Now showing items 1-20 of 321

    • A VKORC1‐based SNP survey of anticoagulant rodenticide resistance in the house mouse, Norway rat and roof rat in the USA 

      Diaz, Juan C.; Kohn, Michael H. (2021)
      BACKGROUND: We conducted a vitamin K epoxide reductase subcomponent 1 (Vkorc1)‐based nonsynonymous Single Nucleotide Polymorphism (nsSNP) screen with focus on the house mouse (Mus musculus domesticus), but that also considered the Norway rat (Rattus norvegicus) and roof rat (R. rattus) in the USA. RESULTS: We detected six Vkorc1 nsSNPs underlying the ...
    • An In Vitro Cell Culture Model for Pyoverdine-Mediated Virulence 

      Kang, Donghoon; Kirienko, Natalia V. (2021)
      Pseudomonas aeruginosa is a multidrug-resistant, opportunistic pathogen that utilizes a wide-range of virulence factors to cause acute, life-threatening infections in immunocompromised patients, especially those in intensive care units. It also causes debilitating chronic infections that shorten lives and worsen the quality of life for cystic fibrosis ...
    • Novel Immune Modulators Enhance Caenorhabditis elegans Resistance to Multiple Pathogens 

      Hummell, Nicholas A.; Revtovich, Alexey V.; Kirienko, Natalia V. (2021)
      Traditionally, treatments for bacterial infection have focused on killing the microbe or preventing its growth. As antimicrobial resistance becomes more ubiquitous, the feasibility of this approach is beginning to wane and attention has begun to shift toward disrupting the host-pathogen interaction by improving the host defense. Using a high-throughput, ...
    • Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system 

      Rao, Satyajit D.; Igoshin, Oleg A.; Center for Theoretical Biological Physics (2021)
      Bacteria use two-component systems (TCSs) to sense environmental conditions and change gene expression in response to those conditions. To amplify cellular responses, many bacterial TCSs are under positive feedback control, i.e. increase their expression when activated. Escherichia coli Mg2+ -sensing TCS, PhoPQ, in addition to the positive feedback, ...
    • Functional diversity and redundancy of tropical forest mammals over time 

      Gorczynski, Daniel; Beaudrot, Lydia; Program in Ecology & Evolutionary Biology (2021)
      Globally, tropical rain forests comprise some of the most diverse and functionally rich ecosystems but are increasingly degraded by human impacts. Protected areas have been shown to conserve species diversity, but their effectiveness at maintaining functional diversity over time is less well known, despite the fact that functional diversity likely ...
    • Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences 

      Del Valle, Ilenne; Fulk, Emily M.; Kalvapalle, Prashant; Silberg, Jonathan J.; Masiello, Caroline A.; (2021)
      The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open ...
    • A zero-dimensional view of atmospheric degradation of levoglucosan (LEVCHEM_v1) using numerical chamber simulations 

      Suciu, Loredana G.; Griffin, Robert J.; Masiello, Caroline A. (2021)
      Here, we developed a zero-dimensional (0-D) modeling framework (LEVCHEM_v1) to provide insights into the atmospheric degradation of a key tracer emitted during biomass burning – levoglucosan (LEV), while additionally exploring its effects on the dynamics of secondary organic aerosols (SOA) and other gases. For this, we updated existing chemical ...
    • Programmable human histone phosphorylation and gene activation using a CRISPR/Cas9-based chromatin kinase 

      Li, Jing; Mahata, Barun; Escobar, Mario; Goell, Jacob; Wang, Kaiyuan; (2021)
      Histone phosphorylation is a ubiquitous post-translational modification that allows eukaryotic cells to rapidly respond to environmental stimuli. Despite correlative evidence linking histone phosphorylation to changes in gene expression, establishing the causal role of this key epigenomic modification at diverse loci within native chromatin has been ...
    • Ontogenetic development underlies population response to mortality 

      Toscano, Benjamin J.; Figel, Alexandra S.; Rudolf, Volker H.W. (2021)
      Understanding demographic responses to mortality is crucial to predictive ecology. While classic ecological theory posits reductions in population biomass in response to extrinsic mortality, models containing realistic developmental change predict the potential for counterintuitive increase in stage‐specific biomass, i.e. biomass overcompensation. ...
    • Comprehensive genetic analysis of adhesin proteins and their role in virulence of Candida albicans 

      Rosiana, Sierra; Zhang, Liyang; Kim, Grace H.; Revtovich, Alexey V.; Uthayakumar, Deeva; (2021)
      Candida albicans is a microbial fungus that exists as a commensal member of the human microbiome and an opportunistic pathogen. Cell surface-associated adhesin proteins play a crucial role in C. albicans’ ability to undergo cellular morphogenesis, develop robust biofilms, colonize, and cause infection in a host. However, a comprehensive analysis of ...
    • A suppressor tRNA-mediated feedforward loop eliminates leaky gene expression in bacteria 

