ORCID Profile
0000-0002-4223-8450
Current Organisation
Australian National University
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Genetics | Developmental Genetics (incl. Sex Determination) | Genome Structure and Regulation | Molecular Evolution | Ecosystem Function | Environmental Science and Management | Environmental Management | Genetic Development (Incl. Sex Determination) | Conservation and Biodiversity | Invertebrate Biology | Molecular Evolution |
Ecosystem Adaptation to Climate Change | Expanding Knowledge in the Biological Sciences | Marine Flora, Fauna and Biodiversity | Cancer and related disorders | Biological sciences | Inherited diseases (incl. gene therapy) | Ecosystem Assessment and Management of Marine Environments
Publisher: Wiley
Date: 10-09-2014
Publisher: Public Library of Science (PLoS)
Date: 10-10-2007
Publisher: John Benjamins Publishing Company
Date: 31-12-2022
Abstract: In many languages, nouns need a numeral classifier to combine with number words or quantifiers. Even though languages may have an elaborate system of numeral classifiers, there usually are exceptional nouns that combine directly with number words. This paper deals with the following questions: Which nouns trigger a numeral classifier when counted? Which nouns are more likely to occur without an additional classifier in a numeral context? Data from 32 languages reveal a classifiability scale of nouns depending on their semantics. The more animate a noun, the more likely is the occurrence of a classifier. With inanimate nouns, classifiers often may or must be omitted. The investigation extends to units, with units of time being much more likely to be accompanied by a numeral classifier than other units. These findings are surprising in the light of the predominant view that numeral classifiers are in iduating units in languages where nouns appear to be uncountable mass nouns. I discuss several approaches, of which animacy and the form-frequency correspondence principle are most promising.
Publisher: Springer Science and Business Media LLC
Date: 17-06-2007
DOI: 10.1038/NATURE05876
Publisher: Wiley
Date: 23-09-2008
Publisher: Public Library of Science (PLoS)
Date: 06-06-2007
Publisher: Oxford University Press (OUP)
Date: 28-01-2019
Abstract: Resolving the relationships of animals (Metazoa) is crucial to our understanding of the origin of key traits such as muscles, guts, and nerves. However, a broadly accepted metazoan consensus phylogeny has yet to emerge. In part, this is because the genomes of deeply erging and fast-evolving lineages may undergo significant gene turnover, reducing the number of orthologs shared with related phyla. This can limit the usefulness of traditional phylogenetic methods that rely on alignments of orthologous sequences. Phylogenetic analysis of gene content has the potential to circumvent this orthology requirement, with binary presence/absence of homologous gene families representing a source of phylogenetically informative characters. Applying binary substitution models to the gene content of 26 complete animal genomes, we demonstrate that patterns of gene conservation differ markedly depending on whether gene families are defined by orthology or homology, that is, whether paralogs are excluded or included. We conclude that the placement of some deeply erging lineages may exceed the limit of resolution afforded by the current methods based on comparisons of orthologous protein sequences, and novel approaches are required to fully capture the evolutionary signal from genes within genomes.
Publisher: Elsevier BV
Date: 10-2007
Publisher: Springer Science and Business Media LLC
Date: 14-10-2016
Publisher: Springer Netherlands
Date: 2015
Publisher: Springer International Publishing
Date: 2018
DOI: 10.1007/978-3-319-92486-1_12
Abstract: Over 100 years of sponge biology research has demonstrated spectacular ersity of cell behaviors during embryonic development, metamorphosis and regeneration. The past two decades have allowed the first glimpses into molecular and cellular mechanisms of these processes. We have learned that while embryonic development of sponges utilizes a conserved set of developmental regulatory genes known from other animals, sponge cell differentiation appears unusually labile. During normal development, and especially as a response to injury, sponge cells appear to have an uncanny ability to transdifferentiate. Here, I argue that sponge cell differentiation plasticity does not preclude homology of cell types and processes between sponges and other animals. Instead, it does provide a wonderful opportunity to better understand transdifferentiation processes in all animals.
