Nealson Kenneth H.

No Thumbnail Available
Last Name
Nealson
First Name
Kenneth H.
ORCID

Filters

2009 - 2009 2 2020 - 2022 1
2 1
3
Reset filters

Settings

Search Results

Now showing 1 - 3 of 3
  • Preprint
    Comparative systems biology across an evolutionary gradient within the Shewanella genus
    ( 2009-07) Konstantinidis, Konstantinos T. ; Serres, Margrethe H. ; Romine, Margaret F. ; Rodrigues, Jorge L. M. ; Auchtung, Jennifer ; McCue, Lee-Ann ; Lipton, Mary S. ; Obraztsova, Anna Y. ; Giometti, Carol S. ; Nealson, Kenneth H. ; Fredrickson, James K. ; Tiedje, James M.
    To what extent genotypic differences translate to phenotypic variation remains a poorly understood issue of paramount importance for several cornerstone concepts of microbiology including the species definition. Here, we take advantage of the completed genomic sequences, expressed proteomic profiles, and physiological studies of ten closely related Shewanella strains and species to provide quantitative insights into this issue. Our analyses revealed that, despite extensive horizontal gene transfer within these genomes, the genotypic and phenotypic similarities among the organisms were generally predictable from their evolutionary relatedness. The power of the predictions depended on the degree of ecological specialization of the organisms evaluated. Using the gradient of evolutionary relatedness formed by these genomes, we were able to partly isolate the effect of ecology from that of evolutionary divergence and rank the different cellular functions in terms of their rates of evolution. Our ranking also revealed that whole-cell protein expression differences among these organisms when grown under identical conditions were relatively larger than differences at the genome level, suggesting that similarity in gene regulation and expression should constitute another important parameter for (new) species description. Collectively, our results provide important new information towards beginning a systems-level understanding of bacterial species and genera.
  • Article
    Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes
    (Springer, 2009-10-03) Karpinets, Tatiana V. ; Obraztsova, Anna Y. ; Wang, Yanbing ; Schmoyer, Denise D. ; Kora, Guruprasad H. ; Park, Byung H. ; Serres, Margrethe H. ; Romine, Margaret F. ; Land, Miriam L. ; Kothe, Terence B. ; Fredrickson, James K. ; Nealson, Kenneth H. ; Uberbacher, Edward C.
    Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.
  • Article
    Science goals and mission architecture of the Europa Lander mission concept
    (IOP Publishing, 2022-01-26) Hand, Kevin P. ; Phillips, Cynthia B. ; Murray, Alison E. ; Garvin, James B. ; Maize, Earl H. ; Gibbs, Roger G. ; Reeves, Glenn ; San Martin, A. Miguel ; Tan-Wang, Grace H. ; Krajewski, Joel ; Hurst, Kenneth ; Crum, Ray ; Kennedy, Brett A. ; McElrath, Timothy P. ; Gallon, John C. ; Sabahi, Dara ; Thurman, Sam W. ; Goldstein, Barry ; Estabrook, Polly ; Lee, Steven W. ; Dooley, Jennifer A. ; Brinckerhoff, William B. ; Edgett, Kenneth