wide range of damage and are also valuable tools for the identification of repair intermediates.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-09T07:33:47.976177-05:
      DOI: 10.1111/php.12685
  • Damaging Effects of Ultraviolet Radiation on the Cornea
    • Authors: Naomi C. Delic; J. Guy Lyons, Nick Di Girolamo, Gary M. Halliday
      Abstract: The cornea sits at the anterior aspect of the eye and additionally to the skin, is highly exposed to ultraviolet radiation (UVR). The cornea blocks a significant proportion of UVB from reaching the posterior structures of the eye. However, UVA can penetrate the full thickness of the cornea, even reaching the anterior portion of the lens. Epidemiological data indicate that UVR is a contributing factor for a multitude of corneal diseases of the cornea including pterygium, photokeratitis, climatic droplet keratopathy, (CDK) and ocular surface squamous neoplasia (OSSN), although the pathogenic mechanisms of each require further elucidation. UVR is a well-known genotoxic agent and its effects have been well characterized in organs such as the skin. However, we are only beginning to identify its effects on the cornea, such as the UVR signature CT and CCTT transversions identified by sequencing and increased proliferative and shedding rates in response to UVR exposure. Alarmingly, a single low dose exposure of UVR to the cornea is sufficient to elicit genetic, molecular and cellular changes, supporting the consideration of using protective measures, such as wearing sunglasses when outdoors. The aim of this review is to describe the adverse effects of UVR on the cornea.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-09T07:27:24.988054-05:
      DOI: 10.1111/php.12686
  • Sub-cellular Targeting as a Determinant of the Efficacy of Photodynamic
    • Authors: David Kessel
      Abstract: In prior studies, we have identified the ability of low-level lysosomal photodamage to potentiate the phototoxic effect of subsequent photodamage to mitochondria. The mechanism involves calpain-mediated cleavage of the autophagy-associated protein ATG5 to form a pro-apoptotic fragment (tATG5). In this report, we explore the permissible time lag between the two targeting procedures along with the effect of simultaneously targeting both lysosomes and mitochondria. This was found to be as effective as the sequential protocol with no gap between the irradiation steps. Inhibition of calpain reversed the enhanced efficacy of the ‘simultaneous’ protocol. It appears that even a minor level of lysosomal photodamage can have a significant effect on the efficacy of subsequent mitochondrial photodamage. We propose that these results may explain the efficacy of Photofrin, a photosensitizing product that also targets both lysosomes and mitochondria for photodamage.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-09T07:26:36.980765-05:
      DOI: 10.1111/php.12692
  • RNA Polymerase-I Dependent Transcription-coupled Nucleotide Excision
           Repair of UV Induced DNA Lesions at Transcription Termination Sites, in
           Saccharomyces cerevisiae
    • Authors: François Peyresaubes; Carlos Zeledon, Laetitia Guintini, Romain Charton, Alexia Muguet, Antonio Conconi
      Abstract: If not repaired, ultraviolet light induced DNA damage can lead to genome instability. Nucleotide excision repair (NER) of UV photoproducts is generally fast in the coding region of genes, where RNA polymerase-II (RNAP2) arrest at damage sites and trigger transcription-coupled NER (TC-NER). In Saccharomyces cerevisiae there is RNA polymerase-I (RNAP1) dependent TC-NER, but this process remains elusive. Therefore, we wished to characterize TC-NER efficiency in different regions of the rDNA locus: where RNAP1 are present at high density and start transcription elongation, where the elongation rate is slow, and in the transcription terminator where RNAP1 pause, accumulate and then are released. The Rpa12 subunit of RNAP1 and the Nsi1 protein participate in transcription termination, and NER efficiency was compared between wild type and cells lacking Rpa12 or Nsi1. The presence of RNAP1 was determined by chromatin endogenous cleavage and chromatin immuno-precipitation, repair was followed at nucleotide precision with an assay that is based on the blockage of Taq polymerase by UV photoproducts. We describe that TC-NER, which is modulated by the RNAP1 level and elongation rate, ends at the 35S rRNA gene transcription termination-site.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-09T07:24:34.960825-05:
      DOI: 10.1111/php.12690
  • Autophagy in UV Damage Response
    • Authors: Ashley Sample; Yu-Ying He
      Abstract: UV radiation exposure from sunlight and artificial tanning beds is the major risk factor for the development of skin cancer and skin photoaging. UV-induced skin damage can trigger a cascade of DNA damage response signaling pathways, including cell cycle arrest, DNA repair, and, if damage is irreparable, apoptosis. Compensatory proliferation replaces the apoptotic cells to maintain skin barrier integrity. Disruption of these processes can be exploited to promote carcinogenesis by allowing the survival and proliferation of damaged cells. UV radiation also induces autophagy, a catabolic process that clears unwanted or damaged proteins, lipids, and organelles. The mechanisms by which autophagy is activated following UV exposure, and the functions of autophagy in UV response are only now being clarified. Here, we summarize the current understanding of the mechanisms governing autophagy regulation by UV, the roles of autophagy in regulating cellular response to UV-induced photodamage, and the implications of autophagy modulation in the treatment and prevention of photoaging and skin cancer.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-09T07:22:45.727659-05:
      DOI: 10.1111/php.12691
  • An Ethenoadenine FAD Analog Accelerates UV Dimer Repair by DNA Photolyase
    • Authors: Madhavan Narayanan; Vijay R. Singh, Goutham Kodali, Kimberly Jacoby, Katarina Moravcevic, Robert J. Stanley
      Abstract: Reduced anionic flavin adenine dinucleotide (FADHˉ) is the critical cofactor in DNA photolyase (PL) for the repair of cyclobutane pyrimidine dimers (CPD) in UV-damaged DNA. The initial step involves photoinduced electron transfer from *FADHˉ to the CPD. The adenine (Ade) moiety is nearly stacked with the flavin ring, an unusual conformation compared to other FAD-dependent proteins. The role of this proximity has not been unequivocally elucidated. Some studies suggest that Ade is a radical intermediate, but others conclude that Ade modulates the electron transfer rate constant (kET) through superexchange. No study has succeeded in removing or modifying this Ade to test these hypotheses. Here, FAD analogs containing either an ethano- or etheno-bridged Ade between the AN1 and AN6 atoms (e-FAD and ε-FAD respectively) were used to reconstitute apo-PL, giving e-PL and ε-PL respectively. The reconstitution yield of e-PL was very poor, suggesting that the hydrophobicity of the ethano group prevented its uptake, while ε-PL showed 50% reconstitution yield. The substrate binding constants for ε-PL and rPL were identical. ε-PL showed a 15% higher steady-state repair yield compared to FAD-reconstituted photolyase (rPL). The acceleration of repair in ε-PL is discussed in terms of an ε-Ade radical intermediate vs. superexchange mechanism.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-09T07:07:50.531513-05:
