Now showing items 1-20 of 98

    • Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays 

      Suzuki, Yoko; Lu, Mingyang; Ben-Jacob, Eshel; Onuchic, José N. (2016)
      Regulatory gene circuit motifs play crucial roles in performing and maintaining vital cellular functions. Frequently, theoretical studies of gene circuits focus on steady-state behaviors and do not include time delays. In ...
    • Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin 

      Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.; Heins, Richard A.; McAndrew, Ryan P.; Bingman, Craig; Deng, Kai; Holland, Keefe C.; Noguera, Daniel R.; Simmons, Blake A.; Sale, Kenneth L.; Ralph, John; Donohue, Timothy J.; Adams, Paul D.; Phillips, George N. Jr. (2016)
      Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion ...
    • The Atlastin C-terminal Tail is an Amphipathic Helix that Perturbs Bilayer Structure during Endoplasmic Reticulum Homotypic Fusion 

      Faust, Joseph E.; Desai, Tanvi; Verma, Avani; Ulengin, Idil; Sun, Tzu-Lin; Moss, Tyler J.; Betancourt, Miguel A.; Huang, Huey W.; Lee, Tina; McNew, James A. (2015)
      Fusion of tubular membranes is required to form three-way junctions found in reticular subdomains of the endoplasmic reticulum (ER). The large GTPase Atlastin has recently been shown to drive ER membrane fusion and three-way ...
    • LucY: A Versatile New Fluorescent Reporter Protein 

      Auldridge, Michele E.; Cao, Hongnan; Sen, Saurabh; Franz, Laura P.; Bingman, Craig A.; Yennamalli, Ragothaman M.; Phillips, George N. Jr.; Mead, David; Steinmetz, Eric J. (2015)
      We report on the discovery, isolation, and use of a novel yellow fluorescent protein. Lucigen Yellow (LucY) binds one FAD molecule within its core, thus shielding it from water and maintaining its structure so that ...
    • Sources of Variability in a Synthetic Gene Oscillator 

      Veliz-Cuba, Alan; Hirning, Andrew J.; Atanas, Adam A.; Hussain, Faiza; Vancia, Flavia; Josić, Krešimir; Bennett, Matthew R. (2015)
      Synthetic gene oscillators are small, engineered genetic circuits that produce periodic variations in target protein expression. Like other gene circuits, synthetic gene oscillators are noisy and exhibit fluctuations in ...
    • Structural Basis for the Stereochemical Control of Amine Installation in Nucleotide Sugar Aminotransferases 

      Wang, Fengbin; Singh, Shanteri; Xu, Weijun; Helmich, Kate E.; Miller, Mitchell D.; Cao, Hongnan; Bingman, Craig A.; Thorson, Jon S.; Phillips, George N. Jr. (2015)
      Sugar aminotransferases (SATs) are an important class of tailoring enzymes that catalyze the 5'-pyridoxal phosphate (PLP)-dependent stereo- and regiospecific installation of an amino group from an amino acid donor (typically ...
    • Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble 

      Fisher, Kaitlin M.; Haglund, Ellinor; Noel, Jeffrey K.; Hailey, Kendra L.; Onuchic, José N.; Jennings, Patricia A. (2015)
      Interleukin-33 (IL-33) is currently the focus of multiple investigations into targeting pernicious inflammatory disorders. This mediator of inflammation plays a prevalent role in chronic disorders such as asthma, rheumatoid ...
    • Genetic and Chemical Activation of TFEB Mediates Clearance of Aggregated α-Synuclein 

      Kilpatrick, Kiri; Zeng, Yimeng; Hancock, Tommy; Segatori, Laura (2015)
      Aggregation of α-synuclein (α-syn) is associated with the development of a number of neurodegenerative diseases, including Parkinson’s disease (PD). The formation of α-syn aggregates results from aberrant accumulation of ...
    • Size-dependent impacts of silver nanoparticles on the lifespan, fertility, growth, and locomotion of Caenorhabditis elegans 

      Contreras, Elizabeth Q.; Puppala, Hema L.; Escalera, Gabriela; Zhong, Weiwei; Colvin, Vicki L. (2014)
      The increased bioavailability of nanoparticles engineered for good dispersion in water may have biological and environmental impacts. To examine this issue, the authors assessed the biological effects in nematodes as they ...
    • Total Synthesis of Viridicatumtoxin B and Analogues Thereof: Strategy Evolution, Structural Revision, and Biological Evaluation 

      Nicolaou, K.C.; Hale, Christopher R.H.; Nilewski, Christian; Ioannidou, Heraklidia A.; ElMarrouni, Abdelatif; Nilewski, Lizanne G.; Beabout, Kathryn; Wang, Tim T.; Shamoo, Yousif (2014)
      The details of the total synthesis of viridicatumtoxin B (1) are described. Initial synthetic strategies toward this intriguing tetracycline antibiotic resulted in the development of key alkylation and Lewis acid-mediated ...
    • Modular, Multi-Input Transcriptional Logic Gating with Orthogonal LacI/GalR Family Chimeras 

