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

Recent Submissions

  • A deep learning solution for crystallographic structure determination 

    Pan, T.; Jin, S.; Miller, M. D.; Kyrillidis, A.; Phillips, G. N. (2023)
    The general de novo solution of the crystallographic phase problem is difficult and only possible under certain conditions. This paper develops an initial pathway to a deep learning neural network approach for the phase problem in protein crystallography, based on a synthetic dataset of small fragments derived from a large well curated subset of ...
  • Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes 

    Veglia, Alex J.; Bistolas, Kalia S. I.; Voolstra, Christian R.; Hume, Benjamin C. C.; Ruscheweyh, Hans-Joachim; (2023)
    Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 ...
  • Stony coral tissue loss disease induces transcriptional signatures of in situ degradation of dysfunctional Symbiodiniaceae 

    Beavers, Kelsey M.; Van Buren, Emily W.; Rossin, Ashley M.; Emery, Madison A.; Veglia, Alex J.; (2023)
    Stony coral tissue loss disease (SCTLD), one of the most pervasive and virulent coral diseases on record, affects over 22 species of reef-building coral and is decimating reefs throughout the Caribbean. To understand how different coral species and their algal symbionts (family Symbiodiniaceae) respond to this disease, we examine the gene expression ...
  • How to tuna fish: constraint, convergence, and integration in the neurocranium of pelagiarian fishes 

    Knapp, Andrew; Rangel-de Lázaro, Gizéh; Friedman, Matt; Johanson, Zerina; Evans, Kory M; (2023)
    Morphological evolution of the vertebrate skull has been explored across a wide range of tetrapod clades using geometric morphometrics, but the application of these methods to teleost fishes, accounting for roughly half of all vertebrate species, has been limited. Here we present the results of a study investigating 3D morphological evolution of the ...
  • Building consensus around the assessment and interpretation of Symbiodiniaceae diversity 

    Davies, Sarah W.; Gamache, Matthew H.; Howe-Kerr, Lauren I.; Kriefall, Nicola G.; Baker, Andrew C.; (2023)
    Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with ...
  • SARS-CoV-2 Exposure in Norway Rats (Rattus norvegicus) from New York City 

    Wang, Yang; Lenoch, Julianna; Kohler, Dennis; DeLiberto, Thomas J.; Tang, Cynthia Y.; (2023)
    Millions of Norway rats (Rattus norvegicus) inhabit New York City (NYC), presenting the potential for transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to rats. We evaluated SARS-CoV-2 exposure among 79 rats captured from NYC during the fall of 2021. Our results showed that 13 of the 79 rats (16.5%) tested IgG- ...
  • Examining Sporadic Cancer Mutations Uncovers a Set of Genes Involved in Mitochondrial Maintenance 

    Moreno, Armando; Taffet, Allison; Tjahjono, Elissa; Anderson, Quinton L.; Kirienko, Natalia V. (2023)
    Mitochondria are key organelles for cellular health and metabolism and the activation of programmed cell death processes. Although pathways for regulating and re-establishing mitochondrial homeostasis have been identified over the past twenty years, the consequences of disrupting genes that regulate other cellular processes, such as division and ...
  • DNA supercoiling-induced shapes alter minicircle hydrodynamic properties 

    Waszkiewicz, Radost; Ranasinghe, Maduni; Fogg, Jonathan M; Catanese, Daniel J, Jr.; Ekiel-Jeżewska, Maria L; (2023)
    DNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand ...
  • Consumer feces impact coral health in guild-specific ways 

    Grupstra, Carsten G. B.; Howe-Kerr, Lauren I.; van der Meulen, Jesse A.; Veglia, Alex J.; Coy, Samantha R.; (2023)
    Animal waste products are an important component of nutrient cycles and result in the trophic transmission of diverse microorganisms. There is growing recognition that the feces of consumers, such as predators, may impact resource species, their prey, via physical effects and/or microbial activity. We tested the effect of feces from distinct fish ...
  • Bacterial and fungal inhibitor interacted impacting growth of invasive Triadica sebifera and soil N2O emissions 

    Lai, Xiaoqin; Luo, Laicong; Fang, Haifu; Zhang, Ling; Shad, Nasir; (2023)
    Plant invasions affect biodiversity and seriously endanger the stability of ecosystems. Invasive plants show strong adaptability and growth advantages but are influenced by various factors. Soil bacteria and fungi are critical to plant growth and are important factors affecting plant invasions. Plant invasions also affect soil N2O emissions, but the ...
  • Impact of a natural disturbance on the performance and microbial communities in a full-scale constructed wetland for industrial wastewater treatment 

    Hollstein, Marielle; Comerford, Mattheau; Uhl, Michael; Abel, Michael; Egan, Scott P.; (2023)
    Constructed Wetlands (CWs) are a cost-effective, versatile and sustainable choice for wastewater treatment. In these environments, microbial communities play a significant role in pollutant removal. However, little is known about how microbial communities in full-scale CWs contribute to maintaining water quality or how their dynamics change in response ...
  • pYtags enable spatiotemporal measurements of receptor tyrosine kinase signaling in living cells 