      DOI: 10.1111/php.12684
  • Bimodal Targeting Using Sulfonated, Mannosylated PEI for Combined Gene
           Delivery and Photodynamic Therapy
    • Authors: Upendra Chitgupi; Yi Li, Mingfu Chen, Shuai Shao, Marie Beitelshees, Myles Joshua Tan, Sriram Neelamegham, Blaine A. Pfeifer, Charles Jones, Jonathan F. Lovell
      Abstract: Photodynamic therapy (PDT) and gene delivery have both been used to target both cancer cells and tumor-associated macrophages (TAMs). Given the complex nature of tumor tissue, there could be merit in combining these strategies simultaneously. In this study, we developed a bimodal targeting approach to both cancer cells and macrophages, employing materials conducive to both gene delivery and PDT. Polymers libraries were created that consisted of cationic polyethyleneimine (PEI) conjugated to the photosensitizer pyropheophorbide-α, with sulfonation (to target selectin-expressing cells) and mannosylation (to target TAMs). Polyplexes, consisting of these polymers electrostatically bound to DNA, were analyzed for transfection efficacy and cytotoxicity towards epithelial cells and macrophages to assess dual-targeting. This study provides preliminary proof of principle for using modified PEI for targeted gene delivery and PDT.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-09T07:00:49.685743-05:
      DOI: 10.1111/php.12688
  • Insights into Light-driven DNA Repair by Photolyases: Challenges and
           Opportunities for Electronic Structure Theory
    • Authors: Shirin Faraji; Andreas Dreuw
      Abstract: UV radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photoproducts. (6-4) photolyases are light-activated enzymes that selectively bind to DNA and trigger repair of mutagenic 6-4 photoproducts via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH−) to the lesion triggering repair. This review provides an overview of the sequential steps of the repair process, i.e. light absorption and resonance energy transfer, photo-induced electron transfer, and electron-induced splitting mechanisms, with an emphasis on the role of theory and computation. In addition, theoretical calculations and physical properties that can be used to classify specific mechanism are discussed in an effort to trace the fundamental aspects of each individual step and assist the interpretation of experimental data. The current challenges and suggested future directions are outlined for each step, concluding with a view on the future.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-07T07:43:34.816469-05:
      DOI: 10.1111/php.12679
  • Fluorescent Protein-photoprotein Fusions and Their Applications in Calcium
    • Authors: Adil Bakayan; Beatriz Domingo, Cecilia F. Vaquero, Nadine Peyriéras, Juan Llopis
      Abstract: Calcium-activated photoproteins, such as aequorin, have been used as luminescent Ca2+ indicators since 1967. After the cloning of aequorin in 1985, microinjection was substituted by its heterologous expression, which opened the way for a widespread use. Molecular fusion of GFP to aequorin recapitulated the nonradiative energy transfer process that occurs in the jellyfish Aequorea victoria, from which these two proteins were obtained, resulting in an increase of light emission and a shift to longer wavelength. The abundance and location of the chimera are seen by fluorescence, whereas its luminescence reports Ca2+ levels. GFP-aequorin is broadly used in an increasing number of studies, from organelles and cells to intact organisms. By fusing other fluorescent proteins to aequorin, the available luminescence color palette has been expanded for multiplexing assays and for in vivo measurements. In this report, we will attempt to review the various photoproteins available, their reported fusions with fluorescent proteins, and their biological applications to image Ca2+ dynamics in organelles, cells, tissue explants and in live organisms.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-07T07:38:02.120714-05:
      DOI: 10.1111/php.12682
  • Conformational and Intermolecular Interaction Dynamics of
           Photolyase/Cryptochrome Proteins Monitored by the Time-resolved Diffusion
    • Authors: Masato Kondoh; Masahide Terazima
      Abstract: Cryptochrome (CRY), a blue light sensor protein, possesses a similar domain structure to photolyase (PHR) that, upon absorption of light, repairs DNA damage. In this review, we compare the reaction dynamics of these systems by monitoring the reaction kinetics of conformation change and intermolecular interaction change based on time-dependent diffusion coefficient measurements obtained by using the pulsed laser-induced transient grating technique. Using this method, time-dependent biomolecular interactions, such as transient dissociation reactions in solution, have been successfully detected in real time. Conformation change of (6-4) PHR has not been detected after the photoexcitation by monitoring the diffusion coefficient. However, the repaired DNA dissociates from PHR with a time constant of 50 μs, which must relate to a minor conformation change. However, CRY exhibits a considerable diffusion change with a time constant of 400 ms, which indicates that the protein–solvent interaction is changed by the conformation change. The C-terminus domain of CRY is shown to be responsible for this change.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-07T07:37:39.444705-05:
      DOI: 10.1111/php.12681
  • Light Regulation of Alternative Pre-mRNA Splicing in Plants
    • Authors: Hangxiao Zhang; Chentao Lin, Lianfeng Gu
      Abstract: Alternative splicing (AS) is a major post-transcriptional mechanism to enhance the diversity of proteome in response to environmental signals. Among the numerous external signals perceived by plants, light is the most crucial one. Plants utilize complex photoreceptor signaling networks to sense different light conditions and adjust their growth and development accordingly. Although light-mediated gene expression has been widely investigated, little is known regarding the mechanism of light affecting AS to modulate mRNA at the post-transcriptional level. In this mini-review, we summarize current progresses on how light affects AS, and how sensory photoreceptors and retrograde signaling pathways may coordinately regulate AS of pre-mRNAs. In addition, we also discuss the possibility that AS of the mRNAs encoding photoreceptors may be involved in feedback control of AS. We hypothesize that light regulation of the expression and activity of splicing factors would be a major mechanism of light-mediated AS. The combination of genetic study and high-throughput analyses of AS and splicing complexes in response to light is likely to further advance our understanding of the molecular mechanisms underlying light control of AS and plant development.This article is protected by copyright. All rights reserved.
