Now showing items 1-20 of 382

    • Rates of Future Climate Change in the Gulf of Mexico and the Caribbean Sea: Implications for Coral Reef Ecosystems 

      Lawman, A.E.; Dee, S.G.; DeLong, K.L.; Correa, A.M.S. (2022)
      Rising temperatures and ocean acidification due to anthropogenic climate change pose ominous threats to coral reef ecosystems in the Gulf of Mexico (GoM) and the western Caribbean Sea. Unfortunately, the once structurally complex coral reefs in the GoM and Caribbean have dramatically declined since the 1970s; relatively few coral reefs still exhibit ...
    • A de novo matrix for macroscopic living materials from bacteria 

      Molinari, Sara; Tesoriero, Robert F.; Li, Dong; Sridhar, Swetha; Cai, Rong; (2022)
      Engineered living materials (ELMs) embed living cells in a biopolymer matrix to create materials with tailored functions. While bottom-up assembly of macroscopic ELMs with a de novo matrix would offer the greatest control over material properties, we lack the ability to genetically encode a protein matrix that leads to collective self-organization. ...
    • Unleashing the potential of noncanonical amino acid biosynthesis to create cells with precision tyrosine sulfation 

      Chen, Yuda; Jin, Shikai; Zhang, Mengxi; Hu, Yu; Wu, Kuan-Lin; (2022)
      Despite the great promise of genetic code expansion technology to modulate structures and functions of proteins, external addition of ncAAs is required in most cases and it often limits the utility of genetic code expansion technology, especially to noncanonical amino acids (ncAAs) with poor membrane internalization. Here, we report the creation of ...
    • Bone Marrow Endothelial Cells Increase Prostate Cancer Cell Apoptosis in 3D Triculture Model of Reactive Stroma 

      Sablatura, Lindsey K.; Tellman, Tristen V.; Kim, Aemin; Farach-Carson, Mary C. (2022)
      The bone marrow tumor microenvironment (BMTE) is a complex network of cells, extracellular matrix, and sequestered signaling factors that initially act as a hostile environment for disseminating tumor cells (DTCs) from the cancerous prostate. Three-dimensional (3D) culture systems offer an opportunity to better model these complex interactions in ...
    • Mean-field model for nematic alignment of self-propelled rods 

      Perepelitsa, Misha; Timofeyev, Ilya; Murphy, Patrick; Igoshin, Oleg A.; Center for Theoretical Biological Physics (2022)
      Self-propelled rods are a facet of the field of active matter relevant to many physical systems ranging in scale from shaken granular media and bacterial alignment to the flocking dynamics of animals. In this paper we develop a model for nematic alignment of self-propelled rods interacting through binary collisions. We avoid phenomenological descriptions ...
    • Soil bacterial communities and co-occurrence changes associated with multi-nutrient cycling under rice-wheat rotation reclamation in coastal wetland 

      Zhang, Kaoping; Shi, Yu; Lu, Haiying; He, Minyan; Huang, Wei; (2022)
      Coastal reclamation is a global threat to coastal wetland ecosystems, but the impacts of coastal reclamation on belowground biodiversity and their consequences for ecosystem nutrient cycling remain poorly understood. In this study, we examined soil bacterial communities, bacterial co-occurrence pattern and soil multi-nutrient cycling index after ...
    • Artificial Soils Reveal Individual Factor Controls on Microbial Processes 

      Del Valle, Ilenne; Gao, Xiaodong; Ghezzehei, Teamrat A.; Silberg, Jonathan J.; Masiello, Caroline A. (2022)
      Soil matrix properties influence microbial behaviors that underlie nutrient cycling, greenhouse gas production, and soil formation. However, the dynamic and heterogeneous nature of soils makes it challenging to untangle the effects of different matrix properties on microbial behaviors. To address this challenge, we developed a tunable artificial soil ...
    • A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology 

      Sridhar, Swetha; Ajo-Franklin, Caroline M.; Masiello, Caroline A. (2022)
      Microbial biosensors sense and report exposures to stimuli, thereby facilitating our understanding of environmental processes. Successful design and deployment of biosensors hinge on the persistence of the microbial host of the genetic circuit, termed the chassis. However, model chassis organisms may persist poorly in environmental conditions. In ...
    • Real-time detection of response regulator phosphorylation dynamics in live bacteria 

      Butcher, Ryan J.; Tabor, Jeffrey J. (2022)
      Bacteria utilize two-component system (TCS) signal transduction pathways to sense and adapt to changing environments. In a typical TCS, a stimulus induces a sensor histidine kinase (SHK) to phosphorylate a response regulator (RR), which then dimerizes and activates a transcriptional response. Here, we demonstrate that oligomerization-dependent ...
    • Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions 

      Wang, Kaiyuan; Escobar, Mario; Li, Jing; Mahata, Barun; Goell, Jacob; (2022)
      Nuclease-inactivated CRISPR/Cas-based (dCas-based) systems have emerged as powerful technologies to synthetically reshape the human epigenome and gene expression. Despite the increasing adoption of these platforms, their relative potencies and mechanistic differences are incompletely characterized, particularly at human enhancer–promoter pairs. Here, ...
    • Measuring understorey vegetation structure using a novel mixed-reality device 

