Rice ragged stunt oryzavirus genome segments S7 and S10 encode non-structural proteins of M(r) 68 025 (Pns7) and M(r) 32364 (Pns10) : brief report

The nucleotide sequences of genome segments S7 and S10 of a Thai-isolate of rice ragged stunt virus (RRSV) were determined. The 1938 bp S7 sequence contains a single large open reading frame (ORF) spanning nucleotides 20 to 1 843 that is predicted to encode a protein of M(r) 68 025. The 1 162 bp S10 sequence has a major ORF spanning nucleotides 142 to 1 032 that is predicted to encode a protein of M(r) 32364. This S10 ORF is preceded by a small ORF (nt 20-55) which is probably a minicistron. Coupled in vitro transcription-translation from the two major ORFs gave protein products of the expected sizes. However, no protein was visualised from S10 when the small ORF sequence was included. Proteins were expressed in Escherichia coli from the full length ORF of S7 (P7) and from a segment of the S10 ORF (P10) fused to the ORF of glutathione S-transferase (GST). Neither fusion protein was recognised by polyclonal antibodies raised against RRSV particles. Furthermore, polyclonal antibodies raised against GST-P7 fusion protein did not recognise any virion structural polypeptides. These data strongly suggest that the proteins P7 and P10 do not form part of RRSV particle. This is further supported by observed sequence homology (though very weak) of predicted.

The M(r) 43K major capsid protein of rice ragged stunt oryzavirus is a post-translationally processed product of a M(r) 67 348 polypeptide encoded by genome segment 8

The nucleotide sequence of DNA complementary to rice ragged stunt oryzavirus (RRSV) genome segment 8 (S8) of an isolate from Thailand was determined. RRSV S8 is 1 914 bp in size and contains a single large open reading frame (ORF) spanning nucleotides 23 to 1 810 which is capable of encoding a protein of M(r) 67 348. The N-terminal amino acid sequence of a ~43K virion polypeptide matched to that inferred for an internal region of the S8 coding sequence. These data suggest that the 43K protein is encoded by S8 and is derived by a proteolytic cleavage. Predicted polypeptide sizes from this possible cleavage of S8 protein are 26K and 42K. Polyclonal antibodies raised against a maltose binding protein (MBP)-S8 fusion polypeptide (expressed in Escherichia coli) recognised four RRSV particle associated polypeptides of M(r) 67K, 46K, 43K and 26K and all except the 26K polypeptide were also highly immunoreactive to polyclonal antibodies raised against purified RRSV particles. Cleavage of the MBP-S8 fusion polypeptide with protease Factor X produced the expected 40K MBP and two polypeptides of apparent M(r) 46K and 26K. Antibodies to purified RRSV particles reacted strongly with the intact fusion protein and the 46K cleavage product but weakly to the 26K product. Furthermore, in vitro transcription and translation of the S8 coding region revealed a post-translational self cleavage of the 67K polypeptide to 46K and 26K products. These data indicate that S8 encodes a structural polypeptide, the majority of which is auto- catalytically cleaved to 26K and 46K proteins. The data also suggest that the 26K protein is the self cleaving protease and that the 46K product is further processed or undergoes stable conformational changes to a ~43K major capsid protein.

The Use of Ecological Design to Achieve Sustainable Development in Queensland, Australia

This series of technical papers arose out of the action by a private entrepreneur to initiate a process beyond mere regulatory compliance in order to achieve best environmental practice at proposed large new visitor gateways to Australia’s Great Barrier Reef. Because of the complexity of issues involved at such urbanized downstream sites, the range of topics covered is wide – though still only those considered at this juncture to be of management priority. Included on this platform is one introductory paper reviewing the history of environmental management in the field in Queensland, and three papers which seek to appreciate the main techniques by which government contributes to the solutions viz. through the national park, threatened species list, and environmental impact assessment. The history paper was designed to allow the present series to be considered in broad context as well as performance to date. The work emphasizes that much of the fertile land that must be sustained nowadays lies in the province of the private sector, and that the initiative to create any new cost-effective paradigm in ecologically-sustainable practices lies mostly in their hands. In all instances, this strategic approach to large-scale property planning is through ecological design – using field case studies around the immediate biophysical catchment of the development, with attendant focus on the associated legal catchment (the actual development site) and the social catchment (the effective land managers). The first of these has given rise to a document termed a Regional Landscape Strategy, its implementation planned in concert with an Environmental Impact Assessment of the site and with a Strategic Regional Initiative (still being tested in the field) for community engagement. The first document takes into account the aspirations of government as expressed in its broad-scale regional plans.

