ORCID Profile
0000-0002-9762-6573
Current Organisations
CSIRO Marine and Atmospheric Research
,
University of Technology Sydney
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Ecology | Ecological Physiology | Phycology (incl. Marine Grasses) | Gene Expression (incl. Microarray and other genome-wide approaches) | Environmental Chemistry (incl. Atmospheric Chemistry) | Global Change Biology
Ecosystem Assessment and Management of Marine Environments | Ecosystem Adaptation to Climate Change | Physical and Chemical Conditions of Water in Marine Environments |
Publisher: Cold Spring Harbor Laboratory
Date: 11-03-2021
DOI: 10.1101/2021.03.10.434861
Abstract: Quality control checks are the first step in RNA-Sequencing analysis, which enable the identification of common issues that occur in the sequenced reads. Checks for sequence quality, contamination, and complexity are commonplace, and allow users to implement steps downstream which can account for these issues. Strand-specificity of reads is frequently overlooked and is often unavailable even in published data, yet when unknown or incorrectly specified can have detrimental effects on the reproducibility and accuracy of downstream analyses. We present how_are_we_stranded_here, a Python library that helps to quickly infer strandedness of paired-end RNA-Sequencing data.
Publisher: Springer Science and Business Media LLC
Date: 2012
Publisher: Open Science Framework
Date: 2017
Publisher: Zenodo
Date: 2018
Publisher: Cold Spring Harbor Laboratory
Date: 03-01-2023
DOI: 10.1101/2023.01.02.522487
Abstract: Diatoms are photosynthetic unicellular microalgae that drive global ecological phenomena in the biosphere and are emerging sustainable feedstock for an increasing number of industrial applications. Diatoms exhibit enormous taxonomic and genetic ersity, which often result in peculiar biochemical and biological traits. Transposable elements (TE) represent a substantial portion of diatom genomes and have been hypothesized to exert a relevant role in enriching genetic ersity and centrally contribute to genome evolution. Here, through long-read whole genome sequencing, we identified a novel Mutator-Like Element (MULE) in the model diatom Phaeodactylum tricornutum, and we report the direct observation of its mobilization within the course of one single laboratory experiment. Under selective conditions, this novel TE inactivated the uridine monophosphate synthase ( UMPS ) gene of P. tricornutum, one of the two only endogenous genetic loci currently targeted for selectable auxotrophy in functional genetics and genome editing applications. We report the first, real-time observation of the mobilization of a transposon in diatoms that possesses novel peculiar features. These include the combined presence of a MULE transposase domain with Zinc finger, SWIM-type domains, and of a diatom-specific E3 ubiquitin ligase of the zinc finger UBR type, which indicate a novel mobilization mechanism. Our findings provide new elements for the understanding of the role of TEs in diatom genome evolution and in the enrichment of intraspecific genetic variability. Ultimately, this raises relevant concerns on the targeting of loci such as UMPS as selectable markers for functional genetics and biotechnological applications in diatoms. We identified a novel DNA transposon in the diatom Phaeodactylum tricornutum . This new Mutator-Like Element encodes a transposase and a diatom-specific E3 ubiquitin ligase, which suggest a novel mobilization mechanism. We documented independent insertions in real-time, which spontaneously inactivated the uridine monophosphate synthase ( UMPS ) locus, a common selectable marker. We provide new insights on the role of transposons in diatom genome dynamics and evolution and on the unsuitability of UMPS as selection locus in diatoms.
Publisher: Frontiers Media SA
Date: 15-11-2018
Publisher: Elsevier BV
Date: 04-2016
DOI: 10.1016/J.CUB.2016.01.007
Abstract: Kahle and Umbers introduce the ways by which organisms emit light though chemical reactions.
