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https://www.readbyqxmd.com/read/29475157/the-role-of-the-n-terminal-domain-of-human-apurinic-apyrimidinic-endonuclease-1-ape1-in-dna-glycosylase-stimulation
#1
Olga A Kladova, Milena Bazlekowa-Karaban, Sonia Baconnais, Olivier Piétrement, Alexander A Ishchenko, Bakhyt T Matkarimov, Danila A Iakovlev, Andrey Vasenko, Olga S Fedorova, Eric Le Cam, Barbara Tudek, Nikita A Kuznetsov, Murat Saparbaev
The base excision repair (BER) pathway consists of sequential action of DNA glycosylase and apurinic/apyrimidinic (AP) endonuclease necessary to remove a damaged base and generate a single-strand break in duplex DNA. Human multifunctional AP endonuclease 1 (APE1, a.k.a. APEX1, HAP-1, or Ref-1) plays essential roles in BER by acting downstream of DNA glycosylases to incise a DNA duplex at AP sites and remove 3'-blocking sugar moieties at DNA strand breaks. Human 8-oxoguanine-DNA glycosylase (OGG1), methyl-CpG-binding domain 4 (MBD4, a...
February 11, 2018: DNA Repair
https://www.readbyqxmd.com/read/29475072/digital-gene-expression-profiling-reveals-transcriptional-responses-to-acute-cold-stress-in-chinese-soft-shelled-turtle-pelodiscus-sinensis-juveniles
#2
Wen-Yi Zhang, Cui-Juan Niu, Bo-Jian Chen, Kenneth B Storey
Turtles are well known for their stress tolerance, including an ability to deal with temperature extremes or rapid thermal change. To know more about the comprehensive molecular basis of thermal stress responses in turtles, we assessed differentially expressed genes (DEGs) in the brain, liver and kidney of juvenile soft-shelled turtles, Pelodiscus sinensis, after acute cold stress (28 °C-8 °C acute transfer and held for 12 h) and following recovery (back to 28 °C and held for 24 h) by digital gene expression profiling...
February 20, 2018: Cryobiology
https://www.readbyqxmd.com/read/29474974/structural-and-biophysical-insight-into-dual-site-binding-of-the-protoberberine-alkaloid-palmatine-to-parallel-g-quadruplex-dna-using-nmr-fluorescence-and-circular-dichroism-spectroscopy
#3
Kumar Padmapriya, Ritu Barthwal
Plant derived small molecules, which interact with and stabilize G-quadruplex DNA, act as inhibitors of telomere elongation and oncogene expression in humans. The inhibition of telomerase enzyme has immense potential since it is over expressed in most cancer cells. Interaction of palmatine, an antitumor alkaloid, to parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4 , has been investigated using Nuclear Magnetic Resonance (NMR), fluorescence and Circular Dichroism (CD) spectroscopy. Titrations were monitored by recording1 H and31 P NMR spectra and solution structure of palmatine-[d(TTGGGGT)]4 complex was obtained by restrained Molecular Dynamics (rMD) simulations using distance restraints from 2D NOESY spectra...
February 20, 2018: Biochimie
https://www.readbyqxmd.com/read/29474667/the-transcription-factor-csbhlh18-of-sweet-orange-citrus-sinensis-functions-in-modulation-of-cold-tolerance-and-reactive-oxygen-species-homeostasis-by-regulating-the-antioxidant-gene
#4
Jingjing Geng, Ji-Hong Liu
The basic helix-loop-helix (bHLH) transcription factors (TFs) comprise one of the largest gene families in plants and participate in various physiological processes, but physiological role and regulatory function of the majority of bHLHs remain poorly understood. Here, a total of 56 putative CsbHLH genes were identified in sweet orange (Citrus sinensis) based on a genome-wide analysis. The CsbHLHs, except four members, were distributed throughout nine chromosomes and divided into 19 subgroups. Most of the CsbHLH genes were responsive to cold stress, with the greatest upregulation being observed in CsbHLH18...
February 21, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29474483/correction-gadolinium-enhanced-cardiac-mr-exams-of-human-subjects-are-associated-with-significant-increases-in-the-dna-repair-marker-53bp1-but-not-the-damage-marker-%C3%AE-h2ax
#5
Jennifer S McDonald, Robert J McDonald, Jacob B Ekins, Antony S Tin, Sylvain Costes, Tamara M Hudson, Dana J Schroeder, Kevin Kallmes, Scott H Kaufmann, Philip M Young, Aiming Lu, Ramanathan Kadirvel, David F Kallmes
[This corrects the article DOI: 10.1371/journal.pone.0190890.].
