ORCID Profile
0000-0002-5829-6655
Current Organisation
Garvan Institute of Medical Research
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Publisher: Cold Spring Harbor Laboratory
Date: 02-06-2021
DOI: 10.1101/2021.06.02.444084
Abstract: Telopea speciosissima, the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for T. speciosissima . Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8 % of Embryophyta BUSCOs complete. We present a new method in Diploidocus ( limsuite/diploidocus ) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer ( limsuite/depthsizer ), for genome size estimation from the read depth of single copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2 n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA ( CYC ) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 ‘Duplicated’ BUSCO genes suggest almost all are real duplications, increasing confidence in protein family analysis using annotated protein-coding genes, and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level T. speciosissima reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.
Publisher: Springer Science and Business Media LLC
Date: 03-01-2022
DOI: 10.1038/S41587-021-01147-4
Abstract: Nanopore sequencing depends on the FAST5 file format, which does not allow efficient parallel analysis. Here we introduce SLOW5, an alternative format engineered for efficient parallelization and acceleration of nanopore data analysis. Using the ex le of DNA methylation profiling of a human genome, analysis runtime is reduced from more than two weeks to approximately 10.5 h on a typical high-performance computer. SLOW5 is approximately 25% smaller than FAST5 and delivers consistent improvements on different computer architectures.
Publisher: Wiley
Date: 10-11-2021
Abstract: Actinobacteria and Proteobacteria are important producers of bioactive natural products (NP), and these phyla dominate in the arid soils of Antarctica, where metabolic adaptations influence survival under harsh conditions. Biosynthetic gene clusters (BGCs) which encode NPs, are typically long and repetitious high G + C regions difficult to sequence with short‐read technologies. We sequenced 17 Antarctic soil bacteria from multi‐genome libraries, employing the long‐read PacBio platform, to optimize capture of BGCs and to facilitate a comprehensive analysis of their NP capacity. We report 13 complete bacterial genomes of high quality and contiguity, representing 10 different cold‐adapted genera including novel species. Antarctic BGCs exhibited low similarity to known compound BGCs (av. 31%), with an abundance of terpene, non‐ribosomal peptide and polyketide‐encoding clusters. Comparative genome analysis was used to map BGC variation between closely related strains from geographically distant environments. Results showed the greatest biosynthetic differences to be in a psychrotolerant Streptomyces strain, as well as a rare Actinobacteria genus, Kribbella , while two other Streptomyces spp. were surprisingly similar to known genomes. Streptomyces and Kribbella BGCs were predicted to encode antitumour, antifungal, antibacterial and biosurfactant‐like compounds, and the synthesis of NPs with antibacterial, antifungal and surfactant properties was confirmed through bioactivity assays.
Publisher: EMBO
Date: 11-11-2016
Abstract: RNA sequencing studies have identified hundreds of non‐coding RNA s in bacteria, including regulatory small RNA ( sRNA ). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high‐throughput analysis of RNA – RNA interactions in bacteria. Here we demonstrate that in vivo sRNA – mRNA duplexes can be recovered using UV ‐crosslinking, ligation and sequencing of hybrids ( CLASH ). Many sRNA s recruit the endoribonuclease, RN ase E, to facilitate processing of mRNA s. We were able to recover base‐paired sRNA – mRNA duplexes in association with RN ase E, allowing proximity‐dependent ligation and sequencing of cognate sRNA – mRNA pairs as chimeric reads. We verified that this approach captures bona fide sRNA – mRNA interactions. Clustering analyses identified novel sRNA seed regions and sets of potentially co‐regulated target mRNA s. We identified multiple mRNA targets for the pathotype‐specific sRNA Esr41, which was shown to regulate colicin sensitivity and iron transport in E. coli . Numerous sRNA interactions were also identified with non‐coding RNA s, including sRNA s and tRNA s, demonstrating the high complexity of the sRNA interactome.
