Gene duplication is an evolutionary mechanism for expanding spectral diversity in the long-wavelength photopigments of butterflies

Butterfly long-wavelength (L) photopigments are interesting for comparative studies of adaptive evolution because of the tremendous phenotypic variation that exists in their wavelength of peak absorbance (lambda(max) value). Here we present a comprehensive survey of L photopigment variation by measuring lambda(max) in 12 nymphalid and 1 riodinid species using epi-microspectrophotometry. Together with previous data, we find that L photopigment lambda(max) varies from 510-565 nm in 22 nymphalids, with an even broader 505- to 600-nm range in riodinids. We then surveyed the L opsin genes for which lambda(max) values are available as well as from related taxa and found 2 instances of L opsin gene duplication within nymphalids, in Hermeuptychia hermes and Amathusia phidippus, and 1 instance within riodinids, in the metalmark butterfly Apodemia mormo. Using maximum parsimony and maximum likelihood ancestral state reconstructions to map the evolution of spectral shifts within the L photopigments of nymphalids, we estimate the ancestral pigment had a lambda(max) = 540 nm +/- 10 nm standard error and that blueshifts in wavelength have occurred at least 4 times within the family. We used ancestral state reconstructions to investigate the importance of several amino acid substitutions (Ile17Met, Ala64Ser, Asn70Ser, and Ser137Ala) previously shown to have evolved under positive selection that are correlated with blue spectral shifts. These reconstructions suggest that the Ala64Ser substitution has indeed occurred along the newly identified blueshifted L photopigment lineages. Substitutions at the other 3 sites may also be involved in the functional diversification of L photopigments. Our data strongly suggest that there are limits to the evolution of L photopigment spectral shifts among species with only one L opsin gene and that opsin gene duplication broadens the potential range of lambda(max) values.

Adaptive evolution of color vision as seen through the eyes of butterflies

Butterflies and primates are interesting for comparative color vision studies, because both have evolved middle- (M) and long-wavelength- (L) sensitive photopigments with overlapping absorbance spectrum maxima (lambda(max) values). Although positive selection is important for the maintenance of spectral variation within the primate pigments, it remains an open question whether it contributes similarly to the diversification of butterfly pigments. To examine this issue, we performed epimicrospectrophotometry on the eyes of five Limenitis butterfly species and found a 31-nm range of variation in the lambda(max) values of the L-sensitive photopigments (514-545 nm). We cloned partial Limenitis L opsin gene sequences and found a significant excess of replacement substitutions relative to polymorphisms among species. Mapping of these L photopigment lambda(max) values onto a phylogeny revealed two instances within Lepidoptera of convergently evolved L photopigment lineages whose lambda(max) values were blue-shifted. A codon-based maximum-likelihood analysis indicated that, associated with the two blue spectral shifts, four amino acid sites (Ile17Met, Ala64Ser, Asn70Ser, and Ser137Ala) have evolved substitutions in parallel and exhibit significant d(N)/d(S) >1. Homology modeling of the full-length Limenitis arthemis astyanax L opsin placed all four substitutions within the chromophore-binding pocket. Strikingly, the Ser137Ala substitution is in the same position as a site that in primates is responsible for a 5- to 7-nm blue spectral shift. Our data show that some of the same amino acid sites are under positive selection in the photopigments of both butterflies and primates, spanning an evolutionary distance >500 million years.

Supporting research at QUT : a tale of three librarians and a Creative Industries super-faculty

