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Professor David Adelson

Telephone +61 8 8313 7555
Email david.adelson@adelaide.edu.au
Fax +61 8 8313 4362
Building The Braggs
Floor/Room 2 11
Campus North Terrace
Org Unit School of Molecular and Biomedical Science

To link to this page, please use the following URL:
http://www.adelaide.edu.au/directory/david.adelson

Biography/ Background

1978 A.B (Biology, Cum Laude) University of California at San Diego, Revelle College.

1985 Ph.D. (Biomedical Science) John A. Burns School of Medicine, University of Hawaii at Manoa

1986 - 88 Postoctoral training, Dept of Zoology, Duke University.

1988 - 2001 Research Scientist - CSIRO. 

2001 - 2007 Associate Professor of Animal Genomics, Dept of Animal Science, Texas A&M University.

2007 - present Professor and Chair of Bioinformatics and Computational Genetics, School of Molecular and Biomedical Science.

2012 - present Zhendong Professor of Molecular Chinese Medicine and Director, Zhendong Australia - China Centre for Molecular Traditional Chinese Medicine.

Research Interests

Research interests are 1. genome evolution and architecture of mammals and 2. Elucidation of genetic networks that respond to Traditional Chinese Medicine.  Biological mechanisms underlying genome evolution are believed to originate with retrotransposon insertions that can ultimately lead to segmental (gene) duplications/deletions, incorporation of retrotransposons into protein coding genes (exaptation) or gene duplication via retro-gene formation.  The resulting "churning" of both non-protein coding regions and protein domains are believed to be two of the major forces that drive speciation and adaptation.  My current primary research aim is to understand the magnitude and rate of change associated with retrotransposon insertion. 

This is an important research problem both in terms of our understanding of evolutionary mechanisms and processes but also because these processe frequently give rise to mutations or structural variation affecting gene regulation and function.  These alterations can result in disease or alter economically important agricultural traits.  We have identified horizontal transfer of retrotransposons as a much more common event than previously realised and are pursuing the implications of this finding with respect to genome evolution in higher organisms.

Current research projects in genome evolution include characterizing the degree of horizontal gene transfer in vertebrates, model organism databases, data mining and determining the effect of disregulated retrotransposons on genome stability.

Current projects in the Zhendong Australia - China Centre for the Molecular Basis of Traditional Chinese Medicine include identifying the alterations to gene expresson networks induced by the Yanshu Injection, also referred to as the Compound Kushen Injection (CKI). The Yanshu injection is an aqueous extract of Kushen (Sophora flavescens) and Baituling (Smilax glabra) roots that contains a complex mixture of alkaloids, flavonoids and saponins, some of which have been demonstrated to kill cancer cells or boost the immune response. Yanshu injection is used as an adjunct to Western chemotherapy in the treatment of gastric and liver cancer in China.  The exact formulation of the Yanshu injection varies from batch to batch and existing specifications only indicate the minimum concentration of alkaloids required to pass quality control. This variation in bioactive content is a function of environmental effects such as different growth locales, precipitation, temperature that interact with the genotype of the plants to cause the production of varying levels of bioactives. The existing project plan for the Yanshu injection work is aimed at describing and quantifying the gene expression changes in immortalised cancer cell cultures as they undergo cell death induced by Yanshu. Whilst the primary objective of this work is to identify the multiplicity of pathways targeted by Yanshu in order to identify a likely molecular mechanism for its effect, this is only one aspect of this work. The other significant aspect of the work is to demonstrate a quantitative molecular fingerprint based on gene expression changes that can be used to assay the effect of different batches of Yanshu injection. The molecular fingerprint will serve as an enabling technology for agricultural research to improve yields and production methods of Kushen and Baituling.

