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Browsing Faculty Research Publications (Biochemistry and Biophysics) by Title

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Browsing Faculty Research Publications (Biochemistry and Biophysics) by Title

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  • Saldivar, Joshua C.; Miuma, Satoshi; Bene, Jessica; Hosseini, Seyed Ali; Shibata, Hidetaka; Sun, Jin; Wheeler, Linda J.; Mathews, Christopher K.; Huebner, Kay (Public Library of Science, 2012-11-29)
    Genomic instability drives tumorigenesis, but how it is initiated in sporadic neoplasias is unknown. In early preneoplasias, alterations at chromosome fragile sites arise due to DNA replication stress. A frequent, perhap ...
  • Sun, Guihua; Li, Haitang; Wu, Xiwei; Covarrubias, Maricela; Scherer, Lisa; Meinking, Keith; Luk, Brian; Chomchan, Pritsana; Alluin, Jessica; Gombart, Adrian F.; Rossi, John J. (Oxford University Press, 2012-03)
    Using microRNA array analyses of in vitro HIV-1-infected CD4(+) cells, we find that several host microRNAs are significantly up- or downregulated around the time HIV-1 infection peaks in vitro. While microRNA-223 levels ...
  • Fok, Wilson C.; Chen, Yidong; Bokov, Alex; Zhang, Yiqiang; Salmon, Adam B.; Diaz, Vivian; Javors, Martin; Wood, William H., III; Zhang, Yongqing; Becker, Kevin G.; Pérez, Viviana I.; Richardson, Arlan (Public Library of Science, 2014-01-07)
    Rapamycin was found to increase (11% to 16%) the lifespan of male and female C57BL/6J mice most likely by reducing the increase in the hazard for mortality (i.e., the rate of aging) term in the Gompertz mortality analys ...
  • Mourino-Perez, Rosa R.; Linacre-Rojas, Lorena P.; Roman-Gavilanes, Ariana I.; Lew, Thomas K.; Callejas-Negrete, Olga A.; Roberson, Robert W.; Freitag, Michael (Public Library of Science, 2013-08-12)
    The microtubule (MT) "plus end" constitutes the platform for the accumulation of a structurally and functionally diverse group of proteins, collectively called "MT plus-end tracking proteins" (+TIPs). +TIPs control MT dy ...
  • Schaaper, Roel M.; Mathews, Christopher K. (Elsevier, 2012-12-06)
    The accuracy of DNA synthesis depends on the accuracy of the polymerase as well as the quality and concentration(s) of the available 5'-deoxynucleoside-triphosphate DNA precursors (dNTPs). The relationships between dNTPs ...
  • Michels, Alexander J.; Frei, Balz (MDPI - Multidisciplinary Digital Publishing Institute, 2013-12-16)
    Research progress to understand the role of vitamin C (ascorbic acid) in human health has been slow in coming. This is predominantly the result of several flawed approaches to study design, often lacking a full appreci ...
  • Drechsel, Derek A.; Estevez, Alvaro G.; Barbeito, Luis; Beckman, Joseph S. (Springer, 2012-11)
    Oxidative damage is a common and early feature of Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis (ALS) and other neurodegenerative disorders. Dr. Mark Smith and his colleagues have built the case ...
  • Roberts, Blaine R.; Lim, Nastasia K. H.; McAllum, Erin J.; Rhoads, Timothy W.; Williams, Jared R.; Beckman, Joseph S.; et al. (Society for Neuroscience, 2014-06-04)
    Mutations in the metallo-protein Cu/Zn-superoxide dismutase (SOD1) cause amyotrophic lateral sclerosis (ALS) in humans and an expression level-dependent phenotype in transgenic rodents. We show that oral treatment with ...
  • Gretes, Michael C.; Poole, Leslie B.; Karplus, P. Andrew (Mary Ann Liebert, Inc., 2012-08)
    Significance: Parasite survival and virulence relies on effective defenses against reactive oxygen and nitrogen species produced by the host immune system. Peroxiredoxins (Prxs) are ubiquitous enzymes now thought to be c ...
  • Trias, Emiliano; Díaz-Amarilla, Pablo; Olivera-Bravo, Silvia; Isasi, Eugenia; Drechsel, Derek A.; Lopez, Nathan; Bradford, C. Samuel; Ireton, Kyle E.; Beckman, Joseph S.; Barbeito, Luis (Frontiers Research Foundation, 2013-12-24)
