Completion of the genome sequence of Lettuce necrotic yellows virus, type species of the genus Cytorhabdovirus

We completed the genome sequence of Lettuce necrotic yellows virus (LNYV) by determining the nucleotide sequences of the 4a (putative phosphoprotein), 4b, M (matrix protein), G (glycoprotein) and L (polymerase) genes. The genome consists of 12,807 nucleotides and encodes six genes in the order 3' leader-N-4a(P)-4b-M-G-L-5' trailer. Sequences were derived from clones of a cDNA library from LNYV genomic RNA and from fragments amplified using reverse transcription-polymerase chain reaction. The 4a protein has a low isoelectric point characteristic for rhabdovirus phosphoproteins. The 4b protein has significant sequence similarities with the movement proteins of capillo- and trichoviruses and may be involved in cell-to-cell movement. The putative G protein sequence contains a predicted 25 amino acids signal peptide and endopeptidase cleavage site, three predicted glycosylation sites and a putative transmembrane domain. The deduced L protein sequence shows similarities with the L proteins of other plant rhabdoviruses and contains polymerase module motifs characteristic for RNA-dependent RNA polymerases of negative-strand RNA viruses. Phylogenetic analysis of this motif among rhabdoviruses placed LNYV in a group with other sequenced cytorhabdoviruses, most closely related to Strawberry crinkle virus. (c) 2005 Elsevier B.V. All rights reserved.

Confirmation of the existence of alloparasitoids in nature - host relationships of an Australian Coccophagus species that parasitizes mealy bugs

Heteronomous hyperparasitoids are parasitic wasps with sex-related host relationships that are unique to a group of genera in the chalcidoid family Aphelinidae. Females are primary parasitoids of various sedentary bugs (mainly, scale insects, mealy bugs, and whiteflies). Males, in contrast, are hyperparasitic, and they frequently develop at the expense of female conspecifics. Alloparasitoids constitute a special category of heteronomous hyperparasitoids, for their males never develop through female conspecifics. The existence of alloparasitic host relationships and the utility of the category 'alloparasitoid' have both been questioned. Here, we present results that confirm the existence of the alloparasitic way of life among heteronomous aphelinids. We investigated an undescribed species of Coccophagus (Hymenoptera: Aphelinidae), an Australian parasitoid that attacks the introduced lantana mealy bug, Phenacoccus parvus Morrison (Homoptera: Pseudococcidae), in Queensland. A year-long field survey regularly returned large numbers of female Coccophagus spec. near gurneyi individuals from P. parvus (total n = 4212), but only few males (n = 11). Males emerged from samples only when the encyrtid parasitoid Anagyrus diversicornis (Howard) (Hymenoptera: Encyrtidae) was present in samples in relatively high numbers. Laboratory oviposition tests confirmed that A. diversicornis is a male host and showed that males do not develop at the expense of conspecific females. Other studies show that males are attracted in numbers to virgin females held in cages above mealy bug-infested Lantana montevidensis (Spreng.) Briq. (Verbenaceae) in the field, demonstrating that they are common in the population as a whole. This confirms that the males need hosts other than conspecific females and that their usual hosts are present outside of the lantana/P. parvus system. The implications of these results for developing a realistic classification of heteronomous host relationships are discussed.

Diverse members of the Ralstonia solanacearum species complex cause bacterial wilts of banana

The bacterial wilts of banana known as Moko disease, Bugtok disease and blood disease are caused by members of the R. solanacearum species complex. R. solanacearum is a heterogeneous species which has been divided into 4 genetic groups known as phylotypes. Within the R. solanacearum species complex, strains that cause Moko and Bugtok diseases belong to phylotype II. The blood disease bacterium, the cause of blood disease, belongs to phylotype IV. This study employs phylogenetic analysis of partial endoglucanase gene sequences to further assess the evolutionary relationships between strains of R. solanacearum causing Moko disease and Bugtok disease and the relationship of the blood disease bacterium to other R. solanacearum strains within phylotype IV of the R. solanacearum species complex. These analyses showed that R. solanacearum Moko disease-causing strains are polyphyletic, forming four related, but distinct, clusters of strains. One of these clusters is a previously unrecognised group of R. solanacearum Moko disease-causing strains. It was also found that R. solanacearum strains that cause Bugtok disease are indistinguishable from strains causing Moko disease in the Philippines. Phylogenetic analysis of partial endoglucanase gene sequences of the strains of the blood disease confirms a close relationship of these strains to R. solanacearum strains within phylotype IV of the R. solanacearum species complex.