Publisher: Elsevier BV
Date: 12-2019
DOI: 10.1016/J.MARPOLBUL.2019.110556
Abstract: Copper (Cu) in an essential trace metal but it can also contaminate coastal waters at high concentrations mainly from agricultural run-off and mining activities which are detrimental to marine organisms including seagrasses. The molecular mechanisms driving Cu toxicity in seagrasses are not clearly understood yet. Here, we investigated the molecular responses of the Australian seagrass, Z. muelleri at the whole transcriptomic level after 7 days of exposure to 250 μg Cu L
Publisher: Springer Science and Business Media LLC
Date: 04-02-2015
Publisher: Portland Press Ltd.
Date: 06-2017
DOI: 10.1042/CS20170063
Abstract: Phosphoinositide 3-kinase [PI3K (p110α)] is able to negatively regulate the diabetes-induced increase in NADPH oxidase in the heart. Patients affected by diabetes exhibit significant cardiovascular morbidity and mortality, at least in part due to a cardiomyopathy characterized by oxidative stress and left ventricular (LV) dysfunction. Thus, PI3K (p110α) may represent a novel approach to protect the heart from diabetes-induced cardiac oxidative stress and dysfunction. In the present study, we investigated the therapeutic potential of a delayed intervention with cardiac-targeted PI3K gene therapy, administered to mice with established diabetes-induced LV diastolic dysfunction. Diabetes was induced in 6-week-old male mice by streptozotocin (STZ). After 8 weeks of untreated diabetes, LV diastolic dysfunction was confirmed by a reduction in echocardiography-derived transmitral E/A ratio. Diabetic and non-diabetic mice were randomly allocated to receive either recombinant adeno-associated viral vector-6 carrying a constitutively-active PI3K construct (recombinant adeno-associated-virus 6-constitutively active PI3K (p110α) (caPI3K) (rAAV6-caPI3K), single i.v. injection, 2 × 1011 vector genomes) or null vector, and were followed for a further 6 or 8 weeks. At study endpoint, diabetes-induced LV dysfunction was significantly attenuated by a single administration of rAAV6-caPI3K, administered 8 weeks after the induction of diabetes. Diabetes-induced impairments in each of LV NADPH oxidase, endoplasmic reticulum (ER) stress, apoptosis, cardiac fibrosis and cardiomyocyte hypertrophy, in addition to LV systolic dysfunction, were attenuated by delayed intervention with rAAV6-caPI3K. Hence, our demonstration that cardiac-targeted PI3K (p110α) gene therapy limits diabetes-induced up-regulation of NADPH oxidase and cardiac remodelling suggests new insights into promising approaches for the treatment of diabetic cardiomyopathy, at a clinically relevant time point (after diastolic dysfunction is manifested).
Publisher: Oxford University Press (OUP)
Date: 17-07-2014
DOI: 10.1093/JAC/DKU271
Publisher: Springer International Publishing
Date: 2020
Publisher: Frontiers Media SA
Date: 09-05-2017
Publisher: Wiley
Date: 17-01-2019
DOI: 10.1002/ECE3.4662
Publisher: Wiley
Date: 10-10-2019
Publisher: Public Library of Science (PLoS)
Date: 17-12-2012
Publisher: Elsevier BV
Date: 03-2020
DOI: 10.1016/J.WATRES.2019.115405
Abstract: While the significance of Arcobacter in clinical settings grows, the ecological dynamics of potentially pathogenic Arcobacter in coastal marine environments remains unclear. In this study, we monitored the temporal dynamics of Arcobacter at an urban beach subject to significant stormwater input and wet weather sewer overflows (WWSO). Weekly monitoring of bacterial communities over 24 months using 16S rRNA licon sequencing revealed large, intermittent peaks in the relative abundance of Arcobacter. Quantitative PCR was subsequently employed to track absolute abundance of Arcobacter 23S rRNA gene copies, revealing peaks in abundance reaching up to 10
Publisher: Springer Science and Business Media LLC
Date: 17-07-2018
Abstract: Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Bio ersity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic licon sequencing data describing Bacteria , Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. S les are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30 ° of latitude and ~38 ° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 s les are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 s les are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.
