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https://www.readbyqxmd.com/read/28323522/detection-of-cytosine-and-cpg-density-in-proto-oncogenes-and-tumor-suppressor-genes-in-promoter-sequences-of-acute-myeloid-leukemia
#1
Senol Dogan, Anis Cilic, Damir Marjanovic, Amina Kurtovic-Kozaric
Aberrant methylation is one of the driving forces of cancer genome development. Although the rate of methylation appears massively variable across the genome, it is mainly observed in histone modification, chromatin organization, DNA accessibility, or promoter sequence. Methylation of promoter sequence occurs mostly to cytosine nucleotides, which can affect transcription factors' binding affinities. In this study, we demonstrated that cytosine repeats (C types density), consisting of CC, CCC, CCCC, CCCCC, CCCCCC, CCCCCCC motifs and CpG islands density in 25 proto-oncogenes, tumor suppressor genes and control genes may play a role in the pathogenesis of acute myeloid leukemia...
March 21, 2017: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/28157182/efficient-genome-replication-of-hepatitis-b-virus-using-adenovirus-vector-a-compact-pregenomic-rna-expression-unit
#2
Mariko Suzuki, Saki Kondo, Manabu Yamasaki, Norie Matsuda, Akio Nomoto, Tetsuro Suzuki, Izumu Saito, Yumi Kanegae
The complicated replication mechanisms of hepatitis B virus (HBV) have impeded HBV studies and anti-HBV therapy development as well. Herein we report efficient genome replication of HBV applying adenovirus vectors (AdVs) showing high transduction efficiency. Even in primary hepatocytes derived from humanized mice the transduction efficiencies using AdVs were 450-fold higher compared than those using plasmids. By using an expression unit consisting of the CMV promoter, 1.03-copy HBV genome and foreign poly(A) signal, we successfully generated an improved AdV (HBV103-AdV) that efficiently provided 58 times more pregenomic RNA than previously reported AdVs...
February 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28116699/pelmo-an-optimised-in-house-cloning-vector
#3
Andrea E Ramos, Marina Muñoz, Darwin A Moreno-Pérez, Manuel A Patarroyo
DNA cloning is an essential tool regarding DNA recombinant technology as it allows the replication of foreign DNA fragments within a cell. pELMO was here constructed as an in-house cloning vector for rapid and low-cost PCR product propagation; it is an optimally designed vector containing the ccdB killer gene from the pDONR 221 plasmid, cloned into the pUC18 vector's multiple cloning site (Thermo Scientific). The ccdB killer gene has a cleavage site (CCC/GGG) for the SmaI restriction enzyme which is used for vector linearisation and cloning blunt-ended products...
December 2017: AMB Express
https://www.readbyqxmd.com/read/27975303/ntcp-reconstituted-in-vitro-hbv-infection-system
#4
Yinyan Sun, Yonghe Qi, Bo Peng, Wenhui Li
Sodium taurocholate cotransporting polypeptide (NTCP) has been identified as a functional receptor for hepatitis B virus (HBV). Expressing human NTCP in human hepatoma HepG2 cells (HepG2-NTCP) renders these cells susceptible for HBV infection. The HepG2-NTCP stably transfected cell line provides a much-needed and easily accessible platform for studying the virus. HepG2-NTCP cells could also be used to identify chemicals targeting key steps of the virus life cycle including HBV covalent closed circular (ccc) DNA, and enable the development of novel antivirals against the infection...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27873496/ovarian-clear-cell-carcinoma-sub-typing-by-arid1a-expression
#5
Jae Yoon Choi, Hyun Ho Han, Young Tae Kim, Joo Hyun Lee, Baek Gil Kim, Suki Kang, Nam Hoon Cho
PURPOSE: Loss of AT-rich DNA-interacting domain 1A (ARID1A) has been identified as a driving mutation of ovarian clear cell carcinoma (O-CCC), a triple-negative ovarian cancer that is intermediary between serous and endometrioid subtypes, in regards to molecular and clinical behaviors. However, about half of O-CCCs still express BAF250a, the protein encoded by ARID1A. Herein, we aimed to identify signatures of ARID1A-positive O-CCC in comparison with its ARID1A-negative counterpart. MATERIALS AND METHODS: Seventy cases of O-CCC were included in this study...
January 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/27797587/the-current-status-and-future-directions-of-hepatitis-b-antiviral-drug-discovery
#6
Liudi Tang, Qiong Zhao, Shuo Wu, Junjun Cheng, Jinhong Chang, Ju-Tao Guo
The current standard care of chronic hepatitis B fails to induce a durable off-drug control of hepatitis B virus (HBV) replication in the majority of treated patients. The primary reasons are its inability to eliminate the covalently closed circular (ccc) DNA, the nuclear form of HBV genome, and restoration of the dysfunctional host antiviral immune response against the virus. Accordingly, discovery and development of therapeutics to completely stop HBV replication, eliminate or functionally inactivate cccDNA as well as activate a functional antiviral immune response against HBV are the primary efforts for finding a cure for chronic hepatitis B...
