97 results on '"Elizabeth J Duncan"'
Search Results
2. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.
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Ariel D Chipman, David E K Ferrier, Carlo Brena, Jiaxin Qu, Daniel S T Hughes, Reinhard Schröder, Montserrat Torres-Oliva, Nadia Znassi, Huaiyang Jiang, Francisca C Almeida, Claudio R Alonso, Zivkos Apostolou, Peshtewani Aqrawi, Wallace Arthur, Jennifer C J Barna, Kerstin P Blankenburg, Daniela Brites, Salvador Capella-Gutiérrez, Marcus Coyle, Peter K Dearden, Louis Du Pasquier, Elizabeth J Duncan, Dieter Ebert, Cornelius Eibner, Galina Erikson, Peter D Evans, Cassandra G Extavour, Liezl Francisco, Toni Gabaldón, William J Gillis, Elizabeth A Goodwin-Horn, Jack E Green, Sam Griffiths-Jones, Cornelis J P Grimmelikhuijzen, Sai Gubbala, Roderic Guigó, Yi Han, Frank Hauser, Paul Havlak, Luke Hayden, Sophie Helbing, Michael Holder, Jerome H L Hui, Julia P Hunn, Vera S Hunnekuhl, LaRonda Jackson, Mehwish Javaid, Shalini N Jhangiani, Francis M Jiggins, Tamsin E Jones, Tobias S Kaiser, Divya Kalra, Nathan J Kenny, Viktoriya Korchina, Christie L Kovar, F Bernhard Kraus, François Lapraz, Sandra L Lee, Jie Lv, Christigale Mandapat, Gerard Manning, Marco Mariotti, Robert Mata, Tittu Mathew, Tobias Neumann, Irene Newsham, Dinh N Ngo, Maria Ninova, Geoffrey Okwuonu, Fiona Ongeri, William J Palmer, Shobha Patil, Pedro Patraquim, Christopher Pham, Ling-Ling Pu, Nicholas H Putman, Catherine Rabouille, Olivia Mendivil Ramos, Adelaide C Rhodes, Helen E Robertson, Hugh M Robertson, Matthew Ronshaugen, Julio Rozas, Nehad Saada, Alejandro Sánchez-Gracia, Steven E Scherer, Andrew M Schurko, Kenneth W Siggens, DeNard Simmons, Anna Stief, Eckart Stolle, Maximilian J Telford, Kristin Tessmar-Raible, Rebecca Thornton, Maurijn van der Zee, Arndt von Haeseler, James M Williams, Judith H Willis, Yuanqing Wu, Xiaoyan Zou, Daniel Lawson, Donna M Muzny, Kim C Worley, Richard A Gibbs, Michael Akam, and Stephen Richards
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Biology (General) ,QH301-705.5 - Abstract
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
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- 2014
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3. The development of an unsupervised hierarchical clustering analysis of dual‐polarization weather surveillance radar observations to assess nocturnal insect abundance and diversity
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Maryna Lukach, Thomas Dally, William Evans, Christopher Hassall, Elizabeth J. Duncan, Lindsay Bennett, Freya I. Addison, William E. Kunin, Jason W. Chapman, and Ryan R. Neely III
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Abundance ,biodiversity ,dual‐polarization ,insects ,moths ,nocturnal ,Technology ,Ecology ,QH540-549.5 - Abstract
Abstract Contemporary analyses of insect population trends are based, for the most part, on a large body of heterogeneous and short‐term datasets of diurnal species that are representative of limited spatial domains. This makes monitoring changes in insect biomass and biodiversity difficult. What is needed is a method for monitoring that provides a consistent, high‐resolution picture of insect populations through time over large areas during day and night. Here, we explore the use of X‐band weather surveillance radar (WSR) for the study of local insect populations using a high‐quality, multi‐week time series of nocturnal moth light trapping data. Specifically, we test the hypotheses that (i) unsupervised data‐driven classification algorithms can differentiate meteorological and biological phenomena, (ii) the diversity of the classes of bioscatterers are quantitatively related to the diversity of insects as measured on the ground and (iii) insect abundance measured at ground level can be predicted quantitatively based on dual‐polarization Doppler WSR variables. Adapting the quasi‐vertical profile analysis method and data clustering techniques developed for the analysis of hydrometeors, we demonstrate that our bioscatterer classification algorithm successfully differentiates bioscatterers from hydrometeors over a large spatial scale and at high temporal resolutions. Furthermore, our results also show a clear relationship between biological and meteorological scatterers and a link between the abundance and diversity of radar‐based bioscatterer clusters and that of nocturnal aerial insects. Thus, we demonstrate the potential utility of this approach for landscape scale monitoring of biodiversity.
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- 2022
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4. High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus
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Thomas W. R. Harrop, Joseph Guhlin, Gemma M. McLaughlin, Elizabeth Permina, Peter Stockwell, Josh Gilligan, Marissa F. Le Lec, Monica A. M. Gruber, Oliver Quinn, Mackenzie Lovegrove, Elizabeth J. Duncan, Emily J. Remnant, Jens Van Eeckhoven, Brittany Graham, Rosemary A. Knapp, Kyle W. Langford, Zev Kronenberg, Maximilian O. Press, Stephen M. Eacker, Erin E. Wilson-Rankin, Jessica Purcell, Philip J. Lester, and Peter K. Dearden
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vespula germanica ,vespula pensylvanica ,vespula vulgaris ,hymenoptera ,social insects ,genomes ,Genetics ,QH426-470 - Abstract
Social wasps of the genus Vespula have spread to nearly all landmasses worldwide and have become significant pests in their introduced ranges, affecting economies and biodiversity. Comprehensive genome assemblies and annotations for these species are required to develop the next generation of control strategies and monitor existing chemical control. We sequenced and annotated the genomes of the common wasp (Vespula vulgaris), German wasp (Vespula germanica), and the western yellowjacket (Vespula pensylvanica). Our chromosome-level Vespula assemblies each contain 176–179 Mb of total sequence assembled into 25 scaffolds, with 10–200 unanchored scaffolds, and 16,566–18,948 genes. We annotated gene sets relevant to the applied management of invasive wasp populations, including genes associated with spermatogenesis and development, pesticide resistance, olfactory receptors, immunity and venom. These genomes provide evidence for active DNA methylation in Vespidae and tandem duplications of venom genes. Our genomic resources will contribute to the development of next-generation control strategies, and monitoring potential resistance to chemical control.
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- 2020
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5. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome
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Kristen A. Panfilio, Iris M. Vargas Jentzsch, Joshua B. Benoit, Deniz Erezyilmaz, Yuichiro Suzuki, Stefano Colella, Hugh M. Robertson, Monica F. Poelchau, Robert M. Waterhouse, Panagiotis Ioannidis, Matthew T. Weirauch, Daniel S. T. Hughes, Shwetha C. Murali, John H. Werren, Chris G. C. Jacobs, Elizabeth J. Duncan, David Armisén, Barbara M. I. Vreede, Patrice Baa-Puyoulet, Chloé S. Berger, Chun-che Chang, Hsu Chao, Mei-Ju M. Chen, Yen-Ta Chen, Christopher P. Childers, Ariel D. Chipman, Andrew G. Cridge, Antonin J. J. Crumière, Peter K. Dearden, Elise M. Didion, Huyen Dinh, Harsha Vardhan Doddapaneni, Amanda Dolan, Shannon Dugan, Cassandra G. Extavour, Gérard Febvay, Markus Friedrich, Neta Ginzburg, Yi Han, Peter Heger, Christopher J. Holmes, Thorsten Horn, Yi-min Hsiao, Emily C. Jennings, J. Spencer Johnston, Tamsin E. Jones, Jeffery W. Jones, Abderrahman Khila, Stefan Koelzer, Viera Kovacova, Megan Leask, Sandra L. Lee, Chien-Yueh Lee, Mackenzie R. Lovegrove, Hsiao-ling Lu, Yong Lu, Patricia J. Moore, Monica C. Munoz-Torres, Donna M. Muzny, Subba R. Palli, Nicolas Parisot, Leslie Pick, Megan L. Porter, Jiaxin Qu, Peter N. Refki, Rose Richter, Rolando Rivera-Pomar, Andrew J. Rosendale, Siegfried Roth, Lena Sachs, M. Emília Santos, Jan Seibert, Essia Sghaier, Jayendra N. Shukla, Richard J. Stancliffe, Olivia Tidswell, Lucila Traverso, Maurijn van der Zee, Séverine Viala, Kim C. Worley, Evgeny M. Zdobnov, Richard A. Gibbs, and Stephen Richards
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Phytophagy ,Transcription factors ,Gene structure ,Lateral gene transfer ,RNAi ,Gene family evolution ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Background The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. Results The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. Conclusions With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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- 2019
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6. One genome, multiple phenotypes: decoding the evolution and mechanisms of environmentally induced developmental plasticity in insects
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Kane J. Yoon, Christopher B. Cunningham, Amanda Bretman, and Elizabeth J. Duncan
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Biochemistry - Abstract
Plasticity in developmental processes gives rise to remarkable environmentally induced phenotypes. Some of the most striking and well-studied examples of developmental plasticity are seen in insects. For example, beetle horn size responds to nutritional state, butterfly eyespots are enlarged in response to temperature and humidity, and environmental cues also give rise to the queen and worker castes of eusocial insects. These phenotypes arise from essentially identical genomes in response to an environmental cue during development. Developmental plasticity is taxonomically widespread, affects individual fitness, and may act as a rapid-response mechanism allowing individuals to adapt to changing environments. Despite the importance and prevalence of developmental plasticity, there remains scant mechanistic understanding of how it works or evolves. In this review, we use key examples to discuss what is known about developmental plasticity in insects and identify fundamental gaps in the current knowledge. We highlight the importance of working towards a fully integrated understanding of developmental plasticity in a diverse range of species. Furthermore, we advocate for the use of comparative studies in an evo-devo framework to address how developmental plasticity works and how it evolves.
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- 2023
7. Simulation of the Radar Cross Section of a Noctuid Moth.
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Freya I. Addison, Thomas Dally, Elizabeth J. Duncan, James Rouse, William L. Evans, Christopher Hassall, and Ryan R. Neely
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- 2022
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8. Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution
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Chen Wu, Melissa D. Jordan, Richard D. Newcomb, Neil J. Gemmell, Sarah Bank, Karen Meusemann, Peter K. Dearden, Elizabeth J. Duncan, Sefanie Grosser, Kim Rutherford, Paul P. Gardner, Ross N. Crowhurst, Bernd Steinwender, Leah K. Tooman, Mark I. Stevens, and Thomas R. Buckley
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Hexapoda ,Neanuridae ,Genome assembly ,Phylogenomics ,Methylation ,Epigenetics ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events. Results Our genome assembly was ~375 Mbp in size with a scaffold N50 of ~230 Kbp and sequencing coverage of ~180×. DNA elements, LTRs and simple repeats and LINEs formed the largest components and SINEs were very rare. Phylogenomics (370,877 amino acids) placed H. duospinosa within the Neanuridae. We recovered orthologs of the conserved sex determination genes thought to play a role in sex determination. Analysis of CpG content suggested the absence of DNA methylation, and consistent with this we were unable to detect orthologs of the DNA methyltransferase enzymes. The small subunit rRNA gene contained a possible retrotransposon. The Hox gene complex was broken over two scaffolds. For chemosensory ability, at least 15 and 18 ionotropic glutamate and gustatory receptors were identified, respectively. However, we were unable to identify any odorant receptors or their obligate co-receptor Orco. Twenty-three chitinase-like genes were identified from the assembly. Members of this multigene family may play roles in the digestion of fungal cell walls, a common food source for these saproxylic organisms. We also detected 59 and 96 genes that blasted to bacteria and fungi, respectively, but were located on scaffolds that otherwise contained arthropod genes. Conclusions The genome of H. duospinosa contains some unusual features including a Hox complex broken over two scaffolds, in a different manner to other arthropod species, a lack of odorant receptor genes and an apparent lack of environmentally responsive DNA methylation, unlike many other arthropods. Our detection of candidate horizontal gene transfer candidates confirms that this phenomenon is occurring across Collembola. These findings allow us to narrow down the regions of the arthropod phylogeny where key innovations have occurred that have facilitated the evolutionary success of Hexapoda.