Restricted mating dispersal and strong breeding group structure in a mid-sized marsupial mammal (Petrogale penicillata)

Ecological genetic studies have demonstrated that spatial patterns of mating dispersal, the dispersal of gametes through mating behaviour, can facilitate inbreeding avoidance and strongly influence the structure of populations, particularly in highly philopatric species. Elements of breeding group dynamics, such as strong structuring and sex-biased dispersal among groups, can also minimize inbreeding and positively influence levels of genetic diversity within populations. Rock-wallabies are highly philopatric mid-sized mammals whose strong dependence on rocky terrain has resulted in series of discreet, small colonies in the landscape. Populations show no signs of inbreeding and maintain high levels of genetic diversity despite strong patterns of limited gene flow within and among colonies. We used this species to investigate the importance of mating dispersal and breeding group structure to inbreeding avoidance within a 'small' population. We examined the spatial patterns of mating dispersal, the extent of kinship within breeding groups, and the degree of relatedness among brush-tailed rock-wallaby breeding pairs within a colony in southeast Queensland. Parentage data revealed remarkably restricted mating dispersal and strong breeding group structuring for a mid-sized mammal. Breeding groups showed significant levels of female kinship with evidence of male dispersal among groups. We found no evidence for inbreeding avoidance through mate choice; however, anecdotal data suggest the importance of life history traits to inbreeding avoidance between first-degree relatives. We suggest that the restricted pattern of mating dispersal and strong breeding group structuring facilitates inbreeding avoidance within colonies. These results provide insight into the population structure and maintenance of genetic diversity within colonies of the threatened brush-tailed rock-wallaby.

Characterisation of Aeromonas strains and species by pulsed field gel electrophoresis and principal components analysis

Aeromonas genomes were investigated by restriction digesting chromosomal DNA with the endonuclease XbaI, separation of restriction fragments by pulsed field gel electrophoresis (PFGE) and principal components analysis (PCA) of resulting separation patterns. A. salmonicida salmonicida were unique amongst the isolates investigated. Separation profiles of these isolates were similar and all characterised by a distinct absence of bands in the 250kb region. Principal components analysis represented these strains as a clearly defined homogeneous group separated by insignificant Euclidian distances. However, A. salmonicida achromogenes isolates in common with those of A. hydrophila and A. sobria were shown by principal components analysis to be more heterogeneous in nature. Fragments from these isolates were more uniform in size distribution but as demonstrated by the Euclidian distances attained through PCA potentially characteristic of each strain. Furthermore passaging of Aeromonas isolates through an appropriate host did not greatly modify fragment separation profiles, indicative of the genomic stability of test aeromonads and the potential of restriction digesting/PFGE/PCA in Aeromonas typing.

Studying green spectacular environmentalisms group

Natural History filmmaking has a long history but the generic boundaries between it and environmental and conservation filmmaking are blurred. Nature, environment and animal imagery has been a mainstay of television, campaigning organisations and conservation bodies from Greenpeace to the Sierra Club, with vibrant images being used effectively on posters, leaflets and postcards, and in coffee table books, media releases, short films and viral emails to educate and inform the general public. However, critics suggest that wildlife film and photography frequently convey a false image of the state of the world’s flora and fauna. The environmental educator David Orr once remarked that all education is environmental education, and it is possible to see all image-based communication in the same way. The Media, Animal Conservation and Environmental Education has contributions from filmmakers, photographers, researchers and academics from across the globe. It explores the various ways in which film, television and video are, and can be, used by conservationists and educators to encourage both a greater awareness of environmental and conservation issues, and practical action designed to help endangered species. This book is based on a special issue of the journal Environmental Education Research.

