Improved molecular tools for sugar cane biotechnology

Sugar cane is a major source of food and fuel worldwide. Biotechnology has the potential to improve economically-important traits in sugar cane as well as diversify sugar cane beyond traditional applications such as sucrose production. High levels of transgene expression are key to the success of improving crops through biotechnology. Here we describe new molecular tools that both expand and improve gene expression capabilities in sugar cane. We have identified promoters that can be used to drive high levels of gene expression in the leaf and stem of transgenic sugar cane. One of these promoters, derived from the Cestrum yellow leaf curling virus, drives levels of constitutive transgene expression that are significantly higher than those achieved by the historical benchmark maize polyubiquitin-1 (Zm-Ubi1) promoter. A second promoter, the maize phosphonenolpyruvate carboxylate promoter, was found to be a strong, leaf-preferred promoter that enables levels of expression comparable to Zm-Ubi1 in this organ. Transgene expression was increased approximately 50-fold by gene modification, which included optimising the codon usage of the coding sequence to better suit sugar cane. We also describe a novel dual transcriptional enhancer that increased gene expression from different promoters, boosting expression from Zm-Ubi1 over eightfold. These molecular tools will be extremely valuable for the improvement of sugar cane through biotechnology.

An improved chemically inducible gene switch that functions in the monocotyledonous plant sugar cane

Chemically inducible gene switches can provide precise control over gene expression, enabling more specific analyses of gene function and expanding the plant biotechnology toolkit beyond traditional constitutive expression systems. The alc gene expression system is one of the most promising chemically inducible gene switches in plants because of its potential in both fundamental research and commercial biotechnology applications. However, there are no published reports demonstrating that this versatile gene switch is functional in transgenic monocotyledonous plants, which include some of the most important agricultural crops. We found that the original alc gene switch was ineffective in the monocotyledonous plant sugar cane, and describe a modified alc system that is functional in this globally significant crop. A promoter consisting of tandem copies of the ethanol receptor inverted repeat binding site, in combination with a minimal promoter sequence, was sufficient to give enhanced sensitivity and significantly higher levels of ethanol inducible gene expression. A longer CaMV 35S minimal promoter than was used in the original alc gene switch also substantially improved ethanol inducibility. Treating the roots with ethanol effectively induced the modified alc system in sugar cane leaves and stem, while an aerial spray was relatively ineffective. The extension of this chemically inducible gene expression system to sugar cane opens the door to new opportunities for basic research and crop biotechnology.

How much geological detail is needed for gasifier success?

The incipient Underground Coal Gasification (UCG) industry in Queensland, Australia, undertook three trial projects in two Mesozoic basins of southeast Queensland. The experiences of these three operations provide useful retrospective insight into gasifier productivity. This paper identifies key output measures of gasifier ‘success’ including output gas composition, presence of contaminants in groundwater and consistency of chamber operation. Likewise, a review of the geological and hydrogeological understanding of each site prior to gasifier commissioning was undertaken. Productivity parameters from gasification were then correlated against the level of baseline geological/hydrogeological understanding for each site. The aim of the study was to identify the optimum scope of geological and hydrogeological understanding required at the site assessment phase to ensure safe, maximum gasifier output during production phase. This approach allows identification of poor or unexpected performance that is attributable to pre-existing uncertainty. A historical review of gasifier conditions inferred from the three trial projects is presented. Hence from the Queensland experiences it is possible to identify what aspects of baseline geological understanding should be clearly understood at the site selection phase in order to limit anomalous gasifier performance and undesirable deviations, and maximise production output.

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16–45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.

A multi-scaling approach to predict hydraulic damage of poromaterials

The purpose of this paper is to introduce the concept of hydraulic damage and its numerical integration. Unlike the common phenomenological continuum damage mechanics approaches, the procedure introduced in this paper relies on mature concepts of homogenization, linear fracture mechanics, and thermodynamics. The model is applied to the problem of fault reactivation within resource reservoirs. The results show that propagation of weaknesses is highly driven by the contrasts of properties in porous media. In particular, it is affected by the fracture toughness of host rocks. Hydraulic damage is diffused when it takes place within extended geological units and localized at interfaces and faults.

