Royal Commission on Human Relationships

This controversial Royal Commission from the 1970s found that many Australian families were failing to protect their most valuable members, and helped change the shape of public discussion around families, gender and sexuality. This is the first time a digitised version of the Royal Commission on Human Relationships\u27 five-volume final report has been made publically available. The Royal Commission was initiated in 1974, following a failed attempt by the Whitlam government to reform abortion law. The terms of reference were: To inquire into and report upon the family, social, educational, legal and sexual aspects of male and female relationships, so far as those matters are relevant to the powers and functions of the Australian Parliament and Government, including powers and functions in relation to the Territories: To give particular emphasis to the concept of responsible parenthood, to have regard to experience in other countries and to include in your inquiry the following aspects of the said matters: (a) the extent of relevant existing education programs, including sex education programs, and their effectiveness in promoting responsible sexual behaviour and providing a sound basis in the fundamentals of male and female relationships in the Australian social environment; (b) the extent of relevant existing programs in medical schools and their adequacy to provide comprehensive medical training in contraceptive techniques, in the physical, psychological and sexual problems experienced by women in adapting to marriage and before, during and after menstruation and in matters relating to pregnancy, fertility control, spontaneous and induced abortions and childbirth and to encourage acceptance by the medical profession of its responsibilities in the field of contraceptive counselling; (c) the provision, adequacy and effectiveness of existing family planning facilities, educational and activational information on family planning and methods of evaluation of all family planning techniques; (d) the social, economic, psychological and medical pressures on women in determining whether to proceed with unplanned or unwanted pregnancies, having regard to: (i) the adequacy of housing, child-minding centres, pre-school centres, domestic assistance for families and working mothers, assistance to single parent families, other forms of assistance for mothers employed in industry, and adoption procedures; (ii) the disabilities of families with handicapped children; and (iii) the social status of women in the community; the social, psychological and medical results of termination of, or and failure to terminate such pregnancies; (e) the adequacy and effectiveness of existing medico-legal determinations in relation to termination of pregnancy, the incidence of such terminations, the factors influencing their occurrence, the adequacy of medical training in an evaluation of methods of termination, consultative rights of the family or other persons concerned and the adequacy and effectiveness of pregnancy support services; and (f) any other matters in relation to the family, social, educational, legal and sexual aspects of male and female relationships to which the attention of the Commission is directed by the Prime Minister in the course of the inquiry. To make recommendations as to measures that are desirable with respect to the foregoing matters under existing or future laws of the Australian Parliament or of the Territories (including laws providing for grants to the States) and to indicate whether these measures should be implemented through existing bodies or through government instrumentalities to be created. The final report, presented to Governor-General John Kerr in 1977, contained over 500 recommendations relating to "contraception (access and use), unwanted pregnancies, childbirth, attitudes to sexuality, sexual knowledge, sex education, domestic violence, rape and the police and courts’ treatment of rape victims, the changing roles of women, child care, child abuse, and homosexuality – especially discrimination faced by gays and lesbians." The report was highly controversial when released and many of its recommendations were not acted on. However, the Royal Commission had a lasting influence. It was said to have brought taboo topics like abortion, rape and child abuse into public discussion, and to have opened up conversations about private life to this day.   ---------------   Part of the Policy History Collection. Digitisation of this report has been supported by the National Library of Australia.   Reproduced with permission of the Department of Prime Minister and Cabinet

Where’s the Science in this? The problem with attempting to isolate aspects of Indigenous practice and thinking as examples of 'Indigenous Science'

This paper reconstructs a voyage of discovery. It is the story of a workshop organised by community educators at the Yirrkala school, (the Yirrkala CEC or Community Education Centre), in NE Arnhem Land. It is a story about a different way of teaching and learning. It also tells of a learning process that I have gone through in making a film about the renewal of the Yambirrpa at Yamuna

Expression of human ARGONAUTE 2 inhibits endogenous microRNA activity in Arabidopsis

