BioSciences faculty publications. For works published before Summer 2014, please see the Biochemistry & Cell Biology and Ecology & Evolutionary Biology collections.

Recent Submissions

  • 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 ...
  • Fast and parallel nanoscale three-dimensional tracking of heterogeneous mammalian chromatin dynamics 

    Gustavsson, Anna-Karin; Ghosh, Rajarshi P.; Petrov, Petar N.; Liphardt, Jan T.; Moerner, W. E.; (2022)
    Chromatin organization and dynamics are critical for gene regulation. In this work we present a methodology for fast and parallel three-dimensional (3D) tracking of multiple chromosomal loci of choice over many thousands of frames on various timescales. We achieved this by developing and combining fluorogenic and replenishable nanobody arrays, ...
  • Activating natural product synthesis using CRISPR interference and activation systems in Streptomyces 

    Ameruoso, Andrea; Villegas Kcam, Maria Claudia; Cohen, Katherine Piper; Chappell, James (2022)
    The rise of antibiotic-resistant bacteria represents a major threat to global health, creating an urgent need to discover new antibiotics. Natural products derived from the genus Streptomyces represent a rich and diverse repertoire of chemical molecules from which new antibiotics are likely to be found. However, a major challenge is that the biosynthetic ...
  • Long-Term Dominance of Carbapenem-Non-Susceptible Pseudomonas aeruginosa ST111 in Hematologic Malignancy Patients and Hematopoietic Cell Transplant Recipients 

    Zhang, Liyang; Tan, Filemon C.; Strasfeld, Lynne; Hakki, Morgan; Kirienko, Natalia V. (2022)
    An epidemiological study uncovered that fluoroquinolone (FQ) neutropenic prophylaxis in hematopoietic cell transplant and hematologic malignancy (HCT/HM) patients was associated with breakthrough Pseudomonas aeruginosa bloodstream infections (BSIs) with isolates non-susceptible to both FQs and meropenem. The molecular epidemiology of the FQ/meropen ...
  • Opposing global change drivers counterbalance trends in breeding North American monarch butterflies 

    Crossley, Michael S.; Meehan, Timothy D.; Moran, Matthew D.; Glassberg, Jeffrey; Snyder, William E.; (2022)
    Many insects are in clear decline, with monarch butterflies (Danaus plexippus) drawing particular attention as a flagship species. It is well documented that, among migratory populations, numbers of overwintering monarchs have been falling across several decades, but trends among breeding monarchs are less clear. Here, we compile >135,000 monarch ...
  • Annotation-free delineation of prokaryotic homology groups 

    Yin, Yongze; Ogilvie, Huw A.; Nakhleh, Luay (2022)
    Phylogenomic studies of prokaryotic taxa often assume conserved marker genes are homologous across their length. However, processes such as horizontal gene transfer or gene duplication and loss may disrupt this homology by recombining only parts of genes, causing gene fission or fusion. We show using simulation that it is necessary to delineate ...
  • When function is biological: Discerning how silver nanoparticle structure dictates antimicrobial activity 

    Zhang, Qingbo; Hu, Yue; Masterson, Caitlin M.; Jang, Wonhee; Xiao, Zhen; (2022)
    Silver nanomaterials have potent antibacterial properties that are the foundation for their wide commercial use as well as for concerns about their unintended environmental impact. The nanoparticles themselves are relatively biologically inert but they can undergo oxidative dissolution yielding toxic silver ions. A quantitative relationship between ...
  • Mutational Switch-Backs Can Accelerate Evolution of Francisella to a Combination of Ciprofloxacin and Doxycycline 

    Mehta, Heer H.; Ibarra, David; Marx, Christopher J.; Miller, Craig R.; Shamoo, Yousif (2022)
    Combination antimicrobial therapy has been considered a promising strategy to combat the evolution of antimicrobial resistance. Francisella tularensis is the causative agent of tularemia and in addition to being found in the nature, is recognized as a threat agent that requires vigilance. We investigated the evolutionary outcome of adapting the Live ...
  • Species-specific plant-mediated effects between herbivores converge at high damage intensity 

    Wan, Jinlong; Yi, Jiahui; Tao, Zhibin; Ren, Zhikun; Otieno, Evans O.; (2022)
    Plants are often exposed to multiple herbivores and densities of these attackers (or corresponding damage intensities) often fluctuate greatly in the field. Plant-mediated interactions vary among herbivore species and with changing feeding intensity, but little is known about how herbivore identity and density interact to determine plant responses ...

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