      PubDate: 2016-12-07T07:35:26.830712-05:
      DOI: 10.1111/php.12680
  • A Review of Spectroscopic and Biophysical Chemical Studies of the Complex
           of CPD Photolyase and Cryptochrome DASH with Substrate DNA
    • Authors: Johannes P. M. Schelvis; Yvonne M. Gindt
      Abstract: CPD photolyase (PL) is a structure-specific DNA repair enzyme that uses blue light to repair cyclobutane pyrimidine dimers (CPD) on DNA. Cryptochrome (CRY) DASH enzymes use blue light for the repair of CPD lesions on single-stranded (ss) DNA, though some may also repair these lesions on double-stranded (ds) DNA. In addition, CRY DASH may be involved in blue-light signaling, similar to cryptochromes. The focus of this review is on spectroscopic and biophysical chemical experiments of the enzyme-substrate complex that have contributed to a more detailed understanding of all the aspects of the CPD repair mechanism of CPD photolyase and CRY DASH. This will be done in the backdrop of the available X-ray crystal structures of these enzymes bound to a CPD-like lesion. These structures helped to confirm conclusions that were drawn earlier from spectroscopic and biophysical chemical experiments, and they have a critical function as a framework to design new experiments and to interpret new experimental data. This review will show the important synergy between X-ray crystallography and spectroscopic/biophysical chemical investigations that is essential to obtain a sufficiently detailed picture of the overall mechanism of CPD photolyases and CRY DASH proteins.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-28T02:35:32.673145-05:
      DOI: 10.1111/php.12678
  • Animal Cryptochromes: Divergent Roles in Light Perception, Circadian
           Timekeeping and Beyond
    • Authors: Alicia K. Michael; Jennifer L. Fribourgh, Russell N. Van Gelder, Carrie L. Partch
      Abstract: Cryptochromes are evolutionarily related to the light-dependent DNA repair enzyme photolyase, serving as major regulators of circadian rhythms in insects and vertebrate animals. There are two types of cryptochromes in the animal kingdom: Drosophila-like CRYs that act as non-visual photopigments linking circadian rhythms to the environmental light/dark cycle, and vertebrate-like CRYs that do not appear to sense light directly, but control the generation of circadian rhythms by acting as transcriptional repressors. Some animals have both types of CRYs, while others possess only one. Cryptochromes have two domains, the photolyase homology region (PHR) and an extended, intrinsically disordered C-terminus. While all animal CRYs share a high degree of sequence and structural homology in their PHR domains, the C-termini are divergent in both length and sequence identity. Recently, cryptochrome function has been shown to extend beyond its pivotal role in circadian clocks, participating in regulation of the DNA damage response, cancer progression, and glucocorticoid signaling, as well as being implicated as possible magnetoreceptors. In this review, we provide a historical perspective on the discovery of animal cryptochromes, examine similarities and differences of the two types of animal cryptochromes, and explore some of the divergent roles for this class of proteins.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-28T02:30:49.595109-05:
      DOI: 10.1111/php.12677
  • Phylogenetic and Functional Classification of the Photolyase/Cryptochrome
    • Authors: Nuri Ozturk
      Abstract: The Photolyase/Cryptochrome (PHR/CRY) family is a large group of proteins with similar structure and but very diverge functions such as in DNA repair, circadian clock resetting, and regulation of transcription. As a result of advances in the biochemistry of the CRY/PHR family and identification of new members, several adjustments have been made to the classification of this protein family. For example, a new class of PHRs, Class III, has been proposed. Furthermore, CRYs have been suggested to function as photosensory proteins in the primordial eye of sponge larvae. Additionally, a magnetosensory function has been attributed to certain CRYs. Recent advances in the field enabled us to propose a comprehensive classification scheme and nomenclatural system for this family.This review focuses on the computational and biochemical classifications of the PHR/CRY family. Several examples show that computational analysis can give a hinge about the function of newly discovered members before performing any biochemical study.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-19T08:15:21.469454-05:
      DOI: 10.1111/php.12676
  • Mfd Protein and Transcription-Repair Coupling in E. coli
    • Authors: Christopher P. Selby
      Abstract: In 1989, transcription-repair coupling (TRC) was first described in Escherichia coli, as the transcription-dependent, preferential nucleotide excision repair (NER) of UV photoproducts located in the template DNA strand. This finding led to pioneering biochemical studies of TRC in the laboratory of Professor Aziz Sancar, where, at the time, major contributions were being made toward understanding the roles of the UvrA, UvrB and UvrC proteins in NER. When the repair studies were extended to TRC, template but not coding strand lesions were found to block RNA polymerase (RNAP) in vitro, and unexpectedly, the blocked RNAP inhibited NER. A transcription-repair coupling factor, also called Mfd protein, was found to remove the blocked RNAP, deliver the repair enzyme to the lesion, and thereby mediate more rapid repair of the transcription-blocking lesion compared to lesions elsewhere. Structural and functional analyses of Mfd protein revealed helicase motifs responsible for ATP hydrolysis and DNA binding, and regions that interact with RNAP and UvrA. These and additional studies provided a basis upon which other investigators, in following decades, have characterized fascinating and unexpected structural and mechanistic features of Mfd, revealed the possible existence of additional pathways of TRC, and discovered additional roles of Mfd in the cell.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-19T07:25:22.825099-05:
      DOI: 10.1111/php.12675
  • Solving Blue-light Riddles: New Lessons from Flavin-binding LOV
    • Authors: Aba Losi; Wolfgang Gärtner
      Abstract: Detection of blue light (BL) via flavin-binding photoreceptors (Fl-Blues) has evolved throughout all three domains of life. Although the main BL players, i.e. LOV (Light, Oxygen and Voltage), BLUF (Blue Light Sending using Flavins) and Cry (Cryptochrome) proteins have been characterized in great detail with respect to structure and function, still several unresolved issues at different levels of complexity remain and novel unexpected findings were reported. Here, we review the most prevailing riddles of LOV-based photoreceptors, for example: the relevance of water and/or small metabolites for the dynamics of the photocycle; molecular details of light-to-signal transduction events; the interplay of BL sensing by LOV domains with other environmental stimuli, such as BL plus oxygen mediating photodamage and its impact on microbial life-styles; the importance of the cell or chromophore redox state in determining the fate of BL-driven reactions; the evolutionary pathways of LOV-based BL sensing and associated functions through the diverse phyla. We will discuss major novelties emerged during the last few years on these intriguing aspects of LOV proteins by presenting paradigmatic examples from prokaryotic photosensors that exhibit the largest complexity and richness in associated functions.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-18T13:00:30.807519-05:
      DOI: 10.1111/php.12674
  • Convergence of The Nobel Fields of Telomere Biology and DNA Repair
    • Authors: Elise Fouquerel; Patricia Opresko
      Abstract: The fields of telomere biology and DNA repair have enjoyed a great deal of cross-fertilization and convergence in recent years. Telomeres function at chromosome ends to prevent them from being falsely recognized as chromosome breaks by the DNA damage response and repair machineries. Conversely, both canonical and non-conical functions of numerous DNA repair proteins have been found to be critical for preserving telomere structure and function. In 2009 Elizabeth Blackburn, Carol Greider, and Jack Szostak were awarded the Nobel prize in Physiology or Medicine for the discovery of telomeres and telomerase. Four years later pioneers in the field of DNA repair, Aziz Sancar, Tomas Lindahl and Paul Modrich, were recognized for their seminal contributions by being awarded the Nobel Prize in Chemistry. This review is part of a special issue meant to celebrate this amazing achievement, and will focus in particular on the convergence of nucleotide excision repair and telomere biology, and will discuss the profound implications for human health.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-18T12:50:29.211448-05:
      DOI: 10.1111/php.12672
  • Cation and Anion Substituted Potassium Manganese Phosphate, KMnP3O9:
