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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
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
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
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...
July 21, 2016: Histopathology
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
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...
June 20, 2016: Oncotarget
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
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
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
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
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
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
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
Li Zong, Yanli Qin, Haodi Jia, Huailiang Zhou, Chaoyang Chen, Ke Qiao, Jiming Zhang, Yongxiang Wang, Jisu Li, Shuping Tong
Replication of the 3.2-kb hepatitis B virus (HBV) genome is driven by the covalently closed circular (ccc) DNA in the nucleus, from which four classes of co-terminal RNAs are transcribed. Genome replication requires just the 3.5-kb pregenomic RNA, which is terminally redundant. Cloning the full-length HBV genome into a vector disrupts its continuity, thus preventing genome replication at the step of pregenomic RNA transcription. This can be overcome by converting the monomeric construct into a tandem dimer, yet the need to ligate two molecules of the HBV genome with vector DNA makes it inefficient and even unsuccessful...
July 2016: Journal of Virological Methods
Shirley Wong, Peggy Lam, Nafiseh Nafissi, Steven Denniss, Roderick Slavcev
We constructed linear covalently closed (LCC) DNA minivectors as a non-viral gene-delivery vector alternative produced via a simple platform in vivo. DNA ministrings possess a heightened safety profile and also efficiently deliver DNA cargo to targeted cells. Conventional DNA vectors carry undesirable prokaryotic sequences, including antibiotic resistance genes, CpG motifs, and bacterial origins of replication, which may lead to the stimulation of host immunological responses. The bioavailability of conventional DNA vectors is also compromised due to their larger molecular size...
2016: Journal of Visualized Experiments: JoVE
Magdalena Szopa, Agnieszka H Ludwig-Galezowska, Piotr Radkowski, Jan Skupien, Julita Machlowska, Tomasz Klupa, Pawel Wolkow, Maciej Borowiec, Wojciech Mlynarski, Maciej T Malecki
UNLABELLED: Until now only a few families with early onset autosomal diabetes due to the NEUROD1 gene mutations have been identified. Moreover, only some of them meet strict MODY (maturity-onset diabetes of the young) criteria. Next-generation sequencing (NGS) provides an opportunity to detect more pathogenic mutations in this gene. Here, we evaluated the segregation of the Arg103Pro mutation in the NEUROD1 gene in a pedigree in which it was detected, and described the clinical characteristics of the mutation carriers...
February 2016: European Journal of Medical Genetics
S Y Cheng, L L Li, H H Yuan, F Xu, H Cheng
Ginkgolides are key pharmaceutical components in Ginkgo biloba. Using the cDNA sequence of the MECP and MECT genes to design primers, we obtained the promoters of these genes from Ginkgo genomic DNA using the genome walking method. The two promoters were 744 and 982 bp in length, respectively. The cis-elements of the GbMECPs and GbMECT promoters were predicted and analyzed using the plant cis-acting regulatory element database. We found major cis-elements in the sequence of the GbMECT and GbMECPs promoters...
2015: Genetics and Molecular Research: GMR
Jincai Wu, Feng Yu, Zheng Zhang, Yong Chen, Jie Du, Atsushi Maruyama
Dimerization of two homologous strands of genomic DNA/RNA is an essential feature of retroviral replication. Herein we show that a cationic comb-type copolymer (CCC), poly(L-lysine)-graft-dextran, accelerates the dimerization of self-complementary stem-loop DNA, frequently found in functional DNA/RNA molecules, such as aptamers. Furthermore, an anionic polymer poly(sodium vinylsulfonate) (PVS) dissociates CCC from the duplex shortly within a few seconds. Then single stem-loop DNA spontaneously transforms from its dimer...
January 7, 2016: Nanoscale
Chi Hong Sum, Nafiseh Nafissi, Roderick A Slavcev, Shawn Wettig
In combination with novel linear covalently closed (LCC) DNA minivectors, referred to as DNA ministrings, a gemini surfactant-based synthetic vector for gene delivery has been shown to exhibit enhanced delivery and bioavailability while offering a heightened safety profile. Due to topological differences from conventional circular covalently closed (CCC) plasmid DNA vectors, the linear topology of LCC DNA ministrings may present differences with regards to DNA interaction and the physicochemical properties influencing DNA-surfactant interactions in the formulation of lipoplexed particles...
2015: PloS One
Martin Köbel, Bo Meng, Lien N Hoang, Noorah Almadani, Xiaodong Li, Robert A Soslow, C Blake Gilks, Cheng-Han Lee
Mixed endometrial carcinoma refers to a tumor that comprises 2 or more distinct histotypes. We studied 18 mixed-type endometrial carcinomas-11 mixed serous and low-grade endometrioid carcinomas (SC/EC), 5 mixed clear cell and low-grade ECs (CCC/EC), and 2 mixed CCC and SCs (CCC/SC), using targeted next-generation sequencing and immunohistochemistry to compare the molecular profiles of the different histotypes present in each case. In 16 of 18 cases there was molecular evidence that both components shared a clonal origin...
February 2016: American Journal of Surgical Pathology
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