Now showing items 1-20 of 364

    • The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina 

      Kosgei, A. J.; Miller, M. D.; Bhardwaj, M.; Xu, W.; Thorson, J. S.; (2022)
      Dynemicin is an enediyne natural product from Micromonospora chersina ATCC53710. Access to the biosynthetic gene cluster of dynemicin has enabled the in vitro study of gene products within the cluster to decipher their roles in assembling this unique molecule. This paper reports the crystal structure of DynF, the gene product of one of the genes ...
    • DNA Polymerase-Parental DNA Interaction Is Essential for Helicase-Polymerase Coupling during Bacteriophage T7 DNA Replication 

      Lo, Chen-Yu; Gao, Yang (2022)
      DNA helicase and polymerase work cooperatively at the replication fork to perform leading-strand DNA synthesis. It was believed that the helicase migrates to the forefront of the replication fork where it unwinds the duplex to provide templates for DNA polymerases. However, the molecular basis of the helicase-polymerase coupling is not fully understood. ...
    • Grand Challenges in Coevolution 

      Medina, Mónica; Baker, David M.; Baltrus, David A.; Bennett, Gordon M.; Cardini, Ulisse; (2022)
    • Strategies for Improving Small-Molecule Biosensors in Bacteria 

      Miller, Corwin A.; Ho, Joanne M. L.; Bennett, Matthew R. (2022)
      In recent years, small-molecule biosensors have become increasingly important in synthetic biology and biochemistry, with numerous new applications continuing to be developed throughout the field. For many biosensors, however, their utility is hindered by poor functionality. Here, we review the known types of mechanisms of biosensors within bacterial ...
    • DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases 

      Tripathi, Shubham; Brahmachari, Sumitabha; Onuchic, José N; Levine, Herbert; Center for Theoretical Biological Physics (2022)
      Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be driven by a physical interaction or ‘push’ between closely spaced RNAPs. However, recent studies have ...
    • Alphaflexivirus Genomes in Stony Coral Tissue Loss Disease-Affected, Disease-Exposed, and Disease-Unexposed Coral Colonies in the U.S. Virgin Islands 

      Veglia, A. J.; Beavers, K.; Buren, E. W. Van; Meiling, S. S.; Muller, E. M.; (2022)
      Stony coral tissue loss disease (SCTLD) is decimating Caribbean corals. Here, through the metatranscriptomic assembly and annotation of two alphaflexivirus-like strains, we provide genomic evidence of filamentous viruses in SCTLD-affected, -exposed, and -...
    • Elevated Hoxb5b Expands Vagal Neural Crest Pool and Blocks Enteric Neuronal Development in Zebrafish 

      Howard, Aubrey G. A.; Nguyen, Aaron C.; Tworig, Joshua; Ravisankar, Priya; Singleton, Eileen W.; (2022)
      Neural crest cells (NCCs) are a migratory, transient, and multipotent stem cell population essential to vertebrate embryonic development, contributing to numerous cell lineages in the adult organism. While great strides have been made in elucidating molecular and cellular events that drive NCC specification, comprehensive knowledge of the genetic ...
    • Nodal is a short-range morphogen with activity that spreads through a relay mechanism in human gastruloids 

      Liu, Lizhong; Nemashkalo, Anastasiia; Rezende, Luisa; Jung, Ji Yoon; Chhabra, Sapna; (2022)
      Morphogens are signaling molecules that convey positional information and dictate cell fates during development. Although ectopic expression in model organisms suggests that morphogen gradients form through diffusion, little is known about how morphogen gradients are created and interpreted during mammalian embryogenesis due to the combined difficulties ...
    • Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism 

      Tejedor-Sanz, Sara; Stevens, Eric T; Li, Siliang; Finnegan, Peter; Nelson, James; (2022)
      Energy conservation in microorganisms is classically categorized into respiration and fermentation; however, recent work shows some species can use mixed or alternative bioenergetic strategies. We explored the use of extracellular electron transfer for energy conservation in diverse lactic acid bacteria (LAB), microorganisms that mainly rely on ...
    • Does ant–plant mutualism have spillover effects on the non-partner ant community? 