Publisher: Elsevier BV
Date: 2016
DOI: 10.1016/J.CUB.2015.11.043
Abstract: One of the unusual features of DNA-containing organelles in general and mitochondria in particular is the frequent occurrence of RNA editing [1]. The term "RNA editing" refers to a variety of mechanistically unrelated biochemical processes that alter RNA sequence during or after transcription [2]. The editing can be insertional, deletional, or substitutional and has been found in all major types of RNAs [3, 4]. Although mitochondrial mRNA editing is widespread in some eukaryotic lineages [5-7], it is rare in animals, with reported cases limited both in their scope and in phylogenetic distribution [8-11] (see also [12]). While analyzing genomic data from calcaronean sponges Sycon ciliatum and Leucosolenia complicata, we were perplexed by the lack of recognizable mitochondrial coding sequences. Comparison of genomic and transcriptomic data from these species revealed the presence of mitochondrial cryptogenes whose transcripts undergo extensive editing. This editing consisted of single or double uridylate (U) insertions in pre-existing short poly(U) tracts. Subsequent analysis revealed the presence of similar editing in Sycon coactum and the loss of editing in Petrobiona massiliana, a hypercalcified calcaronean sponge. In addition, mitochondrial genomes of at least some calcaronean sponges were found to have a highly unusual architecture, with nearly all genes located on in idual and likely linear chromosomes. Phylogenetic analysis of mitochondrial coding sequences revealed accelerated rates of sequence evolution in this group. The latter observation presents a challenge for the mutational-hazard hypothesis [13], which posits that mRNA editing should not occur in lineages with an elevated mutation rate.
Publisher: Elsevier BV
Date: 03-2003
DOI: 10.1016/S0012-1606(02)00114-8
Abstract: doubleridge is a transgene-induced mutation characterized by polydactyly and syndactyly of the forelimbs. The transgene insertion maps to the proximal region of chromosome 19. During embryonic development of the mutant forelimb, delayed elevation and compaction of the apical ectodermal ridge (AER) produces a ridge that is abnormally broad and flat. Fgf8 expression persists in the ventral forelimb ectoderm of the mutant until E10.5. Strong expression of Fgf8 and other markers at the borders of the AER at E11.5 gives the appearance of a double ridge. At E11.5, apoptotic cells are distributed across the broadened ridge, but at E13.5, there is reduced apoptosis in the interdigital regions. The Shh expression domain is widely spaced at the posterior margin of the AER. The doubleridge AER is morphologically similar to that of En1 null mice, but the expression of En1 and Wnt7a is properly restricted in doubleridge, and the dorsal and ventral structures are correctly determined. doubleridge thus exhibits an unusual limb phenotype combining abnormal compaction of the AER with normal dorsal/ventral patterning.
Publisher: Elsevier BV
Date: 08-2002
Abstract: In the mouse embryo, Dlx5 is expressed in the otic placode and vesicle, and later in the semicircular canals of the inner ear. In mice homozygous for a null Dlx5/LacZ allele, a severe dysmorphogenesis of the vestibular region is observed, characterized by the absence of semicircular canals and the shortening of the endolymphatic duct. Minor defects are observed in the cochlea, although Dlx5 is not expressed in this region. Cristae formation is severely impaired however, sensory epithelial cells, recognized by calretinin immunostaining, are present in the vestibular epithelium of Dlx5(-/-) mice. The maculae of utricle and saccule are present but cells appear sparse and misplaced. The abnormal morphogenesis of the semicircular canals is accompanied by an altered distribution of proliferating and apoptotic cells. In the Dlx5(-/-) embryos, no changes in expression of Nkx5.1(Hmx3), Pax2, and Lfng have been seen, while expression of bone morphogenetic protein-4 (Bmp4) was drastically reduced. Notably, BMP4 has been shown to play a fundamental role in vestibular morphogenesis of the chick embryo. We propose that development of the semicircular canals and the vestibular inner ear requires the independent control of several homeobox genes, which appear to exert their function via tight regulation of BPM4 expression and the regional organization of cell differentiation, proliferation, and apoptosis.