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- 2017
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9. What Do Studies of Insect Polyphenisms Tell Us about Nutritionally-Triggered Epigenomic Changes and Their Consequences?
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Andrew G. Cridge, Megan P. Leask, Elizabeth J. Duncan, and Peter K. Dearden
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polyphenisms ,epigenetics ,DNA methylation ,chromatin structure ,insect models ,Nutrition. Foods and food supply ,TX341-641 - Abstract
Many insects are capable of remarkable changes in biology and form in response to their environment or diet. The most extreme example of these are polyphenisms, which are when two or more different phenotypes are produced from a single genotype in response to the environment. Polyphenisms provide a fascinating opportunity to study how the environment affects an animal’s genome, and how this produces changes in form. Here we review the current state of knowledge of the molecular basis of polyphenisms and what can be learnt from them to understand how nutrition may influence our own genomes.
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- 2015
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10. Noggin proteins are multifunctional extracellular regulators of cell signaling
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Prashath Karunaraj, Olivia Tidswell, Elizabeth J Duncan, Mackenzie R Lovegrove, Grace Jefferies, Travis K Johnson, Caroline W Beck, and Peter K Dearden
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animal structures ,embryonic structures ,Bone Morphogenetic Proteins ,Genetics ,Animals ,Gene Expression Regulation, Developmental ,Proteins ,Protein-Tyrosine Kinases ,Body Patterning ,Signal Transduction - Abstract
Noggin is an extracellular cysteine knot protein that plays a crucial role in vertebrate dorsoventral patterning. Noggin binds and inhibits the activity of bone morphogenetic proteins via a conserved N-terminal clip domain. Noncanonical orthologs of Noggin that lack a clip domain (“Noggin-like” proteins) are encoded in many arthropod genomes and are thought to have evolved into receptor tyrosine kinase ligands that promote Torso/receptor tyrosine kinase signaling rather than inhibiting bone morphogenic protein signaling. Here, we examined the molecular function of noggin/noggin-like genes (ApNL1 and ApNL2) from the arthropod pea aphid using the dorso-ventral patterning of Xenopus and the terminal patterning system of Drosophila to identify whether these proteins function as bone morphogenic protein or receptor tyrosine kinase signaling regulators. Our findings reveal that ApNL1 from the pea aphid can regulate both bone morphogenic protein and receptor tyrosine kinase signaling pathways, and unexpectedly, that the clip domain is not essential for its antagonism of bone morphogenic protein signaling. Our findings indicate that ancestral noggin/noggin-like genes were multifunctional regulators of signaling that have specialized to regulate multiple cell signaling pathways during the evolution of animals.
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- 2022
11. A multicentre assessment of contemporary laboratory assays for heparin induced thrombocytopenia
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Sara Ng, Soma Mohammed, Samira Moosavi, Nathan Klose, P. Motum, Dea Donikian, Olivia Yacoub, Elizabeth J. Duncan, Erica Malan, Diane Zebeljan, Timothy A. Brighton, Emmanuel J. Favaloro, Kent Chapman, Joanne Beggs, Robyn Coleman, Leonardo Pasalic, Agnes Yuen, Lauren Cavanaugh, Mayuko Kondo, and Chee Wee Tan
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Male ,0301 basic medicine ,medicine.medical_specialty ,Platelet Aggregation ,Enzyme-Linked Immunosorbent Assay ,Gastroenterology ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,Heparin-induced thrombocytopenia ,Internal medicine ,medicine ,False positive paradox ,Humans ,Platelet activation ,Receiver operating characteristic ,Diagnostic Tests, Routine ,Heparin ,business.industry ,Area under the curve ,Anticoagulants ,Thrombosis ,Gold standard (test) ,Laboratories, Hospital ,medicine.disease ,Thrombocytopenia ,030104 developmental biology ,ROC Curve ,030220 oncology & carcinogenesis ,Female ,Complication ,business - Abstract
Heparin induced thrombocytopenia (HIT) is a rare but potentially fatal complication of heparin therapy. In some patients, HIT causes platelet activation and thrombosis (sometimes abbreviated HITT), which leads to adverse clinical sequalae ('pathological HIT'). The likelihood of HIT is initially assessed clinically, typically using a scoring system, of which the 4T score is that most utilised. Subsequent laboratory testing to confirm or exclude HIT facilitates exclusion or diagnosis and management. The current investigation comprises a multicentre (n=9) assessment of contemporary laboratory testing for HIT, as performed over the past 1-3 years in each site and comprising testing of over 1200 samples. The primary laboratory test used by study participants (n=8) comprised a chemiluminescence procedure (HIT-IgG(PF4-H)) performed on an AcuStar instrument. Additional immunological testing performed by study sites included lateral flow (STiC, Stago), enzyme linked immunosorbent assay (ELISA), Asserachrom (HPIA IgG), PaGIA (BioRad), plus functional assays, primarily serotonin release assay (SRA) or platelet aggregation methods. The chemiluminescence procedure yielded a highly sensitive screening method for identifying functional HIT, given high area under the curve (AUC, generally ≥0.9) in a receiver operator characteristic (ROC) analysis against SRA as gold standard. ELISA testing resulted in lower ROC AUC scores (
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- 2021
12. Honeybee queen mandibular pheromone induces a starvation response in Drosophila melanogaster
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Mackenzie R. Lovegrove, Peter K. Dearden, and Elizabeth J. Duncan
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Insect Science ,Molecular Biology ,Biochemistry - Published
- 2023
13. Genomic Signatures of Recent Adaptation in a Wild Bumblebee
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Thomas J Colgan, Andres N Arce, Richard J Gill, Ana Ramos Rodrigues, Abdoulie Kanteh, Elizabeth J Duncan, Li Li, Lars Chittka, and Yannick Wurm
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Genetics ,Animals ,Genomics ,Bees ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Ecosystem - Abstract
Environmental changes threaten insect pollinators, creating risks for agriculture and ecosystem stability. Despite their importance, we know little about how wild insects respond to environmental pressures. To understand the genomic bases of adaptation in an ecologically important pollinator, we analyzed genomes of Bombus terrestris bumblebees collected across Great Britain. We reveal extensive genetic diversity within this population, and strong signatures of recent adaptation throughout the genome affecting key processes including neurobiology and wing development. We also discover unusual features of the genome, including a region containing 53 genes that lacks genetic diversity in many bee species, and a horizontal gene transfer from a Wolbachia bacteria. Overall, the genetic diversity we observe and how it is distributed throughout the genome and the population should support the resilience of this important pollinator species to ongoing and future selective pressures. Applying our approach to more species should help understand how they can differ in their adaptive potential, and to develop conservation strategies for those most at risk.
- Published
- 2022
14. High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus
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Marissa F. Le Lec, Phillip J Lester, Jessica Purcell, Zev N. Kronenberg, Joshua Gilligan, Emily J. Remnant, Maximilian O. Press, Gemma M. McLaughlin, Oliver Quinn, Monica A. M. Gruber, Peter K. Dearden, Erin E. Wilson-Rankin, Thomas W. R. Harrop, Elizabeth Permina, Stephen M. Eacker, Jens Van Eeckhoven, Joseph Guhlin, Peter A. Stockwell, Kyle W. Langford, Rosemary A. Knapp, Brittany Graham, Elizabeth J. Duncan, and Mackenzie Lovegrove
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0106 biological sciences ,AcademicSubjects/SCI01140 ,AcademicSubjects/SCI00010 ,Wasps ,Vespula vulgaris ,Vespula germanica ,Hymenoptera ,QH426-470 ,AcademicSubjects/SCI01180 ,010603 evolutionary biology ,01 natural sciences ,Genome ,Vespula ,03 medical and health sciences ,Genetics ,Animals ,Yellowjacket ,Vespula pensylvanica ,Molecular Biology ,Genetics (clinical) ,030304 developmental biology ,0303 health sciences ,social insects ,biology ,Vespidae ,Genomics ,biology.organism_classification ,Corrigenda ,Genome Report ,Evolutionary biology ,AcademicSubjects/SCI00960 ,genomes - Abstract
Social wasps of the genus Vespula have spread to nearly all landmasses worldwide and have become significant pests in their introduced ranges, affecting economies and biodiversity. Comprehensive genome assemblies and annotations for these species are required to develop the next generation of control strategies and monitor existing chemical control. We sequenced and annotated the genomes of the common wasp (Vespula vulgaris), German wasp (Vespula germanica), and the western yellowjacket (Vespula pensyl- vanica). Our chromosome-level Vespula assemblies each contain 176–179 Mb of total sequence assembled into 25 scaffolds, with 10–200 unanchored scaffolds, and 16,566–18,948 genes. We annotated gene sets relevant to the applied management of invasive wasp populations, including genes associated with spermatogenesis and development, pesticide resistance, olfactory receptors, immunity and venom. These genomes provide evidence for active DNA methylation in Vespidae and tandem duplications of venom genes. Our genomic resources will contribute to the development of next-generation control strategies, and monitoring potential resistance to chemical control.
- Published
- 2020
15. The diversity and distribution of D1 proteins in cyanobacteria
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Kevin J Sheridan, Julian J. Eaton-Rye, Tina C. Summerfield, and Elizabeth J. Duncan
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Chlorophyll ,0106 biological sciences ,0301 basic medicine ,Cyanobacteria ,Gene isoform ,Photosystem II ,Plant Science ,Biology ,01 natural sciences ,Biochemistry ,Evolution, Molecular ,03 medical and health sciences ,Phylogenetics ,Gene cluster ,Protein Isoforms ,Gene family ,Photosynthesis ,Gene ,Phylogeny ,Genetics ,chemistry.chemical_classification ,Genetic Variation ,Photosystem II Protein Complex ,Cell Biology ,General Medicine ,biology.organism_classification ,Amino acid ,030104 developmental biology ,chemistry ,010606 plant biology & botany - Abstract
The psbA gene family in cyanobacteria encodes different forms of the D1 protein that is part of the Photosystem II reaction centre. We have identified a phylogenetically distinct D1 group that is intermediate between previously identified G3-D1 and G4-D1 proteins (Cardona et al. Mol Biol Evol 32:1310–1328, 2015). This new group contained two subgroups: D1INT, which was frequently in the genomes of heterocystous cyanobacteria and D1FR that was part of the far-red light photoacclimation gene cluster of cyanobacteria. In addition, we have identified subgroups within G3, the micro-aerobically expressed D1 protein. There are amino acid changes associated with each of the subgroups that might affect the function of Photosystem II. We show a phylogenetically broad range of cyanobacteria have these D1 types, as well as the genes encoding the G2 protein and chlorophyll f synthase. We suggest identification of additional D1 isoforms and the presence of multiple D1 isoforms in phylogenetically diverse cyanobacteria supports the role of these proteins in conferring a selective advantage under specific conditions.
