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

Recent Submissions

  • Triple reassortment increases compatibility among viral ribonucleoprotein genes of contemporary avian and human influenza A viruses 

    Waters, Kaitlyn; Gao, Cheng; Ykema, Matthew; Han, Lei; Voth, Lynden; (2021)
    Compatibility among the influenza A virus (IAV) ribonucleoprotein (RNP) genes affects viral replication efficiency and can limit the emergence of novel reassortants, including those with potential pandemic risks. In this study, we determined the polymerase activities of 2,451 RNP reassortants among three seasonal and eight enzootic IAVs by using a ...
  • Simplified Communities of Seed-Dispersers Limit the Composition and Flow of Seeds in Edge Habitats 

    Razafindratsima, Onja H.; Raoelinjanakolona, Nasandratra Nancia; Heriniaina, Rio R.; Nantenaina, Rindra H.; Ratolojanahary, Tianasoa H.; (2021)
    Edge effects, driven by human modification of landscapes, can have critical impacts on ecological processes such as species interactions, with cascading impacts on biodiversity as a whole. Characterizing how edges affect vital biotic interactions such as seed dispersal by frugivores is important for better understanding potential mechanisms that drive ...
  • BMP-treated human embryonic stem cells transcriptionally resemble amnion cells in the monkey embryo 

    Chhabra, Sapna; Warmflash, Aryeh (2021)
    Human embryonic stem cells (hESCs) possess an immense potential to generate clinically relevant cell types and unveil mechanisms underlying early human development. However, using hESCs for discovery or translation requires accurately identifying differentiated cell types through comparison with their in vivo counterparts. Here, we set out to determine ...
  • Structural characterization of DynU16, a START/Bet v1-like protein involved in dynemicin biosynthesis 

    Alvarado, S. K.; Miller, M. D.; Bhardwaj, M.; Thorson, J. S.; Van Lanen, S. G.; (2021)
    The 1.5 Å resolution crystal structure of DynU16, a protein identified in the dynemicin-biosynthetic gene cluster, is reported. The structure adopts a di-domain helix-grip fold with a uniquely positioned open cavity connecting the domains. The elongated dimensions of the cavity appear to be compatible with the geometry of a linear polyene, suggesting ...
  • Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia 

    Winkle, James J.; Karamched, Bhargav R.; Bennett, Matthew R.; Ott, William; Josić, Krešimir (2021)
    The increased complexity of synthetic microbial biocircuits highlights the need for distributed cell functionality due to concomitant increases in metabolic and regulatory burdens imposed on single-strain topologies. Distributed systems, however, introduce additional challenges since consortium composition and spatiotemporal dynamics of constituent ...
  • CHAF1A Blocks Neuronal Differentiation and Promotes Neuroblastoma Oncogenesis via Metabolic Reprogramming 

    Tao, Ling; Moreno-Smith, Myrthala; Ibarra-García-Padilla, Rodrigo; Milazzo, Giorgio; Drolet, Nathan A.; (2021)
    Neuroblastoma (NB) arises from oncogenic disruption of neural crest (NC) differentiation. Treatment with retinoic acid (RA) to induce differentiation has improved survival in some NB patients, but not all patients respond, and most NBs eventually develop resistance to RA. Loss of the chromatin modifier chromatin assembly factor 1 subunit p150 (CHAF1A) ...
  • Direct evidence of sex and a hypothesis about meiosis in Symbiodiniaceae 

    Figueroa, R.I.; Howe-Kerr, L.I.; Correa, A.M.S. (2021)
    Dinoflagellates in the family Symbiodiniaceae are obligate endosymbionts of diverse marine invertebrates, including corals, and impact the capacity of their hosts to respond to climate change-driven ocean warming. Understanding the conditions under which increased genetic variation in Symbiodiniaceae arises via sexual recombination can support efforts ...
  • Phylogenetic Underpinning of Groundwater Use by Trees 

    Knighton, James; Fricke, Evan; Evaristo, Jaivime; de Boer, Hugo Jan; Wassen, Martin Joseph (2021)
    Root water uptake (RWU) strategies shape climate-vegetation feedbacks and ecosystem productivity. A fundamental relationship between RWU strategies and evolutionary histories (phylogeny) of trees, however, remains poorly understood. Establishing a phylogenetic basis for tree RWU, particularly groundwater use, could improve their representation in ...
  • Cryptic diversity in the North American Dromochorus tiger beetles (Coleoptera: Carabidae: Cicindelinae): a congruence-based method for species discovery 

    Duran, Daniel P; Herrmann, David P; Roman, Stephen J; Gwiazdowski, Rodger A; Drummond, Jennifer A; (2019)
    A fundamental problem in biodiversity science is determining the number of species in any taxon, and there is a growing awareness that cryptic diversity contributes to this problem – even in well-studied groups. Discovering cryptic species requires several lines of evidence to elucidate congruent patterns across data-types, and distinguish unrecognized ...
  • Primary cilia deficiency in neural crest cells models anterior segment dysgenesis in mouse 