Publisher: F1000 Research Ltd
Date: 06-12-2018
DOI: 10.12688/F1000RESEARCH.16905.1
Abstract: High-throughput molecular methods such as quantitative polymerase chain reaction (qPCR) and environmental microarrays are cost-effective methods for semi-quantitative assessment of bacterial community structure and the identification of specific target organisms. Both techniques rely on short nucleotide sequences, so-called oligonucleotide probes, which require high specificity to the organisms in question to avoid cross-hybridization with non-target taxa. However, designing oligonucleotide probes for novel taxa or marker genes that show sufficient phylogenetic sensitivity and specificity is often time- and labor-intensive, as each probe has to be in-silico tested for its specificity and sensitivity. Here we present ProbeSpec, to our knowledge the first batch sensitivity and specificity estimation and visualization tool for oligonucleotide probes integrated into the widely used ARB software. Using ProbeSpec’s interactive “mismatch threshold” and “clade marked threshold” we were able to reduce the development time of highly specific probes for a recently published environmental oligonucleotide microarray from several months to one week.
Publisher: Cold Spring Harbor Laboratory
Date: 11-04-2022
DOI: 10.1101/2022.04.10.487810
Abstract: Coral reefs are fundamentally sustained by symbioses involving dinoflagellate algae in the Family Symbiodiniaceae. The coral symbiont Durusdinium trenchii is notable for enhancing the resilience of coral holobionts under thermal stress. Believed to have experienced whole-genome duplication (WGD), D. trenchii offers a valuable model system to understand how selection acts on the genome of a facultative symbiont after WGD. We present genome assemblies for two isolates of D. trenchii and confirm WGD in these taxa, providing the first ex le of this phenomenon in a single-celled eukaryotic symbiont. We assess how the facultative lifestyle has contributed to the retention and ergence of duplicated genes, and how these results intersect with the observed thermotolerance of corals hosting D. trenchii symbionts. Our findings reveal that the free-living lifestyle is the main driver of post-WGD evolution, however, they also implicate symbiosis in this process, with both lifestyles increasing algal fitness. Our results demonstrate that WGD, driven by selection in the free-living phase, has converted D. trenchii into a coral symbiont that serendipitously provides increased thermal stress protection to the host coral.
Publisher: Wiley
Date: 04-11-2016
DOI: 10.1111/MMI.13229
Abstract: Prior to the discovery of a minimal ATP-dependent DNA ligase in Haemophilus influenzae, bacteria were thought to only possess a NAD-dependent ligase, which was involved in sealing of Okazaki fragments. We now know that a erse range of bacterial species possess up to six of these accessory bacterial ATP-dependent DNA ligases (b-ADLs), which vary in size and enzymatic domain associations. Here we compare the domain structure of different types of b-ADLs and investigate their distribution among the bacterial domain to describe possible evolutionary trajectories that gave rise to the sequence and structural ersity of these enzymes. Previous biochemical and genetic analyses have delineated three main classes of these enzymes: Lig B, Lig C and Lig D, which appear to have descended from a common ancestor within the bacterial domain. In the present study, we delineate a fourth group of b-ADLs, Lig E, which possesses a number of unique features at the primary and tertiary structural levels. The biochemical characteristics, domain structure and inferred extracellular location sets this group apart from the other b-ADLs. The results presented here indicate that the Lig E type ligases were horizontally transferred into bacteria in a separate event from other b-ADLs possibly from a bacteriophage.
