Research Group for Molecular Biology

About Us

The focus of the Group is the use of molecular biology to study areas of importance to human health, agriculture and industry. The goals are to develop and maintain high quality, outside-funded research projects, to train graduate students, and to strengthen undergraduate teaching in this area.

Molecular techniques are being used to investigate a range of biological aspects: from bone biology and homeostasis to auxin production in rice and microbial interactions. Microorganisms under study include the anaerobic bacterium Dichelobacter nodosus, which causes footrot in sheep, filamentous fungi from the genus Aspergillus, and the fungus Thielaviopsis basicola, which causes black root rot in plants, Azospirillum, plant growth promoting soil bacteria and both pathogens and probiotic species associated with lobster aquaculture.

This work was published in 1995 (Gene 162:53-58) and attracted international attention, with an invitation to write a review for the leading journal in this field, Molecular Microbiology (Cheetham, B.F. and Katz, M.E., 1995, Mol. Microbiol. 18: 201-20). At about this time, it was discovered that, in several different bacteria, genes associated with virulence were located on genetic elements integrated into tRNA genes, and the concept of "Pathogenicity Islands" was proposed. They were subsequently invited to present their work at the 12 European Meeting on Bacterial Gene Transfer and Expression, in Siena, Italy, September, 1996, and to write a chapter for a book on Pathogenicity Islands and Other Mobile Virulence Elements (Publications, 1). The Molecular Microbiology review was cited 122 times in the period 1997-2004 (Science Citation Index). One aspect of the work was adapted for the improved diagnosis of footrot, and they have then filed a full patent application, and have received substantial industry funding to evaluate their new diagnostic test for which accreditation had been sought from SCAHLS in 2005/2006.

Associate Researchers

Introducing the Group's associate researchers

Dr David Backhouse

David's main research interests are in the ecology of soil fungi and in the epidemiology and management of plant diseases caused by soilborne fungi. David did my PhD on the biology of Botrytis species. This was followed by a postdoc at the University of Auckland working on biological control of onion white rot, and another postdoc at the University of Sydney working on the effects of farming practices on the health of wheat root systems. Since joining UNE in 1998 David has had funded research and supervised postgraduate projects on topics including:

  • Epidemiology and management of crown rot in wheat
  • Population genetics of Fusarium species from cereals
  • Effects of climate on the geographical distribution of fungi and plant diseases
  • Fungal-plant interactions in soilborne diseases
  • Biological control of soilborne diseases.

Monochramtic scan showing series of black dots with id labels and lines on x and y axis reading

Two-dimensional electrophoresis gel of proteins extracted from cotton root harvested after inoculation with Thielaviopsis basicola. Labelled proteins were found to be up-regulated following inoculation with the fungi.

Dr Joelle Coumans-Moens

My interest resides in the regulation of protein expression in response to external cues. Currently, my goal is to enhance short- and long-term plant disease management strategies through an understanding of cotton resistance mechanisms towards a soil-borne fungal pathogen Thielaviopsis basicola. We have found that cotton plants activate diverse defence responses following infection with T. basicola and we are currently investigating the possibility of triggering these responses through the application of plant defence elicitors. Defence can be induced through two regulatory pathways; the salicylic acid (SA) and jasmonic acid (JA)-dependent pathway. SA defence responses are often efficient against biotrophic pathogens, whereas the JA response is mostly effective against necrotrophic pathogens and insects. However, extensive cross-talk between the different signalling pathways is believed to fine-tune this inducible defence response leading to the most favourable response to the invader encountered. Using a proteomic approach, we anticipate identifying proteins expressed in cotton root following treatment with different elicitors providing a better understanding of the molecular mechanisms by which these elicitors protect plants against pathogens.


Book Chapters

Cheetham, B.F., Whittle, G., Ting, M., and Katz, M.E. (2010)Interactions between bacteriophage DinoHI and a network of integrated elements which control virulence in Dichelobacter nodosus, the causative agent of ovine footrot. In: Biocommunication of soil bacteria. Soil Biology Vol. 23. Witzany, G., Ed, Springer Publishing, New York, NY, Chapter 9, pp. 237-253.

Dalton, S. J., Harrison, M., Carroll, A. G., Smith, S. D. A., and Pereg, L. (2010). Spatial and temporal patterns of Australian subtropical white syndrome at eastern Australian reefs: host range, prevalence and progression of tissue necrosis. In 'Emerging infectious diseases: global trends, surveillance and eradication' (Ed. F. Columbus). Nova Science Publishers Inc: New York.

