Now showing items 1-20 of 38

    • 24-Hour Rhythms of DNA Methylation and Their Relation with Rhythms of RNA Expression in the Human Dorsolateral Prefrontal Cortex 

      Lim, Andrew S. P.; Srivastava, Gyan P.; Yu, Lei; Chibnik, Lori B.; Xu, Jishu; Buchman, Aron S.; Schneider, Julie A.; Myers, Amanda J.; Bennett, David A.; De Jager, Philip L. (Public Library of Science, 2014)
      Circadian rhythms modulate the biology of many human tissues, including brain tissues, and are driven by a near 24-hour transcriptional feedback loop. These rhythms are paralleled by 24-hour rhythms of large portions of ...
    • 53BP1 Protects against CtIP-Dependent Capture of Ectopic Chromosomal Sequences at the Junction of Distant Double-Strand Breaks 

      Guirouilh-Barbat, Josée; Gelot, Camille; Xie, Anyong; Dardillac, Elodie; Scully, Ralph; Lopez, Bernard S. (Public Library of Science, 2016)
      DNA double-strand breaks (DSB) are very harmful lesions that can generate genome rearrangements. In this study, we used intrachromosomal reporters to compare both the efficiency and accuracy of end-joining occurring with ...
    • Allele-Specific Methylation Occurs at Genetic Variants Associated with Complex Disease 

      Hutchinson, John N.; Raj, Towfique; Fagerness, Jes; Stahl, Eli; Viloria, Fernando T.; Gimelbrant, Alexander; Seddon, Johanna; Daly, Mark; Chess, Andrew; Plenge, Robert (Public Library of Science, 2014)
      We hypothesize that the phenomenon of allele-specific methylation (ASM) may underlie the phenotypic effects of multiple variants identified by Genome-Wide Association studies (GWAS). We evaluate ASM in a human population ...
    • Analysis of genetic systems using experimental evolution and whole-genome sequencing 

      Hegreness, Matthew; Kishony, Roy (BioMed Central, 2007)
      The application of whole-genome sequencing to the study of microbial evolution promises to reveal the complex functional networks of mutations that underlie adaptation. A recent study of parallel evolution in populations ...
    • Association of Matrix Metalloproteinase-9 (MMP9) Variants with Primary Angle Closure and Primary Angle Closure Glaucoma 

      Chen, Xueli; Chen, Yuhong; Wiggs, Janey L.; Pasquale, Louis R.; Sun, Xinghuai; Fan, Bao Jian (Public Library of Science, 2016)
      Shorter axial length observed in patients with primary angle closure glaucoma (PACG) might be due to altered matrix metalloproteinase-9 (MMP9) activity resulting in ECM remodeling during eye growth and development. This ...
    • Binary DNA Nanostructures for Data Encryption 

      Halvorsen, Kenneth A; Wong, Wesley Philip (Public Library of Science, 2012)
      We present a simple and secure system for encrypting and decrypting information using DNA self-assembly. Binary data is encoded in the geometry of DNA nanostructures with two distinct conformations. Removing or leaving out ...
    • COLD-PCR Amplification of Bisulfite-Converted DNA Allows the Enrichment and Sequencing of Rare Un-Methylated Genomic Regions 

      Castellanos-Rizaldos, Elena; Milbury, Coren A.; Karatza, Elli; Chen, Clark C.; Makrigiorgos, G. Mike; Merewood, Anne (Public Library of Science, 2014)
      Aberrant hypo-methylation of DNA is evident in a range of human diseases including cancer and diabetes. Development of sensitive assays capable of detecting traces of un-methylated DNA within methylated samples can be ...
    • Complex Breakpoints and Template Switching Associated with Non-canonical Termination of Homologous Recombination in Mammalian Cells 

      Hartlerode, Andrea J.; Willis, Nicholas A.; Rajendran, Anbazhagan; Manis, John P.; Scully, Ralph (Public Library of Science, 2016)
      A proportion of homologous recombination (HR) events in mammalian cells resolve by “long tract” gene conversion, reflecting copying of several kilobases from the donor sister chromatid prior to termination. Cells lacking ...
    • CRISPR/Cas9-Mediated Phage Resistance Is Not Impeded by the DNA Modifications of Phage T4 

