The functional significance of fruit exocarp on host selection and oviposition by Queensland fruit fly, Bactrocera tryoni (Froggatt) (Tephritidae: Diptera)

Queensland fruit fly is Australia's most serious insect pest of horticulture. The fly lays its eggs into fruit, where they hatch into maggots which destroy the fruit. Understanding egg laying behaviour, known as oviposition, is a critical but under-researched aspect of fruit fly biology. This thesis focused on three aspects of oviposition: the role of fruit peel as a physical barrier to oviposition; the quality of fruit for maggot development; and the structure and wear of the egg laying organ – the ovipositor. Results showed that flies selected fruit based on their suitability for offspring survival, not because of the softness or hardness of fruit peel. Previously reported use of holes or wounds in fruit peel by ovipositing females was determined to be a mechanism which saved the female time, not a mechanism to reduce ovipositor wear. The results offer insights into the evolution of host use by fruit flies and their sustainable management.

A transcriptome resource for the koala (Phascolarctos cinereus) : insights into koala retrovirus transcription and sequence diversity

Background The koala, Phascolarctos cinereus, is a biologically unique and evolutionarily distinct Australian arboreal marsupial. The goal of this study was to sequence the transcriptome from several tissues of two geographically separate koalas, and to create the first comprehensive catalog of annotated transcripts for this species, enabling detailed analysis of the unique attributes of this threatened native marsupial, including infection by the koala retrovirus. Results RNA-Seq data was generated from a range of tissues from one male and one female koala and assembled de novo into transcripts using Velvet-Oases. Transcript abundance in each tissue was estimated. Transcripts were searched for likely protein-coding regions and a non-redundant set of 117,563 putative protein sequences was produced. In similarity searches there were 84,907 (72%) sequences that aligned to at least one sequence in the NCBI nr protein database. The best alignments were to sequences from other marsupials. After applying a reciprocal best hit requirement of koala sequences to those from tammar wallaby, Tasmanian devil and the gray short-tailed opossum, we estimate that our transcriptome dataset represents approximately 15,000 koala genes. The marsupial alignment information was used to look for potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene. Koala retrovirus (KoRV) transcripts were detected in the transcriptomes. These were analysed in detail and the structure of the spliced envelope gene transcript was determined. There was appreciable sequence diversity within KoRV, with 233 sites in the KoRV genome showing small insertions/deletions or single nucleotide polymorphisms. Both koalas had sequences from the KoRV-A subtype, but the male koala transcriptome has, in addition, sequences more closely related to the KoRV-B subtype. This is the first report of a KoRV-B-like sequence in a wild population. Conclusions This transcriptomic dataset is a useful resource for molecular genetic studies of the koala, for evolutionary genetic studies of marsupials, for validation and annotation of the koala genome sequence, and for investigation of koala retrovirus. Annotated transcripts can be browsed and queried at http://koalagenome.org

Safety envelope for security

We present an approach for detecting sensor spoofing attacks on a cyber-physical system. Our approach consists of two steps. In the first step, we construct a safety envelope of the system. Under nominal conditions (that is, when there are no attacks), the system always stays inside its safety envelope. In the second step, we build an attack detector: a monitor that executes synchronously with the system and raises an alarm whenever the system state falls outside the safety envelope. We synthesize safety envelopes using a modified machine learning procedure applied on data collected from the system when it is not under attack. We present experimental results that show effectiveness of our approach, and also validate the several novel features that we introduced in our learning procedure.

