Publications by authors named "Alun Jones"

155 Publications

Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype.

Nat Commun 2021 05 11;12(1):2678. Epub 2021 May 11.

Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.

Intellectual disability (ID) and autism spectrum disorder (ASD) are the most common neurodevelopmental disorders and are characterized by substantial impairment in intellectual and adaptive functioning, with their genetic and molecular basis remaining largely unknown. Here, we identify biallelic variants in the gene encoding one of the Elongator complex subunits, ELP2, in patients with ID and ASD. Modelling the variants in mice recapitulates the patient features, with brain imaging and tractography analysis revealing microcephaly, loss of white matter tract integrity and an aberrant functional connectome. We show that the Elp2 mutations negatively impact the activity of the complex and its function in translation via tRNA modification. Further, we elucidate that the mutations perturb protein homeostasis leading to impaired neurogenesis, myelin loss and neurodegeneration. Collectively, our data demonstrate an unexpected role for tRNA modification in the pathogenesis of monogenic ID and ASD and define Elp2 as a key regulator of brain development.
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http://dx.doi.org/10.1038/s41467-021-22888-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8113450PMC
May 2021

In vivo proteomic mapping through GFP-directed proximity-dependent biotin labelling in zebrafish.

Elife 2021 Feb 16;10. Epub 2021 Feb 16.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.

Protein interaction networks are crucial for complex cellular processes. However, the elucidation of protein interactions occurring within highly specialised cells and tissues is challenging. Here, we describe the development, and application, of a new method for proximity-dependent biotin labelling in whole zebrafish. Using a conditionally stabilised GFP-binding nanobody to target a biotin ligase to GFP-labelled proteins of interest, we show tissue-specific proteomic profiling using existing GFP-tagged transgenic zebrafish lines. We demonstrate the applicability of this approach, termed BLITZ (Biotin Labelling In Tagged Zebrafish), in diverse cell types such as neurons and vascular endothelial cells. We applied this methodology to identify interactors of caveolar coat protein, cavins, in skeletal muscle. Using this system, we defined specific interaction networks within in vivo muscle cells for the closely related but functionally distinct Cavin4 and Cavin1 proteins.
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http://dx.doi.org/10.7554/eLife.64631DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7906605PMC
February 2021

Structural Changes in Cell-Wall and Cell-Membrane Organic Materials Following Exposure to Free Nitrous Acid.

Environ Sci Technol 2020 08 6;54(16):10301-10312. Epub 2020 Aug 6.

Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, QLD 4072, Australia.

Previous studies demonstrate that free nitrous acid (FNA, i.e., HNO) is biocidal for a range of microorganisms. The biocidal mechanisms of FNA are largely unknown. In this work, it is hypothesized that FNA will break bonds in molecules found in the cell envelope, thus causing cell lysis. Selected molecules representing components found in the cell envelope were treated with FNA at 6.09 mg N/L (NO = 250 mg N/L, pH 5.0) for 24 h (conditions typically used in applications) to evaluate the hypothesized chemical interactions. Molecular changes were observed using analytical techniques including proton (H) nuclear magnetic resonance spectroscopy (NMR) and electrospray ionization mass spectrometry (ESI-MS). It was found that FNA broke down a range of cell envelope molecules. The spectral data demonstrated that the FNA reactions proceeded via two general pathways. One consisted of electrophilic substitution, whereby the nitrosonium ion (NO) was the reactive electrophile. The other was via oxidative reactions involving nitrogen radicals (e.g., •NO and •NO) formed from the decomposition of FNA. We further revealed that it was HNO that caused the breakdown, rather than the exclusive action of the acid (H) or nitrite (NO) counterparts. The fragmentation of these representative cell envelope molecules provides insight into the biocidal effects of FNA on microorganisms.
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http://dx.doi.org/10.1021/acs.est.0c01453DOI Listing
August 2020

Evidence of capacitation in the parasitoid wasp, and its potential role in sex allocation.

Ecol Evol 2020 Jul 1;10(14):7212-7220. Epub 2020 Jun 1.

Department of Genetics and Genome Biology University of Leicester Leicester UK.

The allocation of resources to the production of one sex or another has been observed in a large variety of animals. Its theoretical basis allows accurate predictions of offspring sex ratios in many species, but the mechanisms by which sex allocation is controlled are poorly understood. Using previously published data, we investigated whether alternative splicing, combined with differential gene expression, was involved with sex allocation in the parasitoid wasp, . We found that sex allocation is not controlled by alternative splicing but changes in gene and transcript-specific expression, which were identified to be involved with oviposition, were shown to be similar to those involved in sperm motility and capacitation. Genes involved in cholesterol efflux, a key component of capacitation, along with calcium transport, neurotransmission, trypsin, and MAPKinase activity were regulated in ovipositing wasps. The results show evidence for regulation of sperm motility and of capacitation in an insect which, in the context of the physiology of the spermatheca, could be important for sex allocation.
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http://dx.doi.org/10.1002/ece3.6422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391552PMC
July 2020

Bumblebee Workers Show Differences in Allele-Specific DNA Methylation and Allele-Specific Expression.

