Now showing items 1-20 of 40

    • 4-Phenylbutyrate Attenuates the ER Stress Response and Cyclic AMP Accumulation in DYT1 Dystonia Cell Models 

      Cho, Jin A.; Zhang, Xuan; Miller, Gregory M.; Lencer, Wayne I.; Nery, Flavia C. (Public Library of Science, 2014)
      Dystonia is a neurological disorder in which sustained muscle contractions induce twisting and repetitive movements or abnormal posturing. DYT1 early-onset primary dystonia is the most common form of hereditary dystonia ...
    • Added Mass in Rat Plantaris Muscle Causes a Reduction in Mechanical Work 

      Ross, Stephanie A.; Rimkus, Barbora; Konow, Nicolai; Biewener, Andrew; Wakeling, James M. (The Company of Biologists, 2020-07-31)
      Most of what we know about whole muscle behaviour comes from experiments on single fibres or small muscles that are scaled up in size without considering the effects of the additional muscle mass. Previous modelling studies ...
    • Aquatic and terrestrial takeoffs require different hindlimb kinematics and muscle function in mallard ducks 

      Biewener, Andrew; Taylor-Burt, Kari (The Company of Biologists, 2020-06-25)
      Mallard ducks are capable of performing a wide range of behaviors including nearly vertical takeoffs from both terrestrial and aquatic habitats. The hindlimb plays a key role during takeoffs from both media. However, because ...
    • Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models 

      Jacquin, Hugo; Gilson, Amy; Shakhnovich, Eugene; Cocco, Simona; Monasson, Rémi (Public Library of Science, 2016)
      Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship ...
    • Bright and stable luminescent probes for target engagement profiling in live cells 

      Mazitschek, Ralph; Payne, N. Connor; Kalyakina, Alena S.; Singh, Kritika; Tye, Mark (Springer Science and Business Media LLC, 2021-10-21)
    • Co-evolution-based prediction of metal-binding sites in proteomes by machine learning 

      Cheng, Yao; Wang, Haobo; Xu, Hua; Liu, Yuan; Ma, Bin; Chen, Xuemin; Zeng, Xin; Wang, Xianghe; Wang, Bo; Shiau, Carina; Ovchinnikov, Sergey; Su, Xiao-Dong; Wang, Chu (Springer Science and Business Media LLC, 2023-01-02)
      Metal ions play various important biological role in proteins including structural maintenance, molecular recognition and catalysis. Previous methods of predicting metal-binding sites in proteomes were based on either ...
    • Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC 

      Jaratlerdsiri, Weerachai; Deakin, Janine; Godinez, Ricardo M.; Shan, Xueyan; Peterson, Daniel G.; Marthey, Sylvain; Lyons, Eric; McCarthy, Fiona M.; Isberg, Sally R.; Higgins, Damien P.; Chong, Amanda Y.; John, John St; Glenn, Travis C.; Ray, David A.; Gongora, Jaime (Public Library of Science, 2014)
      The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes ...
    • Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus 

      Tully, Damien C.; Ogilvie, Colin B.; Batorsky, Rebecca E.; Bean, David J.; Power, Karen A.; Ghebremichael, Musie; Bedard, Hunter E.; Gladden, Adrianne D.; Seese, Aaron M.; Amero, Molly A.; Lane, Kimberly; McGrath, Graham; Bazner, Suzane B.; Tinsley, Jake; Lennon, Niall J.; Henn, Matthew R.; Brumme, Zabrina L.; Norris, Philip J.; Rosenberg, Eric S.; Mayer, Kenneth H.; Jessen, Heiko; Kosakovsky Pond, Sergei L.; Walker, Bruce D.; Altfeld, Marcus; Carlson, Jonathan M.; Allen, Todd M. (Public Library of Science, 2016)
      Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the ...
    • Discovery and molecular basis of subtype-selective cyclophilin inhibitors 

      Peterson, Alexander A.; Rangwala, Aziz M.; Thakur, Manish K.; Ward, Patrick S.; Hung, Christie; Outhwaite, Ian R.; Chan, Alix I.; Usanov, Dmitry L.; Mootha, Vamsi K.; Seeliger, Markus A.; Liu, David (Springer Science and Business Media LLC, 2022-09-26)
      <jats:title>Abstract</jats:title><jats:p>Although cyclophilins are attractive targets for probing biology and therapeutic intervention, no subtype-selective cyclophilin inhibitors have been described. We discovered novel ...
    • Dnmt1 Has De Novo Activity Targeted to Transposable Elements 

      Haggerty, Chuck; Kretzmer, Helene; Riemenschneider, Christina; Kumar, Abhishek Sampath; Mattei, Alexandra; Bailly, Nina; Gottfreund, Judith; Giesselmann, Pay; Weigert, Raha; Brändl, Björn; Giehr, Pascal; Buschow, René; Galonska, Christina; von Meyenn, Ferdinand; Pappalardi, Melissa B.; McCabe, Michael T.; Wittler, Lars; Giesecke-Thiel, Claudia; Mielke, Thorsten; Meierhofer, David; Timmermann, Bernd; Müller, Franz-Josef; Walter, Jörn; Meissner, Alexander (Springer Science and Business Media LLC, 2021-06-17)
      <jats:title>Abstract</jats:title><jats:p>DNA methylation plays a critical role during development, particularly in repressing retrotransposons. The mammalian methylation landscape is dependent on the combined activities ...
    • The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation 

      Loevenich, Sandra N; Brunner, Erich; King, Nichole L; Deutsch, Eric W; Stein, Stephen E; Aebersold, Ruedi; Hafen, Ernst (Springer Science and Business Media LLC, 2009-02-11)
      Background: Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn ...
    • Drug addiction unveils a repressive methylation ceiling in EZH2-mutant lymphoma 