- Published
- 2020
16. Evolution and genomic organization of the insect sHSP gene cluster and coordinate regulation in phenotypic plasticity
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Peter K. Dearden, Elizabeth J. Duncan, Abigail Walker, Megan Leask, and Mackenzie Lovegrove
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0106 biological sciences ,Insecta ,Evolution ,Lineage (evolution) ,H3K27me3 ,Honeybee ,Genome, Insect ,Biology ,01 natural sciences ,Genome ,Synteny ,Evolution, Molecular ,03 medical and health sciences ,Phylogenetics ,Gene cluster ,QH359-425 ,Animals ,sHSP ,Gene ,Arthropods ,QH540-549.5 ,Phylogeny ,030304 developmental biology ,Genomic organization ,Birth-and-death evolution ,0303 health sciences ,Phylogenetic tree ,Ecology ,fungi ,General Medicine ,Genomics ,Bees ,Adaptation, Physiological ,Evolutionary biology ,Multigene Family ,Female ,010606 plant biology & botany ,Research Article - Abstract
Background Conserved syntenic gene complexes are rare in Arthropods and likely only retained due to functional constraint. Numerous sHSPs have been identified in the genomes of insects, some of which are located clustered in close proximity. Previous phylogenetic analyses of these clustered sHSP have been limited to a small number of holometabolous insect species and have not determined the pattern of evolution of the clustered sHSP genes (sHSP-C) in insect or Arthropod lineages. Results Using eight genomes from representative insect orders and three non-insect arthropod genomes we have identified that a syntenic cluster of sHSPs (sHSP-C) is a hallmark of most Arthropod genomes. Using 11 genomes from Hymenopteran species our phylogenetic analyses have refined the evolution of the sHSP-C in Hymenoptera and found that the sHSP-C is order-specific with evidence of birth-and-death evolution in the hymenopteran lineage. Finally we have shown that the honeybee sHSP-C is co-ordinately expressed and is marked by genomic features, including H3K27me3 histone marks consistent with coordinate regulation, during honeybee ovary activation. Conclusions The syntenic sHSP-C is present in most insect genomes, and its conserved coordinate expression and regulation implies that it is an integral genomic component of environmental response in arthropods.
- Published
- 2021
17. Environmentally responsive reproduction: neuroendocrine signalling and the evolution of eusociality
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Rosemary A, Knapp, Victoria C, Norman, James L, Rouse, and Elizabeth J, Duncan
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Insecta ,Reproduction ,Insect Science ,Animals ,Female ,Life History Traits ,Pheromones ,Ecology, Evolution, Behavior and Systematics - Abstract
Eusociality is a rare but successful life-history strategy that is defined by the reproductive division of labour. In eusocial species, most females forgo their own reproduction to support that of a dominant female or queen. In many eusocial insects, worker reproduction is inhibited via dominance hierarchies or by pheromones produced by the queen and her brood. Here, we consider whether these cues may act as generic 'environmental signals', similar to temperature or nutrition stress, which induce a state of reproductive dormancy in some solitary insects. We review the recent findings regarding the mechanisms of reproductive dormancy in insects and highlight key gaps in our understanding of how environmental cues inhibit reproduction.
- Published
- 2022
18. Corrigendum to 'High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus'
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Mackenzie Lovegrove, Stephen M. Eacker, Kyle W. Langford, Thomas W. R. Harrop, Jens Van Eeckhoven, Emily J. Remnant, Elizabeth Permina, Rosemary A. Knapp, Peter K. Dearden, Brittany Graham, Gemma M. McLaughlin, Josh Gilligan, Elizabeth J. Duncan, Monica A. M. Gruber, Erin E. Wilson-Rankin, Maximilian O. Press, Marissa F. Le Lec, Zev N. Kronenberg, Philip J. Lester, Jessica Purcell, Oliver Quinn, Joseph Guhlin, and Peter A. Stockwell
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Genus ,media_common.quotation_subject ,Genetics ,Zoology ,Quality (business) ,Biology ,QH426-470 ,biology.organism_classification ,Molecular Biology ,Genetics (clinical) ,Vespula ,media_common - Published
- 2021
19. Development of a multiplex microsatellite marker set for the study of the solitary red mason bee, Osmia bicornis (Megachilidae)
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Elizabeth J. Duncan, Gavin J. Horsburgh, Kathryn Mayer, Deborah A. Dawson, Amanda Bretman, and Jens Van Eeckhoven
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Conservation genetics ,Male ,Megachilidae ,Genotype ,Genotyping Techniques ,Short Communication ,Genome, Insect ,Biology ,Population structure ,Gene Frequency ,Pollinator ,Germany ,Genetics ,Mason bee ,Polymorphic Microsatellite Marker ,Animals ,Molecular Biology ,Alleles ,Ecosystem ,Genetic diversity ,Polymorphism, Genetic ,Microsatellite marker ,General Medicine ,Bees ,biology.organism_classification ,United Kingdom ,Red mason bee ,Evolutionary biology ,Genetic Loci ,Osmia bicornis ,Genetic structure ,Microsatellite ,Female ,Microsatellite Repeats - Abstract
Background Solitary bees, such as the red mason bee (Osmia bicornis), provide important ecosystem services including pollination. In the face of global declines of pollinator abundance, such haplodiploid Hymenopterans have a compounded extinction risk due to the potential for limited genetic diversity. In order to assess the genetic diversity of Osmia bicornis populations, we developed microsatellite markers and characterised them in two populations. Methods and results Microsatellite sequences were mined from the recently published Osmia bicornis genome, which was assembled from DNA extracted from a single male bee originating from the United Kingdom. Sequences were identified that contained dinucleotide, trinucleotide, and tetranucleotide repeat regions. Seventeen polymorphic microsatellite markers were designed and tested, sixteen of which were developed into four multiplex PCR sets to facilitate cheap, fast and efficient genotyping and were characterised in unrelated females from Germany (n = 19) and England (n = 14). Conclusions The microsatellite markers are highly informative, with a combined exclusion probability of 0.997 (first parent), which will enable studies of genetic structure and diversity to inform conservation efforts in this bee.
- Published
- 2021
20. Genomic signatures of recent adaptation in a wild bumblebee
- Author
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Lars Chittka, Li L, Andres N. Arce, Thomas J. Colgan, Kanteh A, Yannick Wurm, Elizabeth J. Duncan, Ramos Rodrigues A, and Richard J. Gill
- Subjects
Ecological stability ,education.field_of_study ,Genetic diversity ,biology ,Evolutionary biology ,Bombus terrestris ,Population ,Wolbachia ,Adaptation ,biology.organism_classification ,education ,Genome ,Bumblebee - Abstract
Behavioral experiments and analyses of observation records have shown that environmental changes threaten insect pollinators, creating risks for agriculture and ecosystem stability. Despite their importance, we know little about how wild insects or other animals can adapt in response to environmental pressures. To understand the genomic bases of adaptation in an ecologically important pollinator, we analyzed genomes ofBombus terrestrisbumblebees collected across Great Britain. We reveal extensive genetic diversity within this population, and strong signatures of recent adaptation throughout the genome. More specifically, we find that selection recently affected key processes underpinning environmental interactions, including neurobiology, wing development, and response to xenobiotics. We also discover unusual features of the genome, including a 53-gene region that lacks genetic diversity in many bee species, and a horizontal gene transfer from aWolbachiabacteria. The genetic diversity and gene flow we observe for this species could support its resilience to ongoing and future challenges. Overall, we provide important insight on the genetic health of an ecologically and economically important pollinator and reveal mechanisms by which it has recently adapted. The approach we used could help to understand how species differ in their adaptive potential, and to develop conservation strategies for those most at risk.
- Published
- 2021
21. Ethnicity and media: a study of English and non-English language print media coverage of water issues in Sydney
- Author
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Liping Yan, Phil McManus, and Elizabeth J. Duncan
- Subjects
Environmental justice ,ethnically diverse media ,1604 Human Geography ,Print media ,05 social sciences ,Geography, Planning and Development ,0211 other engineering and technologies ,0507 social and economic geography ,Ethnic group ,Media studies ,Water ,021107 urban & regional planning ,ethnic media ,02 engineering and technology ,English language ,Management, Monitoring, Policy and Law ,Ethnically diverse ,Newspaper ,environmental management ,Situated ,Sociology ,environmental justice ,050703 geography - Abstract
It is critical to understand how matters relating to water are reported, or ignored, among linguistically diverse media and to understand the possible influence this may have on the conception of water issues among ethnically diverse groups. This research analysed five daily newspapers published in Sydney between 2011 and 2012 in three languages (English, Chinese and Korean) and found that water issues were presented differently by newspapers across language divides in Sydney. These differences may contribute to diverse conceptual constructions of water problems and water management among ethnically diverse communities. After allowing for the influence of other variables, this research highlights the necessity to investigate media construction of water issues in various Non-English language publications as an important approach to improving situated and place-based water awareness in an ethnically diverse city.
- Published
- 2019
22. (Re)presenting urban heat islands in Australian cities: A study of media reporting and implications for urban heat and climate change debates
- Author
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Elizabeth J. Duncan, Phil McManus, Alice Simpson-Young, Alexander Iping, and Juliette Kidston-Lattari
- Subjects
Atmospheric Science ,010504 meteorology & atmospheric sciences ,business.industry ,Geography, Planning and Development ,Climate change ,Distribution (economics) ,Context (language use) ,010501 environmental sciences ,Environmental Science (miscellaneous) ,Private sector ,01 natural sciences ,Urban Studies ,Effects of global warming ,Argument ,Political science ,Science communication ,Urban heat island ,business ,Environmental planning ,0105 earth and related environmental sciences - Abstract
The effects of climate change and urban heat islands are predicted to grow and compound in the future. In the context of urban heat becoming an increasing problem, this article explores the extent to which this is recognised in media. Our findings show that the issue of the urban heat island (UHI) effect appeared on media agendas over the period studied and that predominantly the issue of UHI was framed in four ways. The top-down mitigation frame focused on the proactive approach of local governments while highlighting inaction at state and national levels. The bottom-up mitigation frame presented a patchwork approach to dealing with UHI with a positive focus on the mitigation actions of individuals and the private sector, while the risks and vulnerabilities frame looked at the distribution and mapping of the health risks posed by the phenomena. However, the media analysis also highlighted two factors which have potentially negative consequences regarding science communication and citizen understandings of science. These are the ambiguous and/or cautious manner in which the UHI effect is referred to and the use of UHI as an alternative argument to climate change in the climate change debate frame.
- Published
- 2019
23. ‘No one has even seen… smelt… or sensed a social licence’: Animal geographies and social licence to operate
- Author
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Raewyn Graham, Phil McManus, and Elizabeth J. Duncan
- Subjects
Resource (biology) ,Sociology and Political Science ,business.industry ,media_common.quotation_subject ,05 social sciences ,0211 other engineering and technologies ,0507 social and economic geography ,021107 urban & regional planning ,02 engineering and technology ,Public relations ,Tipping point (climatology) ,Transparency (behavior) ,Animal welfare ,Institution ,Animal geography ,business ,050703 geography ,Welfare ,Legitimacy ,media_common - Abstract
Traditionally, the concept of SLO has been applied to resource-based industries, when companies seek legitimacy because their practice is seen to cause environmental and/or social harms. Recent use of SLO has extended to animal-based industries to address animal welfare concerns. A framework for discussion of such welfare issues is offered by considering SLO in relation to the Australian thoroughbred racing industry, as an example of an animal-based sporting institution. We focus on the visible issue of whipping horses; exploring how visibility as a factor impacts on four key dimensions of the SLO – legitimacy, trust (procedural), transparency and communication. Concluding, when a SLO is under threat, it is often a result of tension between transparency and communication, which in turn impact trust and legitimacy. Furthermore, our findings illustrate that it is the visibility of practices that are seen to cause ‘harm’ that have the potential to trigger a tipping point for a SLO. Our conclusions contribute to an understanding of how the ethical framework of human-animal relations is constructed and to debates about the potential and limitations of applying the concept of SLO in a range of animal-based industries.
