Now showing items 1-20 of 199

    • A PEX5 missense allele preferentially disrupts PTS1 cargo import into Arabidopsis peroxisomes 

      Patel, Khushali J.; Kao, Yun‐Ting; Llinas, Roxanna J.; Bartel, Bonnie (2019-03-20)
      The sorting of eukaryotic proteins to various organellar destinations requires receptors that recognize cargo protein targeting signals and facilitate transport into the organelle. One such receptor is the peroxin PEX5, ...
    • Within-Host Priority Effects Systematically Alter Pathogen Coexistence 

      Clay, Patrick A.; Dhir, Kailash; Rudolf, Volker H.W.; Duffy, Meghan A. (2019)
      Coinfection of host populations alters pathogen prevalence, host mortality, and pathogen evolution. Because pathogens compete for limiting resources, whether multiple pathogens can coexist in a host population can depend ...
    • Biology in Bloom: A Primer on the Arabidopsis thaliana Model System 

      Woodward, Andrew W.; Bartel, Bonnie (2018-04-01)
      Arabidopsis thaliana could have easily escaped human scrutiny. Instead, Arabidopsis has become the most widely studied plant in modern biology despite its absence from the dinner table. Pairing diminutive stature and genome ...
    • Synthetic Biology and the Gut Microbiome 

      Dou, Jennifer; Bennett, Matthew R. (2018)
      The gut microbiome plays a crucial role in maintaining human health. Functions performed by gastrointestinal microbes range from regulating metabolism to modulating immune and nervous system development. Scientists have ...
    • Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors 

      Chen, Ye; Ho, Joanne M.L.; Shis, David L.; Gupta, Chinmaya; Long, James; Wagner, Daniel S.; Ott, William; Josić, Krešimir; Bennett, Matthew R. (2018)
      One challenge for synthetic biologists is the predictable tuning of genetic circuit regulatory components to elicit desired outputs. Gene expression driven by ligand-inducible transcription factor systems must exhibit the ...
    • Lactose repressor hinge domain independently binds DNA 

      Xu, Joseph S.; Hewitt, Madeleine N.; Gulati, Jaskeerat S.; Cruz, Matthew A.; Zhan, Hongli; Liu, Shirley; Matthews, Kathleen S. (2018)
      The short 8–10 amino acid “hinge” sequence in lactose repressor (LacI), present in other LacI/GalR family members, links DNA and inducer‐binding domains. Structural studies of full‐length or truncated LacI‐operator DNA ...
    • Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+-binding 

      Guo, Hou-Fu; Tsai, Chi-Lin; Terajima, Masahiko; Tan, Xiaochao; Banerjee, Priyam; Miller, Mitchell D.; Liu, Xin; Yu, Jiang; Byemerwa, Jovita; Alvarado, Sarah; Kaoud, Tamer S.; Dalby, Kevin N.; Bota-Rabassedas, Neus; Chen, Yulong; Yamauchi, Mitsuo; Tainer, John A.; Phillips, George N. Jr.; Kurie, Jonathan M. (2018)
      Collagen lysyl hydroxylases (LH1-3) are Fe2+- and 2-oxoglutarate (2-OG)-dependent oxygenases that maintain extracellular matrix homeostasis. High LH2 levels cause stable collagen cross-link accumulations that promote ...
    • Diversity and distribution ofᅠWolbachiaᅠin relation to geography, host plant affiliation and life cycle of a heterogonic gall wasp 

      Schuler, Hannes; Egan, Scott P.; Hood, Glen R.; Busbee, Robert W.; Driscoe, Amanda L.; Ott, James R. (2018)
      Background: The maternally inherited endosymbiont Wolbachia is widespread in arthropods and nematodes and can play an important role in the ecology and evolution of its host through reproductive manipulation. Here, we ...
    • Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis 

      Atkinson, Joshua T.; Jones, Alicia M.; Zhou, Quan; Silberg, Jonathan J. (2018)
      Deep mutational scanning has been used to create high-resolution DNA sequence maps that illustrate the functional consequences of large numbers of point mutations. However, this approach has not yet been applied to libraries ...
    • Elucidating the Metabolic Plasticity of Cancer: Mitochondrial Reprogramming and Hybrid Metabolic States 

      Jia, Dongya; Park, Jun Hyoung; Jung, Kwang Hwa; Levine, Herbert; Kaipparettu, Benny Abraham (2018)
      Aerobic glycolysis, also referred to as the Warburg effect, has been regarded as the dominant metabolic phenotype in cancer cells for a long time. More recently, it has been shown that mitochondria in most tumors are not ...
    • Modularity of the metabolic gene network as a prognostic biomarker for hepatocellular carcinoma 

