Research Topics
| Torsten ThomasSummaryAffiliation: University of New South Wales Country: Australia Publications
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Detail Information
Publications
The use of functional genomics for the identification of a gene cluster encoding for the biosynthesis of an antifungal tambjamine in the marine bacterium Pseudoalteromonas tunicataCatherine Burke
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
Environ Microbiol 9:814-8. 2007..A biosynthetic pathway has been proposed based on analysis and annotation of the gene cluster...
Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosisTorsten Thomas
Centre for Marine Bio Innovation, The University of New South Wales, Sydney, Australia
ISME J 4:1557-67. 2010..These data provide new insight into the evolution of symbiotic diversity, microbial metabolism and host-microbe interactions in sponges...
Metagenomics - a guide from sampling to data analysisTorsten Thomas
School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, The University of New South Wales, Sydney, NSW 2052, Australia
Microb Inform Exp 2:3. 2012..As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared...- Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environmentTorsten Thomas
Centre of Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
PLoS ONE 3:e3252. 2008..As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions... - Cold adaptation of archaeal elongation factor 2 (EF-2) proteinsTorsten Thomas
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, UNSW, 2052, Australia
Curr Protein Pept Sci 3:223-30. 2002..A key finding from these studies is that in addition to inherent properties of the EF-2 proteins, intracellular factors (e.g. ribosomes and intracellular solutes) play a central role in thermal adaptation... - An integrative study of a meromictic lake ecosystem in AntarcticaFederico M Lauro
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
ISME J 5:879-95. 2011..By exhaustively describing and modelling interactions in Ace Lake, we have developed an approach that may be applicable to learning how environmental perturbations affect the microbial dynamics in more complex aquatic systems... - Global biogeography of SAR11 marine bacteriaMark V Brown
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
Mol Syst Biol 8:595. 2012..Our data demonstrate the importance of adaptive radiation in the organism's ability to proliferate throughout the world's oceans, and describe genomic traits characteristic of different phylotypes in specific marine biomes... - Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbiontsLu Fan
School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
Proc Natl Acad Sci U S A 109:E1878-87. 2012..Our data thus demonstrate evolutionary convergence in complex symbiont communities and reveal the details and mechanisms that underpin the process... - Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australisCatherine Burke
School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio Innovation, University of New South Wales, Sydney, New South Wales, Australia
ISME J 5:590-600. 2011..The competitive lottery model, originally derived to explain diversity in coral reef fishes, may explain the pattern of colonization of this algal surface... - The genomic basis of trophic strategy in marine bacteriaFederico M Lauro
Environmental Microbiology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia
Proc Natl Acad Sci U S A 106:15527-33. 2009..Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining... - Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean algaNiina A Tujula
Centre for Marine Bio Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
ISME J 4:301-11. 2010.... - Bacterial community assembly based on functional genes rather than speciesCatherine Burke
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
Proc Natl Acad Sci U S A 108:14288-93. 2011.... - Novel antibacterial proteins from the microbial communities associated with the sponge Cymbastela concentrica and the green alga Ulva australisPui Yi Yung
Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
Appl Environ Microbiol 77:1512-5. 2011..The results suggest that uncultured alpha- and gammaproteobacteria contain new classes of proteins that may be a source of antibacterial agents... - Genomes and virulence factors of novel bacterial pathogens causing bleaching disease in the marine red alga Delisea pulchraNeil Fernandes
The Centre for Marine Bio Innovation CMB, University of New South Wales, Sydney, Australia
PLoS ONE 6:e27387. 2011.... - Virophage control of antarctic algal host-virus dynamicsSheree Yau
School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio Innovation, and Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, New South Wales 2052, Australia