- Published
- 2018
24. Honeybee Queen mandibular pheromone induces starvation in Drosophila melanogaster, implying a role for nutrition signalling in the evolution of eusociality
- Author
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Elizabeth J. Duncan, Mackenzie Lovegrove, and Peter K. Dearden
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Evolution of eusociality ,Queen mandibular pheromone ,biology ,media_common.quotation_subject ,Sex pheromone ,Melanogaster ,Insect ,Drosophila melanogaster ,biology.organism_classification ,Starvation response ,Eusociality ,media_common ,Cell biology - Abstract
Eusocial insect societies are defined by the reproductive division of labour, a social structure that is generally enforced by the reproductive dominant or ‘queen’. Reproductive dominance is maintained through behavioural dominance in some species as well as production of queen pheromones in others, or a mixture of both. Queen mandibular pheromone (QMP) is produced by honeybee (Apis mellifera) queens and has been characterised chemically. How QMP acts to repress worker reproduction, and how it has evolved this activity, remains less well understood. Surprisingly, QMP is capable of repressing reproduction in non-target arthropods which have not co-evolved with QMP, are never exposed to QMP in nature, and are up to 530 million years diverged from the honeybee. Here we show that, in Drosophila melanogaster, QMP treatment mimics nutrient limiting conditions, leading to disrupted reproduction. Exposure to QMP induces an increase in food consumption, consistent with that observed in D. melanogaster in response to starvation conditions. This response induces the activation of two checkpoints within the ovary that inhibit oogenesis. The first is the 2a/b ovarian checkpoint in the germarium, which reduces the flow of presumptive oocytes. A stage 9 ovarian checkpoint is also activated, causing degradation of oocytes. The magnitude of activation of both checkpoints is indistinguishable between QMP treated and starved individuals. As QMP seems to trigger a starvation response in an insect highly diverged from honeybees, we propose that QMP originally evolved by co-opting nutrition signalling pathways to regulate reproduction, a key step in the evolution of eusociality.
- Published
- 2021
25. Evolution and genomic organization of the sHSP gene cluster in Arthropods
- Author
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Elizabeth J. Duncan, Megan Leask, Peter K. Dearden, Mackenzie Lovegrove, and Abigail Walker
- Subjects
fungi ,Gene cluster ,Computational biology ,Biology ,Genomic organization - Abstract
Background Conserved syntenic gene complexes are rare in Arthropods and likely only retained due to functional constraint. Numerous sHSPs have been identified in the genomes of insects, some of which are located clustered in close proximity. Previous phylogenetic analyses of these clustered sHSP have been limited to a small number of holometabolous insect species and have not determined the pattern of evolution of the clustered sHSP genes (sHSP-C) in insect or Arthropod lineages. Results Using eight genomes from representative insect orders and three non-insect arthropod genomes we have identified that a syntenic cluster of sHSPs (sHSP-C) is a hallmark of most Arthropod genomes. Using 11 genomes from Hymenopteran species our phylogenetic analyses have refined the evolution of the sHSP-C in Hymenoptera and found that the sHSP-C is order-specific with evidence of birth-and-death evolution in the hymenopteran lineage. Finally we have shown that the honeybee sHSP-C is co-ordinately expressed and is marked by genomic features, including H3K27me3 histone marks consistent with coordinate regulation, during honeybee ovary activation. Conclusions The syntenic sHSP-C is present in most insect genomes, and its conserved coordinate expression and regulation implies that it is an integral genomic component of environmental response in arthropods.
- Published
- 2021
26. COVID-19 as a Stress Test: Assessing the Bank Regulatory Framework
- Author
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Diana Iercosan, Carlo Wix, Francis Martinez, Alice Abboud, Elizabeth J. Duncan, Missaka Warusawitharana, Akos Horvath, Bert Loudis, Timothy Mooney, Ben Ranish, and Ke Wang
- Subjects
History ,Coronavirus disease 2019 (COVID-19) ,Polymers and Plastics ,Bank capital ,Financial system ,Industrial and Manufacturing Engineering ,Market liquidity ,Test (assessment) ,Stress test ,Capital (economics) ,Financial crisis ,Capital requirement ,Business ,Business and International Management ,General Economics, Econometrics and Finance ,Finance - Abstract
The widespread economic damage caused by the ongoing COVID-19 pandemic poses the first major test of the bank regulatory reforms put in place following the global financial crisis. This study assesses this framework, with an emphasis on capital and liquidity requirements. Leading up to the COVID-19 crisis, banks were well-capitalized and held ample liquid assets, reflecting in part heightened requirements. Capital requirements were comparable across major jurisdictions, despite differences in the implementation of the international Basel standards. The overall robust capital and liquidity levels resulted in a resilient banking system, which maintained lending through the early stages of the pandemic. Furthermore, trading activity was a source of strength for banks, reflecting in part a prudent regulatory approach. Areas for potential improvement include addressing the cyclicality of requirements.
- Published
- 2021
27. Drosophila melanogaster and worker honeybees (Apis mellifera) do not require olfaction to be susceptible to honeybee queen mandibular pheromone
- Author
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Peter K. Dearden, Elizabeth J. Duncan, Rosemary A. Knapp, and Mackenzie Lovegrove
- Subjects
0106 biological sciences ,0301 basic medicine ,Queen mandibular pheromone ,Physiology ,Zoology ,Olfaction ,Biology ,01 natural sciences ,Pheromones ,03 medical and health sciences ,Melanogaster ,Animals ,Bees ,biology.organism_classification ,Olfactory Perception ,Eusociality ,Smell ,010602 entomology ,030104 developmental biology ,Drosophila melanogaster ,Insect Science ,Sex pheromone ,Pheromone ,Female ,Trophallaxis - Abstract
Eusociality is characterised by the reproductive division of labour; a dominant female (queen) or females are responsible for the majority of reproduction, and subordinate females are reproductively constrained. Reproductive constraint can be due to behavioural aggression and/or chemical cues, so-called queen pheromones, produced by the dominant females. In the honeybee, Apis mellifera, this repressive queen pheromone is queen mandibular pheromone (QMP). The mechanism by which honeybee workers are susceptible to QMP is not yet completely understood, however it is thought to be through olfaction via the antennae and/or gustation via trophallaxis. We have investigated whether olfaction is key to sensing of QMP, using both Drosophila melanogaster- a tractable non-eusocial insect which is also reproductively repressed by QMP- and the target species, A. mellifera worker honeybees. D. melanogaster are still capable of sensing and responding to QMP without their antenna and maxillary palps, and therefore without olfactory receptors. When worker honeybees were exposed to QMP but unable to physically interact with it, therefore required to use olfaction, they were similarly not reproductively repressed. Combined, these findings support either a non-olfactory based mechanism for the repression of reproduction via QMP, or redundancy via non-olfactory mechanisms in both D. melanogaster and A. mellifera. This study furthers our understanding of how species are susceptible to QMP, and provides insight into the mechanisms governing QMP responsiveness in these diverse species.
- Published
- 2020
28. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera
- Author
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Sebastian Martin, Huyen Dinh, Kim C. Worley, Björn M. von Reumont, Tanja Ziesmann, Elena N. Elpidina, Cameron Gudobba, Alexander G. Martynov, Patrice Baa-Puyoulet, Cornelis J. P. Grimmelikhuijzen, Elizabeth Cash, Olivia R.A. Tidswell, Federica Calevro, Aaron Stahl, Markus Friedrich, Jiaxin Qu, Andrew J. Rosendale, Joshua B. Benoit, Leo W. Beukeboom, Shwetha C. Murali, Mackenzie Lovegrove, Panagiotis Ioannidis, Brenda Oppert, Daniel Dowling, Mei-Ju May Chen, Peter Lesný, Elzemiek Geuverink, Jan Philip Oeyen, Bernhard Misof, Maarten J.M.F. Reijnders, Masatsugu Hatakeyama, Emily C. Jennings, Christoph Mayer, Lucia Vedder, Daisuke S. Yamamoto, Anja Buttstedt, Hsu Chao, Elizabeth J. Duncan, Louis van de Zande, Daniel S.T. Hughes, Monica Munoz-Torres, Erich Bornberg-Bauer, Richard A. Gibbs, Lars Podsiadlowski, Peter K. Dearden, Alexandros G Sotiropoulos, Ralph S. Peters, Nicolas Montagné, Jeanne Wilbrandt, Andrew G. Cridge, Stephen Richards, John H. Werren, Yi Han, Sandra L. Lee, Megumi Sumitani, Victoria C. Moris, Oliver Niehuis, Ewald Große-Wilde, Amanda Dolan, Elise M. Szuter, Nicolas Parisot, Christopher P. Childers, Emmanuelle Jacquin-Joly, Sonja Grath, Panagiotis Provataris, Donna M. Muzny, Thomas Pauli, Joshua D. Gibson, Steffen Klasberg, Frank Hauser, John Skelly, Robert M. Waterhouse, Alexander Donath, Monica F. Poelchau, Shannon Dugan, Bill S. Hansson, Hubert Charles, Harshavardhan Doddapaneni, Malte Petersen, Evgeny M. Zdobnov, Evangelos Tsitlakidis, Christian Pick, Felipe A. Simão, Emma Persyn, Jeffery W. Jones, Lavrov, Dennis, Beukeboom lab, Evolutionary Genetics, Development & Behaviour, Van de Zande lab, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Westfälische Wilhelms-Universität Münster (WWU), Biochemistry Department, University of Otago [Dunedin, Nouvelle-Zélande], Max-Planck-Institut für Kernphysik (MPIK), Max-Planck-Gesellschaft, Max Planck Institute for Chemical Ecology, Physiologie de l'Insecte : Signalisation et Communication (PISC), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech, Institute for Evolution and Biodiversity (IEB), Department of Chemistry [Vancouver] (UBC Chemistry), University of British Columbia (UBC), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Human Genome Sequencing Center, Baylor College of Medicine, Baylor College of Medicine (BCM), Baylor University-Baylor University, Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Department of Biology, Georgetown University, Université de Lausanne (UNIL), Human Genome Sequencing Center [Houston] (HGSC), Grad Sch Life Sci, Div Neurogenet, Tohoku University [Sendai], Department of Genetic Medicine and Development [Geneva], Université de Genève (UNIGE), Zoologisches Forschungsmuseum Alexander Koenig, Center for Molecular Biodiversity Research, Lavrov, Dennis (ed.), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Zdobnov, Evgeny
- Subjects
AcademicSubjects/SCI01140 ,0106 biological sciences ,Most recent common ancestor ,Male ,Vision ,Genome, Insect ,Gene Dosage ,Hymenoptera ,JEWEL WASP NASONIA ,Receptors, Odorant ,01 natural sciences ,Genome ,Parasitoid ,MULTIPLE SEQUENCE ALIGNMENT ,opsin ,Receptors ,phytophagy ,ddc:576.5 ,Apocrita ,Conserved Sequence ,0303 health sciences ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,HOST LOCATION ,Eusociality ,ROYAL JELLY PROTEIN ,ATHALIA-ROSAE ,Sawfly ,Odorant ,APIS-MELLIFERA ,Multigene Family ,Insect Proteins ,Female ,Research Article ,Genetics ,Ecology, Evolution, Behavior and Systematics ,hexamerin ,major royal jelly protein ,microsynteny ,odorant receptor ,CHEMORECEPTOR SUPERFAMILY ,Genetic Speciation ,Biology ,010603 evolutionary biology ,Host-Parasite Interactions ,03 medical and health sciences ,Ocular ,Animals ,Amino Acid Sequence ,Herbivory ,Social Behavior ,DRAFT GENOME ,Life Below Water ,Vision, Ocular ,030304 developmental biology ,MODEL SELECTION ,Glycoproteins ,Orussidae ,Evolutionary Biology ,fungi ,Human Genome ,AcademicSubjects/SCI01130 ,Immunity ,biology.organism_classification ,MOLECULAR EVOLUTION ,Evolutionary biology ,DNA Transposable Elements ,Biochemistry and Cell Biology ,Insect ,[SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis ,Developmental Biology - Abstract
The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.