Publisher: Elsevier BV
Date: 02-2011
DOI: 10.1016/J.ZOOL.2010.10.003
Abstract: Sponges are one of the simplest, and probably the oldest (earliest branching) multicellular lineage of extant animals. Although their embryonic development has been intensively studied in the late 19th and early 20th century, they have been mostly neglected by modern developmental biology. Recent interest in the evolution of development, aided by advances in sequencing technology, has brought the sponges back into the spotlight. It is known that the developmental toolkit of sponges includes signalling pathways, transcription factors and cell adhesion molecules that are employed during development of more complex animals (i.e. bilaterians). We are now beginning to understand how these conserved regulatory genes are used during the development of sponges. Methodological resources are now being developed for model species representing all major sponge lineages, potentially allowing us to gain insight into the evolutionary origin of animal developmental mechanisms.
Publisher: Springer Science and Business Media LLC
Date: 08-2010
DOI: 10.1038/NATURE09201
Publisher: Springer Science and Business Media LLC
Date: 22-11-2016
DOI: 10.1038/SREP37546
Abstract: In many marine invertebrates, larval metamorphosis is induced by environmental cues that activate sensory receptors and signalling pathways. Nitric oxide (NO) is a gaseous signalling molecule that regulates metamorphosis in erse bilaterians. In most cases NO inhibits or represses this process, although it functions as an activator in some species. Here we demonstrate that NO positively regulates metamorphosis in the poriferan Amphimedon queenslandica . High rates of A. queenslandica metamorphosis normally induced by a coralline alga are inhibited by an inhibitor of nitric oxide synthase (NOS) and by a NO scavenger. Consistent with this, an artificial donor of NO induces metamorphosis even in the absence of the alga. Inhibition of the ERK signalling pathway prevents metamorphosis in concert with, or downstream of, NO signalling a NO donor cannot override the ERK inhibitor. NOS gene expression is activated late in embryogenesis and in larvae, and is enriched in specific epithelial and subepithelial cell types, including a putative sensory cell, the globular cell DAF-FM staining supports these cells being primary sources of NO. Together, these results are consistent with NO playing an activating role in induction of A. queenslandica metamorphosis, evidence of its highly conserved regulatory role in metamorphosis throughout the Metazoa.
Publisher: De Gruyter
Date: 16-01-2023
Publisher: Wiley
Date: 2005
DOI: 10.1002/DVDY.20437
Abstract: Wnt7a and the Wnt coreceptor Lrp6 are both required for development of posterior digits and dorsal structures of the limb. We report that Lrp6 null mice lack Lmx1b expression in the distal mesenchyme, as previously described for Wnt7a mutants. The loss of Lmx1b expression in Wnt7a-/-Lrp6+/- double mutants did not differ from that in Wnt7a-/- mice. These data suggest that Wnt7a acts through Lrp6 to regulate Lmx1b expression during dorsal specification. The loss of posterior skeletal elements in the Wnt7a-/-Lrp6+/- double mutant was much more severe than in Wnt7a-/- mice, suggesting that the Wnt7a-/- limb is protected by the action of other Lrp6 ligands. The data are consistent with the view that Wnt7a acts through Lrp6 and the canonical Wnt signaling pathway during dorsal and posterior limb development in the mouse.
Publisher: Springer Science and Business Media LLC
Date: 23-06-2014
Publisher: Oxford University Press (OUP)
Date: 15-10-2002
Abstract: Scn8a encodes an abundant, widely distributed voltage-gated sodium channel found throughout the central and peripheral nervous systems. Mice with different mutant alleles of Scn8a provide models of the movement disorders ataxia, dystonia, tremor and progressive paralysis. We previously reported that the phenotype of the hypomorphic allele of Scn8a, medJ, is dependent upon an unlinked modifier locus, Scnm1. Strain C57BL/6J carries a sensitive allele of the modifier locus that results in juvenile lethality. We now provide evidence that the modifier acts on the splicing efficiency of the mutant splice donor site. Mutant mice display either 90% or 95% reduction in the proportion of correctly spliced mRNA, depending on modifier genotype. The abundance of the channel protein, Na(v)1.6, is also reduced by an order of magnitude in medJ mice, resulting in delayed maturation of nodes of Ranvier, slowed nerve conduction velocity, reduced muscle mass and reduction of brain metabolic activity. medJ mice provide a model for the physiological effects of sodium channel deficiency and the molecular mechanism of bigenic disease.