Anatomy of sand beach ridges : evidence from severe Tropical Cyclone Yasi and its predecessors, northeast Queensland, Australia

[1] Four well-identified tropical cyclones over the past century have been responsible for depositing distinct units of predominantly quartzose sand and gravel to form the most seaward beach ridge at several locations along the wet tropical coast of northeast Queensland, Australia. These units deposited by tropical cyclones display a key sedimentary signature characterized by a sharp basal erosional contact, a coarser grain size than the underlying facies and a coarse-skewed trend toward the base. Coarse-skewed distributions with minimal change in mean grain size also characterize the upper levels of the high-energy deposited units at locations within the zone of maximum onshore winds during the tropical cyclone. These same coarse skew distributions are not apparent in sediments deposited at locations where predominantly offshore winds occurred during the cyclone, which in the case of northeast Australia is north of the eye-crossing location. These sedimentary signatures, along with the geochemical indicators and the degraded nature of the microfossil assemblages, have proven to be useful proxies to identify storm-deposited units within the study site and can also provide useful proxies in older beach ridges where advanced pedogenesis has obscured visual stratigraphic markers. As a consequence, more detailed long-term histories of storms and tropical cyclones can now be developed.

Landscape ecology of the lesser grain borer, Rhyzopertha dominica

The Lesser Grain Borer is a major pest of stored grain with a global distribution. This project has, for the first time recorded this pest throughout broad spatial areas, tens of kilometres from grain production or storage. Statistical analysis revealed that different factors such as ambient temperature and the availability of food resources affect R. dominica differently between different habitats. This suggests that, contrary to the prevailing view, this pest is not solely dependent on stored wheat and can continue to persist throughout a range of habitats. These findings have important management implications for Australia's wheat industry.

Mid-Holocene sea-level and coral reef demise : U-Th dating of subfossil corals in Moreton Bay, Australia

It is increasingly apparent that sea-level data (e.g. microfossil transfer functions, dated coral microatolls and direct observations from satellite and tidal gauges) vary temporally and spatially at regional to local scales, thus limiting our ability to model future sea-level rise for many regions. Understanding sealevel response at ‘far-field’ locations at regional scales is fundamental for formulating more relevant sea-level rise susceptibility models within these regions under future global change projections. Fossil corals and reefs in particular are valuable tools for reconstructing past sea levels and possible environmental phase shifts beyond the temporal constraints of instrumental records. This study used abundant surface geochronological data based on in situ subfossil corals and precise elevation surveys to determine previous sea level in Moreton Bay, eastern Australia, a far-field site. A total of 64 U-Th dates show that relative sea level was at least 1.1 m above modern lowest astronomical tide (LAT) from at least ˜6600 cal. yr BP. Furthermore, a rapid synchronous demise in coral reef growth occurred in Moreton Bay ˜5800 cal. yr BP, coinciding with reported reef hiatus periods in other areas around the Indo-Pacific region. Evaluating past reef growth patterns and phases allows for a better interpretation of anthropogenic forcing versus natural environmental/climatic cycles that effect reef formation and demise at all scales and may allow better prediction of reef response to future global change.