In 2012 the existing eight disciplines of Creative Industries Faculty, QUT combined with the School of Design (formerly a component of the Faculty of Built Environment and Engineering) to create a super faculty that includes the following disciplines: Architecture, Creative Writing & Literary Studies, Dance, Drama, Fashion, Film & Television, Industrial Design, Interior Design, Journalism, Media & Communication, Landscape Architecture, Music & Sound and Urban Design. The university’s research training unit AIRS (Advanced Information Retrieval Skills) is a systematic introduction to research level information literacies. It is currently being redesigned to reflect today’s new data intensive research environment and facilitate the capacity for life-long learning. Upon completion participants are expected to be able to: 1. Demonstrate an understanding of the theory of advanced search and evaluative strategies to efficiently yield appropriate resources to create original research. 2. Apply appropriate data management strategies to organise and utilize your information proficiently, ethically and legally. 3. Identify strategies to ensure best practice in the use of information sources, information technologies, information access tools and investigative methods. All Creative Industries Faculty research students must complete this unit into which CI Librarians teach discipline specific material. The library employs a team of research specific experts as well as Liaison Librarians for each faculty. Together they develop and deliver a generic research training program that provides researcher training in the following areas: Managing Research Data, QUT ePrints: New features for tracking your research impact, Tracking Research Impact, Research Students and the Library: Overview of Library Research Support Services, Technologies for Research Collaboration, Open Access Publishing, Greater Impact via Creative Commons Licence, CAMBIA - Navigating the patent literature, Uploading Publications to QUT ePrints Workshop, AIRS for supervisors, Finding Existing Research Data, Keeping up to date:Discovering and managing current awareness information and Getting Published. In 2011 Creative Industries initiated a new faculty specific research training program to promote capacity building for research within their Faculty, with workshops designed and developed with Faculty Research Leaders, The Office of Research and Liaison Librarians. “Show me the money” which assists staff to pursue alternative funding sources was one such session that was well attended and generated much discussion and interest. Drop in support sessions for ePrints, EndNote referencing software and Tracking Research Impact for the Creative Industries were also popular options on the menu. Liaison Librarians continue to provide one-on-one consultations with individual researchers as requested. This service assists Librarians greatly with getting to know and monitoring their researchers’ changing needs. The CI Faculty has enlisted two Research Leaders, one for each of the two Schools (Design and Media, Entertainment & Creative Arts) whose role it is to mentor newer research staff. Similarly within the CI library liaison team one librarian is assigned the role of Research Coordinator, whose responsibility it is to be the primary liaison with the Assistant Dean, Research and other key Faculty research managers and is the one most likely to attend Faculty committees and meetings relating to research support.

Tax evasion, inequality, and progressive taxes : a political economy perspective

The standard approach to tax compliance applies the economics-of-crime methodology pioneered by Becker (1968): in its first application, due to Allingham and Sandmo (1972) it models the behaviour of agents as a decision involving a choice of the extent of their income to report to tax authorities, given a certain institutional environment, represented by parameters such as the probability of detection and penalties in the event the agent is caught. While this basic framework yields important insights on tax compliance behavior, it has some critical limitations. Specifically, it indicates a level of compliance that is significantly below what is observed in the data. This thesis revisits the original framework with a view towards addressing this issue, and examining the political economy implications of tax evasion for progressivity in the tax structure. The approach followed involves building a macroeconomic, dynamic equilibrium model for the purpose of examining these issues, by using a step-wise model building procedure starting with some very simple variations of the basic Allingham and Sandmo construct, which are eventually integrated to a dynamic general equilibrium overlapping generations framework with heterogeneous agents. One of the variations involves incorporating the Allingham and Sandmo construct into a two-period model of a small open economy of the type originally attributed to Fisher (1930). A further variation of this simple construct involves allowing agents to initially decide whether to evade taxes or not. In the event they decide to evade, the agents then have to decide the extent of income or wealth they wish to under-report. We find that the ‘evade or not’ assumption has strikingly different and more realistic implications for the extent of evasion, and demonstrate that it is a more appropriate modeling strategy in the context of macroeconomic models, which are essentially dynamic in nature, and involve consumption smoothing across time and across various states of nature. Specifically, since deciding to undertake tax evasion impacts on the consumption smoothing ability of the agent by creating two states of nature in which the agent is ‘caught’ or ‘not caught’, there is a possibility that their utility under certainty, when they choose not to evade, is higher than the expected utility obtained when they choose to evade. Furthermore, the simple two-period model incorporating an ‘evade or not’ choice can be used to demonstrate some strikingly different political economy implications relative to its Allingham and Sandmo counterpart. In variations of the two models that allow for voting on the tax parameter, we find that agents typically choose to vote for a high degree of progressivity by choosing the highest available tax rate from the menu of choices available to them. There is, however, a small range of inequality levels for which agents in the ‘evade or not’ model vote for a relatively low value of the tax rate. The final steps in the model building procedure involve grafting the two-period models with a political economy choice into a dynamic overlapping generations setting with more general, non-linear tax schedules and a ‘cost-of evasion’ function that is increasing in the extent of evasion. Results based on numerical simulations of these models show further improvement in the model’s ability to match empirically plausible levels of tax evasion. In addition, the differences between the political economy implications of the ‘evade or not’ version of the model and its Allingham and Sandmo counterpart are now very striking; there is now a large range of values of the inequality parameter for which agents in the ‘evade or not’ model vote for a low degree of progressivity. This is because, in the ‘evade or not’ version of the model, low values of the tax rate encourages a large number of agents to choose the ‘not-evade’ option, so that the redistributive mechanism is more ‘efficient’ relative to the situations in which tax rates are high. Some further implications of the models of this thesis relate to whether variations in the level of inequality, and parameters such as the probability of detection and penalties for tax evasion matter for the political economy results. We find that (i) the political economy outcomes for the tax rate are quite insensitive to changes in inequality, and (ii) the voting outcomes change in non-monotonic ways in response to changes in the probability of detection and penalty rates. Specifically, the model suggests that changes in inequality should not matter, although the political outcome for the tax rate for a given level of inequality is conditional on whether there is a large or small or large extent of evasion in the economy. We conclude that further theoretical research into macroeconomic models of tax evasion is required to identify the structural relationships underpinning the link between inequality and redistribution in the presence of tax evasion. The models of this thesis provide a necessary first step in that direction.