Genome Biol Evol 2020 08;12(8):1471-1481

Department of Genetics and Genome Biology, University of Leicester, United Kingdom.

Allele-specific expression is when one allele of a gene shows higher levels of expression compared with the other allele, in a diploid organism. Recent work has identified allele-specific expression in a number of Hymenopteran species. However, the molecular mechanism which drives this allelic expression bias remains unknown. In mammals, DNA methylation is often associated with genes which show allele-specific expression. DNA methylation systems have been described in species of Hymenoptera, providing a candidate mechanism. Using previously generated RNA-Seq and whole-genome bisulfite sequencing from reproductive and sterile bumblebee (Bombus terrestris) workers, we have identified genome-wide allele-specific expression and allele-specific DNA methylation. The majority of genes displaying allele-specific expression are common between reproductive and sterile workers and the proportion of allele-specific expression bias generally varies between genetically distinct colonies. We have also identified genome-wide allele-specific DNA methylation patterns in both reproductive and sterile workers, with reproductive workers showing significantly more genes with allele-specific methylation. Finally, there is no significant overlap between genes showing allele-specific expression and allele-specific methylation. These results indicate that cis-acting DNA methylation does not directly drive genome-wide allele-specific expression in this species.
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http://dx.doi.org/10.1093/gbe/evaa132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7502211PMC
August 2020

Class IIa Histone Deacetylases Drive Toll-like Receptor-Inducible Glycolysis and Macrophage Inflammatory Responses via Pyruvate Kinase M2.

Cell Rep 2020 02;30(8):2712-2728.e8

Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia. Electronic address:

Histone deacetylases (HDACs) drive innate immune cell-mediated inflammation. Here we identify class IIa HDACs as key molecular links between Toll-like receptor (TLR)-inducible aerobic glycolysis and macrophage inflammatory responses. A proteomic screen identified the glycolytic enzyme pyruvate kinase M isoform 2 (Pkm2) as a partner of proinflammatory Hdac7 in murine macrophages. Myeloid-specific Hdac7 overexpression in transgenic mice amplifies lipopolysaccharide (LPS)-inducible lactate and promotes a glycolysis-associated inflammatory signature. Conversely, pharmacological or genetic targeting of Hdac7 and other class IIa HDACs attenuates LPS-inducible glycolysis and accompanying inflammatory responses in macrophages. We show that an Hdac7-Pkm2 complex acts as an immunometabolism signaling hub, whereby Pkm2 deacetylation at lysine 433 licenses its proinflammatory functions. Disrupting this complex suppresses inflammatory responses in vitro and in vivo. Class IIa HDACs are thus pivotal intermediates connecting TLR-inducible glycolysis to inflammation via Pkm2.
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http://dx.doi.org/10.1016/j.celrep.2020.02.007DOI Listing
February 2020

Multiple Reaction Monitoring for the Accurate Quantification of Amino Acids: Using Hydroxyproline to Estimate Collagen Content.

Methods Mol Biol 2019 ;2030:33-45

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.

Multiple reaction monitoring (MRM) mass spectrometry may be regarded as the gold standard methodology for quantitative mass spectrometry and has been adopted for the analysis of small molecules especially within the pharmaceutical industry. It can also be applied to the analysis of peptides and proteins and to measurement of the basic building blocks of proteins, amino acids. Here we describe the application of MRM mass spectrometry to the measurement of hydroxyproline after acid hydrolysis of various animal tissues. We show that measurement of hydroxyproline provides an accurate and reliable estimate of the collagen content of such tissues and may be a useful indicator of meat tenderness.
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http://dx.doi.org/10.1007/978-1-4939-9639-1_4DOI Listing
April 2020

Investigation of the estuarine stonefish (Synanceia horrida) venom composition.

J Proteomics 2019 06 4;201:12-26. Epub 2019 Apr 4.

Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia. Electronic address:

The Estuarine stonefish (Synanceia horrida) is recognised as one of the most venomous fish species in the world but the overall venom composition has yet to be investigated using in-depth transcriptomic and proteomic methods. To date, known venom components are restricted to a hyaluronidase and a large, pore-forming toxin known as Stonustoxin (SNTX). Transcriptomic sequencing of the venom gland resulted in over 170,000 contigs with only 0.4% that were homologous to putative venom proteins. Integration of the transcriptomic data with proteomic data from the S. horrida venom confirmed the hyaluronidase and SNTX to be present, together with several other protein families including major contributions from C-type lectins. Other protein families observed included peroxiredoxin and several minor protein families such as Golgi-associated plant pathogenesis related proteins, tissue pathway factor inhibitors, and Kazal-type serine protease inhibitors that, although not putative venom proteins, may contribute to the venom's adverse effects. BIOLOGICAL SIGNIFICANCE: Proteomic analysis of milked Synanceia horrida venom, paired with transcriptomic analysis of the venom gland tissue revealed for the first time the composition of one of the world's most dangerous fish venoms. The results demonstrate that the venom is relatively less complex compared to other well-studied venomous animals with a number of unique proteins not previously found in animal venoms.
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http://dx.doi.org/10.1016/j.jprot.2019.04.002DOI Listing
June 2019

Transcriptomic-Proteomic Correlation in the Predation-Evoked Venom of the Cone Snail, .

Mar Drugs 2019 Mar 19;17(3). Epub 2019 Mar 19.

Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia.

Individual variation in animal venom has been linked to geographical location, feeding habit, season, size, and gender. Uniquely, cone snails possess the remarkable ability to change venom composition in response to predatory or defensive stimuli. To date, correlations between the venom gland transcriptome and proteome within and between individual cone snails have not been reported. In this study, we use 454 pyrosequencing and mass spectrometry to decipher the transcriptomes and proteomes of the venom gland and corresponding predation-evoked venom of two specimens of . Transcriptomic analyses revealed 17 conotoxin gene superfamilies common to both animals, including 5 novel superfamilies and two novel cysteine frameworks. While highly expressed transcripts were common to both specimens, variation of moderately and weakly expressed precursor sequences was surprisingly diverse, with one specimen expressing two unique gene superfamilies and consistently producing more paralogs within each conotoxin gene superfamily. Using a quantitative labelling method, conotoxin variability was compared quantitatively, with highly expressed peptides showing a strong correlation between transcription and translation, whereas peptides expressed at lower levels showed a poor correlation. These results suggest that major transcripts are subject to stabilizing selection, while minor transcripts are subject to diversifying selection.
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http://dx.doi.org/10.3390/md17030177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6471084PMC
March 2019

Discovering proteins for chemoprevention and chemotherapy by curcumin in liver fluke infection-induced bile duct cancer.

PLoS One 2018 15;13(11):e0207405. Epub 2018 Nov 15.

Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.

Modulation or prevention of protein changes during the cholangiocarcinoma (CCA) process induced by Opisthorchis viverrini (Ov) infection may become a key strategy for prevention and treatment of CCA. Monitoring of such changes could lead to discovery of protein targets for CCA treatment. Curcumin exerts anti-inflammatory and anti-CCA activities partly through its protein-modulatory ability. To support the potential use of curcumin and to discover novel target molecules for CCA treatment, we used a quantitative proteomic approach to investigate the effects of curcumin on protein changes in an Ov-induced CCA-harboring hamster model. Isobaric labelling and tandem mass spectrometry were used to compare the protein expression profiles of liver tissues from CCA hamsters with or without curcumin dietary supplementation. Among the dysregulated proteins, five were upregulated in liver tissues of CCA hamsters but markedly downregulated in the CCA hamsters supplemented with curcumin: S100A6, lumican, plastin-2, 14-3-3 zeta/delta and vimentin. Western blot and immunohistochemical analyses also showed similar expression patterns of these proteins in liver tissues of hamsters in the CCA and CCA + curcumin groups. Proteins such as clusterin and S100A10, involved in the NF-κB signaling pathway, an important signaling cascade involved in CCA genesis, were also upregulated in CCA hamsters and were then suppressed by curcumin treatment. Taken together, our results demonstrate the important changes in the proteome during the genesis of O. viverrini-induced CCA and provide an insight into the possible protein targets for prevention and treatment of this cancer.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0207405PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237386PMC
April 2019

Elongator mutation in mice induces neurodegeneration and ataxia-like behavior.

Nat Commun 2018 08 10;9(1):3195. Epub 2018 Aug 10.

Institute for Molecular Bioscience, the University of Queensland, Brisbane, QLD, 4072, Australia.

