Showing papers by "Commonwealth Scientific and Industrial Research Organisation published in 2005"

The Transcriptional Landscape of the Mammalian Genome

Abstract: This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.

Genes and salt tolerance: bringing them together.

Abstract: Salinity tolerance comes from genes that limit the rate of salt uptake from the soil and the transport of salt throughout the plant, adjust the ionic and osmotic balance of cells in roots and shoots, and regulate leaf development and the onset of senescence. This review lists some candidate genes for salinity tolerance, and draws together hypotheses about the functions of these genes and the specific tissues in which they might operate. Little has been revealed by gene expression studies so far, perhaps because the studies are not tissue-specific, and because the treatments are often traumatic and unnatural. Suggestions are made to increase the value of molecular studies in identifying genes that are important for salinity tolerance.

Living radical polymerization by the RAFT process

Abstract: This paper presents a review of living radical polymerization achieved with thiocarbonylthio compounds [ZC(=S)SR] by a mechanism of reversible addition–fragmentation chain transfer (RAFT). Since we first introduced the technique in 1998, the number of papers and patents on the RAFT process has increased exponentially as the technique has proved to be one of the most versatile for the provision of polymers of well defined architecture. The factors influencing the effectiveness of RAFT agents and outcome of RAFT polymerization are detailed. With this insight, guidelines are presented on how to conduct RAFT and choose RAFT agents to achieve particular structures. A survey is provided of the current scope and applications of the RAFT process in the synthesis of well defined homo-, gradient, diblock, triblock, and star polymers, as well as more complex architectures including microgels and polymer brushes.

Determinants of woody cover in African savannas

Abstract: Savannas are globally important ecosystems of great significance to human economies. In these biomes, which are characterized by the co-dominance of trees and grasses, woody cover is a chief determinant of ecosystem properties1–3. The availability of resources (water, nutrients) and disturbance regimes (fire, herbivory) are thought to be important in regulating woody cover1,2,4,5, but perceptions differ on which of these are the primary drivers of savanna structure. Here we show, using data from 854 sites across Africa, that maximum woody cover in savannas receiving a mean annual precipitation (MAP) of less than ,650mm is constrained by, and increases linearly with, MAP. These arid and semi-arid savannas may be considered ‘stable' systems in which water constrains woody cover and permits grasses to coexist, while fire, herbivory and soil properties interact to reduce woody cover below the MAP-controlled upper bound. Above a MAP of ,650mm, savannas are ‘unstable' systems in which MAP is sufficient for woody canopy closure, and disturbances (fire, herbivory) are required for the coexistence of trees and grass. These results provide insights into the nature of African savannas and suggest that future changes in precipitation6 may considerably affect their distribution and dynamics.

Strong, Transparent, Multifunctional, Carbon Nanotube Sheets

Abstract: Individual carbon nanotubes are like minute bits of string, and many trillions of these invisible strings must be assembled to make useful macroscopic articles. We demonstrated such assembly at rates above 7 meters per minute by cooperatively rotating carbon nanotubes in vertically oriented nanotube arrays (forests) and made 5-centimeter-wide, meter-long transparent sheets. These self-supporting nanotube sheets are initially formed as a highly anisotropic electronically conducting aerogel that can be densified into strong sheets that are as thin as 50 nanometers. The measured gravimetric strength of orthogonally oriented sheet arrays exceeds that of sheets of high-strength steel. These nanotube sheets have been used in laboratory demonstrations for the microwave bonding of plastics and for making transparent, highly elastomeric electrodes; planar sources of polarized broad-band radiation; conducting appliques; and flexible organic light-emitting diodes.

Climate change and marine plankton

Abstract: Understanding how climate change will affect the planet is a key issue worldwide. Questions concerning the pace and impacts of climate change are thus central to many ecological and biogeochemical studies, and addressing the consequences of climate change is now high on the list of priorities for funding agencies. Here, we review the interactions between climate change and plankton communities, focusing on systematic changes in plankton community structure, abundance, distribution and phenology over recent decades. We examine the potential socioeconomic impacts of these plankton changes, such as the effects of bottom-up forcing on commercially exploited fish stocks (i.e. plankton as food for fish). We also consider the crucial roles that plankton might have in dictating the future pace of climate change via feedback mechanisms responding to elevated atmospheric CO 2 levels. An important message emerges from this review: ongoing plankton monitoring programmes worldwide will act as sentinels to identify future changes in marine ecosystems.