Plant and animal microRNA (miRNA) pathways share many analogous components, the ARGONAUTE (AGO) proteins being foremost among them. We sought to ascertain the degree of functional conservation shared by Homo sapiens ARGONAUTE 2 (HsAGO2) and Arabidopsis thaliana ARGONAUTE 1 (AtAGO1), which are the predominant AGO family members involved with miRNA activity in their respective species. Transgenic Arabidopsis plants expressing HsAGO2 were indistinguishable from counterparts over-expressing AtAGO1, each group exhibiting the morphological and molecular hallmarks of miRNA-pathway loss-of-function alleles. However, unlike AtAGO1, HsAGO2 was unable to rescue the ago1-27 allele. We conclude that, despite the evolutionary gulf between them, HsAGO2 is likely capable of interacting with some component/s of the Arabidopsis miRNA pathway, thereby perturbing its operation, although differences have arisen such that HsAGO2 alone is insufficient to confer efficient silencing of miRNA targets in planta

Parasites, politics and public science: the promotion of biological control in Western Australia, 1900-1910

Biological control of arthropods emerged as a scientific enterprise in the late nineteenth century and the orchard industry of California was an early centre of expertise. In 1900, as the Australian colonies prepared for federation, each had a government entomologist attached to its agriculture department. The hiring of George Compere from California by the Western Australian Department of Agriculture began a controversial chapter in the early history of biological control that was linked to a late, local popularization of acclimatization. Compere became known as the 'travelling entomologist' and for a decade brought 'parasites' of pest insects from overseas and released them in Perth. His antagonistic disciplinary rhetoric and inflated claims for the 'parasite theory' created conflict with his counterparts in the eastern states. The resulting inter-state entomological controversy was played out in the press, revealing the political use of science for institutional and even state identity. It is a story of transnational exchanges, chance discoveries and popular public science: popular because of the promise of a simple, natural solution to agricultural insect pests and because of the public nature of the disputes it generated between the experts. This microcosm contributes to the global historiography of acclimatization, biological control, scientific exposition and the professionalization of agricultural science

Plagues and Players: an Environmental and Scientific History of Australia's Southern Locusts

This thesis traces the changing course of locust and grasshopper outbreaks in southern Australia and relates them to environmental changes. It also examines the creation and use of scientific knowledge about locusts over more than a century of research. Together, these historical investigations show how the insects’ responses to environmental change influenced the course of ecological and agricultural science. Digitised newspaper records of locust occurrence allow a more complete reconstruction of historic plagues and a new interpretation of the species involved and the environmental correlates of their changing incidence. They also provide a different view of the scientific players who investigated locusts in Australia. These sources are complemented by the writings of many entomologists about locust outbreaks and ecologies from the 1840s to the 1970s. The popular and scientific sources reveal the complexity of ecological ideas, technologies and institutional settings, framed by the common material context of environmental change. This is a history of entomological, ecological and public agricultural science as well as an analysis of the environments in which the outbreaks developed. European settlers encountered grasshoppers and locusts soon after establishing pastoral and agricultural land use. Swarming populations developed patterns of occurrence that were observed by farmers and naturalists, and there is evidence that their incidence increased during the nineteenth century. Two species, Austroicetes cruciata and Chortoicetes terminifera, developed frequent outbreak populations on the southern grasslands, making them significant agricultural pests, but they responded differently to changes of climate, landscape and land use. The former swarmed almost annually soon after livestock altered grassland ecosystems within its range, but it declined during the twentieth century. The latter first swarmed across the southern grasslands in the 1870s, but has since maintained irregular outbreak populations through migratory exchanges. They are taxonomically related native locusts with a similar appearance but distinct ecologies. Untangling their identities was historically marked by scientific confusion. However, the two species can sometimes be distinguished in newspaper reports by diagnostic morphological features, and can often be separated by differences in their seasonal occurrence, abundance, phenology and behaviour. This thesis argues that the fundamental changes to grassy ecosystems resulting from the rapid expansion of the pastoral industry favoured the development of swarming populations of both Australian species. Evidence comes from early Aboriginal comments, thousands of newspaper and official reports, climatic sequences and the nature of landscape changes, as well as the subsequent contraction in outbreak extent and frequency when land use and land cover stabilised in the second half of the twentieth century. The writings of many investigators reveal overlapping trends in ecological and technological investigations, and place each player within their scientific era. These are examined in the context of international developments and the broader public discourse about locusts and the importance and relevance of science. In this long relationship of feedbacks, the materiality of the insects allowed scientists to discern their ecologies. Science directed government policy on how to respond and governments sponsored more science in managing the politics of successive agricultural crises

Can climate models capture the structure of extratropical cyclones?