           Luminescence and Photocatalytic studies
    • Authors: C. H. Sudhakar Reddy; G. Ravi, K. Sreenu, Ravinder Guje, M. Malathi, Muga Vithal
      Abstract: Phosphates as multi-functional materials were of vital importance in the environmental and energy fields. In the present work, a new cyclophosphate, potassium-manganese-phosphate (KMnP3O9) (hereafter KMPO), was prepared by solid state method. Cations (Ag+ and Cu2+) and anion (N3-) were substituted into KMPO lattice via ion-exchange and solid state methods respectively. The as-prepared materials were characterized by powder X–ray diffraction, SEM–EDS and UV–visible diffuse reflectance spectra. Rietveld refinement was carried out for parent material. All the prepared materials were found to crystallize in the hexagonal lattice and isomorphous with KCoP3O9. The nitrogen content in N3- substituted KMPO was estimated by EDS and O-N-H analysis. The bandgap energy of the cation and anion substituted samples was lower compared to that of pristine KMPO. Gouy method was employed to determine the magnetic susceptibility of KMPO. The photoluminescence property of Mn2+ in all the samples was studied, and the color coordinates were calculated using CIE 1931 chromaticity. The photocatalytic activity of visible light active material, N3- substituted KMPO, was examined against the degradation of methylene blue and methyl violet at ambient conditions.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-18T12:50:27.638856-05:
      DOI: 10.1111/php.12673
  • Cloning of the Orange Light-Producing Luciferase from Photinus scintillans
           - A New Proposal on how Bioluminescence Color is Determined
    • Authors: Bruce R. Branchini; Tara L. Southworth, Danielle M. Fontaine, Martha H. Murtiashaw, Alex McGurk, Munya H. Talukder, Rakhshi Qureshi, Deniz Yetil, Jesse A. Sundlov, Andrew M. Gulick
      Abstract: Unlike the enchanting yellow-green flashes of light produced on warm summer evenings by Photinus pyralis, the most common firefly species in North America, the orange lights of Photinus scintillans are infrequently observed. These Photinus species, and likely all bioluminescent beetles, use the same substrates beetle luciferin, ATP, and oxygen to produce light. It is the structure of the particular luciferase enzyme that is the key to determining the color of the emitted light. We report here the molecular cloning of the P. scintillans luc gene and the expression and characterization of the corresponding novel recombinant luciferase enzyme. A comparison of the amino acid sequence with that of the highly similar P. pyralis enzyme and subsequent mutagenesis studies revealed that the single conservative amino acid change tyrosine to phenylalanine at position 255 accounted for the entire emission color difference. Additional mutagenesis and crystallographic studies were performed on a H-bond network, which includes the position 255 residue and 5 other stringently conserved beetle luciferase residues, that is proximal to the substrate/emitter binding site. The results are interpreted in the context of a speculative proposal that this network is key to the understanding of bioluminescence color determination.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-18T12:45:31.449821-05:
      DOI: 10.1111/php.12671
  • Daily Variation of UV-induced Erythema and the Action of Solar Filters
    • Authors: Ana Flo; Ana C. Calpena, Antoni Díez-Noguera, Alfons del Pozo, Trinitat Cambras
      Abstract: UV rays may cause several degrees of skin damage, which makes sunscreen research necessary. In addition, skin sensitivity shows daily variations, which can interfere in the detection of the efficacy of the filters. Here we studied the UV-induced erythema in hairless rats at two times of the day (light and darkness) using a colorimeter method. The effect of an emulsion with solar filters, with or without melatonin was also assayed. Results indicate that the value of a* (from CIELAB color space values L* a* b) was the most useful variable to evaluate the erythema. However, at the UV intensity used, erythema was only detected when irradiation was carried out during the activity phase of the animal, enabling the detection of the protective action of the sunscreen at this time. Thus, daily variations in skin sensitivity have been demonstrated and should be taken into account in dermatological research.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-16T07:58:23.652143-05:
      DOI: 10.1111/php.12670
  • The Photolyase/cryptochrome Family of Proteins as DNA Repair Enzymes and
           Transcriptional Repressors
    • Authors: Ibrahim Halil Kavakli; Ibrahim Barış, Mehmet Tardu, Şeref Gül, Haşimcan Öner, Sibel Çal, Selma Bulut, Darya Yarparvar, Çağlar Berkel, Pınar Ustaoğlu, Cihan Aydın
      Abstract: Light is a very important environmental factor that governs many cellular responses in organisms. As a consequence, organisms possess different kinds of light-sensing photoreceptors to regulate their physiological variables and adapt to a given habitat. The cryptochrome/photolyase family (CPF) includes photoreceptors that perform different functions in different organisms. Photolyases repair ultraviolet-induced DNA damage by a process known as photoreactivation using photons absorbed from the blue end of the light spectrum. On the other hand, cryptochromes act as blue-light circadian photoreceptors in plants and Drosophila to regulate growth and development. In mammals, cryptochromes have light-independent functions and are very important transcriptional regulators that act at the molecular level as negative transcriptional regulators of the circadian clock. In this review, we highlight current knowledge concerning the structural and functional relationships of CPF members.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-16T07:53:49.861192-05:
      DOI: 10.1111/php.12669
  • The Cartography of UV-induced DNA Damage Formation and DNA Repair
    • Authors: Jinchuan Hu; Sheera Adar
      Abstract: DNA damage present a barrier to DNA-templated biochemical processes, including gene expression and faithful DNA replication. Compromised DNA repair leads to mutations, enhancing the risk for genetic diseases and cancer development. Conventional experimental approaches to study DNA damage required a researcher to choose between measuring bulk damage over the entire genome, with little or no resolution regarding a specific location, and obtaining data specific to a locus of interest, without a global perspective. Recent advances in high-throughput genomic tools overcame these limitations and provide high-resolution measurements simultaneously across the genome. In this review, we discuss the available methods for measuring DNA damage and their repair, focusing on genome-wide assays for pyrimidine photodimers, the major types of damage induced by ultraviolet irradiation. These new genomic assays will be a powerful tool in identifying key components of genome stability and carcinogenesis.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-14T10:01:58.528917-05:
      DOI: 10.1111/php.12668
  • Bringing It All Together: Coupling Excision Repair to the DNA Damage
    • Authors: Laura A. Lindsey-Boltz
      Abstract: Nucleotide excision repair and the ATR-mediated DNA damage checkpoint are two critical cellular responses to the genotoxic stress induced by ultraviolet (UV) light and are important for cancer prevention. In vivo genetic data indicate that these global responses are coupled. Aziz Sancar and colleagues developed an in vitro coupled repair-checkpoint system to analyze the basic steps of these DNA damage stress responses in a biochemically defined system. The minimum set of factors essential for repair-checkpoint coupling include damaged DNA, the excision repair factors (XPA, XPC, XPF-ERCC1, XPG, TFIIH, RPA), the 5’-3’ exonuclease EXO1, and the damage checkpoint proteins ATR-ATRIP and TopBP1. This coupled repair-checkpoint system was used to demonstrate that the ~30 nucleotide single-stranded DNA (ssDNA) gap generated by nucleotide excision repair is enlarged by EXO1 and bound by RPA to generate the signal that activates ATR.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-14T09:51:15.684592-05:
      DOI: 10.1111/php.12667
  • A Novel Streptavidin–luciferase Fusion Protein: Preparation, Properties,
           and Application in Hybridization Analysis of DNA
    • Authors: D. V. Smirnova; M. Y. Rubtsova, V. G. Grigorenko, N. N. Ugarova
