• An integrated systems and synthetic biology platform to expand the product spectrum of acetogens

    Project keywords

    Systems Biology, Manufacturing, Energy, Sustainability, Aviation fuel, Gas fermentation, Acetogens, Clostridia, Proteomics, Metabolomics, Transcriptomics

    Project summary

    Greenhouse gases that are currently environmental pollutants can be converted into aviation fuel and other valuable chemicals through bacterial fermentation. Some specialized bacteria, known as acetogens, are capable of fixing CO, CO2 and H2 and naturally convert it into ethanol and acetate. Using systems and synthetic biology we can fundamentally understand the metabolism of these organisms to improve the scope of its products into higher value-added molecules. This project aims to construct the world’s first systems biology platform for actegens to understand and overcome fundamental energy limitations in their metabolism. Achieving this aim will be of direct relevance to the aviation industry in Australia on their path to deliver sustainable jet-fuels.

    Publications

    Marcellin E, Behrendorff JB, Nagaraju S, DeTissera S, Segovia S, Palfreyman RW, Daniell J, Licona-Cassani C, Quek LE, Speight R, Hodson MP, Simpson SD, Mitchell WP, Köpke M, Nielsen LK (2016) Low carbon fuels and commodity chemicals from waste gases – Systematic approach to understand energy metabolism in a model acetogen. Green Chemistry. Accepted 05.01.2016.

    Project contacts

    Lead investigator Dr Esteban Marcellin, Professor Lars Nielsen
    Research group AIBN Systems & Synthetic Biology
    Contact email e.marcellin@uq.edu.au

     

    Project keywords Systems Biology, Manufacturing, Energy, Sustainability, Aviation fuel, Gas fermentation, Acetogens, Clostridia, Proteomics, Metabolomics, Transcriptomics Project summary Greenhouse gases that are currentl...
  • Baculovirus biopesticides

    Project keywords

    Systems Biology, Systems Biotechnology, Sustainability, Fermentation, Baculovirus, Biopesticide

    Project summary

    Many of the most significant pests of agriculture and forestry, and vectors of human disease, have developed resistance to multiple conventional chemical insecticides; six species now account for more than US$5 billion worth of chemical insecticides (see Table 1). At the same time, pesticides based on new chemistries has become harder and more costly to develop, register and commercialise. "Wild-Type" Baculoviruses are one of the most promising biocontrol options for insect pests resistant to chemical insecticides, since the hosts are rarely able to develop resistance. However, conventional production in insectaries do not offer the necessary scale benefit to compete with selective chemicals.

    We are developing an in vitro (within bioreactors) production process that can produce large quantities of Baculovirus Biopesticides at costs comparable to selective chemicals (i.e. $20/Ha). It has the potential to transform agriculture, allowing farmers to choose an insect control option that is safe and efficacious to use, as well as economically and environmentally superior to chemicals. The project combines conventional biochemical engineering R&D with a systems biology approach to identify process parameters as well as cell line gene targets for yield improvements.

    Table 1: Economically important insect pests (Crop Protection Compendium 2006)1
    Insect pests Infected regions Effect Pesticides (US$/year)
    Helicoverpa Complex:(armigera, zea,virescens, assulta) Africa, Asia- Pacific, Europe, Middle East, North and South America Maize, sorghum, soybean, cotton, sunflower, pulses, hort., tobacco, $1.7 Billion
    Diamondback moth (Plutella xylostella) Africa, Asia- Pacific, Europe, Middle East, North and South America crucifers, particularly cabbages, broccoli and cauliflowers $1 Billion
    Spodoptera Species (exigua,frugiperda, littoralis, litura) Asia, Middle East, North and South America cotton, soybeans, sugar beet, lucerne, maize $800 Million
    Culex culex mosquitos (C.nigripalpus, C.tarsalis etc) Temperate regions of Europe and North America Encephalitis &. West Nile River Virus > 7,000 cases in US in 2003 $700 Million
    Codling Moth (Cydia pomonella) Australia, Europe, Central and South America pome fruit (i.e. apple, pear) $500 Million
    Velvetbean Caterpillar (Anticarsia gemmatalis) Central and South America beans (e.g. soybean) $350 Million

    1 Crop Protection Compendium. 2006. Reports on Helicoverpa, Spodoptera, Plutella, Cydia, Anticarsia and Culex. http://www.cabicompendium.org/cpc/datasheet.asp?CCODE=HELIAR&COUNTRY=0. Accessed 2007 April 21.

    Publications

     

    Huynh HT, Tran TT, Chan LC, Nielsen LK, Reid S (2015) Decline in Helicoverpa armigera nucleopolyhedrovirus occlusion body yields with increasing infection cell density in vitro is strongly correlated with viral DNA levels. Arch Virol 160: 2169-80. PMID: 26092423

    Huynh HT, Tran TT, Chan LC, Nielsen LK, Reid S (2015) Effect of the peak cell density of recombinant AcMNPV-infected Hi5 cells on baculovirus yields. Appl Microbiol Biotechnol 99:1687-1700. PMID: 25472440

    Matindoost L, Hu H, Chan LC, Nielsen LK, Reid S (2014) The effect of cell line, phylogenetics and medium on baculovirus budded virus yield and quality. Arch Virol. 159: 91-102. PMID: 23884632

    Nguyen Q, Nielsen LK, Reid S (2013) Genome Scale Transcriptomics of Baculovirus-Insect Interactions. Viruses 5: 2721-2747. PMID: 24226166. PMC3856412

    Nguyen QH, Chan LCL, Nielsen LK, Reid S (2013) Genome scale analysis of differential mRNA expression of Helicoverpa zea insect cells infected with a H. armigera baculovirus. Virology 444: 158-170. PMID: 23827436

    Huynh HT, Tran TTB, Chan LCL, Nielsen LK, Reid S  (2013) Decline in baculovirus-expressed recombinant protein production with increasing cell density is strongly correlated to impairment of virus replication and mRNA expression. Appl Microbiol Biotechnol 97:5245–5257. PMID: 23519736

    Matindoost L, Chan LCL, Qi YM, Nielsen LK, Reid S (2012) Suspension culture titration: A simple method for measuring baculovirus titers. Journal of Virological Methods 183: 201–209. PMID: 22561639

    Huynh HT, Chan LCL, Tran TTB, Nielsen LK, Reid S  (2012) Improving the robustness of a low-cost insect cell medium for baculovirus biopesticides production, via hydrolysate streamlining using a tube bioreactor-based statistical optimization routine. Biotechnology Prog 28: 788-802. PMID: 22323401

    Nguyen QH, Palfreyman RW, Chan LCL, Reid S, Nielsen LK (2012) Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions. PloS ONE 7(5):e36324. PMID: 22629315. PMC3356360

    Tran TTB, Dietmair S, Chan LCL, Huynh HT, Nielsen LK, Reid S (2012) Development of quenching and washing protocols for quantitative intracellular metabolite analysis of uninfected and baculovirus-infected insect cells. Methods 56: 396-407. PMID: 22166686

    Nguyen Q, Qi YM, Wu Y, Chan LCL, Nielsen LK, Reid S (2011) In vitro production of Helicoverpa baculovirus biopesticides - Automated selection of insect cell clones for manufacturing and systems biology studies. J. Virol. Meth. 175: 197-205. PMID: 21616093.

    Pedrini MRS, Reid S, Nielsen LK, Chan LCL (2010) Kinetic characterization of the Group II Helicoverpa armigera nucleopolyhedrovirus propagated in suspension cell cultures: implications for development of a biopesticides production process. Biotechnology Progress 27: 614-24. PMID: 21644255.

    Chen LCL, Reid S, Nielsen LK (2010) Baculovirus virus kinetics in insect cell culture. In: Encyclopedia of Industrial Biotechnology: Bioprocess, Bioseparation, and Cell Technology, ed. MC Flickinger. John Wiley & Sons. ISBN: 978-0-471-79930-6. Publication date: March 2010. 

    Pedrini MRD, Chan LCL, Nielsen LK, Reid S, (2006) In vitro production of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus. Brazilian Archives of Biology and Technology 49: 35-41SI.

    Pedrini MRD, Christian P, Nielsen LK, Reid S, Chan LCL (2006) Importance of virus-medium interactions on the biological activity of wild-type Heliothine nucleopolyhedroviruses propagated via suspension insect cell cultures. Journal of Virological Methods 136:267-272.

    Haas R, Nielsen LK (2005) A Physiological Product-Release Model for Baculovirus Infected Insect Cells. Bioengineering & Biotechnology 91: 768-772.

    Pedrini MRS, Nielsen LK, Reid S, Chan LCL (2005) Properties of a unique mutant of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus that exhibits both Many Polyhedra and Few Polyhedra phenotypes upon extended serial passaging in cell cultures. In Vitro Cellular & Developmental Biology – Animal 41:289-297.

    Project contacts

    Lead investigator Dr Steve Reid, Professor Lars Nielsen
    Research group AIBN Systems & Synthetic Biology
    Contact email steven.reid@uq.edu.au

     

     

    Project keywords Systems Biology, Systems Biotechnology, Sustainability, Fermentation, Baculovirus, Biopesticide Project summary Many of the most significant pests of agriculture and forestry, and vectors of human disease...
  • Beer Systems Biology

    Project keywords

    Systems Biology, Systems Biotechnology, Manufacturing, Beer

    Project summary

    Humankind has been brewing beer - or what could reasonably pass as beer - for at least 5,000 years. We know a great deal about the bioprocess requirements for beer brewing, but we know much less about the biology. Beer brewing requires three different living organisms: barley, hops, and yeast. We are using systems biology to investigate the interactions between these three different organisms throughout the brewing process. These interactions are critical for a number of different beer quality trains, including foam quality, staling, flavours and aromas.

