This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The 330 kb genome of Paramecium bursaria Chlorella Virus-1 (PBCV-1) has been completely sequenced. It was found to contain 373 large open reading frames (ORFs) that putatively code for proteins. About half of these ORFs have no counterparts in any of the databases. During this past year I arranged for the design and synthesis of 50-mer ssDNA probes for each of the 371 non-redundant ORFs. These PBCV-1 DNA probes have been spotted onto microarray plates by the Genomics Core Facility at the University of Nebraska Medical Center. I spent the past summer learning how to isolate total RNA from Chlorella cells infected with PBCV-1. I have now developed a protocol that yields high quality total RNA (A260/280 1.9, concentration 2 ?g/?L, formaldehyde RNA gels). I have collected total RNA from uninfected Chlorella cells (control), and from cells that have been infected with PBCV-1 for 30, 75, 120 and 240 minutes. Total RNA from all 5 groups have been sent to the Genomics Core Facility where they have been reverse transcribed, labeled with Cy3 and Cy5 dyes and competitively hybridized to the probes on the microarray plate. For example, the cDNA reverse transcribed from total RNA isolated from cells infected for 0 minutes (i.e., uninfected cells that contains only host RNA) were labeled with Cy3 (green), while cDNA reverse transcribed from total RNA isolated from cells infected for 30 minutes were labeled with Cy5 (red);the two groups of cDNAs were mixed and hybridized to the PBCV-1 probes on a microarray. Expression profiles for each gene are being developed. While the analysis is not yet complete, it is clear that some PBCV-1 mRNAs are expressed early, while others are expressed late. Perhaps the biggest surprise is the approximately 10% of the virus genome appears to be shared with its Chlorella host as evidenced by annealing of the uninfected (0 minutes) Chlorella cells to the PBCV-1 microarray probes. Those shared ORFs (genes) are now being characterized. Among the genes common to the virus and its host is the major viral coat protein.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Exploratory Grants (P20)
Project #
2P20RR016469-09
Application #
7960275
Study Section
Special Emphasis Panel (ZRR1-RI-4 (01))
Project Start
2009-05-01
Project End
2010-04-30
Budget Start
2009-05-01
Budget End
2010-04-30
Support Year
9
Fiscal Year
2009
Total Cost
$27,894
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
Barta, Cody L; Liu, Huizhan; Chen, Lei et al. (2018) RNA-seq transcriptomic analysis of adult zebrafish inner ear hair cells. Sci Data 5:180005
Liu, Huizhan; Chen, Lei; Giffen, Kimberlee P et al. (2018) Cell-Specific Transcriptome Analysis Shows That Adult Pillar and Deiters' Cells Express Genes Encoding Machinery for Specializations of Cochlear Hair Cells. Front Mol Neurosci 11:356
Wehrkamp, Cody J; Natarajan, Sathish Kumar; Mohr, Ashley M et al. (2018) miR-106b-responsive gene landscape identifies regulation of Kruppel-like factor family. RNA Biol 15:391-403
Lopez, Wilfredo; Page, Alexis M; Carlson, Darby J et al. (2018) Analysis of immune-related genes during Nora virus infection of Drosophila melanogaster using next generation sequencing. AIMS Microbiol 4:123-139
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
Lu, Guoqing; Luhr, Jamie; Stoecklein, Andrew et al. (2017) Complete Genome Sequences ofPseudomonas fluorescensBacteriophages Isolated from Freshwater Samples in Omaha, Nebraska. Genome Announc 5:
Azadmanesh, Jahaun; Trickel, Scott R; Weiss, Kevin L et al. (2017) Preliminary neutron diffraction analysis of challenging human manganese superoxide dismutase crystals. Acta Crystallogr F Struct Biol Commun 73:235-240
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
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
Bonham-Carter, Oliver; Thapa, Ishwor; From, Steven et al. (2017) A study of bias and increasing organismal complexity from their post-translational modifications and reaction site interplays. Brief Bioinform 18:69-84

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