Proc Natl Acad Sci U S A 108:6163-8. 2011..These findings indicate that virophages regulate host-virus interactions, influence overall carbon flux in Organic Lake, and play previously unrecognized roles in diverse aquatic ecosystems... - Pathogenic archaea: do they exist?Ricardo Cavicchioli
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
Bioessays 25:1119-28. 2003..The present optimistic view that there are no archaeal pathogens is tainted by a severe lack of relevant knowledge, which may have important consequences in the future... - A polyphasic approach to the exploration of collagenolytic activity in the bacterial community associated with the marine sponge Cymbastela concentricaPui Yi Yung
Centre for Marine Bio Innovation, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
FEMS Microbiol Lett 321:24-9. 2011..concentrica, and that some low-abundance bacteria have collagenase activities that have the potential to harm the sponge through tissue degradation... - Hydrogen peroxide linked to lysine oxidase activity facilitates biofilm differentiation and dispersal in several gram-negative bacteriaAnne Mai-Prochnow
School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, Biological Sciences Building, University of New South Wales, Kensington, Sydney, NSW 2052, Australia
J Bacteriol 190:5493-501. 2008..We propose that biofilm killing through hydrogen peroxide can be linked to AlpP homologue activity and plays an important role in dispersal and colonization across a range of gram-negative bacteria... - Identification of compounds with bioactivity against the nematode Caenorhabditis elegans by a screen based on the functional genomics of the marine bacterium Pseudoalteromonas tunicata D2Francesco Ballestriero
School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney 2052, New South Wales, Australia
Appl Environ Microbiol 76:5710-7. 2010..The novel functional genomic screen presented here therefore detects new eukaryotic inhibitors with different chemical structures, kinetics, and predicted modes of actions... - The seaweed holobiont: understanding seaweed-bacteria interactionsSuhelen Egan
School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio Innovation, The University of New South Wales, Sydney, NSW, Australia
FEMS Microbiol Rev 37:462-76. 2013.... - Identification of the antibacterial compound produced by the marine epiphytic bacterium Pseudovibrio sp. D323 and related sponge-associated bacteriaAnahit Penesyan
School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney 2052, New South Wales, Australia
Mar Drugs 9:1391-402. 2011..We propose that TDA in isolate D323 and related eukaryote-associated bacteria plays a role in defending the host organism against unwanted microbial colonisation and, possibly, bacterial pathogens... - Thermodynamic activation properties of elongation factor 2 (EF-2) proteins from psychrotolerant and thermophilic ArchaeaKhawar Sohail Siddiqui
Microbiology and Immunology, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
Extremophiles 6:143-50. 2002.... - Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtoniiNeil F W Saunders
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
Genome Res 13:1580-8. 2003..This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles... - Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, AntarcticaCharmaine Ng
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
ISME J 4:1002-19. 2010..As a result we are able to propose an explanation of the active biological processes promoted by cold-adapted GSB and the adaptive strategies they use to thrive under the severe physiochemical conditions prevailing in polar environments... - Unlocking the diversity and biotechnological potential of marine surface associated microbial communitiesSuhelen Egan
School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney, NSW 2052, Australia
Curr Opin Microbiol 11:219-25. 2008.... - Assessing the effectiveness of functional genetic screens for the identification of bioactive metabolitesAnahit Penesyan
School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney 2052, New South Wales, Australia
Mar Drugs 11:40-9. 2013..Here we demonstrate that constructing libraries with strains known to produce bioactives can greatly enhance the screening efficiency, by increasing the "hit-rate" and unmasking multiple activities from the same bacterial source... - Community structure and functional gene profile of bacteria on healthy and diseased thalli of the red seaweed Delisea pulchraNeil Fernandes
The Centre for Marine Bio Innovation, University of New South Wales, Sydney, Australia
PLoS ONE 7:e50854. 2012.... - Reconstruction of ribosomal RNA genes from metagenomic dataLu Fan
School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney, New South Wales, Australia
PLoS ONE 7:e39948. 2012..Our approach is readily applicable to existing metagenomic datasets and is expected to lead to the discovery of new microbial phylotypes... - Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lungSharna Naughton