Katz, M.E. and Kelly, J.M. (2010) Glucose. In: Cellular and Molecular Biology of Filamentous Fungi. Borkovich, K. and Ebbole, D., Eds, American Society for Microbiology Press, Herndon, VA, Chapter 21, pp. 291-311.

Katz, M.E. and Cheetham, B.F. (2009) Isolation of nucleic acids from filamentous fungi. In: Handbook of Nucleic Acid Purification, Liu, D., Ed., CRC Press, Boca Raton, FL, Chapter 10, pp. 189-207

Refereed Journal Articles

Coumans J.V.F., Harvey J., Backhouse D.,Poljak A., Raftery M.J., Nehl D., Katz M.E., Pereg L. Proteomic assessment of host-associated microevolution in the fungus Thielaviopsis basicola, Environmental Microbiology, published on-line in advance of print, DOI: 10.1111/j.1462-2920.2010.02358.x.

Nonhebel, H.,Yuan, Y., Al-Amier, H., Pieck, M., Akor, E., Ahamed, A., Cohen, J. D., Celenza, J. L., Normanly, J. (2011) Redirection of tryptophan metabolism in tobacco by ectopic expression of an Arabidopsis indolic glucosinolate biosynthetic gene. Phytochemistry 72:37-48.

Coumans, P. D. J. Moens, A. Poljak, L. Peregand M. J. Raftery (2010). Plant extract induced changes in the proteome of the soilborne pathogenic fungus Thielaviopsis basicola. Molecular and Cellular Proteomics, 10:1573-1591.

Endo-Munoz L, Cumming A, Rickwood D, Wilson D, Cueva C, Ng C, Strutton G, Cassady AI, Evdokiou A, Sommerville S, Dickinson I, Guminski A & Saunders NA. (2010) Loss of osteoclasts contributes to development of osteosarcoma pulmonary metastases. Cancer Research. 15:7063-7072.

Dalton, S. J., Godwin, S., Smith, S. D. A., and Pereg, L. (2010). Australian subtropical white syndrome: A transmissible, temperature-dependent coral disease. Marine and Freshwater Research, 61:342-350.

Rahmanpour, S., Backhouse, D., & Nonhebel, H. M. (2010). Reaction of glucosinolate-myrosinase defence system in Brassica plants to pathogenicity factor of Sclerotinia sclerotiorum. European Journal of Plant Pathology, 128(4), 429-433.

Palanisamy, S. K.A., Fletcher, C., Tanjung, L., Katz, M.E.,and Cheetham, B.F. (2010) Deletion of the C-terminus of polynucleotide phosphorylase increases twitching motility, a virulence characteristic of the anaerobic bacterial pathogen Dichelobacter nodosus. FEMSMicrobiol. Lett. 302: 39-45.

Coumans, A. Poljak, M.J. Raftery, D. Backhouse and L. Pereg-Gerk (2009) Analysis of cotton (Gossypium hirsutum) root proteomes during a compatible interaction with the black root rot fungus Thielaviopsis basicola. Proteomics 9(2): 335-349.

Way K, Dinh H, Keene M, White K, Clanchy F, Lusby P, Roiniotis J, Cook A, Cassady AI, Curtis D & Hamilton J. (2009) The generation and properties of human macrophage populations from hemopoietic stem cells. Journal of Leukocyte Biology. 85:766-778.

Wu CKA, Pettit, AR., Toulson, S, Mackie EJ, Grøndahl L& Cassady AI. (2009) Analysis of in vivo responses to purified PHBV implanted in a murine tibial defect. Journal of Biomedical Materials Research Part A. 91:845-854.

Rahmanpour, S., Backhouse, D., & Nonhebel, H. M. (2009). Induced tolerance of Sclerotinia sclerotiorum to isothiocyanates and toxic volatiles from Brassica species. Plant Pathology, 58(3), 479-486.

Katz, M.E., Evans, C.J., Heagney, E.E., vanKuyk, P.A., Kelly, J.M., and Cheetham, B.F. (2009) Mutations in genes encoding sorting nexins alter production of intracellular and extracellular proteases in Aspergillus nidulans. Genetics 181: 1239-1247.

Tanjung, L.R., Whittle, G., Shaw, B.E., Bloomfield, G.A., Katz, M.E. and Cheetham, B.F. (2009). The intD mobile genetic element from Dichelobacter nodosus, the causative agent of ovine footrot, is associated with the benign phenotype. Anaerobe 15: 219-224.