Publisher: American Astronomical Society
Date: 31-07-2023
Publisher: De Gruyter
Date: 07-02-2022
Publisher: Elsevier BV
Date: 12-2001
DOI: 10.1016/S0925-4773(01)00550-0
Abstract: FGF2 or FGF8 applied ectopically, close to the developing otic placode enhances transcription of a subset of ear marker genes such as Nkx5-1, SOHo1 and Pax2. Other ear expressed genes (Dlx5 and BMP4) are not up-regulated by FGFs. Ectopic FGFs lead to an increase in size of the vestibulo-cochlear ganglion. This phenotypic change is due to an increased recruitment of epithelial cells to the neuronal fate rather than to an enhanced proliferation. We also observed an induction of additional, vesicle-like structures upon ectopic FGF treatment, but this induction never led to enrolment of a full ear program. We further demonstrate that FGF8 is expressed in two separate, short waves, first at the otic placode stage and later at the vesicle stage. Both activities correspond to critical morphogenetic events in ear development. We propose that FGF8 is an important regulator of otocyst patterning.
Publisher: Oxford University Press (OUP)
Date: 16-01-2014
DOI: 10.1093/GBE/EVU011
Publisher: Elsevier BV
Date: 08-2004
Publisher: Springer Science and Business Media LLC
Date: 26-09-2019
Publisher: Cold Spring Harbor Laboratory
Date: 12-2008
DOI: 10.1101/PDB.PROT5096
Abstract: Developmental gene expression is analyzed predominantly via whole-mount in situ hybridization using digoxigenin-labeled RNA probes. This protocol describes how to perform this procedure in Amphimedon queenslandica , including fixation, hybridization, and sectioning of embryonic, larval, and post-larval juvenile stages.
Publisher: Cold Spring Harbor Laboratory
Date: 12-2008
DOI: 10.1101/PDB.PROT5097
Abstract: Although attempts to culture prepigmentation-stage embryos (i.e., blastulas and early gastrulas) outside of brood chambers have so far been unsuccessful in Amphimedon , it is possible to manipulate embryos within the brood chamber and follow their development under laboratory conditions. This protocol describes microinjection of lipophilic tracers such as 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate (DiI) into embryos embedded in their native brood chamber. DiI does not appear to perturb embryonic development and is relatively resistant to photobleaching. As long as care is taken not to damage the fragile embryos during observation and photography, the same embryo can be photographed multiple times, permitting its development to be tracked (up to 4 wk) from early cleavage stages to hatching of free-swimming parenchymella larvae. The embryos or larvae also can be fixed without loss of fluorescence. This method also can be used to deliver other types of solutions to embryos or in idual cells of early embryos.
Publisher: Springer Science and Business Media LLC
Date: 20-05-2014
DOI: 10.1038/NCOMMS4905
Abstract: Elucidation of macroevolutionary transitions between erse animal body plans remains a major challenge in evolutionary biology. We address the sponge-eumetazoan transition by analyzing expression of a broad range of eumetazoan developmental regulatory genes in Sycon ciliatum (Calcispongiae). Here we show that many members of surprisingly numerous Wnt and Tgfβ gene families are expressed higher or uniquely in the adult apical end and the larval posterior end. Genes involved in formation of the eumetazoan endomesoderm, such as β-catenin, Brachyury and Gata, as well as germline markers Vasa and Pl10, are expressed during formation and maintenance of choanoderm, the feeding epithelium of sponges. Similarity in developmental gene expression between sponges and eumetazoans, especially cnidarians, is consistent with Haeckel's view that body plans of sponges and cnidarians are homologous. These results provide a framework for further studies aimed at deciphering ancestral developmental regulatory networks and their modifications during animal body plans evolution.
