This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The major goal of this research endeavor is to search for novel genes among the Nucleocytoplasmic Large DNA Viruses (NCLDV). The model virus of this group, Paramecium bursaria chlorella virus-1 (PBVC-1), which infect a green alga, has been sequenced, as have 7 other viruses of this group. These viruses contain many novel genes/proteins, some of which are the smallest known, several of which have commercial applications (next paragraph and section B.3.). PBCV-1 belongs to an ancient family of eukaryotic viruses that infect a chlorella-like green alga, a symbiont of Paramecium bursaria. PBVC-1 is a plaque-forming virus that has proven to be very amenable to laboratory study. James Van Etten, (JVE) the mentor/collaborator for this project (see section E below), has 25+ years working on this virus and has current NIH funding to investigate the DNA replication and gene expression of this virus. Furthermore, JVE has a network of collaborators who are studying a wide variety of PBVC-1 properties. This virus will be used as a reference against all newly sequenced viruses. The reasons for focusing on the NCLDV group of viruses are that they have, by definition, large genomes (the mimivirus encodes over 1000 proteins) and they are ancient. Their large genomes have come about by high jacking genes from a variety of sources and by gene duplication. Their ancient history and short life cycles have enabled them to evolve some of the smallest functional proteins, while other proteins have been shown to have medical importance (see section B.3.). For example, PBCV-1 has genes that encode proteins involved in DNA replication, recombination and repair, cell signaling, DNA restriction/modification, to name a few. The PBCV-1 type II DNA topoisomerase is the smallest one to be described to date and yet has very high activity levels (Lavrukhin et al., 2000). Topoisomerase II from PBCV-1 has been of interest in the study of cancer cells. Its restriction and methylation enzymes are commercially sold by New England Biolabs. This virus also encodes the smallest K+ channel protein. Plugge et al. (2000) have extensively characterized this protein from PBCV-1. Ion channel proteins affect ion concentrations and are the target of channel blockers for muscles, including the heart. As well, potassium ion (K+) channels play a key role in the proliferations of breast cancer (Abdul, Santo, and Hoosein, 2003). The primary objectives towards this proposal are: (i.) sequence additional viruses from this group;(ii.) conduct genomic, bioinformatic and phylogenetic analyses of these newly sequenced genomes. The analyses will be ongoing as new databanks and methods emerge. (iii.) Upon identification of novel or unusual genes, hand them off to others in the Van Etten lab and their colleagues who will clone, express and characterize them.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Exploratory Grants (P20)
Project #
5P20RR016469-11
Application #
8360012
Study Section
Special Emphasis Panel (ZRR1-RI-4 (01))
Project Start
2011-05-01
Project End
2012-04-30
Budget Start
2011-05-01
Budget End
2012-04-30
Support Year
11
Fiscal Year
2011
Total Cost
$6,624
Indirect Cost
Name
University of Nebraska Medical Center
Department
Genetics
Type
Schools of Medicine
DUNS #
168559177
City
Omaha
State
NE
Country
United States
Zip Code
68198
Gerald, Gary W; Thompson, Moriah M; Levine, Todd D et al. (2017) Interactive effects of leg autotomy and incline on locomotor performance and kinematics of the cellar spider, Pholcus manueli. Ecol Evol 7:6729-6735
Gong, Qiang; Wang, Chao; Zhang, Weiwei et al. (2017) Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data. Sci Rep 7:11301
Bouska, A; Zhang, W; Gong, Q et al. (2017) Combined copy number and mutation analysis identifies oncogenic pathways associated with transformation of follicular lymphoma. Leukemia 31:83-91
Lu, Guoqing; Luhr, Jamie; Stoecklein, Andrew et al. (2017) Complete Genome Sequences of Pseudomonas fluorescens Bacteriophages Isolated from Freshwater Samples in Omaha, Nebraska. Genome Announc 5:
Azadmanesh, Jahaun; Trickel, Scott R; Borgstahl, Gloria E O (2017) Substrate-analog binding and electrostatic surfaces of human manganese superoxide dismutase. J Struct Biol 199:68-75
Donze-Reiner, Teresa; Palmer, Nathan A; Scully, Erin D et al. (2017) Transcriptional analysis of defense mechanisms in upland tetraploid switchgrass to greenbugs. BMC Plant Biol 17:46
Quispe, Cristian F; Esmael, Ahmed; Sonderman, Olivia et al. (2017) Characterization of a new chlorovirus type with permissive and non-permissive features on phylogenetically related algal strains. Virology 500:103-113
Carlson, Kimberly A; Zhang, Chi; Harshman, Lawrence G (2016) A dataset for assessing temporal changes in gene expression during the aging process of adult Drosophila melanogaster. Data Brief 7:1652-7
Tietze, S M; Gerald, G W (2016) Trade-offs between salinity preference and antipredator behaviour in the euryhaline sailfin molly Poecilia latipinna. J Fish Biol 88:1918-31
Ericson, Brad L; Carlson, Darby J; Carlson, Kimberly A (2016) Characterization of Nora Virus Structural Proteins via Western Blot Analysis. Scientifica (Cairo) 2016:9067848

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