Using biplots to interpret gene expression patterns in plants

Sum: Plant biologists in fields of ecology, evolution, genetics and breeding frequently use multivariate methods. This paper illustrates Principal Component Analysis (PCA) and Gabriel's biplot as applied to microarray expression data from plant pathology experiments. Availability: An example program in the publicly distributed statistical language R is available from the web site (www.tpp.uq.edu.au) and by e-mail from the contact. Contact: scott.chapman@csiro.au.

Are we too busy to volunteer? The relationship between time and volunteering using the 1997 ABS Time Use Data

Time availability is a key concept in relation to volunteering, leading to organisations and governments targeting those outside paid work as a potential source of volunteers. It may be that factors such as a growth in female participation in the labour market and an increase in work hours will lead to more people saying they are simply too busy to volunteer This paper discusses how social and economic change, such as changing work patterns, are impacting on time availability. Using the 1997 ABS Time Use data, it identifies a predictive model of spare time by looking at demographic, life stage and employment related variables. Results confirm that those outside paid work, particularly the young, males and those without partners or children, are the groups most likely to have time to spare. These groups do not currently report high rates of volunteering. The paper concludes by questioning the premise that people will volunteer simply because they have time to spare. This is just one component of a range of motivations and factors that influence the decision to volunteer.

Characterization of a novel protein with homology to C-type lectins expressed by the Cotesia rubecula bracovirus in larvae of the lepidopteran host, Pieris rapae

Polydnaviruses are essential for the survival of many Ichneumonoid endoparasitoids, providing active immune suppression of the host in which parasitoid larvae develop. The Cotesia rubecula bracovirus is unique among polydnaviruses in that only four major genes are detected in parasitized host ( Pieris rapae) tissues, and gene expression is transient. Here we describe a novel C. rubecula bracovirus gene (CrV3) encoding a lectin monomer composed of 159 amino acids, which has conserved residues consistent with invertebrate and mammalian C-type lectins. Bacterially expressed CrV3 agglutinated sheep red blood cells in a divalent ion-dependent but Ca2+-independent manner. Agglutination was inhibited by EDTA but not by biological concentrations of any saccharides tested. Two monomers of similar to14 and similar to17 kDa in size were identified on SDS-PAGE in parasitized P. rapae larvae. The 17-kDa monomer was found to be an N-glyscosylated form of the 14-kDa monomer. CrV3 is produced in infected hemocytes and fat body cells and subsequently secreted into hemolymph. We propose that CrV3 is a novel lectin, the first characterized from an invertebrate virus. CrV3 shows over 60% homology with hypothetical proteins isolated from polydnaviruses in two other Cotesia wasps, indicating that these proteins may also be C-type lectins and that a novel polydnavirus lectin family exists in Cotesia-associated bracoviruses. CrV3 is probably interacting with components in host hemolymph, resulting in suppression of the Pieris immune response. The high similarity of CrV3 with invertebrate lectins, as opposed to those from viruses, may indicate that some bracovirus functions were acquired from their hosts.

Causes and consequences of long-term climatic variability on the Australian continent

1. Ice-volume forced glacial-interglacial cyclicity is the major cause of global climate variation within the late Quaternary period. Within the Australian region, this variation is expressed predominantly as oscillations in moisture availability. Glacial periods were substantially drier than today with restricted distribution of mesic plant communities, shallow or ephemeral water bodies and extensive aeolian dune activity. 2. Superimposed on this cyclicity in Australia is a trend towards drier and/or more variable climates within the last 350 000 years. This trend may have been initiated by changes in atmospheric and ocean circulation resulting from Australia's continued movement into the Southeast Asian region and involving the onset or intensification of the El Nino-Southern Oscillation system and a reduction in summer monsoon activity. 3. Increased biomass burning, stemming originally from increased climatic variability and later enhanced by activities of indigenous people, resulted in a more open and sclerophyllous vegetation, increased salinity and a further reduction in water availability. 4. Past records combined with recent observations suggest that the degree of environmental variability will increase and the drying trend will be enhanced in the foreseeable future, regardless of the extent or nature of human intervention.

Identification of novel "pathologs" (human disease-related gene candidates) from the RIKEN full-length mouse cDNA data set

The majority of common diseases such as cancer, allergy, diabetes, or heart disease are characterized by complex genetic traits, in which genetic and environmental components contribute to disease susceptibility. Our knowledge of the genetic factors underlying most of such diseases is limited. A major goal in the post-genomic era is to identify and characterize disease susceptibility genes and to use this knowledge for disease treatment and prevention. More than 500 genes are conserved across the invertebrate and vertebrate genomes. Because of gene conservation, various organisms including yeast, fruitfly, zebrafish, rat, and mouse have been used as genetic models.