Trading water for carbon with biological carbon sequestration

Abstract: Carbon sequestration strategies highlight tree plantations without considering their full environmental consequences. We combined field research, synthesis of more than 600 observations, and climate and economic modeling to document substantial losses in stream flow, and increased soil salinization and acidification, with afforestation. Plantations decreased stream flow by 227 millimeters per year globally (52%), with 13% of streams drying completely for at least 1 year. Regional modeling of U.S. plantation scenarios suggests that climate feedbacks are unlikely to offset such water losses and could exacerbate them. Plantations can help control groundwater recharge and upwelling but reduce stream flow and salinize and acidify some soils.

Zero tolerance ecology: improving ecological inference by modelling the source of zero observations

Abstract: A common feature of ecological data sets is their tendency to contain many zero values. Statistical inference based on such data are likely to be inefficient or wrong unless careful thought is given to how these zeros arose and how best to model them. In this paper, we propose a framework for understanding how zero-inflated data sets originate and deciding how best to model them. We define and classify the different kinds of zeros that occur in ecological data and describe how they arise: either from 'true zero' or 'false zero' observations. After reviewing recent developments in modelling zero-inflated data sets, we use practical examples to demonstrate how failing to account for the source of zero inflation can reduce our ability to detect relationships in ecological data and at worst lead to incorrect inference. The adoption of methods that explicitly model the sources of zero observations will sharpen insights and improve the robustness of ecological analyses.

Vegetation patches and runoff–erosion as interacting ecohydrological processes in semiarid landscapes

Abstract: Ecological and hydrological processes can interact strongly in landscapes, yet these processes are often studied separately. One particularly important interaction between these processes in patchy semiarid lands is how vegetation patches serve to obstruct runoff and then how this retained water increases patch growth that, in turn, provides feedbacks to the system. Such ecohydrological interactions have been mostly demonstrated for semiarid landscapes with distinctly banded vegetation patterns. In this paper, we use data from our studies and from the literature to evaluate how strongly four ecohydrological interactions apply across other patchy semiarid vegetations, and how these interactions are affected by disturbances. We specifically address four questions concerning ecohydrological interactions: (1) if vegetation patches obstruct runoff flows during rainfall events, how much more soil water is stored in these patches compared to open interpatch areas; (2) if inputs of water are higher in patches, how much stronger is the pulse of plant growth compared to interpatches; (3) if more soil water in patches promotes greater biological activity by organisms such as earthworms that create macropores, how much does this improve soil infiltrability; and (4) if vegetation patches are damaged on a hillslope, how much does this increase runoff and erosion and decrease biomass production? We used the trigger-transfer-reserve-pulse framework developed for Australian semiarid woodlands to put these four questions into a landscape context. For a variety of patchy semiarid vegetation types in Australia, Europe, and North America, we found that patches significantly stored more soil water, produced more growth and had better infiltrability than interpatches, and that runoff and erosion can markedly increase on disturbed hillslopes. However, these differences varied greatly and appeared to depend on factors such as the intensity and amount of input events (rainstorms) and type of topography, soils, and vegetation. Exper- imental and modeling studies are needed to better quantify how these factors specifically affect ecohydrological interactions. Our current findings do support the conclusion that vegetation patches and runoff-erosion processes do strongly interact in many semiarid landscapes across the globe, not just banded landscapes.