Composites of wind speeds, equivalent potential temperature, mean sea level pressure, vertical velocity, and relative humidity have been produced for the 100 most intense extratropical cyclones in the Northern Hemisphere winter for the 40-yr ECMWF Re-Analysis (ERA-40) and the high resolution global environment model (HiGEM). Features of conceptual models of cyclone structure—the warm conveyor belt, cold conveyor belt, and dry intrusion—have been identified in the composites from ERA-40 and compared to HiGEM. Such features can be identified in the composite fields despite the smoothing that occurs in the compositing process. The surface features and the three-dimensional structure of the cyclones in HiGEM compare very well with those from ERA-40. The warm conveyor belt is identified in the temperature and wind fields as a mass of warm air undergoing moist isentropic uplift and is very similar in ERA-40 and HiGEM. The rate of ascent is lower in HiGEM, associated with a shallower slope of the moist isentropes in the warm sector. There are also differences in the relative humidity fields in the warm conveyor belt. In ERA-40, the high values of relative humidity are strongly associated with the moist isentropic uplift, whereas in HiGEM these are not so strongly associated. The cold conveyor belt is identified as rearward flowing air that undercuts the warm conveyor belt and produces a low-level jet, and is very similar in HiGEM and ERA-40. The dry intrusion is identified in the 500-hPa vertical velocity and relative humidity. The structure of the dry intrusion compares well between HiGEM and ERA-40 but the descent is weaker in HiGEM because of weaker along-isentrope flow behind the composite cyclone. HiGEM’s ability to represent the key features of extratropical cyclone structure can give confidence in future predictions from this model