Cerebellar ataxias are severe neurodegenerative disorders with an early onset and progressive and inexorable course of the disease. Here, we report a single point mutation in the gene encoding Elongator complex subunit 6 causing Purkinje neuron degeneration and an ataxia-like phenotype in the mutant wobbly mouse. This mutation destabilizes the complex and compromises its function in translation regulation, leading to protein misfolding, proteotoxic stress, and eventual neuronal death. In addition, we show that substantial microgliosis is triggered by the NLRP3 inflammasome pathway in the cerebellum and that blocking NLRP3 function in vivo significantly delays neuronal degeneration and the onset of ataxia in mutant animals. Our data provide a mechanistic insight into the pathophysiology of a cerebellar ataxia caused by an Elongator mutation, substantiating the increasing body of evidence that alterations of this complex are broadly implicated in the onset of a number of diverse neurological disorders.
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http://dx.doi.org/10.1038/s41467-018-05765-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086839PMC
August 2018

Proteomic and functional variation within black snake venoms (Elapidae: Pseudechis).

Comp Biochem Physiol C Toxicol Pharmacol 2018 Feb 17;205:53-61. Epub 2018 Jan 17.

Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia. Electronic address:

Pseudechis (black snakes) is an Australasian elapid snake genus that inhabits much of mainland Australia, with two representatives confined to Papua New Guinea. The present study is the first to analyse the venom of all 9 described Pseudechis species (plus one undescribed species) to investigate the evolution of venom composition and functional activity. Proteomic results demonstrated that the typical Pseudechis venom profile is dominated by phospholipase A toxins. Strong cytotoxicity was the dominant function for most species. P. porphyriacus, the most basal member of the genus, also exhibited the most divergent venom composition, being the only species with appreciable amounts of procoagulant toxins. The relatively high presence of factor Xa recovered in P. porphyriacus venom may be related to a predominantly amphibian diet. Results of this study provide important insights to guide future ecological and toxinological investigations.
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http://dx.doi.org/10.1016/j.cbpc.2018.01.001DOI Listing
February 2018

Venom Profiling of a Population of the Theraphosid Spider Phlogius crassipes Reveals Continuous Ontogenetic Changes from Juveniles through Adulthood.

Toxins (Basel) 2017 03 25;9(4). Epub 2017 Mar 25.

Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.

Theraphosid spiders (tarantulas) are venomous arthropods found in most tropical and subtropical regions of the world. Tarantula venoms are a complex cocktail of toxins with potential use as pharmacological tools, drugs and bioinsecticides. Although numerous toxins have been isolated from tarantula venoms, little research has been carried out on the venom of Australian tarantulas. We therefore investigated the venom profile of the Australian theraphosid spider and examined whether there are ontogenetic changes in venom composition. Spiders were divided into four ontogenic groups according to cephalothorax length, then the venom composition of each group was examined using gel electrophoresis and mass spectrometry. We found that the venom of changes continuously during development and throughout adulthood. Our data highlight the need to investigate the venom of organisms over the course of their lives to uncover and understand the changing functions of venom and the full range of toxins expressed. This in turn should lead to a deeper understanding of the organism's ecology and enhance the potential for biodiscovery.
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http://dx.doi.org/10.3390/toxins9040116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408190PMC
March 2017

Differential Protein Expression Marks the Transition From Infection With to Cholangiocarcinoma.

Mol Cell Proteomics 2017 05 23;16(5):911-923. Epub 2017 Feb 23.

QIMR Berghofer Medical Research Institute, Infectious Disease Program, Brisbane 4006, Australia;

Parts of Southeast Asia have the highest incidence of intrahepatic cholangiocarcinoma (CCA) in the world because of infection by the liver fluke (Ov). Ov-associated CCA is the culmination of chronic Ov-infection, with the persistent production of the growth factors and cytokines associated with persistent inflammation, which can endure for years in Ov-infected individuals prior to transitioning to CCA. Isobaric labeling and tandem mass spectrometry of liver tissue from a hamster model of CCA was used to compare protein expression profiles from inflammed tissue (Ovinfected but not cancerous) cancerous tissue (Ov-induced CCA). Immunohistochemistry and immunoblotting were used to verify dysregulated proteins in the animal model and in human tissue. We identified 154 dysregulated proteins that marked the transition from Ov-infection to Ov-induced CCA, proteins dysregulated during carcinogenesis but not Ov-infection. The verification of dysregulated proteins in resected liver tissue from humans with Ov-associated CCA showed the numerous parallels in protein dysregulation between human and animal models of Ov-induced CCA. To identify potential circulating markers for CCA, dysregulated proteins were compared with proteins isolated from exosomes secreted by a human CCA cell line (KKU055) and 27 proteins were identified as dysregulated in CCA and present in exosomes. These data form the basis of potential diagnostic biomarkers for human Ov-associated CCA. The profile of protein dysregulation observed during chronic Ovinfection and then in Ov-induced CCA provides insight into the etiology of an infection-induced inflammation-related cancer.
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http://dx.doi.org/10.1074/mcp.M116.064576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5417829PMC
May 2017

Combining Sense and Nonsense Codon Reassignment for Site-Selective Protein Modification with Unnatural Amino Acids.