Late Quaternary Milankovitch-scale climatic change and variability and its impact on monsoonal Australasia

Four pollen and charcoal records derived from marine cores around the northern perimeter of Australia are examined to provide a regional picture of patterns, causes and impacts of climate change over the last 100-300 ka. The availability of radiocarbon dates and oxygen isotope records for the cores provides primary chronological control. Spectral analysis of components of these records demonstrates an overall importance of Milankovitch frequencies with clear glacial-interglacial cyclicity dominated by variation in precipitation. In addition, a number of pollen taxa, as well as charcoal particles, exhibit a 30 ka frequency that is considered, from its relationship with biomass burning and with results of past modelling, to reflect changes in the intensity of El Nino-Southern Oscillation (ENSO) variability. Pollen components of all records show a decline, frequently stepwise, in more fire-sensitive vegetation and its replacement with more fire-tolerant vegetation. There is some evidence that this trend is linked to an onset or general increase in ENSO activity and perhaps also to variation in monsoon activity dating from about 300 ka BP that was caused by changes to oceanic circulation within the Indonesian region. The trend may have accelerated within the last 45 ka due to burning by indigenous people. (C) 2003 Elsevier B.V. All rights reserved.

Effects of settler size and density on early post-settlement survival of Ciona intestinalis in the field

Effects of variation in larval quality on post-metamorphic performance in marine invertebrates are increasingly apparent. Recently, it has been shown that variation in offspring size can also strongly affect post-settlement survival, but variation in environmental conditions can mediate this effect. The quality of habitat into which marine invertebrate larvae settle can vary markedly, and 1 influence on quality is the number of conspecifics present. We tested the effects of settler size and settler density on early (1 wk after settlement) post-settlement survival in the field for the solitary ascidian Ciona intestinalis. Larger settlers survived better than smaller settlers, within and among groups of siblings. Increases in the density of settlers decreased survival, but the density-dependent effects were much stronger for smaller settlers. We suggest that larger settlers are better able to cope with intra-specific competition because they have greater energetic reserves or a greater capacity to feed than smaller settlers.

Analysis of soil wetting and solute transport in subsurface trickle irrigation

The increased use of trickle or drip irrigation is seen as one way of helping to improve the sustainability of irrigation systems around the world. However, soil water and solute transport properties and soil profile characteristics are often not adequately incorporated in the design and management of trickle systems. In this paper, we describe results of a simulation study designed to highlight the impacts of soil properties on water and solute transport from buried trickle emitters. The analysis addresses the influence of soil hydraulic properties, soil layering, trickle discharge rate, irrigation frequency, and timing of nutrient application on wetting patterns and solute distribution. We show that (1) trickle irrigation can improve plant water availability in medium and low permeability fine-textured soils, providing that design and management are adapted to account for their soil hydraulic properties, (2) in highly permeable coarse-textured soils, water and nutrients move quickly downwards from the emitter, making it difficult to wet the near surface zone if emitters are buried too deep, and (3) changing the fertigation strategy for highly permeable coarse-textured soils to apply nutrients at the beginning of an irrigation cycle can maintain larger amounts of nutrient near to and above the emitter, thereby making them less susceptible to leaching losses. The results demonstrate the need to account for differences in soil hydraulic properties and solute transport when designing irrigation and fertigation management strategies. Failure to do this will result in inefficient systems and lost opportunities for reducing the negative environmental impacts of irrigation.

Potential triggers for akinete differentiation in an Australian strain of the cyanobacterium Cylindrospermopsis raciborskii (AWT 205/1)

Understanding the triggers for some cyanobacteria of the Nostocales and Stigonematales orders to produce specialised reproductive cells termed akinetes, is very important to gain further insights into their ecology. By improving our understanding of their life cycle, appropriate management options may be devised to control the formation of these cells, and therefore the potential bloom inoculum which they are thought to provide, may be reduced. This study investigated the effect of chemical (phosphorus limitation), and environmental variables (temperature shock) on akinete differentiation in the freshwater cyanobacterium Cylindrospermopsis raciborskii (AWT 205/1). From the preliminary results, it is suggested that the availability of phosphorus and changes in temperature were a necessary requirement for the formation of akinetes in this particular strain of C. raciborskii. In the four phosphorus treatments investigated (0, 3, 38 and 75 mug l(-1) P), only the two higher treatments produced akinetes (approximately 220 ml(-1)). When the first akinetes were observed in the 38 and 75 mug l(-1) P treatments, filterable reactive phosphorus (FRP) concentrations in the medium were approximately 22 and 52 mug l(-1) P, respectively, indicating that there was no phosphorus limitation. In the temperature shock experiment, akinetes were observed in the 15 and 20degreesC treatments. However, akinetes were degraded (pale yellow colour, limited swelling and shrivelled edges) and in much lower concentrations, which was thought to be a result of the daily temperature shock. We suggest that the formation of akinetes in C. raciborskii (AWT 205/1) can be triggered by an initial temperature shock and that phosphorus is a necessary requirement to allow further growth and full development of akinetes.