Indoor air: Contemporary sources, exposures and global implications

Recent 'Global Burden of Disease' studies have provided quantitative evidence of the significant role air pollution plays as a human health risk factor (Lim et al., The Lancet, 380: 2224–2260, 2012). Tobacco smoke, including second hand smoke, household air pollution from solid fuels and ambient particulate matter are among the top risks, leading to lower life expectancy around the world. Indoor air constitutes an environment particularly rich in different types of pollutants, originating from indoor sources, as well as penetrating from outdoors, mixing, interacting or growing (when considering microbes) under the protective enclosure of the building envelope. Therefore, it is not a simple task to follow the dynamics of the processes occurring there, or to quantify the outcomes of the processes in terms of pollutant concentrations and other characteristics. This is further complicated by limitations such as building access for the purpose of air quality monitoring, or the instrumentation which can be used indoors, because of their possible interference with the occupants comfort (due to their large size, noise generated or amount of air drawn). European studies apportioned contributions of indoor versus outdoor sources of indoor air contaminants in 26 European countries and quantified IAQ associated DALYs (Disability-Adjusted Life Years) in those countries (Jantunen et al., Promoting actions for healthy indoor air (IAIAQ), European Commission Directorate General for Health and Consumers, Luxembourg, 2011). At the same time, there has been an increase in research efforts around the world to better understand the sources, composition, dynamics and impacts of indoor air pollution. Particular focus has been directed towards the contemporary sources, novel pollutants and new detection methods. The importance of exposure assessment and personal exposure, the majority of which occurs in various indoor micro¬environments, has also been realized. Overall, this emerging knowledge has been providing input for global assessments of indoor environments, the impact of indoor pollutants and their science based management and control. It was a major outcome of recent international conferences that interdisciplinarity and especially a better colla¬boration between exposure and indoor sciences would be of high benefit for the health related evaluation of environmental stress factors and pollutants. A very good example is the combination of biomonitoring and indoor air, particle and dust analysis to study the exposure routes of semi volatile organic compounds (SVOCs). We have adopted the idea of combining the forces of exposure and indoor sciences for this Special Issue, identified new and challenging topics and have attracted colleagues who are top researchers in their field to provide their inputs. The Special Issue includes papers, which collectively present advances in current research topics and in our view, build the bridge between indoor and exposure sciences.

Multi-rotor with suspended load: System dynamics and control toolbox

There is an increasing demand for Unmanned Aerial Systems (UAS) to carry suspended loads as this can provide significant benefits to several applications in agriculture, law enforcement and construction. The load impact on the underlying system dynamics should not be neglected as significant feedback forces may be induced on the vehicle during certain flight manoeuvres. The constant variation in operating point induced by the slung load also causes conventional controllers to demand increased control effort. Much research has focused on standard multi-rotor position and attitude control with and without a slung load. However, predictive control schemes, such as Nonlinear Model Predictive Control (NMPC), have not yet been fully explored. To this end, we present a novel controller for safe and precise operation of multi-rotors with heavy slung load in three dimensions. The paper describes a System Dynamics and Control Simulation Toolbox for use with MATLAB/SIMULINK which includes a detailed simulation of the multi-rotor and slung load as well as a predictive controller to manage the nonlinear dynamics whilst accounting for system constraints. It is demonstrated that the controller simultaneously tracks specified waypoints and actively damps large slung load oscillations. A linear-quadratic regulator (LQR) is derived and control performance is compared. Results show the improved performance of the predictive controller for a larger flight envelope, including aggressive manoeuvres and large slung load displacements. The computational cost remains relatively small, amenable to practical implementations.

Monoclonal antibody screening of a phage-displayed random peptide library reveals mimotopes of chemokine receptor CCR5: Implications for the tertiary structure of the receptor and for an n-terminal binding site for HIV-1 gp120

The chemokine receptor CCR5 contains seven transmembrane-spanning domains. It binds chemokines and acts as co-receptor for macrophage (m)-tropic (or R5) strains of HIV-1. Monoclonal antibodies (mAb) to CCR5, 3A9 and 5C7, were used for biopanning a nonapeptide cysteine (C)-constrained phage-displayed random peptide library to ascertain contact residues and define tertiary structures of possible epitopes on CCR5. Reactivity of antibodies with phagotopes was established by enzyme-linked immunosorbent assay (ELISA). mAb 3A9 identified a phagotope C-HASIYDFGS-C (3A9/1), and 5C7 most frequently identified C-PHWLRDLRV-C (5C7/1). Corresponding peptides were synthesized. Phagotopes and synthetic peptides reacted in ELISA with corresponding antibodies and synthetic peptides inhibited antibody binding to the phagotopes. Reactivity by immunofluorescence of 3A9 with CCR5 was strongly inhibited by the corresponding peptide. Both mAb 3A9 and 5C7 reacted similarly with phagotopes and the corresponding peptide selected by the alternative mAb. The sequences of peptide inserts of phagotopes could be aligned as mimotopes of the sequence of CCR5. For phage 3A9/1, the motif SIYD aligned to residues at the N terminus and FG to residues on the first extracellular loop; for 5C7/1, residues at the N terminus, first extracellular loop, and possibly the third extracellular loop could be aligned and so would contribute to the mimotope. The synthetic peptides corresponding to the isolated phagotopes showed a CD4-dependent reactivity with gp120 of a primary, m-tropic HIV-1 isolate. Thus reactivity of antibodies raised to CCR5 against phage-displayed peptides defined mimotopes that reflect binding sites for these antibodies and reveal a part of the gp120 binding sites on CCR5.