ACS Synth Biol 2017 03 30;6(3):535-544. Epub 2016 Dec 30.

Institute for Molecular Bioscience, The University of Queensland , St Lucia, QLD 4072, Australia.

Incorporation of unnatural amino acids (uAAs) via codon reassignment is a powerful approach for introducing novel chemical and biological properties to synthesized polypeptides. However, the site-selective incorporation of multiple uAAs into polypeptides is hampered by the limited number of reassignable nonsense codons. This challenge is addressed in the current work by developing Escherichia coli in vitro translation system depleted of specific endogenous tRNAs. The translational activity in this system is dependent on the addition of synthetic tRNAs for the chosen sense codon. This allows site-selective uAA incorporation via addition of tRNAs pre- or cotranslationally charged with uAA. We demonstrate the utility of this system by incorporating the BODIPY fluorophore into the unique AGG codon of the calmodulin(CaM) open reading frame using in vitro precharged BODIPY-tRNA. The deacylated tRNA is a poor substrate for Cysteinyl-tRNA synthetase, which ensures low background incorporation of Cys into the chosen codon. Simultaneously, p-azidophenylalanine mediated amber-codon suppression and its post-translational conjugation to tetramethylrhodamine dibenzocyclooctyne (TAMRA-DIBO) were performed on the same polypeptide. This simple and robust approach takes advantage of the compatibility of BODIPY fluorophore with the translational machinery and thus requires only one post-translational derivatization step to introduce two fluorescent labels. Using this approach, we obtained CaM nearly homogeneously labeled with two FRET-forming fluorophores. Single molecule FRET analysis revealed dramatic changes in the conformation of the CaM probe upon its exposure to Ca or a chelating agent. The presented approach is applicable to other sense codons and can be directly transferred to eukaryotic cell-free systems.
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http://dx.doi.org/10.1021/acssynbio.6b00245DOI Listing
March 2017

Deep venomics of the Pseudonaja genus reveals inter- and intra-specific variation.

J Proteomics 2016 Feb 26;133:20-32. Epub 2015 Nov 26.

Institute for Molecular Bioscience, The University of Queensland, QLD 4072, Australia. Electronic address:

Unlabelled: Australian elapid venom remains an under-investigated resource of novel bioactive peptides. In this study, the venom gland transcriptomes and proteomes of the Australian western brown snakes, Pseudonaja aspidorhyncha and Pseudonaja nuchalis, were compared to Pseudonaja textilis. A deep venomics strategy incorporating high throughput 454 pyrosequencing gave a total of 200,911 raw reads for the three venoms. Subsequent annotation identified 5716 transcripts from 20 different toxin families with inter-specific variation between species observed in eight of the less abundant families. Integration of each venom proteome with the corresponding annotated reads identified 65 isoforms from six toxin families; high sequence coverage highlighted subtle differences between sequences and intra and inter-specific variation between species. High quality MS/MS data identified unusual glycoforms with natriuretic peptides from P. aspidorhyncha and P. nuchaliscontaining O-linked trisaccharides with high homology to the glycosylated region of TNPc. Molecular evolutionary assessments indicated the accelerated evolution of all toxin families with the exception of both natriuretic peptides and P. aspidorhyncha PLA2s that were found to be evolutionarily constrained under purifying selection pressures. This study has revealed a wide range of novel peptide sequences from six bioactive peptide families and highlights the subtle differences between toxins in these closely related species.

Biological Significance: Mining Australia's vastly untapped source of toxins from its venomous creatures has been significantly advanced by employing deep venomics methodology. Technological advances in transcriptome analysis using next generation sequencing platforms and proteome analysis by highly sensitive tandem mass spectrometry allowed a more comprehensive interrogation of three underinvestigated brown snake (Pseudonaja) venoms uncovering many novel peptide sequences that are unique to these closely related species. This generic strategy will provide invaluable information when applied to other venomous snakes for a deeper understanding of venom composition, envenomation, venom evolution, as well as identifying research tools and drug leads.
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http://dx.doi.org/10.1016/j.jprot.2015.11.019DOI Listing
February 2016

Mammalian farnesyltransferase α subunit regulates vacuolar protein sorting-associated protein 4A (Vps4A)--dependent intracellular trafficking through recycling endosomes.

