scholarly journals Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses

2021 ◽  
Author(s):  
Jackie E Mahar ◽  
Maria Jenckel ◽  
Nina Huang ◽  
Elena Smertina ◽  
Edward C Holmes ◽  
...  
Keyword(s):  
Antigenic Variation ◽  
Major Capsid Protein ◽  
New South ◽  
Phylogenetic Analyses ◽  
Single Amino Acid ◽  
Structural Genes ◽  
South Wales ◽  
Competition Study ◽  
Single Amino Acid Change ◽  
Key Drivers

AbstractThe diversity of lagoviruses (Caliciviridae) in Australia has increased considerably. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the interactions between these lagovirus variants we monitored their geographical distribution and relative incidence over time through a landscape-scale competition study, and from this, revealed potential drivers of epidemiological fitness. Within three years of the arrival of GI.1bP-GI.2 (RHDV2) into Australia, we observed the emergence of two novel recombinant lagovirus variants, GI.4eP-GI.2 (4e-recombinant) in New South Wales and GI.4cP-GI.2 (4c-recombinant) in Victoria. Although both novel recombinants contain the non-structural genes from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the 4c-recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both new recombinant variants replaced the previous dominant parental RHDV2 in their respective geographical areas, despite sharing an identical or near-identical (i.e., single amino acid change) major capsid protein with the parental virus. This suggests that epidemiological fitness of these recombinants was not driven by antigenic variation in the capsid, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the GI4.e recombination event in early to mid-2015, while the five GI.4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a two-year period highlights an unprecedented frequency of these events, detectable only due to intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.

scholarly journals Frequent Intergenotypic Recombination Between the Non-Structural and Structural Genes is a Major Driver of Epidemiological Fitness in Caliciviruses

2021 ◽  
Author(s):  
Jackie E Mahar ◽  
Maria Jenckel ◽  
Nina Huang ◽  
Elena Smertina ◽  
Edward C Holmes ◽  
...  
Keyword(s):  
Antigenic Variation ◽  
Phylogenetic Analyses ◽  
Single Amino Acid ◽  
Structural Genes ◽  
Continental Scale ◽  
South Wales ◽  
Competition Study ◽  
Rabbit Haemorrhagic Disease ◽  
Single Amino Acid Change ◽  
Haemorrhagic Disease

Abstract The diversity of lagoviruses (Caliciviridae) in Australia has increased considerably in recent years. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the evolutionary interactions among these lagovirus variants we monitored their geographical distribution and relative incidence over time in a continental-scale competition study. Within three years of the incursion of rabbit haemorrhagic disease virus 2 (RHDV2, denoted genotype GI.1bP-GI.2 [polymerase genotype]P-[capsid genotype]) into Australia, two novel recombinant lagovirus variants emerged: RHDV2-4e (genotype GI.4eP-GI.2) in New South Wales and RHDV2-4c (genotype GI.4cP-GI.2) in Victoria. Although both novel recombinants contain non-structural genes related to those from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that the determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the RHDV2-4c recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both the new RHDV2-4e and 4c recombinant variants replaced the previous dominant parental RHDV2 (genotype GI.1bP-GI.2) in their respective geographical areas, despite sharing an identical or near-identical (i.e. single amino acid change) VP60 major capsid protein with the parental virus. This suggests that the observed replacement by these recombinants was not driven by antigenic variation in VP60, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the RHDV2-4e recombination event in early to mid-2015, while the five RHDV2-4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a two-year period highlights the high frequency of these events, detectable only through intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.