Publications

Recent Publications (Since 2009)

  1. Adelson DL, Rayson JM, Edgar RC (2009) Characterization and Distribution of Retrotransposons and Simple Sequence Repeats In The Bovine Genome. Proc Natl Acad Sci 106(31), pp.12855-60.
  2. Satterfield C, Song G, Kochan K, Riggs P, Simmons R, Elsik C, Adelson DL, Bazer FW, Zhou H, and Spencer TE (2009) Discovery of candidate genes in the endometrium regulating ovine blastocyst growth and conceptus elongation. Physiol. Genomics 39(2):85-99. 
  3. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear T, Adelson DL, Penedo MCT , Bellone RR, Bailey E,  Mauceli E, Garber M, MacLeod JN, Sharpe T, Vogel J,  Andersson L, Antczak DF, Biagi T, Binns MM, Blöcker H, Chowdhary BP, Coleman SJ, Della Valle G, Distl O, Edgar RC, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Leeb T, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze  SG, Onofrio R, Pedroni S, Piras MF, Raison J, Raudsepp T, Rocchi M,  Røed KH, Ryder O, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JS, Zody MC,  Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Lander ES, and Lindblad-Toh K (2009) Genome sequence, comparative analysis and population genetics of the domestic horse. Science 326(5954):865-7.  
  4. Rios JJ, Fleming JG, Bryant UK, Carter CN, Huber JC, Long MT, Spencer TE, Adelson DL (2010) OAS1 and RNASEL Polymorphisms Are Associated With Susceptibility To West Nile Encephalitis In Horses. PLoS ONE 5(5): e10537. doi:10.1371/journal.pone.0010537.
  5. Adelson DL, Rayson JM, Edgar RC (2010) Characterization and Distribution of Retrotransposons and Simple Sequence Repeats In The Equine Genome.  Animal Genetics 41 (Suppl. 2):91–99. doi:10.1111/j.1365-2052.2010.02115.x
  6. Childers, C, Reese, J, Jaideep, S, Vile, D, Dickens, C, Childs, K, Salih, H, Bennett, A, Hagen D, Adelson, D, Elsik, C. (2010) Bovine Genome Database: Integrated Tools for Genome Annotation and Discovery. Nucleic Acids Research 39(1): 830-834.
  7. Appels, R, Adelson, DL, Moolhuijzen, P, Webster, R, Barrero, R, and Bellgard, M (2011) Genome studies at the PAG 2011 conference Funct Integr Genomics, 11:1-11.
  8. Ling, KH, Brautigan, PJ, Hahn, CH, Daish, T, Rayner, JR, Cheah, PS, Raison, JM, Piltz, S, Mann, JR, Mattiske, DM, Thomas, PQ, Adelson, DL and Scott, HS (2011) Deep sequencing analysis of the developing mouse brain reveals a novel microRNA BMC Genomics, 12:176.
  9. Vidale P, Piras FM, Nergadze FG, Bertoni L, Verini-Supplizi A, Adelson D, Guerin G and Giulotto E (2011) Chromosomal Assignment of Six Genes (EIF4G3, HSP90, RBBP6, IL8, TERT, and TERC) in Four Species of the Genus Equus. Animal Biotechnology, 22: 119–123. 
  10. Qu Z, Adelson DL (2012) Bovine ncRNAs Are Abundant, Primarily Intergenic, Conserved and Associated with Regulatory Genes. PLoS ONE 7(8): e42638. doi:10.1371/journal.pone.0042638
  11. Qu Z, Adelson DL (2012) Evolutionary conservation and functional roles of ncRNA. Front. Gene., doi: 10.3389/fgene.2012.00205
  12. Walsh, A, Kortschak, RD, Gardner, MG, Bertozzi, T and  Adelson DL (2012), Widespread horizontal transfer of Retrotransposons, Proc Natl Acad Scipublished ahead of print December 31, 2012,doi:10.1073/pnas.1205856110. 
  13. Qu Z, Adelson DL (2012) Identification And Comparative Analysis Of ncRNAs In Human, Mouse And Zebrafish Indicate A Conserved Role In Regulation Of Genes Expressed In Brain. PLoS ONE 7(12): e52275. doi:10.1371/journal.pone.0052275
  14. Fruzangohar M, Ebrahimie E, Ogunniyi AD, Mahdi LK, Paton JC, Adelson DL (2013) Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria. PLoS ONE 8(3):e58759. doi: 10.1371/journal.pone.0058759. 
  15. Ivancevic, AM, Walsh AM, Kortschak RD, Adelson DL (2013) Jumping the fine LINE between species: horizontal transfer of transposable elements in animals catalyses genome evolution. BioEssays 35(12):1071-82. doi: 10.1002/bies.201300072. 