Publisher: F1000 Research Limited
Date: 2018
Publisher: F1000 Research Limited
Date: 2018
Publisher: Frontiers Media SA
Date: 15-08-2017
Publisher: Cold Spring Harbor Laboratory
Date: 14-04-2021
DOI: 10.1101/2021.04.12.439551
Abstract: ORF prediction in de-novo assembled transcriptomes is a critical step for RNA-Seq analysis and transcriptome annotation. However, current approaches do not appropriately account for factors such as strand-specificity and incompletely assembled transcripts. Strand-specific RNA-Seq libraries should produce assembled transcripts in the correct orientation, and therefore ORFs should only be annotated on the sense strand. Additionally, start site selection is more complex than appreciated as sequences upstream of the first start codon need to be correctly annotated as 5’ UTR in completely assembled transcripts, or part of the main ORF in incomplete transcripts. Both of these factors influence the accurate annotation of ORFs and therefore the transcriptome as a whole. We generated four de-novo transcriptome assemblies of well annotated species as a gold-standard dataset to test the impact strand specificity and start site selection have on ORF prediction in real data. Our results show that prediction of ORFs on the antisense strand in data from stranded RNA libraries results in false-positive ORFs with no or very low similarity to known proteins. In addition, we found that up to 23% of assembled transcripts had no stop codon upstream and in-frame of the first start codon, instead comprising a sequence of upstream codons. We found the optimal length cutoff of these upstream sequences to accurately classify these transcripts as either complete (upstream sequence is 5’ UTR) or 5’ incomplete (transcript is incompletely assembled and upstream sequence is part of the ORF). Here, we present Borf, the better ORF finder, specifically designed to minimise false-positive ORF prediction in stranded RNA-Seq data and improve annotation of ORF start-site prediction accuracy. Borf is written in Python3 and freely available at etsig/borf .
Publisher: Springer Science and Business Media LLC
Date: 21-03-2017
DOI: 10.1038/NCOMMS14774
Abstract: We have previously shown higher-than-expected rates of schizophrenia in relatives of patients with amyotrophic lateral sclerosis (ALS), suggesting an aetiological relationship between the diseases. Here, we investigate the genetic relationship between ALS and schizophrenia using genome-wide association study data from over 100,000 unique in iduals. Using linkage disequilibrium score regression, we estimate the genetic correlation between ALS and schizophrenia to be 14.3% (7.05–21.6 P =1 × 10 −4 ) with schizophrenia polygenic risk scores explaining up to 0.12% of the variance in ALS ( P =8.4 × 10 −7 ). A modest increase in comorbidity of ALS and schizophrenia is expected given these findings (odds ratio 1.08–1.26) but this would require very large studies to observe epidemiologically. We identify five potential novel ALS-associated loci using conditional false discovery rate analysis. It is likely that shared neurobiological mechanisms between these two disorders will engender novel hypotheses in future preclinical and clinical studies.
Publisher: Springer Science and Business Media LLC
Date: 06-02-2009
Publisher: Wiley
Date: 23-01-2020
Abstract: The intimate relationship between scleractinian corals and their associated microorganisms is fundamental to healthy coral reef ecosystems. Coral-associated microbes (Symbiodiniaceae and other protists, bacteria, archaea, fungi and viruses) support coral health and resilience through metabolite transfer, inter-partner signalling, and genetic exchange. However, much of our understanding of the coral holobiont relationship has come from studies that have investigated either coral-Symbiodiniaceae or coral-bacteria interactions in isolation, while relatively little research has focused on other ecological and metabolic interactions potentially occurring within the coral multi-partner symbiotic network. Recent evidences of intimate coupling between phytoplankton and bacteria have demonstrated that obligate resource exchange between partners fundamentally drives their ecological success. Here, we posit that similar associations with bacterial consortia regulate Symbiodiniaceae productivity and are in turn central to the health of corals. Indeed, we propose that this bacteria-Symbiodiniaceae-coral relationship underpins the coral holobiont's nutrition, stress tolerance and potentially influences the future survival of coral reef ecosystems under changing environmental conditions. Resolving Symbiodiniaceae-bacteria associations is therefore a logical next step towards understanding the complex multi-partner interactions occurring in the coral holobiont.