Co-occurrence of two tadpole shrimp, Triops cf. australiensis (Branchiopoda:Notostraca), lineages in middle Paroo, north-western New South Wales, with the first record of Triops hermaphrodites for the Australian continent

2009 ◽  
Vol 57 (2) ◽  
pp. 77 ◽  
Author(s):  
Gopal Murugan ◽  
Hortencia Obregón-Barboza ◽  
Alejandro M. Maeda-Martínez ◽  
Brian V. Timms
Keyword(s):  
New South ◽  
Phylogenetic Analyses ◽  
Molecular Genetic ◽  
New South Wales ◽  
First Record ◽  
Testicular Tissue ◽  
12S Rrna ◽  
South Wales ◽  
Australian Continent ◽  
North Western

The only species of the genus Triops in Australia, T. australiensis, is found to reproduce by gonochorism. Morphological and reproductive data and molecular analyses of fragments of mitochondrial genes 12S rRNA (12S) and cytochrome oxidase I (COI) indicate that a Triops population from the middle Paroo in north-western New South Wales is composed of two different entities, Triops cf. australiensis lineage A, and T. cf. australiensis lineage B. Gonad histology in individuals with ovisacs of lineage A revealed no evidence of testicular tissue; however, large testicular lobes were found in individuals with ovisacs of lineage B, indicating that they were anatomically hermaphrodites. This is the first record of Australian hermaphroditic Triops. For each lineage, a single haplotype of each gene was obtained. Molecular genetic distance and phylogenetic analyses confirmed the closer relationship and monophyly of the two lineages with T. australiensis (GenBank) when compared with Triops species from other continents. COI haplotypes of lineage A and lineage B differed by 7.7% from each other and differed by 10.2% and 9.6% from a published T. australiensis sequence, respectively. The 12S haplotypes of lineage A and lineage B differed by 3.3% from each other and differed by 2% and 2.5% from a published T. australiensis sequence, respectively. Our results suggest that the two co-occurring Triops lineages probably represent two species that are distinct from T. australiensis.

Phylogeography of the freshwater catfish Tandanus tandanus (Plotosidae): a model species to understand evolution of the eastern Australian freshwater fish fauna

2008 ◽  
Vol 59 (4) ◽  
pp. 351 ◽  
Author(s):  
Dean R. Jerry
Keyword(s):  
New South ◽  
Phylogenetic Analyses ◽  
New South Wales ◽  
Fish Fauna ◽  
Freshwater Fishes ◽  
Phylogeographic Structure ◽  
Biogeographic Patterns ◽  
South Wales ◽  
Eastern Australia ◽  
Australian Freshwater

The geologically complex eastern Australian coastal margin supports the highest taxonomic diversity of freshwater fishes on the continent. However, mechanisms leading to coastal biogeographic patterns are poorly understood. A 399-bp fragment of the hypervariable mtDNA control region was sequenced from populations of eel-tailed catfish (Tandanus tandanus) to determine their phylogeographic structure and to relate this to proposed biogeographic mechanisms and landform evolution. Genetic structure in Tandanus is complex, with haplotypes clustering into three lineages: a phylogenetically distant, northern Queensland clade that is probably a new species; a mid-northern New South Wales clade corresponding to the recently discovered ‘Bellinger’ Tandanus cryptic species; and a third ‘derived’ clade T. tandanus. Phylogenetic analyses suggest that eastern Australian Tandanus originally invaded freshwaters from the coast where volcanic activity in the north and increasing aridity from the Paleocene reduced inter-fluvial connections, causing genetic divergence of northern Queensland and mid-northern New South Wales populations. The haplotypes represented by Murray–Darling drainage T. tandanus were the most derived, indicating that this species originally evolved on the coast and subsequently colonised the Murray–Darling basin. Tandanus in eastern Australia is phylogenetically structured and possibly comprises three species in this region; a pattern potentially shared by other eastern Australian freshwater fishes.

Yarning up: Stories of challenges and success

2018 ◽  
Vol 62 (3) ◽  
pp. 266-275 ◽  
Author(s):  
Janet Mooney ◽  
Lyn Riley ◽  
Fabri Blacklock
Keyword(s):  
Social Life ◽  
New South ◽  
Culturally Appropriate ◽  
Women In Academia ◽  
Aboriginal Women ◽  
What Works ◽  
South Wales ◽  
Leadership Experiences ◽  
Key Drivers ◽  
Ways Of Being