- Published
- 2020
29. Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera)
- Author
-
Elizabeth J. Duncan, Megan Leask, and Peter K. Dearden
- Subjects
0106 biological sciences ,H3K27me3 ,Genome, Insect ,RNA-Seq ,honeybee ,010603 evolutionary biology ,01 natural sciences ,Genome ,phenotypic plasticity ,gene cluster ,genomic regulatory domain ,03 medical and health sciences ,Gene cluster ,Genetics ,Animals ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Discoveries ,030304 developmental biology ,0303 health sciences ,Phenotypic plasticity ,biology ,Receptors, Notch ,Ovary ,reproductive constraint ,Histone-Lysine N-Methyltransferase ,Bees ,Phenotype ,Adaptation, Physiological ,ChIP-seq ,Histone ,evolution of gene expression ,Evolutionary biology ,biology.protein ,Insect Proteins ,Female ,sense organs ,Adaptation ,RNA-seq ,Apis mellifera ,polycomb - Abstract
Phenotypic plasticity, the ability of an organism to alter its phenotype in response to an environmental cue, facilitates rapid adaptation to changing environments. Plastic changes in morphology and behavior are underpinned by widespread gene expression changes. However, it is unknown if, or how, genomes are structured to ensure these robust responses. Here, we use repression of honeybee worker ovaries as a model of plasticity. We show that the honeybee genome is structured with respect to plasticity; genes that respond to an environmental trigger are colocated in the honeybee genome in a series of gene clusters, many of which have been assembled in the last 80 My during the evolution of the Apidae. These clusters are marked by histone modifications that prefigure the gene expression changes that occur as the ovary activates, suggesting that these genomic regions are poised to respond plastically. That the linear sequence of the honeybee genome is organized to coordinate widespread gene expression changes in response to environmental influences and that the chromatin organization in these regions is prefigured to respond to these influences is perhaps unexpected and has implications for other examples of plasticity in physiology, evolution, and human disease.
- Published
- 2020
30. Phenotypic Plasticity: What Has DNA Methylation Got to Do with It?
- Author
-
Elizabeth J. Duncan, Christopher B. Cunningham, and Peter K. Dearden
- Subjects
Insect Science - Abstract
How does one genome give rise to multiple, often markedly different, phenotypes in response to an environmental cue? This phenomenon, known as phenotypic plasticity, is common amongst plants and animals, but arguably the most striking examples are seen in insects. Well-known insect examples include seasonal morphs of butterfly wing patterns, sexual and asexual reproduction in aphids, and queen and worker castes of eusocial insects. Ultimately, we need to understand how phenotypic plasticity works at a mechanistic level; how do environmental signals alter gene expression, and how are changes in gene expression translated into novel morphology, physiology and behaviour? Understanding how plasticity works is of major interest in evolutionary-developmental biology and may have implications for understanding how insects respond to global change. It has been proposed that epigenetic mechanisms, specifically DNA methylation, are the key link between environmental cues and changes in gene expression. Here, we review the available evidence on the function of DNA methylation of insects, the possible role(s) for DNA methylation in phenotypic plasticity and also highlight key outstanding questions in this field as well as new experimental approaches to address these questions.
- Published
- 2022
31. Understanding ethnic differences in perceptions, attitudes, and behaviours: a study of domestic water use in Sydney
- Author
-
Liping Yan, Elizabeth J. Duncan, and Phil McManus
- Subjects
Sustainable development ,Value (ethics) ,media_common.quotation_subject ,05 social sciences ,Geography, Planning and Development ,0507 social and economic geography ,Ethnic group ,010501 environmental sciences ,01 natural sciences ,Social studies ,Water conservation ,Variation (linguistics) ,Cultural diversity ,Perception ,Psychology ,050703 geography ,Social psychology ,0105 earth and related environmental sciences ,Earth-Surface Processes ,media_common - Abstract
There is growing realisation among environmental and social studies researchers that people's decision-making about water use conforms to their internal norms and beliefs, which are developed in social and cultural contexts. Little research, however, has addressed the possible impacts that ethnic and cultural diversity may have on domestic water use and management. This paper presents the results of a study conducted in Sydney, with specific reference to questionnaire findings. Among respondents from different ethnic and cultural backgrounds, significant differences were observed in terms of perceptions, specific knowledge, attitudes, and self-reported behaviours in relation to water use and conservation. The disparities identified were not masking socio-demographic and economic characteristics but were the result of a series of constructs closely tied to ethnicity, including cultural value, environmental experience, language preference, and information access. As a factor explaining variation in the engagement of pro-conservation behaviour, ethnic status was found to be more useful than some socio-economic factors. The study highlights the importance of including ethnicity and cultural sensitivity issues in the decision-making process of environmental management.
- Published
- 2017
32. Understanding the dynamics of sustainability transitions: the Home Insulation Program
- Author
-
Lisa Smoleniec, Elizabeth J. Duncan, and Phil McManus
- Subjects
Government ,Economic growth ,020209 energy ,05 social sciences ,Geography, Planning and Development ,02 engineering and technology ,Political ecology ,Occupational safety and health ,Greenhouse gas ,0502 economics and business ,Sustainability ,Financial crisis ,0202 electrical engineering, electronic engineering, information engineering ,Economics ,050203 business & management ,Earth-Surface Processes ,Efficient energy use - Abstract
The Home Insulation Program (HIP) in Australia is an outstanding example of a contemporary attempt to intervene in a socio-technical regime. The program, implemented in 2009 under the then Australian Labor Party government led by Kevin Rudd, was targeted at stimulating the retrofit insulation industry. The objective was to both improve the energy efficiency of homes and thereby contribute to Australia’s emissions reduction targets by reducing greenhouse gas emissions and to stimulate the Australian economy at the time of the global financial crisis. The program ended early following a number of economic issues and health and safety concerns. Despite previous investigation into the HIP reviewing its design and implementation, the focus has been on economic issues and health and safety concerns. To date there has been no investigation of the HIP as a sustainability transition. This article integrates socio-technical transition theory (STTT) and political ecology (PE) approaches to analyse the HIP an...
- Published
- 2017
33. Urban Sustainability Indicators: how do Australian city decision makers perceive and use global reporting standards?
- Author
-
Derui Deng, Shiyao Liu, Elizabeth J. Duncan, Phil McManus, and Lawrence Wallis
- Subjects
business.industry ,Geography, Planning and Development ,Environmental resource management ,0211 other engineering and technologies ,021107 urban & regional planning ,02 engineering and technology ,Benchmarking ,010501 environmental sciences ,01 natural sciences ,Variety (cybernetics) ,Sustainable city ,Local government ,Sustainability ,Metric (unit) ,Business ,Adaptation (computer science) ,Set (psychology) ,Environmental planning ,0105 earth and related environmental sciences ,Earth-Surface Processes - Abstract
The introduction in 2014 of the first globally standardised sustainability metric for cities, ISO 37120, transformed the concept of scalability for sustainable city indicators. Our study uses original research involving producers and consumers of urban sustainability indicators (USIs), including ISO 37120, to review the current use of sustainability indicators (SIs) in Sydney and ascertain the use-value of internationally standardised USIs as perceived by professionals in the field. Our findings show that managers of cities use SIs in a variety of ways, yet links between SIs and organisational decision making are often weak. The cost of adaptation to a new indicator set may be prohibitive, especially for smaller city governments. Larger cities are seen to benefit more from international exposure and comparison. Highlighting ISO 37120 should be valued for the opportunity it presents for comparative learning regarding the nature of a sustainable city rather than its benchmarking potential. This arti...
- Published
- 2017
34. Ancestral hymenopteran queen pheromones do not share the broad phylogenetic repressive effects of honeybee queen mandibular pheromone
- Author
-
Elizabeth J. Duncan, Mackenzie Lovegrove, and Peter K. Dearden
- Subjects
0106 biological sciences ,0301 basic medicine ,Queen mandibular pheromone ,Physiology ,01 natural sciences ,Pheromones ,03 medical and health sciences ,Oogenesis ,Phylogenetics ,Alkanes ,Melanogaster ,Animals ,biology ,Reproduction ,Bees ,biology.organism_classification ,Eusociality ,010602 entomology ,030104 developmental biology ,Drosophila melanogaster ,Evolutionary biology ,Insect Science ,Sex pheromone ,Queen (butterfly) ,Female ,Social evolution - Abstract
Queen pheromones effect the reproductive division of labour, a defining feature of eusociality. Reproductive division of labour ensures that one, or a small number of, females are responsible for the majority of reproduction within a colony. Much work on the evolution and function of these pheromones has focussed on Queen Mandibular Pheromone (QMP) which is produced by the Western or European honeybee (Apis mellifera). QMP has phylogenetically broad effects, repressing reproduction in a variety of arthropods, including those distantly related to the honeybee such as the fruit fly Drosophila melanogaster. QMP is highly derived and has little chemical similarity to the majority of hymenopteran queen pheromones which are derived from cuticular hydrocarbons. This raises the question of whether the phylogenetically widespread repression of reproduction by QMP also occurs with more basal saturated hydrocarbon-based queen-pheromones. Using D. melanogaster we show that saturated hydrocarbons, are incapable of repressing reproduction, unlike QMP. We also show no interaction between the four saturated hydrocarbons tested or between the saturated hydrocarbons and QMP, implying that there is no conservation in the mechanism of detection or action between these compounds. We propose that the phylogenetically broad reproductive repression seen in response to QMP is not a feature of all queen pheromones, but unique to QMP itself, which has implications for our understanding of how queen pheromones act and evolve.
- Published
- 2019
35. Including health impacts in environmental impact assessments for three Australian coal-mining projects: a documentary analysis
- Author
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Emily Riley, Francesca Viliani, Tracy Pham, Ruth Colagiuri, Phil McManus, Patrick Harris, Elizabeth J. Duncan, Angus Dawson, Peter Sainsbury, and Yolande Stone
- Subjects
Government ,Health (social science) ,Health Equity ,business.industry ,Public Health, Environmental and Occupational Health ,Coal mining ,Equity (finance) ,010501 environmental sciences ,Environment ,01 natural sciences ,Coal Mining ,03 medical and health sciences ,Environmental impact statement ,0302 clinical medicine ,Content analysis ,Intergenerational equity ,Humans ,Environmental impact assessment ,030212 general & internal medicine ,Business ,Health Impact Assessment ,New South Wales ,Environmental planning ,Inclusion (education) ,0105 earth and related environmental sciences - Abstract
Notwithstanding the historical benefits of coal in aiding human and economic development, the negative health and environmental impacts of coal extraction and processing are of increasing concern. Environmental impact assessments (EIAs) are a regulated policy mechanism that can be used to predict and consider the health impacts of mining projects to determine if consent is given. The ways in which health is considered within EIA is unclear. This research investigated ‘How and to what extent are health, well-being and equity issues considered in Environmental Impact Assessments (EIAs) of major coal mining projects in New South Wales, Australia’. To this end we developed and applied a comprehensive coding framework designed to interrogate the publicly available environmental impact statements (EISs) of three mines in New South Wales (NSW), Australia, for their inclusion of health, well-being and equity issues. Analysis of the three EISs demonstrates that: the possible impacts of each mine on health and well-being were narrowly and inadequately considered; when health and well-being were considered there was a failure to assess the possible impacts specific to the particular mine and the communities potentially affected; the cumulative impacts on human health of multiple mines in the same geographical area were almost completely ignored; the discussions of intragenerational and intergenerational equity did not demonstrate a sound understanding of equity and, it is essential that governments’ requirements for the EIA include detailed analysis of the health, well-being, equity and cumulative impacts specific to the proposed mine and relevant communities.