Target RNA Secondary Structure Is a Major Determinant of miR159 Efficacy

In plants, microRNA (miRNA)-target complementarity has long been considered the predominant factor determining the silencing outcome of the miRNA-target interaction, although the efficacy of such interactions have rarely been appraised in plants. Here, we perform in planta silencing efficacy assays on seven Arabidopsis MYB genes, all of which contain conserved miR159-binding sites of analogous complementarity. These genes were found to be differentially silenced by miR159; MYB81, MYB97, MYB101, MYB104, and DUO1 were all poorly silenced, whereas MYB33 and MYB65 were strongly silenced. Curiously, this is consistent with previous genetic analysis defining MYB33 and MYB65 as the major functional targets of miR159. Neither the free energy of miR159-target complementarity, nor miRNA binding site accessibility, as determined by flanking region AU content, could fully explain the discrepancy of miR159 silencing efficacy. Instead, we found that MYB33 and MYB65 were both predicted to contain a distinctive RNA secondary structure abutting the miR159 binding site. The structure is composed of two stem-loops (SLs) that are predicted to form in MYB33/65 homologs of species as evolutionary distant as gymnosperms. Functional analysis found that the RNA structure in MYB33 correlated with strong silencing efficacy; introducing mutations to disrupt either SL attenuated miR159 efficacy, while introducing complementary mutations to restore the SLs, but not the sequence, restored strong miR159-mediated silencing. Therefore, it appears that this RNA secondary structure demarcates MYB33/65 as sensitive targets of miR159, which underpins the narrow functional specificity of Arabidopsis miR159. MicroRNAs (miRNAs) are small 20- to 24-nucleotide (nt) RNAs that guide the RNA-Induced Silencing Complex to target mRNAs and mediate their silencing through a combination of transcript degradation and translational repression (Axtell, 2013). In plants, miRNAs have been shown to be involved in a multitude of critical developmental events and stress responses, and are often referred to as master regulators of gene expression. Central to understanding miRNA function has been identifying their target mRNAs (Sun et al., 2014). In plants, it is clear that high sequence complementarity between a miRNA and its target mRNA is compulsory for a miRNA-target interaction (Mallory et al., 2004; Schwab et al., 2005; Addo-Quaye et al., 2008; German et al., 2008), with most experimentally validated miRNA-target pairs having very few mismatches (Schwab et al., 2005; Liu et al., 2014). Consequently, miRNA-target complementarity has been the cornerstone of plant miRNA biology, determining miRNA target prediction (Dai and Zhao, 2011), the design of artificial miRNAs (amiRNAs; Schwab et al., 2005), the design of artificial miRNA decoys such as target MIMICs (Todesco et al., 2010), or the identification of endogenous target MIMICs (Karakülah et al., 2016). However, bioinformatic prediction of target genes often fails to accurately predict functionally relevant targets, where from numerous predicted targets, only a select few appear functionally significant (for review, see Li et al., 2014a). Likewise, it has been reported that amiRNAs with high complementarity to their intended targets perform with considerable variability in plants (Li et al., 2013; Deveson et al., 2013). Finally, different miRNA decoys that contain identical miRNA binding sites work with widely varying efficacies (Reichel et al., 2015). These and other observations argue that miRNA-target interaction is not simply a product of complementarity, but additional factors are required for functional miRNA-target interactions (Wang et al., 2015). In animals, it has long been known that the contextual sequence features in which a miRNA-binding site resides can strongly impact silencing. For example, miRNA-binding site accessibility was shown to be important, where introduction of mutations to decrease predicted accessibility disrupted efficient regulation, with impacts being as strong as mutations within the binding site itself (Kertesz et al., 2007). Furthermore, it has been shown that for certain animal miRNA-target interactions, strong regulation only occurs when the binding sites are within specific sequence arrangements or contexts (Didiano and Hobert, 2006; Vella et al., 2004). Other factors impacting the efficiency of regulation include RNA-binding proteins (RBPs), which can either attenuate or facilitate the access of the miRNA to its binding site (Kedde et al., 2010). Factors such as these have been studied less in plants, but evidence is accumulating that sequence context of miRNA binding sites may also be important in plants. First, Gu et al. (2012) found a synonymous codon bias favoring AU-richness, and hence reduced RNA secondary structure, around predicted miRNA target sites in several plant species. Second, Li et al. (2012) have found that miRNA binding sites in Arabidopsis (Arabidopsis thaliana) are generally less structured than their flanking regions, indicating a preference for high accessibility. Indeed, Fei et al. (2015) found that target site accessibility may explain select regulation of only a few targets from a large number of predicted target genes. Therefore, it would be of interest to functionally test these potential factors on miRNA-target interactions. In plants, the Arabidopsis miR159 family has been extensively studied as a model for plant miRNA-mediated gene regulation (Palatnik et al., 2003, 2007; Allen et al., 2007, 2010). The family has two major isoforms, miR159a and miR159b, which are strongly expressed throughout Arabidopsis (Palatnik et al., 2007; Li et al., 2016). Such expression is consistent with a loss-of-function mir159ab double mutant that displays strong pleiotropic developmental defects. In Arabidopsis, miR159 is bioinformatically predicted to regulate more than 20 targets, including eight genes encoding conserved R2R3 domain MYB transcription factors (Palatnik et al., 2007). Despite this, genetic analysis revealed that miR159-mediated regulation of only two of the predicted target genes, MYB33 and MYB65, account for the developmental defects of mir159ab, as all defects are suppressed in a myb33.myb65.mir159ab quadruple mutant (Allen et al., 2007). This defined the functional specificity of Arabidopsis miR159 being restricted to MYB33 and MYB65, but also raised the question of the functional significance of miR159-mediated regulation of the additional bioinformatically predicted targets, including those that have a strongly conserved miR159 binding site (Allen et al., 2007, 2010). Curiously, this narrower functional specificity as defined by genetics has also been found in other plant and animal miRNA systems, suggesting the functional scope of miRNA-mediated silencing is narrower than generally assumed (Seitz, 2009; Li et al., 2014a). For miR159, it is likely that multiple factors contribute to this apparent narrow functional specificity, including nonoverlapping transcriptional domains of the miR159 and MYB target genes (Allen et al., 2007), whether regulation of other targets is important under certain untested growth conditions or certain miR159 isoforms have become obsolete (Allen at al., 2010). However, one untested hypothesis is that MYB33 and MYB65 are more sensitive to miR159 regulation than the other MYB target genes. Recently, we have shown that factors beyond complementary govern the efficacy of the miR159-MYB33 silencing outcome (Li et al., 2014b). This not only included the miR159:MYB33 transcript stoichiometry, but also the sequence context of the miR159 binding site in MYB33. We showed that mutation of nts that immediately flank the miR159-binding site attenuated silencing to a similar extent to mutating nts within the binding site itself (Li et al., 2014b). This is further evidence that sequence complementarity alone does not guarantee strong miRNA regulation and that additional factor(s) are at play impacting miRNA-mediated regulation in plants. Here, by carrying out in planta miR159 efficacy assays, we show that MYB33 and MYB65 are indeed much more sensitive to miR159 regulation than the other MYB genes with conserved miR159 binding sites. Neither flanking AU content nor predicted accessibility of the miR159 binding site underlie this sensitivity. Rather, MYB33 and MYB65 are shown to share a predicted RNA secondary structure consisting of two stem-loops that partially overlap with the miR159 binding site. Structure-function analysis demonstrates that both these stem-loops are required for efficient miR159 mediated silencing of MYB33. We hypothesize that having strong RNA stem-loops adjacent to a miRNA binding site may facilitate accessibility of the binding site to the miRNA, which in turn promotes efficient silencing of the target gene.This work was supported by a Research School of Biology International student Ph.D. scholarship to Z.Z., an International ANU Ph.D. scholarship to M.R., and an Australian Research Council Discovery Grant (No. DP110103493) to A.A.M