      Donald, Marion L.; Miller, Tom E. X.; Program in Ecology and Evolutionary Biology (2022)
      Mutualism benefits partner species, and theory predicts these partnerships can affect the abundance, diversity, and composition of partner and non-partner species. We used 16 years of monitoring data to determine the ant partner species of tree cholla cacti (Cylindropuntia imbricata), which reward ants with extrafloral nectar in exchange for ...
    • A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics 

      Karmi, Ola; Marjault, Henri-Baptiste; Bai, Fang; Roy, Susmita; Sohn, Yang-Sung; (2022)
      Mitochondrial inner NEET (MiNT) and the outer mitochondrial membrane (OMM) mitoNEET (mNT) proteins belong to the NEET protein family. This family plays a key role in mitochondrial labile iron and reactive oxygen species (ROS) homeostasis. NEET proteins contain labile [2Fe-2S] clusters which can be transferred to apo-acceptor proteins. In eukaryotes, ...
    • The Structure of the Arabidopsis PEX4-PEX22 Peroxin Complex—Insights Into Ubiquitination at the Peroxisomal Membrane 

      Traver, Melissa S.; Bradford, Sarah E.; Olmos, Jose Luis; Wright, Zachary J.; Miller, Mitchell D.; (2022)
      Peroxisomes are eukaryotic organelles that sequester critical oxidative reactions and process the resulting reactive oxygen species into less toxic byproducts. Peroxisome function and formation are coordinated by peroxins (PEX proteins) that guide peroxisome biogenesis and division and shuttle proteins into the lumen and membrane of the organelle. ...
    • Post-Acquisition Hyperpolarized 29Silicon Magnetic Resonance Image Processing for Visualization of Colorectal Lesions Using a User-Friendly Graphical Interface 

      McCowan, Caitlin V.; Salmon, Duncan; Hu, Jingzhe; Pudakalakatti, Shivanand; Whiting, Nicholas; (2022)
      Medical imaging devices often use automated processing that creates and displays a self-normalized image. When improperly executed, normalization can misrepresent information or result in an inaccurate analysis. In the case of diagnostic imaging, a false positive in the absence of disease, or a negative finding when disease is present, can produce a ...
    • The energy cost and optimal design of networks for biological discrimination 

      Yu, Qiwei; Kolomeisky, Anatoly B.; Igoshin, Oleg A.; Center for Theoretical Biological Physics (2022)
      Many biological processes discriminate between correct and incorrect substrates through the kinetic proofreading mechanism that enables lower error at the cost of higher energy dissipation. Elucidating physico-chemical constraints for global minimization of dissipation and error is important for understanding enzyme evolution. Here, we identify ...
    • Box C/D small nucleolar ribonucleoproteins regulate mitochondrial surveillance and innate immunity 

      Tjahjono, Elissa; Revtovich, Alexey V.; Kirienko, Natalia V. (2022)
      Monitoring mitochondrial function is crucial for organismal survival. This task is performed by mitochondrial surveillance or quality control pathways, which are activated by signals originating from mitochondria and relayed to the nucleus (retrograde response) to start transcription of protective genes. In Caenorhabditis elegans, several systems are ...
    • Bone-Specific Enhancement of Antibody Therapy for Breast Cancer Metastasis to Bone 

      Tian, Zeru; Yu, Chenfei; Zhang, Weijie; Wu, Kuan-Lin; Wang, Chenhang; (2022)
      Despite the rapid evolution of therapeutic antibodies, their clinical efficacy in the treatment of bone tumors is hampered due to the inadequate pharmacokinetics and poor bone tissue accessibility of these large macromolecules. Here, we show that engineering therapeutic antibodies with bone-homing peptide sequences dramatically enhances their ...
    • In crystallo observation of three metal ion promoted DNA polymerase misincorporation 

      Chang, Caleb; Lee Luo, Christie; Gao, Yang (2022)
      Error-free replication of DNA is essential for life. Despite the proofreading capability of several polymerases, intrinsic polymerase fidelity is in general much higher than what base-pairing energies can provide. Although researchers have investigated this long-standing question with kinetics, structural determination, and computational simulations, ...
    • Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes 

      Yan, Zhi; Cao, Zhen; Liu, Yushu; Ogilvie, Huw A; Nakhleh, Luay (2022)
      Phylogenetic networks provide a powerful framework for modeling and analyzing reticulate evolutionary histories. While polyploidy has been shown to be prevalent not only in plants but also in other groups of eukaryotic species, most work done thus far on phylogenetic network inference assumes diploid hybridization. These inference methods have been ...
    • Nrf2 Modulates the Hybrid Epithelial/Mesenchymal Phenotype and Notch Signaling During Collective Cancer Migration 

      Vilchez Mercedes, Samuel A.; Bocci, Federico; Ahmed, Mona; Eder, Ian; Zhu, Ninghao; (2022)
      Hybrid epithelial/mesenchymal cells (E/M) are key players in aggressive cancer metastasis. It remains a challenge to understand how these cell states, which are mostly non-existent in healthy tissue, become stable phenotypes participating in collective cancer migration. The transcription factor Nrf2, which is associated with tumor progression and ...
    • 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 ...