    Project contacts

    Lead investigator Dr Claudia Vickers
    Research group AIBN Systems & Synthetic Biology
    Contact email c.vickers@uq.edu.au
    Project keywords Systems Biology, Systems Biotechnology, Manufacturing, Beer Project summary Humankind has been brewing beer - or what could reasonably pass as beer - for at least 5,000 years. We know a great deal about t...
  • Blood cell production

    Project keywords

    Cell and Tissue Engineering, Systems Biology, Systems Biotechnology, Manufacturing, Health, Blood, Cancer, Stem Cells

    Project summary

    Millions of people are saved every year through the transfusion of blood products. Supported by the generosity of donors, transfussion of blood products demonstrate that inexpensive, generic cell therapies are possible. However, some blood cells are difficult to obtain from donors and this project develops bioprocesses suitable for routine clinical scale manufacture of blood cells from haematopoietic progenitor cells (HPC).

    Ex vivo manufacture of neutrophils

    Many anti-cancer drugs are so toxic that the body's blood generating tissues are severely damaged. When this happens, the number of infection fighting neutrophils (a type of white blood cell) can become so low that life-threatening fungal and bacterial infections occur. This condition is known as neutropaenia, and is a major cause of chemotherapy associated morbidity and mortality. By manufacturing neutrophils ex vivo, and giving these to chemotherapy patients, it may be possible to prevent neutropaenia and associated infections.

    Dose-intensive chemotherapy results in an obligatory period of neutropaenia (less than 0.1 x 109 neutrophils/L of whole blood), during which patients are at high risk of infection. While transfusion support with donor neutrophils appears to be an obvious solution to the problem (analogous to red blood cell and platelet transfusions for anaemia and thrombocytopaenia), obtaining sufficiently large numbers of neutrophils for efficacious dosing is challenging. The limited number of neutrophils that can be obtained from a single donor, combined with an inability to store neutrophil collections, results in a single dose/donation situation at best. Neutrophil transfusion is practised in only a few specialist centres around the world, and only in a therapeutic setting. Ideally, neutrophils should be provided as infection prophylaxis to all patients undergoing chemotherapy associated with severe neutropaenia.

    Several research groups have trialed the administration of ex vivo expanded haematopoietic progenitor cells in an attempt to accelerate recovery of endogenous neutrophil production. While clinical benefit was obtained, this approach does not address the imbalance between supply and demand. Precursor cells retain the ability to differentiate into a variety blood cell types, some of which are linked to immunological rejection and graft-versus-host disease (GVHD). As such these products can only be used in an autologous setting, or for recipients that are immunologically matched and receiving immunosuppressive treatments. Thus, a single HPC donation can provide only a single dose of transfusable precursor cells.

    In a combination of the two approaches described above (transfusion of donor derived neutrophils and ex vivo expansion), we have developed a bioprocess for ex vivo production of a mature neutrophil product. A readily available supply of neutrophils could enable routine administration as infection prophylaxis in chemotherapy patients. Routine production of neutrophils for clinical use depends on the availability of cultivation system capable of operating at 10’s to 100’s of litres. By screening multiple culture parameters, we developed and optimized a process allowing us to conduct multi litre neutrophil cultures in Wave bioreactors. We are able to obtain cell yields equivalent to as many 20 – 40 doses of neutrophils from a single HPC donation. The process itself is amenable to routine production of a therapeutic product and has been demonstrated at volumes up to 10 L. This is the first ever demonstration of clinical scale manufacture of neutrophils from HPC. The process is currently undergoing pre-clinical evaluation at the Centre for Commercialization of Regenerative Medicine (CCRM) in Toronto.

    High efficiency generation of RBC from HPC

    Increasing demand for transfusable red blood cells is paralleled by increasingly stringent donor exclusion criteria and prevalence of blood borne disease, placing pressures on global blood supply. Logistical considerations and donor distribution further hinder supply, with only 45% of whole blood donations collected in regions accounting for 80% of world population. It has been proposed for some time that ex vivo manufactured RBC could provide a secure and safe alternative to donor RBC. While in principle this is true, the numbers of cells that are required to have any significant impact are extremely large. A number of processes have been developed for the generation of RBC from umbilical cord blood derived HPC, but the methods used yield only several transfusion units per donation at best, and are not well suited to routine manufacture. In order to have any meaningful impact on global blood supply, it would be necessary to generate several hundreds of units of RBC from a single umbilical cord blood donation.

    We are developing high efficiency culture methods for production of very large numbers of RBC from umbilical blood derived HPC. We have developed a culture process capable of generating over 200 RBC units/donation. In conjunction with the development of advanced bioprocess technologies, these methods could enable large scale manufacture of RBC. While it will be many years before we see ex vivo manufactured RBC replacing routine donor blood transfusion used in the clinic, development of a high yield process may find application in the supply of rare blood types.

    Publications

    Schwaber JL, Brunck ME, Levesque JP, Nielsen LK (2016) Filling the void: allogeneic myeloid cells for transplantation. Current Opinion in Hematology 23: 72-7. PMID: 26554894

    Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KAL, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME (2015) Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Nature Methods 12: 339-342. PMID: 25751143

    Mercer TR, Clark MB, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS (2015) Genome-wide discovery of human splicing branchpoints. Genome Res 25: 290-303. PMID: 25561518

    Brunck MEG, Andersen SB, Timmins NE, Osborne GW, Nielsen LK (2014) Absolute counting of neutrophils in whole blood using flow cytometry. Cytometry 85: 1057-64. PMID: 24995861.

    Brunck MEG, Nielsen LK (2014) Next generation cell therapies to prevent infections in neutropenic patients. Stem cells translational medicine 3: 541-548. PMID: 24598780

    Peatey CL, Watson JA, Trenholme KR, Brown CL, Nielsen LK, Guenther M, Timmins NE, Watson GS, Gardiner DL (2013) Enhanced gametocyte formation in erythrocyte progenitor cells: a site specific adaptation by Plasmodium falciparum. J Infect Dis 208: 1170-1174. PMID: 23847056

    Doran M, Aird I, Marturana F, Timmins NE, Atkinson K, Nielsen LK (2012) Bioreactor for Blood Production. Cell Transplantation 21: 1235-1244. PMID: 22405378

    Timmins NE, Nielsen LK (2012) Large scale manufacture of blood cells. In N. Jenkins, N Barron, PM Alves (Ed.) Proceedings of the 21st Annual Meeting of the European Society for Animal Cell Technology (ESACT), Dublin, Ireland, June 7-10, 2009 (pp. 557-571) Dordrecht, Netherlands: Springer.

    Timmins NE, Athanasas S, G?nther M, Buntine P, Nielsen LK (2011) Ultra high yield manufacture of red blood cells from hematopoietic stem cells. Tissue Engineering, Part C 17: 1131-7. PMID: 21736478.

    Timmins NE, Nielsen LK (2011) Manufactured RBC - rivers of blood, or an oasis in the desert? Biotechnology Advances 29: 661-6. PMID: 21609758.

    Marturana F, Timmins NE, Nielsen LK (2011) Short term exposure of umbilical cord blood CD34+ cells to GM-CSF early in culture improves ex vivo expansion of neutrophils. Cytotherapy 13: 366-77. PMID: 20860426.

    Osiecki M, Ghanavi P, Atkinson K, Nielsen LK, Doran M (2010) The Ascorbic Acid Paradox. Biochemical and Biophysical Research Communications 400: 466-470. PMID: 20732307

    Doran MR, Markway B, Clark A, Athanasas-Platsis S, Brooke G, Atkinson K, Nielsen LK, Cooper-White JJ (2010) Membrane Bioreactors Enhance Microenvironmental Conditioning and Tissue Development. Tissue Engineering Part C: Methods. 16:407-415. PMID: 19622005.

    Timmins NE, Palfreyman E, Marturana F, Dietmair S, Luikenga S, Lopez G, Fung YL, Minchinton R, Nielsen LK (2009) Clinical Scale Ex vivo Manufacture of Neutrophils from Hematopoietic Progenitor Cells. Biotechnol Bioeng 104:832-40. PMID: 19591208.

    Timmins NE, Nielsen LK (2009) Blood cell manufacture: current methods and future challenges. Trends Biotechnol 27:415-422. PMID: 19500866.

    Doran MR, Markway BD, Aird IA, Rowlands AS, George PA, Nielsen LK, Cooper-White JJ (2009) Surface-bound stem cell factor and the promotion of hematopoietic cell expansion. Biomaterials 30:4047-52. PMID: 19481255.

    Hines M, Nielsen LK, Cooper-White J (2008) The hematopoietic stem cell niche: what are we trying to replicate? Journal of Chemical Technology and Biotechnology 83: 421-443. doi: 10.1002/jctb.1856

    Peng JC, Hyde C, Pai S, O’Sullivan BJ, Nielsen LK, Thomas R (2006) Monocyte-derived DC primed with TLR agonists secrete IL-12p70 in a CD40-dependent manner under hyperthermic conditions. Journal of Immunotherapy 29:606-615.