2018: PloS One
https://www.readbyqxmd.com/read/29474423/seasonal-variability-in-the-persistence-of-dissolved-environmental-dna-edna-in-a-marine-system-the-role-of-microbial-nutrient-limitation
#6
Ian Salter
Environmental DNA (eDNA) can be defined as the DNA pool recovered from an environmental sample that includes both extracellular and intracellular DNA. There has been a significant increase in the number of recent studies that have demonstrated the possibility to detect macroorganisms using eDNA. Despite the enormous potential of eDNA to serve as a biomonitoring and conservation tool in aquatic systems, there remain some important limitations concerning its application. One significant factor is the variable persistence of eDNA over natural environmental gradients, which imposes a critical constraint on the temporal and spatial scales of species detection...
2018: PloS One
https://www.readbyqxmd.com/read/29473918/metal-nanoparticles-porous-silicon-microcavity-enhanced-surface-plasmon-resonance-fluorescence-for-the-detection-of-dna
#7
Jiajia Wang, Zhenhong Jia
A porous silicon microcavity (PSiMC) with resonant peak wavelength of 635 nm was fabricated by electrochemical etching. Metal nanoparticles (NPs)/PSiMC enhanced fluorescence substrates were prepared by the electrostatic adherence of Au NPs that were distributed in PSiMC. The Au NPs/PSiMC device was used to characterize the target DNA immobilization and hybridization with its complementary DNA sequences marked with Rhodamine red (RRA). Fluorescence enhancement was observed on the Au NPs/PSiMC device substrate; and the minimum detection concentration of DNA ran up to 10 pM...
February 23, 2018: Sensors
https://www.readbyqxmd.com/read/29473176/the-b-allele-with-a-5%C3%A2-8-kb-deletion-in-intron-1-of-the-abo-gene-is-the-major-allele-in-japanese-individuals-with-b-m-and-a-1-b-m-phenotypes
#8
K Ogasawara, T Miyazaki, S Ito, R Yabe, M Uchikawa, T Enomoto, N Yokoya, Y Hori, M Kumamoto, S Watanabe, M Satake
Bm and A1 Bm phenotypes are the most frequent ABO variants in the Japanese population. The B antigen on Bm red blood cells is only detectable by adsorption and elution tests, and plasma B-transferase activity is usually detected at half or less levels compared with that of common B. Recently, a B allele lacking an erythroid cell-specific transcription enhancer in intron 1 of the ABO gene was identified from individuals with Bm and A1 Bm phenotypes, which could explain the unique serologic properties of Bm ...
February 23, 2018: Vox Sanguinis
https://www.readbyqxmd.com/read/29473044/cardiotoxicity-of-anticancer-therapeutics
#9
REVIEW
Jerry Dong, Hong Chen
As cancer therapeutics continues to improve and progress, the adverse side effects associated with anticancer treatments have also attracted more attention and have become extensively explored. Consequently, the importance of posttreatment follow-ups is becoming increasingly relevant to the discussion. Contemporary treatment methods, such as tyrosine kinase inhibitors, anthracycline chemotherapy, and immunotherapy regimens are effective in treating different modalities of cancers; however, these reagents act through interference with DNA replication or prevent DNA repair, causing endothelial dysfunction, generating reactive oxygen species, or eliciting non-specific immune responses...
2018: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/29472543/dznep-inhibits-h3k27me3-deposition-and-delays-retinal-degeneration-in-the-rd1-mice
#10
Shijie Zheng, Lirong Xiao, Yu Liu, Yujiao Wang, Lin Cheng, Junjun Zhang, Naihong Yan, Danian Chen
Retinitis pigmentosa (RP) is a group of inherited retinal degenerative diseases causing progressive loss of photoreceptors. Numerous gene mutations are identified to be related with RP, but epigenetic modifications may also be involved in the pathogenesis. Previous studies suggested that both DNA methylation and histone acetylation regulate photoreceptor cell death in RP mouse models. However, the role of histone methylation in RP has never been investigated. In this study, we found that trimethylation of several lysine sites of histone H3, including lysine 27 (H3K27me3), increased in the retinas of rd1 mice...