Publisher: Research Square Platform LLC
Date: 14-04-2022
DOI: 10.21203/RS.3.RS-1495587/V1
Abstract: Chimeric antigen receptor (CAR) T cells have demonstrable efficacy in treating B-cell malignancies. Factors such as product composition, lymphodepletion and immune reconstitution are known to influence functional persistence of CAR+ T cells. However, little is known about the determinants of differentiation and phenotypic plasticity of CAR+ T and immune cells early post-infusion. We report single cell multi-omics analysis of molecular, clonal, and phenotypic profiles of CAR+ T and other immune cells circulating in patients receiving donor-derived products. We used these data to reconstruct a differentiation trajectory, which explained the observed phenotypic plasticity and identified cell fate of CAR+ and CAR- T cells. Following lympho-depletion, endogenous CAR- CD8+ and 𝛾ẟ T cells, clonally expand, and differentiate across heterogenous phenotypes, from a dominant resting or proliferating state into precursor of exhausted T cells, and notably into a terminal NK-like phenotype. In parallel, following infusion, CAR+ T cells undergo a similar differentiation trajectory, showing increased proliferation, metabolic activity and exhaustion when compared to circulating CAR- T cells. The subset of NK-like CAR+ T cells was associated with increasing levels of circulating proinflammatory cytokines, including innate-like IL-12 and IL-18. These results demonstrate that differentiation and phenotype of CAR+ T cells are determined by non-CAR induced signals that are shared with endogenous T cells, and condition the patients’ immune-recovery.
Publisher: Cold Spring Harbor Laboratory
Date: 23-06-2021
DOI: 10.1101/2021.06.22.449521
Abstract: Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a erse family of Australo-Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae erged from Asian elapids ∼30 Mya and have since rapidly ersified into six hibious, ∼60 marine and ∼100 terrestrial species which fill a broad range of ecological niches. We find TE ersity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.
Publisher: Cold Spring Harbor Laboratory
Date: 17-09-2023
Publisher: MDPI AG
Date: 25-01-2022
Abstract: Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a erse family of Australo–Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae erged from Asian elapids ~30 Mya and have since rapidly ersified into six hibious, ~60 marine and ~100 terrestrial species that fill a broad range of ecological niches. We find TE ersity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.
Publisher: Cold Spring Harbor Laboratory
Date: 20-06-2022
DOI: 10.1101/2022.06.19.496732
Abstract: Nanopore sequencing is an emerging technology that is being rapidly adopted in research and clinical genomics. We recently developed SLOW5, a new file format for storage and analysis of raw data from nanopore sequencing experiments. SLOW5 is a community-centric, open source format that offers considerable performance benefits over the existing nanopore data format, known as FAST5. Here we introduce slow5tools , a simple, intuitive toolkit for handling nanopore raw signal data in SLOW5 format. Slow5tools enables lossless FAST5-to-SLOW5 and SLOW5-to-FAST5 data conversion, and a range of tools for structuring, indexing, viewing and querying SLOW5 files. Slow5tools uses multi-threading, multi-processing and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We outline a series of ex les and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its high performance. Slow5tools is an essential toolkit for handling nanopore signal data, which was developed to support adoption of SLOW5 by the nanopore community. Slow5tools is written in C/C++ with minimal dependencies and is freely available as an open-source program under an MIT licence: asindu2008/slow5tools .
Publisher: Wiley
Date: 11-01-2022
Abstract: Telopea speciosissima , the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome‐level genome for T . speciosissima . Combining Oxford Nanopore long‐reads, 10x Genomics Chromium linked‐reads and Hi‐C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8% of Embryophyta BUSCOs “Complete”. We present a new method in Diploidocus ( limsuite/diploidocus ) for classifying, curating and QC‐filtering scaffolds, which combines read depths, k ‐mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer ( limsuite/depthsizer ), for genome size estimation from the read depth of single‐copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1% of the assembly, conforming to the expected number of chromosomes (2 n = 22). Genome annotation predicted 40,158 protein‐coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA ( CYC ) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 “Duplicated” BUSCO genes using a new tool, DepthKopy ( limsuite/depthkopy ), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome‐level T . speciosissima reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.