S. ; German, Christopher R. ; Hoehler, Tori M. ; Hörst, Sarah M. ; Lunine, Jonathan I. ; Paranicas, Christopher ; Nealson, Kenneth H. ; Smith, David E. ; Templeton, Alexis S. ; Russell, Michael J. ; Schmidt, Britney E. ; Christner, Brent C. ; Ehlmann, Bethany L. ; Hayes, Alexander ; Rhoden, Alyssa R. ; Willis, Peter ; Yingst, R. Aileen ; Craft, Kathleen L. ; Cameron, Marissa E. ; Nordheim, Tom A. ; Pitesky, Jo ; Scully, Jennifer ; Hofgartner, Jason D. ; Sell, Steve W. ; Barltrop, Kevin J. ; Izraelevitz, Jacob ; Brandon, Erik J. ; Seong, J. ; Jones, John-Paul ; Pasalic, Jasmina ; Billings, Keith J. ; Ruiz, John Paul ; Bugga, Ratnakumar V. ; Graham, Dan ; Arenas, L. A. ; Takeyama, Deidre ; Drummond, Mai ; Aghazarian, Hrand ; Andersen, Allen J. ; Andersen, Kayla B. ; Anderson, E. W. ; Babuscia, Alessandra ; Backes, Paul G. ; Bailey, Elizabeth S. ; Balentine, Daniel ; Ballard, Christopher G. ; Berisford, Daniel F. ; Bhandari, Pradeep ; Blackwood, Krys ; Bolotin, Gary S. ; Bovre, Emilee A. ; Bowkett, Joseph ; Boykins, Kobie T. ; Bramble, Michael S. ; Brice, Timothy M. ; Briggs, Paul ; Brinkman, Alexander P. ; Brooks, Shawn M. ; Buffington, Brent B. ; Burns, Brandon ; Cable, Morgan L. ; Campagnola,Stefano ; Cangahuala, Laureano A. ; Carr, Gregory A. ; Casani, John R. ; Chahat, Nacer E. ; Chamberlain-Simon, Brendan K. ; Cheng, Yun-Ting ; Chien, Steve A. ; Cook, B. T. ; Cooper, Moogega ; Dinicola, Michael ; Clement, Brian G. ; Dean, Zachary S. ; Cullimore, Emily A. ; Curtis, Aaron G. ; de la Croix, Jean-Pierre ; Di Pasquale, Peter ; Dodd, Emma M. ; Dubord, Luke A. ; Edlund, Jeffrey A. ; Ellyin, Raymond ; Emanuel, Blair ; Foster, Jeffrey T. ; Ganino, Anthony J. ; Garner, Gregory J. ; Gibson, Matt T. ; Gildner, Matt ; Glazebrook, Kenneth J. ; Greco, Martin E. ; Green, W. M. ; Hatch, Sara J. ; Hetzel, Mark M. ; Hoey, William A. ; Hofmann, Amy E. ; Ionasescu, Rodica ; Jain, Abhinandan ; Jasper, Jay D. ; Johannesen, Jennie R. ; Johnson, Glenn K. ; Jun, Insoo ; Katake, Anup B. ; Kim-Castet, So Young ; Kim, David Inkyu ; Kim, Wousik ; Klonicki, Emily F. ; Kobeissi, Brad ; Kobie, Bryan D. ; Kochocki, Joseph ; Kokorowski, Michael ; Kosberg, Jacob A. ; Kriechbaum, Kristopher ; Kulkarni, Tejas P. ; Lam, Rebekah L. ; Landau, Damon F. ; Lattimore, Myra A. ; Laubach, Sharon L. ; Lawler, Christopher R. ; Lim, Grace ; Li, Jui-Lin ; Litwin, Todd E. ; Lo, Martin W. ; Logan, Cambria A. ; Maghasoudi, Elham ; Mandrake, Lukas ; Marchetti, Yuliya ; Marteau, Eloise ; Maxwell, Kimberly A. ; McNamee, John B. ; McIntyre, Ocean ; Meacham, Michael ; Melko, Joseph P. ; Mueller, Juergen ; Muliere, David ; Mysore, Aprameya ; Nash, Jeremy ; Ono, Masahiro ; Parker, Jay M. ; Perkins, Rebecca C. ; Petropoulos, Anastassios E. ; Gaut, Aaron ; Piette Gomez, Marie Y. ; Casillas, Raul Polit ; Preudhomme, Michael ; Pyrzak, Guy ; Rapinchuk, Jacqueline ; Ratliff, John Martin ; Ray, T. L. ; Roberts, Eric T. ; Roffo, Kenneth ; Roth, Duane C. ; Russino, Joseph A. ; Schmidt, Tyler M. ; Schoppers, Marcel J. ; Senent, Juan S. ; Serricchio, Fred ; Sheldon, Douglas J. ; Shiraishi, Lori