      Gorczynski, Daniel; Beaudrot, Lydia; Program in Ecology and Evolutionary Biology (2022)
      Most ecological studies of vegetation structure have relied on manual field measurements that are labour-intensive and time-consuming. Many current alternatives to classical measurements are expensive or difficult to transport to field settings. Here we evaluated a new method for measuring understorey vegetation with a novel mixed-reality, remote ...
    • Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA 

      Jin, Shikai; Bueno, Carlos; Lu, Wei; Wang, Qian; Chen, Mingchen; (2022)
      Bacteriophage T7 gp4 helicase has served as a model system for understanding mechanisms of hexameric replicative helicase translocation. The mechanistic basis of how nucleoside 5′-triphosphate hydrolysis and translocation of gp4 helicase are coupled is not fully resolved. Here, we used a thermodynamically benchmarked coarse-grained protein force ...
    • Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway 

      Galbraith, Madeline; Bocci, Federico; Onuchic, José N.; Center for Theoretical Biological Physics (2022)
      The Notch-Delta signaling pathway mediates cell differentiation implicated in many regulatory processes including spatiotemporal patterning in tissues by promoting alternate cell fates between neighboring cells. At the multicellular level, this "lateral inhibition” principle leads to checkerboard patterns with alternation of Sender and Receiver cells. ...
    • Speciation in Nearctic oak gall wasps is frequently correlated with changes in host plant, host organ, or both 

      Ward, Anna K. G.; Bagley, Robin K.; Egan, Scott P.; Hood, Glen Ray; Ott, James R.; (2022)
      Quantifying the frequency of shifts to new host plants within diverse clades of specialist herbivorous insects is critically important to understand whether and how host shifts contribute to the origin of species. Oak gall wasps (Hymenoptera: Cynipidae: Cynipini) comprise a tribe of ∼1000 species of phytophagous insects that induce gall formation on ...
    • Contact map dependence of a T-cell receptor binding repertoire 

      Chau, Kevin Ng; George, Jason T.; Onuchic, José N.; Lin, Xingcheng; Levine, Herbert; (2022)
      The T-cell arm of the adaptive immune system provides the host protection against unknown pathogens by discriminating between host and foreign material. This discriminatory capability is achieved by the creation of a repertoire of cells each carrying a T-cell receptor (TCR) specific to non-self-antigens displayed as peptides bound to the major ...
    • An Arabidopsis pre-RNA processing8a (prp8a) missense allele restores splicing of a subset of mis-spliced mRNAs 

      Llinas, Roxanna J.; Xiong, Jia Qi; Clark, Natalie M.; Burkhart, Sarah E.; Bartel, Bonnie (2022)
      Eukaryotic precursor mRNAs often harbor noncoding introns that must be removed prior to translation. Accurate splicing of precursor messenger RNA depends on placement and assembly of small nuclear ribonucleoprotein (snRNP) sub-complexes of the spliceosome. Yeast (Saccharomyces cerevisiae) studies established a role in splice-site selection for PRE-RNA ...
    • Plant peroxisome proteostasis—establishing, renovating, and dismantling the peroxisomal proteome 

      Muhammad, DurreShahwar; Smith, Kathryn A.; Bartel, Bonnie (2022)
      Plant peroxisomes host critical metabolic reactions and insulate the rest of the cell from reactive byproducts. The specialization of peroxisomal reactions is rooted in how the organelle modulates its proteome to be suitable for the tissue, environment, and developmental stage of the organism. The story of plant peroxisomal proteostasis begins with ...
    • Multidecadal, continent-level analysis indicates agricultural practices impact wheat aphid loads more than climate change 

      Sun, Xiao; Sun, Yumei; Ma, Ling; Liu, Zhen; Wang, Qiyun; (2022)
      Temperature has a large influence on insect abundances, thus under climate change, identifying major drivers affecting pest insect populations is critical to world food security and agricultural ecosystem health. Here, we conducted a meta-analysis with data obtained from 120 studies across China and Europe from 1970 to 2017 to reveal how climate and ...
    • BMP3 inhibits TGFβ2-mediated myofibroblast differentiation during wound healing of the embryonic cornea 

      Spurlin, James W.; Garis, Matthew R.; Lwigale, Peter Y. (2022)
      Often acute damage to the cornea initiates drastic tissue remodeling, resulting in fibrotic scarring that disrupts light transmission and precedes vision impairment. Very little is known about the factors that can mitigate fibrosis and promote scar-free cornea wound healing. We previously described transient myofibroblast differentiation during ...
    • Occupancy winners in tropical protected forests: a pantropical analysis 

      Semper-Pascual, Asunción; Bischof, Richard; Milleret, Cyril; Beaudrot, Lydia; Vallejo-Vargas, Andrea F.; (2022)
      The structure of forest mammal communities appears surprisingly consistent across the continental tropics, presumably due to convergent evolution in similar environments. Whether such consistency extends to mammal occupancy, despite variation in species characteristics and context, remains unclear. Here we ask whether we can predict occupancy patterns ...