FY2020 Annual Report

Genomics and Regulatory Systems Unit
Professor Nicholas M. Luscombe

Abstract

1. Staff

Nicholas M. Luscombe, Professor (Adjunct)
Charles Plessy, Staff Scientist
Michael J. Mansfield, Research Scientist
Andrew W. Liu, Senior Technician
Aki Masunaga, Technician
Yongkai Tan, Technician
Aleksandra Bliznina, Graduate Student
Munissa Sadykova Graduate Student
Yuka Ozaki, Research Unit Administrator

2. Collaborations

3. Activities and Findings

4. Publications

4.1 Journals

Taguchi A, Nagasaka K, Plessy C, Nakamura H, Kawata Y, Kato S, Hashimoto K, Nagamatsu T, Oda K, Kukimoto I, Kawana K, Carninci P, Osuga Y, Fujii T. Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages. Sci Rep. 2020 Oct 22;10(1):17991. doi: 10.1038/s41598-020-75133-2. PMID: 33093512;PMCID: PMC7582169.

Wang K, Tomura R, Chen W, Kiyooka M, Ishizaki H, Aizu T, Minakuchi Y, Seki M, Suzuki Y, Omotezako T, Suyama R, Masunaga A, Plessy C, Luscombe NM, Dantec C, Lemaire P, Itoh T, Toyoda A, Nishida H, Onuma TA. A genome database for a Japanese population of the larvacean Oikopleura dioica. Dev Growth Differ. 2020 Aug;62(6):450-461. doi: 10.1111/dgd.12689. Epub　2020 Aug 14. PMID: 32677034.

Poulain S, Arnaud O, Kato S, Chen I, Ishida H, Carninci P, Plessy C. Machine-driven parameter screen of biochemical reactions. Nucleic Acids Res. 2020 Apr 17;48(7):e37. doi: 10.1093/nar/gkaa079. PMID: 32025730;PMCID: PMC7144897.

GO Bozdag, J Ono, JA Denton, E Karakoc, N Hunter, JY Leu, D Greig.　Breaking a species barrier by enabling hybrid recombination. Current Biology 31 (4), R180-R181

VG Lopez-Huerta, JA Denton, Y Nakano, O Jaidar, M Garcia-Munoz, .... Striatal bilateral control of skilled forelimb movement. Cell Reports 34 (3), 108651

JA Denton, CS Gokhale. Synthetic Symbiosis under Environmental Disturbances.mSystems 5 (3)

Bano, L., Kiel, M., Sales, G., Doxey, A. C., Mansfield, M. J., Wami, H. T., ... & Montecucco, C. (2020). Genome Sequence of the Fish Brain Bacterium Clostridium tarantellae. Microbiology resource announcements, 9(16). https://doi.org/10.1128/MRA.01575-19

Lobb, B., Hodgson, R., Lynch, M. D., Mansfield, M. J., Cheng, J., Charles, T. C., ... & Doxey, A. C. (2020). Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens. MSystems, 5(2). https://doi.org/10.1128/mSystems.00145-20

Aguiar, J. A., Tremblay, B. J., Mansfield, M. J., Woody, O., Lobb, B., Banerjee, A., ... & Hirota, J. A. (2020). Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue. European Respiratory Journal, 56(3). https://doi.org/10.1183/13993003.01123-2020

Bliznina, A., Masunaga, A., Mansfield, M. J., Tan, Y., Liu, A. W., West, C., ... & Luscombe, N. M. (2020). Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing. bioRxiv. https://doi.org/10.1101/2020.09.11.292656

Banerjee, A., Doxey, A. C., Tremblay, B. J. M., Mansfield, M. J., Subudhi, S., Hirota, J. A., ... & Mossman, K. (2020). Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus. Journal of General Virology, 101(12), 1251-1260. https://doi.org/10.1099/jgv.0.001491

Fantauzzi, M. F., Aguiar, J. A., Tremblay, B. J. M., Mansfield, M. J., Yanagihara, T., Chandiramohan, A., ... & Hirota, J. A. (2020). Expression of endocannabinoid system components in human airway epithelial cells: impact of sex and chronic respiratory disease status. ERJ open research, 6(4). https://doi.org/10.1183/23120541.00128-2020

Eckhard, U., Blöchl, C., Jenkins, B. G., Mansfield, M. J., Huber, C. G., Doxey, A. C., & Brandstetter, H. (2020). Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis. Scientific reports, 10(1), 1-13.https://doi.org/10.1038/s41598-020-76010-8

Mansfield, M. J., Tremblay, B. J., Zeng, J., Wei, X., Hodgins, H., Worley, J., ... & Doxey, A. C. (2020). Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B. PLoS pathogens, 16(12), e1009181. https://doi.org/10.1371/journal.ppat.1009181

Masunaga, A., Liu, A. W., Tan, Y., Scott, A., Luscombe, N. M. Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica. J. Vis. Exp.(160), e61279, doi:10.3791/61279 (2020).

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

Plessy, C. 2nd Dec 2020, 43rd annual meeting of the molecular biology society of Japan (MBSJ2020), online: Poster number 1LBA-006 on Flexibility of gene arrangement in the genome of Oikopleura dioica.