      Abstract: A streptavidin–luciferase fusion protein comprising the thermostable mutant form of firefly luciferase Luciola mingrelica and minimal core streptavidin was constructed. The streptavidin–luciferase fusion was mainly produced in a tetrameric form with high luciferase and biotin-binding activities. It was shown, that fusion has the same Km values for ATP and luciferin and the bioluminescence spectra as initial luciferase. The linear dependence of the bioluminescence signal on the content of the fusion was observed within the range of 10-18–10-13 mol per well. Successful application of obtained fusion in a biospecific bioluminescence assay based on biotin–streptavidin interactions was demonstrated by the example of a specific DNA hybridization analysis. A DNA hybridization analysis for E. coli cells identification was developed using unique for these cells gadB fragment encoding glutamate decarboxylase. The amplified biotinylated GadB fragments were hybridized with the immobilized oligonucleotide probes; then, the biotin in the DNA duplexes was detected using the streptavidin-luciferase fusion protein. To reach the high sensitivity of the assay we optimized the conditions of the assay. It was shown, that the use of pluronic for plate modification resulted in a significant reduction of the DNA detection limit which finally was 0.4 ng per well.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-14T09:41:33.57388-05:0
      DOI: 10.1111/php.12666
  • Unanimous Model for Describing the Fast Bioluminescence Kinetics of
           Ca2+-regulated Photoproteins of Different Organisms
    • Authors: Elena V. Eremeeva; Sergey I. Bartsev, Willem J.H. van Berkel, Eugene S. Vysotski
      Abstract: Upon binding their metal ion cofactors, Ca2+-regulated photoproteins display a rapid increase of light signal, which reaches its peak within milliseconds. In the present study we investigate bioluminescence kinetics of the entire photoprotein family. All five recombinant hydromedusan Ca2+-regulated photoproteins—aequorin from Aequorea victoria, clytin from Clytia gregaria, mitrocomin from Mitrocoma cellularia, and obelins from Obelia longissima and Obelia geniculata—demonstrate the same bioluminescent kinetics pattern. Based on these findings, for the first time we propose a unanimous kinetic model describing the bioluminescence mechanism of Ca2+-regulated photoproteins.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-12T10:40:20.113139-05:
      DOI: 10.1111/php.12664
  • Impact of the Circadian Clock on UV-Induced DNA Damage Response and
    • Authors: Panshak Dakup; Shobhan Gaddameedhi
      Abstract: The skin is in constant exposure to various external environmental stressors, including solar ultraviolet (UV) radiation. Various wavelengths of UV light are absorbed by the DNA and other molecules in the skin to cause DNA damage and induce oxidative stress. The exposure to excessive ultraviolet (UV) radiation and/or accumulation of damage over time can lead to photocarcinogenesis and photoaging. The nucleotide excision repair (NER) system is the sole mechanism for removing UV photoproduct damage from DNA, and genetic disruption of this repair pathway leads to the photosensitive disorder xeroderma pigmentosum (XP). Interestingly, recent work has shown that NER is controlled by the circadian clock, the body's natural time keeping mechanism, through regulation of the rate-limiting repair factor xeroderma pigmentosum group A (XPA). Studies have shown reduced UV-induced skin cancer after UV exposure in the evening compared to the morning, which corresponds with times of high and low repair capacities, respectively. However, most studies of the circadian clock-NER connection have utilized murine models, and it is therefore important to translate these findings to humans to improve skin cancer prevention and chronotherapy.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-12T10:30:26.915192-05:
      DOI: 10.1111/php.12662
  • Cryptochromes Orchestrate Transcription Regulation of Diverse Blue Light
           Responses in Plants
    • Authors: Zhaohe Yang; Bobin Liu, Jun Su, Jiakai Liao, Chentao Lin, Yoshito Oka
      Abstract: Blue light affects many aspects of plant growth and development throughout the plant lifecycle. Plant cryptochromes (CRYs) are UV-A/blue light photoreceptors that play pivotal roles in regulating blue light-mediated physiological responses via the regulated expression of more than one thousand genes. Photoactivated CRYs regulate transcription via two distinct mechanisms: indirect promotion of the activity of transcription factors by inactivation of the COP1/SPA E3 ligase complex or direct activation or inactivation of at least two sets of basic helix-loop-helix transcription factor families by physical interaction. Hence, CRYs govern intricate mechanisms that modulate activities of transcription factors to regulate multiple aspects of blue light-responsive photomorphogenesis. Here, we review recent progress in dissecting the pathways of CRY signaling and discuss accumulating evidence that shows how CRYs regulate broad physiological responses to blue light.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-12T10:30:21.057996-05:
      DOI: 10.1111/php.12663
  • From Mfd to TRCF and Back Again – A Perspective on Bacterial
           Transcription-Coupled Nucleotide Excision Repair
    • Authors: Alexandra M. Deaconescu; Margaret M. Suhanovsky
      Abstract: Photochemical and other reactions on DNA cause damage and corrupt genetic information. To counteract this damage, organisms have evolved intricate repair mechanisms that often crosstalk with other DNA-based processes, such as transcription. Intriguing observations in the late 1980s and early 1990s led to the discovery of transcription-coupled repair (TCR), a subpathway of nucleotide excision repair (NER). TCR, found in all domains of life prioritizes for repair lesions located in the transcribed DNA strand, directly read by RNA polymerase. Here we give a historical overview of developments in the field of bacterial TCR, starting from the pioneering work of Evelyn Witkin and Aziz Sancar, which led to the identification of the first transcription-repair coupling factor (the Mfd protein), to recent studies that have uncovered alternative TCR pathways and regulators.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-12T10:20:22.717076-05:
      DOI: 10.1111/php.12661
  • Targeted Inactivation of DNA Photolyase Genes in Medaka Fish (Oryzias
    • Authors: Tomoko Ishikawa-Fujiwara; Eri Shiraishi, Yoshihiro Fujikawa, Toshio Mori, Tohru Tsujimura, Takeshi Todo
      Abstract: Proteins of the cryptochrome/photolyase family (CPF) exhibit sequence and structural conservation, but their functions are divergent. Photolyase is a DNA repair enzyme that catalyzes the light-dependent repair of ultraviolet (UV)-induced photoproducts, whereas cryptochrome acts as a photoreceptor or circadian clock protein. Two types of DNA photolyase exist: CPD photolyase, which repairs cyclobutane pyrimidine dimers (CPDs), and 6-4 photolyase, which repairs 6-4 pyrimidine–pyrimidone photoproducts (6-4PPs). Although the Cry-DASH protein is classified as a cryptochrome, it also has light-dependent DNA repair activity. To determine the significance of the three light-dependent repair enzymes in recovering from solar UV-induced DNA damage at the organismal level, we generated mutants in each gene in medaka using the CRISPR genome editing technique. The light-dependent repair activity of the mutants was examined in vitro in cultured cells and in vivo in skin tissue. Light-dependent repair of CPD was lost in the CPD photolyase–deficient mutant, whereas weak repair activity against 6-4PPs persisted in the 6-4 photolyase–deficient mutant. These results suggest the existence of a heretofore unknown 6-4PP repair pathway, and thus improve our understanding of the mechanisms of defense against solar UV in vertebrates.This article is protected by copyright. All rights reserved.
      PubDate: 2016-11-10T02:10:54.413626-05:
      DOI: 10.1111/php.12658
  • Theoretical Study of Dinoflagellate Bioluminescence
    • Authors: Ming-Yu Wang; Ya-Jun Liu
      Abstract: Dinoflagellates are the most ubiquitous luminescent protists in the marine environment and have drawn much attention for their crucial roles in marine ecosystems. Dinoflagellate bioluminescence has been applied in underwater target detection. The luminescent system of dinoflagellates is a typical luciferin-luciferase one. However, the excited-state oxyluciferin is not the light emitter of dinoflagellate bioluminescence as in most luciferin-luciferase bioluminescent organisms. The oxyluciferin of bioluminescent dinoflagellates is not fluorescent, whereas its luciferin emits bright fluorescence with similar wavelength of the bioluminescence. What is the light emitter of dinoflagellate bioluminescence and what is the chemical process of the light emission like? These questions have not be answered by the limited experimental evidence so far. In this study, for the first time, the density functional calculation is employed to investigate the geometries and properties of luciferin and oxyluciferin of bioluminescent dinoflagellate. The calculated results agree with the experimental observations and indicate the luciferin or its analogue, rather than oxyluciferin, is the bioluminophore of dinoflagellate bioluminescence. A rough mechanism involving energy transfer is proposed for dinoflagellate bioluminescence.This article is protected by copyright. All rights reserved.