R. ; Shirvanian, James ; Siegel, Katherine J. ; Singh, Gurjeet ; Sirota, Allen R. ; Skulsky, Eli D. ; Stehly, Joseph S. ; Strange, Nathan J. ; Stevens, Sarah U. ; Sunada, Eric T. ; Tepsuporn, Scott P. ; Tosi, Luis Phillipe C. ; Trawny, Nikolas ; Uchenik, Igor ; Verma, Vandi ; Volpe, Richard A. ; Wagner, Caleb T. ; Wang, D. ; Willson, Reg G. ; Wolff, John Luke ; Wong, A. T. ; Zimmer, Aline K. ; Sukhatme, Kalyani G. ; Bago, Kevin A. ; Chen, Yang ; Deardorff, Alyssa M. ; Kuch, Roger S. ; Lim, Christopher ; Syvertson, Marguerite L. ; Arakaki, Genji A. ; Avila, Art ; DeBruin, Kevin J. ; Frick, Andreas ; Harris, Joby R. ; Heverly, Matthew C. ; Kawata, Jessie M. ; Kim‬, Sung-Kyun ; Kipp, Devin M. ; Murphy, Juliana ; Smith, Matthew W. ; Spaulding, Matthew D. ; Thakker, Rohan ; Warner, Noah Z. ; Yahnker, Chris R. ; Young, M. E. ; Magner, Tom ; Adams, Danica ; Bedini, Peter ; Mehr, Lauren ; Sheldon, Colin ; Vernon, Steven ; Bailey, Vince ; Briere, Marc ; Butler, Michael ; Davis, Amanda ; Ensor, Susan ; Gannon, Michele ; Haapala-Chalk, Amanda ; Hartka, Ted ; Holdridge, Mark ; Hong, Albert ; Hunt, J. ; Iskow, Joe ; Kahler, Faith ; Murray, Kimberly ; Napolillo, David ; Norkus, Michael ; Pfisterer, Rick ; Porter, Jamie ; Roth, David ; Schwartz, Paul ; Wolfarth, Lawrence ; Cardiff, Eric ; Davis, Anita ; Grob, Eric W. ; Adam, Jason R. ; Betts, Erin ; Norwood, Jason ; Heller, M. M. ; Voskuilen, Tyler ; Sakievich, Philip ; Gray, L. ; Hansen, D. J. ; Irick, Kevin W. ; Hewson, John C. ; Lamb, Joshua ; Stacy, S. C. ; Brotherton, Chris M. ; Tappan, Alexander S. ; Benally, Darryl ; Thigpen, Hannah ; Ortiz, Erick ; Sandoval, Dan ; Ison, Aaron M. ; Warren, M. ; Stromberg, Peter G. ; Thelen, Paul Mark ; Blasy, B. ; Nandy, Prabal ; Haddad, Alexandria W. ; Trujillo, Lynna B. ; Wiseley, T. H. ; Bell, S. A. ; Teske, Nicholas P. ; Post, C. ; Torres-Castro, Loraine ; Grosso, Chris ; Wasiolek, Maryla
    Europa is a premier target for advancing both planetary science and astrobiology, as well as for opening a new window into the burgeoning field of comparative oceanography. The potentially habitable subsurface ocean of Europa may harbor life, and the globally young and comparatively thin ice shell of Europa may contain biosignatures that are readily accessible to a surface lander. Europa's icy shell also offers the opportunity to study tectonics and geologic cycles across a range of mechanisms and compositions. Here we detail the goals and mission architecture of the Europa Lander mission concept, as developed from 2015 through 2020. The science was developed by the 2016 Europa Lander Science Definition Team (SDT), and the mission architecture was developed by the preproject engineering team, in close collaboration with the SDT. In 2017 and 2018, the mission concept passed its mission concept review and delta-mission concept review, respectively. Since that time, the preproject has been advancing the technologies, and developing the hardware and software, needed to retire risks associated with technology, science, cost, and schedule.