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Browsing Faculty Research Publications (Biochemistry and Biophysics) by Issue Date

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Browsing Faculty Research Publications (Biochemistry and Biophysics) by Issue Date

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  • 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 ...
  • 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 ...
  • Benison, Gregory; Karplus, P. Andrew; Barbar, Elisar (Elsevier, 2008-12-26)
    Dynein light chain LC8 is a small, dimeric, and very highly conserved globular protein that is an integral part of the dynein and myosin molecular motors but appears to have a broader role in multiple protein complexes u ...
  • Visioli, Francesco; Hagen, Tory M. (Elsevier, 2011)
    The use of antioxidants is now often used as a pharmacological adjunct to limit infertility. Indeed, the lay public rightly perceives oxidative stress and, thus, antioxidant treatment as important modulators of inferti ...
  • Voinov, Valery G.; Deinzer, Max L.; Beckman, Joseph S.; Barofsky, Douglas F. (Springer, 2011-04)
    Recently, we demonstrated that a radio-frequency-free electromagnetostatic (RF-free EMS) cell could be retrofitted into a triple quad mass spectrometer to allow electron-capture dissociation (ECD) without the aid of cool ...
  • Ma, Liping; Greenwood, Jeffrey A.; Schachner, Melitta (Society for Neuroscience, 2011-11-16)
    The cysteine-rich protein (CRP) family is a subgroup of LIM domain proteins. CRP1, which cross-links actin filaments to make actin bundles, is the only CRP family member expressed in the CNS with little known about its f ...
  • Ishikawa, Francine H.; Souza, Elaine A.; Shoji, Jun-ya; Connolly, Lanelle; Freitag, Michael; Read, Nick D.; Roca, M. Gabriela (2012-02-02)
    It has been hypothesized that horizontal gene/chromosome transfer and parasexual recombination following hyphal fusion between different strains may contribute to the emergence of wide genetic variability in plant patho ...
  • Lepesant, Julie M. J.; Cosseau, Celine; Boissier, Jerome; Freitag, Michael; Portela, Julien; Climent, Deborah; Perrin, Cecile; Zerlotini, Adhemar; Grunau, Christoph (BioMed Central Ltd., 2012-02-29)
    Background: In the leuphotrochozoan parasitic platyhelminth Schistosoma mansoni, male individuals are homogametic (ZZ) whereas females are heterogametic (ZW). To elucidate the mechanisms that led to the emergence of sex ...
  • 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 ...
  • 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 ...
  • 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 ...
  • Frei, Balz; Birlouez-Aragon, Ines; Lykkesfeldt, Jens (Taylor & Francis, 2012-06-14)
    The recommended dietary allowance (RDA) of vitamin C has traditionally been based on the prevention of the vitamin C deficiency disease, scurvy. While higher intakes of vitamin C may exert additional health benefits, the ...
  • 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 ...
  • Kyme, Pierre; Thoennissen, Nils H.; Tseng, Ching Wen; Thoennissen, Gabriela B.; Wolf, Andrea J.; Shimada, Kenichi; Krug, Utz O.; Lee, Kunik; Muller-Tidow, Carsten; Berdel, Wolfgang E.; Hardy, W. David; Gombart, Adrian F.; Koeffler, H. Phillip; Liu, George Y. (American Society for Clinical Investigation, 2012-09)
    The myeloid-specific transcription factor, CCAAT/enhancer-binding protein epsilon (C/EBPε) is a critical mediator of myelopoiesis. Mutation of this gene is responsible for neutrophil-specific granule deficiency in humans ...
  • Wheeler, Linda J.; Mathews, Christopher K. (American Society for Biochemistry and Molecular Biology, 2012-09-07)
    Saccharomyces cerevisiae contains three NAD⁺/NADH kinases, one of which is localized in mitochondria and phosphorylates NADH in preference to NAD⁺. Strand et al (Euk. Cell 2:809 (2003)) reported that a yeast mutation i ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...

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