Tomer Ventura

Gene Silencing in Crustaceans: From Basic Research to Biotechnologies

Publisher: MDPI AG

Date: 07-11-2013

DOI: 10.3390/GENES4040620

Two Homogametic Genotypes – One Crayfish: On the Consequences of Intersexuality

Publisher: Elsevier BV

Date: 11-2020

DOI: 10.1016/J.ISCI.2020.101652

Toward the identification of female gonad-stimulating factors in crustaceans

Publisher: Springer Science and Business Media LLC

Date: 07-02-2018

DOI: 10.1007/S10750-017-3497-4

Insulin and gender: An insulin-like gene expressed exclusively in the androgenic gland of the male crayfish

Publisher: Elsevier BV

Date: 2007

DOI: 10.1016/J.YGCEN.2006.09.006

Abstract: Members of the insulin family of hormones are generally not regarded as gender-specific, although there is sporadic evidence for the possible involvement of insulin pathways in sexual differentiation. In crustaceans, sexual differentiation is controlled by the androgenic gland (AG), an organ unique to males. To date, attempts to identify active AG factors in decapods through either classical purification methods or sequence similarity with isopod AG hormones have proven unsuccessful. In the present study, the first subtractive cDNA library from a decapod AG was constructed from the red-claw crayfish Cherax quadricarinatus. During library screening, an AG-specific gene, expressed exclusively in males even at early stages of maturation and termed Cq-IAG (C. quadricarinatus insulin-like AG factor), was discovered. In situ hybridization of Cq-IAG confirmed the exclusive localization of its expression to the AG. Following cloning and complete sequencing of the gene, its cDNA was found to contain 1445 nucleotides encoding a deduced translation product of 176 amino acids. The proposed protein sequence encompasses Cys residue and putative cleaved peptide patterns whose linear and 3D organization are similar to those of members of the insulin/insulin-like growth factor/relaxin family and their receptor recognition surface. The identification of Cq-IAG is the first report of a pro-insulin-like gene expressed in a decapod crustacean in a gender-specific manner. Its expression in a male-specific endocrine gland controlling sex differentiation supports the notion that insulin may have evolved in the context of regulating sexual differentiation.

Physiological status and nutritional condition of cultured juvenile Thenus australiensis over the moult cycle

Publisher: Elsevier BV

Date: 12-2020

DOI: 10.1016/J.CBPB.2020.110504

Transcriptomic changes across vitellogenesis in the black tiger prawn (Penaeus monodon), neuropeptides and G protein-coupled receptors repertoire curation

Publisher: Elsevier BV

Date: 11-2020

DOI: 10.1016/J.YGCEN.2020.113585

A sexual shift induced by silencing of a single insulin-like gene in crayfish: Ovarian upregulation and testicular degeneration

Publisher: Public Library of Science (PLoS)

Date: 09-12-2010

DOI: 10.1371/JOURNAL.PONE.0015281

Crustacean nuclear localization signals help facilitating the delivery of DNA into Australian red-claw crayfish cells

Publisher: Elsevier BV

Date: 2019

DOI: 10.1016/J.AQUACULTURE.2018.09.030

Multi-Tissue Transcriptome Analysis Identifies Key Sexual Development-Related Genes of the Ornate Spiny Lobster (Panulirus ornatus)

Publisher: MDPI AG

Date: 29-09-2020

DOI: 10.3390/GENES11101150

Abstract: Sexual development involves the successive and overlapping processes of sex determination, sexual differentiation, and ultimately sexual maturation, enabling animals to reproduce. This provides a mechanism for enriched genetic variation which enables populations to withstand ever-changing environments, selecting for adapted in iduals and driving speciation. The molecular mechanisms of sexual development display a bewildering ersity, even in closely related taxa. Many sex determination mechanisms across animals include the key family of “doublesex- and male abnormal3-related transcription factors” (Dmrts). In a few exceptional species, a single Dmrt residing on a sex chromosome acts as the master sex regulator. In this study, we provide compelling evidence for this model of sex determination in the ornate spiny lobster Panulius ornatus, concurrent with recent reports in the eastern spiny lobster Sagmariasus verreauxi. Using a multi-tissue transcriptomic database established for P. ornatus, we screened for the key factors associated with sexual development (by homology search and using previous knowledge of these factors from related species), providing an in-depth understanding of sexual development in decapods. Further research has the potential to close significant gaps in our understanding of reproductive development in this ecologically and commercially significant order.

Double-Stranded RNA Binding Proteins in Serum Contribute to Systemic RNAi Across Phyla—Towards Finding the Missing Link in Achelata

Publisher: MDPI AG

Date: 22-09-2020

DOI: 10.3390/IJMS21186967

Abstract: RNA interference (RNAi) has become a widely utilized method for studying gene function, yet despite this many of the mechanisms surrounding RNAi remain elusive. The core RNAi machinery is relatively well understood, however many of the systemic mechanisms, particularly double-stranded RNA (dsRNA) transport, are not. Here, we demonstrate that dsRNA binding proteins in the serum contribute to systemic RNAi and may be the limiting factor in RNAi capacity for species such as spiny lobsters, where gene silencing is not functional. Incubating sera from a variety of species across phyla with dsRNA led to a gel mobility shift in species in which systemic RNAi has been observed, with this response being absent in species in which systemic RNAi has never been observed. Proteomic analysis suggested lipoproteins may be responsible for this phenomenon and may transport dsRNA to spread the RNAi signal systemically. Following this, we identified the same gel shift in the slipper lobster Thenus australiensis and subsequently silenced the insulin androgenic gland hormone, marking the first time RNAi has been performed in any lobster species. These results pave the way for inducing RNAi in spiny lobsters and for a better understanding of the mechanisms of systemic RNAi in Crustacea, as well as across phyla.

A Placemaking Framework for the Social Sustainability of Master-Planned Communities: A Case Study from Australia

Publisher: Cambridge University Press

Date: 13-01-2022

DOI: 10.1017/9780511977961.018

Discovery of a novel insulin-like peptide and insulin binding proteins in the Eastern rock lobster Sagmariasus verreauxi

Publisher: Elsevier BV

Date: 05-2015

DOI: 10.1016/J.YGCEN.2014.08.018

Abstract: This study reports, for the first time in any of the commercially important decapod species, the identification of an insulin-like peptide (ILP), distinct from the androgenic gland hormone. Bioinformatics analysis of the de novo assembled spiny lobster, (Sagmariasus verreauxi) transcriptome, allowed identification of Sv-ILP1 as well as eight binding proteins. Binding proteins were termed as Sv-IGFBP, due to homology with the vertebrate insulin-like growth-factor binding protein and Sv-SIBD1-7, single insulin-binding domain protein (SIBD), similar to those identified in other invertebrate species. Sv-ILP1 was found to be expressed in the eyestalk, gonads and antennal gland of both sexes and to a lesser extent in male muscle, androgenic gland and hepatopancreas. The expression profiles of each binding protein were found to vary across tissues, with Sv-SIBD5, 6 and 7 showing higher expression in the gonad, demonstrated by PCR and digital gene expression. Further spatial investigations, using in-situ hybridisation, found Sv-ILP1 to be expressed in the neurosecretory cells of the thoracic ganglia, in keeping with the tissue expression of Drosophila ILP7 (DILP7). This correlative tissue expression, considered with the phylogenetic clustering of Sv-ILP1 and DILP7, suggests Sv-ILP1 to be a DILP7 orthologue. The broad expression of Sv-ILP1 strongly suggests that ILPs have a role beyond that of masculinisation in decapods. The function of these novel peptides may have application in enhancing aquaculture practices in the commercially important decapod species.

Concurrence of lower jaw skeletal anomalies in triploid Atlantic salmon (Salmo salar L.) and the effect on growth in freshwater

Publisher: Wiley

Date: 04-05-2016

DOI: 10.1111/JFD.12492

Abstract: Triploid Atlantic salmon populations are associated with higher prevalence of lower jaw skeletal anomalies affecting fish performance, welfare and value deleteriously. Anomalous lower jaw can be curved downward (LJD), shortened (SJ) or misaligned (MA). Two separate groups of triploid Atlantic salmon (~12 g) with either normal lower jaw (NOR) or SJ were visually assessed four times over three months for presence and concurrence of jaw anomalies (with severity classified) and opercular shortening to understand the relatedness of these anomalous developmental processes. The prevalence of jaw anomalies increased in both groups over time (NOR group - SJ, LJD and MA combined 0-24.5% SJ group - LJD and MA combined 17-31%). SJ and LJD occurred both independently and concurrently whereas MA exclusively concurred with them. All three anomalies could be concurrent. Severity of both LJD and SJ increased in the SJ group only. Opercular shortening recovery was observed in both groups but at a slower rate in the SJ group. The SJ group specific growth rate (SGR) was significantly (P < 0.05) lower than the NOR group. This study demonstrated the concurrence of SJ, LJD and MA and showed possible deleterious consequences deriving from the conditions.