Biochem Biophys Res Commun 2015 Dec 10;468(4):580-6. Epub 2015 Nov 10.

Institute for Molecular Bioscience, University of Queensland, Brisbane, St. Lucia, Queensland, 4072, Australia. Electronic address:

The protein farnesyltransferase (FTase) mediates posttranslational modification of proteins with isoprenoid lipids. FTase is a heterodimer and although the β subunit harbors the active site, it requires the α subunit for its activity. Here we explore the other functions of the FTase α subunit in addition to its established role in protein prenylation. We found that in the absence of the β subunit, the α subunit of FTase forms a stable autonomous dimeric structure in solution. We identify interactors of FTase α using mass spectrometry, followed by rapid in vitro analysis using the Leishmania tarentolae cell - free system. Vps4A was validated for direct binding to the FTase α subunit both in vitro and in vivo. Analysis of the interaction with Vps4A in Hek 293 cells demonstrated that FTase α controls trafficking of transferrin receptor upstream of this protein. These results point to the existence of previously undetected biological functions of the FTase α subunit that includes control of intracellular membrane trafficking.
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http://dx.doi.org/10.1016/j.bbrc.2015.10.148DOI Listing
December 2015

Flexibility versus Rigidity for Orally Bioavailable Cyclic Hexapeptides.

Chembiochem 2015 Nov 7;16(16):2289-93. Epub 2015 Oct 7.

Division of Chemistry and Structural Biology, University of Queensland, Brisbane, QLD, 4072, Australia.

Cyclic peptides and macrocycles have the potential to be membrane permeable and orally bioavailable, despite often not complying with the "rule of five" used in medicinal chemistry to guide the discovery of oral drugs. Here we compare solvent-dependent three-dimensional structures of three cyclic hexapeptides containing d-amino acids, prolines, and intramolecular hydrogen bonds. Conformational rigidity rather than flexibility resulted in higher membrane permeability, metabolic stability and oral bioavailability, consistent with less polar surface exposure to solvent and a reduced entropy penalty for transition between polar and nonpolar environments.
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http://dx.doi.org/10.1002/cbic.201500441DOI Listing
November 2015

New Approaches to Marine Conservation Through the Scaling Up of Ecological Data.

Ann Rev Mar Sci 2016 7;8:435-61. Epub 2015 Aug 7.

Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom; email: ,

In an era of rapid global change, conservation managers urgently need improved tools to track and counter declining ecosystem conditions. This need is particularly acute in the marine realm, where threats are out of sight, inadequately mapped, cumulative, and often poorly understood, thereby generating impacts that are inefficiently managed. Recent advances in macroecology, statistical analysis, and the compilation of global data will play a central role in improving conservation outcomes, provided that global, regional, and local data streams can be integrated to produce locally relevant and interpretable outputs. Progress will be assisted by (a) expanded rollout of systematic surveys that quantify species patterns, including some carried out with help from citizen scientists; (b) coordinated experimental research networks that utilize large-scale manipulations to identify mechanisms underlying these patterns;
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http://dx.doi.org/10.1146/annurev-marine-122414-033921DOI Listing
October 2016

Optimized deep-targeted proteotranscriptomic profiling reveals unexplored Conus toxin diversity and novel cysteine frameworks.

Proc Natl Acad Sci U S A 2015 Jul 6;112(29):E3782-91. Epub 2015 Jul 6.

Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;

Cone snails are predatory marine gastropods characterized by a sophisticated venom apparatus responsible for the biosynthesis and delivery of complex mixtures of cysteine-rich toxin peptides. These conotoxins fold into small highly structured frameworks, allowing them to potently and selectively interact with heterologous ion channels and receptors. Approximately 2,000 toxins from an estimated number of >70,000 bioactive peptides have been identified in the genus Conus to date. Here, we describe a high-resolution interrogation of the transcriptomes (available at www.ddbj.nig.ac.jp) and proteomes of the diverse compartments of the Conus episcopatus venom apparatus. Using biochemical and bioinformatic tools, we found the highest number of conopeptides yet discovered in a single Conus specimen, with 3,305 novel precursor toxin sequences classified into 9 known superfamilies (A, I1, I2, M, O1, O2, S, T, Z), and identified 16 new superfamilies showing unique signal peptide signatures. We were also able to depict the largest population of venom peptides containing the pharmacologically active C-C-CC-C-C inhibitor cystine knot and CC-C-C motifs (168 and 44 toxins, respectively), as well as 208 new conotoxins displaying odd numbers of cysteine residues derived from known conotoxin motifs. Importantly, six novel cysteine-rich frameworks were revealed which may have novel pharmacology. Finally, analyses of codon usage bias and RNA-editing processes of the conotoxin transcripts demonstrate a specific conservation of the cysteine skeleton at the nucleic acid level and provide new insights about the origin of sequence hypervariablity in mature toxin regions.
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http://dx.doi.org/10.1073/pnas.1501334112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517256PMC
July 2015

Some unbeautiful aspects about 'The Game'.