The Arecibo Legacy Fast ALFA survey. I. Science goals, survey design, and strategy

Abstract: The recently initiated Arecibo Legacy Fast ALFA (ALFALFA) survey aims to map ~7000 deg2 of the high Galactic latitude sky visible from Arecibo, providing a H I line spectral database covering the redshift range between -1600 and 18,000 km (s-1) with ~5 km s(-1) resolution. Exploiting Arecibo's large collecting area and small beam size, ALFALFA is specifically designed to probe the faint end of the H I mass function in the local universe and will provide a census of H I in the surveyed sky area to faint flux limits, making it especially useful in synergy with wide-area surveys conducted at other wavelengths. ALFALFA will also provide the basis for studies of the dynamics of galaxies within the Local Supercluster and nearby superclusters, allow measurement of the H I diameter function, and enable a first wide-area blind search for local H I tidal features, H I absorbers at z < 0.06, and OH megamasers in the redshift range 0.16 < z < 0.25. Although completion of the survey will require some 5 years, public access to the ALFALFA data and data products will be provided in a timely manner, thus allowing its application for studies beyond those targeted by the ALFALFA collaboration. ALFALFA adopts a two-pass, minimum intrusion, drift scan observing technique that samples the same region of sky at two separate epochs to aid in the discrimination of cosmic signals from noise and terrestrial interference. Survey simulations, which take into account large-scale structure in the mass distribution and incorporate experience with the ALFA system gained from tests conducted during its commissioning phase, suggest that ALFALFA will detect on the order of 20,000 extragalactic H I line sources out to z ~ 0.06, including several hundred with H I masses M(HI) < 10(7.5) M ?.

Giant Porphyry Deposits: Characteristics, Distribution, and Tectonic Controls

Abstract: More than half of the 25 largest known porphyry copper deposits, defined in terms of contained copper metal, formed during three time periods: the Paleocene to Eocene, Eocene to Oligocene, and middle Miocene to Pliocene. These giant deposits are clustered within three provinces, central Chile, northern Chile, and southwest Arizona-northern Mexico. Other giant deposits occur in Montana, Utah, Panama, Peru, Argentina, Irian Jaya, Mongolia, and Iran. Compressive tectonic environments, thickened continental crust, and active uplift and erosion were associated with the formation of many of these deposits. Calc-alkalic magmas are most favorable for the formation of giant porphyry copper deposits, although several of the largest systems are associated with high K calc-alkalic intrusions. The 25 largest gold-rich porphyry deposits are concentrated in the southwest Pacific and South America, with other occurrences in Eurasia, British Columbia, Alaska, and New South Wales. Many of the deposits formed in the last 13 m.y. The largest of the deposits are associated with high K calc-alkalic intrusions. Many calc-alkalic porphyritic intrusions have also produced giant gold-rich porphyries. In the last 20 m.y., the formation of giant porphyry copper-molybdenum and copper-gold deposits in the circum-Pacific region has been closely associated with subduction of aseismic ridges, seamount chains, and oceanic plateaus beneath oceanic island and continental arcs. In several examples, these tectonic perturbations have promoted flat-slab subduction, crustal thickening, uplift and erosion, and adakitic magmatism coeval with the formation of well-endowed porphyry and/or epithermal mineral provinces. Similar tectonic features are inferred to be associated with the giant porphyry copper-molybdenum provinces of northern Chile (Eocene-Oligocene) and southwest United States (Cretaceous-Paleocene). Topographic and thermal anomalies on the downgoing slab appear to act as tectonic triggers for porphyry ore formation. Other factors, such as sutures in the overriding plate, permeability architecture of the upper crust, efficient processes of ore transport and deposition, and, in some cases, formation and preservation of supergene enrichment blankets are also vital for the development of high-grade giant ore deposits. A low-grade geochemical anomaly may be the final product of mineralization, if ore-forming processes do not operate efficiently, even in the most favorable geodynamic settings.

Data collection, storage, and retrieval with an underwater sensor network

Abstract: In this paper we present a novel platform for underwater sensor networks to be used for long-term monitoring of coral reefs and fisheries. The sensor network consists of static and mobile underwater sensor nodes. The nodes communicate point-to-point using a novel high-speed optical communication system integrated into the TinyOS stack, and they broadcast using an acoustic protocol integrated in the TinyOS stack. The nodes have a variety of sensing capabilities, including cameras, water temperature, and pressure. The mobile nodes can locate and hover above the static nodes for data muling, and they can perform network maintenance functions such as deployment, relocation, and recovery. In this paper we describe the hardware and software architecture of this underwater sensor network. We then describe the optical and acoustic networking protocols and present experimental networking and data collected in a pool, in rivers, and in the ocean. Finally, we describe our experiments with mobility for data muling in this network.