      PubDate: 2016-10-31T00:46:11.701811-05:
      DOI: 10.1111/php.12657
  • Firefly Luciferase-Based Fusion Proteins and their Applications in
    • Authors: Daria V. Smirnova; Natalia N. Ugarova
      Abstract: Firefly luciferase is widely used in molecular biology and bioanalytical systems as a reporter molecule due to the high quantum yield of the bioluminescence, availability of stable mutant forms of the enzyme with prescribed spectral characteristics, and abundance of bacterial expression systems suitable for production of recombinant proteins in limitless quantities. In this review we described fusion proteins of luciferase with biotin-binding domain and streptavidin, with proteins A and G, antibodies, with DNA- and RNA-binding proteins, as well as fusion proteins designed for BRET-systems. The firefly luciferase-based fusion proteins are represented as an effective tool for the development of different bioanalytical systems such as: 1) systems in which luciferase is attached to the surface of the target and the bioluminescence signal is detected from the specific complexes formed; 2) BRET-based systems, in which the specific interaction induces changes in the bioluminescence spectrum; 3) systems that use modified or split-luciferases, in which the luciferase activity changes under the action of the analyte. All these systems have wide application in biochemical analysis of physiologically important compounds, for the detection of pathogenic bacteria and viruses, for evaluation of protein–protein interactions, assaying of metabolites involved in cell communication and cell signaling.This article is protected by copyright. All rights reserved.
      PubDate: 2016-10-31T00:46:07.356715-05:
      DOI: 10.1111/php.12656
  • Spectroscopic properties of amine-substituted analogues of firefly
           luciferin and oxyluciferin
    • Authors: Michio Kakiuchi; Soichiro Ito, Minoru Yamaji, Vadim R. Viviani, Shojiro Maki, Takashi Hirano
      Abstract: Spectroscopic and photophysical properties of firefly luciferin and oxyluciferin analogues with an amine substituent (NH2, NHMe and NMe2) at the C6′ position were studied based on absorption and fluorescence measurements. Their π-electronic properties were investigated by DFT and TD-DFT calculations. These compounds showed fluorescence solvatochromism with good quantum yields. An increase in the electron donating strength of the substituent led to the bathochromic shift of the fluorescence maximum. The fluorescence maxima of the luciferin analogues and the corresponding oxyluciferin analogues in a solvent were well correlated to each other. Based on the obtained data, the polarity of a luciferase active site was explained. As a result, the maximum wavelength of bioluminescence for a luciferin analogue was readily predicted by measuring the photoluminescence of the luciferin analogue in place of that of the corresponding oxyluciferin analogue.This article is protected by copyright. All rights reserved.
      PubDate: 2016-10-31T00:46:04.151239-05:
      DOI: 10.1111/php.12654
  • Facilitators and Repressors of Transcription Coupled DNA Repair in
           Saccharomyces cerevisiae
    • Authors: Wentao Li; Shisheng Li
      Abstract: Nucleotide excision repair is a well-conserved DNA repair pathway that removes bulky and/or helix-distorting DNA lesions, such as UV induced cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts. Transcription coupled repair (TCR) is a subpathway of nucleotide excision repair that is dedicated to rapid removal of DNA lesions in the transcribed strand of actively transcribed genes. In eukaryotic cells, TCR is triggered by RNA polymerase II (RNAP II). Rad26, a DNA-dependent ATPase, Rpb9, a nonessential subunit of RNAP II, and Sen1, a 5′ to 3′ RNA/DNA and DNA helicase, have been shown to facilitate TCR in Saccharomyces cerevisiae. In contrast, a number of factors have also been found to repress TCR in the yeast. These TCR repressors include Rpb4, another nonessential subunit of RNAP II, Spt4/5, a transcription elongation factor complex, and the RNAP II associated factor complex (PAFc). It appears that the eukaryotic TCR process involves intricate interplays of RNAP II with TCR facilitators and repressors. In this minireview, we summarize recent advances in TCR in S. cerevisiae.This article is protected by copyright. All rights reserved.
      PubDate: 2016-10-31T00:35:58.983834-05:
      DOI: 10.1111/php.12655
  • Perspectives on Bioluminescence Mechanisms
    • Authors: John Lee
      Abstract: The molecular mechanisms of the bioluminescence systems of the firefly, bacteria, and those utilizing imidazopyrazinone luciferins such as coelenterazine, are gradually being uncovered using modern biophysical methods such as dynamic (ns—ps) fluorescence spectroscopy, NMR, X-ray crystallography, and computational chemistry. The chemical structures of all reactants are well defined and the spatial structures of the luciferases are providing important insight into interactions within the active cavity. It is generally accepted that the firefly and coelenterazine systems, although proceeding by different chemistries, both generate a dioxetanone high energy species that undergoes decarboxylation to form directly the product in its S1 state, the bioluminescence emitter. More work is still needed to establish the structure of the products completely. In spite of the bacterial system receiving the most research attention, the chemical pathway for excitation remains mysterious except that it is clearly not by a decarboxylation. Both the coelenterazine and bacterial systems have in common of being able to employ “antenna proteins”, lumazine protein and the green-fluorescent protein, for tuning the color of the bioluminescence. Spatial structure information has been most valuable in informing the mechanism of the Ca2+-regulated photoproteins and the antenna protein interactions.This article is protected by copyright. All rights reserved.
      PubDate: 2016-10-17T09:35:21.666291-05:
      DOI: 10.1111/php.12650
  • Cloning of the Blue Ghost (Phausis reticulata) Luciferase Reveals a
           Glowing Source of Green Light
    • Authors: Bruce R. Branchini; Tara L. Southworth, Leah J. Salituro, Danielle M. Fontaine, Yuichi Oba
      Abstract: In the southern Appalachian area of the United States, the Phausis reticulata firefly, commonly known as the “Blue Ghost,” performs a unique display of bioluminescence. Adult male organisms are observed darting rapidly along paths and riverbeds in dark forests producing long-lasting and mesmerizing bluish-white luminous streaks. Starting with eighteen adult male firefly lanterns, we used a reverse transcriptase and rapid amplification of cDNA ends (RACE) approach to clone the 1635 base pair open reading frame of the P. reticulata luc gene corresponding to a 545 residue protein. Expression of the recombinant luciferase protein in E. coli and characterization studies revealed the true color of the light emission to be green (λmax = 552 nm), strongly suggesting that the field observations result from a Purkinje shift. While the P. reticulata luciferase amino acid sequence is 74.3% identical to the North American P. pyralis luciferase, we were surprised to find that it was 88.4% and 87.7% identical to luciferases from C. ruficollis and D. axillaris both native to mainland Japan. Phylogenetic analysis confirmed the close relationship of the three enzymes that is surprising given the great distance between their natural habitats and the inability of the Japanese fireflies to produce bright bioluminescence.This article is protected by copyright. All rights reserved.
      PubDate: 2016-10-01T10:23:59.50573-05:0
      DOI: 10.1111/php.12649
  • Hybrid Minimal Core Streptavidin-obelin as a Versatile Reporter for
           Bioluminescence-based Bioassay
    • Authors: Eugenia E. Bashmakova; Vasilisa V. Krasitskaya, Alexander N. Kudryavtsev, Vitaly G. Grigorenko, Ludmila A. Frank
      Abstract: Ca2+-regulated photoprotein obelin was genetically fused with a minimum-sized core streptavidin. Hybrid protein (SAV-OL) was produced by bacterial expression and applied as a specific bioluminescent probe in diverse solid-phase assays. The obtained results clearly demonstrate specific activity of each domain indicating its proper folding with favorable space orientation. SAV-OL has been shown to be a much more sensitive label than the chemical conjugate of a full-length streptavidin with obelin.This article is protected by copyright. All rights reserved.