    Portal, Céline; Rompolas, Panteleimos; Lwigale, Peter; Iomini, Carlo (2019)
    Defects affecting tissues of the anterior segment (AS) of the eye lead to a group of highly debilitating disorders called Anterior Segment Dysgenesis (ASD). Despite the identification of some causative genes, the pathogenesis of ASD remains unclear. Interestingly, several ciliopathies display conditions of the AS. Using conditional targeting of Ift88 ...
  • Mitochondria-affecting small molecules ameliorate proteostasis defects associated with neurodegenerative diseases 

    Tjahjono, Elissa; Pei, Jingqi; Revtovich, Alexey V.; Liu, Terri-Jeanne E.; Swadi, Alisha; (2021)
    Macroautophagic recycling of dysfunctional mitochondria, known as mitophagy, is essential for mitochondrial homeostasis and cell viability. Accumulation of defective mitochondria and impaired mitophagy have been widely implicated in many neurodegenerative diseases, and loss-of-function mutations of PINK1 and Parkin, two key regulators of mitophagy, ...
  • Synthesis of precision antibody conjugates using proximity-induced chemistry 

    Cao, Yu J.; Yu, Chenfei; Wu, Kuan-Lin; Wang, Xuechun; Liu, Dong; (2021)
    Rationale: Therapeutic antibody conjugates allow for the specific delivery of cytotoxic agents or immune cells to tumors, thus enhancing the antitumor activity of these agents and minimizing adverse systemic effects. Most current antibody conjugates are prepared by nonspecific modification of antibody cysteine or lysine residues, inevitably resulting ...
  • Climate warming promotes pesticide resistance through expanding overwintering range of a global pest 

    Ma, Chun-Sen; Zhang, Wei; Peng, Yu; Zhao, Fei; Chang, Xiang-Qian; (2021)
    Climate change has the potential to change the distribution of pests globally and their resistance to pesticides, thereby threatening global food security in the 21st century. However, predicting where these changes occur and how they will influence current pest control efforts is a challenge. Using experimentally parameterised and field-tested models, ...
  • Quantification of Myxococcus xanthus Aggregation and Rippling Behaviors: Deep-Learning Transformation of Phase-Contrast into Fluorescence Microscopy Images 

    Zhang, Jiangguo; Comstock, Jessica A.; Cotter, Christopher R.; Murphy, Patrick A.; Nie, Weili; (2021)
    Myxococcus xanthus bacteria are a model system for understanding pattern formation and collective cell behaviors. When starving, cells aggregate into fruiting bodies to form metabolically inert spores. During predation, cells self-organize into traveling cell-density waves termed ripples. Both phase-contrast and fluorescence microscopy are used to ...
  • DNA Helicase–Polymerase Coupling in Bacteriophage DNA Replication 

    Lo, Chen-Yu; Gao, Yang (2021)
    Bacteriophages have long been model systems to study the molecular mechanisms of DNA replication. During DNA replication, a DNA helicase and a DNA polymerase cooperatively unwind the parental DNA. By surveying recent data from three bacteriophage replication systems, we summarized the mechanistic basis of DNA replication by helicases and polymerases. ...
  • Phylogenomic assessment of the role of hybridization and introgression in trait evolution 

    Wang, Yaxuan; Cao, Zhen; Ogilvie, Huw A.; Nakhleh, Luay (2021)
    Trait evolution among a set of species—a central theme in evolutionary biology—has long been understood and analyzed with respect to a species tree. However, the field of phylogenomics, which has been propelled by advances in sequencing technologies, has ushered in the era of species/gene tree incongruence and, consequently, a more nuanced understanding ...
  • Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion 

    Dodero-Rojas, Esteban; Onuchic, Jose N; Whitford, Paul Charles; Center for Theoretical Biological Physics (2021)
    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious, and transmission involves a series of processes that may be targeted by vaccines and therapeutics. During transmission, host cell invasion is controlled by a large-scale (200–300 Å) conformational change of the Spike protein. This conformational rearrangement leads to ...
  • Editorial: Gulf of Mexico Reefs: Past, Present and Future 

    Martindale, Rowan C.; Holstein, Daniel; Knowlton, Nancy; Voss, Joshua D.; Weiss, Anna M.; (2021)
  • Mammalian herbivores restrict the altitudinal range limits of alpine plants 

    Lynn, Joshua S.; Miller, Tom E. X.; Rudgers, Jennifer A. (2021)
    Although rarely experimentally tested, biotic interactions have long been hypothesised to limit low-elevation range boundaries of species. We tested the effects of herbivory on three alpine-restricted plant species by transplanting plants below (novel), at the edge (limit), or in the centre (core) of their current elevational range and factorially ...
  • A protocol for whole-mount immuno-coupled hybridization chain reaction (WICHCR) in zebrafish embryos and larvae 

    Ibarra-García-Padilla, Rodrigo; Howard, Aubrey Gaylon Adam; Singleton, Eileen Willey; Uribe, Rosa Anna (2021)
    Characterizing mRNA and protein expression with temporal and spatial resolution is a valuable component of nearly every developmental study. Here, we describe a protocol that combines in situ hybridization chain reaction (HCR) and immunofluorescence, allowing for the detection of mRNAs and proteins simultaneously, in zebrafish embryos and larvae. ...

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