Continuous reproduction and recruitment in the narrowback mud crab Panopeus americanus (Brachyura, Panopeidae) in a remnant human-impacted mangrove area

The population structure, reproductive period, and juvenile recruitment of Panopeus americanus were studied in order to enhance knowledge of its life cycle and reproductive strategy and promote the maintenance of its natural stocks in an impacted region. Specimens were collected in the remnant human-impacted mangrove at Araca, state of Sao Paulo, Brazil, at two-month intervals from January to November 2005, at low tide, with a capture effort by three people. The crabs were measured (carapace width, CW) and sexed. The total catch was 275 animals, including 132 males (48.0%); 127 females (46.2%), of which 39 were ovigerous (14.2% of total catch); and 16 individuals whose sex could not be identified (5.8%). No correlation was observed between water temperature and the number of collected individuals; however, there was a significant, positive correlation with salinity. Males were significantly larger than females. The size-frequency distribution was bimodal, reflecting the occurrende of more than one recruitment pulse and the differential abundance of adults during the period of study. The overall sex ratio was 1:0.97 favoring males, and was not significantly different from the expected value, i.e., this population fits the anomalous pattern of sex occurrence in size classes. Ovigerous females were captured in all sampled months, which explain the continuous recruitment observed. Expected low levels of individuals of different size classes in the population were not confirmed. All population aspects found here allowed us to infer that this population of P. americanus is well established in the impacted mangrove by virtue of its reproductive strategy.

Cost-effectiveness of dexamphetamine and methylphenidate for the treatment of childhood attention deficit hyperactivity disorder

Objective: To analyze from a health sector perspective the cost-effectiveness of dexamphetamine (DEX) and methylphenidate (MPH) interventions to treat childhood attention deficit hyperactivity disorder (ADHD), compared to current practice. Method: Children eligible for the interventions are those aged between 4 and 17 years in 2000, who had ADHD and were seeking care for emotional or behavioural problems, but were not receiving stimulant medication. To determine health benefit, a meta-analysis of randomized controlled trials was performed for DEX and MPH, and the effect sizes were translated into utility values. An assessment on second stage filter criteria ('equity', 'strength of evidence', 'feasibility' and 'acceptability to stakeholders') is also undertaken to incorporate additional factors that impact on resource allocation decisions. Simulation modelling techniques are used to present a 95% uncertainty interval (UI) around the incremental cost-effectiveness ratio (ICER), which is calculated in cost (in A$) per DALY averted. Results: The ICER for DEX is A$4100/DALY saved (95% UI: negative to A$14 000) and for MPH is A$15 000/DALY saved (95% UI: A$9100-22 000). DEX is more costly than MPH for the government, but much less costly for the patient. Conclusions: MPH and DEX are cost-effective interventions for childhood ADHD. DEX is more cost-effective than MPH, although if MPH were listed at a lower price on the Pharmaceutical Benefits Scheme it would become more cost-effective. Increased uptake of stimulants for ADHD would require policy change. However, the medication of children and wider availability of stimulants may concern parents and the community.

Shelter association between the hermit crab Sympagurus dimorphus and the zoanthid Epizoanthus paguricola in the southwestern Atlantic Ocean

Schejter, L. and Mantelatto, F.L. 2011. Shelter association between the hermit crab Sympagurus dimorphus and the zoanthid Epizoanthus paguricola in the southwestern Atlantic Ocean. -Acta Zoologica (Stockholm) 92: 141-149. The available literature on zoanthid-hermit crab associations deals only with records of this phenomenon, providing no detailed information. We describe, for the first time, the shell-like colonies of Epizoanthus paguricola associated with the hermit crab Sympagurus dimorphus from benthic samples taken in the Argentine Sea, between 85 and 131 m depth, and provide information about morphometric relationships between the hermits and the zoanthids. In total, 260 specimens (137 males and 123 females) of S. dimorphus were collected, 240 (92.3%) of which were living in symbiosis with E. paguricola. The remaining 20 (7.7%) were living inside gastropod shells. As the initial structure of the pseudoshell, 12 different gastropod species were found (all were almost totally covered with colonies of E. paguricola). The hermit crab lives in the spiral cavity inside the soft colony, which seemed to be slightly different depending on the initial gastropod. Aperture pseudoshell morphology did not seem to be related to the sex of the hermit crab host, although males showed larger apertures for a given colony size. This fact is probably related to a larger size of male`s cheliped (sexual dimorphic character) used like a gastropod operculum and that may serve as a template for the growing of the aperture pseudoshell edge. The number of epizoanthid polyps per colony increased in relation to the weight of the colony and to the size of the hermit crab. A process of selection of the initial shell was evident, because species of Naticidae were not the most common gastropods in this benthic community, but were those most used by hermit crabs (> 60%). The puzzling association between hermit crab, shell and zoanthid presumably occurs during the hermit juvenile phase, when the crab occupies a small shell, and a zoanthid larva settles on it. Given the close relationship between S. dimorphus and E. paguricola found in this region, we support the idea that due to the low availability of adequate gastropod shells for hermit life cycle, this association allows the establishment and the continuity of the hermit crab population in the studied area.