Department of Infectious Diseases and Immunology, University of Sydney, Sydney, Australia
PLoS ONE 6:e24526. 2011..Elucidation of these genes' roles could lead to targeted treatment strategies for chronically infected CF patients... - Simple high-throughput annotation pipeline (SHAP)Matthew Z DeMaere
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
Bioinformatics 27:2431-2. 2011..The software provides Grid capable analysis, relational storage and Web-based full-text searching of annotation results. Implemented in Java, SHAP recognizes the limited resources of many smaller research groups... - Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stressLu Fan
Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
ISME J 7:991-1002. 2013..High symbiont specialization and low functional redundancy, thus make these holobionts extremely vulnerable to environmental perturbations, including climate change... - Metaproteogenomic analysis of a community of sponge symbiontsMichael Liu
Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, NSW, Australia
ISME J 6:1515-25. 2012..Our data clearly show that a combined metaproteogenomic approach can provide novel information on the activities, physiology and interactions of sponge-associated microbial communities... - Functional genomic analysis of an uncultured δ-proteobacterium in the sponge Cymbastela concentricaMichael Yizhe Liu
Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
ISME J 5:427-35. 2011.... - The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptationMichelle A Allen
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
ISME J 3:1012-35. 2009.... - Metagenomic studies reveal the critical and wide-ranging ecological importance of uncultivated Archaea: the role of ammonia oxidizersRicardo Cavicchioli
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
Bioessays 29:11-4. 2007..1 These findings not only highlight the undoubtedly critical yet unknown roles that archaea play in global nutrient cycles but illustrate the importance of genomic studies for informing us about the functional capacity of life on Earth... - Harnessing single cell sorting to identify cell division genes and regulators in bacteriaCatherine Burke
The ithree Institute, University of Technology, Sydney, New South Wales, Australia
PLoS ONE 8:e60964. 2013..This novel screening strategy is applicable to a wide range of organisms, including pathogenic bacteria, where cell division genes and regulators are attractive drug targets for antibiotic development... - Draft Genome Sequence of the Chronic, Nonclonal Cystic Fibrosis Isolate Pseudomonas aeruginosa Strain 18AJerry K K Woo
School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio Innovation, University of New South Wales, Sydney, Australia
Genome Announc 1:e0000113. 2013..The genome of 18A was sequenced for comparison with environmental and clinical isolates to identify genes that might facilitate its persistence during infection... - An experimental model for the spatial structuring and selection of bacterial communitiesTorsten Thomas
Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
J Microbiol Methods 87:165-8. 2011..8 under conditions of protozoan grazing. The competitive benefit provided by spatial structuring has implications for the evolution of natural bacterial communities in the environment... - Primer fabrication using polymerase mediated oligonucleotide synthesisMurray J Cairns
Schizophrenia Research Institute, Sydney, NSW 2006, Australia
BMC Genomics 10:344. 2009..PMOS can be used to generate primers directly in the end-users laboratory within the context of any DNA polymerase chemistry such as in PCR or sequencing reactions.. - Selective extraction of bacterial DNA from the surfaces of macroalgaeCatherine Burke
School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, The University of New South Wales, Sydney 2052, Australia
Appl Environ Microbiol 75:252-6. 2009..The DNA is suitable for a variety of subsequent applications, including the construction of large-insert clone libraries and metagenomic sequencing... - GemSIM: general, error-model based simulator of next-generation sequencing dataKerensa E McElroy
Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
BMC Genomics 13:74. 2012..Empirical fragment length and quality score distributions are also used. Reads may be drawn from one or more genomes or haplotype sets, facilitating simulation of deep sequencing, metagenomic, and resequencing projects... - Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertionPui Yi Yung
Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2035 NSW, Australia
Nucleic Acids Res 37:e144. 2009..Our approach represents a valuable tool for the analysis of rapidly increasing, environmental DNA sequencing information... - A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomesSusanne M D Goldberg
J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 103:11240-5. 2006....