Publisher: Springer Science and Business Media LLC
Date: 06-06-2016
Publisher: Springer Science and Business Media LLC
Date: 11-08-2017
Publisher: Cold Spring Harbor Laboratory
Date: 30-06-2021
DOI: 10.1101/2021.06.29.450255
Abstract: Nanopore sequencing is an emerging genomic technology with great potential. However, the storage and analysis of nanopore sequencing data have become major bottlenecks preventing more widespread adoption in research and clinical genomics. Here, we elucidate an inherent limitation in the file format used to store raw nanopore data – known as FAST5 – that prevents efficient analysis on high-performance computing (HPC) systems. To overcome this, we have developed SLOW5, an alternative file format that permits efficient parallelisation and, thereby, acceleration of nanopore data analysis. For ex le, we show that using SLOW5 format, instead of FAST5, reduces the time and cost of genome-wide DNA methylation profiling by an order of magnitude on common HPC systems, and delivers consistent improvements on a wide range of different architectures. With a simple, accessible file structure and a ~ 25% reduction in size compared to FAST5, SLOW5 format will deliver substantial benefits to all areas of the nanopore community.
Publisher: Springer Science and Business Media LLC
Date: 06-07-2021
DOI: 10.1038/S41467-021-24442-9
Abstract: Spi-1 Proto-Oncogene (SPI1) fusion genes are recurrently found in T-cell acute lymphoblastic leukemia (T-ALL) cases but are insufficient to drive leukemogenesis. Here we show that SPI1 fusions in combination with activating NRAS mutations drive an immature T-ALL in vivo using a conditional bone marrow transplant mouse model. Addition of the oncogenic fusion to the NRAS mutation also results in a higher leukemic stem cell frequency. Mechanistically, genetic deletion of the β-catenin binding domain within Transcription factor 7 ( TCF7)-SPI1 or use of a TCF/β-catenin interaction antagonist abolishes the oncogenic activity of the fusion. Targeting the TCF7-SPI1 fusion in vivo with a doxycycline-inducible knockdown results in increased differentiation. Moreover, both pharmacological and genetic inhibition lead to down-regulation of SPI1 targets. Together, our results reveal an ex le where TCF7-SPI1 leukemia is vulnerable to pharmacological targeting of the TCF/β-catenin interaction.
Publisher: The American Association of Immunologists
Date: 15-02-2016
Abstract: CMV is the most common congenital infection in the United States. The major target of congenital CMV is the brain, with clinical manifestations including mental retardation, vision impairment, and sensorineural hearing loss. Previous reports have shown that CD8+ T cells are required to control viral replication and significant numbers of CMV-specific CD8+ T cells persist in the brain even after the initial infection has been cleared. However, the dynamics of CD8+ T cells in the brain during latency remain largely undefined. In this report, we used TCR sequencing to track the development and maintenance of neonatal clonotypes in the brain and spleen of mice during chronic infection. Given the discontinuous nature of tissue-resident memory CD8+ T cells, we hypothesized that neonatal TCR clonotypes would be locked in the brain and persist into adulthood. Surprisingly, we found that the Ag-specific T cell repertoire in neonatal-infected mice ersified during persistent infection in both the brain and spleen, while maintaining substantial similarity between the CD8+ T cell populations in the brain and spleen in both early and late infection. However, despite the ersification of, and potential interchange between, the spleen and brain Ag-specific T cell repertoires, we observed that germline-encoded TCR clonotypes, characteristic of neonatal infection, persisted in the brain, albeit sometimes in low abundance. These results provide valuable insights into the evolution of CD8+ T cell repertoires following neonatal CMV infection and thus have important implications for the development of therapeutic strategies to control CMV in early life.
Publisher: Research Square Platform LLC
Date: 13-07-2021
DOI: 10.21203/RS.3.RS-668517/V1
Abstract: Nanopore sequencing is an emerging genomic technology with great potential. However, the storage and analysis of nanopore sequencing data have become major bottlenecks preventing more widespread adoption in research and clinical genomics. Here, we elucidate an inherent limitation in the file format used to store raw nanopore data – known as FAST5 – that prevents efficient analysis on high-performance computing (HPC) systems. To overcome this we have developed SLOW5, an alternative file format that permits efficient parallelisation and, thereby, acceleration of nanopore data analysis. For ex le, we show that using SLOW5 format, instead of FAST5, reduces the time and cost of genome-wide DNA methylation profiling by an order of magnitude on common HPC systems, and delivers consistent improvements on a wide range of different architectures. With a simple, accessible file structure and a ~25% reduction in size compared to FAST5, SLOW5 format will deliver substantial benefits to all areas of the nanopore community.
No related grants have been discovered for Timothy Amos.