Longitudinal assessment of neuropathy in diabetes using novel ophthalmic markers (LANDMark) : baseline findings

Purpose Over the past decade, corneal nerve morphology and corneal sensation threshold have been explored as potential surrogate markers for the evaluation of diabetic neuropathy. We present the baseline findings of a Longitudinal Assessment of Neuropathy in Diabetes using novel ophthalmic Markers (LANDMark). Methods The LANDMark Study is a 5-year, two-site, natural history (observational) study of individuals with Type 1 diabetes stratified into those with (T1W) and without (T1WO) neuropathy according to the Toronto criteria, and control subjects. All study participants undergo detailed annual assessment of neuropathy including corneal nerve parameters measured using corneal confocal microscopy and corneal sensitivity measured using non-contact corneal esthesiometry. Results 396 eligible individuals (208 in Brisbane and 188 in Manchester) were assessed: 76 T1W, 166 T1WO and 154 controls. Corneal sensation threshold (mbars) was significantly higher in T1W (1.0 ± 1.1) than T1WO (0.7 ± 0.7) and controls (0.6 ± 0.4) (P=0.002); post-hoc analysis (PHA) revealed no difference between T1WO and controls (Tukey HSD, P=0.502). Corneal nerve fiber length (mm/mm2) (CNFL) was lower in T1W (13.8 ± 6.4) than T1WO (19.1 ± 5.8) and controls (23.2 ± 6.3) (P<0.001); PHA revealed CNFL to be lower in T1W than T1WO, and lower in both of these groups than controls (P<0.001). Corneal nerve branch density (branches/mm2) (CNBD) was significantly lower in T1W (40 ± 32) than T1WO (62 ± 37) and controls (83 ± 46) (P<0.001); PHA showed CNBD was lower in T1W than T1WO, and lower in both groups than controls (P<0.001). Alcohol and cigarette consumption did not differ between groups, although age, BMI, BP, waist circumference, HbA1c, albumin-creatinine ratio, and cholesterol were slightly greater in T1W than T1WO (p<0.05). Some site differences were observed. Conclusions The LANDMark baseline findings confirm that corneal sensitivity and corneal nerve morphometry can detect differences in neuropathy status in individuals with Type 1 diabetes and healthy controls. Corneal nerve morphology is significantly abnormal even in diabetic patients ‘without neuropathy’ compared to control participants. Results of the longitudinal trial will assess the capability of these tests for monitoring change in these parameters over time as potential surrogate markers for neuropathy.

Integrin αvβ3 upregulates integrin-linked kinase expression in human ovarian cancer cells via enhancement of ILK gene transcription

We previously showed that integrin alphavbeta3 overexpression and engagement by its ligand vitronectin increased adhesion, motility, and proliferation of human ovarian cancer cells. In search of differentially regulated genes involved in these tumor biological events, we previously identified the integrin-linked kinase (ILK) to be under control of alphavbeta3. In the present investigation we demonstrated significantly upregulated ILK protein as a function of alphavbeta3 in two ovarian cancer cell lines, OV-MZ-6 and OVCAR-3, and proved co-localization at the surface of alphavbeta3-overexpressing cells adherent to vitronectin. Increase of ILK protein was reflected by enhanced ILK promoter activity, an effect, which we further characterized with regard to transcriptional response elements involved. Abrogation of NF-kappaB/c-rel or p53 binding augmented ILK promoter activity and preserved induction by alphavbeta3. The AP1-mutant exhibited decreased promoter activity but was also still inducible by alphavbeta3. Disruption of the two DNA consensus motifs for Ets proteins led to divergent observations: mutation of the Ets motif at promoter position -462 bp did not significantly alter promoter activity but still allowed response to alphavbeta3. In contrast, disruption of the second Ets motif at position -85 bp did not only lead to slightly diminished promoter activity but also, in that case, abrogated ILK promoter induction by alphavbeta3. Subsequent co-transfection studies with ets-1 in the presence of the second Ets motif led to additional induction of ILK promoter activity. Taken together, these data suggest that ets-1 binding to the second Ets DNA motif strongly contributes to alphavbeta3-mediated ILK upregulation. By increasing ILK as an important integrin-proximal kinase, alphavbeta3 may promote its intracellular signaling and tumor biological processes arising thereof in favor of ovarian cancer metastasis.