The Black-tailed Antechinus, Antechinus arktos sp. nov.: a new species of carnivorous marsupial from montane regions of the Tweed Volcano caldera, eastern Australia

We describe a new species of dasyurid marsupial within the genus Antechinus that was previously known as a northern outlier of Dusky Antechinus (A. swainsonii). The Black-tailed Antechinus, Antechinus arktos sp. nov., is known only from areas of high altitude and high rainfall on the Tweed Volcano caldera of far south-east Queensland and north-east New South Wales, Australia. Antechinus arktos formerly sheltered under the taxonomic umbrella of A. swainsonii mimetes, the widespread mainland form of Dusky Antechinus. With the benefit of genetic hindsight, some striking morphological differences are herein resolved: A. s. mimetes is more uniformly deep brown-black to grizzled grey-brown from head to rump, with brownish (clove brown—raw umber) hair on the upper surface of the hindfoot and tail, whereas A. arktos is more vibrantly coloured, with a marked change from greyish-brown head to orange-brown rump, fuscous black on the upper surface of the hindfoot and dense, short fur on the evenly black tail. Further, A. arktos has marked orange-brown fur on the upper and lower eyelid, cheek and in front of the ear and very long guard hairs all over the body; these characters are more subtle in A. s. mimetes. There are striking genetic differences between the two species: at mtDNA, A. s. mimetes from north-east New South Wales is 10% divergent to A. arktos from its type locality at Springbrook NP, Queensland. In contrast, the Ebor A. s. mimetes clades closely with conspecifics from ACT and Victoria. A. arktos skulls are strikingly different to all subspecies of A. swainsonii. A. arktos are markedly larger than A. s. mimetes and A. s. swainsonii (Tasmania) for a range of craniodental measures. Antechinus arktos were historically found at a few proximate mountainous sites in south-east Queensland, and have only recently been recorded from or near the type locality. Even there, the species is likely in low abundance. The Black-tailed Antechinus has plausibly been detrimentally affected by climate change in recent decades, and will be at further risk with increasing warming trends.

A new dasyurid marsupial from Kroombit Tops, south-east Queensland, Australia : the Silver-headed Antechinus, Antechinus argentus sp. nov. (Marsupialia: Dasyuridae)

Antechinus argentus sp. nov. is currently only known from the plateau at the eastern escarpment of Kroombit Tops National Park, about 400km NNW of Brisbane and 60km SSW of Gladstone, south-east Queensland, Australia. Antechinus flavipes (Waterhouse) is also known from Kroombit Tops NP, 4.5km W of the nearest known population of A. argentus; A. mysticus Baker, Mutton and Van Dyck has yet to be found within Kroombit Tops, but is known from museum specimens taken at Bulburin NP, just 40km ESE, as well as extant populations about 400km to both the south-east and north-west of Kroombit NP. A. argentus can be easily distinguished in the field, having an overall silvery/grey appearance with much paler silver feet and drabber deep greyish-olive rump than A. flavipes, which has distinctive yellow-orange toned feet, rump and tail-base; A. argentus fur is also less coarse than that of A. flavipes. A. argentus has a striking silver-grey head, neck and shoulders, with pale, slightly broken eye-rings, which distinguish it from A. mysticus which has a more subtle greyish-brown head, pale buff dabs of eyeliner and more colourful brownish-yellow rump. Features of the dentary can also be used for identification: A. argentus differs from A. flavipes in having smaller molar teeth, as well as a narrower and smaller skull and from A. mysticus in having on average a narrower snout, smaller skull and dentary lengths and smaller posterior palatal vacuities in the skull. A. argentus is strongly divergent genetically (at mtDNA) from both A. flavipes (9.0–11.2%) and A. mysticus (7.2–7.5%), and forms a very strongly supported clade to the exclusion of all other antechinus species, in both mtDNA and combined (mtDNA and nDNA) phylogenies inferred here. We are yet to make detailed surveys in search of A. argentus from forested areas to the immediate east and north of Kroombit Tops. However, A. mysticus has only been found at these sites in low densities in decades past and not at all in several recent trapping expeditions conducted by the authors. With similar habitat types in close geographic proximity, it is plausible that A. argentus may be found outside Kroombit. Nevertheless, it is striking that from a range of surveys conducted at Kroombit Tops in the last 15 years and intensive surveys by the authors in the last 3 years, totalling more than 5 080 trap nights, just 13 A. argentus have been captured from two sites less than 6 km apart. If this is even close to the true geographic extent of the species, it would possess one of the smallest distributions of an Australian mammal species. With several threats identified, we tentatively recommend that A. argentus be listed as Endangered, pending an exhaustive trapping survey of Kroombit and surrounds.