    Peng JC, Abu Bakar S, Richardson MM, Jonsson JJ, Frazer IH, Nielsen LK, Morahan G, Thomas R (2006) IL10 and IL12B polymorphisms each influence IL-12p70 secretion by dendritic cells in response to LPS. Immunology and Cell Biology 84: 227-232. doi:10.1111/j.1440-1711.2006.01419.x

    Peng JC, Thomas R, Nielsen LK (2005) Generation and maturation of DC for clinical application under serum-free conditions. Journal of Immunotherapy 28:599-609.

    Project contacts

    Lead investigator Professor Lars Nielsen
    Research group AIBN Systems & Synthetic Biology
    Contact email lars.nielsen@uq.edu.au

     

    Production of blood cells from haematopoietic stem cells
  • Carbon Flow through Mesophyll and Bundle Sheath Cells of Sugarcane to Produce Poly-3-Hydroxybutyrate

    Project keywords

    Cell and Tissue Engineering, Systems Biology, Systems Biotechnology, Materials, Manufacturing, Sustainability, Sugarcane, Renewable, Polyhydroxybutyrate, Transgenic, Sustainable, Biopolymer, Biofactory, Synthetic biology, Metabolic engineering

    Project summary

    This project focuses on producing the biodegradable plastic polyhydroxybutyrate in the leaves of sugarcane at commercially relevant levels. This biodegradable plastic is currently produced by bacterial fermentation, however in planta production is expected to provide economies of scale and make the polymer more cost competitive with petroleum based plastics. A systems biology approach is being used to understand how polymer production affects central metabolism so that polymer production can be fine-tuned. A major milestone was recently achieved as polymer production in sugarcane exceeded the level considered necessary for commercial viability. The project will next focus on risk proofing the plastic producing sugarcane against any potential biomass penalty resulting from the introduction of the novel carbon sink.

    Publications

    McQualter RB, Bellasio C, Gebbie LK, Petrasovits LA, Palfreyman RW, Hodson MP, Plan MR, Blackman DM, Brumbley SM, Nielsen LK (2015) Systems biology and metabolic modelling unveils limitations to polyhydroxybutyrate accumulation in sugarcane leaves; lessons for C4 engineering. Plant Biotechnology Journal. Accepted, 16.04.2015. PMID: 26015295

    Dal'Molin CGDO, Quek LE, Saa PA, Nielsen LK (2015) A multi-tissue genome-scale metabolic modelling framework for the analysis of whole plant systems. Front. Plant Sci. 6:4. PMID: 25657653

    McQualter RB, Petrasovits LA, Gebbie LK, Schweitzer D, Blackman DM, Plan MR, Hodson MP, Riches JD, Snell KD, Brumbley SM, Nielsen LK (2015) The use of an acetoacetyl-CoA synthase in place of a β-ketothiolase enhances poly-3-hydroxybutyrate production in sugarcane mesophyll cells. Plant Biotechnology Journal 13: 700-7. PMID: 25532451

    McQualter RB, Somleva MN, Gebbie LK, Li X, Petrasovits LA, Snell KD, Nielsen LK, Brumbley SM (2014) Factors affecting polyhydroxybutyrate accumulation in mesophyll cells of sugarcane and switchgrass. BMC Biotechnology 14: 83.PMID: 25209261. Online.

    Petrasovits LA, McQualter RB, Gebbie L, Blackman D, Nielsen LK, Brumbley SM (2013) Chemical inhibition of Acetyl Coenzyme A Carboxylase as a strategy to increase polyhydroxybutyrate yields in transgenic sugarcane. Plant Biotechnol J 11: 1146-1151. PMID: 24112832

    O’Neill BP, Purnell MP, Kurniawan ND, Cowin GJ, Galloway GJ, Nielsen LK, Brumbley SM (2013) Non-Invasive Monitoring of Sucrose Mobilization from Culm Storage Parenchyma by Magnetic Resonance Spectroscopy. Bioscience, Biotechnology, and Biochemistry 77:487-496. PMID: 23470752

    O’Neill BP, Purnell MP, Nielsen LK, Brumbley SM (2012) RNAi-mediated abrogation of trehalase expression does not affect trehalase activity in sugarcane. SpringerPlus 1:74. PMID: 23539210. PMC3606522

    O’Neill BP, Purnell MP, Anderson DJ, Nielsen LK, Brumbley SM (2012) Sucrose mobilisation in sugarcane stalk induced by heterotrophic axillary bud growth. Tropical Plant Biology 5:173-182.

    Petrasovits LA, Zhao L, McQualter RB, Snell KD, Somleva MN, Patterson NA, Nielsen LK, Brumbley SM (2012) Enhanced polyhydroxybutryate production in transgenic sugarcane. Plant Biotechnol J 10: 569-578..PMID: 22369516

    Anderson DJ, Gnanasambandam A, Williams E, O’Shea MG, Nielsen LK, Brumbley SM (2011) Synthesis of short-chain-length/medium-chain length polyhydroxyalkanoate (PHA) copolymers in peroxisomes of transgenic sugarcane plants. Tropical Plant Biology 4: 170-184.

    de Oliveira Dal'molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010) C4GEM - Genome-Scale Metabolic Model to study C4 plant metabolism. Plant Physiol. 154:1871-85. PMID: 20974891.

    de Oliveira Dal'molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010) AraGEM - a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis thaliana. Plant Physiol. 152: 579–589.  PMID: 20044452.

    Gnanasambandam A, Anderson DJ, Purnell M, Nielsen LK, Brumbley SM (2008)The N-terminal presequence from F1-ATPase -subunit of Nicotiana plumbaginifolia efficiently targets green fluorescent fusion protein to the mitochondria in diverse commercial crops. Functional Plant Biology 35: 166-170.

    Brumbley SM, Purnell MP, Petrasovits LA, Nielsen LK, Twine PH (2007) Developing the sugarcane biofactory for high-value biomaterials. Int Sugar J 109: 5-15.

    Purnell MP, Petrasovits LA, Nielsen LK, Brumbley SM (2007) Spatio-temporal characterisation of polyhydroxybutyrate accumulation in sugarcane. Plant Biotechnology Journal 5:173-184. doi: 10.1111/j.1467-7652.2006.00230.x

    Petrasovits LA, Purnell MP, Nielsen LK, Brumbley SM (2007) Production of polyhydroxybutyrate in sugarcane. Plant Biotechnology Journal 5:162-172. doi: 10.1111/j.1467-7652.2006.00229.x

    Brumbley SM, Twine PE, Nielsen LK (2006) Plastics from Plant Cells: The High-Carb Economy. Australasian Science 27:19-22. 

    Project contacts

    Lead investigator Professor Lars Nielsen
    Research group AIBN Systems & Synthetic Biology
    Contact email lars.nielsen@uq.edu.au

     

    We are studying the potential use of "green plants" as manufacturing plants for making useful chemicals. The aim of this project is to produce polyhydroxybutyrate (PHB) in genetically modified sugarcane plants at commercially significant levels.
  • Improving clostridial toxoid production through molecular fermentation maps

    Project keywords

    Systems Biology, Health, Manufacturing, Toxoid, Clostridia, Livestock, Vaccine, Proteomics, Metabolomics, Transcriptomics

    Project summary

    Toxoid vaccines are used routinely in the livestock industry to prevent animal-disease caused by pathogenic clostridia. Vaccines are produced using batch fermentation processes, which have undergone limited optimization over the past five decades. Low titres and frequent batch failures greatly affect capital utilization and represent a significant cost factor. This project uses high-throughput chemistry (omics) to produce ‘molecular maps of fermentation’, which will be used to design a new generation of superior fermentation processes. Achieving the aims will be of direct relevance to diagnose causes of batch failure (e.g., raw material failures) and engineer productive, high density fermentation for the production of toxins use in vaccine formulation to prevent multiple animal diseases.

    Project contacts

    Lead investigator Dr Esteban Marcellin, Professor Lars Nielsen
    Research group AIBN Systems & Synthetic Biology
    Contact email e.marcellin@uq.edu.au
    Project keywords Systems Biology, Health, Manufacturing, Toxoid, Clostridia, Livestock, Vaccine, Proteomics, Metabolomics, Transcriptomics Project summary Toxoid vaccines are used routinely in the livestock industry to pr...
  • Isoprenoid Biofuels and Industrial Biochemicals

    Project keywords

    Systems Biology, Systems Biotechnology, Energy, Materials, Manufacturing, Sustainability, Sucrose, Renewable, Isoprenoids, Synthetic biology, Metabolic engineering

    Project summary

    Isoprenoids are a very large class of natural products. Their chemical and structural diversity lends them to a wide variety of industrial applications (e.g. as pharmaceuticals, fuels, rubbers, nutraceuticals, agricultural chemicals, flavours, fragrances, colorants, etc.). We are interested in several industrially-useful isoprenoids. Examples include isoprene, a C5 hydrocarbon that can be polymerised to make synthetic rubber, and various C10 (monoterpene) and C15 (sesquiterpene) hydrocarbons that can be used to produce bio-jet fuel/bio-diesel (and in other applications). Production of these compounds is non-trivial, since they are not naturally made by E. coli and yeast, and some, notably the monoterpenes, are highly toxic.