  16. Roberts, ND, Kortschak, RD, Parker, WT, Schreiber, AW, Branford, S, Scott, HS, Glonek, G, Adelson, DL (2013) A Comparative Analysis of Algorithms for Somatic SNV Detection in Cancer. Bioinformatics doi: 10.1093/bioinformatics/btt375.
  17. Bellone, RR, Holl, H, Setaluri, V, Devi, S, Maddodi, N, Archer, S, Sandmeyer, L, Ludwig, A, Foerster, D, Pruvost, M, Reissmann, M, Bortfeldt, R, Adelson, DL, Lim, SL, Nelson, J, Haase, B, Engensteiner, M, Leeb, T, Forsyth, G, Mienaltowski, MJ, Hofreiter, M, Paijmans, JLA, Gonzalez-Fortes, G, Grahn, B, Brooks, SA (2013) LTR Driven Premature Poly-adenylation in TRPM1 Causes Congenital Stationary Night Blindness and Leopard Complex Spotting in Horse: An Ancient Example of Balancing Selection. PLoS ONE 8(10):e78280. doi: 10.1371/journal.pone.0078280.
  18. Fruzangohar, M, Kroeger, T, Adelson DL. (2013) Improved Part-of-Speech Tagging for Biological Articles using a Novel Suffix Analysis Method. PloS ONE8(10):e76042. doi: 10.1371/journal.pone.0076042.
  19. Mahdi, LK, Ebrahimie, E, Adelson, DL, Paton, JC, Ogunniyi, AD (2013) A Transcriptional Factor Contributes to Pathogenesis and Virulence in Streptococcus pneumonia. PLoS ONE 8(8):e70862. doi: 10.1371/journal.pone.0070862.
  20. Alanazi, I, Ebrahimie, E, Hoffmann, P, Adelson, DL. (2013) Combined gene expression and proteomic analysis of EGF induced apoptosis in A431 cells suggests multiple pathways trigger apoptosis. Apoptosis, (DOI) 10.1007/s10495-013-0887-6
  21. Lim, Sl, Kortschak, RD and Adelson, DL (2014) Discovery of a novel long terminal repeat (LTR2i_SS) in Sus Scrofa.  Animal Genetics 45(3):367-372. doi: 10.1111/age.12138. Epub 2014 Mar 12.
  22. Ebrahimi M, Aghagolzadeh P, Shamabadi N, Tahmasebi A, Alsharifi M, Adelson DL, Hemmatzadeh F, Ebrahimie E. (2014) Understanding the underlying mechanism of HA-subtyping in the level of physic-chemical characteristics of protein. PLoS One. 2014 May 8;9(5):e96984. doi: 10.1371/journal.pone.0096984. 
  23. Wang D, Qu Z, Adelson DL, Zhu JK, Timmis JN. (2014) Transcription of nuclear organellar DNA in a model plant system. Genome Biol Evol. 2014 May 27;6(6):1327-34. doi: 10.1093/gbe/evu111.
  24. Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton JA, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SM, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Fuentes-Utrilla P, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristiansen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, Oddy VH, Nicholas FW, McEwan JC, Kijas JW, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP. (2014) The sheep genome illuminates biology of the rumen and lipid metabolism. Science. 2014 Jun 6;344(6188):1168-73. doi: 10.1126/science.1252806.
  25. Gagliardi L, Schreiber AW, Hahn CN, Feng J, Cranston T, Boon H, Hotu C, Oftedal BE, Cutfield R, Adelson DL, Braund WJ, Gordon RD, Rees DA, Grossman AB, Torpy DJ, Scott HS.(2014) ARMC5 mutations are common in familial bilateral macronodular adrenal hyperplasia. J Clin Endocrinol Metab. 2014 Jun 6:jc20141265. [Epub ahead of print]
  26. Buckley RM, Adelson DL (2014) Mammalian genome evolution as a result of epigenetic regulation of transposable elements. Biomolecular Concepts.5(3):183–194, DOI: 10.1515/bmc-2014-0013,
  27. Fruzangohar M, Ebrahimie E, Adelson DL (2014) Application of Global Transcriptome Data in Gene Ontology Classification and Construction of a Gene Ontology Interaction Network. bioRxiv doi: http://dx.doi.org/10.1101/004911
  28. Kortschak RD, Adelson DL (2014) biogo: a simple high-performance bioinformatics toolkit for the Go language. bioRxiv doi: http://dx.doi.org/10.1101/005033

Entry last updated: Tuesday, 1 Jul 2014

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