Lång P, van Harmelen V, Rydén M, Kaaman, M, Carneheim C, Cassady AI, Hume DA, Andersson G & Arner P. (2008) Macrophages promote adipogenesis and obesity through secretion of monomeric tartrate-resistant acid phosphatase (TRAP).Plos One. 3(3):e1713.

Ripoll VM, MeadowsNM, RaggattLJ, ChangMK, CassadyAI & HumeDA. (2008) Microphthalmia Transcription Factor Regulates the Expression of the Novel Osteoclast Factor GPNMB.Gene. 413:32-41.

Hadler KS, Huber T, Cassady AI, Weber JE, Robinson J, Burrows A, Guddat LW, Hume D, Schenk, G & Flanagan J. (2008) Identification of a putative non-purple binuclear metalloesterase distantly related to plant purple acid phosphatases. BMC Research Notes. 1:78.

Katz, M. E., S. M. Bernardo, and B. F. Cheetham. (2008) The interaction of induction, repression and starvation in the regulation of extracellular proteases in Aspergillus nidulans: evidence for a role for CreA in the response to carbon starvation. Current Genetics54: 47-55.

Cheetham, B.F., Parker, D., Bloomfield, G.A., Shaw, B.E., Sutherland, M., Hyman, J.A., Druitt, J., Kennan, R.M., Rood, J.I. and Katz, M.E. (2008). Isolation of the bacteriophage DinoHI from Dichelobacter nodosus and its interactions with other integrated genetic elements. Open Microbiol. J. 2:1-9.

Cool SM, Kenny B, Wu A, Nurcombe V, Trau M, Cassady AI & Grøndahl L. (2007) Composite biomaterials for bone tissue regeneration: In vitro performance assessed by osteoblast proliferation, osteoclast adhesion and resorption and macrophage pro-inflammatory response. Journal of Biomedical Materials Research Part A. 82:599-610.

Meadows N, Sharma SM, Faulkner G, Ostrowski MC, HumeDA & Cassady AI. (2007) The expression of chloride channel 7 (CLCN7) and ostm1 in osteoclasts is co-regulated by microphthalmia transcription factor. Journal of Biological Chemistry. 282:1891–1904.

Bernardo, S.M.H., Gray, K.A., Todd, R.B., Cheetham, B.F. and Katz, M.E. (2007) Characterization of regulatory non-catalytic hexokinases in Aspergillus nidulans, Molec. Genet. Genomics 277: 519-532.

Katz, M.E., Gray, K.-A, and Cheetham, B.F. (2006) The Aspergillus nidulans xprG (phoG) gene encodes a putative transcriptional activator involved in the response to nutrient limitation. Fungal Genet. Biol., 43: 190-199.

Cheetham, B.F., Tanjung, L.R., Sutherland, M., Druitt, J., Green, G., McFarlane, J., Bailey, G.D., Seaman J.T, and Katz, M.E. (2006). Improved diagnosis of virulent ovine footrot using the intA gene. Vet. Microbiol., 116:166-174.

Flanagan JU, Cassady AI,Schenk G, Guddat LW & Hume DA. (2006) Identification and molecular modeling of a novel, plant-like, human purple acid phosphatase. Gene. 377:12-20.

SharmaSM, HuR, Bronisz A, Meadows N, Lusby P, Fletcher B, Hume DA, Cassady AI, & Ostrowski MC. (2006) Genetics and Genomics of Osteoclast Differentiation: Integrating Cell Signaling Pathways and Gene Networks. Critical Reviews in Eukaryotic Gene Expression. 16:253-278.

Wu ACK, GrøndahlL, JackKS, Foo MX, Trau M, HumeDA & Cassady AI. (2006) Reduction of the in vitro pro-inflammatory response by macrophages to poly(3-hydroxybutyrate-co-3-hydroxyvalerate). Biomaterials. 27:4715-4725.


Pereg-Gerk, L., Backhouse, D., Katz, M., Nehl, D and Driessen, S. (2007-2011) Linking cotton-pathogen molecular interactions and black root rot management. Cotton Research and Development Corp. $476,405.

Cheetham, B.F. and Katz, M.E. (2005-2008) Commercialisation of improved footrot diagnosis. Australian Wool Innovation, $441,161.

Pereg-Gerk, L., Backhouse, D, Katz, M. and Nehl, D.. (2004-2007) Molecular Factors determining Thielaviopsis basicola-cotton interactions leading to Black Root Rot disease. Cotton Research and Development Corp. $181,119

Forwood MR & Cassady AI. (2004-2006) Investigation of COX-2 regulation of bone turnover and mechanically induced bone formation by genetic overexpression in mice. NHMRC $432,500.