Modeling spatiotemporal dynamics of outbreaking species: influence of environment and migration in a locust

Many pest species exhibit huge fluctuations in population abundance. Understanding their large-scale and long-term dynamics is necessary to develop effective control and management strategies. Occupancy models represent a promising approach to unravel interactions between environmental factors and spatiotemporal dynamics of outbreaking populations. Here, we investigated population dynamics of the Australian plague locust, Chortoicetes terminifera, using density data collected between 1988 and 2010 by the Australian Plague Locust Commission over more than 3 million km2 in eastern Australia. We applied multistate and autologistic multi-season occupancy models to test competing hypotheses about environmental and demographic processes affecting the large-scale dynamics of the Australian plague locust. We found that rainfall and land cover predictors best explained the spatial variability in outbreak probability across eastern Australia. Outbreaks are more likely to occur in temperate than tropical regions, with a faster and more continuous response to rainfall in desert than in agricultural areas. Our results also support the hypothesis that migration tends to propagate outbreaks only locally (over distances lower than 400 km) rather than across climatic regions. Our study suggests that locust outbreak forecasting and management systems could be improved by implementing key environmental factors and migration in hierarchical spatial models. Finally, our modeling framework can be seen as a step towards bridging the gap between mechanistic and more phenomenological models in the spatial analysis of fluctuating populations

Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing

More than 50 neurological and neuromuscular diseases are caused by short tandem repeat (STR) expansions, with 37 different genes implicated to date. We describe the use of programmable targeted long-read sequencing with Oxford Nanopore's ReadUntil function for parallel genotyping of all known neuropathogenic STRs in a single assay. Our approach enables accurate, haplotype-resolved assembly and DNA methylation profiling of STR sites, from a list of predetermined candidates. This correctly diagnoses all individuals in a small cohort (n = 37) including patients with various neurogenetic diseases (n = 25). Targeted long-read sequencing solves large and complex STR expansions that confound established molecular tests and short-read sequencing and identifies noncanonical STR motif conformations and internal sequence interruptions. We observe a diversity of STR alleles of known and unknown pathogenicity, suggesting that long-read sequencing will redefine the genetic landscape of repeat disorders. Last, we show how the inclusion of pharmacogenomic genes as secondary ReadUntil targets can further inform patient care

DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity

DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher-order levels of genome architecture is still unclear. Here, using Repli-Seq, single-cell Repli-Seq, and Hi-C, we show that genome-wide methylation loss is associated with both concordant loss of replication timing precision and deregulation of 3D genome organization. Notably, we find distinct disruption in 3D genome compartmentalization, striking gains in cell-to-cell replication timing heterogeneity and loss of allelic replication timing in cancer hypomethylation models, potentially through the gene deregulation of DNA replication and genome organization pathways. Finally, we identify ectopic H3K4me3-H3K9me3 domains from across large hypomethylated domains, where late replication is maintained, which we purport serves to protect against catastrophic genome reorganization and aberrant gene transcription. Our results highlight a potential role for the methylome in the maintenance of 3D genome regulation