This paper explores the lives of three New South Wales Aboriginal women, mothers, artists and academics. It will identify the women’s success in academia as demonstrated by their pathways to education, employment, job satisfaction, commitment and leadership experiences. In addition, the challenges they have faced, together with balancing family and community commitments and the importance and influence of mentors who assisted them on their pathway to success will be discussed. They employ Aboriginal methodologies that privilege Aboriginal ways of being, knowing and doing utilising a yarning methodology which is a culturally appropriate conversational process of sharing stories to develop knowledge and educate younger generations. In this way, they generate new knowledge on what works and why for Aboriginal women in academia, identifying historical pathways and platforms to success, revealing common significant influences in order to uncover key drivers of success and aspects of cultural and social life, which have enabled them as Aboriginal women to succeed.

scholarly journals A single amino acid switch converts the Sleeping Beauty transposase into an efficient unidirectional excisionase with utility in stem cell reprogramming

2019 ◽  
Vol 48 (1) ◽  
pp. 316-331 ◽  
Author(s):  
Lisa Kesselring ◽  
Csaba Miskey ◽  
Cecilia Zuliani ◽  
Irma Querques ◽  
Vladimir Kapitonov ◽  
...  
Keyword(s):  
Amino Acid ◽  
Signal Sequence ◽  
Phylogenetic Analyses ◽  
Sleeping Beauty ◽  
Single Amino Acid ◽  
Amino Acid Residues ◽  
Dna Transposition ◽  
Dead End ◽  
Single Amino Acid Change ◽  
Induced Pluripotent

Abstract The Sleeping Beauty (SB) transposon is an advanced tool for genetic engineering and a useful model to investigate cut-and-paste DNA transposition in vertebrate cells. Here, we identify novel SB transposase mutants that display efficient and canonical excision but practically unmeasurable genomic re-integration. Based on phylogenetic analyses, we establish compensating amino acid replacements that fully rescue the integration defect of these mutants, suggesting epistasis between these amino acid residues. We further show that the transposons excised by the exc+/int− transposase mutants form extrachromosomal circles that cannot undergo a further round of transposition, thereby representing dead-end products of the excision reaction. Finally, we demonstrate the utility of the exc+/int− transposase in cassette removal for the generation of reprogramming factor-free induced pluripotent stem cells. Lack of genomic integration and formation of transposon circles following excision is reminiscent of signal sequence removal during V(D)J recombination, and implies that cut-and-paste DNA transposition can be converted to a unidirectional process by a single amino acid change.

scholarly journals Looking Behind the Increase in Custodial Remand Populations

2013 ◽  
Vol 2 (2) ◽  
pp. 80-99 ◽  
Author(s):  
David Brown
Keyword(s):  
New South ◽  
Individual Case ◽  
Law Reform ◽  
South Wales ◽  
Wide Range ◽  
Commission Report ◽  
Key Drivers ◽  
The Individual

Numbers, rates and proportions of those remanded in custody have increased significantly in recent decades across a range of jurisdictions. In Australia they have doubled since the early 1980s, such that close to one in four prisoners is currently unconvicted. Taking NSW as a case study and drawing on the recent New South Wales Law Reform Commission Report on Bail (2012), this article will identify the key drivers of this increase in NSW, predominantly a form of legislative hyperactivity involving constant changes to the Bail Act 1978 (NSW), changes which remove or restrict the presumption in favour of bail for a wide range of offences. The article will then examine some of the conceptual, cultural and practice shifts underlying the increase. These include: a shift away from a conception of bail as a procedural issue predominantly concerned with securing the attendance of the accused at trial and the integrity of the trial, to the use of bail for crime prevention purposes; the diminishing force of the presumption of innocence; the framing of a false opposition between an individual interest in liberty and a public interest in safety; a shift from determination of the individual case by reference to its own particular circumstances to determination by its classification within pre-set legislative categories of offence types and previous convictions; a double jeopardy effect arising in relation to people with previous convictions for which they have already been punished; and an unacknowledged preventive detention effect arising from the increased emphasis on risk. Many of these conceptual shifts are apparent in the explosion in bail conditions and the KPI-driven policing of bail conditions and consequent rise in revocations, especially in relation to juveniles. The paper will conclude with a note on the NSW Government’s response to the NSW LRC Report in the form of a Bail Bill (2013) and brief speculation as to its likely effects.