Biological activities of compounds from Piper species

It is well established that secondary metabolites play an important role in plant chemical defense. In an effort to find natural herbicides research on plant growth regulatory activity of secondary metabolites has received more and more attention recently. The genus Piper has been an important source for useful secondary metabolites.^ Crude extracts from Piper species inhibited gram-positive bacteria and higher plant growth under laboratory conditions. Bioassay-guided isolation and purification lead to the identification of safrole, a phenylpropene, as the responsible agent for the inhibitory activity. Safrole was found to leach from naturally fallen leaves with water. Mechanisms of plant growth inhibition by safrole were investigated. Disassociation of cell membrane from cell walls was determined to be a major cause.^ Phenylpropenes structurally similar to safrole had similar phytogrowth inhibitory activity. It is postulated that phenylpropanoids are an important group of naturally occurring secondary metabolites in plant-plant interactions. ^

Advanced oxidation of arsenic species in aqueous solutions

Ingestion of arsenic from contaminated water is a serious problem and affects the health of more than 100 million people worldwide. Traditional water purification technologies are generally not effective or cost prohibitive for the removal of arsenic to acceptable levels (≤10 ppb). Current multi-step arsenic removal processes involve oxidation, precipitation and/or adsorption. Advanced Oxidation Technologies (AOTs) may be attractive alternatives to existing treatments. The reactions of inorganic and organic arsenic species with reactive oxygen species were studied to develop a fundamental mechanistic understanding of these reactions, which is critical in identifying an effective and economical technology for treatment of arsenic contaminated water. ^ Detailed studies on the conversion of arsenite in aqueous media by ultrasonic irradiation and TiO2 photocatalytic oxidation (PCO) were conducted, focusing on the roles of hydroxyl radical and superoxide anion radical formed during the irradiation. ·OH plays the key role, while O2 -· has little or no role in the conversion of arsenite during ultrasonic irradiation. The reaction of O2-· does not contribute in the rapid conversion of As(III) when compared to the reaction of As(III) with ·OH radical during TiO2 PCO. Monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA) are readily degraded upon TiO2 PCO. DMA is oxidized to MMA as the intermediate and arsenate as the final product. For dilute solutions, TiO2 also may be applicable as an adsorbent for direct removal of arsenic species, namely As(III), As(V), MMA and DMA, all of which are strongly adsorbed, thus eliminating the need for a multi-step treatment process. ^ Phenylarsonic acid (PA) was subjected to gamma radiolysis under hydroxyl radical generating conditions, which showed rapid degradation of PA. Product analysis and computational calculation both indicate the arsenate group is an ortho, para director. Our results indicate · OH radical mediated processes should be effective for the remediation of phenyl substituted arsonic acids. ^ While hydroxyl radical generating methods, specifically AOTs, appear to be promising methods for the treatment of a variety of arsenic compounds in aqueous media, pilot studies and careful economic analyses will be required to establish the feasibility of AOTs applications in the removal of arsenic. ^