Climate Change and the Resilience of Commodity Food Production in Australia

The current view of Australian state and national governments about the effects of climate change on agriculture is that farmers – through the adoption of mitigation and adaptation strategies – will remain resilient, and agricultural production will continue to expand. The assumption is that neoliberalism will provide the best ‘free market’ options for climate change mitigation and adaptation in farming. In contrast, we argue that neoliberalism will increase the move towards productivis (‘high-tech’) agriculture – the very system that has caused major environmental damage to the Australian continent. High-tech farming is highly dependent upon access to water and fossil fuels, both of which would appear to be the main limits to production in future decades. Productivist agriculture is a system highly reliant upon fertilizers and fuels that are derived from the petrochemical industry, and are currently increasing in cost as the price of oil increases.

Molecular characterization of "Candidatus Parilichlamydia carangidicola," a novel Chlamydia-like epitheliocystis agent in yellowtail kingfish, Seriola lalandi (Valenciennes), and the proposal of a new family, "Candidatus Parilichlamydiaceae" fam. nov. (order Chlamydiales).

Three cohorts of farmed yellowtail kingfish (Seriola lalandi) from South Australia were examined for Chlamydia-like organisms associated with epitheliocystis. To characterize the bacteria, 38 gill samples were processed for histopathology, electron microscopy, and 16S rRNA amplification, sequencing, and phylogenetic analysis. Microscopically, the presence of membrane-enclosed cysts was observed within the gill lamellae. Also observed was hyperplasia of the epithelial cells with cytoplasmic vacuolization and fusion of the gill lamellae. Transmission electron microscopy revealed morphological features of the reticulate and intermediate bodies typical of members of the order Chlamydiales. A novel 1,393-bp 16S chlamydial rRNA sequence was amplified from gill DNA extracted from fish in all cohorts over a 3-year period that corresponded to the 16S rRNA sequence amplified directly from laser-dissected cysts. This sequence was only 87% similar to the reported "Candidatus Piscichlamydia salmonis" (AY462244) from Atlantic salmon and Arctic charr. Phylogenetic analysis of this sequence against 35 Chlamydia and Chlamydia-like bacteria revealed that this novel bacterium belongs to an undescribed family lineage in the order Chlamydiales. Based on these observations, we propose this bacterium of yellowtail kingfish be known as "Candidatus Parilichlamydia carangidicola" and that the new family be known as "Candidatus Parilichlamydiaceae."

The mitochondrial genome of the Russian wheat aphid Diuraphis noxia : large repetitive sequences between trnE and trnF in aphids

To characterize aphid mitochondrial genome (mitogenome) features, we sequenced the complete mitogenome of the Russian wheat aphid, Diuraphis noxia. The 15,784-bp mitogenome with a high A + T content (84.76%) and strong C skew (− 0.26) was arranged in the same gene order as that of the ancestral insect. Unlike typical insect mitogenomes, D. noxia possessed a large tandem repeat region (644 bp) located between trnE and trnF. Sequencing partial mitogenome of the cotton aphid (Aphis gossypii) further confirmed the presence of the large repeat region in aphids, but with different repeat length and copy number. Another motif (58 bp) tandemly repeated 2.3 times in the control region of D. noxia. All repeat units in D. noxia could be folded into stem-loop secondary structures, which could further promote an increase in copy numbers. Characterization of the D. noxia mitogenome revealed distinct mitogenome architectures, thus advancing our understanding of insect mitogenomic diversities and evolution.

A history of environmental management in the field in Queensland : episodes of activity

This paper reviews a wide range of literature on environmental management in the field in Queensland, and analyzes this by period and by author. An episodic pattern of activities since European settlement is evident. Periods of exploration (pre-1950) and inventory- compilation (ca. 1950-1970) were followed by two decades of media and non-government organization campaigning (ca. 1970-1990), then an era dominated by government regulatory action (ca. 1990-2010). These eras dominated public perception of what was happening in environmental practice. They were delineated by historic ‘interventions’ (summarily, the end of World War II, the 1971 inflationary crisis, and computerization respectively).

Benchmarking the standard of environmental management practised in marinas

Most existing marinas are boat parking/storing and servicing facilities that have been built over a long period of time for the convenience of local boat owners.