      Ho, Joanne M.L.; Miller, Corwin A.; Parks, Sydney E.; Mattia, Jacob R.; Bennett, Matthew R. (2021)
      Ligand-inducible genetic systems are the mainstay of synthetic biology, allowing gene expression to be controlled by the presence of a small molecule. However, ‘leaky’ gene expression in the absence of inducer remains a persistent problem. We developed a leak dampener tool that drastically reduces the leak of inducible genetic systems while retaining ...
    • Theoretical Analysis Reveals the Cost and Benefit of Proofreading in Coronavirus Genome Replication 

      Mallory, Joel D.; Mallory, Xian F.; Kolomeisky, Anatoly B.; Igoshin, Oleg A.; Center for Theoretical Biological Physics (2021)
      Severe acute respiratory syndrome coronaviruses have unusually large RNA genomes replicated by a multiprotein complex containing an RNA-dependent RNA polymerase (RdRp). Exonuclease activity enables the RdRp complex to remove wrongly incorporated bases via proofreading, a process not utilized by other RNA viruses. However, it is unclear why the RdRp ...
    • Roadmap for the multiscale coupling of biochemical and mechanical signals during development 

      Lenne, Pierre-François; Munro, Edwin; Heemskerk, Idse; Warmflash, Aryeh; Bocanegra-Moreno, Laura; (2021)
      The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly ...
    • Controlled and Stable Patterning of Diverse Inorganic Nanocrystals on Crystalline Two-Dimensional Protein Arrays 

      Mann, Victor R.; Manea, Francesca; Borys, Nicholas J.; Ajo-Franklin, Caroline M.; Cohen, Bruce E. (2021)
      Controlled patterning of nanoparticles on bioassemblies enables synthesis of complex materials for applications in optics, nanoelectronics, and sensing. Biomolecular self-assembly offers molecular control for engineering patterned nanomaterials, but current approaches have been limited in their ability to combine high nanoparticle coverage with ...
    • A platform for post-translational spatiotemporal control of cellular proteins 

      Jayanthi, Brianna; Bachhav, Bhagyashree; Wan, Zengyi; Martinez Legaspi, Santiago; Segatori, Laura; (2021)
      Mammalian cells process information through coordinated spatiotemporal regulation of proteins. Engineering cellular networks thus relies on efficient tools for regulating protein levels in specific subcellular compartments. To address the need to manipulate the extent and dynamics of protein localization, we developed a platform technology for the ...
    • Self-organized signaling in stem cell models of embryos 

      Liu, Lizhong; Warmflash, Aryeh (2021)
      Mammalian embryonic development is a complex process driven by self-organization. Understanding how a fertilized egg develops into an embryo composed of more than 200 cell types in precise spatial patterns remains one of the fundamental challenges in biology. Pluripotent stem cells have been used as in vitro models for investigating mammalian ...
    • Stem cell-based models of embryos: The need for improved naming conventions 

      Matthews, Kirstin R. W.; Wagner, Daniel S.; Warmflash, Aryeh; Baker Institute for Public Policy-Center for Health and Biosciences (2021)
      Stem cell-based models of embryos are known by various names, with different naming conventions, leading to confusion regarding their composition and potential. We propose the need for a general term for the field to promote public engagement and the development of a systematic nomenclature system to differentiate between specific models.
    • High-Throughput Approaches for the Identification of Pseudomonas aeruginosa Antivirulents 

      Kang, Donghoon; Zhang, Liyang; Kirienko, Natalia V. (2021)
      Antimicrobial resistance is a serious medical threat, particularly given the decreasing rate of discovery of new treatments. Although attempts to find new treatments continue, it has become clear that merely discovering new antimicrobials, even if they are new classes, will be insufficient. It is essential that new strategies be aggressively pursued. ...
    • Lagged and dormant season climate better predict plant vital rates than climate during the growing season 

      Evers, Sanne M.; Knight, Tiffany M.; Inouye, David W.; Miller, Tom E. X.; Salguero‐Gómez, Roberto; (2021)
      Understanding the effects of climate on the vital rates (e.g., survival, development, reproduction) and dynamics of natural populations is a long-standing quest in ecology, with ever-increasing relevance in the face of climate change. However, linking climate drivers to demographic processes requires identifying the appropriate time windows during ...
    • Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice 

      Huang, Kun; Zhang, Yufei; Hui, Xianfeng; Zhao, Ya; Gong, Wenxiao; (2021)
      Background: An ideal animal model to study SARS-coronavirus 2 (SARS-CoV-2) pathogenesis and evaluate therapies and vaccines should reproduce SARS-CoV-2 infection and recapitulate lung disease like those seen in humans. The angiotensin-converting enzyme 2 (ACE2) is a functional receptor for SARS-CoV-2, but mice are resistant to the infection because ...