Development and Interrogation of a Transcriptomic Resource for the Giant Triton Snail (Charonia tritonis)

Publisher: Springer Science and Business Media LLC

Date: 06-2021

DOI: 10.1007/S10126-021-10042-7

Abstract: Gastropod molluscs are among the most abundant species that inhabit coral reef ecosystems. Many are specialist predators, along with the giant triton snail Charonia tritonis (Linnaeus, 1758) whose diet consists of Acanthaster planci (crown-of-thorns starfish), a corallivore known to consume enormous quantities of reef-building coral. C. tritonis are considered vulnerable due to overexploitation, and a decline in their populations is believed to have contributed to recurring A. planci population outbreaks. Aquaculture is considered one approach that could help restore natural populations of C. tritonis and mitigate coral loss however, numerous questions remain unanswered regarding their life cycle, including the molecular factors that regulate their reproduction and development. In this study, we have established a reference C. tritonis transcriptome derived from developmental stages (embryo and veliger) and adult tissues. This was used to identify genes associated with cell signalling, such as neuropeptides and G protein-coupled receptors (GPCRs), involved in endocrine and olfactory signalling. A comparison of developmental stages showed that several neuropeptide precursors are exclusively expressed in post-hatch veligers and functional analysis found that FFamide stimulated a significant (20.3%) increase in larval heart rate. GPCRs unique to veligers, and a ersity of rhodopsin-like GPCRs located within adult cephalic tentacles, all represent candidate olfactory receptors. In addition, the cytochrome P450 superfamily, which participates in the biosynthesis and degradation of steroid hormones and lipids, was also found to be expanded with at least 91 genes annotated, mostly in gill tissue. These findings further progress our understanding of C. tritonis with possible application in developing aquaculture methods.

Apparent digestibility of raw materials by yellowtail kingfish (Seriola lalandi)

Publisher: Elsevier BV

Date: 09-2019

DOI: 10.1016/J.AQUACULTURE.2019.734233

Production, gene structure and characterization of two orthologs of leptin and a leptin receptor in tilapia

Publisher: Elsevier BV

Date: 10-2014

DOI: 10.1016/J.YGCEN.2014.05.006

Abstract: Full-length cDNA encoding two leptin sequences (tLepA and tLepB) and one leptin receptor sequence (tLepR) were identified in tilapia (Oreochromis niloticus). The full-length cDNA of tLepR was 3423bp, encoding a protein of 1140 amino acid (aa) which contained all functionally important domains conserved among vertebrate leptin receptors. The cDNAs of tLepA and tLepB were 486bp and 459bp in length, encoding proteins of 161 aa and 152 aa, respectively. Modeling the three-dimensional structures of tLepA and tLepB predicted strong conservation of tertiary structure with that of human leptin, comprised of four helixes. Using synteny, the tLeps were found near common genes, such as IMPDH1 and LLRC4. The cDNA for tLepA and tLepB was cloned and synthetic cDNA optimized for expression in Escherichia coli was prepared according to the cloned sequence. The tLepA- and tLepB-expressing plasmids were transformed into E. coli and expressed as recombinant proteins upon induction with nalidixic acid, found almost entirely in insoluble inclusion bodies (IBs). The proteins were solubilized, refolded and purified to homogeneity by anion-exchange chromatography. In the case of tLepA, the fraction eluted contained a mixture of monomers and dimers. The purified tLepA and tLepB monomers and tLepA dimer showed a single band of ∼15kDa on an SDS-polyacrylamide gel in the presence of reducing agent, whereas the tLepA dimer showed one band of ∼30kDa in the absence of reducing agent, indicating its formation by S-S bonds. The three tLeps were biologically active in promoting proliferation of BAF/3 cells stably transfected with the long form of human leptin receptor (hLepR), but their activity was four orders of magnitude lower than that of mammalian leptin. Furthermore, the three tLeps were biologically active in promoting STAT-LUC activation in COS7 cells transfected with the identified tLepR but not in cells transfected with hLepR. tLepA was more active than tLepB. Low or no activity likely resulted from low identity (9-22%) to mammalian leptins. In an in vivo experiment in which tilapia were fed ad libitum or fasted, there was no significant difference in the expressions of tLepA, tLepB or tLepR in the brain between the two groups examined both by real-time PCR and RNA next generation sequencing. In conclusion, in the present report we show novel, previously unknown sequences of tilapia leptin receptor and two leptins and prepare two biologically active recombinant leptin proteins.

Intestinal Transcriptome Analysis Highlights Key Differentially Expressed Genes Involved in Nutrient Metabolism and Digestion in Yellowtail Kingfish (Seriola lalandi) Fed Terrestrial Animal and Plant Proteins

Publisher: MDPI AG

Date: 05-06-2020

DOI: 10.3390/GENES11060621

Abstract: This study investigated the effects of dietary terrestrial animal and plant proteins on the intestinal transcriptomes of yellowtail kingfish (YTK), Seriola lalandi, an ecologically and economically important marine species in Australia. Five diets containing fish meal (FM), poultry by-product meal (PBM), blood meal (BLM), faba bean meal (FBM) and corn gluten meal (CGM) were formulated and fed over a period of 4 weeks. The Illumina RNA-sequencing (RNA-Seq) results identified a suite of differentially expressed genes involved in nutrient metabolism and protein digestion pathways, reinforced by quantitative polymerase chain reaction (qPCR) results. These findings provide molecular support to the notion that PBM and FBM are useful raw materials in commercial diets for YTK. Using the same evidence, we have demonstrated that BLM and CGM may be less useful and their incorporation into commercial aquafeeds for this species should be done cautiously. The differentially expressed genes showed a subtle difference and high correlation with apparent nutrient digestibility of raw materials. Further, our results indicate that transcriptome profiling provides a useful tool to evaluate alternative protein sources for use in aquaculture feeds.

Double Stranded RNA Binding Proteins in the Serum Contribute to Systemic RNAi across Phyla – Towards Finding the Missing Link in Achelata

Publisher: MDPI AG

Date: 13-09-2020

DOI: 10.20944/PREPRINTS202009.0283.V1

Abstract: RNA interference (RNAi) has become a widely utilised method to study gene function, yet despite this, many of the mechanisms surrounding RNAi remain elusive. The core RNAi machinery is relatively well understood, however many of the systemic mechanisms, particularly double stranded RNA (dsRNA) transport, are not. Here, we demonstrate that dsRNA binding proteins in the serum contribute to systemic RNAi, and may be the limiting factor in RNAi capacity for species such as spiny lobsters where gene silencing is not functional. Incubating serum from a variety of species across phyla with dsRNA led to a gel mobility shift in species where systemic RNAi has been observed, with this response being absent in species where systemic RNAi has never been observed. Proteomic analysis suggested lipoproteins may be responsible for this phenomenon, and may transport dsRNA to spread the RNAi signal systemically. Following this, we identified the same gel shift in the slipper lobster Thenus australiensis and subsequently silenced the insulin androgenic gland hormone, marking the first time RNAi has been performed in any lobster species. These results pave the way for inducing RNAi in spiny lobsters, and better understanding the mechanisms of systemic RNAi in Crustacea, as well as across phyla.

Transcriptomic Changes Following Induced De-Masculinisation of Australian Red Claw Crayfish Cherax quadricarinatus

Publisher: MDPI AG

Date: 07-02-2023

DOI: 10.3390/IJMS24043292

Abstract: The Australian red claw crayfish Cherax quadricarinatus, an emerging species within the freshwater aquaculture trade, is not only an ideal species for commercial production due to its high fecundity, fast growth, and physiological robustness but also notoriously invasive. Investigating the reproductive axis of this species has been of great interest to farmers, geneticists, and conservationists alike for many decades however, aside from the characterisation of the key masculinising insulin-like androgenic gland hormone (IAG) produced by the male-specific androgenic gland (AG), little remains known about this system and the downstream signalling cascade involved. This investigation used RNA interference to silence IAG in adult intersex C. quadricarinatus (Cq-IAG), known to be functionally male but genotypically female, successfully inducing sexual redifferentiation in all in iduals. To investigate the downstream effects of Cq-IAG knockdown, a comprehensive transcriptomic library was constructed, comprised of three tissues within the male reproductive axis. Several factors known to be involved in the IAG signal transduction pathway, including a receptor, binding factor, and additional insulin-like peptide, were found to not be differentially expressed in response to Cq-IAG silencing, suggesting that the phenotypic changes observed may have occurred through post-transcriptional modifications. Many downstream factors displayed differential expression on a transcriptomic level, most notably related to stress, cell repair, apoptosis, and cell proliferation. These results suggest that IAG is required for sperm maturation, with necrosis of arrested tissue occurring in its absence. These results and the construction of a transcriptomic library for this species will inform future research involving reproductive pathways as well as biotechnological developments in this commercially and ecologically significant species.