High pressure studies on group VI metal hexacarbonyl molecular solids

Group VI metal hexacarbonyls, M(CO)6 (M = Cr, Mo and W), are of extreme importance as catalysts in industry and also of fundamental interest due to the established charge transfer mechanism between the carbon monoxide and the metal. They condense to molecular solids at ambient conditions retaining the octahedral (Oh) symmetry of gas phase and have been extensively investigated by previous workers to understand their fundamental chemical bonding and possible industrial applications. However little is known about their behavior at high pressures which is the focus of this dissertation. Metal hexacarbonyls were subjected to high pressures in Diamond-Anvil cells to understand the pressure effect on chemical bonding using Raman scattering in situ. The high-pressure results on each of the three metal hexacarbonyls are presented and are followed by a critical analysis of the entire family. The Raman study was conducted at pressures up to 45 GPa and X-ray up to 58 GPa. This is followed by a discussion on infra red spectra in conjunction with Raman and X-ray analysis to provide a rationale for polymerization. Finally the probable synthesis of extremely reactive species under high-pressures and as identified via Raman is discussed. The high-pressure Raman scattering, up to 30 GPa, demonstrated the absence of Π-backbonding. The disappearance of parental Raman spectra for (M = Cr, Mo and W) at 29.6, 23.3 and 22.2 GPa respectively was attributed to the total collapse of the Oh symmetry. This collapse under high-pressure lead to metal-mediated polymeric phase characterized by Raman active δ(OCO) feature, originating from intermolecular vibrational coupling in the parent sample. Further increase in pressures up to 45 GPa, did not affect this feature. The pressure quenched Raman spectra, revealed various chemical groups non-characteristic of the parent sample and adsorption of CO in addition to the characteristic δ(OCO) feature. The thus recorded Raman, complemented with the far and mid-infrared pressure quenched spectra, reveal the formation of novel metal-mediated polymers. The X-ray diffraction on W(CO)6 up to 58 GPa revealed the generation of amorphous polymeric pattern which was retained back to ambient conditions.

Interactions of different arsenic species with thols: Chemical and biological implications

Arsenic has been classified as a group I carcinogen. It has been ranked number one in the CERCLA priority list of hazardous substances due to its frequency, toxicity and potential for human exposure. Paradoxically, arsenic has been employed as a successful chemotherapeutic agent for acute promyelocytic leukemia and has found some success in multiple myeloma. Since arsenic toxicity and efficacy is species dependent, a speciation method, based on the complementary use of reverse phase and cation exchange chromatography, was developed. Inductively coupled plasma mass spectrometer (ICP-MS), as an element specific detector, and electrospray ionization mass spectrometer (ESI-MS), as a molecule specific detector, were employed. Low detection limits in the µg. L−1 range on the ICP-MS and mg. L−1 range on the ESI-MS were obtained. The developed methods were validated against each other through the use of a Deming plot. With the developed speciation method, the effects of both pH on the stability of As species and reduced glutathione (GSH) concentration on the formation and stability of arsenic glutathione complexes were studied. To identify arsenicals in multiple myeloma (MM) cell lines post arsenic trioxide (ATO) and darinaparsin (DAR) incubation, an extraction method based on the use of ultrasonic probe was developed. Extraction tools and solvents were evaluated and the effect of GSH concentration on the quantitation of arsenic glutathione (As-GSH) complexes in MM cell extracts was studied. The developed method was employed for the identification of metabolites in DAR incubated cell lines where the effect of extraction pH, DAR incubation concentration and incubation time on the relative distribution of the As metabolites was assessed. A new arsenic species, dimethyarsinothioyl glutathione (DMMTA V-GS), a pentavalent thiolated arsenical, was identified in the cell extracts through the use of liquid chromatography tandem mass spectrometry. The formation of the new metabolite in the extracts was dependent on the decomposition of s-dimethylarsino glutathione (DMA(GS)). These results have major implications in both the medical and toxicological fields of As because they involve the metabolism of a chemotherapeutic agent and the role sulfur compounds play in this mechanism.

Fire and grazing in a mesic tallgrass prairie: impacts on plant species and functional traits