The Arabidopsis GAMYB-Like Genes, MYB33 and MYB65, Are MicroRNA-Regulated Genes That Redundantly Facilitate Anther Development

Abstract: The functions of the vast majority of genes encoding R2R3 MYB domain proteins remain unknown. The closely related MYB33 and MYB65 genes of Arabidopsis thaliana have high sequence similarity to the barley (Hordeum vulgare) GAMYB gene. T-DNA insertional mutants were isolated for both genes, and a myb33 myb65 double mutant was defective in anther development. In myb33 myb65 anthers, the tapetum undergoes hypertrophy at the pollen mother cell stage, resulting in premeiotic abortion of pollen development. However, myb33 myb65 sterility was conditional, where fertility increased both under higher light or lower temperature conditions. Thus, MYB33/MYB65 facilitate, but are not essential for, anther development. Neither single mutant displayed a phenotype, implying that MYB33 and MYB65 are functionally redundant. Consistent with functional redundancy, promoter–β-glucuronidase (GUS) fusions of MYB33 and MYB65 gave identical expression patterns in flowers (sepals, style, receptacle, anther filaments, and connective but not in anthers themselves), shoot apices, and root tips. By contrast, expression of a MYB33:GUS translational fusion in flowers was solely in young anthers (consistent with the male sterile phenotype), and no staining was seen in shoot meristems or root tips. A microRNA target sequence is present in the MYB genes, and mutating this sequence in the MYB33:GUS fusion results in an expanded expression pattern, in tissues similar to that observed in the promoter-GUS lines, implying that the microRNA target sequence is restricting MYB33 expression. Arabidopsis transformed with MYB33 containing the mutated microRNA target had dramatic pleiotrophic developmental defects, suggesting that restricting MYB33 expression, especially in the shoot apices, is essential for proper plant development.

Synthesis and properties of crosslinked recombinant pro-resilin.

Abstract: The elastic properties of the protein called resilin were discovered about 40 years ago during studies of the flight systems of locusts and dragonflies. It is used in repetitive tasks by most insects, including jumping fleas and chirping cicadas. Resilin is formed by crosslinking of a precursor protein, pro-resilin. The elastic region of pro-resilin has now been isolated in pure form in large quantities following expression of its gene in Escherichia coli. The recombinant pro-resilin can be photochemically crosslinked into a rubber-like material with many of the properties of natural resilin. The synthetic material can be cast into useful shapes, and its capacity to recover after deformation exceeds that of high-resilience rubber, making it a promising candidate for industrial and in situ biomedical applications. Resilin is a member of a family of elastic proteins that includes elastin, as well as gluten, gliadin, abductin and spider silks. Resilin is found in specialized regions of the cuticle of most insects, providing low stiffness, high strain and efficient energy storage1,2; it is best known for its roles in insect flight3,4 and the remarkable jumping ability of fleas5,6 and spittle bugs7. Previously, the Drosophila melanogaster CG15920 gene was tentatively identified as one encoding a resilin-like protein8,9 (pro-resilin). Here we report the cloning and expression of the first exon of the Drosophila CG15920 gene as a soluble protein in Escherichia coli. We show that this recombinant protein can be cast into a rubber-like biomaterial by rapid photochemical crosslinking. This observation validates the role of the putative elastic repeat motif in resilin function. The resilience (recovery after deformation) of crosslinked recombinant resilin was found to exceed that of unfilled synthetic polybutadiene, a high resilience rubber. We believe that our work will greatly facilitate structural investigations into the functional properties of resilin and shed light on more general aspects of the structure of elastomeric proteins. In addition, the ability to rapidly cast samples of this biomaterial may enable its use in situ for both industrial and biomedical applications.

MINISEED3 (MINI3), a WRKY family gene, and HAIKU2 (IKU2), a leucine-rich repeat (LRR) KINASE gene, are regulators of seed size in Arabidopsis.