      Ye, Fengdan; Jia, Dongya; Lu, Mingyang; Levine, Herbert; Deem, Michael W. (2018)
      Abnormal metabolism is an emerging hallmark of cancer. Cancer cells utilize both aerobic glycolysis and oxidative phosphorylation (OXPHOS) for energy production and biomass synthesis. Understanding the metabolic reprogramming ...
    • Bayesian inference of phylogenetic networks from bi-allelic genetic markers 

      Zhu, Jiafan; Wen, Dingqiao; Yu, Yun; Meudt, Heidi M.; Nakhleh, Luay (2018)
      Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence ...
    • PqsA Promotes Pyoverdine Production via Biofilm Formation 

      Kang, Donghoon; Turner, Kelly E.; Kirienko, Natalia V. (2018)
    • Orsay δ protein is required for non-lytic viral egress 

      Yuan, Wang; Zhou, Ying; Fan, Yanlin; Tao, Yizhi J.; Zhong, Weiwei (2018)
      Nonenveloped gastrointestinal viruses, such as human rotavirus, can exit infected cells from the apical surface without cell lysis. The mechanism of such nonlytic exit is poorly understood. The nonenveloped Orsay virus is ...
    • Latitudinal variation in soil biota: testing the biotic interaction hypothesis with an invasive plant and a native congener 

      Lu, Xinmin; He, Minyan; Ding, Jianqing; Siemann, Evan (2018)
      Soil biota community structure can change with latitude, but the effects of changes on native plants, invasive plants, and their herbivores remain unclear. Here, we examined latitudinal variation in the soil biota community ...
    • Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes 

      Di Pierro, Michele; Potoyan, Davit A.; Wolynes, Peter G.; Onuchic, José N. (2018)
      The nucleus of a eukaryotic cell is a nonequilibrium system where chromatin is subjected to active processes that continuously rearrange it over the cell's life cycle. Tracking the motion of chromosomal loci provides ...
    • Development and field validation of an environmental DNA (eDNA) assay for invasive clams of the genus Corbicula 

      Cowart, Dominique A.; Renshaw, Mark A.; Gantz, Crysta A.; Umek, John; Chandra, Sudeep; Egan, Scott P.; Lodge, David M.; Larson, Eric R. (2018)
      Early detection is imperative for successful control or eradication of invasive species, but many organisms are difficult to detect at the low abundances characteristic of recently introduced populations. Environmental DNA ...
    • A High-throughput, High-content, Liquid-based C. elegans Pathosystem 

      Anderson, Quinton L.; Revtovich, Alexey V.; Kirienko, Natalia V. (2018)
      The number of new drugs identified by traditional, in vitro screens has waned, reducing the success of this approach in the search for new weapons to combat multiple drug resistance. This has led to the conclusion that ...
    • Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography 

      Olmos, Jose L. Jr.; Pandey, Suraj; Martin-Garcia, Jose M.; Calvey, George; Katz, Andrea; Knoska, Juraj; Kupitz, Christopher; Hunter, Mark S.; Liang, Mengning; Oberthuer, Dominik; Yefanov, Oleksandr; Wiedorn, Max; Heyman, Michael; Holl, Mark; Pande, Kanupriya; Barty, Anton; Miller, Mitchell D.; Stern, Stephan; Roy-Chowdhury, Shatabdi; Coe, Jesse; Nagaratnam, Nirupa; Zook, James; Verburgt, Jacob; Norwood, Tyler; Poudyal, Ishwor; Xu, David; Koglin, Jason; Seaberg, Matthew H.; Zhao, Yun; Bajt, Saša; Grant, Thomas; Mariani, Valerio; Nelson, Garrett; Subramanian, Ganesh; Bae, Euiyoung; Fromme, Raimund; Fung, Russell; Schwander, Peter; Frank, Matthias; White, Thomas A.; Weierstall, Uwe; Zatsepin, Nadia; Spence, John; Fromme, Petra; Chapman, Henry N.; Pollack, Lois; Tremblay, Lee; Ourmazd, Abbas; Phillips, George N. Jr.; Schmidt, Marius (2018)
      BACKGROUND: Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular ...
    • A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells and Notch-Jagged signaling 

      Bocci, Federico; Jolly, Mohit Kumar; George, Jason Thomas; Levine, Herbert; Onuchic, José Nelson (2018)
      Epithelial-mesenchymal transition (EMT) and cancer stem cell (CSCs) formation are two fundamental and well-studied processes contributing to cancer metastasis and tumor relapse. Cells can undergo a partial EMT to attain a ...