Authors:
Alun Jones

Nurse Educ Today 2015 Sep 24;35(9):961-2. Epub 2015 Mar 24.

BCUHB, United Kingdom; Chester University, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.nedt.2015.03.007DOI Listing
September 2015

PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization.

J Proteome Res 2015 May 17;14(5):2255-66. Epub 2015 Apr 17.

§Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland G61 1BD, United Kingdom.

We describe PGTools, an open source software suite for analysis and visualization of proteogenomic data. PGTools comprises applications, libraries, customized databases, and visualization tools for analysis of mass-spectrometry data using combined proteomic and genomic backgrounds. A single command is sufficient to search databases, calculate false discovery rates, group and annotate proteins, generate peptide databases from RNA-Seq transcripts, identify altered proteins associated with cancer, and visualize genome scale peptide data sets using sophisticated visualization tools. We experimentally confirm a subset of proteogenomic peptides in human PANC-1 cells and demonstrate the utility of PGTools using a colorectal cancer data set that led to the identification of 203 novel protein coding regions missed by conventional proteomic approaches. PGTools should be equally useful for individual proteogenomic investigations as well as international initiatives such as chromosome-centric Human Proteome Project (C-HPP). PGTools is available at http://qcmg.org/bioinformatics/PGTools.
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http://dx.doi.org/10.1021/acs.jproteome.5b00029DOI Listing
May 2015

A defined α-helix in the bifunctional O-glycosylated natriuretic peptide TcNPa from the venom of Tropidechis carinatus.

Angew Chem Int Ed Engl 2015 Apr 3;54(16):4828-31. Epub 2015 Mar 3.

Institute for Molecular Bioscience, The University of Queensland, Queensland 4072 (Australia).

Natriuretic peptides (NP) play important roles in human cardiac physiology through their guanylyl cyclase receptors NPR-A and NPR-B. Described herein is a bifunctional O-glycosylated natriuretic peptide, TcNPa, from Tropidechis carinatus venom and it unusually targets both NPR-A and NPR-B. Characterization using specific glycosidases and ETD-MS identified the glycan as galactosyl-β(1-3)-N-acetylgalactosamine (Gal-GalNAc) and was α-linked to the C-terminal threonine residue. TcNPa contains the characteristic NP 17-membered disulfide ring with conserved phenylalanine and arginine residues. Both glycosylated and nonglycosylated forms were synthesized by Fmoc solid-phase peptide synthesis and NMR analysis identified an α-helix within the disulfide ring containing the putative pharmacophore for NPR-A. Surprisingly, both forms activated NPR-A and NPR-B and were relatively resistant towards proteolytic degradation in plasma. This work will underpin the future development of bifunctional NP peptide mimetics.
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http://dx.doi.org/10.1002/anie.201411914DOI Listing
April 2015

What evidence is there for the use of workplace-based assessment in surgical training?

J Surg Educ 2015 May-Jun;72(3):367-8. Epub 2015 Jan 13.

Royal Victoria Infirmary, Newcastle upon Tyne, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jsurg.2014.11.011DOI Listing
May 2016

A HIV-1 Tat mutant protein disrupts HIV-1 Rev function by targeting the DEAD-box RNA helicase DDX1.

Retrovirology 2014 Dec 14;11:121. Epub 2014 Dec 14.

QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.

Background: Previously we described a transdominant negative mutant of the HIV-1 Tat protein, termed Nullbasic, that downregulated the steady state levels of unspliced and singly spliced viral mRNA, an activity caused by inhibition of HIV-1 Rev activity. Nullbasic also altered the subcellular localizations of Rev and other cellular proteins, including CRM1, B23 and C23 in a Rev-dependent manner, suggesting that Nullbasic may disrupt Rev function and trafficking by intervening with an unidentified component of the Rev nucleocytoplasmic transport complex.

