SCORPION2: A database for structure-function analysis of scorpion toxins

Scorpion toxins are important experimental tools for characterization of vast array of ion channels and serve as scaffolds for drug design. General public database entries contain limited annotation whereby rich structure-function information from mutation studies is typically not available. SCORPION2 contains more than 800 records of native and mutant toxin sequences enriched with binding affinity and toxicity information, 624 three-dimensional structures and some 500 references. SCORPION2 has a set of search and prediction tools that allow users to extract and perform specific queries: text searches of scorpion toxin records, sequence similarity search, extraction of sequences, visualization of scorpion toxin structures, analysis of toxic activity, and functional annotation of previously uncharacterized scorpion toxins. The SCORPION2 database is available at http://sdmc.i2r.a-star.edu.sg/scorpion/. (c) 2006 Elsevier Ltd. All rights reserved.

Tree species diversity and ecosystem function: Can tropical multi-species plantations generate greater productivity?

Results from the humid tropics of Australia demonstrate that diverse plantations can achieve greater productivity than monocultures. We found that increases in both the observed species number and the effective species richness were significantly related to increased levels of productivity as measured by stand basal area or mean individual tree basal area. Four of five plantation species were more productive in mixtures with other species than in monocultures, offering on average, a 55% increase in mean tree basal area. A general linear model suggests that species richness had a significant effect on mean individual tree basal area when environmental variables were included in the model. As monoculture plantations are currently the preferred reforestation method throughout the tropics these results suggest that significant productivity and ecological gains could be made if multi-species plantations are more broadly pursued. (c) 2006 Elsevier B.V. All rights reserved.

Establishment of native ecosystems after mining - Australian experience across diverse biogeographic zones

The Australian minerals industry, which is dominated by coal, gold, bauxite, iron ore, base metals and mineral sand operations, is widely scattered across a continent which has a wide range of climatic zones ranging from moist temperate in the south through hot deserts in the centre to moist tropical in the north. There is an emphasis at most mines on establishing native ecosystems after mining, and technologies have had to be developed to ensure successful establishment and stability of these ecosystems under often adverse climatic conditions. This paper describes some of the innovative practices used to establish native ecosystenms in bauxite, mineral sand and coal operations across diverse biogeographic zones. Additionally, brief reference is made to an ecosystem function analysis, which has been developed to assess the success of establishment of these ecosystems. (C) 2001 Elsevier Science B.V. All rights reserved.

Links between tree species, symbiotic fungal diversity and ecosystem functioning in simplified tropical ecosystems

We studied the relationships among plant and arbuscular mycorrhizal (AM) fungal diversity, and their effects on ecosystem function, in a series of replicate tropical forestry plots in the La Selva Biological Station, Costa Rica. Forestry plots were 12 yr old and were either monocultures of three tree species, or polycultures of the tree species with two additional understory species. Relationships among the AM fungal spore community, host species, plant community diversity and ecosystem phosphorus-use efficiency (PUE) and net primary productivity (NPP) were assessed. Analysis of the relative abundance of AM fungal spores found that host tree species had a significant effect on the AM fungal community, as did host plant community diversity (monocultures vs polycultures). The Shannon diversity index of the AM fungal spore community differed significantly among the three host tree species, but was not significantly different between monoculture and polyculture plots. Over all the plots, significant positive relationships were found between AM fungal diversity and ecosystem NPP, and between AM fungal community evenness and PUE. Relative abundance of two of the dominant AM fungal species also showed significant correlations with NPP and PUE. We conclude that the AM fungal community composition in tropical forests is sensitive to host species, and provide evidence supporting the hypothesis that the diversity of AM fungi in tropical forests and ecosystem NPP covaries.