Ecological design with respect to the environment of large-scale marina developments in Queensland

Ecological principles have been employed to assist in the sustainability of a suite of 'gateway' marinas currently being developed in Queensland. Tasks included (a) location and fostering of core remnant native vegetation areas, (b) understanding the dynamic patterns of region behaviour using the ecological strategies employed by key flora and fauna species, (c) promoting those native wildlife species best characterising the region, and (d) allocating management actions along elongated buffer zones to the catchment headwaters (rather than only peripheral to the property). The design of infrastructure and its relationship to sustainable landscape development is lacking such a response int eh planning and detailing of new marinas. This paper distinguishes between the practice of landscape ecology and the design of ecological landscapes, offering examples of the principles of the latter in support of the concept of ecological landscape practice.

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.

Fast re-parameterisation of Gaussian mixture models for robotics applications

Autonomous navigation and picture compilation tasks require robust feature descriptions or models. Given the non Gaussian nature of sensor observations, it will be shown that Gaussian mixture models provide a general probabilistic representation allowing analytical solutions to the update and prediction operations in the general Bayesian filtering problem. Each operation in the Bayesian filter for Gaussian mixture models multiplicatively increases the number of parameters in the representation leading to the need for a re-parameterisation step. A computationally efficient re-parameterisation step will be demonstrated resulting in a compact and accurate estimate of the true distribution.

Apple skin patterning is associated with differential expression of MYb10

Background Some apple (Malus × domestica Borkh.) varieties have attractive striping patterns, a quality attribute that is important for determining apple fruit market acceptance. Most apple cultivars (e.g. 'Royal Gala') produce fruit with a defined fruit pigment pattern, but in the case of 'Honeycrisp' apple, trees can produce fruits of two different kinds: striped and blushed. The causes of this phenomenon are unknown. Results Here we show that striped areas of 'Honeycrisp' and 'Royal Gala' are due to sectorial increases in anthocyanin concentration. Transcript levels of the major biosynthetic genes and MYB10, a transcription factor that upregulates apple anthocyanin production, correlated with increased anthocyanin concentration in stripes. However, nucleotide changes in the promoter and coding sequence of MYB10 do not correlate with skin pattern in 'Honeycrisp' and other cultivars differing in peel pigmentation patterns. A survey of methylation levels throughout the coding region of MYB10 and a 2.5 Kb region 5' of the ATG translation start site indicated that an area 900 bp long, starting 1400 bp upstream of the translation start site, is highly methylated. Cytosine methylation was present in all three contexts, with higher methylation levels observed for CHH and CHG (where H is A, C or T) than for CG. Comparisons of methylation levels of the MYB10 promoter in 'Honeycrisp' red and green stripes indicated that they correlate with peel phenotypes, with an enrichment of methylation observed in green stripes. Conclusions Differences in anthocyanin levels between red and green stripes can be explained by differential transcript accumulation of MYB10. Different levels of MYB10 transcript in red versus green stripes are inversely associated with methylation levels in the promoter region. Although observed methylation differences are modest, trends are consistent across years and differences are statistically significant. Methylation may be associated with the presence of a TRIM retrotransposon within the promoter region, but the presence of the TRIM element alone cannot explain the phenotypic variability observed in 'Honeycrisp'. We suggest that methylation in the MYB10 promoter is more variable in 'Honeycrisp' than in 'Royal Gala', leading to more variable color patterns in the peel of this cultivar.

Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples

Mutations in the genes encoding for either the biosynthetic or transcriptional regulation of the anthocyanin pathway have been linked to color phenotypes. Generally, this is a loss of function resulting in a reduction or a change in the distribution of anthocyanin. Here, we describe a rearrangement in the upstream regulatory region of the gene encoding an apple (Malus x domestica) anthocyanin-regulating transcription factor, MYB10. We show that this modification is responsible for increasing the level of anthocyanin throughout the plant to produce a striking phenotype that includes red foliage and red fruit flesh. This rearrangement is a series of multiple repeats, forming a minisatellite-like structure that comprises five direct tandem repeats of a 23-bp sequence. This MYB10 rearrangement is present in all the red foliage apple varieties and species tested but in none of the white fleshed varieties. Transient assays demonstrated that the 23-bp sequence motif is a target of the MYB10 protein itself, and the number of repeat units correlates with an increase in transactivation by MYB10 protein. We show that the repeat motif is capable of binding MYB10 protein in electrophoretic mobility shift assays. Taken together, these results indicate that an allelic rearrangement in the promoter of MYB10 has generated an autoregulatory locus, and this autoregulation is sufficient to account for the increase in MYB10 transcript levels and subsequent ectopic accumulation of anthocyanins throughout the plant.