From the discovery of the crustacean androgenic gland to the insulin-like hormone in six decades

Publisher: Elsevier BV

Date: 09-2011

DOI: 10.1016/J.YGCEN.2011.05.018

Abstract: Over the past six decades, a unique crustacean endocrine organ, the androgenic gland (AG), has occupied the minds of groups researching Crustacea the world over. Unlike male sexual differentiation and maintenance of sexual characteristics in other arthropods, in crustaceans these processes are regulated by the unique male AG. Crustaceans present a particular case in which the gametogenic organ (testis) is clearly separated from the organ regulating sex differentiation (the AG), enabling endocrine manipulations. The AG was first discovered in a decapod species and later investigated in detail not only in decapods but also in hipods and isopods. The key role of the AG in regulating sex differentiation was subsequently validated in a number of representative species of a wide array of Malacostraca. It was in an isopod species that the AG hormone was first discovered. Later, orthologous genes were found in isopods and decapods, with all these genes sharing the key features of the insulin-like superfamily of peptides. This review unfolds the story of the AG and AG-specific insulin-like factors (IAGs) from a historical perspective, highlighting the main achievements in the field and giving a glimpse of future challenges to be addressed.

Epidermal growth factor receptor in the prawn Macrobrachium rosenbergii: Function and putative signaling cascade

Publisher: The Endocrine Society

Date: 09-2013

DOI: 10.1210/EN.2013-1259

Abstract: Epidermal growth factor receptors (EGFRs) are highly conserved members of the tyrosine kinase receptor superfamily found in metazoans and plants. In arthropods, EGFRs are vital for the proper development of embryos and of adult limbs, gonads, and eyes as well as affecting body size. In searching for genes involved in the growth and development of our model organism, the decapod crustacean (Macrobrachium rosenbergii), a comprehensive transcript library was established using next-generation sequencing. Using this library, the expression of several genes assigned to the signal transduction pathways mediated by EGFRs was observed, including a transcript encoding M. rosenbergii EGFR (Mr-EGFR), several potential ligands upstream to the receptor, and most of the putative downstream signal transducer genes. The deduced protein encoded by Mr-EGFR, representing the first such receptor reported thus far in crustaceans, shows sequence similarity to other arthropod EGFRs. The M. rosenbergii gene is expressed in most tested tissues. The role of Mr-EGFR was revealed by temporarily silencing the transcript through weekly injections of double-stranded Mr-EGFR RNA. Such treatment resulted in a significant reduction in growth and a delay in the appearance of a male secondary sexual characteristic, namely the appendix masculina. An additional function of Mr-EGFR was revealed with respect to eye development. Although the optic ganglion appeared to have retained its normal morphology, Mr-EGFR-silenced in iduals developed abnormal eyes that presented irregular organization of the ommatidia, reflected by unorganized receptor cells occupying large areas of the dioptric portion and by a shortened crystalline tract layer.

Crustacean metamorphosis: an omics perspective

Publisher: Springer Science and Business Media LLC

Date: 27-11-2017

DOI: 10.1007/S10750-017-3445-3

Characterization of Shed genes encoding ecdysone 20-monooxygenase (CYP314A1) in the Y-organ of the blackback land crab, Gecarcinus lateralis

Publisher: Elsevier BV

Date: 2021

DOI: 10.1016/J.YGCEN.2020.113658

Assessing the Pyloric Caeca and Distal Gut Microbiota Correlation with Flesh Color in Atlantic Salmon (Salmo salar L., 1758)

Publisher: MDPI AG

Date: 16-08-2020

DOI: 10.3390/MICROORGANISMS8081244

Abstract: The Atlantic salmon (Salmo salar L., 1758) is a temperate fish species native to the northern Atlantic Ocean. The distinctive pink–red flesh color (i.e., pigmentation) significantly affects the market price. Flesh paleness leads to customer dissatisfaction, a loss of competitiveness, a drop in product value and, consequently, severe economic losses. This work extends our knowledge on salmonid carotenoid dynamics to include the interaction between the gut microbiota and flesh color. A significant association between the flesh color and abundance of specific bacterial communities in the gut microbiota suggests that color may be affected either by seeding resilient beneficial bacteria or by inhibiting the negative effect of pathogenic bacteria. We s led 96 fish, which covered all phenotypes of flesh color, including the average color and the evenness of color of different areas of the fillet, at both the distal intestine and the pyloric caeca of each in idual, followed by 16S rRNA sequencing at the V3-V4 region. The microbiota profiles of these two gut regions were significantly different however, there was a consistency in the microbiota, which correlated with the flesh color. Moreover, the pyloric caeca microbiota also showed high correlation with the evenness of the flesh color (beta ersity index, PERMANOVA, p = 0.002). The results from the pyloric caeca indicate that Carnobacterium, a group belonging to the lactic acid bacteria, is strongly related to the flesh color and the evenness of the color between the flesh areas.

In silico prediction of the G-protein coupled receptors expressed during the metamorphic molt of Sagmariasus verreauxi (Crustacea: Decapoda) by mining transcriptomic data: RNA-seq to repertoire

Publisher: Elsevier BV

Date: 03-2016

DOI: 10.1016/J.YGCEN.2016.02.001

Abstract: Against a backdrop of food insecurity, the farming of decapod crustaceans is a rapidly expanding and globally significant source of food protein. Sagmariasus verreauxi spiny lobster, the subject of this study, are decapods of underdeveloped aquaculture potential. Crustacean neuropeptide G-protein coupled receptors (GPCRs) mediate endocrine pathways that are integral to animal fecundity, growth and survival. The potential use of novel biotechnologies to enhance GPCR-mediated physiology may assist in improving the health and productivity of farmed decapod populations. This study catalogues the GPCRs expressed in the early developmental stages, as well as adult tissues, with a view to illuminating key neuropeptide receptors. De novo assembled contiguous sequences generated from transcriptomic reads of metamorphic and post metamorphic S. verreauxi were filtered for seven transmembrane domains, and used as a reference for iterative re-mapping. Subsequent putative GPCR open reading frames (ORFs) were BLAST annotated, categorised, and compared to published orthologues based on phylogenetic analysis. A total of 85 GPCRs were digitally predicted, that represented each of the four arthropod subfamilies. They generally displayed low-level and non-differential metamorphic expression with few exceptions that we examined using RT-PCR and qPCR. Two putative CHH-like neuropeptide receptors were annotated. Three dimensional structural modelling suggests that these receptors exhibit a conserved extracellular ligand binding pocket, providing support to the notion that these receptors co-evolved with their ligands across Decapoda. This perhaps narrows the search for means to increase productivity of farmed decapod populations.

Atlantic Salmon (Salmo salar L., 1758) Gut Microbiota Profile Correlates with Flesh Pigmentation: Cause or Effect?

Publisher: Springer Science and Business Media LLC

Date: 15-01-2020

DOI: 10.1007/S10126-019-09939-1

Abstract: In Tasmania (Australia), during the marine phase, it has been observed that flesh pigmentation significantly drops in summer, possibly due to high water temperatures (> 20 °C). Although this deleterious effect of summer temperatures has been ascertained, there is a lack of knowledge of the actual mechanisms behind the impaired uptake and/or loss of pigments in Atlantic salmon in a challenging environment. Since the microbial community in the fish intestine significantly changes in relation to the variations of water temperature, this study was conducted to assess how the gut microbiota profile also correlates with the flesh color during temperature fluctuation. We s led 68 fish at three time points covering the end of summer to winter at a marine farm in Tasmania, Australia. Flesh color was examined in two ways: the average color throughout and the evenness of the color between different areas of the fillet. Using 16S rRNA sequencing of the v3-v4 region, we determined that water temperature corresponded to changes in the gut microbiome both with alpha ersity (Kruskal-Wallis tests P = 0.05) and beta ersity indices (PERMANOVA P = 0.001). Also, there was a significant correlation between the microbiota and the color of the fillet (PERMANOVA P = 0.016). There was a high abundance of Pseudoalteromonadaceae, Enterobacteriaceae, Microbacteriaceae, and Vibrionaceae in the pale in iduals. Conversely, carotenoid-synthesizing bacteria families (Bacillaceae, Mycoplasmataceae, Pseudomonas, Phyllobacteriaceae, and Comamonadaceae) were found in higher abundance in in iduals with darker flesh color.

Transcriptional profiling of spiny lobster metamorphosis reveals three new additions to the nuclear receptor superfamily

Publisher: Springer Science and Business Media LLC

Date: 28-06-2019

DOI: 10.1186/S12864-019-5925-5

Insights into sexual maturation and reproduction in the Norway lobster (nephrops norvegicus) via in silico prediction and characterization of neuropeptides and G protein-coupled receptors

Publisher: Frontiers Media SA

Date: 27-07-2018

DOI: 10.3389/FENDO.2018.00430

Androgenic gland implantation promotes growth and inhibits vitellogenesis in cherax quadricarinatus females held in individual compartments

Publisher: Informa UK Limited

Date: 07-2004

DOI: 10.1080/07924259.2004.9652584

Neural remodelling in spiny lobster larvae is characterized by broad neuropeptide suppression

Publisher: Elsevier BV

Date: 08-2020

DOI: 10.1016/J.YGCEN.2020.113496

Multigenic delineation of lower jaw deformity in triploid Atlantic salmon (Salmo salar L.)