Cassady AI. (2005) Biocompatibility assessment of libraries of oral drug candidates capable of regulating osteoblasts and osteoclasts. Bone Medical Ltd. $88,000.

PhD Students

Honours Students

  • Rebecca Buckland (Katz) Completed 2012
  • Sarah Cooper (Katz) Completed 2012
  • Karina Bennett (Nonhebel) Completed 2011
  • Robert Gentile, Fungal genetic transformation (Pereg) Competed 2011

PhD Students

  • Sarah Cooper (2016) Microbial applications for sustainable crop production and managing soil health (Pereg)
  • Aimee Grace (2014) Investigation of methods for non-viral transformation of bovine cells to induce pluripotency (Cassady)
  • João Fidalgo, Characterization of the Role of Peroxisome Proliferator Activator Receptor (PPAR)-Delta in Osteoclast Biology (Cassady)
  • Salih Wajid (Katz/Walkden-Brown/Renz)
  • Evan Goulden (2011) Potential use of probiotics in ornate spiny lobster (Panulirus ornatus) larviculture (Pereg)
  • Getachew Mohammed Ali, Genetic factors involved in the pathogenicity of Thielaviopsis basicola towards cotton (Pereg/Katz/Backhouse)
  • Blkeas Jawad, Molecular Factors Involved in Pathogen Suppression by probiotic Bacteria (Pereg)
  • Ganisan Krishnen, Molecular interactions between plant growth promoting organisms and rice, submitted (Pereg with USYD)
  • Khanok-on Amprayn, Quantifying plant response to plant-growth promoting (PGP) organisms (Pereg with USYD)
  • Lisa Kidd (2008) Investigation of activated remodelling in the healing of experimental stress fractures and the influence of anti-inflammatory treatments (Cassady)
  • Simon Smart (2008) Carbon nanotube/thermoplastic polyurethane nanocomposites (Cassady)
  • Eleanor Leung (2008) Structure-function relationships in metal dependent enzymes(Cassady)
  • Arjuna Kumarasuriyar (2007) Exploring novel bioactive bone repair strategies (Cassady)
  • Andy Wu (2007) In vitro and in vivo characterization of cellular responses to PHBV and hydroxyapatite/PHBV composites as bone biomaterials (Cassady)
  • Nicholas Meadows (2006) The role of microphthalmia transcription factor (Mitf) in osteoclast gene regulation (Cassady)
  • Kapil Chousalkar (2008) Effects of infectious bronchitis virus on the oviduct of laying hens (Roberts/Walkden-Brown/Cheetham)
  • Katrin Renz (2008) In vitro and in vivo characterization of selected Australian isolates of Marek's disease virus (Wlakden-Brown/Islam/ Cheetham)
  • Suresh Kumar (2007) Molecular analysis of the role of polynucleotide phosphorylase in the virulence of Dichelobacter nodosus (Cheetham /Katz)
  • Aminul Islam (2006) Molecular detection and quantitative surveillance of Marek's disease viruses in broiler chickens and their environment (Walkden-Brown/Cheetham)
  • Elizabeth Farrell (2008) The biological and genetic variation amongst 25 Australian isolates of the nematophagous fungus Duddingtonia flagrans (Katz/Knox)
  • Yousef Abu Zaitoon (2010) Characterisation of the tryptamine pathway of auxin biosynthesis in developing rice grains (Nonhebel)
  • Siamak Rahmanpour, 2008 (Nonhebel/Backhouse)
  • Steve Dalton (2010) Stressors of Eastern Australian subtropical corals: Australian subtropical white syndrome and coral bleaching (Pereg)
  • Xingsheng Hou (2009) FlcA regulation of metabolism and stress response in Azospirillum brasilense Sp7 (Pereg)
  • Jason Moulynox (2009) Biocontrol agents for managing black root rot in Australian cotton(Pereg)
  • Amar Padney (2009) Microbiological and molecular factors involved in the interactions of disease suppressive bacteria Pantoea, Exigubacterium and Microbacterium with wheat (Backhouse/Pereg)
  • Scott Godwin (2008) The Pathology and Bacterial Ecology of Subtropical White Syndrome: A Disease of Scleractinian Corals in Subtropical Eastern Australia (Pereg)
  • Samiya Al-Jaaidi (2007) Transformation of Thielaviopsis basicola to study host-pathogen interactions(Pereg/Katz/Backhouse)

Contact Us

Dr Heather Nonhebel
Phone: +61 2 6773 2083Call through Skype