January 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/27783675/dna-polymerase-%C3%AE%C2%BA-is-a-key-cellular-factor-for-the-formation-of-covalently-closed-circular-dna-of-hepatitis-b-virus
#7
Yonghe Qi, Zhenchao Gao, Guangwei Xu, Bo Peng, Chenxuan Liu, Huan Yan, Qiyan Yao, Guoliang Sun, Yang Liu, Dingbin Tang, Zilin Song, Wenhui He, Yinyan Sun, Ju-Tao Guo, Wenhui Li
Hepatitis B virus (HBV) infection of hepatocytes begins by binding to its cellular receptor sodium taurocholate cotransporting polypeptide (NTCP), followed by the internalization of viral nucleocapsid into the cytoplasm. The viral relaxed circular (rc) DNA genome in nucleocapsid is transported into the nucleus and converted into covalently closed circular (ccc) DNA to serve as a viral persistence reservoir that is refractory to current antiviral therapies. Host DNA repair enzymes have been speculated to catalyze the conversion of rcDNA to cccDNA, however, the DNA polymerase(s) that fills the gap in the plus strand of rcDNA remains to be determined...
October 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27711445/structures-of-the-kinetically-trapped-i-motif-dna-intermediates
#8
Alyssa Garabedian, David Butcher, Jennifer L Lippens, Jaroslava Miksovska, Prem P Chapagain, Daniele Fabris, Mark E Ridgeway, Melvin A Park, Francisco Fernandez-Lima
In the present work, the conformational dynamics and folding pathways of i-motif DNA were studied in solution and in the gas-phase as a function of the solution pH conditions using circular dichroism (CD), photoacoustic calorimetry analysis (PAC), trapped ion mobility spectrometry-mass spectrometry (TIMS-MS), and molecular dynamics (MD). Solution studies showed at thermodynamic equilibrium the existence of a two-state folding mechanism, whereas during the pH = 7.0 → 4.5 transition a fast and slow phase (ΔHfast + ΔHslow = 43 ± 7 kcal mol(-1)) with a volume change associated with the formation of hemiprotonated cytosine base pairs and concomitant collapse of the i-motif oligonucleotide into a compact conformation were observed...
September 29, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27602323/mitochondrial-copy-number-and-d-loop-variants-in-pompe-patients
#9
Fatemeh Bahreini, Massoud Houshmand, Mohammad Hossein Modaresi, Hassan Tonekaboni, Shahriar Nafissi, Ferdoss Nazari, Seyed Mohammad Akrami
OBJECTIVE: Pompe disease is a rare neuromuscular genetic disorder and is classified into two forms of early and late-onset. Over the past two decades, mitochondrial abnor- malities have been recognized as an important contributor to an array of neuromuscular diseases. We therefore aimed to compare mitochondrial copy number and mitochondrial displacement-loop sequence variation in infantile and adult Pompe patients. MATERIALS AND METHODS: In this retrospective study, the mitochondrial D-loop sequence was analyzed by polymerase chain reaction (PCR) and direct sequencing to detect pos- sible variation in 28 Pompe patients (17 infants and 11 adults)...
2016: Cell Journal
https://www.readbyqxmd.com/read/27471731/in-vivo-and-in-vitro-genotoxic-and-epigenetic-effects-of-two-types-of-cola-beverages-and-caffeine-a-multiassay-approach
#10
Marcos Mateo-Fernández, Tania Merinas-Amo, Miguel Moreno-Millán, Ángeles Alonso-Moraga, Sebastián Demyda-Peyrás
The aim of this work was to assess the biological and food safety of two different beverages: Classic Coca Cola™ (CCC) and Caffeine-Free Coca Cola (CFCC). To this end, we determined the genotoxicological and biological effects of different doses of lyophilised CCC and CFCC and Caffeine (CAF), the main distinctive constituent. Their toxic/antitoxic, genotoxic/antigenotoxic, and chronic toxicity (lifespan assay) effects were determined in vivo using the Drosophila model. Their cytotoxic activities were determined using the HL-60 in vitro cancer model...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27442838/long-term-survival-of-patients-with-mismatch-repair-protein-deficient-high-stage-ovarian-clear-cell-carcinoma
#11
Colin J R Stewart, David D L Bowtell, Dorota A Doherty, Yee C Leung
AIMS: Gynaecological cancer patients with germline mutations appear to have a better prognosis than those with sporadic malignancies. Following the observation of long-term survival in a patient with stage III ovarian clear cell carcinoma (CCC) and possible Lynch syndrome (LS), DNA mismatch repair (MMR) protein immunohistochemistry was performed in a series of high-stage CCC and correlated with patient outcomes. METHODS AND RESULTS: Thirty-two consecutive cases of stage III/IV ovarian CCCs accessioned between 1992 and 2015 were examined...