    Isoprenoids are produced by two distinct metabolic pathways: the mevalonate (MVA) pathway present in all higher organisms as well as yeast and the methylerythritol phosphate (MEP) pathway found in many microbes and plastids. We are using synthetic biology engineering approaches to improve carbon flux through both of these pathways for production of industrially-useful isoprenoids. The aim of this program is to increase conversion of bioprocess feedstocks (such as sucrose) into desired end products by whole cell biocatalysts. We have reconstructed synthetic pathways with improved flux in both yeast and E. coli. We are also examining approaches to minimise carbon loss to competing pathways, redirect carbon into the pathways, and scavenge carbon lost to nonspecific reactions. 

    Publications

    Bongers M, Chrysanthopoulos PK, Behrendorff JBYH, Hodson MP, Vickers CE, Nielsen LK (2015) Systems analysis of methylerythritol-phosphate pathway flux in E. coli: insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite. Microbial Cell Factories 14: 193. PMID: 26610700

    Brennan TCR, Williams TC, Schulz BL, Palfreyman RW, Krömer JO, Nielsen LK (2015) Evolutionary engineering improves tolerance for replacement jet fuels in Saccharomyces cerevisiae. Appl Environ Microbiol 81: 3316 –3325. PMID: 25746998

    Vickers CE, Behrendorff JBYH, Bongers M, Brennan TCR, Bruschi M, Nielsen LK (2015) Production of industrially relevant isoprenoid compounds in engineered microbes. In: Kamm B (ed) Microorganisms in Biorefineries. Series: Microbiology Monographs, vol. 26. Chapter 11: 303-334.

    Vickers CE, Bongers M, Liu Q, Delatte T, Bouwmeester H (2014) Metabolic engineering of volatile isoprenoids in plants and microbes. Plant, Cell and Environment, 37 8: 1753-1775. doi:10.1111/pce.12316

    Brennan TCR, Kroemer JO, Nielsen LK (2013) Physiological and transcriptional response to d-limonene in Saccharomyces cerevisiae shows changes to the cell wall, not the plasma membrane. Appl Env Microbiol 79: 3590-3600. PMID: 23542628

    Behrendorff JBYH, Vickers CE, Chrysanthopoulos P, Nielsen LK (2013) 2,2-Diphenyl-1-picrylhydrazyl as a screening tool for recombinant monoterpene biosynthesis. Microbial Cell Factories 12:76. PMID: 23968454. PMC3847554

    Brennan TCR, Turner CD, Kroemer JO, Nielsen LK (2012) Alleviating monoterpene toxicity using a two-phase extractive fermentation for the bioproduction of jet fuel mixtures in Saccharomyces cerevisiae. Biotechnology & Bioengineering 109: 2513-2522. PMID: 22539043

    Project contacts

    Lead investigator Dr Claudia Vickers, Professor Lars Nielsen
    Research group AIBN Systems & Synthetic Biology
    Contact email c.vickers@uq.edu.au
    Project keywords Systems Biology, Systems Biotechnology, Energy, Materials, Manufacturing, Sustainability, Sucrose, Renewable, Isoprenoids, Synthetic biology, Metabolic engineering Project summary Isoprenoids are a very l...
  • Mammalian Systems Biology

    Project keywords

    Cell and Tissue Engineering, Systems Biology, Systems Biotechnology, Manufacturing, Health, CHO, HEK293, MAb, Biofactory, Metabolic engineering

    Project summary

    Mammalian cells are important hosts for the production of a wide range of biopharmaceuticals due to their ability to produce correctly folded and glycosylated proteins. Compared to microbes and yeast, however, the productivity of mammalian cells is low because of their comparatively slow growth rate, tendency to undergo apoptosis, and low production capacities. While much effort has been invested in the engineering of mammalian cells with superior production characteristics, the success of these approaches has been limited to date. One factor responsible for this lack of success is our limited understanding of the cellular basis for high productivity, and of how discrete mechanisms within a cell contribute to the overall phenotype. Aiming to measure and characterize all cellular components at different functional levels, omics technologies have the potential to improve our understanding of mammalian cell physiology, elucidating new targets for the generation of a superior host cell line.

    In the past 5 years, the release of the CHO genome and advances in omics technologies have enabled the generation of high-resolution, high-quality data, which together with advances in mammalian genome engineering tools will greatly change production of high value biopharmaceuticals. 

    Publications

    Song MC, Hou JJ, Nielsen LK, Gray PP (2015) Novel cell engineering of the Unfolded Protein Response to achieve efficient therapeutic protein production cell line. BMC Proceedings 9 (S9):P14. doi:10.1186/1753-6561-9-S9-P14.

    Orellana CA, Marcellin E, Munro T, Gray PP, Nielsen LK (2015) Multi-omics approach for comparative studies of monoclonal antibody producing CHO cells. BMC Proceedings 9 (S9):O8. doi:10.1186/1753-6561-9-S9-O8.

    Martínez VS, Buchsteiner M, Gray P, Nielsen LK, Quek LE (2015) Dynamic Metabolic Flux Analysis using B-splines to study the effects of temperature shift on CHO cell metabolism. Met Eng Comm 2: 46-57.

    Orellana CA, Marcellin E, Schulz BL, Nouwens AS, Gray PP, Nielsen LK (2015) High antibody producing Chinese hamster ovary cells up-regulate intracellular protein transport and glutathione synthesis. J Proteome Res 14: 609–618. PMID: 25495469

    Turner J, Quek LE, Titmarsh D, Krömer JO, Kao LP, Nielsen LK, Wolvetang E, Cooper-White J (2014) Metabolic profiling and flux analysis of MEL-2 human embryonic stem cells during exponential growth at physiological and atmospheric oxygen concentrations. PLoS ONE 9: e112757. PMID: 25412279. Online.

    Fearnley LG, Davis MJ, Ragan MA, Nielsen LK (2014) Extracting Reaction Networks from Databases – Opening Pandora’s Box. Briefings in Bioinformatics 15: 973-983. PMID: 23946492. Online

    Quek LE, Nielsen LK (2014) Steady-State 13C Fluxomics Using OpenFLUX. In: Krömer JO, Nielsen LK, Blank LM (eds) Metabolic Flux Analysis: Methods and Protocols. Series: Methods in Molecular Biology, vol. 1191. Chapter 13: 65-78. PMID: 25178793.

    Quek LE, Nielsen LK (2014) Customization of 13C-MFA Strategy According to Cell Culture System. In: Krömer JO, Nielsen LK, Blank LM (eds) Metabolic Flux Analysis: Methods and Protocols. Series: Methods in Molecular Biology, vol. 1191. Chapter 5: 81-90. PMID: 25178785.

    Martinez VS, Nielsen LK (2014) NExT: Integration of Thermodynamic Constraints and Metabolomics Data into a Metabolic Network. In: Krömer JO, Nielsen LK, Blank LM (eds) Metabolic Flux Analysis: Methods and Protocols. Series: Methods in Molecular Biology, vol. 1191. Chapter 4: 209-224. PMID: 25178784.

    Quek LE, Nielsen LK (2014) A depth-first search algorithm to compute elementary flux modes by linear programming. BMC Systems Biology 8:94. PMID: 25074068. Online.

    Martínez VS, Quek LE, Nielsen LK ( 2014) Network thermodynamic curation of human and yeast genome-scale metabolic models. Biophys J 107:493-503. PMID: 25028891.

    Quek LE, Dietmair S, Hanscho M, Martinez VS, Borth N, Nielsen LK (2014) Reducing Recon 2 for steady-state flux analysis of HEK cell culture. J Biotech 184: 172-178. PMID: 24907410.

    Mercer TR, Clark MB, Crawford J, Brunck ME, Gerhardt D, Taft R, Nielsen LK, Dinger M, Mattick JS (2014) Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nat Protoc 9: 989-1009. PMID: 24705597

    Fearnley LG, Ragan MA, Nielsen LK (2014) Towards a Large Integrated Model of Signal Transduction and Gene Regulation Events in Mammalian Cells. In: Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, pg 117-122.

    Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen LK, Mattick JS, Stamatoyannopoulos JA (2013) DNase I-hypersensitive exons co-localize with promoters and distal regulatory elements. Nature Genetics 45:852-9. PMID: 23793028

    Dietmair S, Hodson MP, Quek L-E, Timmins NE, Gray P, Nielsen LK (2012) A multi-omics analysis of recombinant protein production in Hek293 cells. PLoS ONE 7(8):e43394. PMID: 22937046. PMC3427347

    Fearnley LG, Nielsen LK (2012) PATHLOGIC-S: A scalable Boolean framework for modelling cellular signalling. PLoS ONE 7(8): e41977. PMID: 22879903. PMC3413702

    Martinez VS, Dietmair S, Quek L-E, Hodson MP, Gray P, Nielsen LK (2012) Flux balance analysis of CHO cells before and after a metabolic switch from lactate production to consumption. Biotechnol. Bioeng. 110: 660-666. PMID: 22991240

    Dietmair S, Hodson MP, Quek LE, Timmins NE, Chrysanthopoulos P, Jacob SS, Gray P, Nielsen LK (2012)Metabolite profiling of CHO cells with different growth characteristics. Biotechnol. Bioeng. 109: 1404-1414. PMID: 22407794

    Dietmair S, Timmins NE, Chrysanthopoulos P, Gray PP, Kr?mer JO, Nielsen LK (2012) Metabolomic analysis of CHO cultures with different growth characteristics - Development of a metabolite extraction protocol for suspension adapted mammalian cells In N. Jenkins, N Barron, PM Alves (Ed.) Proceedings of the 21st Annual Meeting of the European Society for Animal Cell Technology (ESACT), Dublin, Ireland, June 7-10, 2009 (pp. 37-41) Dordrecht, Netherlands: Springer.