scholarly journals Colletotrichum Species Causing Anthracnose of Citrus in Australia

2021 ◽  
Vol 7 (1) ◽  
pp. 47
Author(s):  
Weixia Wang ◽  
Dilani D. de Silva ◽  
Azin Moslemi ◽  
Jacqueline Edwards ◽  
Peter K. Ades ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
New South ◽  
Phylogenetic Analyses ◽  
New South Wales ◽  
Morphological Characters ◽  
Postharvest Disease ◽  
Colletotrichum Species ◽  
South Wales ◽  
Culture Characteristics ◽  
Colletotrichum Spp

Colletotrichum spp. are important pathogens of citrus that cause dieback of branches and postharvest disease. Globally, several species of Colletotrichum have been identified as causing anthracnose of citrus. One hundred and sixty-eight Colletotrichum isolates were collected from anthracnose symptoms on citrus stems, leaves, and fruit from Victoria, New South Wales, and Queensland, and from State herbaria in Australia. Colletotrichum australianum sp. nov., C. fructicola, C. gloeosporioides, C. karstii, C. siamense, and C. theobromicola were identified using multi-gene phylogenetic analyses based on seven genomic loci (ITS, gapdh, act, tub2, ApMat, gs, and chs-1) in the gloeosporioides complex and five genomic loci (ITS, tub2, act, chs-1, and his3) in the boninense complex, as well as morphological characters. Several isolates pathogenic to chili (Capsicum annuum), previously identified as C. queenslandicum, formed a clade with the citrus isolates described here as C. australianum sp. nov. The spore shape and culture characteristics of the chili and citrus isolates of C. australianum were similar and differed from those of C. queenslandicum. This is the first report of C. theobromicola isolated from citrus and the first detection of C. karstii and C. siamense associated with citrus anthracnose in Australia.

scholarly journals Phylogenetic revision of Backhousieae (Myrtaceae): Neogene divergence, a revised circumscription of Backhousia and two new species

2012 ◽  
Vol 25 (6) ◽  
pp. 404 ◽  
Author(s):  
Mark G. Harrington ◽  
Betsy R. Jackes ◽  
Matthew D. Barrett ◽  
Lyn A. Craven ◽  
Russell L. Barrett
Keyword(s):  
New Species ◽  
New South ◽  
Phylogenetic Analyses ◽  
Internal Transcribed Spacers ◽  
Molecular Dating ◽  
Undescribed Species ◽  
South Wales ◽  
Bayesian Relaxed Clock ◽  
Phylogenetic Revision ◽  
Relaxed Clock

Backhousieae is a small tribe of Myrtaceae composed of two genera (Backhousia and Choricarpia) endemic to Australia. Phylogenetic analyses (parsimony, maximum likelihood and Bayesian) were performed on a combined chloroplast (matK, trnH–psbA, trnC–psbM, trnL–F, rps16) and nuclear (internal transcribed spacers) dataset for all nine species of Backhousia, two species of Choricarpia and two undescribed species. Backhousieae is monophyletic; however, Choricarpia is embedded within Backhousia. In all analyses there were four strongly supported clades containing two to four taxa, with no support for relationships among clades, and the relationships of B. bancroftii and B. citriodora remain unresolved. Bayesian relaxed-clock molecular dating indicated that the Backhousieae has been potentially present in rainforest across Australia for more than 50 million years. The current distribution of Backhousia is inferred to be largely due to the contraction of Australian rainforest in the Neogene. New combinations in Backhousia are made for the two species of Choricarpia, and B. gundarara and B. tetraptera are described as new species. B. gundarara is known only from the Kimberley region of Western Australia, widely disjunct from the remaining Backhousia in eastern Queensland and New South Wales, and appears to be a lineage isolated by increasing aridity during the Miocene.

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