Multiple alignment and sorting of peptides derived from phage-displayed random peptide libraries with polyclonal sera allows discrimination of relevant phagotopes

Biopanning of phage-displayed random peptide libraries is a powerful technique for identifying peptides that mimic epitopes (mimotopes) for monoclonal antibodies (mAbs). However, peptides derived using polyclonal antisera may represent epitopes for a diverse range of antibodies. Hence following screening of phage libraries with polyclonal antisera, including autoimmune disease sera, a procedure is required to distinguish relevant from irrelevant phagotopes. We therefore applied the multiple sequence alignment algorithm PILEUP together with a matrix for scoring amino acid substitutions based on physicochemical properties to generate guide trees depicting relatedness of selected peptides. A random heptapeptide library was biopanned nine times using no selecting antibodies, immunoglobulin G (IgG) from sera of subjects with autoimmune diseases (primary biliary cirrhosis (PBC) and type 1 diabetes) and three murine ascites fluids that contained mAbs to overlapping epitope(s) on the Ross River Virus envelope protein 2. Peptides randomly sampled from the library were distributed throughout the guide tree of the total set of peptides whilst many of the peptides derived in the absence of selecting antibody aligned to a single cluster. Moreover peptides selected by different sources of IgG aligned to separate clusters, each with a different amino acid motif. These alignments were validated by testing all of the 53 phagotopes derived using IgG from PBC sera for reactivity by capture ELISA with antibodies affinity purified on the E2 subunit of the pyruvate dehydrogenase complex (PDC-E2), the major autoantigen in PBC: only those phagotopes that aligned to PBC-associated clusters were reactive. Hence the multiple sequence alignment procedure discriminates relevant from irrelevant phagotopes and thus a major difficulty with biopanning phage-displayed random peptide libraries with polyclonal antibodies is surmounted.

Mating compatibility between bactrocera invadens and bactrocera dorsalis (Diptera: Tephritidae)

The invasive fruit fly, Bactrocera invadens Drew, Tsuruta & White, is a highly polyphagous fruit pest that occurs predominantly in Africa yet has its origins in the Indian subcontinent. It is extremely morphologically and genetically similar to the Oriental fruit fly, Bactrocera dorsalis (Hendel); as such the specific relationship between these two species is unresolved. We assessed prezygotic compatibility between B. dorsalis and B. invadens using standardized field cage mating tests, which have proven effectiveness in tephritid cryptic species studies. These tests were followed by an assessment of postzygotic compatibility by examining egg viability, larval and pupal survival, and sex ratios of offspring produced from parental and subsequent F1 crosses to examine for hybrid breakdown as predicted under a two-species hypothesis. B. dorsalis was sourced from two countries (Pakistan and China), and each population was compared with B. invadens from its type locality of Kenya. B. invadens mated randomly with B. dorsalis from both localities, and there were generally high levels of hybrid viability and survival resulting from parental and F1 crosses. Furthermore, all but one hybrid cross resulted in equal sex ratios, with the single deviation in favor of males and contrary to expectations under Haldane's rule. These data support the hypothesis that B. dorsalis and B. invadens represent the same biological species, an outcome that poses significant implications for pest management and international trade for sub-Saharan Africa.

Ship Seakeeping Operability, Motion Control, and Autonomy - A Bayesian Perspective

Ship seakeeping operability refers to the quantification of motion performance in waves relative to mission requirements. This is used to make decisions about preferred vessel designs, but it can also be used as comprehensive assessment of the benefits of ship-motion-control systems. Traditionally, operability computation aggregates statistics of motion computed over over the envelope of likely environmental conditions in order to determine a coefficient in the range from 0 to 1 called operability. When used for assessment of motion-control systems, the increase of operability is taken as the key performance indicator. The operability coefficient is often given the interpretation of the percentage of time operable. This paper considers an alternative probabilistic approach to this traditional computation of operability. It characterises operability not as a number to which a frequency interpretation is attached, but as a hypothesis that a vessel will attain the desired performance in one mission considering the envelope of likely operational conditions. This enables the use of Bayesian theory to compute the probability of that this hypothesis is true conditional on data from simulations. Thus, the metric considered is the probability of operability. This formulation not only adheres to recent developments in reliability and risk analysis, but also allows incorporating into the analysis more accurate descriptions of ship-motion-control systems since the analysis is not limited to linear ship responses in the frequency domain. The paper also discusses an extension of the approach to the case of assessment of increased levels of autonomy for unmanned marine craft.