      Yaung, Stephanie J.; Esvelt, Kevin M.; Church, George M. (Public Library of Science, 2014)
      Bacteria rely on two known DNA-level defenses against their bacteriophage predators: restriction-modification and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) systems. Certain ...
    • Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure 

      Smith, J. Gustav; Felix, Janine F.; Morrison, Alanna C.; Kalogeropoulos, Andreas; Trompet, Stella; Wilk, Jemma B.; Gidlöf, Olof; Wang, Xinchen; Morley, Michael; Mendelson, Michael; Joehanes, Roby; Ligthart, Symen; Shan, Xiaoyin; Bis, Joshua C.; Wang, Ying A.; Sjögren, Marketa; Ngwa, Julius; Brandimarto, Jeffrey; Stott, David J.; Aguilar, David; Rice, Kenneth M.; Sesso, Howard D.; Demissie, Serkalem; Buckley, Brendan M.; Taylor, Kent D.; Ford, Ian; Yao, Chen; Liu, Chunyu; Sotoodehnia, Nona; van der Harst, Pim; Stricker, Bruno H. Ch.; Kritchevsky, Stephen B.; Liu, Yongmei; Gaziano, J. Michael; Hofman, Albert; Moravec, Christine S.; Uitterlinden, André G.; Kellis, Manolis; van Meurs, Joyce B.; Margulies, Kenneth B.; Dehghan, Abbas; Levy, Daniel; Olde, Björn; Psaty, Bruce M.; Cupples, L. Adrienne; Jukema, J. Wouter; Djousse, Luc; Franco, Oscar H.; Boerwinkle, Eric; Boyer, Laurie A.; Newton-Cheh, Christopher; Butler, Javed; Vasan, Ramachandran S.; Cappola, Thomas P.; Smith, Nicholas L. (Public Library of Science, 2016)
      Failure of the human heart to maintain sufficient output of blood for the demands of the body, heart failure, is a common condition with high mortality even with modern therapeutic alternatives. To identify molecular ...
    • DISSECT Method Using PNA-LNA Clamp Improves Detection of EGFR T790m Mutation 

      Guha, Minakshi; Castellanos-Rizaldos, Elena; Makrigiorgos, G. Mike (Public Library of Science, 2013)
      Non-small cell lung cancer (NSCLC) patients treated with small molecule EGFR inhibitors, such as gefitinib, frequently develop drug resistance due to the presence of secondary mutations like the T790M mutation on EGFR exon ...
    • DNA Self-Assembly of Targeted Near-Infrared-Responsive Gold Nanoparticles for Cancer Thermo-Chemotherapy 

      Xiao, Zeyu; Ji, Changwei; Shi, Jinjun; Pridgen, Eric M; Frieder, Jillian; Farokhzad, Omid Cameron (WILEY-VCH Verlag, 2012)
      Targeted Cancer Therapy: Inspired by the ability of DNA hybridization, a targeted near-infrared (NIR) light-responsive delivery system has been developed through simple DNA self-assembly (PEG=polyethylene glycol). This ...
    • Dynamic in vivo mutations within the ica operon during persistence of Staphylococcus aureus in the airways of cystic fibrosis patients 

      Schwartbeck, Bianca; Birtel, Johannes; Treffon, Janina; Langhanki, Lars; Mellmann, Alexander; Kale, Devika; Kahl, Janina; Hirschhausen, Nina; Neumann, Claudia; Lee, Jean C.; Götz, Friedrich; Rohde, Holger; Henke, Hanae; Küster, Peter; Peters, Georg; Kahl, Barbara C. (Public Library of Science, 2016)
      Cystic fibrosis (CF) is associated with chronic bacterial airway infections leading to lung insufficiency and decreased life expectancy. Staphylococcus aureus is one of the most prevalent pathogens isolated from the airways ...
    • Engineered Hyperactive Integrase for Concerted HIV-1 DNA Integration 