Publisher: Public Library of Science (PLoS)

Date: 15-12-2016

DOI: 10.1371/JOURNAL.PONE.0168454

Correction to: Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar) (BMC Genomics, (2021), 22, 1, (545), 10.1186/s12864-021-07884-9)

Publisher: Springer Science and Business Media LLC

Date: 30-09-2021

DOI: 10.1186/S12864-021-08031-0

Histological and transcriptomic analysis of muscular atrophy associated with depleted flesh pigmentation in Atlantic salmon (Salmo salar) exposed to elevated seawater temperatures

Publisher: Springer Science and Business Media LLC

Date: 14-03-2023

DOI: 10.1038/S41598-023-31242-2

Abstract: Tasmania is experiencing increasing seawater temperatures during the summer period which often leads to thermal stress-induced starvation events in farmed Atlantic salmon, with consequent flesh pigment depletion. Our previous transcriptomic studies found a link between flesh pigmentation and the expression of genes regulating lipid metabolism accompanied by feeding behavior in the hindgut. However, the impact of prolonged exposure to elevated water temperature on muscle structural integrity and molecular mechanisms in muscle underlying pigment variation has not been elucidated to date. In this study, we investigated the effect of prolonged exposure to elevated water temperature on the farmed salmon flesh pigmentation and structural integrity, using muscle histological and transcriptomic analysis. On April 2019, after the end of the summer, two muscle regions of the fish fillet, front dorsal and back central (usually the most and least affected by depletion, respectively), were s led from fifteen fish (weighing approximately 2 kg and belonging to the same commercial population split in two cages). The fish represented three flesh color intensity groups (n = 5 fish per group) categorized according to general level of pigmentation and presence of banding (i.e. difference in color between the two regions of interest) as follows: high red color-no banding (HN), high red color-banded (HB) and Pale fish. Histological analysis showed a distinction between the flesh color intensity phenotypes in both muscle regions. Muscle fibers in the HB fish were partly degraded, while they were atrophied and smaller in size in Pale fish compared to HN fish. In the Pale fish, interstitial spaces between muscle fibers were also enlarged. Transcriptomic analysis showed that in the front dorsal region of the HN fish, genes encoding collagens, calcium ion binding and metabolic processes were upregulated while genes related to lipid and fatty acid metabolism were downregulated when compared to HB fish. When comparing the back central region of the three phenotypes, actin alpha skeletal muscle and myosin genes were upregulated in the HN and HB fish, while tropomyosin genes were upregulated in the Pale fish. Also, genes encoding heat shock proteins were upregulated in the HN fish, while genes involving lipid metabolism and proteolysis were upregulated in the Pale fish. Starvation, likely caused by thermal stress during prolonged periods of elevated summer water temperatures, negatively affects energy metabolism to different extents, leading to localized or almost complete flesh color depletion in farmed Atlantic salmon. Based on our results, we conclude that thermal stress is responsible not only for flesh discoloration but also for loss of muscle integrity, which likely plays a key role in pigment depletion.

In-vitro and in-vivo biological activity of recombinant yellowtail kingfish (Seriola lalandi) follicle stimulating hormone

Publisher: Elsevier BV

Date: 2017

DOI: 10.1016/J.YGCEN.2016.03.001

Abstract: Biologically active recombinant yellowtail kingfish follicle stimulating hormone (rytkFsh) was produced in yeast Pichia pastoris and its biological activity was demonstrated by both in-vitro and in-vivo bioassays. Incubation of ovarian and testicular fragments with the recombinant hormone stimulated E

CrustyBase: An interactive online database for crustacean transcriptomes

Publisher: Springer Science and Business Media LLC

Date: 14-09-2020

DOI: 10.1186/S12864-020-07063-2

Abstract: Transcriptome sequencing has opened the field of genomics to a wide variety of researchers, owing to its efficiency, applicability across species and ability to quantify gene expression. The resulting datasets are a rich source of information that can be mined for many years into the future, with each dataset providing a unique angle on a specific context in biology. Maintaining accessibility to this accumulation of data presents quite a challenge for researchers. The primary focus of conventional genomics databases is the storage, navigation and interpretation of sequence data, which is typically classified down to the level of a species or in idual. The addition of expression data adds a new dimension to this paradigm – the s ling context. Does gene expression describe different tissues, a temporal distribution or an experimental treatment? These data not only describe an in idual, but the biological context surrounding that in idual. The structure and utility of a transcriptome database must therefore reflect these attributes. We present an online database which has been designed to maximise the accessibility of crustacean transcriptome data by providing intuitive navigation within and between datasets and instant visualization of gene expression and protein structure. The site is accessible at crustybase.org and currently holds 10 datasets from a range of crustacean species. It also allows for upload of novel transcriptome datasets through a simple web interface, allowing the research community to contribute their own data to a pool of shared knowledge.

Sex and tissue specific gene expression patterns identified following de novo transcriptomic analysis of the Norway lobster, Nephrops norvegicus

Publisher: Springer Science and Business Media LLC

Date: 16-08-2017

DOI: 10.1186/S12864-017-3981-2

Correction to: Transcriptional profiling of spiny lobster metamorphosis reveals three new additions to the nuclear receptor superfamily

Publisher: Springer Science and Business Media LLC

Date: 31-07-2019

DOI: 10.1186/S12864-019-5990-9

Isolation and characterization of a female-specific DNA marker in the giant freshwater prawn Macrobrachium rosenbergii

Publisher: Springer Science and Business Media LLC

Date: 27-04-2011

DOI: 10.1038/HDY.2011.32

Characterization of G-protein coupled receptors from the blackback land crab Gecarcinus lateralis Y organ transcriptome over the molt cycle

Publisher: Springer Science and Business Media LLC

Date: 22-01-2019

DOI: 10.1186/S12864-018-5363-9

Production of recombinant insulin-like androgenic gland hormones from three decapod species: In vitro testicular phosphorylation and activation of a newly identified tyrosine kinase receptor from the

Publisher: Elsevier BV

Date: 04-2016

DOI: 10.1016/J.YGCEN.2016.02.013

Abstract: In crustaceans the insulin-like androgenic gland hormone (IAG) is responsible for male sexual differentiation. To date, the biochemical pathways through which IAG exerts its effects are poorly understood and could be elucidated through the production of a functional recombinant IAG (rIAG). We have successfully expressed glycosylated, biologically active IAG using the Pichia pastoris yeast expression system. We co-expressed recombinant single-chain precursor molecules consisting of the B and A chains (the mature hormone) tethered by a flexible linker, producing rIAGs of the following commercially important species: Eastern spiny lobster Sagmariasus verreauxi (Sv), redclaw crayfish Cherax quadricarinatus (Cq) and giant freshwater prawn Macrobrachium rosenbergii (Mr). We then tested the biological activity of each, through the ability to increase phosphorylation in the testis both Sv and Cq rIAGs significantly elevated phosphorylation specific to their species, and in a dose-dependent manner. Mr rIAG was tested on Macrobrachium australiense (Ma), eliciting a similar response. Moreover, using bioinformatics analyses of the de novo assembled spiny lobster transcriptome, we identified a spiny lobster tyrosine kinase insulin receptor (Sv-TKIR). We validated this discovery with a receptor activation assay in COS-7 cells expressing Sv-TKIR, using a reporter SRE-LUC system designed for RTKs, with each of the rIAG proteins acting as the activation ligand. Using recombinant proteins, we aim to develop specific tools to control sexual development through the administration of IAG within the critical sexual differentiation time window. The biologically active rIAGs generated might facilitate commercially feasible solutions for the long sought techniques for sex-change induction and monosex population culture in crustaceans and shed new light on the physiological mode of action of IAG in crustaceans.

Alternative Feed Raw Materials Modulate Intestinal Microbiota and Its Relationship with Digestibility in Yellowtail Kingfish Seriola lalandi

Publisher: MDPI AG

Date: 11-05-2020

DOI: 10.3390/FISHES5020014

Abstract: Gut microbiota plays a crucial role in nutrient digestibility and fish health. This study aimed to investigate the effects of alternative feed raw materials on the bacterial communities in the distal intestine and its relationship with nutrient digestibility in yellowtail kingfish (YTK), Seriola lalandi. Two 4-week digestibility trials were conducted to evaluate fish meal (FM), two sources of poultry by-product meal (PBM-1 & PBM-2), blood meal (BLM), faba bean meal (FBM), corn gluten meal (CGM), soy protein concentrate (SPC) and wheat flour (WH). The nutrient digestibility value was determined using the stripping fecal collection method. Bacterial communities were characterized by high-throughput sequencing based on V3-V4 region of the 16S rRNA gene. The most abundant phylum identified in the present study was Proteobacteria. A significant change in the distal intestine was observed in fish fed diets containing CGM and BLM, characterized by a reduction of species richness and ersity. Additionally, significant correlation between nutrient digestibility and intestinal microbiota was observed. Allivibrio, Vibrio, Curvibacter, Ruminococcaceae, and Clostridium were positively correlated, whereas Ralstonia genus was negatively correlated with nutrient digestibility. This study demonstrated that intestinal microbiota could be a useful tool for evaluating the digestibility of feed raw materials however, further culture-based study is needed to confirm this observation.