    Li J, Wijffels G, Yu Y, Nielsen LK, Niemeyer DO, Fisher AD, Ferguson DM, Schirra HJ (2011) Altered Fatty Acid Metabolism in Long Duration Road Transport: An NMR-based Metabonomics Study in Sheep. J Proteome Res. 10: 1073-87. PMID: 21142080.

    Krömer JO, Dietmair S, Jacob SS, Nielsen LK (2011) Quantification of L-alanyl-L-glutamine in mammalian cell culture broth - evaluation of different detectors. Analytical Biochemistry 416:129-31. PMID: 21651886.

    Dietmair S, Nielsen LK, Timmins NE (2010) Engineering a mammalian super producer. Journal of Chemical Technology & Biotechnology 86: 905–914.

    Dietmair S, Timmins NE, Gray PP, Nielsen LK, Krömer JO (2010) Toward quantitative metabolomics of mammalian cells: Development of a metabolite extraction protocol. Analytical Biochemistry 404:155-164. PMID: 20435011.

    Quek L-E, Dietmair S; Krömer JO, Nielsen LK (2010) Metabolic flux analysis in mammalian cell culture. Metabolic Engineering 12: 161-171. PMID: 19833223.

    Quek L-E, Nielsen LK (2009) Metabolic engineering of mammalian cells. In: The Metabolic Pathway Engineering Handbook, ed. CD Smolke. CRC Press. Chapter 26. ISBN 978-1-4398-0296-0.  Publication Date: 28/07/2009.

    Quek L-E, Wittmann C, Nielsen LK, Krömer JO (2009) OpenFLUX: Efficient Modelling Software for 13C-Based Metabolic Flux Analysis. Microbial Cell Factories 8:25. PMID: 19409084.

    Quek L-E, Nielsen LK (2008) On the reconstruction of the Mus musculus genome-scale metabolic network model. Genome Informatics 21:89-100.

    Dinnis DM, Stansfield SH, Schlatter S, Smales CM, Alete D, Birch JR, Racher AJ, Marshall CT, Nielsen LK, James DC (2006) Functional proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate. Biotechnology and Bioengineering 94: 830-841. DOI 10.1002/bit. 20899

    Sheikh K, Förster J, Nielsen LK (2005) Modeling Hybridoma Cell Metabolism Using a Generic Genome-Scale Metabolic Model of Mus musculus. Biotechnology Progress 21:112-121. DOI: 10.1021/bp0498138

    Project contacts

    Lead investigator Professor Lars Nielsen
    Research group AIBN Systems & Synthetic Biology
    Contact email lars.nielsen@uq.edu.au

     

    The aim of this project is to model and analyse mammalian cell metabolism using genome scale models and metabolomics.
  • Metabolic engineering of hyaluronic acid production

    Project keywords

    Systems Biology, Systems Biotechnology, Sustainability, Fermentation, Synthetic Biology, Hyaluronic Acid

    Project summary

    Hyaluronic acid (HA) is a biopolymer with valuable applications in the pharmaceutical and cosmetic industries. It is a linear molecule comprising of unbranched, polyanionic disaccharide units consisting of glucuronic acid (GlcUA) an N-acetyl glucosamine (GlcNAc) joined alternately by beta 1-3 and beta 1-4 glycosidic bonds. The in vivo functions of HA and the industrial applications relate directly to its rheological properties (viscoelastic and pseudoplastic), which are dictated by the molecular weight (MW) of the polymer. Currently, HA is produced commercially by either extraction from animal tissues (e.g. rooster comb) or bacterial fermentation. Increased concerns over the contamination of animal derived products with infectious agents have made bacterial fermentation a more desirable production system to meet future demands.However, HA from bacterial sources are of a lower grade (lower molecular weight) compared with the product extracted from animal tissues. The aim of this project is to produce HA of comparable or higher molecular weight to the one currently extracted from rooster comb (used in the pharmaceutical industry).

    Little is known about what controls the molecular weight of beta-polysaccharides such as HA during bacterial fermentations. This is also true for abundant beta-polysaccharides such as chitin and cellulose. Several groups including ours have pursued various hypotheses for the past decade, but no hypothesis adequately describes the MW regulation observed in bioreactors.Given previous failures of direct approaches, a systems biology approach was adopted. A genome scale model of an HA-producing bacterium was constructed. This was coupled with a range of ‘omics tools including metabolomics, transcriptomics and proteomics, thereby providing a global view of the entire system. 

    Publications

    Zhang Y, Luo K, Zhao Q, Qi Z, Nielsen LK, Liu H (2015) Genetic and biochemical characterization of genes involved in hyaluronic acid synthesis in Streptococcus zooepidemicus. Appl Microbiol Biotechnol. Accepted 29.12.2015. PMID: 26758299

    Zhu Y, Pham TH, Nhiep THN, Vu NMT, Marcellin E, Chakrabortti A, Wang Y, Waanders J, Lo R, Huston WM, Bansal N, Nielsen LK, Liang ZX, Turner MS (2015) Cyclic-di-AMP synthesis by the diadenylate cyclase CdaA is modulated by the peptidoglycan biosynthesis enzyme GlmM in Lactococcus lactis. Molecular Microbiology. Accepted: 17.11.2015. PMID: 26585449

    Marcellin E, Steen JA, Nielsen LK (2014) Insight into hyaluronic acid molecular weight control. Applied Microbiology and Biotechnology 98: 6947-56. PMID: 24957250.

    Chen WY, Marcellin E, Steen JA, Nielsen LK (2014) The role of hyaluronic acid precursor concentrations in molecular weight control in Streptococcus zooepidemicus. Mol Biotechnol 56:147–156.PMID: 23903961

    Marcellin E, Chen WY, Nielsen LK (2011) Metabolic Pathway Engineering for Hyaluronic Acid Production. In: Carbohydrate Modifying Biocatalysts, ed. P. Grundwald. Pan Stanford Publishing. ISBN: 978-9814241670. Published 30.9.2011. Chapter 15, pp. 571-584.

    Marcellin E, Chen W, Nielsen LK (2010) Understanding plasmid effect on hyaluronic acid molecular weight produced by Streptococcus equi subsp. zooepidemicus. Metabolic Engineering 12: 62–69. PMID: 19782148.

    Chen WY, Marcellin E, Nielsen LK (2009) Hyaluronan molecular weight is controlled by UDP-N- acetylglucosamine concentration in Streptococcus zooepidemicus. J Biol Chem 284:18007-14. PMID: 19451654.

    Marcellin E, Gruber CW, Archer C, Craik DJ, Nielsen LK (2009) Proteome analysis of the hyaluronic acid-producing bacterium, Streptococcus zooepidemicus. Proteome Science 7:13. PMID: 19327162.

    Marcellin E, Nielsen LK, Abeydeera P, Kroemer JO (2009) Quantitative analysis of intracellular sugar phosphates and sugar nucleotides in encapsulated Streptococci using HPAEC-PAD. Biotechnol. J. 4: 58-63. PMID: 19156726.

    Marcellin E, Chen W, Nielsen LK (2009) Microbial hyaluronic acid biosynthesis. In: Microbial Production of Biopolymers and Polymer Precursors: Applications and Perspectives, ed. BHA Rehm. Norwich: Caister Academic Press. Pp. 163-180.

    Blank LM, Hugenholtz P, Nielsen LK (2008) Evolution of the hyaluronic acid synthesis (has) operon in Streptococcus zooepidemicus and other pathogenic streptococci. Journal of Molecular Evolution 67: 13-22.

    Blank LM, McLaughlin RL, Nielsen LK (2005) Stable production of hyaluronic acid in Streptoccus zooepidemicus chemostats operated at high dilution rate. Biotechnology & Bioengineering 90: 685-693.

    Fong Chong B, Blank LM, McLaughlin R, Nielsen LK (2005) Microbial hyaluronic acid production. Applied Microbiology and Biotechnology 66:341-351. DOI: 10.1007/s00253-004-1774-4.

    Project contacts

    Lead investigator Professor Lars Nielsen, Dr Esteban Marcellin
    Research group AIBN Systems & Synthetic Biology
    Contact email lars.nielsen@uq.edu.au

     

    Engineering superior hyaluronic acid production host
  • Microtissue Culture

    Project keywords

    Cell and Tissue Engineering, Systems Biology, Systems Biotechnology, Health, Cancer

    Project summary

    Microtissue culture recaptures many tissue features lost in conventional 2D tissue systems. The hanging-drop method for generating microtissues was developed in our lab more than  a decade ago and benefits from the ability to generate homogenous spheroids without artificial matrix material as well as the potential of introducing multiple tissue types. Dr Jens Kelm, who conceived the technique in our lab, went on to co-found InSphero, a developer and supplier of microtissue technologies for drug screening.