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- 2019
36. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome
- Author
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Shwetha C. Murali, Hsiao-ling Lu, Siegfried Roth, Huyen Dinh, Peter K. Dearden, Barbara M. I. Vreede, M. Emília Santos, Evgeny M. Zdobnov, Viera Kovacova, Christopher J. Holmes, Stefano Colella, Yuichiro Suzuki, Tamsin E. M. Jones, Chun-che Chang, Stefan Koelzer, Jeffery W. Jones, Essia Sghaier, Thorsten Horn, Richard A. Gibbs, Mackenzie Lovegrove, Panagiotis Ioannidis, Lucila Traverso, Subba Reddy Palli, Megan L. Porter, Olivia Tidswell, Peter Nagui Refki, Neta Ginzburg, Rolando Rivera-Pomar, Sandra L. Lee, Chris Jacobs, Cassandra G. Extavour, Jan Seibert, Amanda Dolan, David Armisén, Jayendra Nath Shukla, Kristen A. Panfilio, Christopher P. Childers, Matthew T. Weirauch, Daniel S.T. Hughes, Jiaxin Qu, Kim C. Worley, Hugh M. Robertson, Monica Munoz-Torres, Markus Friedrich, Emily C. Jennings, Elizabeth J. Duncan, Andrew G. Cridge, Hsu Chao, J. Spencer Johnston, Maurijn van der Zee, Mei-Ju May Chen, John H. Werren, Abderrahman Khila, Shannon Dugan, Stephen Richards, Lena Sachs, Joshua B. Benoit, Antonin J.J. Crumière, Nicolas Parisot, Megan Leask, Yen-Ta Chen, Harshavardhan Doddapaneni, Gérard Febvay, Donna M. Muzny, Ariel D. Chipman, Rose Richter, Robert M. Waterhouse, Leslie Pick, Monica F. Poelchau, Patricia J. Moore, Chloé Suzanne Berger, Richard J. Stancliffe, Yi Min Hsiao, Séverine Viala, Chien-Yueh Lee, Yi Han, Iris M. Vargas Jentzsch, Elise M. Didion, Deniz F. Erezyilmaz, Yong Lu, Andrew J. Rosendale, Peter Heger, Patrice Baa-Puyoulet, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), University of Illinois [Chicago] (UIC), University of Illinois System, Department of Biology, Georgetown University, Université de Lausanne (UNIL), Cincinnati Children's Hospital Medical Center, Biochemistry Department, University of Otago [Dunedin, Nouvelle-Zélande], Human Genome Sequencing Center, Baylor College of Medicine, Baylor College of Medicine (BCM), Baylor University-Baylor University, University of Edinburgh, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Entomology [Lexington], University of Kentucky, Cologne Biocenter, Institute of Developmental Biology, Institute of Developmental Biology, University of Basel (Unibas), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Human Genome Sequencing Center [Houston] (HGSC), Department of Genetic Medicine and Development [Geneva], Université de Genève (UNIGE), United States Department of Health & Human Services National Institutes of Health (NIH) - USA [U54 HG003273], German Research Foundation (DFG) [PA 2044/1 1 SFB 680], Swiss National Science Foundation (SNSF) [31003A_143936, PP00P3_170664], European Research Council grant ERC-CoG [616346], German Research Foundation (DFG) [SFB 680], National Science Foundation (NSF) [US NSF DEB1257053], United States Department of Health & Human Services National Institutes of Health (NIH) - USA [5R01GM080203, 5R01HG004483, R01GM113230], United States Department of Energy (DOE) [DE-AC02-05CH11231], École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Georgetown University [Washington] (GU), Université de Lausanne = University of Lausanne (UNIL), University of Kentucky (UK), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Genève = University of Geneva (UNIGE), Panfilio, Kristen A [0000-0002-6417-251X], Vargas Jentzsch, Iris M [0000-0003-4527-1560], Benoit, Joshua B [0000-0002-4018-3513], Erezyilmaz, Deniz [0000-0001-8416-8561], Suzuki, Yuichiro [0000-0002-0957-3564], Colella, Stefano [0000-0003-3139-6055], Poelchau, Monica F [0000-0002-4584-6056], Waterhouse, Robert M [0000-0003-4199-9052], Ioannidis, Panagiotis [0000-0003-0939-6745], Weirauch, Matthew T [0000-0001-7977-9122], Werren, John H [0000-0001-9353-2070], Jacobs, Chris GC [0000-0002-3128-2288], Duncan, Elizabeth J [0000-0002-1841-504X], Vreede, Barbara MI [0000-0002-5023-4601], Chang, Chun-Che [0000-0002-3586-1607], Chen, Mei-Ju M [0000-0001-7768-8905], Chen, Yen-Ta [0000-0002-4570-6061], Childers, Christopher P [0000-0002-1253-5550], Chipman, Ariel D [0000-0001-6696-840X], Cridge, Andrew G [0000-0002-1399-5188], Crumière, Antonin JJ [0000-0003-2214-2993], Dearden, Peter K [0000-0001-7790-9675], Didion, Elise M [0000-0002-4987-8901], Dinh, Huyen [0000-0003-0336-0362], Doddapaneni, Harsha Vardhan [0000-0002-2433-633X], Dugan, Shannon [0000-0003-1482-816X], Extavour, Cassandra G [0000-0003-2922-5855], Febvay, Gérard [0000-0002-0654-2340], Friedrich, Markus [0000-0002-5622-7920], Han, Yi [0000-0001-7605-8979], Holmes, Christopher J [0000-0001-9612-366X], Horn, Thorsten [0000-0001-8181-939X], Hsiao, Yi-Min [0000-0002-1817-0302], Jennings, Emily C [0000-0002-7687-5319], Johnston, J Spencer [0000-0003-4792-2945], Jones, Tamsin E [0000-0002-0027-0858], Khila, Abderrahman [0000-0003-0908-483X], Kovacova, Viera [0000-0003-4581-4254], Lee, Chien-Yueh [0000-0002-4304-974X], Lu, Hsiao-Ling [0000-0002-4029-6470], Moore, Patricia J [0000-0001-9802-7217], Munoz-Torres, Monica C [0000-0001-8430-6039], Muzny, Donna M [0000-0002-3055-0359], Palli, Subba R [0000-0002-0873-3247], Parisot, Nicolas [0000-0001-5217-8415], Pick, Leslie [0000-0002-4505-5107], Porter, Megan L [0000-0001-7985-2887], Qu, Jiaxin [0000-0002-1122-9391], Rivera-Pomar, Rolando [0000-0002-7720-7064], Rosendale, Andrew J [0000-0002-2463-8856], Roth, Siegfried [0000-0001-5772-3558], Shukla, Jayendra N [0000-0003-1589-1929], Stancliffe, Richard J [0000-0002-6972-9655], van der Zee, Maurijn [0000-0002-8728-8646], Worley, Kim C [0000-0002-0282-1000], Richards, Stephen [0000-0001-8959-5466], and Apollo - University of Cambridge Repository
- Subjects
gene family evolution ,Lineage (evolution) ,[SDV]Life Sciences [q-bio] ,Genome, Insect ,Gene Transfer ,Gene Dosage ,Insect ,Genome ,purl.org/becyt/ford/1 [https] ,0302 clinical medicine ,CYS2-HIS2 Zinc Fingers ,phytophagy ,ddc:576.5 ,lcsh:QH301-705.5 ,media_common ,[SDV.EE]Life Sciences [q-bio]/Ecology, environment ,0303 health sciences ,biology ,Large milkweed bug ,Ecology ,Pigmentation ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,Genes, Homeobox ,Biological Sciences ,Lygaeidae ,Hemiptera ,séquence du génome ,Smell ,evolution of development ,TRANSCRIPTION FACTORS ,puceron ,Biotechnology ,lcsh:QH426-470 ,Gene Transfer, Horizontal ,ddc:025.063/570 ,Evolution ,Bioinformatics ,media_common.quotation_subject ,1.1 Normal biological development and functioning ,Transcription Factors/genetics ,Zoology ,Amino Acid Sequence ,Animals ,Evolution, Molecular ,Feeding Behavior ,Gene Expression Profiling ,Hemiptera/genetics ,Hemiptera/growth & development ,Hemiptera/metabolism ,Pigmentation/genetics ,Evolution of development ,Gene family evolution ,Gene structure ,Lateral gene transfer ,Phytophagy ,RNAi ,Transcription factors ,GENE FAMILY EVOLUTION ,Genomics ,Biotechnologies ,LATERAL GENE TRANSFER ,Horizontal ,03 medical and health sciences ,Molecular evolution ,Underpinning research ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Information and Computing Sciences ,transcription factors ,RNAI ,Genetics ,Homeobox ,GENE STRUCTURE ,purl.org/becyt/ford/1.6 [https] ,SB ,Genome size ,Ciencias Exactas ,030304 developmental biology ,Whole genome sequencing ,QL ,QH ,Research ,gene structure ,lateral gene transfer ,Human Genome ,fungi ,Molecular ,biology.organism_classification ,Hemiptera/genetics/growth & development/metabolism ,diversité des populations ,lcsh:Genetics ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,PHYTOPHAGY ,lcsh:Biology (General) ,Genes ,Animal ecology ,Evolutionary biology ,EVOLUTION OF DEVELOPMENT ,Evolutionary developmental biology ,030217 neurology & neurosurgery ,Environmental Sciences - Abstract
Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. Conclusions: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes., La lista completa de autores puede verse en el archivo asociado., Facultad de Ciencias Exactas, Centro Regional de Estudios Genómicos
- Published
- 2019
37. Evolution of the Torso activation cassette, a pathway required for terminal patterning and moulting
- Author
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John Skelly, Elizabeth J. Duncan, Peter K. Dearden, and Charlotte Pushparajan
- Subjects
0106 biological sciences ,0301 basic medicine ,Genome evolution ,Insecta ,Genome, Insect ,Ligands ,01 natural sciences ,Genome ,03 medical and health sciences ,Genetics ,Animals ,Prothoracicotropic hormone ,Molecular Biology ,Gene ,Body Patterning ,biology ,Gene Expression Regulation, Developmental ,biology.organism_classification ,Cell biology ,010602 entomology ,030104 developmental biology ,Insect Science ,Ecdysis ,Insect Hormones ,Insect Proteins ,Arthropod ,Moulting ,Holometabola - Abstract
Embryonic terminal patterning and moulting are critical developmental processes in insects. In Drosophila and Tribolium both of these processes are regulated by the Torso‐activation cassette (TAC). The TAC consists of a common receptor, Torso, ligands Trunk and prothoracicotropic hormone (PTTH), and the spatially restricted protein Torso‐like, with combinations of these elements acting mechanistically to activate the receptor in different developmental contexts. In order to trace the evolutionary history of the TAC we determined the presence or absence of TAC components in the genomes of arthropods. Our analyses reveal that Torso, Trunk and PTTH are evolutionarily labile components of the TAC with multiple individual or combined losses occurring in the arthropod lineages leading to and within the insects. These losses are often correlated, with both ligands and receptor missing from the genome of the same species. We determine that the PTTH gene evolved in the common ancestor of Hemiptera and Holometabola, and is missing from the genomes of a number of species with experimentally demonstrated PTTH activity, implying another molecule may be involved in ecdysis in these species. In contrast, the torso‐like gene is a common component of pancrustacean genomes.