Unravelling the neuropeptidome of the ornate spiny lobster Panulirus ornatus: A focus on peptide hormones and their processing enzymes expressed in the reproductive tissues

Publisher: Elsevier BV

Date: 02-2023

DOI: 10.1016/J.YGCEN.2022.114183

Making the Gold Coast a Smart City—An Analysis

Publisher: MDPI AG

Date: 24-09-2021

DOI: 10.3390/SU131910624

Abstract: In recent times, there has been a worldwide trend towards creating smart cities with a focus on the knowledge economy and on information and communication technologies. These technologies have potential applications in managing the built and natural environments more efficiently, promoting economic development, and actively engaging the public, thus helping build more sustainable cities. Whilst the interest in smart cities has been widespread predominantly amongst metropolitan cities, several regional cities such as the Gold Coast in Australia have also recently endeavoured to become smart cities. In response to this emerging trend, this study aimed to investigate key opportunities and challenges associated with developing regional cities into smart cities using the Gold Coast as a case study. It identified key factors critical to the planning and development of smart cities. These factors fall under five broad themes: cultural and natural amenities, technology, knowledge and innovation precincts, people and skills, and governance. The factors were applied to the Gold Coast to analyse the key opportunities and challenges for its development into a smart city. Finally, key lessons, which are potentially applicable to other regional cities seeking to develop into smart cities, are drawn from the case study.

Skeletal anomaly assessment in diploid and triploid juvenile Atlantic salmon (Salmo salar L.) and the effect of temperature in freshwater

Publisher: Wiley

Date: 13-01-2016

DOI: 10.1111/JFD.12438

Abstract: Triploid Atlantic salmon tend to develop a higher prevalence of skeletal anomalies. This tendency may be exacerbated by an inadequate rearing temperature. Early juvenile all-female diploid and triploid Atlantic salmon were screened for skeletal anomalies in consecutive experiments to include two size ranges: the first tested the effect of ploidy (0.2-8 g) and the second the effect of ploidy, temperature (14 °C and 18 °C) and their interaction (8-60 g). The first experiment showed that ploidy had no effect on skeletal anomaly prevalence. A high prevalence of opercular shortening was observed (average prevalence in both ploidies 85.8%) and short lower jaws were common (highest prevalence observed 11.3%). In the second experiment, ploidy, but not temperature, affected the prevalence of short lower jaw (diploids > triploids) and lower jaw deformity (triploids > diploids, highest prevalence observed 11.1% triploids and 2.7% diploids) with a trend indicating a possible developmental link between the two jaw anomalies in triploids. A radiological assessment (n = 240 in iduals) showed that at both temperatures triploids had a significantly (P < 0.05) lower number of vertebrae and higher prevalence of deformed in iduals. These findings (second experiment) suggest ploidy was more influential than temperature in this study.

Male Sexual Development and the Androgenic Gland: Novel Insights through the de novo Assembled Transcriptome of the Eastern Spiny Lobster, Sagmariasus verreauxi

Publisher: S. Karger AG

Date: 2016

DOI: 10.1159/000443943

Abstract: The Eastern spiny lobster, i Sagmariasus verreauxi /i , is commercially important in fisheries, with growing aquaculture potential, driving an interest to better understand male sexual differentiation. Amongst the Decapoda i , /i the androgenic gland (AG) and the insulin-like androgenic gland hormone (IAG) have a well-defined function in male sexual differentiation. However, IAG is not a sex determinant and therefore must be considered as part of a broader, integrated pathway. This work uses a transcriptomic, multi-tissue approach to provide an integrated description of male-biased expression as mediated through the AG. Transcriptomic analyses demonstrate that IAG expression is stage- and eyestalk-regulated (low in immature, high in mature and 6-times higher in hypertrophied glands), with IAG being the predominant AG-specific factor. The low expression of this key factor in immature males suggests the involvement of other tissues in male sexual differentiation. Across tissues, the gonad (87.8%) and antennal gland (73.5%) show the highest male-biased differential expression of transcripts and also express 4 sex-determination regulators, known as i Dmrts /i , with broader expression of i Sv-Sxl /i and i Sv-TRA-2. /i In order to better understand male sexual differentiation, tissues other than the AG must also be considered. This research highlights the gonad and antennal gland as showing significant male-biased expression patterns, including the i Sv-Dmrts /i .

Transcriptomic Analysis and Time to Hatch Visual Prediction of Embryo Development in the Ornate Spiny Lobster (Panulirus ornatus)

Publisher: Frontiers Media SA

Date: 12-07-2022

DOI: 10.3389/FMARS.2022.889317

Abstract: The ability to conduct closed life-cycle culture of tropical spiny lobsters, Panulirus ornatus , at the Institute for Marine and Antarctic Studies (IMAS) provides a unique opportunity to investigate specific developmental stages during embryogenesis. The production of closed life-cycle lobsters provides access to embryos at defined time points, yet physical staging is challenging due to their small size and environmental factors impacting their development. A transcriptome comprising 11 distinct stages across the 30-day P. ornatus embryonal development period allowed the establishment of the most detailed transcriptomic library of embryogenesis across decapods. A series of key genes across the 11 stages of embryonal development were characterized. The expression of neuropeptides was reported across P. ornatus embryos, suggesting they are primarily active during the later stages of embryogenesis as the nervous system develops and the animal prepares to hatch. Gastrula-specific genes, nanos and brachyury , presented an expression profile indicating gastrulation occurs early in embryogenesis. In addition to the molecular tools used to characterize embryo development, certain developmental characteristics, such as eye spot development, provide a measurable indicator that can be visualised. Hatch prediction models based on visual characteristics were shown to be an accurate method to predict the timing of the hatch for P. ornatus embryos kept at 26°C. The combination of morphological and visual measures with transcriptomics can be used to further define and establish the groundwork for future characterisation and staging of P. ornatus embryogenesis.

Identification and characterization of an insulin-like receptor involved in crustacean reproduction

Publisher: The Endocrine Society

Date: 02-2016

DOI: 10.1210/EN.2015-1391

Abstract: Sexual differentiation and maintenance of masculinity in crustaceans has been suggested as being regulated by a single androgenic gland (AG) insulin-like peptide (IAG). However, downstream elements involved in the signaling cascade remain unknown. Here we identified and characterized a gene encoding an insulin-like receptor in the prawn Macrobrachium rosenbergii (Mr-IR), the first such gene detected in a decapod crustacean. In mining for IRs and other insulin signaling-related genes, we constructed a comprehensive M. rosenbergii transcriptomic library from multiple sources. In parallel we sequenced the complete Mr-IR cDNA, confirmed in the wide transcriptomic library. Mr-IR expression was detected in most tissues in both males and females, including the AG and gonads. To study Mr-IR function, we performed long-term RNA interference (RNAi) silencing in young male prawns. Although having no effect on growth, Mr-IR silencing advanced the appearance of a male-specific secondary trait. The most noted effects of Mr-IR silencing were hypertrophy of the AG and the associated increased production of Mr-IAG, with an unusual abundance of immature sperm cells being seen in the distal sperm duct. A ligand blot assay using de novo recombinant Mr-IAG confirmed the existence of a ligand-receptor interaction. Whereas these results suggest a role for Mr-IR in the regulation of the AG, we did not see any sexual shift after silencing of Mr-IR, as occurred when the ligand-encoding Mr-IAG gene was silenced. This suggests that sexual differentiation in crustaceans involve more than a single Mr-IAG receptor, emphasizing the complexity of sexual differentiation and maintenance.

Evaluation of genes involved in Norway lobster (Nephrops norvegicus) female sexual maturation using transcriptomic analysis

Publisher: Springer Science and Business Media LLC

Date: 05-02-2018

DOI: 10.1007/S10750-018-3521-3

Molecular characterization of sdf1 and cxcr4 in the Mozambique tilapia, Oreochromis mossambicus

Publisher: Elsevier BV

Date: 2017

DOI: 10.1016/J.ANIREPROSCI.2016.11.007

Abstract: Animal sexual reproduction relies on primordial germ cells (PGCs), the predecessors of the germ cell lineage, giving rise to either spermatogonia or oogonia after the completion of gonadal differentiation. There is limited information on the mechanism of PGC migration leading to the formation of the primordial gonad in Perciform fish. Oreochromis mossambicus, a tilapiine species, was investigated that is a commercially important aquaculture species in many parts of the world while in other areas it has become an invasive pest. Key components involved in PGC migration were identified, including the stromal-cell derived factor 1 (Om-sdf1a, Om-sdf1b) and the CXC receptor 4 (Om-cxcr4): both share conservation with existing model species. The spatial gene expression profiles were determined through transcript and protein analysis and displayed distinct localisation within the region of the developing gonad in larvae and within the adult gonads of certain cell populations. A recombinant Om-sdf1a was produced in Escherichia coli that activates Om-cxcr4 using a BRET-based yeast in vitro assay system, suggesting that it is structurally similar to the native Om-sdf1a and is appropriate for further structural studies. This study has improved understanding of the molecular basis of tilapia reproduction through investigation of gonad development, which may be important in the progression towards reproductive suppression methods to control tilapia populations in the wild. In addition, this research will facilitate developments in germ cell transplantation, an innovative technique that harnesses germ cell migration and allows the uptake of foreign germ cells, which differentiate to produce sperm or ova.