Nature and extent of genetic diversity of dengue viruses determined by 454 pyrosequencing

Dengue virus (DENV) populations are characteristically highly diverse. Regular lineage extinction and replacement is an important dynamic DENV feature, and most DENV lineage turnover events are associated with increased incidence of disease. The role of genetic diversity in DENV lineage extinctions is not understood. We investigated the nature and extent of genetic diversity in the envelope (E) gene of DENV serotype 1 representing different lineages histories. A region of the DENV genome spanning the E gene was amplified and sequenced by Roche/454 pyrosequencing. The pyrosequencing results identified distinct sub-populations (haplotypes) for each DENV-1 E gene. A phylogenetic tree was constructed with the consensus DENV-1 E gene nucleotide sequences, and the sequences of each constructed haplotype showed that the haplotypes segregated with the Sanger consensus sequence of the population from which they were drawn. Haplotypes determined through pyrosequencing identified a recombinant DENV genome that could not be identified through Sanger sequencing. Nucleotide level sequence diversities of DENV-1 populations determined from SNP analysis were very low, estimated from 0.009-0.01. There were also no stop codon, frameshift or non-frameshift mutations observed in the E genes of any lineage. No significant correlations between the accumulation of deleterious mutations or increasing genetic diversity and lineage extinction were observed (p>0.5). Although our hypothesis that accumulation of deleterious mutations over time led to the extinction and replacement of DENV lineages was ultimately not supported by the data, our data does highlight the significant technical issues that must be resolved in the way in which population diversity is measured for DENV and other viruses. The results provide an insight into the within-population genetic structure and diversity of DENV-1 populations.

"The last egg in the basket?" Elderly primiparity: A review of findings

The recent trend of later childbearing among primiparous women is examined with attention to its possible motivations and how they might relate to maternal and infant outcomes. The influence of psychological factors is examined in the context of the inconsistencies in the obstetric literature regarding the risk factors associated with advancing maternal age. An interplay of psychological and biologic factors in determining the outcome of pregnancy and adaptation to motherhood in elderly primiparous women is proposed in terms of the compensatory as opposed to cumulative effect of psychological factors. The adoption of a broad perspective in the study of the experience of later motherhood is recommended as the direction for future research.

The envelope-based cyclic periodogram

Cyclostationary analysis has proven effective in identifying signal components for diagnostic purposes. A key descriptor in this framework is the cyclic power spectrum, traditionally estimated by the averaged cyclic periodogram and the smoothed cyclic periodogram. A lengthy debate about the best estimator finally found a solution in a cornerstone work by Antoni, who proposed a unified form for the two families, thus allowing a detailed statistical study of their properties. Since then, the focus of cyclostationary research has shifted towards algorithms, in terms of computational efficiency and simplicity of implementation. Traditional algorithms have proven computationally inefficient and the sophisticated "cyclostationary" definition of these estimators slowed their spread in the industry. The only attempt to increase the computational efficiency of cyclostationary estimators is represented by the cyclic modulation spectrum. This indicator exploits the relationship between cyclostationarity and envelope analysis. The link with envelope analysis allows a leap in computational efficiency and provides a "way in" for the understanding by industrial engineers. However, the new estimator lies outside the unified form described above and an unbiased version of the indicator has not been proposed. This paper will therefore extend the analysis of envelope-based estimators of the cyclic spectrum, proposing a new approach to include them in the unified form of cyclostationary estimators. This will enable the definition of a new envelope-based algorithm and the detailed analysis of the properties of the cyclic modulation spectrum. The computational efficiency of envelope-based algorithms will be also discussed quantitatively for the first time in comparison with the averaged cyclic periodogram. Finally, the algorithms will be validated with numerical and experimental examples.

Adsorption and Unfolding of Lysozyme at a Polarized Aqueous-Organic Liquid Interface

The adsorption of proteins at the interface between two immiscible electrolyte solutions has been found to be key to their bioelectroactivity at such interfaces. Combined with interfacial complexation of organic phase anions by cationic proteins, this adsorption process may be exploited to achieve nanomolar protein detection. In this study, replica exchange molecular dynamics simulations have been performed to elucidate for the first time the molecular mechanism of adsorption and subsequent unfolding of hen egg white lysozyme at low pH at a polarized 1,2-dichloroethane/water interface. The unfolding of lysozyme was observed to occur as soon as it reaches the organic−aqueous interface,which resulted in a number of distinct orientations at the interface. In all cases, lysozyme interacted with the organic phase through regions rich in nonpolar amino acids, such that the side chains are directed toward the organic phase, whereas charged and polar residues were oriented toward the aqueous phase. By contrast, as expected, lysozyme in neat water at low pH does not exhibit significant structural changes. These findings demonstrate the key influence of the organic phase upon adsorption of lysozyme under the influence of an electric field, which results in the unfolding of its structure.