      PubDate: 2016-10-01T10:23:57.26145-05:0
      DOI: 10.1111/php.12648
  • Nucleotide Excision Repair: Finely Tuned Molecular Orchestra of Early
           Pre-incision Events
    • Authors: Qianzheng Zhu; Altaf A. Wani
      Abstract: Nucleotide excision repair (NER) eliminates a broad variety of helix-distorting DNA lesions that can otherwise cause genomic instability. NER comprises two distinct sub-pathways: global genomic NER (GG-NER) operating throughout the genome, and transcription-coupled NER (TC-NER) preferentially removing DNA lesions from transcribing DNA strands of transcriptionally active genes. Several NER factors undergo post-translational modifications, including ubiquitination, occurring swiftly and reversibly at DNA lesion sites. Accumulating evidence indicates that ubiquitination not only orchestrates the spatio-temporal recruitment of key protein factors to DNA lesion sites but also the productive assembly of NER preincision complex. This review will be restricted to the latest conceptual understanding of ubiquitin-mediated regulation of initial damage sensors of NER, i.e., DDB, XPC, RNAPII and CSB. We project hypothetical NER models in which ubiquitin-specific segregase, valosin-containing protein (VCP)/p97, plays an essential role in timely extraction of the congregated DNA damage sensors to functionally facilitate the DNA lesion elimination from the genome.This article is protected by copyright. All rights reserved.
      PubDate: 2016-10-01T10:15:25.064246-05:
      DOI: 10.1111/php.12647
  • UV‐Induced DNA Damage and Mutagenesis in Chromatin
    • Authors: Peng Mao; John J. Wyrick, Steven A. Roberts, Michael J. Smerdon
      Abstract: UV radiation induces photolesions that distort the DNA double helix and, if not repaired, can cause severe biological consequences, including mutagenesis or cell death. In eukaryotes, both the formation and repair of UV damage occur in the context of chromatin, in which genomic DNA is packaged with histones into nucleosomes and higher‐order chromatin structures. Here, we review how chromatin impacts the formation of UV photoproducts in eukaryotic cells. We describe the initial discovery that nucleosomes and other DNA‐binding proteins induce characteristic ‘photofootprints’ during the formation of UV photoproducts. We also describe recent progress in genome‐wide methods for mapping UV damage, which echoes early biochemical studies, and highlights the role of nucleosomes and transcription factors in UV damage formation and repair at unprecedented resolution. Finally, we discuss our current understanding of how the distribution and repair of UV DNA damage influence mutagenesis in human skin cancers.This article is protected by copyright. All rights reserved.
      PubDate: 2016-09-26T09:00:24.412429-05:
      DOI: 10.1111/php.12646
  • Tibetan Firefly Luciferase With Low Temperature Adaptation
    • Authors: Yasuo Mitani; Ryo Futahashi, Zichao Liu, Xingcai Liang, Yoshihiro Ohmiya
      Abstract: Fireflies are widespread all over the world and a numerous numbers of luciferases have been isolated and characterized. In this study, we identified and characterized the luciferase and luciferase‐like genes from a Tibetan firefly collected in Shangri‐La, China. The altitude of this area is more than 3,300 meters. We saw this Tibetan firefly flying with strong luminescence after sunset at ~10°C. We analyzed the transcriptome of Tibetan firefly using head, thorax, abdomen (without light organ), and light organ tissue by RNA sequencing. We identified one luciferase gene, which was almost identical to luciferase from fireflies Pyrocoelia species, and expressed specifically in the light organ. Interestingly, the optimal temperature of the Tibetan firefly recombinant luciferase was 10°C. The Km for D‐luciferin and ATP of the recombinant luciferase was 23 and 154 μM, respectively. The optimal pH was around 7.0 to 7.5. The emission peak was 556 nm at pH 8.0, while it shifted to 606 nm at pH 6.0. We also found a luciferase‐like gene with 43% identical amino acids to the Tibetan firefly luciferase, which was scarcely expressed in any portion of the adult body. No luciferase activity was detected for this luciferase‐like protein.This article is protected by copyright. All rights reserved.
      PubDate: 2016-09-26T08:50:23.110213-05:
      DOI: 10.1111/php.12643
  • Skin Exposure to Ultraviolet B Rapidly Activates Systemic Neuroendocrine
           and Immunosuppressive Responses
    • Authors: Cezary Skobowiat; Arnold E. Postlethwaite, Andrzej T. Slominski
      Abstract: The back skin of C57BL/6 mice was exposed to a single 400 mJ/cm2 dose of ultraviolet B (UVB), and parameters of hypothalamic‐pituitary‐adrenal (HPA) axis in relation to immune activity were tested after 30‐90 min following irradiation. Levels of brain and/or plasma corticotropin releasing hormone (CRH), β‐endorphin, ACTH and corticosterone (CORT) were enhanced by UVB. Hypophysectomy had no effect on UVB‐induced increases of CORT. Mitogen induced IFNγ production by splenocytes from UVB‐treated mice was inhibited at 30, 90 min and after 24 h. UVB also led to inhibition of IL‐10 production indicating an immunosuppressive effect on both Th1 and Th2 cytokines. Conditioned media from splenocytes isolated from UVB‐treated animals had no effect on IFNγ production in cultured normal splenocytes, however IFNγ increased with conditioned media from sham‐irradiated animals. Sera from UVB‐treated mice suppressed T cell mitogen‐induced IFNγ production as compared to sera from sham‐treated mice. IFNγ production was inhibited in splenocytes isolated from UVB‐treated animals with intact pituitary, while stimulated in splenocytes from UVB‐treated hypophysectomised mice. Thus, cutaneous exposure to UVB rapidly stimulates systemic CRH, ACTH, β‐endorphin, and CORT production accompanied by rapid immunosuppressive effects in splenocytes that appear to be independent of the HPA axis.This article is protected by copyright. All rights reserved.
      PubDate: 2016-09-26T08:45:23.154824-05:
      DOI: 10.1111/php.12642
  • Post‐excision Events in Human Nucleotide Excision Repair
    • Authors: Michael G. Kemp; Jinchuan Hu
      Abstract: The nucleotide excision repair system removes a wide variety of DNA lesions from the human genome, including photoproducts induced by ultraviolet (UV) wavelengths of sunlight. A defining feature of nucleotide excision repair is its dual incision mechanism, in which two nucleolytic incision events on the damaged strand of DNA at sites bracketing the lesion generate a damage‐containing DNA oligonucleotide and a single‐stranded DNA gap approximately 30 nucleotides in length. Although the early events of nucleotide excision repair, which include lesion recognition and the dual incisions, have been explored in detail and are reasonably well understood, the fate of the single‐stranded gaps and excised oligonucleotide products of repair have not been as extensively examined. In this review, recent findings that address these less‐explored aspects of nucleotide excision repair are discussed and support the concept that post‐incision gap and excised oligonucleotide processing are critical steps in the cellular response to DNA damage induced by UV light and other environmental carcinogens. Defects in these latter stages of repair lead to cell death and other DNA damage signaling responses and may therefore contribute to a number of human disease states associated with exposure to UV wavelengths of sunlight, including skin cancer, aging, and autoimmunity.This article is protected by copyright. All rights reserved.