Fire is a globally distributed disturbance that impacts terrestrial ecosystems and has been proposed to be a global “herbivore.” Fire, like herbivory, is a top-down driver that converts organic materials into inorganic products, alters community structure, and acts as an evolutionary agent. Though grazing and fire may have some comparable effects in grasslands, they do not have similar impacts on species composition and community structure. However, the concept of fire as a global herbivore implies that fire and herbivory may have similar effects on plant functional traits. Using 22 years of data from a mesic, native tallgrass prairie with a long evolutionary history of fire and grazing, we tested if trait composition between grazed and burned grassland communities would converge, and if the degree of convergence depended on fire frequency. Additionally, we tested if eliminating fire from frequently burned grasslands would result in a state similar to unburned grasslands, and if adding fire into a previously unburned grassland would cause composition to become more similar to that of frequently burned grasslands. We found that grazing and burning once every four years showed the most convergence in traits, suggesting that these communities operate under similar deterministic assembly rules and that fire and herbivory are similar disturbances to grasslands at the trait-group level of organization. Three years after reversal of the fire treatment we found that fire reversal had different effects depending on treatment. The formerly unburned community that was then burned annually became more similar to the annually burned community in trait composition suggesting that function may be rapidly restored if fire is reintroduced. Conversely, after fire was removed from the annually burned community trait composition developed along a unique trajectory indicating hysteresis, or a time lag for structure and function to return following a change in this disturbance regime. We conclude that functional traits and species-based metrics should be considered when determining and evaluating goals for fire management in mesic grassland ecosystems.

Behavioural profiles of captive capuchin monkeys (Sapajus spp.): analyses at group and individual levels

The use of behavioural indicators of suffering and welfare in captive animals has produced ambiguous results. In comparisons between groups, those in worse condition tend to exhibit increased overall rate of Behaviours Potentially Indicative of Stress (BPIS), but when comparing within groups, individuals differ in their stress coping strategies. This dissertation presents analyses to unravel the Behavioural Profile of a sample of 26 captive capuchin monkeys, of three different species (Sapajus libidinosus, S. flavius and S. xanthosternos), kept in different enclosure types. In total, 147,17 hours of data were collected. We explored four type of analysis: Activity Budgets, Diversity indexes, Markov chains and Sequence analyses, and Social Network Analyses, resulting in nine indexes of behavioural occurrence and organization. In chapter One we explore group differences. Results support predictions of minor sex and species differences and major differences in behavioural profile due to enclosure type: i. individuals in less enriched enclosures exhibited a more diverse BPIS repertoire and a decreased probability of a sequence with six Genus Normative Behaviour; ii. number of most probable behavioural transitions including at least one BPIS was higher in less enriched enclosures; iii. proeminence indexes indicate that BPIS function as dead ends of behavioural sequences, and proeminence of three BPIS (pacing, self-direct, active I) were higher in less enriched enclosures. Overall, these data are not supportive of BPIS as a repetitive pattern, with a mantra-like calming effect. Rather, the picture that emerges is more supportive of BPIS as activities that disrupt organization of behaviours, introducing “noise” that compromises optimal activity budget. In chapter Two we explored individual differences in stress coping strategies. We classified individuals along six axes of exploratory behaviour. These were only weakly correlated indicating low correlation among behavioural indicators of syndromes. Nevertheless, the results are suggestive of two broad stress coping strategies, similar to the bold/proactive and shy/reactive pattern: more exploratory capuchin monkeys exhibited increased values of proeminence in Pacing, aberrant sexual display and Active 1 BPIS, while less active animals exhibited increased probability in significant sequences involving at least one BPIS, and increased prominence in own stereotypy. Capuchin monkeys are known for their cognitive capacities and behavioural flexibility, therefore, the search for a consistent set of behavioural indictors of welfare and individual differences requires further studies and larger data sets. With this work we aim contributing to design scientifically grounded and statistically correct protocols for collection of behavioural data that permits comparability of results and meta-analyses, from whatever theoretical perspective interpretation it may receive.