      Li, Min; Jurado, Kellie A.; Lin, Shiqiang; Engelman, Alan; Craigie, Robert (Public Library of Science, 2014)
      The DNA cutting and joining reactions of HIV-1 integration are catalyzed by integrase (IN), a viral protein that functions as a tetramer bridging the two viral DNA ends (intasome). Two major obstacles for biochemical and ...
    • Enrichment of Mutations in Multiple DNA Sequences Using COLD-PCR in Emulsion 

      Castellanos-Rizaldos, Elena; Milbury, Coren Audrey; Makrigiorgos, G. Mike (Public Library of Science, 2012)
      Background: Multiplex detection of low-level mutant alleles in the presence of wild-type DNA would be useful for several fields of medicine including cancer, pre-natal diagnosis and infectious diseases. COLD-PCR is a ...
    • Essential Developmental, Genomic Stability, and Tumour Suppressor Functions of the Mouse Orthologue of hSSB1/NABP2 

      Shi, Wei; Bain, Amanda L.; Schwer, Bjoern; Al-Ejeh, Fares; Smith, Corey; Wong, Lee; Chai, Hua; Miranda, Mariska S.; Ho, Uda; Kawaguchi, Makoto; Miura, Yutaka; Finnie, John W.; Wall, Meaghan; Heierhorst, Jörg; Wicking, Carol; Spring, Kevin J.; Alt, Frederick W.; Khanna, Kum Kum (Public Library of Science, 2013)
      Single-stranded DNA binding proteins (SSBs) regulate multiple DNA transactions, including replication, transcription, and repair. We recently identified SSB1 as a novel protein critical for the initiation of ATM signaling ...
    • Evaluation of OPEN Zinc Finger Nucleases for Direct Gene Targeting of the ROSA26 Locus in Mouse Embryos 

      Hermann, Mario; Rector, Kyle; Ruiz, Joseph; Becher, Burkhard; Bürki, Kurt; Khayter, Cyd; Aguzzi, Adriano; Buch, Thorsten; Pelczar, Pawel; Maeder, Morgan L.; Joung, Jae Keith (Public Library of Science, 2012)
      Zinc finger nucleases (ZFNs) enable precise genome modification in a variety of organisms and cell types. Commercial ZFNs were reported to enhance gene targeting directly in mouse zygotes, whereas similar approaches using ...
    • Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation 

      Kuzu, Guray; Kaye, Emily G.; Chery, Jessica; Siggers, Trevor; Yang, Lin; Dobson, Jason R.; Boor, Sonia; Bliss, Jacob; Liu, Wei; Jogl, Gerwald; Rohs, Remo; Singh, Nadia D.; Bulyk, Martha L.; Tolstorukov, Michael Y.; Larschan, Erica (Public Library of Science, 2016)
      Dosage compensation is an essential process that equalizes transcript levels of X-linked genes between sexes by forming a domain of coordinated gene expression. Throughout the evolution of Diptera, many different X-chromosomes ...
    • The HoxB1 hexapeptide is a prefolded domain: Implications for the Pbx1/Hox interaction 

      Slupsky, Carolyn M.; Sykes, David Brian; Gay, Grant L.; Sykes, Brian D. (Wiley-Blackwell, 2001)
      Hox proteins are transcriptional regulators that bind consensus DNA sequences. The DNA-binding specificity of many of these Hox proteins is modulated by the heterodimerization with partners, such as the Pbx proteins. This ...
    • Identification of Anziaic Acid, a Lichen Depside from Hypotrachyna sp., as a New Topoisomerase Poison Inhibitor 

      Cheng, Bokun; Cao, Shugeng; Vasquez, Victor; Annamalai, Thirunavukkarasu; Tamayo-Castillo, Giselle; Clardy, Jon C.; Tse-Dinh, Yuk-Ching (Public Library of Science, 2013)
      Topoisomerase inhibitors are effective for antibacterial and anticancer therapy because they can lead to the accumulation of the intermediate DNA cleavage complex formed by the topoisomerase enzymes, which trigger cell ...