January 2017: Histopathology
https://www.readbyqxmd.com/read/27346421/structural-and-calorimetric-studies-demonstrate-that-the-hepatocyte-nuclear-factor-1%C3%AE-hnf1%C3%AE-transcription-factor-is-imported-into-the-nucleus-via-a-monopartite-nls-sequence
#12
Mareike M Wiedmann, Shintaro Aibara, David R Spring, Murray Stewart, James D Brenton
The transcription factor hepatocyte nuclear factor 1β (HNF1β) is ubiquitously overexpressed in ovarian clear cell carcinoma (CCC) and is a potential therapeutic target. To explore potential approaches that block HNF1β transcription we have identified and characterised extensively the nuclear localisation signal (NLS) for HNF1β and its interactions with the nuclear protein import receptor, Importin-α. Pull-down assays demonstrated that the DNA binding domain of HNF1β interacted with a spectrum of Importin-α isoforms and deletion constructs tagged with eGFP confirmed that the HNF1β (229)KKMRRNR(235) sequence was essential for nuclear localisation...
September 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27340867/comprehensive-assessment-of-the-expression-of-the-swi-snf-complex-defines-two-distinct-prognostic-subtypes-of-ovarian-clear-cell-carcinoma
#13
Hisham Abou-Taleb, Ken Yamaguchi, Noriomi Matsumura, Ryusuke Murakami, Hidekatsu Nakai, Koichiro Higasa, Yasuaki Amano, Kaoru Abiko, Yumiko Yoshioka, Junzo Hamanishi, Masafumi Koshiyama, Tsukasa Baba, Ryo Yamada, Fumihiko Matsuda, Ikuo Konishi, Masaki Mandai
Somatic mutations in the ARID1A tumor-suppressor gene have been frequently identified in ovarian clear cell carcinoma (CCC) cases. BAF250a encoded by ARID1A is a member of the SWI/SNF complex, but the expression and mutation status of other SWI/SNF subunits have not been explored. The current study aimed to elucidate the biological and clinical significance of the SWI/SNF complex subunits, by assessing the expression and mutation status of SWI/SNF subunits, and distinct genomic aberrations associated with their expression...
August 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/27338670/sensitivity-of-human-cells-expressing-low-fidelity-or-weak-catalytic-activity-variants-of-dna-polymerase-%C3%AE-to-genotoxic-stresses
#14
Tetsuya Suzuki, Petr Grúz, Masamitsu Honma, Noritaka Adachi, Takehiko Nohmi
Translesion DNA polymerases (TLS pols) play critical roles in defense mechanisms against genotoxic agents. The defects or mutations of TLS pols are predicted to result in hypersensitivity of cells to environmental mutagens. In this study, human cells expressing DNA polymerase ζ (Pol ζ) variants with low fidelity or weak catalytic activity have been established with Nalm-6-MSH+ cells and their sensitivity to mutagenicity and cytotoxicity of benzo[a]pyrene diol epoxide (BPDE) and ultraviolet-C light (UV-C) was examined...
September 2016: DNA Repair
https://www.readbyqxmd.com/read/27272189/complete-hepatitis-b-virus-prophylaxis-withdrawal-in-hepatitis-b-surface-antigen-positive-liver-transplant-recipients-after-longterm-minimal-immunosuppression
#15
Ilaria Lenci, Leonardo Baiocchi, Laura Tariciotti, Daniele Di Paolo, Martina Milana, Francesco Santopaolo, Tommaso Maria Manzia, Luca Toti, Valentina Svicher, Giuseppe Tisone, Carlo Federico Perno, Mario Angelico
Tailored approaches have been attempted to prevent hepatitis B virus (HBV) reinfection in antibodies against hepatitis B surface antigen (HBsAg)-positive liver transplantation (LT) recipients in order to minimize the use of hepatitis B immune globulin (HBIG) and nucleoside analogues (NAs). We report the results of complete HBV prophylaxis withdrawal after a follow-up of at least 6 years in LT recipients with undetectable serum HBV DNA and intrahepatic total HBV DNA and covalently closed circular DNA at LT. We included 30 HBsAg positive, hepatitis B e antigen-negative recipients, 6 with hepatitis C virus and 7 with hepatitis D virus coinfection, who had received HBIG plus NA for at least 5 years after LT...