February 22, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29472273/a-unified-approach-for-quantifying-and-interpreting-dna-shape-readout-by-transcription-factors
#11
H Tomas Rube, Chaitanya Rastogi, Judith F Kribelbauer, Harmen J Bussemaker
Transcription factors (TFs) interpret DNA sequence by probing the chemical and structural properties of the nucleotide polymer. DNA shape is thought to enable a parsimonious representation of dependencies between nucleotide positions. Here, we propose a unified mathematical representation of the DNA sequence dependence of shape and TF binding, respectively, which simplifies and enhances analysis of shape readout. First, we demonstrate that linear models based on mononucleotide features alone account for 60-70% of the variance in minor groove width, roll, helix twist, and propeller twist...
February 22, 2018: Molecular Systems Biology
https://www.readbyqxmd.com/read/29471857/patterns-of-midichloria-infection-in-avian-borne-african-ticks-and-their-trans-saharan-migratory-hosts
#12
Irene Di Lecce, Chiara Bazzocchi, Jacopo G Cecere, Sara Epis, Davide Sassera, Barbara M Villani, Gaia Bazzi, Agata Negri, Nicola Saino, Fernando Spina, Claudio Bandi, Diego Rubolini
BACKGROUND: Ticks are obligate haematophagous ectoparasites of vertebrates and frequently parasitize avian species that can carry them across continents during their long-distance migrations. Ticks may have detrimental effects on the health state of their avian hosts, which can be either directly caused by blood-draining or mediated by microbial pathogens transmitted during the blood meal. Indeed, ticks host complex microbial communities, including bacterial pathogens and symbionts. Midichloria bacteria (Rickettsiales) are widespread tick endosymbionts that can be transmitted to vertebrate hosts during the tick bite, inducing an antibody response...
February 22, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29471804/genetic-mapping-and-comparative-genomics-to-inform-restoration-enhancement-and-culture-of-southern-flounder-paralichthys-lethostigma
#13
Shannon J O'Leary, Christopher M Hollenbeck, Robert R Vega, John R Gold, David S Portnoy
BACKGROUND: Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Low year-class strengths over the past few years in the western Gulf of Mexico have raised concern that spawning stocks may be overfished. Current management of the resource includes releasing hatchery-raised juveniles to restock bays and estuaries; additionally, there is a growing interest in the potential for commercial aquaculture of the species...
February 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29471497/increased-nk-cell-function-after-cessation-of-long-term-nucleos-t-ide-analogue-treatment-in-chronic-hepatitis-b-associates-with-liver-damage-and-hbsag-loss
#14
Christine L Zimmer, Franziska Rinker, Christoph Höner Zu Siederdissen, Michael P Manns, Heiner Wedemeyer, Markus Cornberg, Niklas K Björkström
Background: Treatment with nucleos(t)ide analogues (NA) efficiently suppress HBV DNA but rarely leads to functional cure of chronic hepatitis B (CHB). Following NA cessation, a fraction of HBeAg-negative CHB-patients experience HBsAg loss. Cellular immune responses, including those by natural killer cells, innate lymphocytes known to respond in CHB, explaining the virological events transpiring following NA treatment cessation remain elusive. Methods: In a single-center prospective trial, 15 HBeAg-negative CHB-patients on long-term NA treatment underwent structured NA cessation and were studied longitudinally...
February 17, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29471255/non-stop-aptasensor-capable-of-rapidly-monitoring-norovirus-in-a-sample
#15
Brian Kim, Kang Wook Chung, Ji Hoon Lee
A cost-effective and simple biosensor was developed for the accurate and rapid monitoring of norovirus GII in a sample. The modified DNA aptamer, 5 guanines linked to conventional DNA aptamer, designed for the research, was able to rapidly capture norovirus GII in tap water as well artificial urine. In addition, the extra guanines of the modified DNA aptamer enhanced the sensitivity of biosensor with guanine chemiluminescence detection based on the principle of intra chemiluminescent resonance transfer (Intra-CRET)...