    We have used the microtissues in solid tumour models, to explore angiogenesis and ductal tissue formation. We also used the models for developing, functionalised coherent microcapsules for cellular therapies.

    Publications

    Leung A, Nielsen LK, Trau M, Timmins NE (2010) Tissue Transplantation by Stealth - Coherent Alginate Microcapsules for Immunoisolation. Biochem Eng J 48:337-347. doi:10.1016/j.bej.2009.10.007.

    Leung A, Trau M, Nielsen LK (2009) Assembly of multilayer PSS/PAH membrane on coherent alginate/PLO microcapsule for long-term graft transplantation. Journal of Biomedical Materials Research: Part A 88A:226-237. PMID: 18286625.

    Leung A, Lawrie G, Nielsen LK, Trau M (2008) Facilitating Specific Functionality on the APA Microcapsule to Control Its Neighborhood: Application in Implementing Local Immunosuppression for Xenotransplanation. Journal of Microencapsulation 25:387-398.

    Timmins NE, Nielsen LK (2007) Generation of Multicellular Tumour Spheroids by the Hanging Drop Method. In: Tissue Engineering 2nd Edition, eds. Fussenegger M, Hauser H. Methods in Molecular Medicine 140:141-151.

    Leung A, Ramaswamy Y, Munro P, Lawrie G, Nielsen LK, Trau M (2005) Emulsion Strategies in the Microencapsulation of Cells: Pathways to Thin Coherent Membranes. Bioengineering & Biotechnology 92:45-53.

    Timmins NE, Maguire TL, Grimmond SM, Nielsen LK (2005). Identification of three gene candidates for multicellular resistance in colon carcinoma. Cytotechnology 46:9-18. http://dx.doi.org/10.1007/s10616-005-1476-5.

    Timmins NE, Harding FJ, Smart C, Brown MA, Nielsen LK (2005) Method for the generation and cultivation of functional 3-dimensional mammary constructs without exogenous extracellular matrix material. Cell & Tissue Research 320:207-210. DOI: 10.1007/s00441-004-1064-6

    Project contacts

    Lead investigator Professor Lars Nielsen
    Research group AIBN Systems & Synthetic Biology
    Contact email lars.nielsen@uq.edu.au

     

    Project keywords Cell and Tissue Engineering, Systems Biology, Systems Biotechnology, Health, Cancer Project summary Microtissue culture recaptures many tissue features lost in conventional 2D tissue systems. The hanging-...
  • Opening Pandora's Box: the world of actinomycetes

    Project keywords

    Systems Biology, Health, Antibiotics, Actinomycetes, S. erythraea, Proteomics, Metabolomics, Transcriptomics

    Project summary

    Actinomycetes are a rich source of secondary metabolites and the origin of half the antibiotics in current use. However, less than 10% of their metabolic potential has been explored to date. Accessing this rich source of bioactives has proven difficult due to the complex regulation of secondary metabolism in actinomycetes. During the actinomycete developmental cycle a ’metabolic switch’, marks the transition from primary to secondary metabolism. The switch presumably dictates the subset of metabolites produced and thus understanding its regulation is of major importance to biotechnology. Using a systems biology platform we are exploring the life cycle of S. erythraea, S. coelicolor and other actinomycetes in bioreactors at the transcriptional, translational and post-translational level. The project aims to systematically characterize and understand the mechanisms underpinning the control of the metabolic switch to guide the rational design of superior strains.

    Publications

    Licona-Cassani C, Morales PC, Manteca A, Barona-Gomez F, Nielsen LK, Marcellin E (2015) Systems biology approaches to understand natural products biosynthesis. Front. Bioeng. Biotechnol. 3:199. PMID: 26697425

    Navone L, Macagno JP, Licona-Cassani C, Marcellin E, Nielsen LK, Gramajo H, Rodriguez E (2015) AllR controls the expression of Streptomyces coelicolor allantoin pathway genes. Appl Env Microbiol 81: 6649-59. PMID: 26187964

    Liao C, Rigali S, Cassani CL, Marcellin E, Nielsen LK, Ye BC (2014) Control of Chitin and N-acetylglucosamine Utilization in Saccharopolyspora erythraea. Microbiology 160: 1914–1928. PMID: 25009237.

    Licona-Cassani C, Lim SA, Marcellin E, Nielsen LK (2014) Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome. Molecular and Cellular Proteomics 13: 1219-1230. PMID: 24615062

    Navone L, Casati P, Licona-Cassani C, Marcellin E, Nielsen LK, Rodriguez E, Gramajo H (2014) Allantoin catabolism influences the production of antibiotics in Streptomyces coelicolor. Appl Microbiol Biotechnol 98:351-360. PMID: 24292080

    Marcellin E, Licona-Cassani C, Mercer TR, Palfreyman RW, Nielsen LK (2013) Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach. BMC Genomics 14:699. PMID: 24118942. Open access

    Marcellin E, Mercer TR, Licona-Cassani C, Palfreyman RW, Dinger M, Steen JA, Mattick JS, Nielsen LK (2013) Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch. BMC Genomics 14:15. PMID: 23324121. PMC3610266

    Licona-Cassani C, Marcellin E, Quek L-E, Jacob S, Nielsen LK (2012) Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production. Antonie van Leeuwenhoek 102: 493-502. PMID: 22847261

    Project contacts

    Lead investigator Dr Esteban Marcellin, Professor Lars Nielsen
    Research group AIBN Systems & Synthetic Biology
    Contact email e.marcellin@uq.edu.au
    Project keywords Systems Biology, Health, Antibiotics, Actinomycetes, S. erythraea, Proteomics, Metabolomics, Transcriptomics Project summary Actinomycetes are a rich source of secondary metabolites and the origin ...
  • Plant Genome Scale Modelling

    Project keywords

    Systems Biotechnology, Systems Biology, Health, Sustainability, Plants, Genome Scale Model

    Project summary

    Plant genome scale modelling considers the reconstruction, pathway analysis and application of genome-scale metabolic models to study complex plant metabolism. Ultimately, such modells may be used for systems-level metabolic engineering, pathway design and in silico analyses for strain improvement. We developed the first genome scale model for plants capable of describing photosynthesis and photorespiration (AraGEM). We subsequently developed models for C4 metabolism in maize, sorghum and sugarcane as well as for the green algae, Chlamydomonas reinhardtii. Multi-tissue interactions were critical to describe C4 metabolism and we have recently expanded the scheme to model whole-plant metabolism.

    Current project includes

    • Arabidopsis Reconstruction Annotation Jamboree: a international community approach to plant systems biology;
    • Pathway curation and study of oil seed metabolism using AraGEM (with CSIRO);
    • Whole plant fluxomics: Multi-tissue genome-scale metabolic modeling for analysis of whole plant systems;
    • Development and applications of algae genome-scale metabolic model reconstruction (AlgaGEM); and
    • Omics analyses, development and application of genome-scale model (C4GEM) to study of metabolism of C4 grasses 

    Publications

    Dal’Molin CGO, Nielsen LK (2016) Algae Genome-Scale Reconstruction, Modelling and Applications. In: M.A. Borowitzka et al. (eds.) The Physiology of Microalgae. Series: Developments in Applied Phycology, vol. 6, pg. 591-598.

    Dal'molin CGO, Quek LE, Saa PA, Nielsen LK (2015) A multi-tissue genome-scale metabolic modelling framework for the analysis of whole plant systems. Front. Plant Sci., online 5.1.2015. doi: 10.3389/fpls.2015.00004.

    Dal’Molin CGO, Quek LE, Palfreyman RW, Nielsen LK (2014) Plant Genome-Scale Modeling and Implementation. In: Dieuaide-Noubhani M, Alonso AP, editors. Plant Metabolic Flux Analysis: Methods & Protocols. Humana Press. Methods in Molecular Biology 1090: 317-32. PMID: 24222424

    Dal’Molin CGO, Nielsen LK (2013) Plant genome-scale metabolic reconstruction and modelling. Curr Opin Biotechnol. 24: 271-277. PMID: 22947602

    Dal’Molin CGO, Quek LE, Palfreyman RW, Nielsen LK (2011) AlgaGEM - A genome-scale metabolic reconstruction of Algae based on Chlamydomonas reinhardtii genome. BMC Genomics 12 (Supp 4): S5. PMID: 22369158. PMC3287588

    de Oliveira Dal'molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010) C4GEM - Genome-Scale Metabolic Model to study C4 plant metabolism. Plant Physiol. 154:1871-85. PMID: 20974891.

    de Oliveira Dal'molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010) AraGEM - a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis thaliana. Plant Physiol. 152: 579-589. PMID: 20044452.

    Project contacts

    Lead investigator Dr Cristiana Dal'Molin, Professor Lars Nielsen
    Research group AIBN Systems & Synthetic Biology
    Contact email c.gomesdeoliveira@uq.edu.au
    Project keywords Systems Biotechnology, Systems Biology, Health, Sustainability, Plants, Genome Scale Model Project summary Plant genome scale modelling considers the reconstruction, pathway analysis and application of ge...
  • Role of isoprene synthesis in plants

    Project keywords

    Systems Biology, Systems Biotechnology, Energy, Sustainability, Greenhouse Gas, Abiotic Stress, Isoprene

    Project summary

    The volatile gas isoprene is emitted in teragrams per annum quantities from the terrestrial biosphere and exerts a large effect on atmospheric chemistry. The physiological role of isoprene in plants continues to be subject to much debate.