Detecting sugarcane 'orange rust' disease using EO-1 Hyperion hyperspectral imagery

This Letter evaluates several narrow-band indices from EO-1 Hyperion imagery in discriminating sugarcane areas affected by 'orange rust' ( Puccinia kuehnii ) disease. Forty spectral vegetation indices (SVIs), focusing on bands related to leaf pigments, leaf internal structure, and leaf water content, were generated from an image acquired over Mackay, Queensland, Australia. Discriminant function analysis was used to select an optimum set of indices based on their correlations with the discriminant function. The predictive ability of each index was also assessed based on the accuracy of classification. Results demonstrated that Hyperion imagery can be used to detect orange rust disease in sugarcane crops. While some indices that only used visible near-infrared (VNIR) bands (e.g. SIPI and R800/R680) offer separability, the combination of VNIR bands with the moisture-sensitive band (1660 nm) yielded increased separability of rust-affected areas. The newly formulated 'Disease-Water Stress Indices' (DWSI-1=R800/R1660; DSWI-2=R1660/R550; DWSI-5=(R800+R550)/(R1660+R680)) produced the largest correlations, indicating their superior ability to discriminate sugarcane areas affected by orange rust disease.

Addressing shortcomings in the Household Responsibility System - Empirical analysis of the Two-Farmland System in Shandong Province

Despite apparent overwhelming benefits, implementation of the Household Responsibility System (HRS) in China contained a number of flaws. The Two-Farmland System (TFS), which originated in Pingdu City in Shandong Province, sought to address the twin problems of land fragmentation and economies of size. A stochastic frontier production function analysis that isolates the impacts of land allocation reforms suggests that the TFS increased efficiency by around 7%. This article highlights the need for empirical analysis to assess objectively the merits or otherwise of particular reforms. (C) 2002 Elsevier Science Inc. All rights reserved.

Stock discrimination and movements of narrow-barred Spanish mackerel across northern Australia as indicated by parasites

The parasite fauna of Spanish mackerel Scomberomorus commerson from 10 sites across northern Australia and one site in Indonesia, was examined to evaluate the degree of movement and subsequent stock structure of the fish. Kupang fish (Indonesia) had very few Terranova spp.. Grillotia branchi, Otobothrium cysticum or Pterobothrium sp. compared to Australian fish, indicating that no Australian fish enter the Kupang fishery. Univariate and discriminant function analysis of four 'temporary' parasite species, the copepod Pseudocyenoides armatus and the monogeneans Gotocotyla bivaginalis, Pricea multae and Pseudothoracocotyla ovalis, demonstrated little similarity between areas of northern Australia, indicating minimal short-term exchange between neighbouring groups of S. commerson. Analyses of five 'permanent' parasite species, the larval helminths G. branchi, O. cysticum, Pterobothrium sp., Callitetrarhynchus gracilis and Paranybelinia balli, also revealed large differences between areas thus indicating long-term separation. There are at least six parasitological stocks across northern Australia: Fog Bay/Bathurst Island, Cape Wessel. Groote/Sir Edward Pellew. Mornington Island, Weipa. and the Torres Strait. The occurrence of a few irregular fish in the samples suggested that LIP to 5% of fish moved between stocks during their lifetime. The similarity of within-school variability to that between schools showed that the fish do not form long-term school associations. (C) 2003 The Fisheries Society of the British Isles.

Probing the S100 protein family through genomic and functional analysis

The EF-hand superfamily of calcium binding proteins includes the S100, calcium binding protein, and troponin subfamilies. This study represents a genome, structure, and expression analysis of the S100 protein family, in mouse, human, and rat. We confirm the high level of conservation between mammalian sequences but show that four members, including S100A12, are present only in the human genome. We describe three new members of the S100 family in the three species and their locations within the S100 genomic clusters and propose a revised nomenclature and phylogenetic relationship between members of the EF-hand superfamily. Two of the three new genes were induced in bone-marrow-derived macrophages activated with bacterial lipopolysaccharide, suggesting a role in inflammation. Normal human and murine tissue distribution profiles indicate that some members of the family are expressed in a specific manner, whereas others are more ubiquitous. Structure-function analysis of the chemotactic properties of murine S100A8 and human S100A12, particularly within the active hinge domain, suggests that the human protein is the functional homolog of the murine protein. Strong similarities between the promoter regions of human S100A12 and murine S100A8 support this possibility. This study provides insights into the possible processes of evolution of the EF-hand protein superfamily. Evolution of the S100 proteins appears to have occurred in a modular fashion, also seen in other protein families such as the C2H2-type zinc-finger family. (C) 2004 Elsevier Inc. All rights reserved.