      PubDate: 2016-09-19T19:25:23.282486-05:
      DOI: 10.1111/php.12641
  • Hormonal Regulation of the Repair of UV Photoproducts in Melanocytes by
           the Melanocortin Signaling Axis
    • Authors: Stuart G. Jarrett; John A. D'Orazio
      Abstract: Melanoma is the deadliest form of skin cancer because of its propensity to spread beyond the primary site of disease and because it resists many forms of treatment. Incidence of melanoma has been increasing for decades. Though ultraviolet radiation (UV) has been identified as the most important environmental causative factor for melanoma development, UV‐protective strategies have had limited efficacy in melanoma prevention. UV mutational burden correlates with melanoma development and tumor progression, underscoring the importance of UV in melanomagenesis. However, besides amount of UV exposure, melanocyte UV mutational load is influenced by the robustness of nucleotide excision repair, the genome maintenance pathway charged with removing UV photoproducts before they cause permanent mutations in the genome. In this review, we highlight the importance of the melanocortin hormonal signaling axis on regulating efficiency of nucleotide excision repair in melanocytes. By understanding the molecular mechanisms by which nucleotide excision repair can be increased, it may be possible to prevent many cases of melanoma by reducing UV mutational burden over time.This article is protected by copyright. All rights reserved.
      PubDate: 2016-09-19T19:25:20.826358-05:
      DOI: 10.1111/php.12640
  • Bioluminescent Enzymatic Assay as a Tool for Studying Antioxidant Activity
           and Toxicity of Bioactive Compounds
    • Authors: Nadezhda S. Kudryasheva; Ekaterina S. Kovel, Anna S. Sachkova, Anna A. Vorobeva, Viktoriya G. Isakova, Grigoriy N. Churilov
      Abstract: A bioluminescent assay based on a system of coupled enzymatic reactions catalyzed by bacterial luciferase and NADH:FMN‐oxidoreductase was developed to monitor toxicity and antioxidant activity of bioactive compounds. The assay enables studying toxic effects at the level of biomolecules and physicochemical processes, as well as determining the toxicity of general and oxidative types. Toxic and detoxifying effects of bioactive compounds were studied. Fullerenols, perspective pharmaceutical agents, nanosized particles, water‐soluble polyhydroxylated fullerene‐60 derivatives were chosen as bioactive compounds. Two homologous fullerenols with different number and type of substituents, C60O2‐4(OH)20‐24 and Fe0.5C60(OH)xOy (x+y=40‐42), were used. They suppressed bioluminescent intensity at concentrations > 0.01 g L−1 and > 0.001 g L−1 for C60O2‐4(OH)20‐24 and Fe0.5C60(OH)xOy, respectively, hence, a lower toxicity of C60O2‐4(OH)20‐24 was demonstrated. Antioxidant activity of fullerenols was studied in model solutions of organic and inorganic oxidizers; changes in toxicities of general and oxidative type were determined; detoxification coefficients were calculated. Fullerenol C60O2‐4(OH)20‐24 revealed higher antioxidant ability at concentrations 10‐17‐10‐5 g L−1. The difference in the toxicity and antioxidant activity of fullerenols was explained through their electron donor/acceptor properties and different catalytic activity. Principles of bioluminescent enzyme assay application for evaluating the toxic effect and antioxidant activity of bioactive compounds were summarized.This article is protected by copyright. All rights reserved.
      PubDate: 2016-09-19T19:20:27.241649-05:
      DOI: 10.1111/php.12639
  • Detection of the Excised, Damage‐containing Oligonucleotide Products of
           Nucleotide Excision Repair in Human Cells
    • Authors: Jimyeong Song; Michael G. Kemp, Jun‐Hyuk Choi
      Abstract: The human nucleotide excision repair system targets a wide variety of DNA adducts for removal from DNA, including photoproducts induced by UV wavelengths of sunlight. A key feature of nucleotide excision repair is its dual incision mechanism, which results in generation of a small, damage‐containing oligonucleotide approximately 24‐ to 32‐nt in length. Detection of these excised oligonucleotides using cell‐free extracts and purified proteins with defined DNA substrates has provided a robust biochemical assay for excision repair activity in vitro. However, the relevance of a number of in vitro findings to excision repair in living cells in vivo has remained unresolved. Over the past few years, novel methods for detecting and isolating the excised oligonucleotide products of repair in vivo have therefore been developed. Here we provide a basic outline of a sensitive and versatile in vivo excision assay and discuss how the assay both confirms previous in vitro findings and offers a number of advantages over existing cell‐based DNA repair assays. Thus, the in vivo excision assay offers a powerful tool for readily monitoring the repair of DNA lesions induced by a large number of environmental carcinogens and anti‐cancer compounds.This article is protected by copyright. All rights reserved.
      PubDate: 2016-09-16T02:30:41.787955-05:
      DOI: 10.1111/php.12638
  • Distinct Role of Sesn2 in Response to UVB‐induced DNA Damage and
           UVA‐induced Oxidative Stress in Melanocytes
    • Authors: Baozhong Zhao; Palak Shah, Lei Qiang, Tong‐Chuan He, Andrey Budanov, Yu‐Ying He
      Abstract: Ultraviolet (UV) radiation, including both UVB and UVA irradiation, is the major risk factor for causing skin cancer including melanoma. Recently we have shown that Sesn2, a member of the evolutionarily conserved stress‐inducible protein family Sestrins (Sesn), is up‐regulated in human melanomas as compared to melanocytes in normal human skin, suggesting an oncogenic role of Sesn2. However, the role of Sesn2 in UVB and UVA response is unknown. Here we demonstrated that both UVB and UVA induce Sesn2 up‐regulation in melanocytes and melanoma cells. UVB induces Sesn2 expression through the p53 and AKT3 pathways. Sesn2 negatively regulates UVB‐induced DNA damage repair. In comparison UVA induces Sesn2 up‐regulation through mitochondria but not Nrf2. Sesn2 ablation increased UVA‐induced Nrf2 induction and inhibits UVA‐induced ROS production, indicating that Sesn2 acts as an upstream regulator of Nrf2. These findings suggest previously unrecognized mechanisms in melanocyte response to UVB and UVA irradiation and potentially in melanoma formation.This article is protected by copyright. All rights reserved.
      PubDate: 2016-07-27T09:50:19.827165-05:
      DOI: 10.1111/php.12624
  • FAD and MTHF are the in‐planta Cofactors of Arabidopsis thaliana
           Cryptochrome 3
    • Authors: Tanja Göbel; Stefan Reisbacher, Alfred Batschauer, Richard Pokorny
      Abstract: Members of the cryptochrome/photolyase family (CPF) of proteins utilize non‐covalently bound light‐absorbing cofactors for their biological function. Usually, the identity of these cofactors is determined after expression in heterologous systems leaving the question unanswered whether these cofactors are identical to the indigenous ones. Here, cryptochrome 3 from Arabidopsis thaliana was expressed as a fusion with the green fluorescent protein in Arabidopsis plants. Besides the confirmation of the earlier report of its localization in chloroplasts, our data indicate that fractions of the fusion protein are present in the stroma and associated with thylakoids, respectively. Furthermore, it is shown that the fusion protein expressed in planta contains the same cofactors as the His6‐tagged protein expressed in Escherichia coli, i.e., flavin adenine dinucleotide and N5,N10‐methenyltetrahydrofolate. This demonstrates that the heterologously‐expressed cryptochrome 3, characterized in a number of previous studies, is a valid surrogate of the corresponding protein expressed in plants. To our knowledge, this is also a first conclusive analysis of cofactors bound to an Arabidopsis protein belonging to the CPF and purified from plant tissue.This article is protected by copyright. All rights reserved.
      PubDate: 2016-07-27T09:45:21.608782-05:
      DOI: 10.1111/php.12622
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