Results: To seek a possible mechanism that could explain how Nullbasic inhibits Rev activity, we used a proteomics approach to identify host cellular proteins that interact with Nullbasic. Forty-six Nullbasic-binding proteins were identified by mass spectrometry including the DEAD-box RNA helicase, DDX1. To determine the effect of DDX1 on Nullbasic-mediated Rev activity, we performed cell-based immunoprecipitation assays, Rev reporter assays and bio-layer interferometry (BLI) assays. Interaction between DDX1 and Nullbasic was observed by co-immunoprecipitation of Nullbasic with endogenous DDX1 from cell lysates. BLI assays showed a direct interaction between Nullbasic and DDX1. Nullbasic affected DDX1 subcellular distribution in a Rev-independent manner. Interestingly overexpression of DDX1 in cells not only restored Rev-dependent mRNA export and gene expression in a Rev reporter assay but also partly reversed Nullbasic-induced Rev subcellular mislocalization. Moreover, HIV-1 wild type Tat co-immunoprecipitated with DDX1 and overexpression of Tat could rescue the unspliced viral mRNA levels inhibited by Nullbasic in HIV-1 expressing cells.

Conclusions: Nullbasic was used to further define the complex mechanisms involved in the Rev-dependent nuclear export of the 9 kb and 4 kb viral RNAs. All together, these data indicate that DDX1 can be sequestered by Nullbasic leading to destabilization of the Rev nucleocytoplasmic transport complex and decreased levels of Rev-dependent viral transcripts. The outcomes support a role for DDX1 in maintenance of a Rev nuclear complex that transports viral RRE-containing mRNA to the cytoplasm. To our knowledge Nullbasic is the first anti-HIV protein that specifically targets the cellular protein DDX1 to block Rev's activity. Furthermore, our research raises the possibility that wild type Tat may play a previously unrecognized but very important role in Rev function.
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http://dx.doi.org/10.1186/s12977-014-0121-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271445PMC
December 2014

Extreme venom variation in Middle Eastern vipers: a proteomics comparison of Eristicophis macmahonii, Pseudocerastes fieldi and Pseudocerastes persicus.

J Proteomics 2015 Feb 18;116:106-13. Epub 2014 Sep 18.

Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, Queensland 4520, Australia; Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4520, Australia. Electronic address:

Unlabelled: Venoms of the viperid sister genera Eristicophis and Pseudocerastes are poorly studied despite their anecdotal reputation for producing severe or even lethal envenomations. This is due in part to the remote and politically unstable regions that they occupy. All species contained are sit and wait ambush feeders. Thus, this study examined their venoms through proteomics techniques in order to establish if this feeding ecology, and putatively low levels of gene flow, have resulted in significant variations in venom profile. The techniques indeed revealed extreme venom variation. This has immediate implications as only one antivenom is made (using the venom of Pseudocerastes persicus) yet the proteomic variation suggests that it would be of only limited use for the other species, even the sister species Pseudocerastes fieldi. The high degree of variation however also points toward these species being rich resources for novel compounds which may have use as lead molecules in drug design and development.

Biological Significance: These results show extreme venom variation between these closely related snakes. These results have direct implications for the treatment of the envenomed patient.
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http://dx.doi.org/10.1016/j.jprot.2014.09.003DOI Listing
February 2015

Response to: Reflections on competency-based education and training for surgical residents.

J Surg Educ 2014 Sep-Oct;71(5):651

Royal Victoria Infirmary, Newcastle upon Tyne, UK.

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http://dx.doi.org/10.1016/j.jsurg.2014.04.007DOI Listing
May 2015

The burden of shame and stigma.

Midwives 2014 ;17(2):50-1

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August 2014

Clawing through evolution: toxin diversification and convergence in the ancient lineage Chilopoda (centipedes).

Mol Biol Evol 2014 Aug 20;31(8):2124-48. Epub 2014 May 20.

Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, AustraliaVenom Evolution Laboratory, School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Australia

Despite the staggering diversity of venomous animals, there seems to be remarkable convergence in regard to the types of proteins used as toxin scaffolds. However, our understanding of this fascinating area of evolution has been hampered by the narrow taxonomical range studied, with entire groups of venomous animals remaining almost completely unstudied. One such group is centipedes, class Chilopoda, which emerged about 440 Ma and may represent the oldest terrestrial venomous lineage next to scorpions. Here, we provide the first comprehensive insight into the chilopod "venome" and its evolution, which has revealed novel and convergent toxin recruitments as well as entirely new toxin families among both high- and low molecular weight venom components. The ancient evolutionary history of centipedes is also apparent from the differences between the Scolopendromorpha and Scutigeromorpha venoms, which diverged over 430 Ma, and appear to employ substantially different venom strategies. The presence of a wide range of novel proteins and peptides in centipede venoms highlights these animals as a rich source of novel bioactive molecules. Understanding the evolutionary processes behind these ancient venom systems will not only broaden our understanding of which traits make proteins and peptides amenable to neofunctionalization but it may also aid in directing bioprospecting efforts.
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http://dx.doi.org/10.1093/molbev/msu162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104317PMC
August 2014
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