Maternal investment in egg production: environmental and population-specific effects on offspring performance in the snapping shrimp Alpheus nuttingi (Schmitt, 1924) (Decapoda, Alpheidae)

Among marine invertebrates, the overall biomass invested in egg production varies widely within populations, which can result from the interaction of endogenous and exogenous factors. Species that have constant reproduction throughout the year can be good models to study the influence of environmental factors on reproductive processes. We conducted a seasonal comparison of egg production in the intertidal snapping shrimp Alpheus nuttingi, which shows a continuous reproductive pattern, to examine the hypothesis that differences in egg production are driven by environmental conditions and population features. This population showed an uncommon strategy, characterized by females that produce eggs of varying sizes within their clutches, with reduced egg volume when the number of eggs is higher (Spring-Summer). In these seasons, higher temperatures and greater food availability may allow the production of more eggs compared to the Autumn-Winter seasons. Compared to other alpheid shrimps, this population produces small eggs, but in larger numbers. Despite the higher fecundity, the reproductive output is relatively low, this production being supported by the large size of females from the southern Atlantic region. Our findings showed that the egg production of A. nuttingi was greatly influenced by environmental factors. Therefore, this shrimp, and probably other decapods that possess continuous reproduction, adopt different reproductive strategies during the year. (C) Koninklijke Brill NV, Leiden, 2010.

Molecular phylogeny of the freshwater prawn genus Macrobrachium (Decapoda, Palaemonidae), with emphasis on the relationships among selected American species

The genus Macrobrachium Bate, 1868 is one of the best examples of widespread crustacean genera distributed globally throughout tropical and subtropical waters. Previous investigators have noted the systematic complexity of the group, and have suggested rearrangements within the family Palaemonidae. Our phylogenetic analysis of new mitochondrial DNA sequences of 58 species of Macrobrachium distributed mainly in America support the hypothesis of monophyly of this genus, if Cryphiops Dana, 1852 is accepted as a generic synonym. We concluded that the independent evolution of different types of life cycle (abbreviated larval development-ALD and extended larval development-ELD) must have occurred more than once in the history of the group. Similarly, we also concluded that the current type species of the genus, Macrobrachium americanum Bate, 1868, should not be considered valid, as previously proposed. The synonymy of two members of the `olfersi` species complex (M. birai Lobao, Melo&Fernandes, 1986 and M. holthuisi Genofre&Lobao, 1978) with M. olfersi (Wiegmann, 1836) was confirmed. Similar results were found in comparing M. petronioi Melo, Lobao&Fernandes, 1986 and M. potiuna (Muller, 1880), in which the genetic divergence placed M. petronioi within the level of intraspecific variation of M. potiuna. The taxonomic status of the genus Cryphiops, as well as theories on the origin of Macrobrachium, is also called into question.

Using multidimensional projection techniques for reaching a high distinguishing ability in biosensing

Recent advances in the control of molecular engineering architectures have allowed unprecedented ability of molecular recognition in biosensing, with a promising impact for clinical diagnosis and environment control. The availability of large amounts of data from electrical, optical, or electrochemical measurements requires, however, sophisticated data treatment in order to optimize sensing performance. In this study, we show how an information visualization system based on projections, referred to as Projection Explorer (PEx), can be used to achieve high performance for biosensors made with nanostructured films containing immobilized antigens. As a proof of concept, various visualizations were obtained with impedance spectroscopy data from an array of sensors whose electrical response could be specific toward a given antibody (analyte) owing to molecular recognition processes. In addition to discussing the distinct methods for projection and normalization of the data, we demonstrate that an excellent distinction can be made between real samples tested positive for Chagas disease and Leishmaniasis, which could not be achieved with conventional statistical methods. Such high performance probably arose from the possibility of treating the data in the whole frequency range. Through a systematic analysis, it was inferred that Sammon`s mapping with standardization to normalize the data gives the best results, where distinction could be made of blood serum samples containing 10(-7) mg/mL of the antibody. The method inherent in PEx and the procedures for analyzing the impedance data are entirely generic and can be extended to optimize any type of sensor or biosensor.