(Table 2) Collection sites and number of specimens of Usnea subgenus Neuropogon species

Usnea species of the Neuropogon group are amongst the most widespread and abundant macrolichens in Antarctic regions. Four principal species, U. antarctica, U. aurantiaco-atra, U. sphacelata and U. subantarctica, have been described on morphological grounds. However, identification to species level is often difficult and atypical morphologies frequently arise. Over 400 specimens were collected on the Antarctic Peninsula and Falkland Islands. Both morphological and molecular characters (ITS and RPB1) were used to compare samples to clarify taxonomic relationships. Morphological characteristics used included presence of apothecia, apothecial rays, soredia, papillae, fibrils, pigmentation and the diameter of the central axis as a proportion of branch diameter. Results revealed a very close relationship between U. antarctica and U. aurantiaco-atra, suggesting that they might constitute a species pair or be conspecific. Usnea sphacelata was comprised of at least two genetically distinct groups with no clear differences in morphology. One group included the first reported fertile specimen of this species. Usnea subantarctica was phylogenetically distinct from the other main Antarctic Usnea species, but clustered with U. trachycarpa. Genetic variation was evident within all species although there was no clear correlation between geographic origin and genetic relatedness. Phylogenetic analyses indicated that species circumscription in the Neuropogon group needs revision, with the principal species being non-monophyletic. None of the morphological characters, or groups of characters, used in this study proved to be completely unambiguous markers for a single species. However, axis thickness was supported as being informative for the identification of monophyletic lineages within the group.

Estimating density of a rare and cryptic high-mountain Galliform species, the Buff-throated Partridge Tetraophasis szechenyii

Estimates of abundance or density are essential for wildlife management and conservation. There are few effective density estimates for the Buff-throated Partridge Tetraophasis szechenyii, a rare and elusive high-mountain Galliform species endemic to western China. In this study, we used the temporary emigration N-mixture model to estimate density of this species, with data acquired from playback point count surveys around a sacred area based on indigenous Tibetan culture of protection of wildlife, in Yajiang County, Sichuan, China, during April–June 2009. Within 84 125-m radius points, we recorded 53 partridge groups during three repeats. The best model indicated that detection probability was described by covariates of vegetation cover type, week of visit, time of day, and weather with weak effects, and a partridge group was present during a sampling period with a constant probability. The abundance component was accounted for by vegetation association. Abundance was substantially higher in rhododendron shrubs, fir-larch forests, mixed spruce-larch-birch forests, and especially oak thickets than in pine forests. The model predicted a density of 5.14 groups/km², which is similar to an estimate of 4.7 – 5.3 groups/km² quantified via an intensive spot-mapping effort. The post-hoc estimate of individual density was 14.44 individuals/km², based on the estimated mean group size of 2.81. We suggest that the method we employed is applicable to estimate densities of Buff-throated Partridges in large areas. Given importance of a mosaic habitat for this species, local logging should be regulated. Despite no effect of the conservation area (sacred) on the abundance of Buff-throated Partridges, we suggest regulations linking the sacred mountain conservation area with the official conservation system because of strong local participation facilitated by sacred mountains in land conservation.

Coccosphere geometry measurements from culture experiments on the coccolithophore species Calcidiscus leptoporus, Calcidiscus quadriperforatus and Helicosphaera carteri

Coccolithophores are a key phytoplankton group that exhibit remarkable diversity in their biology, ecology, and calcitic exoskeletons (coccospheres). An understanding of the physiological processes that underpin coccosphere architecture is essential for maximizing the information that can be retrieved from their extensive fossil record. Using culturing experiments on four modern species from three long-lived families, we investigate how coccosphere architecture responds to population shifts from rapid (exponential) to slowed (stationary) growth phases as nutrients become depleted. These experiments reveal statistical differences in cell size and the number of coccoliths per cell between these two growth phases, specifically that cells in exponential-phase growth are typically smaller with fewer coccoliths, whereas cells experiencing growth-limiting nutrient depletion have larger coccosphere sizes and greater numbers of coccoliths per cell. Although the exact numbers are species-specific, these growth-phase shifts in coccosphere geometry are common to four different coccolithophore families (Calcidiscaceae, Coccolithaceae, Isochrysidaceae, Helicosphaeraceae), demonstrating that this is a core physiological response to nutrient depletion across a representative diversity of this phytoplankton group. Polarised light microscopy was used for all coccosphere geometry measurements.