Identification and characterization of androgenic gland specific insulin-like peptide-encoding transcripts in two spiny lobster species: Sagmariasus verreauxi and Jasus edwardsii

Publisher: Elsevier BV

Date: 04-2015

DOI: 10.1016/J.YGCEN.2014.06.027

Abstract: In this study we describe, for the first time in spiny lobsters, the androgenic gland and its putative hormone. The androgenic gland in crustaceans is the key regulator of crustacean masculinity. The transcript encoding the insulin-like androgenic gland specific factor has recently been identified and characterized in a number of decapod crustacean species including commercially important crabs, crayfish, prawns and shrimps. This insulin-like factor has proven to be the androgenic gland masculinizing hormone, and is absent in females. While the androgenic gland and its putative hormone have been identified in all other commercially valuable groups, none had been identified in lobsters. We identified and characterized the androgenic glands of two spiny lobster species (Sagmariasus verreauxi and Jasus edwardsii) and conducted a transcriptomic analysis of the S. verreauxi androgenic gland. Bioinformatics analysis led to the discovery and characterization of the insulin-like androgenic gland specific factors in both species studied. Changes in androgenic gland cell size and quantity between sub-adult and sexually mature males were evident. The transcriptomic database established for the S. verreauxi androgenic gland might enable to elucidate the mechanisms through which the insulin-like factor is secreted, transported to the target cells and how it triggers the physiological effects of sexual differentiation towards maleness and maintenance of the male gonad.

Tropical rock lobster (Panulirus ornatus) uses chemoreception via the antennular lateral flagellum to identify conspecific ecdysis

Publisher: Springer Science and Business Media LLC

Date: 31-07-2023

DOI: 10.1038/S41598-023-39567-8

Abstract: The tropical rock lobster, Panulirus ornatus , is a commercially important aquaculture species exhibiting complex social interactions in laboratory culture, including cannibalism of moulting conspecifics. Cannibalism of soft-shelled post-moult stage in iduals is a major limitation during the juvenile stage of culture. Not limited to P. ornatus , cannibalism is widespread across farmed decapods, limiting stocking densities in crab, freshwater crayfish, and prawn species. To understand the mechanisms driving this behaviour and reduce its prevalence, we have investigated the role of chemoreception via the aesthetasc-bearing region of the lateral antennular flagellum, in the recognition of conspecific moulting cues. Differential expression analysis of several tissues in P. ornatus shows an upregulation of 70 ionotropic receptor isoforms, including co-receptors (IR25a and IR93a) and ergent receptors (IR4, IR7, and IR21a) in the aesthetasc-bearing region of the antennules. Deafferentation of the aesthetascs via deionised water exposure prevents juveniles from responding to conspecific moulting cues in a two-current choice flume, suggesting chemoreception, possibly olfaction, plays a role in identifying moulting juveniles. This is the first step in understanding the mechanisms via which cannibalism is triggered in juvenile P. ornatus culture. Further work in this area will help discover means to limit cannibalism in laboratory and commercial culture.

The decapod researcher’s guide to the galaxy of sex determination

Publisher: Springer Science and Business Media LLC

Date: 20-12-2018

DOI: 10.1007/S10750-017-3452-4

Monosex in Aquaculture

Publisher: Springer International Publishing

Date: 2018

DOI: 10.1007/978-3-319-92486-1_6

Abstract: Monosex refers to the culture of either all-male or all-female populations, a sought after approach in aquaculture. This chapter reviews the advantages of monosex population culture and details the mechanisms to achieve it based on different modes of sex determination and sexual differentiation. A recent case study for an aquaculture biotechnology based on sexual manipulation in crustaceans serves in this chapter to identify the key elements for a successful application. This application which makes use of RNA interference with a key regulating hormone opens the pathway toward environmentally friendly applications in fish and additional aquacultured species. This chapter portrays the state of the art in sexual manipulations in aquacultured species, starting with vertebrate species, followed by the case study of the crustacean species and discussion on how the techniques used in this study are applicable for other species.

Timing sexual differentiation: Full functional sex reversal achieved through silencing of a single insulin-like gene in the prawn, Macrobrachium rosenbergii

Publisher: Oxford University Press (OUP)

Date: 03-2012

DOI: 10.1095/BIOLREPROD.111.097261

Abstract: In Crustacea, an early evolutionary group (∼50 000 species) inhabiting most ecological niches, sex differentiation is regulated by a male-specific androgenic gland (AG). The identification of AG-specific insulin-like factors (IAGs) and genomic sex markers offers an opportunity for a deeper understanding of the sexual differentiation mechanism in crustaceans and other arthropods. Here, we report, to our knowledge, the first full and functional sex reversal of male freshwater prawns (Macrobrachium rosenbergii) through the silencing of a single IAG-encoding gene. These "neofemales" produced all-male progeny, as proven by sex-specific genomic markers. This finding offers an insight regarding the biology and evolution of sex differentiation regulation, with a novel perspective for the evolution of insulin-like peptides. Our results demonstrate how temporal intervention with a key regulating gene induces a determinative, extreme phenotypic shift. Our results also carry tremendous ecological and commercial implications. Invasive and pest crustacean species represent genuine concerns worldwide without an apparent solution. Such efforts might, therefore, benefit from sexual manipulations, as has been successfully realized with other arthropods. Commercially, such manipulation would be significant in sexually dimorphic cultured species, allowing the use of nonbreeding, monosex populations while dramatically increasing yield and possibly minimizing the invasion of exotic cultured species into the environment.

Guidelines for RNA-seq projects: applications and opportunities in non-model decapod crustacean species

Publisher: Springer Science and Business Media LLC

Date: 03-07-2018

DOI: 10.1007/S10750-018-3682-0

Supporting Active and Healthy Living in Master-planned Communities: A Case Study

Publisher: Informa UK Limited

Date: 03-04-2014

DOI: 10.1080/07293682.2014.901980

HSP60 is transported through the secretory pathway of 3-MCA-induced fibrosarcoma tumour cells and undergoes N-glycosylation

Publisher: Wiley

Date: 08-05-2012

DOI: 10.1111/J.1742-4658.2012.08594.X

Abstract: There is increasing evidence localizes the mitochondrial chaperone heat shock protein (HSP)60, outside the cell, where it mediates interactions between immune cells and other body tissues. However, the mechanisms by which HSP60 is secreted into the extracellular environment are not fully understood. Recent studies have shown that HSP60 is actively released by a nonconventional secretion mechanism, the lipid raft-exosome pathway. In the present study, we show for the first time that HSP60, produced by 3-methylcholantrene-induced fibrosarcoma tumour cells, is secreted through the conventional endoplasmic reticulum-Golgi secretory pathway. Confocal microscopy using anti-TGN38 and anti-HSP60 antibodies together with monensin, a Golgi transport inhibitor, demonstrated the relocation of HSP60 to the Golgi of malignant cells but not primary fibroblast cells subjected to heat shock or fibroblast cell lines. Transmission electron microscopy, flow cytometry and cell fractionation of cell treated with brefeldin A, an inhibitor of endoplasmic reticulum to Golgi protein transport, further indicated that HSP60 is present both in the endoplasmic reticulum and the Golgi complex of malignant cells. We found a single mRNA with a mitochondrial targeting sequence encoding for HSP60 in the malignant cells but two HSP60 translation products, namely the native unmodified protein and a protein post-translationally modified by N-glycosylation. The N-glycans observed were composed of high-mannose structures and bi-, tri- and tetra-antennary complex type structures occupying sites of the three potential glycosylation sites present on HSP60. Accordingly, we propose that HSP60 in malignant cells is transported through the endoplasmic reticulum-Golgi secretion pathway, where it acquires N-glycans, and thus can affect the immunological properties of the proteins in the tumour microenvironment.

Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)

Publisher: Springer Science and Business Media LLC

Date: 17-07-2021

DOI: 10.1186/S12864-021-07884-9

Abstract: The flesh pigmentation of farmed Atlantic salmon is formed by accumulation of carotenoids derived from commercial diets. In the salmon gastrointestinal system, the hindgut is considered critical in the processes of carotenoids uptake and metabolism. In Tasmania, flesh color depletion can noticeably affect farmed Atlantic salmon at different levels of severity following extremely hot summers. In this study, RNA sequencing (RNA-Seq) was performed to investigate the reduction in flesh pigmentation. Library preparation is a key step that significantly impacts the effectiveness of RNA sequencing (RNA-Seq) experiments. Besides the commonly used whole transcript RNA-Seq method, the 3’ mRNA-Seq method is being applied widely, owing to its reduced cost, enabling more repeats to be sequenced at the expense of lower resolution. Therefore, the output of the Illumina TruSeq kit (whole transcript RNA-Seq) and the Lexogen QuantSeq kit (3’ mRNA-Seq) was analyzed to identify genes in the Atlantic salmon hindgut that are differentially expressed (DEGs) between two flesh color phenotypes. In both methods, DEGs between the two color phenotypes were associated with metal ion transport, oxidation-reduction processes, and immune responses. We also found DEGs related to lipid metabolism in the QuantSeq method. In the TruSeq method, a missense mutation was detected in DEGs in different flesh color traits. The number of DEGs found in the TruSeq libraries was much higher than the QuantSeq however, the trend of DEGs in both library methods was similar and validated by qPCR. Flesh coloration in Atlantic salmon is related to lipid metabolism in which apolipoproteins, serum albumin and fatty acid-binding protein genes are hypothesized to be linked to the absorption, transport and deposition of carotenoids. Our findings suggest that Grp could inhibit the feeding behavior of low color-banded fish, resulting in the dietary carotenoid shortage. Several SNPs in genes involving in carotenoid-binding cholesterol and oxidative stress were detected in both flesh color phenotypes. Regarding the choice of the library preparation method, the selection criteria depend on the research design and purpose. The 3’ mRNA-Seq method is ideal for targeted identification of highly expressed genes, while the whole RNA-Seq method is recommended for identification of unknown genes, enabling the identification of splice variants and trait-associated SNPs, as we have found for duox2 and duoxa1 .

The insulin-like androgenic gland hormone in crustaceans: From a single gene silencing to a wide array of sexual manipulation-based biotechnologies

Publisher: Elsevier BV

Date: 11-2012

DOI: 10.1016/J.BIOTECHADV.2012.04.008

Abstract: Due to the over-harvesting and deterioration of wild populations, the ever-growing crustacean market is increasingly reliant on aquaculture, driving the need for better management techniques. Since most cultured crustacean species exhibit sexually dimorphic growth patterns, the culture of monosex populations (either all-male or all-female) is a preferred approach for gaining higher yields, with the ecological benefit of reducing the risk of invasion by the cultured species. Sexual manipulations may also render sustainable solutions to the environmental problems caused by the presence of invasive crustacean species with detrimental impacts ranging from aggressive competition with native species for food and shelter, to affecting aquaculture facilities and harvests and causing structural damage to river banks. Recent discoveries of androgenic gland (AG)-specific insulin-like peptides (IAGs) in crustaceans and the ability to manipulate them and their encoding transcripts (IAGs) have raised the possibility of sexually manipulating crustacean populations. Sexual manipulation is already a part of sustainable solutions in fish aquaculture and in the bio-control of insect pest species, and attempts are also being made to implement it with crustaceans. As recently exemplified in a commercially important prawn species, IAG silencing, a temporal, non-genetically modifying and non-transmissible intervention, has enabled the production of non-breeding all-male monosex populations that are the progeny of sexually reversed males ('neo-females'). IAG manipulations-based biotechnologies therefore have the potential to radically transform the entire industry. We review here how this proof of concept could be broadened to meet both aquacultural and environmental needs. We include the major cultured decapod crustacean groups and suggest a sustainable solution for the management of invasive and pest crustacean species. We also review the key considerations for devising a biotechnological approach that specifically tailors the molecular technological abilities to the management of each target group.

Gonadotropin-releasing hormone and adipokinetic hormone/corazonin-related peptide in the female prawn

Publisher: Elsevier BV

Date: 09-2016

DOI: 10.1016/J.YGCEN.2016.07.008

Abstract: Crustacean neuropeptides (NPs) play important roles in the regulation of most physiological activities, including growth, molting and reproduction. In this study, we have performed an in silico analysis of female prawn (Macrobrachium rosenbergii) neural transcriptomes to identify NPs not previously identified. We predict that approximately 1309 proteins are destined for the secretory pathway, many of which are likely post-translationally processed to generate active peptides. Within this neural secretome, we identified a gene transcript that encoded a precursor protein with striking similarity to a gonadotropin-releasing hormone (GnRH). We additionally identified another GnRH NP superfamily member, the adipokinetic hormone/corazonin-related peptide (ACP). M. rosenbergii GnRH and ACP were widespread throughout the nervous tissues, implicating them as potential neuromodulators. Furthermore, GnRH was found in non-neural tissues, including the stomach, gut, heart, testis and ovary, in the latter most prominently within secondary oocytes. The GnRH/corazonin receptor-like gene is specific to the ovary, whereas the receptor-like gene expression is more widespread. Administration of GnRH had no effect on ovarian development and maturation, nor any effect on total hemolymph lipid levels, while ACP administration decreased oocyte proliferation (at high dose) and stimulated a significant increase in total hemolymph lipids. In conclusion, our targeted analysis of the M. rosenbergii neural secretome has revealed the decapod GnRH and ACP genes. We propose that ACP in crustaceans plays a role in the lipid metabolism and the inhibition of oocyte proliferation, while the role of the GnRH remains to be clearly defined, possibly through experiments involving gene silencing.

The crustacean ecdysone cassette: A gatekeeper for molt and metamorphosis

Publisher: Elsevier BV

Date: 2019

DOI: 10.1016/J.JSBMB.2018.08.012

Abstract: Arthropods have long been utilized as models to explore molecular function, and the findings derived from them can be applied throughout metazoa, including as a basis for medical research. This has led to the adoption of many representative insect models beyond Drosophila, as each lends its own unique perspective to questions in endocrinology and genetics. However, non-insect arthropods are yet to be realised for the potential insight they may provide in such studies. The Crustacea are among the most ancient arthropods from which insects descended, comprising a huge variety of life histories and ecological roles. Of the events in a typical crustacean development, metamorphosis is perhaps the most ubiquitous, challenging and highly studied. Despite this, our knowledge of the endocrinology which underpins metamorphosis is rudimentary at best although several key molecules have been identified and studied in depth, the link between them is quite nebulous and leans heavily on well-explored insect models, which erged from the Pancrustacea over 450 million years ago. As omics technologies become increasingly accessible, they bring the prospect of explorative molecular research which will allow us to uncover components and pathways unique to crustaceans. This review reconciles known components of crustacean metamorphosis and reflects on our findings in insects to outline a future search space, with focus given to the ecdysone cascade. To expand our knowledge of this ubiquitous endocrine system not only aids in our understanding of crustacean metamorphosis, but also provides a deeper insight into the adaptive capacity of arthropods throughout evolution.

Ecdysis triggering hormone modulates molt behaviour in the redclaw crayfish Cherax quadricarinatus, providing a mechanistic evidence for conserved function in molt regulation across Pancrustacea

Publisher: Elsevier BV

Date: 11-2020

DOI: 10.1016/J.YGCEN.2020.113556

The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation

Publisher: Springer Science and Business Media LLC

Date: 22-04-2021

DOI: 10.1038/S41467-021-22604-3

Abstract: The infraorder Brachyura (true or short-tailed crabs) represents a successful group of marine invertebrates yet with limited genomic resources. Here we report a chromosome-anchored reference genome and transcriptomes of the Chinese mitten crab Eriocheir sinensis , a catadromous crab and invasive species with wide environmental tolerance, strong osmoregulatory capacity and high fertility. We show the expansion of specific gene families in the crab, including F-ATPase, which enhances our knowledge on the adaptive plasticity of this successful invasive species. Our analysis of spatio-temporal transcriptomes and the genome of E. sinensis and other decapods shows that brachyurization development is associated with down-regulation of Hox genes at the megalopa stage when tail shortening occurs. A better understanding of the molecular mechanism regulating sexual development is achieved by integrated analysis of multiple omics. These genomic resources significantly expand the gene repertoire of Brachyura, and provide insights into the biology of this group, and Crustacea in general.

Understanding Insulin Endocrinology in Decapod Crustacea: Molecular Modelling Characterization of an Insulin-Binding Protein and Insulin-Like Peptides in the Eastern Spiny Lobster, Sagmariasus verreauxi

Publisher: MDPI AG

Date: 23-08-2017

DOI: 10.3390/IJMS18091832

Post-Embryonic Transcriptomes of the Prawn Macrobrachium rosenbergii: Multigenic Succession through Metamorphosis

Publisher: Public Library of Science (PLoS)

Date: 25-01-2013

DOI: 10.1371/JOURNAL.PONE.0055322

Crustacean larval factor shares structural characteristics with the insect-specific follicle cell protein

Publisher: Springer Science and Business Media LLC

Date: 26-02-2019

DOI: 10.1038/S41598-019-39173-7

Abstract: Literature on the cuticle formation in larval stages of the erse group of decapod crustaceans is lacking, as opposed to a wealth of knowledge in several insect groups. Here we provide the first glimpse of the cuticular organisation in larvae of the eastern spiny lobster Sagmariasus verreauxi . A bioinformatic approach applied to S . verreauxi transcriptome through metamorphosis identified for the first time a small secreted protein with multiple isoforms that is highly expressed in crustacean larvae. This protein, named crustacean larval factor (Clf) shares structural characteristics with insect follicle cell protein 3 (FCP3), an insect-specific, rapidly evolving protein, with spatial-temporal regulated expression that is restricted to follicular cells during the production of the vitellin coat. Furthermore, we identified the FCP3 domain in additional structural proteins in multiple arthropod groups. Recombinant Clf inhibited in vitro calcium carbonate crystalline precipitation, in keeping with the finding that the spiny lobster larval cuticle is mainly composed of amorphous calcium carbonate. In addition, the recombinant Clf was shown to bind chitosan. Taken together, this research identifies two novel structural domains with lineage-specific expansion across arthropods. In crustaceans, Clf is found predominantly in larvae and the spatial-temporal regulated FCP3 factor occurs as a domain identified in multiple structural proteins across arthropods. Given the shared ten cysteines backbone between the Clf and FCP domains, a shared evolution is suggested and should be further explored.

