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Jordan Bird

InstitutionUniversity of Arkansas for Medical Sciences
DepartmentBiochemistry & Molecular Biology, College of Medicine
Address9108 ACRC
4301 W. Markham
Mail Slot # 516
Little Rock AR 72205
ORCID ORCID Icon0000-0001-5753-6058 Additional info
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    R24GM137786     (TACKETT, ALAN)Aug 20, 2020 - May 31, 2025
    IDeA National Resource for Quantitative Proteomics
    Role: Co-Investigator

    NNH19ZDA001N-EXO     (Jay Lennon)Nov 22, 2019 - Nov 22, 2022
    Energy limitation and the evolution of microbial dormancy
    Role Description: Microorganisms are the most abundant and diverse forms of life on Earth. Owing to their metabolic versatility and capacity for rapid growth, they have played a central role in regulating biogeochemical processes that ensure our planet’s habitability. Rarely, however, do species experience conditions that are optimal for growth and reproduction. Many organisms contend with these challenges by engaging in dormancy, a universal process whereby individuals enter a reversible state of reduced metabolic activity. Dormancy generates a “seed bank” of long-lived individuals that buffers a wide range of ecological processes, but dormancy is also a life-history process that is shaped by the forces of evolution. In this proposal, we seek to understand the maintenance of dormancy by studying spore-forming bacteria (i.e., Bacillus) when faced by varying degrees of energy limitation. Sporulation is a complex and conserved trait that originated billions of years ago. Nevertheless, sporulation can easily be lost under “good” conditions in just hundreds of generations, which has consequences for the persistence and evolution of microbial lineages. Advances in high-throughput sequencing technology provide unprecedented opportunity for studying the evolution of dormancy, which will help us better understand the distribution, abundance, and activity of life on Earth and perhaps elsewhere in the universe. From test tubes to the globe, the overarching goal of our research is to identify the key ecological and evolutionary processes that generate and maintain microbial biodiversity (Locey and Lennon 2016). In the current proposal we investigate how sporulation, a hallmark trait of a globally dominant group of microorganisms, is maintained in the face of fluctuating and extreme environmental conditions. Specifically, we address three major objectives pertaining to the evolution of dormancy and energy limitation: 1) Accounting for genomic, transcriptional, and translational expenditures, we will estimate the bioenergetic cost of making a spore and use this information to then model and predict scenarios that favor the evolutionary retention versus loss of sporulation. 2) Using controlled and replicated experimental evolution trials, we will quantify the rate at which sporulation is lost and then characterize how bacteria subsequently evolve when challenged by contrasting energy regimes. 3) Leveraging large existing metagenomic databases, we will evaluate the loss of sporulation in a range of ecosystems and use phylogenetic comparative methods to test theoretical predictions about how trait decay should affect lineage diversification and rates of evolutionary change. Our research team is uniquely qualified to accomplish the objectives of the proposed research. Together, we have expertise in theoretical ecology and evolution, microbiology, genomics, bioinformatics, and the biogeochemistry of energy-limited ecosystems. Novel evolutionary insight into sporulation and alternate forms of dormancy will aid in understanding the long-term survival and resilience of populations in the modern-day biosphere while shedding light on early Earth evolution, including the persistence of life through mass extinction events. In addition to generating basic knowledge regarding the robustness of complex traits, our findings will have practical implications for planetary protection during future NASA missions.
    Role: Other Significant Contributor