February 11, 2018: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29471172/enhancing-glioblastoma-treatment-using-cisplatin-gold-nanoparticle-conjugates-and-targeted-delivery-with-magnetic-resonance-guided-focused-ultrasound
#16
Daniel Coluccia, Carlyn A Figueiredo, Megan YiJun Wu, Alexandra N Riemenschneider, Roberto Diaz, Amanda Luck, Christian Smith, Sunit Das, Cameron Ackerley, Meaghan O'Reilly, Kullervo Hynynen, James T Rutka
Glioblastoma (GBM) is the most common and aggressive primary brain tumor resulting in high rates of morbidity and mortality. A strategy to increase the efficacy of available drugs and enhance the delivery of chemotherapeutics through the blood brain barrier (BBB) is desperately needed. We investigated the potential of Cisplatin conjugated gold nanoparticles (GNP-UP-Cis) in combination with MR-guided Focused Ultrasound (MRgFUS) to intensify GBM treatment. Viability assays demonstrated that GNP-UP-Cis greatly inhibits the growth of GBM cells compared to free cisplatin and shows marked synergy with radiation therapy...
February 19, 2018: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/29471112/evaluation-of-two-commercial-real-time-pcr-kits-a-fumigatus-%C3%A2-bio-evolution-and-mycogenie-%C3%A2-a-fumigatus-for-aspergillus-dna-detection-in-bronchoalveolar-lavage-fluid-in-patients-with-invasive-pulmonary-aspergillosis
#17
Julie Denis, Faezeh Forouzanfar, Raoul Herbrecht, Elise Toussaint, Romain Kessler, Marcela Sabou, Ermanno Candolfi, Valérie Letsher-Bru
Invasive pulmonary aspergillosis (IPA) is a common complication of immunosuppression. Rapid diagnosis using molecular techniques is essential to improve patient survival. PCR techniques are promising in enhancing Aspergillus detection in blood and respiratory samples. Here, we evaluate for the first time the performances of two commercial Real-Time PCR kits, the A. fumigatus® Bio-Evolution and the MycoGENIE® A. fumigatus for the detection of A. fumigatus DNA in broncho-alveolar lavage (BAL) from patients with and without IPA...
February 19, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29470985/cytoplasmic-p53-contributes-to-the-removal-of-uracils-misincorporated-by-hiv-1-reverse-transcriptase
#18
Yossi Saragani, Amnon Hizi, Galia Rahav, Sara Zauch, Mary Bakhanashvili
HIV-1 reverse transcriptase (RT) in the cytoplasm of HIV-infected cells efficiently inserts the non-canonical dUTP into the proviral DNA, and extends the dU-terminated DNA. The misincorporation of dUTP leads to mutagenesis, and uracils can down-regulate viral gene expression. However, uracilation might also protect HIV DNA from auto-integration in the cytoplasm. Tumor suppressor p53 protein, exhibiting inherent 3'→5' exonuclease activity, provides a potential host-derived repair mechanism during HIV reverse transcription for the misincorporation of various wrong nucleotides, leading to both base-base mismatches and incorporated non-canonical ribonucleotides...
February 19, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29470542/functional-fine-tuning-between-bacterial-dna-recombination-initiation-and-quality-control-systems
#19
Veronika Ferencziová, Gábor M Harami, Julianna B Németh, Tibor Vellai, Mihály Kovács
Homologous recombination (HR) is crucial for the error-free repair of DNA double-strand breaks (DSBs) and the restart of stalled replication. However, imprecise HR can lead to genome instability, highlighting the importance of HR quality control. After DSB formation, HR proceeds via DNA end resection and recombinase loading, whereas helicase-catalyzed disruption of a subset of subsequently formed DNA invasions is thought to be essential for maintaining HR accuracy via inhibiting illegitimate (non-allelic) recombination...
2018: PloS One
https://www.readbyqxmd.com/read/29468195/transcriptome-profiling-reveals-interplay-of-multifaceted-stress-response-in-escherichia-coli-on-exposure-to-glutathione-and-ciprofloxacin
#20
Manish Goswami, Akkipeddi Venkat Satya Surya Narayana Rao
We have previously reported that supplementation of exogenous glutathione (GSH) promotes ciprofloxacin resistance in Escherichia coli by neutralizing antibiotic-induced oxidative stress and by enhancing the efflux of antibiotic. In the present study, we used a whole-genome microarray as a tool to analyze the system-level transcriptomic changes of E. coli on exposure to GSH and/or ciprofloxacin. The microarray data revealed that GSH supplementation affects redox function, transport, acid shock, and virulence genes of E...
January 2018: MSystems
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