    Publications

    Jardine, Kolby, Chambers, Jeffrey, Alves, Eliane G., Teixeira, Andrea, Garcia, Sabrina, Holm, Jennifer, Higuchi, Niro, Manzi, Antonio, Abrell, Leif, Fuentes, Jose D., Nielsen, Lars K., Torn, Margaret S. and Vickers, Claudia E. (2014) Dynamic balancing of isoprene carbon sources reflects photosynthetic and photorespiratory responses to temperature stress. Plant Physiology, 166 4: 2051-2064. doi:10.1104/pp.114.247494

    Tattini, Massimiliano, Velikova, Violeta, Vickers, Claudia, Brunetti, Cecilia, Di Ferdinando, Martina, Trivellini, Alice, Fineschi, Silvia, Agati, Giovanni, Ferrini, Francesco and Loreto, Francesco (2014) Isoprene production in transgenic tobacco alters isoprenoid, non-structural carbohydrate and phenylpropanoid metabolism, and protects photosynthesis from drought stress. Plant, Cell and Environment, 37 8: 1950-1964. doi:10.1111/pce.12350

    Ryan, Annette C., Hewitt, C. Nicholas, Possell, Malcolm, Vickers,Claudia E., Purnell, Anna, Mullineaux, Philip M., Davies, William J. and Dodd, Ian C. (2013) Isoprene emission protects photosynthesis but reduces plant productivity during drought in transgenic tobacco (Nicotiana tabacum) plants. New Phytologist, 201 1: 205-216. doi:10.1111/nph.12477

    Jardine, Kolby J., Meyers, Kimberly, Abrell, Leif, Alves, Eliane G., Yanez Serrano, Ana Maria, Kesselmeier, Jurgen, Karl, Thomas, Guenther, Alex, Chambers, Jeffrey Q. and Vickers, Claudia (2013) Emissions of putative isoprene oxidation products from mango branches under abiotic stress. Journal of Experimental Botany, 64 12: 3697-3709. doi:10.1093/jxb/ert202

    Vickers, Claudia E., Possell, Malcolm, Laothawornkitkul, Jullada, Ryan, Annette C., Hewitt, C. Nicholas and Mullineaux, Philip M. (2011) Isoprene synthesis in plants: Lessons from a transgenic tobacco model. Plant, Cell and Environment, 34 6: 1043-1053. doi:10.1111/j.1365-3040.2011.02303.x

    Vickers, Claudia E., Possell, Malcolm, Hewitt, C. Nicholas and Mullineaux, Philip M. (2010) Genetic structure and regulation of isoprene synthase in Poplar (Populus spp.). Plant Molecular Biology, 73 4-5: 547-558. doi:10.1007/s11103-010-9642-3

    Possell, Malcolm, Ryan, Annette, Vickers, Claudia E., Mullineaux, Philip M. and Hewitt, C. Nicholas (2010) Effects of fosmidomycin on plant photosynthesis as measured by gas exchange and chlorophyll fluorescence. Photosynthesis Research, 104 1: 49-59. doi:10.1007/s11120-009-9504-5

    Vickers, Claudia, E., Gershenzon, Jonathan, Lerdau, Manuel T. and Loreto, Francesco (2009) A unified mechanism of action for volatile isoprenoids in plant abiotic stress. Nature Chemical Biology, 5 5: 283-291. doi:10.1038/nchembio.158

    Vickers, Claudia E., Possell, Malcolm, Cojocariu, Cristian I., Velikova, Violeta B., Laothawornkitkul, Jullada, Ryan, Annette, Mullineaux, Philip M. and Hewitt, C. Nicholas (2009) Isoprene synthesis protects transgenic tobacco plants from oxidative stress. Plant, Cell and Environment, 32 5: 520-531. doi:10.1111/j.1365-3040.2009.01946.x

    Laothawornkitkul, Jullada, Paul, Nigel D., Vickers, Claudia E., Possell, Malcolm, Mullineaux, Philip M., Hewitt, C. Nicholas and Taylor, Jane E. (2008) The role of isoprene in insect herbivory. Plant Signalling and Behaviour, 3 12: 1141-1142.

    Laothawornkitkul, Jullada, Paul, Nigel D., Vickers, Claudia E., Possell, Malcolm, Taylor, Jane E., Mullineaux, Philip M. and Hewitt, C. Nicholas (2008) Isoprene emissions influence herbivore feeding decisions. Plant, Cell and Environment, 31 10: 1410-1415. doi:10.1111/j.1365-3040.2008.01849.x

    Vickers, C. E., Schenk, P. M., Li, D., Mullineaux, P. M. and Gresshoff, P. M. (2007) pGFPGUSPlus, a new binary vector for gene expression studies and optimising transformation systems in plants. Biotechnology Letters, 29 11: 1793-1796. doi:10.1007/s10529-007-9467-6

    Wilkinson, Michael J., Owen, Susan M., Possell, Malcolm, Hartwell, James, Gould, Peter, Hall, Anthony, Vickers, Claudia and Hewitt, Nicholas (2006) Circadian control of isoprene emissions from oil palm (Elaeis guineensis). Plant Journal, 47 6: 960-968. doi:10.1111/j.1365-313X.2006.02847.x

    Buzas, Diana Mihaela, Lohar, Dasharath, Sato, Shusei, Nakamura, Yasukazu, Tabata, Satoshi, Vickers, Claudia Estelle, Stiller, Jiri and Gresshoff, Peter Michael (2005) Promoter trapping in Lotus japonicus reveals novel root and nodule GUS expression domains. Plant and Cell Physiology, 46 8: 1202-1212. doi:10.1093/pcp/pci129Schenk, P. M. P., Vickers, C. E. and Manners, J.M. (2004) Rapid cloning of novel genes and promoters for functional analysis in transgenic cells. Transgenics, 4 151-156.

    Vickers, C. E., Xue, G. P. and Gresshoff, P. M. (2003) A synthetic xylanase as a novel reporter in plants. Plant Cell Reports, 22 2: 135-140. doi:10.1007/s00299-003-0667-9

    Project contacts

    Lead investigator Dr Claudia Vickers
    Research group AIBN Systems & Synthetic Biology
    Contact email c.vickers@uq.edu.au
    Project keywords Systems Biology, Systems Biotechnology, Energy, Sustainability, Greenhouse Gas, Abiotic Stress, Isoprene Project summary The volatile gas isoprene is emitted in teragrams per annum quantities from the ter...
  • Sucrose to Bioproducts

    Project keywords

    Systems Biology, Systems Biotechnology, Energy, Materials, Manufacturing, Sustainability, Sucrose, Sugarcane, Renewable, Polyhydroxybutyrate, Surfactant, Synthetic biology, Metabolic engineering

    Project summary

    Carbon source drives the triple bottom line for microbial production of bulk chemicals. Sugarcane is unique in delivering a high quality feedstock with exceptional environmental performance. Like glucose from corn starch, sucrose comes at high concentration and purity enabling high titre, high production rate and low downstream purification cost. Unlike starch, sucrose is not a food stable and sugarcane generally does not compete with food crops. Moreover, waste biomass (bagasse) is harvested with sucrose and is used to produce heat and electricity, hereby greatly reducing the carbon footprint of production.

    Sucrose is a major agricultural product in Australia. However, most industrial strains of E. coli cannot utilise it as a carbon source. To better understand sucrose utilisation, we sequenced the genome of a sucrose-utilising E. coli strain and generated an in silico genome-scale metabolic model. We then developed methods to improve sucrose utilisation in this strain, and to reproducibly engineer efficient sucrose utilisation in industrial E. coli strains. Engineered strains producing polyhydroxybutyrate (a polymer that can be used to make biodegradeable plastics) and peptide bio-surfactants make as much or more bio-product when growing on sucrose than on glucose. 

    Publications

    Lim S, Marcellin E, Jacob S, Nielsen LK (2015) Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions. J Proteomics 126: 24-33. PMID: 26013414

    Bruschi M, Krömer JO, Steen JA, Nielsen LK (2014) Production of the short peptide surfactant DAMP4 from glucose or sucrose in high cell density cultures of Escherichia coli BL21(DE3). Microbial Cell Factories 13:99. PMID: 25134850. Online.

    Arifin Y, Archer C, Lim SA, Quek L-E, Sugiarto H, Marcellin E, Vickers CE, Krömer JO, Nielsen LK (2014) Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation. Applied Microbiology and Biotechnology 98: 9033-44. PMID: 25125039.

    Steen JA, Bohlke N, Vickers CE, Nielsen LK(2014) The trehalose phosphotransferase system (PTS) in E. coli W can transport low levels of sucrose that are sufficient to facilitate induction of the csc sucrose catabolism operon. PLoS ONE 9:e88688.PMID: 24586369. Online

    Sabri S, Nielsen LK, Vickers CE (2013) Molecular control of sucrose utilization in Escherichia coli W, an efficient sucrose-utilizing strain. Appl Env Microbiol 79: 478-487. PMID: 23124236. PMC3553775

    Klein-Marcuschamer D, Turner C, Allen M, Dietzgen RG, Gray P, Gresshoff P, Hankamer B, Heimann K, Scott P, Speight R, Stephens E, Nielsen LK (2013) Analysis of renewable aviation fuel from microalgae, Pongamia pinnata, and sugarcane. Biofuels, Bioproducts & Biorefining 7:416-428.