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- 2018
38. The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water
- Author
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Andrew G. Cridge, Arjuna Rajakumar, Emily C. Jennings, Yi Han, Cédric Finet, Elizabeth J. Duncan, Hsu Chao, Richard A. Gibbs, Li Mei Chiang, Seung-Joon Ahn, Abderrahman Khila, Joshua B. Benoit, Chris Jacobs, Sandra L. Lee, Kim C. Worley, Antonin J.J. Crumière, Markus Friedrich, Séverine Viala, Rajendhran Rajakumar, Andrew J. Rosendale, Harshavardhan Doddapaneni, Maryna P. Lesoway, Travis Chen, Aidamalia Vargas Lowman, Alys M. Cheatle Jarvela, Mackenzie Lovegrove, Daniel S.T. Hughes, Jeffery W. Jones, Shwetha C. Murali, Christopher P. Childers, Donna M. Muzny, Monica Munoz-Torres, Iris M. Vargas Jentzsch, Brenda Oppert, Huyen Dinh, David Armisén, Marie-Julie Favé, Elise M. Didion, Stephen Richards, François Bonneton, William Toubiana, Elena N. Elpidina, Amélie Decaras, Peter N Refki, Monica F. Poelchau, Shannon Dugan, Angelica Lillico-Ouachour, Maria Emilia Santos, Kristen A. Panfilio, Ehab Abouheif, Hugh M. Robertson, Maurijn van der Zee, Alexander G. Martynov, Jiaxin Qu, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, Georgetown University [Washington] (GU), Human Genome Sequencing Center, Baylor College of Medicine, Baylor College of Medicine (BCM), Baylor University-Baylor University, Human Genome Sequencing Center [Houston] (HGSC), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL), Reproduction et développement des plantes (RDP), Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), École pratique des hautes études (EPHE), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Apollo - University of Cambridge Repository
- Subjects
0106 biological sciences ,Genome evolution ,lcsh:QH426-470 ,Evolution ,lcsh:Biotechnology ,[SDV]Life Sciences [q-bio] ,Genomics ,Biology ,010603 evolutionary biology ,01 natural sciences ,Genome ,Evolution, Molecular ,Heteroptera ,03 medical and health sciences ,lcsh:TP248.13-248.65 ,Gene family ,Animals ,14. Life underwater ,Epigenetics ,Adaptation ,Gene ,QH426 ,Phylogeny ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,0303 health sciences ,QL ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,Water striders ,Adaptation, Physiological ,lcsh:Genetics ,Phenotype ,Evolutionary biology ,Genome sequence ,Insect Proteins ,Evolutionary ecology ,Water surface locomotion ,Research Article - Abstract
Background Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. Results Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. Conclusions Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders. Electronic supplementary material The online version of this article (10.1186/s12864-018-5163-2) contains supplementary material, which is available to authorized users.
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- 2018
39. A Raster-Based Subdividing Indicator to Map Urban Heat Vulnerability: A Case Study in Sydney, Australia
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Wei Zhang, Elizabeth J. Duncan, and Phil McManus
- Subjects
demography ,Hot Temperature ,010504 meteorology & atmospheric sciences ,Urban Population ,Computer science ,Health, Toxicology and Mutagenesis ,Vulnerability ,Geographic Mapping ,lcsh:Medicine ,010501 environmental sciences ,01 natural sciences ,Article ,Unit (housing) ,heat vulnerability ,Humans ,Urban heat island ,Cities ,mapping ,Sydney ,Spatial analysis ,0105 earth and related environmental sciences ,Adaptive capacity ,Pixel ,Comparability ,lcsh:R ,public health ,Public Health, Environmental and Occupational Health ,Extreme Heat ,computer.file_format ,indicators ,Raster graphics ,New South Wales ,computer ,Cartography - Abstract
Assessing and mapping urban heat vulnerability has developed significantly over the past decade. Many studies have mapped urban heat vulnerability with a census unit-based general indicator (CGI). However, this kind of indicator has many problems, such as inaccurate assessment results and lacking comparability among different studies. This paper seeks to address this research gap and proposes a raster-based subdividing indicator to map urban heat vulnerability. We created a raster-based subdividing indicator (RSI) to map urban heat vulnerability from 3 aspects: exposure, sensitivity and adaptive capacity. We applied and compared it with a raster-based general indicator (RGI) and a census unit-based general indicator (CGI) in Sydney, Australia. Spatial statistics and analysis were used to investigate the performance among those three indicators. The results indicate that: (1) compared with the RSI framework, 67.54% of very high heat vulnerability pixels were ignored in the RGI framework, and up to 83.63% of very high heat vulnerability pixels were ignored in the CGI framework, (2) Compared with the previous CGI framework, a RSI framework has many advantages. These include more accurate results, more flexible model structure, and higher comparability among different studies. This study recommends using a RSI framework to map urban heat vulnerability in the future.
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- 2018
- Full Text
- View/download PDF
40. On Deadly Tides : A Penny Brannigan Mystery
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Elizabeth J. Duncan and Elizabeth J. Duncan
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- Cozy mysteries, Detective and mystery fiction, Fiction, Mystery fiction, Brannigan, Penny (Fictitious character)--Fiction, Murder--Investigation--Wales--Fiction, Journalists--Crimes against--Fiction, New Zealanders--Wales--Fiction
- Abstract
With a picturesque black and white lighthouse, pebble beaches and stunning views of sea and mountains, the island of Anglesey off the coast of North Wales is the perfect place for an idyllic mid-summer painting holiday.And watercolour artist, businesswoman, and amateur sleuth Penny Brannigan is enjoying the retreat enormously - until she discovers the body of a New Zealand journalist on a secluded beach just as the tide is going out, threatening to take the body with it. The post mortem reveals the victim died from injuries'consistent with a fall from a great height,'and the death is ruled accidental. But Penny thinks there's more to the story. Curious how the victim came to such an untimely end at this most inhospitable spot, she uncovers a link to a mysterious disappearance several years earlier. And as her holiday romance with a wildlife photographer turns to love, she learns some truths about herself, too, that surprise her. As the winds of change blow through Penny's own life, she sets sail on a friendly tide for a future she never dreamed possible, in a beautiful place she never imagined
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- 2020
41. The fundamental basis of a life: a review of ‘The Biology of Reproduction’
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Elizabeth J. Duncan
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Multicellular organism ,Form and function ,Anthropology ,Reproduction (economics) ,Animal Science and Zoology ,Biology ,human activities ,Developmental Biology - Abstract
All life starts with a single cell. In some species, this cell divides and give rise to complex multicellular organisms and the diversity of form and function that we see in the world around us. Bu...
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- 2021
42. Remembering the Dead : A Penny Brannigan Mystery
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Elizabeth J. Duncan and Elizabeth J. Duncan
- Abstract
In award-winning author Elizabeth J. Duncan's tenth Penny Brannigan mystery set in North Wales, Canadian amateur sleuth Penny Brannigan attends a dinner party at a posh country house--where a historic chair disappears and a waiter is murdered.Artist and spa owner Penny Brannigan has been asked to organize a formal dinner to mark the centenary of the armistice that ended World War One. After dinner, the guests adjourn to the library for a private exhibition of the Black Chair, a precious piece of Welsh literary history awarded in 1917 to poet Hedd Wyn. But to the guests'shock, the newly restored bardic chair is missing. And then Penny discovers the rain-soaked body of a waiter.When Penny learns that the victim was the nephew of one of her employees, she is determined to find the killer. Meanwhile, the local police search for the Black Chair. The Prince of Wales is due to open an exhibit featuring the chair in three weeks, so time is not on their side. A visit to a nursing home to consult an ex-thief convinces Penny that the theft of the Black Chair and the waiter's murder are connected. She rushes to Dublin to consult a disagreeable antiquarian, who might know more than he lets on, and during the course of her investigation confronts a gaggle of suspicious travelers and an eccentric herbalist who seems to have something to hide. Can Penny find the chair and the culprit before she is laid to rest in the green grass of Wales?
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- 2019
43. Striatal mRNA expression patterns underlying peak dose l-DOPA-induced dyskinesia in the 6-OHDA hemiparkinsonian rat
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Peter K. Dearden, Neil J. Gemmell, Louise C. Parr-Brownlie, Michael A. Black, L.M. Smith, Elizabeth J. Duncan, and John N. J. Reynolds
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Male ,0301 basic medicine ,Dyskinesia, Drug-Induced ,Levodopa ,Parkinson's disease ,Tyrosine 3-Monooxygenase ,Side effect ,Gene Expression ,Striatum ,Pharmacology ,Functional Laterality ,Antiparkinson Agents ,Benserazide ,Random Allocation ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Parkinsonian Disorders ,medicine ,Animals ,RNA, Messenger ,Rats, Wistar ,Oxidopamine ,Cytoskeleton ,business.industry ,General Neuroscience ,medicine.disease ,Corpus Striatum ,Abnormal involuntary movement ,nervous system diseases ,Drug Combinations ,030104 developmental biology ,chemistry ,Dyskinesia ,medicine.symptom ,business ,030217 neurology & neurosurgery ,medicine.drug - Abstract
L-DOPA is the primary pharmacological treatment for relief of the motor symptoms of Parkinson’s disease (PD). With prolonged treatment (⩾5 years) the majority of patients will develop abnormal involuntary movements as a result of L-DOPA treatment, known as L-DOPA-induced dyskinesia. Understanding the underlying mechanisms of dyskinesia is a crucial step toward developing treatments for this debilitating side effect. We used the 6-hydroxydopamine (6-OHDA) rat model of PD treated with a three-week dosing regimen of L-DOPA plus the dopa decarboxylase inhibitor benserazide (4 mg/kg and 7.5 mg/kg s.c., respectively) to induce dyskinesia in 50% of individuals. We then used RNA-seq to investigate the differences in mRNA expression in the striatum of dyskinetic animals, non-dyskinetic animals, and untreated parkinsonian controls at the peak of dyskinesia expression, 60 min after L-DOPA administration. Overall, 255 genes were differentially expressed; with significant differences in mRNA expression observed between all three groups. In dyskinetic animals 129 genes were more highly expressed and 14 less highly expressed when compared with non-dyskinetic and untreated parkinsonian controls. In L-DOPA treated animals 42 genes were more highly expressed and 95 less highly expressed when compared with untreated parkinsonian controls. Gene set cluster analysis revealed an increase in expression of genes associated with the cytoskeleton and phosphoproteins in dyskinetic animals compared with non-dyskinetic animals, which is consistent with recent studies documenting an increase in synapses in dyskinetic animals. These genes may be potential targets for drugs to ameliorate L-DOPA-induced dyskinesia or as an adjunct treatment to prevent their occurrence.
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- 2016
44. Social competition stimulates cognitive performance in a sex-specific manner
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James Rouse, Zak Mitchell, Laurin McDowall, Amanda Bretman, and Elizabeth J. Duncan
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Male ,0106 biological sciences ,Evolution ,media_common.quotation_subject ,010603 evolutionary biology ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Competition (biology) ,03 medical and health sciences ,Cognition ,Sex Factors ,Visual memory ,Memory ,Animals ,Effects of sleep deprivation on cognitive performance ,Mating ,Social Behavior ,Sperm competition ,030304 developmental biology ,General Environmental Science ,media_common ,0303 health sciences ,General Immunology and Microbiology ,Reproduction ,Social environment ,General Medicine ,Drosophila melanogaster ,Phenotype ,Female ,Olfactory Learning ,Sleep ,General Agricultural and Biological Sciences ,Psychology ,Cognitive psychology - Abstract
Social interactions are thought to be a critical driver in the evolution of cognitive ability. Cooperative interactions, such as pair bonding, rather than competitive interactions have been largely implicated in the evolution of increased cognition. This is despite competition traditionally being a very strong driver of trait evolution. Males of many species track changes in their social environment and alter their reproductive strategies in response to anticipated levels of competition. We predict this to be cognitively challenging. Using a Drosophila melanogaster model, we are able to distinguish between the effects of a competitive environment versus generic social contact by exposing flies to same-sex same-species competition versus different species partners, shown to present non-competitive contacts. Males increase olfactory learning/memory and visual memory after exposure to conspecific males only, a pattern echoed by increased expression of synaptic genes and an increased need for sleep. For females, largely not affected by mating competition, the opposite pattern was seen. The results indicate that specific social contacts dependent on sex, not simply generic social stimulation, may be an important evolutionary driver for cognitive ability in fruit flies.