Distribution and taxonomy of Enterococci from the Davis Station wastewater discharge, Antarctica

This project assessed the potential impact of untreated sewage release in a near-shore marine environment of Antarctica through the distribution and characterisation of the faecal indicator bacteria Enterococcus. Antibiotic resistance and genome sequencing analyses revealed that enterococci resistant to multiple antibiotics closely related to clinical pathogens were introduced to the pristine Antarctic environment by Australia's Davis station.

Integrating 40Ar-39Ar, 87Rb-87Sr and 147Sm-143Nd geochronology of authigenic illite to evaluate tectonic reactivation in an intraplate setting, central Australia

The Warburton-Cooper basins, central Australia, include a multitude of reactivated fracture-fault networks related to a complex, and poorly understood, tectonic evolution. We investigated authigenic illites from a granitic intrusion and sedimentary rocks associated with prominent structural features (Gidgealpa-Merrimelia-Innamincka Ridge and the Nappamerri Trough). These were analysed by 40Ar-39Ar, 87Rb-87Sr and 147Sm-143Nd geochronology to explore the thermal and tectonic histories of central Australian basins. The combined age data provide evidence for three major periods of fault reactivation throughout the Phanerozoic. While Carboniferous (323.3 ± 9.4 Ma) and Late Triassic ages (201.7 ± 9.3 Ma) derive from basin-wide hydrothermal circulation, Cretaceous ages (~128 to ~86 Ma) reflect episodic fluid flow events restricted to the synclinal Nappamerri Trough. Such events result from regional extensional tectonism derived from the transferral of far-field stresses to mechanically and thermally weakened regions of the Australian continent. Specifically, Cretaceous ages reflect continent-wide transmission of tensional stress from a > 2500 km long rifting event on the Eastern (and southern) Australian margin associated with break-up of Gondwana and opening of the Tasman Sea. By integrating 40Ar-39Ar, 87Rb-87Sr and 147Sm-143Nd dating, this study highlights the use of authigenic illite in temporally constraining the tectonic evolution of intracontinental basins that would otherwise remain unknown. Furthermore, combining Sr- and Ar-isotopic systems enables more accurate dating of authigenesis whilst significantly reducing geochemical pitfalls commonly associated with these radioisotopic dating methods.

Development of a Remote Sensing Core Curriculum submitted for the sessions on educational initiatives in Geoscience and Remote Sensing

A Remote Sensing Core Curriculum (RSCC) development project is currently underway. This project is being conducted under the auspices of the National Center for Geographic Information and Analysis (NCGIA). RSCC is an outgrowth of the NCGIA GIS Core Curriculum project. It grew out of discussions begun at NCGIA, Initiative 12 (I-12): 'Integration of Remote Sensing and Geographic Information Systems'. This curriculum development project focuses on providing professors, teachers and instructors in undergraduate and graduate institutions with course materials from experts in specific subject matter for areas use in the class room.

Remote sensing utility expansion through Earth Portal internet browser

A modular, graphic-oriented Internet browser has been developed to enable non-technical client access to a literal spinning world of information and remotely sensed. The Earth Portal (www.earthportal.net) uses the ManyOne browser (www.manyone.net) to provide engaging point and click views of the Earth fully tessellated with remotely sensed imagery and geospatial data. The ManyOne browser technology use Mozilla with embedded plugins to apply multiple 3-D graphics engines, e.g. ArcGlobe or GeoFusion, that directly link with the open-systems architecture of the geo-spatial infrastructure. This innovation allows for rendering of satellite imagery directly over the Earth's surface and requires no technical training by the web user. Effective use of this global distribution system for the remote sensing community requires a minimal compliance with protocols and standards that have been promoted by NSDI and other open-systems standards organizations.