      Kwok, Hui; Freedy, Allyson M.; Siegenfeld, Allison P.; Morriss, Julia W.; Waterbury, Amanda L.; Kissler, Stephen M.; Liau, Brian B. (Springer Science and Business Media LLC, 2023-03-27)
      Drug addiction, a phenomenon where cancer cells paradoxically depend on continuous drug treatment for survival, has uncovered cell signaling mechanisms and cancer co-dependencies. Here, we discover mutations that confer ...
    • The ESX System in Bacillus subtilis Mediates Protein Secretion 

      Huppert, Laura A.; Ramsdell, Talia L.; Chase, Michael R.; Sarracino, David A.; Fortune, Sarah M.; Burton, Briana M. (Public Library of Science, 2014)
      Esat-6 protein secretion systems (ESX or Ess) are required for the virulence of several human pathogens, most notably Mycobacterium tuberculosis and Staphylococcus aureus. These secretion systems are defined by a conserved ...
    • The Evolution of Quorum Sensing as a Mechanism to Infer Kinship 

      Schluter, Jonas; Schoech, Armin P.; Foster, Kevin R.; Mitri, Sara (Public Library of Science, 2016)
      Bacteria regulate many phenotypes via quorum sensing systems. Quorum sensing is typically thought to evolve because the regulated cooperative phenotypes are only beneficial at certain cell densities. However, quorum sensing ...
    • The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima 

      Chipman, Ariel D.; Ferrier, David E. K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S. T.; Schröder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C.; Alonso, Claudio R.; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C. J.; Blankenburg, Kerstin P.; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K.; Du Pasquier, Louis; Duncan, Elizabeth J.; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D.; Extavour, Cassandra G.; Francisco, Liezl; Gabaldón, Toni; Gillis, William J.; Goodwin-Horn, Elizabeth A.; Green, Jack E.; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J. P.; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H. L.; Hunn, Julia P.; Hunnekuhl, Vera S.; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N.; Jiggins, Francis M.; Jones, Tamsin E.; Kaiser, Tobias S.; Kalra, Divya; Kenny, Nathan J.; Korchina, Viktoriya; Kovar, Christie L.; Kraus, F. Bernhard; Lapraz, François; Lee, Sandra L.; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N.; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J.; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H.; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C.; Robertson, Helen E.; Robertson, Hugh M.; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E.; Schurko, Andrew M.; Siggens, Kenneth W.; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J.; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M.; Willis, Judith H.; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M.; Worley, Kim C.; Gibbs, Richard A.; Akam, Michael; Richards, Stephen (Public Library of Science, 2014)
      Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda ...
    • Functional morphology of the ankle extensor muscle‐tendon units in the springhare Pedetes capensis shows convergent evolution with macropods for bipedal hopping locomotion 

      Veiga, Gabriela N.; Biewener, Andrew; Fuller, Andrea; Ven, Tanja M. F. N.; McGowan, Craig P.; Panaino, Wendy; Snelling, Edward P. (Wiley, 2020-06-25)
      This study assesses the functional morphology of the ankle extensor muscle-tendon units of the springhare Pedetes capensis, an African bipedal hopping rodent, to test for convergent evolution with the Australian bipedal ...
    • Geometric Deep Learning Enables 3D Kinematic Profiling Across Species and Environments 

      Dunn, Timothy; Marshall, Jesse; Severson, Kyle S.; Aldarondo, Diego; Hildebrand, David; Chettih, Selmaan; Wang, William; Gellis, Amanda; Carlson, David E.; Aronov, Dmitriy; Freiwald, Winrich; Wang, Fan; Ölveczky, Bence P. (Springer Science and Business Media LLC, 2021-04-19)
      Comprehensive descriptions of animal behavior require precise measurements of 3D whole-body movements. Although 2D approaches can track visible landmarks in restrictive environments, performance drops significantly in ...
    • Goats decrease hindlimb stiffness when walking over compliant surfaces 

      Clites, Tyler; Arnold-rife, Allison; Biewener, Andrew; Arnold, Allison S.; Singh, Nalini M.; Kline, Eric; Chen, Hope; Tugman, Christopher; Billadeau, Brahms; Herr, Hugh M. (The Company of Biologists, 2019-05-13)
      Leg stiffness, commonly estimated as the 'compression' of a defined leg element in response to a load, has long been used to characterize terrestrial locomotion. This study investigated how goats adjust the stiffness of ...
    • Identification of Listeria monocytogenes Determinants Required for Biofilm Formation 

      Alonso, Almaris N.; Perry, Kyle J.; Regeimbal, James M.; Regan, Patrick M.; Higgins, Darren E. (Public Library of Science, 2014)
      Listeria monocytogenes is a Gram-positive, food-borne pathogen of humans and animals. L. monocytogenes is considered to be a potential public health risk by the U.S. Food and Drug Administration (FDA), as this bacterium ...
    • Improved green and red GRAB sensors for monitoring dopaminergic activity in vivo 

      Zhuo, Yizhou; Luo, Bin; Yi, Xinyang; Dong, Hui; Miao, Xiaolei; Wan, Jinxia; Williams, John T; Campbell, Malcolm; Cai, Ruyi; Qian, Tongrui; Wang, Lei; Li, Bozhi; Li, Fengling; Weber, Sophia; Wei, Yu; Li, Guochuan; Wang, Huan; Zheng, Yu; Zhao, Yulin; Wolf, Marina; Zhu, Yingjie; Watabe-Uchida, Mitsuko; Yulong, Li (Springer Science and Business Media LLC, 2023-11-30)
      Dopamine (DA) plays multiple roles in a wide range of physiological and pathological processes via a vast network of dopaminergic projections. To fully dissect the spatiotemporal dynamics of DA release in both dense and ...