    See article for Abstract.
  • Seiboth, Bernhard; Karimi, Razieh Aghcheh; Phatale, Pallavi A.; Linke, Rita; Hartl, Lukas; Sauer, Dominik G.; Smith, Kristina M.; Baker, Scott E.; Freitag, Michael; Kubicek, Christian P. (Wiley-Blackwell, 2012-06)
    Trichoderma reesei is an industrial producer of enzymes that degrade lignocellulosic polysaccharides to soluble monomers, which can be fermented to biofuels. Here we show that the expression of genes for lignocellulose d ...
  • Yu, Zhen; Wang, Rong; Fok, Wilson C.; Coles, Alexander; Salmon, Adam B.; Pérez, Viviana I. (Oxford University Press, 2014-04-22)
    Dietary restriction (DR) is the gold standard intervention used to delay aging, and much recent research has focused on the identification of possible DR mimetics. Energy sensing pathways, including insulin/IGF1 signali ...
  • Campbell, Yan; Fantacone, Mary L.; Gombart, Adrian F. (Springer, 2012-12)
    Background: Antimicrobial peptides (AMPs) are synthesized and secreted by immune and epithelial cells that are constantly exposed to environmental microbes. AMPs are essential for barrier defense and deficiencies lead to ...
  • Tronrud, Dale E.; Allen, James P. (Springer, 2012-04)
    The Fenna-Matthews-Olson antenna protein from the green bacterium Pelodictyon phaeum mediates the energy transfer from a peripheral antenna complex to the membrane-bound reaction center. The three-dimensional structure ...
  • Mannava, Sudha; Moparthy, Kalyana C.; Wheeler, Linda J.; Leonova, Katerina I.; Wawrzyniak, Joseph A.; Bianchi-Smiraglia, Anna; Berman, Albert E.; Flanagan, Sheryl; Shewach, Donna S.; Zeitouni, Nathalie C.; Gudkov, Andrei V.; Mathews, Christopher K.; Nikiforov, Mikhail A. (Impact Journals LLC., 2012-12)
    The down‐regulation of dominant oncogenes, including C‐MYC, in tumor cells often leads to the induction of senescence via mechanisms that are not completely identified. In the current study, we demonstrate that MYC‐depl ...
  • Chimploy, Korakod; Song, Shiwei; Wheeler, Linda J.; Mathews, Christopher K. (American Society for Biochemistry and Molecular Biology, 2013-05-03)
    Deoxyribonucleoside triphosphate pools in mammalian mitochondria are highly asymmetric, and this asymmetry probably contributes toward the elevated mutation rate for the mitochondrial genome as compared with the nuclea ...
  • Hong, Joung-Woo; Hendrix, David A.; Levine, Michael S. (American Association for the Advancement of Science, 2008-09-05)
    The dorsal-ventral patterning of the Drosophila embryo is controlled by Dorsal, a sequence-specific transcription factor that is related to mammalian NF-κB. Previous ChIP-chip assays predicted that as many as a third or ...
  • Fok, Wilson C.; Zhang, Yiqiang; Salmon, Adam B.; Bhattacharya, Arunabh; Gunda, Rakesh; Jones, Dean; Ward, Walter; Fisher, Kathleen; Richardson, Arlan; Perez, Viviana I. (Oxford University Press, 2013-02)
    Because rapamycin, an inhibitor of the nutrient sensor mammalian target of rapamycin, and dietary restriction both increase life span of mice, it has been hypothesized that they act through similar mechanisms. To test th ...
  • Grote, Phillip; Wittler, Lars; Währisch, Sandra; Hendrix, David; Beisaw, Arica; Macura, Karol; Bläss, Gaby; Kellis, Manolis; Werber, Martin; Herrmann, Bernhard G. (Elsevier, 2013-01-28)
    The histone modifying complexes PRC2 and TrxG/MLL play pivotal roles in determining the activation state of genes controlling pluripotency, lineage commitment, and cell differentiation. Long non-coding RNAs (lncRNAs) can ...
  • Mahony, Shaun; Hendrix, David; Golden, Aaron; Smith, Terry J.; Rokhsar, Daniel S. (Oxford University Press, 2005-01-12)
    MOTIVATION: The automatic identification of over-represented motifs present in a collection of sequences continues to be a challenging problem in computational biology. Many existing approaches to motif identification do ...

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