Kallikrein 14 is down-regulated by androgen receptor signalling and harbours genetic variation that is associated with prostate tumour aggressiveness

Kallikrein 14 (KLK14) has been proposed as a useful prognostic marker in prostate cancer, with expression reported to be associated with tumour characteristics such as higher stage and Gleason score. KLK14 tumour expression has also shown the potential to predict prostate cancer patients at risk of disease recurrence after radical prostatectomy. The KLKs are a remarkably hormone-responsive family of genes, although detailed studies of androgen regulation of KLK14 in prostate cancer have not been undertaken to date. Using in vitro studies, we have demonstrated that unlike many other prostatic KLK genes that are strictly androgen responsive, KLK14 is more broadly expressed and inversely androgen regulated in prostate cancer cells. Given these results and evidence that KLK14 may play a role in prostate cancer prognosis, we also investigated whether common genetic variants in the KLK14 locus are associated with risk and/or aggressiveness of prostate cancer in approximately 1200 prostate cancer cases and 1300 male controls. Of 41 single nucleotide polymorphisms assessed, three were associated with higher Gleason score (≥7): rs17728459 and rs4802765, both located upstream of KLK14, and rs35287116, which encodes a p.Gln33Arg substitution in the KLK14 signal peptide region. Our findings provide further support for KLK14 as a marker of prognosis in prostate cancer.

A three-nucleotide mutation altering the Maize streak virus Rep pRBR-interaction motif reduces symptom severity in maize and partially reverts at high frequency without restoring pRBR-Rep binding

Geminivirus infectivity is thought to depend on interactions between the virus replication-associated proteins Rep or RepA and host retinoblastoma-related proteins (pRBR), which control cell-cycle progression. It was determined that the substitution of two amino acids in the Maize streak virus (MSV) RepA pRBR-interaction motif (LLCNE to LLCLK) abolished detectable RepA-pRBR interaction in yeast without abolishing infectivity in maize. Although the mutant virus was infectious in maize, it induced less severe symptoms than the wild-type virus. Sequence analysis of progeny viral DNA isolated from infected maize enabled detection of a high-frequency single-nucleotide reversion of C(601)A in the 3 nt mutated sequence of the Rep gene. Although it did not restore RepA-pRBR interaction in yeast, sequence-specific PCR showed that, in five out of eight plants, the C(601)A reversion appeared by day 10 post-inoculation. In all plants, the C(601)A revertant eventually completely replaced the original mutant population, indicating a high selection pressure for the single-nucleotide reversion. Apart from potentially revealing an alternative or possibly additional function for the stretch of DNA that encodes the apparently non-essential pRBR-interaction motif of MSV Rep, the consistent emergence and eventual dominance of the C(601)A revertant population might provide a useful tool for investigating aspects of MSV biology, such as replication, mutation and evolution rates, and complex population phenomena, such as competition between quasispecies and population turnover. © 2005 SGM.

Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts

Background. Despite the demonstration that geminiviruses, like many other single stranded DNA viruses, are evolving at rates similar to those of RNA viruses, a recent study has suggested that grass-infecting species in the genus Mastrevirus may have co-diverged with their hosts over millions of years. This "co-divergence hypothesis" requires that long-term mastrevirus substitution rates be at least 100,000-fold lower than their basal mutation rates and 10,000-fold lower than their observable short-term substitution rates. The credibility of this hypothesis, therefore, hinges on the testable claim that negative selection during mastrevirus evolution is so potent that it effectively purges 99.999% of all mutations that occur. Results. We have conducted long-term evolution experiments lasting between 6 and 32 years, where we have determined substitution rates of between 2 and 3 × 10 -4substitutions/site/year for the mastreviruses Maize streak virus (MSV) and Sugarcane streak Réunion virus (SSRV). We further show that mutation biases are similar for different geminivirus genera, suggesting that mutational processes that drive high basal mutation rates are conserved across the family. Rather than displaying signs of extremely severe negative selection as implied by the co-divergence hypothesis, our evolution experiments indicate that MSV and SSRV are predominantly evolving under neutral genetic drift. Conclusion. The absence of strong negative selection signals within our evolution experiments and the uniformly high geminivirus substitution rates that we and others have reported suggest that mastreviruses cannot have co-diverged with their hosts. © 2009 Harkins et al; licensee BioMed Central Ltd.

Dating the origins of the maize-adapted strain of maize streak virus, MSV-A

Maize streak virus (MSV), which causes maize streak disease (MSD), is one of the most serious biotic threats to African food security. Here, we use whole MSV genomes sampled over 30 years to estimate the dates of key evolutionary events in the 500 year association of MSV and maize. The substitution rates implied by our analyses agree closely with those estimated previously in controlled MSV evolution experiments, and we use them to infer the date when the maize-adapted strain, MSV-A, was generated by recombination between two grass-adapted MSV strains. Our results indicate that this recombination event occurred in the mid-1800s, ∼20 years before the first credible reports of MSD in South Africa and centuries after the introduction of maize to the continent in the early 1500s. This suggests a causal link between MSV recombination and the emergence of MSV-A as a serious pathogen of maize. © 2009 SGM.

Inhibition of maize streak virus (MSV) replication by transient and transgenic expression of MSV replication-associated protein mutants

Maize streak disease is a severe agricultural problem in Africa and the development of maize genotypes resistant to the causal agent, Maize streak virus (MSV), is a priority. A transgenic approach to engineering MSV-resistant maize was developed and tested in this study. A pathogen-derived resistance strategy was adopted by using targeted deletions and nucleotide-substitution mutants of the multifunctional MSV replication-associated protein gene (rep). Various rep gene constructs were tested for their efficacy in limiting replication of wild-type MSV by co-bombardment of maize suspension cells together with an infectious genomic clone of MSV and assaying replicative forms of DNA by quantitative PCR. Digitaria sanguinalis, an MSV-sensitive grass species used as a model monocot, was then transformed with constructs that had inhibited virus replication in the transient-expression system. Challenge experiments using leafhopper-transmitted MSV indicated significant MSV resistance - from highly resistant to immune - in regenerated transgenic D. sanguinalis lines. Whereas regenerated lines containing a mutated full-length rep gene displayed developmental and growth defects, those containing a truncated rep gene both were fertile and displayed no growth defects, making the truncated gene a suitable candidate for the development of transgenic MSV-resistant maize. © 2007 SGM.

Toward a theory of the architectural subject

The extraordinary event, for Deleuze, is the object becoming subject – not in the manner of an abstract formulation, such as the substitution of one ideational representation for another but, rather, in the introduction of a vast, new, impersonal plane of subjectivity, populated by object processes and physical phenomena that in Deleuze’s discovery will be shown to constitute their own subjectivities. Deleuze’s polemic of subjectivity (the refusal of the Cartesian subject and the transcendental ego of Husserl) – long attempted by other thinkers – is unique precisely because it heralds the dawning of a new species of objecthood that will qualify as its own peculiar subjectivity. A survey of Deleuze’s early work on subjectivity, Empirisme et subjectivité (Deleuze 1953), Le Bergsonisme (Deleuze 1968), and Logique du sens (Deleuze 1969), brings the architectural reader into a peculiar confrontation with what Deleuze calls the ‘new transcendental field’, the field of subjectproducing effects, which for the philosopher takes the place of both the classical and modern subject. Deleuze’s theory of consciousness and perception is premised on the critique of Husserlian phenomenology; and ipso facto his question is an architectural problematic, even if the name ‘architecture’ is not invoked...