Ecosystem response to antibiotics entering the aquatic environment

Awareness of antibiotics in wastewaters and aquatic ecosystems is growing as investigations into alternate pollutants increase and analytical techniques for detecting these chemicals improve. The presence of three antibiotics (ciproffoxacin, norfloxacin and cephalexin) was evaluated in both sewage effluent and environmental waters downstream from a sewage discharge. Bacteria cultured from the sewage bioreactor and receiving waters were tested for resistance against six antibiotics (ciprofloxacin, tetracycline, ampicillin, trimethoprim, erythromycin and trimethoprim/sulphamethoxazole) and effects of short term exposure (24h) to antibiotics on bacterial denitrification rates were examined. Antibiotics were detected entering the sewage treatment plant with varying levels of removal during the treatment process. Antibiotics were also detected in effluent entering receiving waters and detectable 500m from the source. Among the bacteria cultured from the sewage bioreactor, resistance was displayed against all six antibiotics tested and bacteria cultured from receiving waters were resistant against two of the antibiotics tested. Rates of denitrification were observed to decrease in response to some antibiotics and not to others, though this was only observed at concentrations exceeding those likely to be found in the environment. Findings from this preliminary research have indicated that antibiotics are entering our aquatic systems and pose a potential threat to ecosystem function and potentially human health. (c) 2004 Elsevier Ltd. All rights reserved.

Purification and characterization of a plant antimicrobial peptide expressed in Escherichia coli

MiAMP1 is a low-molecular-weight, cysteine-rich, antimicrobial peptide isolated from the nut kernel of Macadamia integrifolia. A DNA sequence encoding MiAMP1 with an additional ATG: start codon was cloned into a modified pET vector under the control of the T7 RNA polymerase promoter. The pET vector was cotransformed together with the vector pSB161, which expresses a rare arginine tRNA. The peptide was readily isolated in high yield from the insoluble fraction of the Escherichia coil extract. The purified peptide was shown to have an identical molecular weight to the native peptide by mass spectroscopy indicating that the N-terminal methionine had been cleaved. Analysis by NMR spectroscopy indicated that the refolded recombinant peptide had a similar overall three-dimensional structure to that of the native peptide. The peptide inhibited the growth of phytopathogenic fungi in vitro in a similar manner to the native peptide. To our knowledge, MiAMP1 is the first antimicrobial peptide from plants to be functionally expressed in E. coil. This will permit a detailed structure-function analysis of the peptide and studies of its mode of action on phytopathogens. (C) 1999 Academic Press.

Biodiversity: bridging the gap between condition and conservation

The aim of this study is to create a two-tiered assessment combining restoration and conservation, both needed for biodiversity management. The first tier of this approach assesses the condition of a site using a standard bioassessment method, AUSRIVAS, to determine whether significant loss of biodiversity has occurred because of human activity. The second tier assesses the conservation value of sites that were determined to be unimpacted in the first step against a reference database. This ensures maximum complementarity without having to set a priori target areas. Using the reference database, we assign site-specific and comparable coefficients for both restoration (Observed/Expected taxa with > 50% probability of occurrence) and conservation values (O/E taxa with < 50%, rare taxa). In a trial on 75 sites on rivers around Sydney, NSW, Australia we were able to identify three regions: (1) an area that may need restoration; (2) an area that had a high conservation value and; (3) a region that was identified as having significant biodiversity loss but with high potential to respond to rehabilitation and become a biodiversity hotspot. These examples highlight the use of the new framework as a comprehensive system for biodiversity assessment.