Publisher: Cold Spring Harbor Laboratory
Date: 27-06-2019
DOI: 10.1101/683383
Abstract: From publicly available next-gen sequencing datasets of non-model organisms, such as marine protists, arise opportunities to explore their evolutionary relationships. In this study we explored the effects that dataset and model selection have on the phylogenetic inference of the Gonyaulacales, single celled marine algae of the phylum Dinoflagellata with genomes that show extensive paralogy. We developed a method for identifying and extracting single copy genes from RNA-seq libraries and compared phylogenies inferred from these single copy genes with those inferred from commonly used genetic markers and phylogenetic methods. Comparison of two datasets and three different phylogenetic models showed that exclusive use of ribosomal DNA sequences, maximum likelihood and gene concatenation showed very different results to that obtained with the multi-species coalescent. The multi-species coalescent has recently been recognized as being robust to the inclusion of paralogs, including hidden paralogs present in single copy gene sets (pseudoorthologs). Comparisons of model fit strongly favored the multi-species coalescent for these data, over a concatenated alignment (single tree) model. Our findings suggest that the multi-species coalescent (inferred either via Maximum Likelihood or Bayesian Inference) should be considered for future phylogenetic studies of organisms where accurate selection of orthologs is difficult.
Publisher: Springer Science and Business Media LLC
Date: 31-07-2021
DOI: 10.1007/S00248-021-01823-7
Abstract: Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef bio ersity and functional complexity. We examined the ersity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp. Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA licon sequencing, bacterial ersity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad ersity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.
Publisher: Wiley
Date: 20-06-2023
DOI: 10.1111/TPJ.16271
Abstract: Diatoms are photosynthetic unicellular microalgae that drive global ecological phenomena in the biosphere and are emerging as sustainable feedstock for an increasing number of industrial applications. Diatoms exhibit enormous taxonomic and genetic ersity, which often results in peculiar biochemical and biological traits. Transposable elements (TEs) represent a substantial portion of diatom genomes and have been hypothesized to exert a relevant role in enriching genetic ersity and making a core contribution to genome evolution. Here, through long‐read whole‐genome sequencing, we identified a mutator‐like element (MULE) in the model diatom Phaeodactylum tricornutum , and we report the direct observation of its mobilization within the course of a single laboratory experiment. Under selective conditions, this TE inactivated the uridine monophosphate synthase ( UMPS ) gene of P. tricornutum , one of the few endogenous genetic loci currently targeted for selectable auxotrophy for functional genetics and genome‐editing applications. We report the observation of a recently mobilized transposon in diatoms with unique features. These include the combined presence of a MULE transposase with zinc‐finger SWIM‐type domains and a diatom‐specific E3 ubiquitin ligase of the zinc‐finger UBR type, which are suggestive of a mobilization mechanism. Our findings provide new elements for the understanding of the role of TEs in diatom genome evolution and in the enrichment of intraspecific genetic variability.
Publisher: Wiley
Date: 12-2018
Abstract: Dinoflagellates of the genus Symbiodinium underpin the survival and ecological success of corals. The use of cultured strains has been particularly important to disentangle the complex life history of Symbiodinium and their contribution to coral host physiology. However, these cultures typically harbour abundant bacterial communities which likely play important, but currently unknown, roles in Symbiodinium biology. We characterized the bacterial communities living in association with a wide phylogenetic ersity of Symbiodinium cultures (18 types spanning 5 clades) to define the core Symbiodinium microbiome. Similar to other systems, bacteria were nearly two orders of magnitude more numerically abundant than Symbiodinium cells and we identified three operational taxonomic units (OTUs) which were present in all cultures. These represented the α-proteobacterium Labrenzia and the γ-proteobacteria Marinobacter and Chromatiaceae. Based on the abundance and functional potential of bacteria harboured in these cultures, their contribution to Symbiodinium physiology can no longer be ignored.
Start Date: 04-2020
End Date: 03-2023
Amount: $511,014.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2016
End Date: 12-2018
Amount: $398,800.00
Funder: Australian Research Council
View Funded Activity