Pearling and aquaculture in the Dampier Archipelago - Existing and proposed operations - a report for public comment

This discussion paper has been prepared by the Fisheries Department of WA as part of a consultative process to enable the public to comment on existing and proposed pearling and aquaculture activities in the Dampier Archipelago. This report follows on from Fisheries Management Report 90 - the Driscoll Report - and provides more detailed information about pearling and aquaculture to enable the public to consider and comment on individual projects

A first-draft human protein-interaction map

BACKGROUND: Protein-interaction maps are powerful tools for suggesting the cellular functions of genes. Although large-scale protein-interaction maps have been generated for several invertebrate species, projects of a similar scale have not yet been described for any mammal. Because many physical interactions are conserved between species, it should be possible to infer information about human protein interactions (and hence protein function) using model organism protein-interaction datasets. RESULTS: Here we describe a network of over 70,000 predicted physical interactions between around 6,200 human proteins generated using the data from lower eukaryotic protein-interaction maps. The physiological relevance of this network is supported by its ability to preferentially connect human proteins that share the same functional annotations, and we show how the network can be used to successfully predict the functions of human proteins. We find that combining interaction datasets from a single organism (but generated using independent assays) and combining interaction datasets from two organisms (but generated using the same assay) are both very effective ways of further improving the accuracy of protein-interaction maps. CONCLUSIONS: The complete network predicts interactions for a third of human genes, including 448 human disease genes and 1,482 genes of unknown function, and so provides a rich framework for biomedical research

Chytrid fungus infection in alpine tree frogs is associated with individual heterozygosity and population isolation but not population-genetic diversity

Chytridiomycosis, a disease caused by the emerging fungus Batrachochytrium dendrobatidis (Bd), has been implicated in the decline of over 500 amphibian species. Population declines could have important genetic consequences, including reduced genetic diversity. We contrasted genetic diversity among both long-Bd-exposed and unexposed populations of the south-east Australian alpine tree frog (Litoria verreauxii alpina) across its range. At the population level, we found no significant differences in genetic diversity between Bd-exposed and unexposed populations. Encouragingly, even Bd-infected remnant populations that are now highly isolated maintain genetic diversity comparable to populations in which Bd is absent. Spatial genetic structure among populations followed an isolation-by-distance pattern, suggesting restricted movement among remnant populations. At the individual level, greater heterozygosity was associated with reduced probability of infection. Loss of genetic diversity in remnant populations that survived chytridiomycosis epidemics does not appear to be a threat to L. v. alpina. We suggest several factors underpinning maintenance of genetic diversity: (1) remnant populations have remained large enough to avoid losses of genetic diversity; (2) many individuals in the population are able to breed once before succumbing to disease; and (3) juveniles in the terrestrial environment have low exposure to Bd, providing an annual ‘reservoir’ of genetic diversity. The association between individual heterozygosity and infection status suggests that, while other work has shown all breeding adults are typically killed by Bd, males with greater heterozygosity may survive longer and obtain fitness benefits through extended breeding opportunities. Our results highlight the critical role of life history in mitigating the impacts of Bd infection for some amphibian species, but we infer that increased isolation as a result of disease-induced population extirpations will enhance population differentiation and thus biogeographic structure

Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution

BACKGROUND: Systematic analyses of loss-of-function phenotypes have been carried out for most genes in Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster. Although such studies vastly expand our knowledge of single gene function, they do not address redundancy in genetic networks. Developing tools for the systematic mapping of genetic interactions is thus a key step in exploring the relationship between genotype and phenotype. RESULTS: We established conditions for RNA interference (RNAi) in C. elegans to target multiple genes simultaneously in a high-throughput setting. Using this approach, we can detect the great majority of previously known synthetic genetic interactions. We used this assay to examine the redundancy of duplicated genes in the genome of C. elegans that correspond to single orthologs in S. cerevisiae or D. melanogaster and identified 16 pairs of duplicated genes that have redundant functions. Remarkably, 14 of these redundant gene pairs were duplicated before the divergence of C. elegans and C. briggsae 80-110 million years ago, suggesting that there has been selective pressure to maintain the overlap in function between some gene duplicates. CONCLUSION: We established a high throughput method for examining genetic interactions using combinatorial RNAi in C. elegans. Using this technique, we demonstrated that many duplicated genes can retain redundant functions for more than 80 million years of evolution. This provides strong support for evolutionary models that predict that genetic redundancy between duplicated genes can be actively maintained by natural selection and is not just a transient side effect of recent gene duplication events

A model for principals' STEM leadership capability

In this paper we develop a model for the capabilities required by principals for effective Science, Technology, Engineering and Mathematics (STEM) leadership. The model underpinned a large national cross-sectional research and development project across Australian states in both primary and secondary schools. This model is developed via synthesis of research literature across leadership and STEM education. The model consists of five dimensions of principals' STEM capability: (1) STEM discipline-specific and integrated knowledge and practices; (2) contexts; (3) dispositions; (4) tools; and (5) critical orientation. These dimensions represent distinct, but interrelated, capacities required by principals to establish and maintain positive STEM learning cultures within schools. Elaborations have been provided, in the form of capabilities, for each of these dimensions. The model has the potential for shaping principals' STEM leadership development trajectories and structuring targeted professional learning programmes for principals, teachers and other members of the school community