- Published
- 2020
45. Much Ado About Murder : A Shakespeare in the Catskills Mystery
- Author
-
Elizabeth J. Duncan and Elizabeth J. Duncan
- Abstract
When a directorial debut turns deadly, it falls to costume designer Charlotte Fairfax to unmask the culprit in award-winning author Elizabeth J. Duncan's third Shakespeare in the Catskills mysteryCharlotte Fairfax has another murder on her hands as she prepares for the latest performance of the Catskills Shakespeare Theater Company, Much Ado About Nothing. The company's steady growth enables them to cast star British actress Audrey Ashley, who arrives on scene to play the lead role of Beatrice. But things immediately get more complicated when Audrey insists the company replace the current director with new, up and coming British director Edmund Albright.Edmund plans to change the popular romantic comedy, which alienates several people associated with the production. And the list of people he upsets only grows: the laid off former director, the hotel owner's secretary, and even Audrey herself. Just as Edmund's plans are about to come to fruition, his body is discovered on his sofa, holding a gun in his hand. His death is quickly ruled a suicide but Charlotte thinks otherwise. Why would Edmund, on the brink of greatness, kill himself? With a whole cast of characters to investigate, Charlotte is determined to unmask each one before it's final curtain call on the whole production.
- Published
- 2017
46. Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution
- Author
-
Ross N. Crowhurst, Neil J. Gemmell, Bernd Steinwender, Karen Meusemann, Mark I. Stevens, L.K. Tooman, Elizabeth J. Duncan, Richard D. Newcomb, Thomas R. Buckley, Chen Wu, Melissa D. Jordan, Sarah Bank, Peter K. Dearden, Paul P. Gardner, Kim Rutherford, Sefanie Grosser, Wu, Chen, Jordan, Melissa D, Newcomb, Richard D, Gemmell, Neil J, Bank, Sarah, Meusemann, Karen, Dearden, Peter K, Duncan, Elizabeth J, Grosser, Sefanie, Rutherford, Kim, Gardner, Paul P, Crowhurst, Ross N, Steinwender, Bernd, Tooman, Leah K, Stevens, Mark I, and Buckley, Thomas R
- Subjects
0106 biological sciences ,0301 basic medicine ,Retrotransposon ,01 natural sciences ,Genome ,chemoreceptors ,Phylogenomics ,Hox gene ,Phylogeny ,Genetics ,Chitinases ,Hexapoda ,Genomics ,Horizontal gene transfer ,Epigenetics ,hexapoda ,Biotechnology ,Research Article ,lcsh:QH426-470 ,Gene Transfer, Horizontal ,lcsh:Biotechnology ,Biology ,010603 evolutionary biology ,Methylation ,Evolution, Molecular ,Neanuridae ,03 medical and health sciences ,developmental biology ,Phylogenetics ,lcsh:TP248.13-248.65 ,Developmental biology ,Animals ,Gene ,Arthropods ,Genome assembly ,epigenetics ,Chemoreceptors ,Gene Expression Profiling ,Molecular Sequence Annotation ,DNA Methylation ,Sex Determination Processes ,Sex determination ,lcsh:Genetics ,030104 developmental biology ,genome assembly ,RNA - Abstract
Background The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events. Results Our genome assembly was ~375 Mbp in size with a scaffold N50 of ~230 Kbp and sequencing coverage of ~180×. DNA elements, LTRs and simple repeats and LINEs formed the largest components and SINEs were very rare. Phylogenomics (370,877 amino acids) placed H. duospinosa within the Neanuridae. We recovered orthologs of the conserved sex determination genes thought to play a role in sex determination. Analysis of CpG content suggested the absence of DNA methylation, and consistent with this we were unable to detect orthologs of the DNA methyltransferase enzymes. The small subunit rRNA gene contained a possible retrotransposon. The Hox gene complex was broken over two scaffolds. For chemosensory ability, at least 15 and 18 ionotropic glutamate and gustatory receptors were identified, respectively. However, we were unable to identify any odorant receptors or their obligate co-receptor Orco. Twenty-three chitinase-like genes were identified from the assembly. Members of this multigene family may play roles in the digestion of fungal cell walls, a common food source for these saproxylic organisms. We also detected 59 and 96 genes that blasted to bacteria and fungi, respectively, but were located on scaffolds that otherwise contained arthropod genes. Conclusions The genome of H. duospinosa contains some unusual features including a Hox complex broken over two scaffolds, in a different manner to other arthropod species, a lack of odorant receptor genes and an apparent lack of environmentally responsive DNA methylation, unlike many other arthropods. Our detection of candidate horizontal gene transfer candidates confirms that this phenomenon is occurring across Collembola. These findings allow us to narrow down the regions of the arthropod phylogeny where key innovations have occurred that have facilitated the evolutionary success of Hexapoda. Electronic supplementary material The online version of this article (10.1186/s12864-017-4197-1) contains supplementary material, which is available to authorized users.
- Published
- 2017
47. Identification of reference genes for RT-qPCR in ovine mammary tissue during late pregnancy and lactation and in response to maternal nutritional programming
- Author
-
Paul R. Kenyon, Paten Am, S. W. Peterson, Elizabeth J. Duncan, Peter K. Dearden, Hugh T. Blair, and Sarah J. Pain
- Subjects
Physiology ,Offspring ,Mammary gland ,Gene Expression ,Biology ,Andrology ,Mammary Glands, Animal ,Pregnancy ,Lactation ,Reference genes ,Gene expression ,Genetics ,medicine ,Animals ,Sheep, Domestic ,Regulation of gene expression ,Sheep ,Models, Genetic ,Reverse Transcriptase Polymerase Chain Reaction ,Gene Expression Profiling ,Maternal Nutritional Physiological Phenomena ,DNA Methylation ,Gene expression profiling ,medicine.anatomical_structure ,Gene Expression Regulation ,DNA methylation ,Pregnancy, Animal ,Female - Abstract
The mammary gland is a complex tissue consisting of multiple cell types which, over the lifetime of an animal, go through repeated cycles of development associated with pregnancy, lactation and involution. The mammary gland is also known to be sensitive to maternal programming by environmental stimuli such as nutrition. The molecular basis of these adaptations is of significant interest, but requires robust methods to measure gene expression. Reverse-transcription quantitative PCR (RT-qPCR) is commonly used to measure gene expression, and is currently the method of choice for validating genome-wide expression studies. RT-qPCR requires the selection of reference genes that are stably expressed over physiological states and treatments. In this study we identify suitable reference genes to normalize RT-qPCR data for the ovine mammary gland in two physiological states; late pregnancy and lactation. Biopsies were collected from offspring of ewes that had been subjected to different nutritional paradigms during pregnancy to examine effects of maternal programming on the mammary gland of the offspring. We evaluated eight candidate reference genes and found that two reference genes ( PRPF3 and CUL1) are required for normalising RT-qPCR data from pooled RNA samples, but five reference genes are required for analyzing gene expression in individual animals ( SENP2, EIF6, MRPL39, ATP1A1, CUL1). Using these stable reference genes, we showed that TET1, a key regulator of DNA methylation, is responsive to maternal programming and physiological state. The identification of these novel reference genes will be of utility to future studies of gene expression in the ovine mammary gland.
- Published
- 2014
48. Capturing embryonic development from metamorphosis: how did the terminal patterning signalling pathway of Drosophila evolve?
- Author
-
Travis K. Johnson, Elizabeth J. Duncan, Peter K. Dearden, Coral G. Warr, and James C. Whisstock
- Subjects
medicine.medical_specialty ,integumentary system ,Context (language use) ,Torso ,Biology ,equipment and supplies ,biology.organism_classification ,Prothoracic gland ,Hedgehog signaling pathway ,Receptor tyrosine kinase ,Cell biology ,body regions ,chemistry.chemical_compound ,medicine.anatomical_structure ,Endocrinology ,chemistry ,Insect Science ,Internal medicine ,medicine ,biology.protein ,Prothoracicotropic hormone ,Drosophila melanogaster ,Ecology, Evolution, Behavior and Systematics ,Ecdysone - Abstract
The Torso receptor tyrosine kinase has two crucial roles in Drosophila melanogaster development. One is in the control of insect moulting, which is regulated by the neuropeptide hormone PTTH (prothoracicotropic hormone). PTTH activates ERK signalling via Torso in the prothoracic gland to stimulate ecdysone secretion. Torso also has a role in control of one of the earliest events in embryogenesis in Drosophila; patterning of the embryonic termini. Here Torso is activated by a different, but related, peptide called Trunk. During terminal patterning another protein, Torso-like, has a key role in mediating activation of Torso by Trunk. Torso-like is also expressed in the prothoracic gland and null-mutants have defective developmental timing in Drosophila. This function, however, has been recently shown to be independent of Torso and PTTH. We refer to these proteins, Trunk, PTTH, Torso and Torso-like, as the Torso-activation module. Outside Drosophila we see that the genes encoding the Torso-activation module have a complex phylogenetic history, with different origins and multiple losses of components of this signalling pathway during arthropod evolution. This, together with expression and functional data in a range of insects, leads us to propose that the terminal patterning pathway in Drosophila and Tribolium arose through co-option of PTTH/Trunk and Torso, which has a role in developmental timing, into a new context, and that Torso-like was recruited specifically in the ovary to modulate the specificity of this pathway.
- Published
- 2014
49. Correction to: From genes to environment in shaping of an embryo: understanding embryonic-extraembryonic interactions at the BSDB autumn meeting in Oxford
- Author
-
Anna Ajduk and Elizabeth J. Duncan
- Subjects
0106 biological sciences ,0301 basic medicine ,Correction ,Embryo ,Biology ,010603 evolutionary biology ,01 natural sciences ,Embryonic stem cell ,Spelling ,03 medical and health sciences ,030104 developmental biology ,Institutional affiliation ,Evolutionary biology ,Genetics ,Gene ,Developmental biology ,Developmental Biology - Abstract
The authors of the article Ajduk & Duncan 2019 sincerely apologize for specifying the incorrect institutional affiliation for Professor Ali Brivanlou and also the incorrect spelling of Professor Brivanlou's surname in the text of the article.
- Published
- 2019
50. Ill Met By Murder : A Shakespeare in the Catskills Mystery
- Author
-
Elizabeth J. Duncan and Elizabeth J. Duncan
- Abstract
Ill Met by Murder, the second in Elizabeth J. Duncan's compelling mystery series, will satisfy every Shakespeare and mystery lover alikeIt's the most important night of the year for costume designer Charlotte Fairfax and the Catskills Shakespeare Theater Company—the annual fund raising performance at the country estate of the wealthy widow Paula Van Dusen. This year, the company will give a moonlight performance of A Midsummer Night's Dream as part of the wedding celebrations for Paula's daughter, Belinda, and her fiance Adrian. But then Hugh Hedley, family friend of the Van Dusens and Adrian's rival in the cutthroat world of high-end Manhattan real estate, is found murdered with a stolen prop from the play.Paula, desperate to keep her daughter's name of out of the paper, enlists Charlotte's help, despite the fact that Charlotte's already got her hands full amidst her costume design responsibilities and finding a home for the company's new theater school. But Charlotte nevertheless throws herself into an investigation of shady business deals, a missing dog, and long buried family secrets because'though she be but little, she is fierce!'
- Published
- 2016
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