Publisher: Cold Spring Harbor Laboratory
Date: 12-2008
DOI: 10.1101/PDB.PROT5095
Abstract: Fertilization occurs internally in Amphimedon and embryos are brooded in multiple chambers throughout the adult. Each chamber contains a mixture of developmental stages, from egg to late ring stages (i.e., prehatch late embryos). At the end of embryogenesis, swimming parenchymella larvae emerge from the adult. After several hours in the water column, the larvae settle and metamorphose into juvenile sponges. This protocol details how to obtain Amphimedon larvae and post-larvae/juveniles as well as embryos. Once isolated, these biological stages can be used for a variety of molecular and cellular analyses.
Publisher: Springer Science and Business Media LLC
Date: 05-08-2019
Publisher: The MIT Press
Date: 12-02-2016
Publisher: La Trobe
Date: 2021
Publisher: Springer Science and Business Media LLC
Date: 23-07-2012
Abstract: Sox genes are HMG-domain containing transcription factors with important roles in developmental processes in animals many of them appear to have conserved functions among eumetazoans. Demosponges have fewer Sox genes than eumetazoans, but their roles remain unclear. The aim of this study is to gain insight into the early evolutionary history of the Sox gene family by identification and expression analysis of Sox genes in the calcareous sponge Sycon ciliatum . Calcaronean Sox related sequences were retrieved by searching recently generated genomic and transcriptome sequence resources and analyzed using variety of phylogenetic methods and identification of conserved motifs. Expression was studied by whole mount in situ hybridization. We have identified seven Sox genes and four Sox-related genes in the complete genome of Sycon ciliatum . Phylogenetic and conserved motif analyses showed that five of Sycon Sox genes represent groups B, C, E, and F present in cnidarians and bilaterians. Two additional genes are classified as Sox genes but cannot be assigned to specific subfamilies, and four genes are more similar to Sox genes than to other HMG-containing genes. Thus, the repertoire of Sox genes is larger in this representative of calcareous sponges than in the demosponge Amphimedon queenslandica . It remains unclear whether this is due to the expansion of the gene family in Sycon or a secondary reduction in the Amphimedon genome. In situ hybridization of Sycon Sox genes revealed a variety of expression patterns during embryogenesis and in specific cell types of adult sponges. In this study, we describe a large family of Sox genes in Sycon ciliatum with dynamic expression patterns, indicating that Sox genes are regulators in development and cell type determination in sponges, as observed in higher animals. The revealed differences between demosponge and calcisponge Sox genes repertoire highlight the need to utilize models representing different sponge lineages to describe sponge development, a prerequisite for deciphering evolution of metazoan developmental mechanisms.
Publisher: Elsevier BV
Date: 12-2015
DOI: 10.1016/J.MARGEN.2015.07.008
Abstract: Developmental transcription factors (DTFs) control development of animals by affecting expression of target genes, some of which are transcription factors themselves. In bilaterians and cnidarians, conserved DTFs are involved in homologous processes such as gastrulation or specification of neurons. The genome of Amphimedon queenslandica, the first sponge to be sequenced, revealed that only a fraction of these conserved DTF families are present in demosponges. This finding was in line with the view that morphological complexity in the animal lineage correlates with developmental toolkit complexity. However, as the phylum Porifera is very erse, Amphimedon's genome may not be representative of all sponges. The recently sequenced genomes of calcareous sponges Sycon ciliatum and Leucosolenia complicata allowed investigations of DTFs in a sponge lineage evolutionarily distant from demosponges. Surprisingly, the phylogenetic analyses of identified DTFs revealed striking differences between the calcareous sponges and Amphimedon. As these differences appear to be a result of independent gene loss events in the two sponge lineages, the last common ancestor of sponges had to possess a much more erse repertoire of DTFs than extant sponges. Developmental expression of sponge homologs of genes involved in specification of the Bilaterian endomesoderm and the neurosensory cells suggests that roles of many DTFs date back to the last common ancestor of all animals. Strikingly, even DTFs displaying apparent pan-metazoan conservation of sequence and function are not immune to being lost from in idual species genomes. The quest for a comprehensive picture of the developmental toolkit in the last common metazoan ancestor is thus greatly benefitting from the increasing accessibility of sequencing, allowing comparisons of multiple genomes within each phylum.