Abstract: We have identified mutant alleles of two sporophytically acting genes, HAIKU2 (IKU2) and MINISEED3 (MINI3). Homozygotes of these alleles produce a small seed phenotype associated with reduced growth and early cellularization of the endosperm. This phenotype is similar to that described for another seed size gene, IKU1. MINI3 encodes WRKY10, a WRKY class transcription factor. MINI3 promoter::GUS fusions show the gene is expressed in pollen and in the developing endosperm from the two nuclei stage at ≈12 hr postfertilization to endosperm cellularization at ≈96 hr. MINI3 is also expressed in the globular embryo but not in the late heart stage of embryo development. The early endosperm expression of MINI3 is independent of its parent of origin. IKU2 encodes a leucine-rich repeat (LRR) KINASE (At3g19700). IKU2::GUS has a similar expression pattern to that of MINI3. The patterns of expression of the two genes and their similar phenotypes indicate they may operate in the same genetic pathway. Additionally, we found that both MINI3 and IKU2 showed decreased expression in the iku1-1 mutant. IKU2 expression was reduced in a mini3-1 background, whereas MINI3 expression was unaltered in the iku2-3 mutant. These data suggest the successive action of the three genes IKU1, IKU2, and MINI3 in the same pathway of seed development.

Governing Water: Contentious Transnational Politics and Global Institution Building

Abstract: Water is a key component of critical ecosystems, a marketable commodity, a foundation of local communities and cultures, and a powerful means of social control. It has become a source of contentious politics and social controversy on a global scale, and the management of water conflicts is one of the biggest challenges in the effort to achieve effective global environmental governance.In Governing Water, Ken Conca examines political struggles to create a global framework for the governance of water. Threats to the world's rivers, watersheds, and critical freshwater ecosystems have resisted the establishment of effective global agreements through intergovernmental bargaining because the conditions for successful interstate cooperation -- effective state authority, stable knowledge frameworks, and a territorialized understanding of nature -- cannot be imposed upon water controversies. But while interstate water diplomacy has faltered, less formalized institutions -- socially and politically embedded rules, roles, and practices -- have emerged to help shape water governance locally and globally.Conca examines the politics of these institutions, presenting a framework for understanding global environmental governance based on key institutional presumptions about territoriality, authority, and knowledge. He maps four distinct processes of institution building: formal international regimes for shared rivers; international networking among water experts and professionals; social movements opposing the construction of large dams; and the struggle surrounding transnational water "marketization." These cases illustrate the potential for alternative institutional forms in situations where traditional interstate regimes are ineffective.

Proanthocyanidin Synthesis and Expression of Genes Encoding Leucoanthocyanidin Reductase and Anthocyanidin Reductase in Developing Grape Berries and Grapevine Leaves

Abstract: Proanthocyanidins (PAs), also called condensed tannins, can protect plants against herbivores and are important quality components of many fruits. Two enzymes, leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR), can produce the flavan-3-ol monomers required for formation of PA polymers. We isolated and functionally characterized genes encoding both enzymes from grapevine (Vitis vinifera L. cv Shiraz). ANR was encoded by a single gene, but we found two highly related genes encoding LAR. We measured PA content and expression of genes encoding ANR, LAR, and leucoanthocyanidin dioxygenase in grape berries during development and in grapevine leaves, which accumulated PA throughout leaf expansion. Grape flowers had high levels of PA, and accumulation continued in skin and seeds from fruit set until the onset of ripening. VvANR was expressed throughout early flower and berry development, with expression increasing after fertilization. It was expressed in berry skin and seeds until the onset of ripening, and in expanding leaves. The genes encoding LAR were expressed in developing fruit, particularly in seeds, but had low expression in leaves. The two LAR genes had different patterns of expression in skin and seeds. During grape ripening, PA levels decreased in both skin and seeds, and expression of genes encoding ANR and LAR were no longer detected. The results indicate that PA accumulation occurs early in grape development and is completed when ripening starts. Both ANR and LAR contribute to PA synthesis in fruit, and the tissue and temporal-specific regulation of the genes encoding ANR and LAR determines PA accumulation and composition during grape berry development.