September 2016: Liver Transplantation
https://www.readbyqxmd.com/read/27210429/decay-of-ccc-dna-marks-persistence-of-intrahepatic-viral-dna-synthesis-under-tenofovir-in-hiv-hbv-co-infected-patients
#16
Anders Boyd, Karine Lacombe, Fabien Lavocat, Sarah Maylin, Patrick Miailhes, Caroline Lascoux-Combe, Constance Delaugerre, Pierre-Marie Girard, Fabien Zoulim
BACKGROUND & AIMS: In the presence of highly-potent antivirals, persistence of hepatitis B virus (HBV) is most well-characterized by covalently-closed circular DNA (cccDNA) and total intrahepatic DNA (IH-DNA). We sought to determine how antiviral therapy could affect their levels during human immunodeficiency virus (HIV)-HBV co-infection. METHODS: Sixty co-infected patients from a well-defined cohort with ⩾1 liver biopsy were studied. HBV cccDNA and total IH-DNA were extracted from biopsies and quantified by real-time PCR...
October 2016: Journal of Hepatology
https://www.readbyqxmd.com/read/27199921/characterization-of-the-deamination-coupled-with-sliding-along-dna-of-anti-hiv-factor-apobec3g-on-the-basis-of-the-ph-dependence-of-deamination-revealed-by-real-time-nmr-monitoring
#17
Keisuke Kamba, Takashi Nagata, Masato Katahira
Human APOBEC3G (A3G) is an antiviral factor that inactivates HIV. The C-terminal domain of A3G (A3G-CTD) deaminates cytosines into uracils within single-stranded DNA (ssDNA), which is reverse-transcribed from the viral RNA genome. The deaminase activity of A3G is highly sequence-specific; the third position (underlined) of a triplet cytosine (CCC) hotspot is converted into CCU. A3G deaminates a CCC that is located close to the 5' end of ssDNA more effectively than ones that are less close to the 5' end, so-called 3' → 5' polarity...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27185623/establishment-of-an-inducible-hbv-stable-cell-line-that-expresses-cccdna-dependent-epitope-tagged-hbeag-for-screening-of-cccdna-modulators
#18
Dawei Cai, Xiaohe Wang, Ran Yan, Richeng Mao, Yuanjie Liu, Changhua Ji, Andrea Cuconati, Haitao Guo
Hepatitis B virus (HBV) covalently closed circular (ccc) DNA is essential to the virus life cycle, its elimination during chronic infection is considered critical to a durable therapy but has not been achieved by current antivirals. Despite being essential, cccDNA has not been the major target of high throughput screening (HTS), largely because of the limitations of current HBV tissue culture systems, including the impracticality of detecting cccDNA itself. In response to this need, we have previously developed a proof-of-concept HepDE19 cell line in which the production of wildtype e antigen (HBeAg) is dependent upon cccDNA...
August 2016: Antiviral Research
https://www.readbyqxmd.com/read/27153553/association-of-nineteen-polymorphisms-from-seven-dna-repair-genes-and-the-risk-for-bladder-cancer-in-gansu-province-of-china
#19
Gongjian Zhu, Haixiang Su, Lingeng Lu, Hongyun Guo, Zhaohui Chen, Zhen Sun, Ruixia Song, Xiaomin Wang, Haining Li, Zhiping Wang
BACKGROUND: Balance of DNA damage and proper repair plays an important role in progression of bladder cancer. Here we aimed to assess the associations of nineteen polymorphisms from seven DNA repair-associated genes (PRAP1, OGG1, APEX1, MUTYH, XRCC1, XRCC2 and XRCC3) with bladder cancer and their interactions in the disease in a Han Chinese population. METHODOLOGY/PRINCIPAL FINDINGS: A chip-based TaqMan genotyping for the candidate genes was performed on 227 bladder cancer patients and 260 healthy controls...
May 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27121283/a-novel-type-2-diabetes-risk-allele-increases-the-promoter-activity-of-the-muscle-specific-small-ankyrin-1-gene
#20
Rengna Yan, Shanshan Lai, Yang Yang, Hongfei Shi, Zhenming Cai, Vincenzo Sorrentino, Hong Du, Huimei Chen
Genome-wide association studies have identified Ankyrin-1 (ANK1) as a common type 2 diabetes (T2D) susceptibility locus. However, the underlying causal variants and functional mechanisms remain unknown. We screened for 8 tag single nucleotide polymorphisms (SNPs) in ANK1 between 2 case-control studies. Genotype analysis revealed significant associations of 3 SNPs, rs508419 (first identified here), rs515071, and rs516946 with T2D (P < 0.001). These SNPs were in linkage disequilibrium (r(2) > 0...
2016: Scientific Reports
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