Publisher: Cold Spring Harbor Laboratory
Date: 12-2008
DOI: 10.1101/PDB.EMO108
Abstract: Sponges are one of the earliest branching metazoans. In addition to undergoing complex development and differentiation, they can regenerate via stem cells and can discern self from nonself (“allorecognition”), making them a useful comparative model for a range of metazoan-specific processes. Molecular analyses of these processes have the potential to reveal ancient homologies shared among all living animals and critical genomic innovations that underpin metazoan multicellularity. Amphimedon queenslandica (Porifera, Demospongiae, Haplosclerida, Niphatidae) is the first poriferan representative to have its genome sequenced, assembled, and annotated. Amphimedon exemplifies many sessile and sedentary marine invertebrates (e.g., corals, ascidians, bryozoans): They disperse during a planktonic larval phase, settle in the vicinity of conspecifics, ward off potential competitors (including incompatible genotypes), and ensure that brooded eggs are fertilized by conspecific sperm. Using genomic and expressed sequence tag (EST) resources from Amphimedon , functional genomic approaches can be applied to a wide range of ecological and population genetic processes, including fertilization, dispersal, and colonization dynamics, host-symbiont interactions, and secondary metabolite production. Unlike most other sponges, Amphimedon produce hundreds of asynchronously developing embryos and larvae year-round in distinct, easily accessible brood chambers. Embryogenesis gives rise to larvae with at least a dozen cell types that are segregated into three layers and patterned along the body axis. In this article, we describe some of the methods currently available for studying A. queenslandica , focusing on the analysis of embryos, larvae, and post-larvae.
Publisher: Springer Science and Business Media LLC
Date: 07-2001
Abstract: We report the identification and characterisation of five different Nkx5-related genes in medaka fish (Oryzias latipes). They constitute homologues of genes previously isolated in higher vertebrates, Nkx5--1, Nkx5--2, Hmx1/Nkx5--3 and SOHo-1, and were named accordingly: OlNkx5--1.1, OlNkx5--2, OlNkx5--3 and OlSOHo. For the Nkx5--1 gene a new, second homologue, OlNkx5--1.2, was isolated. In medaka, Nkx5 and SOHo genes are differentially expressed in three developing sensory organs: eye, ear and lateral line and later in defined brain regions. Phylogenetic analyses of the entire Nkx5 family revealed that four paralogous Nkx5 groups, Nkx5--1, Nkx5--2, Hmx1/Nkx5--3/GH6 and SOHo, are present in vertebrates. Only some of the Nkx5 family members have been identified in singular vertebrate species so far. Here we present, for the first time, the isolation of representatives of each Nkx5 subgroup in one species, the medaka fish. Based on similarities in sequence and expression patterns, and genomic organisation we propose a model of the evolutionary history of the Nkx5 family. The model predicts that the four vertebrate Nkx5 genes arose by a tandem duplication, followed by chromosomal duplication. The two Nkx5--1 genes identified so far exclusively in medaka most probably result from an additional genome duplication in the fish lineage.
Publisher: PeerJ
Date: 25-08-2015
DOI: 10.7717/PEERJ.1211
Publisher: Elsevier BV
Date: 08-2016
DOI: 10.1016/J.GDE.2016.05.026
Abstract: The emergence of complex animal life forms remains poorly understood despite substantial interest and research in this area. To be informative, the ideal models to study transitions from single-cell organisms to the first animals and then to mammalian-level complexity should be phylogenetically strategically placed and retain ancestral characters. Sponges (Porifera) are likely to be the earliest branching animal phylum. When analysed from morphological, genomic and developmental perspectives, sponges appear to combine features of single-cell eukaryotic organisms and the complex multicellular animals (Eumetazoa). Intriguingly, homologues of components of the eumetazoan regulatory networks specifying the endoderm, the germ-cells and stem cells and (neuro) sensory cells are expressed in sponge choanocytes, archaeocytes and larval sensory cells. Studies using sponges as model systems are already bringing insights into animal evolution, and have opened avenues to further research benefitting from the recent spectacular expansion of genomic technologies.