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions. Don't see publications published under other names? Login to add alternative names.
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    1. Venugopal G, Bird JT, Washam CL, Roys H, Bowlin A, Byrum SD, Weinkopff T. In vivo transcriptional analysis of mice infected with Leishmania major unveils cellular heterogeneity and altered transcriptomic profiling at single-cell resolution. PLoS Negl Trop Dis. 2022 07; 16(7):e0010518. PMID: 35789215.
      View in: PubMed
    2. Lin VJT, Hu J, Zolekar A, Salick MR, Mittal P, Bird JT, Hoffmann P, Kaykas A, Byrum SD, Wang YC. Deficiency of N-glycanase 1 perturbs neurogenesis and cerebral development modeled by human organoids. Cell Death Dis. 2022 03 24; 13(3):262. PMID: 35322011.
      View in: PubMed
    3. Chappell K, Manna K, Washam CL, Graw S, Alkam D, Thompson MD, Zafar MK, Hazeslip L, Randolph C, Gies A, Bird JT, Byrd AK, Miah S, Byrum SD. Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer. Mol Omics. 2021 10 11; 17(5):677-691. PMID: 34142686.
      View in: PubMed
    4. Schinke CD, Bird JT, Qu P, Yaccoby S, Lyzogubov VV, Shelton R, Ling W, Boyle EM, Deshpande S, Byrum SD, Washam C, Mackintosh S, Stephens O, Thanendrarajan S, Zangari M, Shaughnessy J, Zhan F, Barlogie B, van Rhee F, Walker BA. PHF19 inhibition as a therapeutic target in multiple myeloma. Curr Res Transl Med. 2021 07; 69(3):103290. PMID: 33894670.
      View in: PubMed
    5. Graw S, Chappell K, Washam CL, Gies A, Bird J, Robeson MS, Byrum SD. Multi-omics data integration considerations and study design for biological systems and disease. Mol Omics. 2021 04 19; 17(2):170-185. PMID: 33347526.
      View in: PubMed
    6. Wallis KF, Morehead LC, Bird JT, Byrum SD, Miousse IR. Differences in cell death in methionine versus cysteine depletion. Environ Mol Mutagen. 2021 03; 62(3):216-226. PMID: 33615565.
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    7. Allensworth-James M, Banik J, Odle A, Hardy L, Lagasse A, Moreira ARS, Bird J, Thomas CL, Avaritt N, Kharas MG, Lengner CJ, Byrum SD, MacNicol MC, Childs GV, MacNicol AM. Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi. Endocrinology. 2021 03 01; 162(3). PMID: 33373440.
      View in: PubMed
    8. Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA. A genomic catalog of Earth's microbiomes. Nat Biotechnol. 2021 04; 39(4):499-509. PMID: 33169036.
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    9. Lloyd KG, Bird JT, Buongiorno J, Deas E, Kevorkian R, Noordhoek T, Rosalsky J, Roy T. Erratum for Lloyd et al., "Evidence for a Growth Zone for Deep-Subsurface Microbial Clades in Near-Surface Anoxic Sediments". Appl Environ Microbiol. 2020 Oct 15; 86(21). PMID: 33060120.
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    10. Lloyd KG, Bird JT, Buongiorno J, Deas E, Kevorkian R, Noordhoek T, Rosalsky J, Roy T. Evidence for a Growth Zone for Deep-Subsurface Microbial Clades in Near-Surface Anoxic Sediments. Appl Environ Microbiol. 2020 09 17; 86(19). PMID: 32709727.
      View in: PubMed
    11. Fritts RK, Bird JT, Behringer MG, Lipzen A, Martin J, Lynch M, McKinlay JB. Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community. ISME J. 2020 11; 14(11):2816-2828. PMID: 32788711.
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    12. Steen AD, Kevorkian RT, Bird JT, Dombrowski N, Baker BJ, Hagen SM, Mulligan KH, Schmidt JM, Webber AT, Royalty TM, Alperin MJ. Kinetics and Identities of Extracellular Peptidases in Subsurface Sediments of the White Oak River Estuary, North Carolina. Appl Environ Microbiol. 2019 10 01; 85(19). PMID: 31324636.
      View in: PubMed
    13. Bird JT, Tague ED, Zinke L, Schmidt JM, Steen AD, Reese B, Marshall IPG, Webster G, Weightman A, Castro HF, Campagna SR, Lloyd KG. Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments. mBio. 2019 04 16; 10(2). PMID: 30992358.
      View in: PubMed
    14. Zinke LA, Glombitza C, Bird JT, Røy H, Jørgensen BB, Lloyd KG, Amend JP, Reese BK. Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry. Appl Environ Microbiol. 2019 02 15; 85(4). PMID: 30504213.
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    15. Vishnivetskaya TA, Buongiorno J, Bird J, Krivushin K, Spirina EV, Oshurkova V, Shcherbakova VA, Wilson G, Lloyd KG, Rivkina EM. Methanogens in the Antarctic Dry Valley permafrost. FEMS Microbiol Ecol. 2018 08 01; 94(8). PMID: 29878114.
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    16. Kevorkian R, Bird JT, Shumaker A, Lloyd KG. Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment. Appl Environ Microbiol. 2018 Jan 01; 84(1). PMID: 29054869.
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    17. Zinke LA, Mullis MM, Bird JT, Marshall IPG, Jørgensen BB, Lloyd KG, Amend JP, Kiel Reese B. Thriving or surviving? Evaluating active microbial guilds in Baltic Sea sediment. Environ Microbiol Rep. 2017 10; 9(5):528-536. PMID: 28836742.
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    18. Wilhelm SW, Bird JT, Bonifer KS, Calfee BC, Chen T, Coy SR, Gainer PJ, Gann ER, Heatherly HT, Lee J, Liang X, Liu J, Armes AC, Moniruzzaman M, Rice JH, Stough JM, Tams RN, Williams EP, LeCleir GR. A Student's Guide to Giant Viruses Infecting Small Eukaryotes: From Acanthamoeba to Zooxanthellae. Viruses. 2017 03 17; 9(3). PMID: 28304329.
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    19. Buongiorno J, Bird JT, Krivushin K, Oshurkova V, Shcherbakova V, Rivkina EM, Lloyd KG, Vishnivetskaya TA. Draft Genome Sequence of Antarctic Methanogen Enriched from Dry Valley Permafrost. Genome Announc. 2016 Dec 08; 4(6). PMID: 27932654.
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    20. Bird JT, Baker BJ, Probst AJ, Podar M, Lloyd KG. Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales. Front Microbiol. 2016; 7:1221. PMID: 27547202.
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    21. Michalska K, Steen AD, Chhor G, Endres M, Webber AT, Bird J, Lloyd KG, Joachimiak A. New aminopeptidase from "microbial dark matter" archaeon. FASEB J. 2015 Sep; 29(9):4071-9. PMID: 26062601.
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