Early immune suppression leads to uncontrolled mite proliferation and potent host inflammatory responses in a porcine model of crusted versus ordinary scabies.

Publisher: Public Library of Science (PLoS)

Date: 04-09-2020

DOI: 10.1371/JOURNAL.PNTD.0008601

Transcriptomic characterization and curation of candidate neuropeptides regulating reproduction in the eyestalk ganglia of the Australian crayfish, Cherax quadricarinatus

Publisher: Springer Science and Business Media LLC

Date: 07-12-2016

DOI: 10.1038/SREP38658

Abstract: The Australian redclaw crayfish ( Cherax quadricarinatus ) has recently received attention as an emerging candidate for sustainable aquaculture production in Australia and worldwide. More importantly, C. quadricarinatus serves as a good model organism for the commercially important group of decapod crustaceans as it is distributed worldwide, easy to maintain in the laboratory and its reproductive cycle has been well documented. In order to better understand the key reproduction and development regulating mechanisms in decapod crustaceans, the molecular toolkit available for model organisms such as C. quadricarinatus must be expanded. However, there has been no study undertaken to establish the C. quadricarinatus neuropeptidome. Here we report a comprehensive study of the neuropeptide genes expressed in the eyestalk in the Australian crayfish C. quadricarinatus . We characterised 53 putative neuropeptide-encoding transcripts based on key features of neuropeptides as characterised in other species. Of those, 14 neuropeptides implicated in reproduction regulation were chosen for assessment of their tissue distribution using RT-PCR. Further insights are discussed in relation to current knowledge of neuropeptides in other species and potential follow up studies. Overall, the resulting data lays the foundation for future gene-based neuroendocrinology studies in C. quadricarinatus .

Molecular aspects of eye development and regeneration in the Australian redclaw crayfish, Cherax quadricarinatus

Publisher: Elsevier BV

Date: 2019

DOI: 10.1016/J.AAF.2018.04.001

Twelve quick steps for genome assembly and annotation in the classroom

Publisher: Public Library of Science (PLoS)

Date: 12-11-2020

DOI: 10.1371/JOURNAL.PCBI.1008325

Abstract: Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of in idual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.

A Tale of Two Lobsters—Transcriptomic Analysis Reveals a Potential Gap in the RNA Interference Pathway in the Tropical Rock Lobster Panulirus ornatus

Publisher: MDPI AG

Date: 04-10-2022

DOI: 10.3390/IJMS231911752

Abstract: RNA interference (RNAi) has been widely utilised in many invertebrate models since its discovery, and in a majority of instances presents as a highly efficient and potent gene silencing mechanism. This is emphasized in crustaceans with almost all taxa having the capacity to trigger effective silencing, with a notable exception in the spiny lobsters where repeated attempts at dsRNA induced RNAi have demonstrated extremely ineffective gene knockdown. A comparison of the core RNAi machinery in transcriptomic data from spiny lobsters (Panulirus ornatus) and the closely related slipper lobsters (Thenus australiensis, where silencing is highly effective) revealed that both lobsters possess all proteins involved in the small interfering and microRNA pathways, and that there was little difference at both the sequence and domain architecture level. Comparing the expression of these genes however demonstrated that T. australiensis had significantly higher expression in the transcripts encoding proteins which directly interact with dsRNA when compared to P. ornatus, validated via qPCR. These results suggest that low expression of the core RNAi genes may be hindering the silencing response in P. ornatus, and suggest that it may be critical to enhance the expression of these genes to induce efficient silencing in spiny lobsters.

Temporal silencing of an androgenic gland-specific insulin-like gene affecting phenotypical gender differences and spermatogenesis

Publisher: The Endocrine Society

Date: 06-11-2009

DOI: 10.1210/EN.2008-0906

Abstract: Androgenic glands (AGs) of the freshwater prawn Macrobrachium rosenbergii were subjected to endocrine manipulation, causing them to hypertrophy. Transcripts from these glands were used in the construction of an AG cDNA subtractive library. Screening of the library revealed an AG-specific gene, termed the M. rosenbergii insulin-like AG (Mr-IAG) gene. The cDNA of this gene was then cloned and fully sequenced. The cysteine backbone of the predicted mature Mr-IAG peptide (B and A chains) showed high similarity to that of other crustacean AG-specific insulin-like peptides. In vivo silencing of the gene, by injecting the prawns with Mr-IAG double-stranded RNA, temporarily prevented the regeneration of male secondary sexual characteristics, accompanied by a lag in molt and a reduction in growth parameters, which are typically higher in males of the species. In terms of reproductive parameters, silencing of Mr-IAG led to the arrest of testicular spermatogenesis and of spermatophore development in the terminal ullae of the sperm duct, accompanied by hypertrophy and hyperplasia of the AGs. This study constitutes the first report of the silencing of a gene expressed specifically in the AG, which caused a transient adverse effect on male phenotypical gender differences and spermatogenesis. Temporal silencing of a newly identified insulin-like gene from prawn androgenic gland inhibits primary spermatogenesis, male secondary sex characteristics, and growth.

A refined roadmap to decapod sexual manipulation

Publisher: Wiley

Date: 14-03-2023

DOI: 10.1111/RAQ.12808

Abstract: Many decapod crustaceans with sexual dimorphism in body size are economically significant species for fisheries and aquaculture, making monosex culture a desirable practice to increase farmers' yield and profits. It is well established that the male‐specific androgenic gland (AG) mediates masculinization in decapods by producing and secreting the insulin‐like AG hormone (IAG). However, IAG is not a sex‐determining factor hence, iag silencing in decapods does not always lead to successful sex change. Since the establishment of monosex populations in the giant freshwater prawn Macrobrachium rosenbergii , the same AG/ iag manipulation approach has been attempted in economically significant penaeid shrimps, crabs, crayfish and spiny lobsters, to no avail. There are many factors at play with species‐specific intricacies which require close examination when addressing monosex production. This review provides a refined roadmap to successful sexual manipulation in decapod crustaceans, highlighting the key caveats to be considered and critical gaps in knowledge such as the timing of iag expression compared to the development of sexual characteristics, the relationship between iag and a master regulator, as well as silencing capacity. Lastly, this review examines what the future might hold for monosex aquaculture in decapods, taking into consideration novel technologies such as gene editing.

Biomolecular changes that occur in the antennal gland of the giant freshwater prawn (Machrobrachium rosenbergii)

Publisher: Public Library of Science (PLoS)

Date: 29-06-2017

DOI: 10.1371/JOURNAL.PONE.0177064

Ben-Gurion University Of The Negev

Location: Israel

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University Of The Sunshine Coast

Location: Australia

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Collaborative Research: Signaling Mechanisms In The Crustacean Molting Gland

Start Date: 2020

End Date: 2023

Funder: Directorate for Biological Sciences

Deep Protein Sequencing, Structure And Quantification Facility

Start Date: 2017

End Date: 2017

Funder: Australian Research Council

The Molecular Mechanism Underlying Crustacean Metamorphosis

Start Date: 2016

End Date: 2017

Funder: Australian Research Council

ARC Research Hub For Sustainable Onshore Lobster Aquaculture

Start Date: 2019

End Date: 2023

Funder: Australian Research Council

An Integrated, Multi-nodal Bio-layer Interferometry Facility

Start Date: 2020

End Date: 2020

Funder: Australian Research Council

Project LE140100012

Start Date: 2014

End Date: 2014

Funder: Australian Research Council

Discovery Early Career Researcher Award - Grant ID: DE130101089

Start Date: 2013

End Date: 12-2015

Amount: $371,800.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE140100012

Start Date: 2014

End Date: 04-2015

Amount: $890,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP160103320

Start Date: 2016

End Date: 03-2018

Amount: $148,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE170100192

Start Date: 05-2017

End Date: 12-2017

Amount: $450,000.00

Funder: Australian Research Council

Industrial Transformation Research Hubs - Grant ID: IH190100014

Start Date: 2020

End Date: 12-2024

Amount: $5,000,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE200100140

Start Date: 03-2020

End Date: 06-2021

Amount: $945,000.00

Funder: Australian Research Council