Publisher: Springer Science and Business Media LLC
Date: 13-04-2017
DOI: 10.1038/SREP45658
Abstract: The ability to form mineral structures under biological control is widespread among animals. In several species, specific proteins have been shown to be involved in biomineralization, but it is uncertain how they influence the shape of the growing biomineral and the resulting skeleton. Calcareous sponges are the only sponges that form calcitic spicules, which, based on the number of rays (actines) are distinguished in diactines, triactines and tetractines. Each actine is formed by only two cells, called sclerocytes. Little is known about biomineralization proteins in calcareous sponges, other than that specific carbonic anhydrases (CAs) have been identified, and that uncharacterized Asx-rich proteins have been isolated from calcitic spicules. By RNA-Seq and RNA in situ hybridization (ISH), we identified five additional biomineralization genes in Sycon ciliatum: two bicarbonate transporters (BCTs) and three Asx-rich extracellular matrix proteins (ARPs). We show that these biomineralization genes are expressed in a coordinated pattern during spicule formation. Furthermore, two of the ARPs are spicule-type specific for triactines and tetractines (ARP1 or SciTriactinin ) or diactines (ARP2 or SciDiactinin ). Our results suggest that spicule formation is controlled by defined temporal and spatial expression of spicule-type specific sets of biomineralization genes.
Publisher: Wiley
Date: 21-02-2014
Publisher: Wiley
Date: 24-01-2013
DOI: 10.1002/JEZ.B.22485
Abstract: We present the discovery of microRNAs (miRNAs) in the calcisponges Sycon and Leucosolenia (phylum Calcarea), and potential miRNAs in the homoscleromorph Oscarella carmela (Phylum Homoscleromorpha), expanding the complement of poriferan miRNAs previously known only from the siliceous sponges (demosponges and hexactinellids). Comparison of these miRNAs with those previously described from silicisponges and eumetazoans reveals that these newly described miRNAs are novel, with each metazoan lineage (Silicea, Calcarea, Homoscleromorpha, and Eumetazoa) characterized by a unique and non-overlapping repertoire of miRNAs (or potential miRNAs as in the case of the homoscleromorphs). Because each group is characterized by a unique repertoire of miRNAs, miRNAs cannot be used to help resolve the contentious issue of sponge mono- versus paraphyly. Further, because all sponges are characterized by a similar repertoire of tissue types and body plan organisation, we hypothesize that the lack of conserved miRNAs amongst the three primary sponge lineages is evidence that cellular differentiation and cell type specificity in sponges are not dependent upon conserved miRNAs, contrary to many known cases in eumetazoans. Finally, we suggest that miRNAs evolved multiple times independently not only among eukaryotes, but even within animals, independently evolved miRNAs representing molecular exaptations of RNAi machinery into pre-existing gene regulatory networks. The role(s) miRNAs play though in sponge biology and evolution remains an open question.
Publisher: The Royal Society
Date: 22-12-2015
Abstract: Long non-coding RNAs (lncRNAs) play important regulatory roles during animal development, and it has been hypothesized that an RNA-based gene regulation was important for the evolution of developmental complexity in animals. However, most studies of lncRNA gene regulation have been performed using model animal species, and very little is known about this type of gene regulation in non-bilaterians. We have therefore analysed RNA-Seq data derived from a comprehensive set of embryogenesis stages in the calcareous sponge Sycon ciliatum and identified hundreds of developmentally expressed intergenic lncRNAs (lincRNAs) in this species. In situ hybridization of selected lincRNAs revealed dynamic spatial and temporal expression during embryonic development. More than 600 lincRNAs constitute integral parts of differentially expressed gene modules, which also contain known developmental regulatory genes, e.g. transcription factors and signalling molecules. This study provides insights into the non-coding gene repertoire of one of the earliest evolved animal lineages, and suggests that RNA-based gene regulation was probably present in the last common ancestor of animals.
Publisher: Springer Science and Business Media LLC
Date: 10-06-2016
Publisher: Elsevier BV
Date: 12-2019
DOI: 10.1016/J.ZOOL.2019.125695
Abstract: It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA licon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A erse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.