Haustorially Expressed Secreted Proteins from Flax Rust Are Highly Enriched for Avirulence Elicitors

Abstract: Rust fungi, obligate biotrophs that cause disease and yield losses in crops such as cereals and soybean (Glycine max), obtain nutrients from the host through haustoria, which are specialized structures that develop within host cells. Resistance of flax (Linum usitatissimum) to flax rust (Melampsora lini) involves the induction of a hypersensitive cell death response at haustoria formation sites, governed by gene-for-gene recognition between host resistance and pathogen avirulence genes. We identified genes encoding haustorially expressed secreted proteins (HESPs) by screening a flax rust haustorium-specific cDNA library. Among 429 unigenes, 21 HESPs were identified, one corresponding to the AvrL567 gene. Three other HESPs cosegregated with the independent AvrM, AvrP4, and AvrP123 loci. Expression of these genes in flax induced resistance gene–mediated cell death with the appropriate specificity, confirming their avirulence activity. AvrP4 and AvrP123 are Cys-rich proteins, and AvrP123 contains a Kazal Ser protease inhibitor signature, whereas AvrM contains no Cys residues. AvrP4 and AvrM induce cell death when expressed intracellularly, suggesting their translocation into plant cells during infection. However, secreted AvrM and AvrP4 also induce necrotic responses, with secreted AvrP4 more active than intracellular AvrP4, possibly as a result of enhanced formation of endoplasmic reticulum–dependent disulfide bonds. Addition of an endoplasmic reticulum retention signal inhibited AvrM-induced necrosis, suggesting that both AvrM and AvrP4 can reenter the plant cell after secretion in the absence of the pathogen.

Crop residue management for nutrient cycling and improving soil productivity in rice-based cropping systems in the tropics

Abstract: Publisher Summary Crop residues, usually considered a problem, when managed correctly can improve soil organic matter dynamics and nutrient cycling, thereby creating a rather favorable environment for plant growth. The intelligent management and utilization of crop residues is essential for the improvement of soil quality and crop productivity under rice-based cropping systems of the tropics. Viable option is to retain residue in the field; burning should be avoided. The major issue is adapting drills to sow into loose residues. Strategies include chopping and spreading of straw during or after combining or the use of disc-type trash drills. Residues rich in lignin and polyphenol contents experience the lowest decay. Decomposition of crop residues occurs at a rapid rate—about 80% of crop residue C is lost in the first year—under the warm and humid conditions of the tropics. Factors that control C decomposition also affect the N mineralization from the crop residues. Decomposition of poor-quality residues with low N contents, high C:N ratios, and high lignin and polyphenol contents generally results in microbial immobilization of soil and fertilizer N. Nutrient cycling in the soil–plant ecosystem is an essential component of sustainable productive agricultural enterprise. Although during the last three decades, fertilization practices have played a dominant role in the rice-based cropping systems, crop residues—the harvest remnants of the previous crop still play an essential role in the cycling of nutrients. Incorporation of crop residues alters the soil environment that in turn influences the microbial population and activity in the soil and subsequent nutrient transformations.

Which ecological indicators can robustly detect effects of fishing

Abstract: Many ecological indicators have been proposed to detect and describe the effects of fishing on marine ecosystems, but few have been evaluated formally. Here, simulation models of two marine systems off southeastern Australia (a large marine embayment, and an EEZ-scale regional marine ecosystem) are used to evaluate the performance of a suite of ecological indicators. The indicators cover species, assemblages, habitats, and ecosystems, including quantities derived from models such as Ecopath. The simulation models, based on the Atlantis framework, incorporate the effects of fishing from several fishing gears, and also the confounding impacts of other broad-scale pressures on the ecosystems (e.g. increased nutrient loads). These models are used to provide fishery-dependent and fishery-independent pseudo-data from which the indicators are calculated. Indicator performance is quantified by the ability to detect and/or predict trends in key variables of interest (“attributes”), the true values of which are known from the simulation models. The performance of each indicator is evaluated across a range of ecological and fishing scenarios. Results suggest that indicators at the community level of organization are the most reliable, and that it is necessary to use a variety of indicators simultaneously to detect the full range of impacts from fishing. Several key functional groups provide a good characterization of ecosystem state, or indicate the cause of broader ecosystem changes in most instances.