    Farahani, Payam E; Yang, Xiaoyu; Mesev, Emily V; Fomby, Kaylan A; Brumbaugh-Reed, Ellen H; (2023)
    Receptor tyrosine kinases (RTKs) are major signaling hubs in metazoans, playing crucial roles in cell proliferation, migration, and differentiation. However, few tools are available to measure the activity of a specific RTK in individual living cells. Here, we present pYtags, a modular approach for monitoring the activity of a user-defined RTK by ...
  • Pathogen-induced dormancy in liquid limits gastrointestinal colonization of Caenorhabditis elegans 

    Zhang, Liyang; Gade, Vyshnavi; Kirienko, Natalia V. (2023)
    Colonization is generally considered a prerequisite for infection, but this event is context-dependent, as evidenced by the differing ability of the human pathogen Pseudomonas aeruginosa to efficiently colonize Caenorhabditis elegans on agar but not in liquid . In this study, we examined the impact of the environment, pathogen, host, and their ...
  • Indirect Enrichment of Desirable, but Less Fit Phenotypes, from a Synthetic Microbial Community Using Microdroplet Confinement 

    Prabhakar, Ramya Ganiga; Fan, Gaoyang; Alnahhas, Razan N.; Hirning, Andrew J.; Bennett, Matthew R.; (2023)
    Spatial structure within microbial communities can provide nearly limitless opportunities for social interactions and are an important driver for evolution. As metabolites are often molecular signals, metabolite diffusion within microbial communities can affect the composition and dynamics of the community in a manner that can be challenging to ...
  • Native diversity contributes to composition heterogeneity of exotic floras 

    Chen, Pengdong; Shen, Changchao; Ren, Jie; Qin, Wenchao; Yi, Jiahui; (2023)
    Variation in species composition among sites (beta diversity) is generally thought to be driven by environmental filtering and dispersal limitation, but the role of biotic interactions has not been sufficiently addressed. Specifically, the early species in a local community may contribute to subsequent beta diversity patterns. Exotic assemblages ...
  • Visualization of RNA virus infection in a marine protist with a universal biomarker 

    Coy, Samantha R.; Utama, Budi; Spurlin, James W.; Kim, Julia G.; Deshmukh, Harshavardhan; (2023)
    Half of the marine virosphere is hypothesized to be RNA viruses (kingdom Orthornavirae) that infect abundant micro-eukaryotic hosts (e.g. protists). To test this, quantitative approaches that broadly track infections in situ are needed. Here, we describe a technique—dsRNA-Immunofluorescence (dsRIF)—that uses a double-stranded RNA (dsRNA) targeting ...
  • Molecular Basis of KAT2A Selecting Acyl-CoA Cofactors for Histone Modifications 

    Li, Sha; Li, Nan; He, Jie; Zhou, Runxin; Lu, Zhimin; (2023)
    Emerging discoveries about undocumented acyltransferase activities of known histone acetyltransferases (HATs) advance our understandings in the regulation of histone modifications. However, the molecular basis of HATs selecting acyl coenzyme A (acyl-CoA) substrates for histone modification is less known. We here report that lysine acetyltransferase ...
  • An associative memory Hamiltonian model for DNA and nucleosomes 

    Lu, Weiqi; Onuchic, José N.; Pierro, Michele Di; Center for Theoretical Biological Physics (2023)
    A model for DNA and nucleosomes is introduced with the goal of studying chromosomes from a single base level all the way to higher-order chromatin structures. This model, dubbed the Widely Editable Chromatin Model (WEChroM), reproduces the complex mechanics of the double helix including its bending persistence length and twisting persistence length, ...
  • A discrete intermediate for the biosynthesis of both the enediyne core and the anthraquinone moiety of enediyne natural products 

    Bhardwaj, Minakshi; Cui, Zheng; Daniel Hankore, Erome; Moonschi, Faruk H.; Saghaeiannejad Esfahani, Hoda; (2023)
    The enediynes are structurally characterized by a 1,5-diyne-3-ene motif within a 9- or 10-membered enediyne core. The anthraquinone-fused enediynes (AFEs) are a subclass of 10-membered enediynes that contain an anthraquinone moiety fused to the enediyne core as exemplified by dynemicins and tiancimycins. A conserved iterative type I polyketide synthase ...
  • Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity 

    Chang, Caleb; Lee Luo, Christie; Eleraky, Sarah; Lin, Aaron; Zhou, Grace; (2023)
    DNA polymerases catalyze DNA synthesis with high efficiency, which is essential for all life. Extensive kinetic and structural efforts have been executed in exploring mechanisms of DNA polymerases, surrounding their kinetic pathway, catalytic mechanisms, and factors that dictate polymerase fidelity. Recent time-resolved crystallography studies on DNA ...

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