Publisher: Wiley
Date: 2005
DOI: 10.1002/DVDY.20498
Publisher: Elsevier BV
Date: 08-2008
DOI: 10.1016/J.CUB.2008.06.074
Abstract: The nerve cell is a eumetazoan (cnidarians and bilaterians) synapomorphy [1] this cell type is absent in sponges, a more ancient phyletic lineage. Here, we demonstrate that despite lacking neurons, the sponge Amphimedon queenslandica expresses the Notch-Delta signaling system and a proneural basic helix loop helix (bHLH) gene in a manner that resembles the conserved molecular mechanisms of primary neurogenesis in bilaterians. During Amphimedon development, a field of subepithelial cells expresses the Notch receptor, its ligand Delta, and a sponge bHLH gene, AmqbHLH1. Cells that migrate out of this field express AmqDelta1 and give rise to putative sensory cells that populate the larval epithelium. Phylogenetic analysis suggests that AmqbHLH1 is descendent from a single ancestral bHLH gene that later duplicated to produce the atonal/neurogenin-related bHLH gene families, which include most bilaterian proneural genes [2]. By way of functional studies in Xenopus and Drosophila, we demonstrate that AmqbHLH1 has a strong proneural activity in both species with properties displayed by both neurogenin and atonal genes. From these results, we infer that the bilaterian neurogenic circuit, comprising proneural atonal-related bHLH genes coupled with Notch-Delta signaling, was functional in the very first metazoans and was used to generate an ancient sensory cell type.
Publisher: Public Library of Science (PLoS)
Date: 30-05-2013
Publisher: Project MUSE
Date: 2021
DOI: 10.1353/OL.2021.0007
Publisher: Elsevier BV
Date: 10-2000
DOI: 10.1016/S0925-4773(00)00414-7
Abstract: An orthologue of the mouse homeobox gene Nkx5-1 was cloned and characterized in the zebrafish. As in the mouse and chick, the zebrafish Nkx5-1 gene is expressed in the ear placode and vesicle and in cells forming the vestibulo-acoustic ganglion. In addition, a novel expression domain, the lateral line, appears in the zebrafish, supporting a common precursor hypothesis for these two organs. In the FGF8 zebrafish mutant ace, expression of Nkx5-1 in the otic structures is diminished. The most significant reduction of zfNkx5-1 expression was observed in cells of the vestibulo-acoustic ganglion.
Publisher: Springer Science and Business Media LLC
Date: 29-10-2014
DOI: 10.1038/NATURE13881
Abstract: Sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors, including homeobox genes belonging to the Antennapedia (ANTP) class, which in bilaterians encompass Hox, ParaHox and NK genes. In the genome of the demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians. It has been proposed that Hox and ParaHox genes originated from NK cluster genes after ergence of sponges from the lineage leading to cnidarians and bilaterians. On the other hand, synteny analysis lends support to the notion that the absence of Hox and ParaHox genes in Amphimedon is a result of secondary loss (the ghost locus hypothesis). Here we analysed complete suites of ANTP-class homeoboxes in two calcareous sponges, Sycon ciliatum and Leucosolenia complicata. Our phylogenetic analyses demonstrate that these calcisponges possess orthologues of bilaterian NK genes (Hex, Hmx and Msx), a varying number of additional NK genes and one ParaHox gene, Cdx. Despite the generation of scaffolds spanning multiple genes, we find no evidence of clustering of Sycon NK genes. All Sycon ANTP-class genes are developmentally expressed, with patterns suggesting their involvement in cell type specification in embryos and adults, metamorphosis and body plan patterning. These results demonstrate that ParaHox genes predate the origin of sponges, thus confirming the ghost locus hypothesis, and highlight the need to analyse the genomes of multiple sponge lineages to obtain a complete picture of the ancestral composition of the first animal genome.
Publisher: Springer Science and Business Media LLC
Date: 25-11-2014
Start Date: 2006
End Date: 12-2009
Amount: $205,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2017
End Date: 12-2020
Amount: $805,168.00
Funder: Australian Research Council
View Funded ActivityStart Date: 10-2014
End Date: 12-2021
Amount: $28,000,000.00
Funder: Australian Research Council
View Funded Activity