Spectroscopy and thermal modelling of the first interstellar object 1I/2017 U1 ‘Oumuamua

During the formation and evolution of the Solar System, significant numbers of cometary and asteroidal bodies were ejected into interstellar space. It is reasonable to expect that the same happened for planetary systems other than our own. Detection of such interstellar objects would allow us to probe the planetesimal formation processes around other stars, possibly together with the effects of long-term exposure to the interstellar medium. 1I/2017 U1 ‘Oumuamua is the first known interstellar object, discovered by the Pan-STARRS1 telescope in October 2017. The discovery epoch photometry implies a highly elongated body with radii of ~ 200 × 20 m when a comet-like geometric albedo of 0.04 is assumed. The observable interstellar object population is expected to be dominated by comet-like bodies in agreement with our spectra, yet the reported inactivity of 'Oumuamua implies a lack of surface ice. Here, we report spectroscopic characterization of ‘Oumuamua, finding it to be variable with time but similar to organically rich surfaces found in the outer Solar System. We show that this is consistent with predictions of an insulating mantle produced by long-term cosmic ray exposure. An internal icy composition cannot therefore be ruled out by the lack of activity, even though ‘Oumuamua passed within 0.25 au of the Sun

Dynamical system analysis and forecasting of deformation produced by an earthquake fault

We present a method of constructing low-dimensional nonlinear models describing the main dynamical features of a discrete 2D cellular fault zone, with many degrees of freedom, embedded in a 3D elastic solid. A given fault system is characterized by a set of parameters that describe the dynamics, rheology, property disorder, and fault geometry. Depending on the location in the system parameter space we show that the coarse dynamics of the fault can be confined to an attractor whose dimension is significantly smaller than the space in which the dynamics takes place. Our strategy of system reduction is to search for a few coherent structures that dominate the dynamics and to capture the interaction between these coherent structures. The identification of the basic interacting structures is obtained by applying the Proper Orthogonal Decomposition (POD) to the surface deformations fields that accompany strike-slip faulting accumulated over equal time intervals. We use a feed-forward artificial neural network (ANN) architecture for the identification of the system dynamics projected onto the subspace (model space) spanned by the most energetic coherent structures. The ANN is trained using a standard back-propagation algorithm to predict (map) the values of the observed model state at a future time given the observed model state at the present time. This ANN provides an approximate, large scale, dynamical model for the fault.Comment: 30 pages, 12 figure

Loss of LIN-35, the Caenorhabditis elegans ortholog of the tumor suppressor p105Rb, results in enhanced RNA interference

BACKGROUND: Genome-wide RNA interference (RNAi) screening is a very powerful tool for analyzing gene function in vivo in Caenorhabditis elegans. The effectiveness of RNAi varies from gene to gene, however, and neuronally expressed genes are largely refractive to RNAi in wild-type worms. RESULTS: We found that C. elegans strains carrying mutations in lin-35, the worm ortholog of the tumor suppressor gene p105Rb, or a subset of the genetically related synMuv B family of chromatin-modifying genes, show increased strength and penetrance for many germline, embryonic, and post-embryonic RNAi phenotypes, including neuronal RNAi phenotypes. Mutations in these same genes also enhance somatic transgene silencing via an RNAi-dependent mechanism. Two genes, mes-4 and zfp-1, are required both for the vulval lineage defects resulting from mutations in synMuv B genes and for RNAi, suggesting a common mechanism for the function of synMuv B genes in vulval development and in regulating RNAi. Enhanced RNAi in the germline of lin-35 worms suggests that misexpression of germline genes in somatic cells cannot alone account for the enhanced RNAi observed in this strain. CONCLUSION: A worm strain with a null mutation in lin-35 is more sensitive to RNAi than any other previously described single mutant strain, and so will prove very useful for future genome-wide RNAi screens, particularly for identifying genes with neuronal functions. As lin-35 is the worm ortholog of the mammalian tumor suppressor gene p105Rb, misregulation of RNAi may be important during human oncogenesis

A critique of game-based definitions of receipt-freeness for voting

We analyse three game-based definitions of receipt-freeness; uncovering soundness issues with two of the definitions and completeness issues with all three. Hence, two of the definitions are too weak, i.e., satisfiable by voting schemes that are not intuitively receipt-free. More precisely, those schemes need not even satisfy ballot secrecy. Consequently, the definitions are satisfiable by schemes that reveal how voters\u27 vote. Moreover, we find that each definition is limited in scope. Beyond soundness and completeness issues, we show that each definition captures a different attacker model and we examine some of those differences