      Shis, David L.; Hussain, Faiza; Meinhardt, Sarah; Swint-Kruse, Liskin; Bennett, Matthew R. (2014)
      In prokaryotes, the construction of synthetic, multi-input promoters is constrained by the number of transcription factors that can simultaneously regulate a single promoter. This fundamental engineering constraint is an ...
    • A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation 

      Desai, Kevin K.; Cheng, Chin L.; Bingman, Craig A.; Phillips, George N. Jr.; Raines, Ronald T. (2014)
      Archease is a 16-kDa protein that is conserved in all three domains of life. In diverse bacteria and archaea, the genes encoding Archease and the tRNA ligase RtcB are localized into an operon. Here we provide a rationale ...
    • Refactoring and Optimization of Light-Switchable Escherichia coli Two-Component Systems 

      Schmidl, Sebastian R.; Sheth, Ravi U.; Wu, Andrew; Tabor, Jeffrey J. (2014)
      Light-switchable proteins enable unparalleled control of molecular biological processes in live organisms. Previously, we have engineered red/far-red and green/red photoreversible two-component signal transduction systems ...
    • Three-dimensional in vitro tumor models for cancer research and drug evaluation 

      Xu, Xian; Farach-Carson, Mary C.; Jia, Xinqiao (2014)
      Cancer occurs when cells acquire genomic instability and inflammation, produce abnormal levels of epigenetic factors/proteins and tumor suppressors, reprogram the energy metabolism and evade immune destruction, leading to ...
    • Structure-Guided Functional Characterization of Enediyne Self-Sacrifice Resistance Proteins, CalU16 and CalU19 

      Elshahawi, Sherif I.; Ramelot, Theresa A.; Seetharaman, Jayaraman; Chen, Jing; Singh, Shanteri; Yang, Yunhuang; Pederson, Kari; Kharel, Madan K.; Xiao, Rong; Lew, Scott; Yennamalli, Ragothaman M.; Miller, Mitchell D.; Wang, Fengbin; Tong, Liang; Montelione, Gaetano T.; Kennedy, Michael A.; Bingman, Craig A.; Zhu, Haining; Phillips, George N. Jr.; Thorson, Jon S. (2014)
      Calicheamicin γ1I (1) is an enediyne antitumor compound produced by Micromonospora echinospora spp. calichensis, and its biosynthetic gene cluster has been previously reported. Despite extensive analysis and biochemical ...
    • Hydrogel-Based 3D Model of Patient-Derived Prostate Xenograft Tumors Suitable for Drug Screening 

      Fong, Eliza L.S.; Martinez, Mariane; Yang, Jun; Mikos, Antonios G.; Navone, Nora M.; Harrington, Daniel A.; Farach-Carson, Mary C. (2014)
      The lack of effective therapies for bone metastatic prostate cancer (PCa) underscores the need for accurate models of the disease to enable the discovery of new therapeutic targets and to test drug sensitivities of individual ...
    • Tunable Protease-Activatable Virus Nanonodes 

      Judd, Justin; Ho, Michelle L.; Tiwari, Abhinav; Gomez, Eric J.; Dempsey, Christopher; Vliet, Kim Van; Igoshin, Oleg A.; Silberg, Jonathan J.; Agbandje-McKenna, Mavis; Suh, Junghae (2014)
      We explored the unique signal integration properties of the self-assembling 60-mer protein capsid of adeno-associated virus (AAV), a clinically proven human gene therapy vector, by engineering proteolytic regulation of ...
    • Nitrogen, biochar, and mycorrhizae: Alteration of the symbiosis and oxidation of the char surface 

      LeCroy, Chase; Masiello, Caroline A.; Rudgers, Jennifer A.; Hockaday, William C.; Silberg, Jonathan J. (2014)
      In some cases amending soil with biochar improves fertility, although the exact mechanisms through which biochar alters soil processes are not well understood. In other cases, however, biochar amendment can have no effect ...
    • Leveraging synthetic biology for tissue engineering applications 

      Lee, Esther J.; Tabor, Jeffrey J.; Mikos, Antonios G. (2014)
      Restoration of damaged tissues and organs requires precise control of cellular processes at the molecular level. Synthetic biology offers genetic tools that can be used to program the molecular biology of the cell, thereby ...
    • Tissue engineering perfusable cancer models 

      Fong, E.L.; Santoro, M.; Farach-Carson, M.C.; Kasper, F.K.; Mikos, A.G. (2014)
      The effect of fluid flow on cancer progression is currently not well understood, highlighting the need for perfused tumor models to close this gap in knowledge. Enabling biological processes at the cellular level to be ...