    Bruschi M, Boyes SJ, Sugiarto H, Nielsen LK, Vickers CE (2012) A transferable sucrose utilization approach for non-sucrose-utilizing Escherichia coli strains. Biotechnology Advances 30: 1001-1010. PMID: 21907272.

    Utrilla J, Licona-Cassani C, Marcellin E, Gosset G, Nielsen LK, Martinez A (2012) Engineering and adaptive evolution of Escherichia coli for D-lactate fermentation reveals GatC as a xylose transporter. Metabolic Engineering 14: 469–476. PMID: 22885034

    Arafin Y, Sabri S, Sugiarto H, Krömer JO, Vickers CE, Nielsen LK (2011) Deletion of cscR in Escherichia coli W improves growth and poly-3-hydroxyburyrate (PHB) production from sucrose in fed batch culture. J. Biotechnol.156: 275-278. PMID: 21782859.

    Vickers CE, Klein-Marcuschamer D, Krömer JO (2011) Examining the feasibility of bulk commodity production in Escherichia coli. Biotechnology Letters 34: 585-96. PMID: 22160295.

    Archer CT, Kim JF, Jeong H, Park JH, Vickers CE, Lee SY, Nielsen LK (2011) The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genomics 12:9. PMID: 21208457.

    Lee JW, Choi S, Park JH, Vickers CE, Nielsen LK, Lee SY (2010) Development of sucrose-utilizing Escherichia coli K-12 strain by cloning β-fructofuranosidases and its application for L-threonine production. Appl Microbiol Biotechnol 88: 905-13. PMID: 20711572.

    Renouf MA, Wegener MK, Nielsen LK (2008) An environmental life cycle assessment comparing Australian sugarcane with US corn and UK sugar beet as producers of sugars for fermentation. Biomass & Bioenergy 32: 1144-1155. doi:10.1016/j.biombioe.2008.02.012

    Project contacts

    Lead investigator Professor Lars Nielsen, Dr Claudia Vickers
    Research group AIBN Systems & Synthetic Biology
    Contact email lars.nielsen@uq.edu.au

     

    Sucrose is an abundant, high-energy carbon source and is ideal for bioproduction in microbial fermentation. The aim of this project is to develop biological replacements for materials currently produced from petrochemical feedstocks.
  • Sustainable dollar notes and other polypropylenes from bio-derived feedstocks

    Project keywords

    Systems Biology, Materials, Manufacturing, Sustainability, Propanol, Polypropylene, Bio-feedstock, Fermentation, Microbes, Proteomics, Metabolomics, Transcriptomics

    Project summary

    Propylene and polypropylenes are essential feedstock chemicals and materials for the global chemical industry, producing  thousands of products of use in our every day lives. These products include fibers, packaging, automotive parts and, in Australia, even bank notes. Propylene is currently derived from fossil feedstocks as a by-product of the oil refining process. In order to decrease dependence on these finite resources and improve sustainability, the chemical industry is seeking green alternatives to produce propylene. This project aims to produce propylene precursors in a biotechnological fermentation process that is optimised to increase yields and productivities using a systems biology approach. The project is also investigating ways to engineer the fermentation microorganisms to improve yields.

    Project contacts

    Lead investigator Professor Lars Nielsen, Dr Esteban Marcellin
    Research group AIBN Systems & Synthetic Biology
    Contact email lars.nielsen@uq.edu.au

     

    Systems Biology, Materials, Sustainability, Propylene, Propanol, Propionic acid, Propionibacterium, Fermentation, Proteomics, Metabolomics, Transcriptomics
  • The Queensland Sustainable Aviation Fuel Initiative

    Project keywords

    Systems Biology, Systems Biotechnology, Energy, Sustainability, Biofuel, Sugarcane, Pongamia, Algae, Technoeconomics, Fermentation, Synthetic Biology

    Project summary

    The Queensland Sustainable Aviation Fuel Initiative was born out of an aviation industry desire for genuinely sustainable aviation fuels that will match current performance standards. The initiative was established through a Queensland Government National and International Research Alliances Program grant that brought together a consortium of university biofuel experts and industry for the AU$6.5 million first stage of the program. The second phase to evaluate a production facility business case is funded through the Queensland Government’s Research Partnerships Program.

    • AIBN has led the development of detailed, open and transparent techno-economic engineering models that evaluate the production of biofuels from three different biomass sources (sucrose from sugar cane; oil from the seeds of the Pongamia tree; and autotrophic microalgae). The results have been published in a leading international journal and will inform researchers and other community stakeholders. The results suggest where future research and development would have the greatest impact on the feasibility and lowering the cost of biofuel production.
    • Boeing has performed detailed lifecycle analyses on the production of biofuel from the three feed stocks to evaluate sustainability.
    • A wiki website is providing a forum to disseminate all of the results and for interactive feedback, review, updating of results and discussion. The aim of the wiki is to provide clarity and consensus on biofuel production feasibility for scientists, engineers, government and the wider community.
    • AIBN has strong expertise in microbe engineering, and systems and synthetic biology, which are being used to develop and improve the process of converting sugarcane to aviation fuel. 

    Project contacts

    Lead investigator Professor Lars Nielsen
    Research group Nielsen Group
    Contact email Professor Lars Nielsen
    Systems Biology, Systems Biotechnology, Energy, Sustainability, Biofuel, Sugarcane, Pongamia, Algae, Technoeconomics, Fermentation, Synthetic Biology
  • Tools for Synthetic Biology

    Project keywords

    Systems Biology, Systems Biotechnology, Energy, Materials, Manufacturing, Sustainability, Sucrose, Renewable, Isoprenoids, Synthetic biology, Metabolic engineering

    Project summary

    We have developed a variety of synthetic biology tools to facilitate metabolic engineering in both yeast and E. coli. Examples include our expression and integration vectors. The pCEV vectors allow over-expression of multiple genes in yeast using antibiotic resistance for selection. This is particularly useful for industrial strains that do not have engineered auxotrophies, or for heavily engineered strains that have no auxotrophic markers remaining for selection. We also have a vector series for rapid, efficient integration of very large DNA sequences onto the E. coli genome. These knock-in/knock-out (KIKO) vectors are particularly useful for introduction of multiple genes, for example when reconstructing long metabolic pathways. We also developed a method to reliably engineer the sucrose utilization phenotype in (previously) non-sucrose-utilizing E. coli strains. The pCSCX plasmid can be used to rapidly transfer a permease-mediated system onto most E. coli genomes.

    Regulating gene expression at appropriate times during cultivation is very important to help avoid/mitigate problems of metabolic burden (excessive competition between production of the biochemical of interest and core metabolism required for cell growth) and/or product toxicity. We have developed synthetic biology circuits to help control appropriate expression patterns. The native yeast system, naturally used to detect cell density (‘quorum sensing’) was hi-jacked to interface with signal amplification and regulation systems, so that sharp switch-like control of gene expression is achieve in response to increased cell density. This engineered quorum-sensing system is now being applied to a variety of problems.

    Plasmids are available from AddGene.

    Publications

    Williams TC, Averesch NJH, Winter G, Plan MR, Vicker CE, Nielsen LK, Krömer JO (2015) Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae. Metabolic Engineering 29: 124-134. PMID: 25792511

    Peng BY, Williams TC, Henry M, Nielsen LK, Vickers CE (2015) Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activities. Microbial Cell Factories 14:91.PMID: 26112740

    Williams TC, Gomez ME, Nielsen LK, Vickers CE (2015) Dynamic regulation of gene expression using sucrose responsive promoters and RNA interference in Saccharomyces cerevisiae. Microbial Cell Factories 14:43. PMID: 25886317

    Williams TC, Nielsen LK, Vickers CE (2013) Engineered quorum-sensing using pheromone-mediated cell-to-cell communication in Saccharomyces cerevisiae. ACS Synthetic Biology 2: 136-149. PMID: 23656437 

    Vickers CE, Bydder SF, Zhou Y, Nielsen LK (2013) Dual gene expression cassette vectors with antibiotic selection markers for engineering in Saccharomyces cerevisiae. Microbial Cell Factories 12: 96. PMID: 24161108. Open access.

    Sabri S, Steen JA, Bongers M, Nielsen LK, Vickers CE (2013) Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci. Microbial Cell Factories 12:60. PMID: 23799955. PMC3706339

    Nielsen LK (2011) METABOLIC ENGINEERING From retrofitting to green field. Nature Chemical Biology 7: 407-408. PMID: 21685882.

    Vickers CE, Blank LM, Kroemer JO (2010) Chassis cells for industrial biochemical production. Nature Chemical Biology 6: 875-877. PMID: 21079595.

    Project contacts

    Lead investigator Dr Claudia Vickers, Professor Lars Nielsen
    Research group AIBN Systems & Synthetic Biology
    Contact email c.vickers@uq.edu.au

     

    Project keywords Systems Biology, Systems Biotechnology, Energy, Materials, Manufacturing, Sustainability, Sucrose, Renewable, Isoprenoids, Synthetic biology, Metabolic engineering Project summary We have developed a vari...