Catalytic cracking of tars derived from rice hull gasification over goethite and palygorskite

Palygorskite (P), goethite (G), and hydrothermally synthesized goethite (HG) were used as supports for Fe and Ni. The catalytic activity of these materials was investigated involving in P, G and HG (supported Fe and Ni) for catalytic decomposition of biomass tar derived from rice hull gasification. The materials were characterized by X-ray diffraction (XRD), X-ray fluorescence (XRF), and transmission electron microscopy (TEM) with an energy dispersive X-ray (EDS). The catalytic activity of P for removal of tar was significantly better than that of G and HG. However, the activity of G with 6 mass% Ni labeled as Ni6/G (tar conversion 94.6%), which was equal to Fe6Ni6/P (94.4%), was better than Ni6/P (64.4%) and Ni6/HG (46.7%). When the loading of Ni (mass%) was 6 mass% on G, tar conversion had the best value (94.6%) and yield of gaseous products reached 486.9, 167.8 and 22.2 mL/(g·tar) for H2, CO, CH4, respectively. The catalytic activity of goethite supported Ni was better in improving tar conversion and improving increased yield of H2, CO, CH4, which was attributed to the existence of Al/Fe substitution of goethite

Genetic association of the KLK4 locus with risk of prostate cancer

The Kallikrein-related peptidase, KLK4, has been shown to be significantly overexpressed in prostate tumours in numerous studies and is suggested to be a potential biomarker for prostate cancer. KLK4 may also play a role in prostate cancer progression through its involvement in epithelial-mesenchymal transition, a more aggressive phenotype, and metastases to bone. It is well known that genetic variation has the potential to affect gene expression and/or various protein characteristics and hence we sought to investigate the possible role of single nucleotide polymorphisms (SNPs) in the KLK4 gene in prostate cancer. Assessment of 61 SNPs in the KLK4 locus (±10 kb) in approximately 1300 prostate cancer cases and 1300 male controls for associations with prostate cancer risk and/or prostate tumour aggressiveness (Gleason score <7 versus ≥7) revealed 7 SNPs to be associated with a decreased risk of prostate cancer at the Ptrend<0.05 significance level. Three of these SNPs, rs268923, rs56112930 and the HapMap tagSNP rs7248321, are located several kb upstream of KLK4; rs1654551 encodes a non-synonymous serine to alanine substitution at position 22 of the long isoform of the KLK4 protein, and the remaining 3 risk-associated SNPs, rs1701927, rs1090649 and rs806019, are located downstream of KLK4 and are in high linkage disequilibrium with each other (r2≥0.98). Our findings provide suggestive evidence of a role for genetic variation in the KLK4 locus in prostate cancer predisposition.

Preliminary study on the stability of highly sensitive fiber Bragg grating temperature sensors [对高灵敏光纤光栅温度传感器的稳定性的初探]

As a novel sensitive element and due to its advantages of immunity to electrical interference, distributed measurement, etc., fiber Bragg grating (FBG) has been researched widely. To realize the substitution of high accurate electronic temperature sensors, high sensitive FBG temperature sensors can be made by taking advantage of its characters of being sensitive to both temperature and strain. Although there are reports about high sensitive FBG temperature sensors, however, few about their stability have been done. We manufactured a high sensitive FBG temperature sensor, and put it together with an average FBG temperature sensor and an electronic crystal temperature sensor into a stainless steel container filled by water to observe the room temperature change. By comparing their results in two weeks, we have found out that: although the high sensitive FBG temperature sensor is in much better agreement with the electronic crystal sensor than the average FBG sensor is, it has occurred some small drifts. Because the drifts appeared in the process of further pulling the FBG, it might be a result of the slip of the FBG fixing points. This contributes some good experiences to the application of FBG in high accuracy temperature measurement.

Vibrational spectroscopic characterization of the phosphate mineral ludlamite (Fe,Mn,Mg)3(PO4)2⋅4H2O – a mineral found in lithium bearing pegmatites

The objective of this work is to analyze ludlamite (Fe,Mn,Mg)3(PO4)2⋅4H2O from Boa Vista mine, Galiléia, Brazil and to assess the molecular structure of the mineral. The phosphate mineral ludlamite has been characterized by EMP-WDS, Raman and infrared spectroscopic measurements. The mineral is shown to be a ferrous phosphate with some minor substitution of Mg and Mn. Raman bands at 917 and 950 cm−1 are assigned to the symmetric stretching mode of and units. Raman bands at 548, 564, 599 and 634 cm−1 are assigned to the ν4 bending modes. Raman bands at 2605, 2730, 2896 and 3190 cm−1 and infrared bands at 2623, 2838, 3136 and 3185 cm−1 are attributed to water stretching vibrations. By using a Libowitzky empirical function, hydrogen bond distances are calculated from the OH stretching wavenumbers. Strong hydrogen bonds in the structure of ludlamite are observed as determined by their hydrogen bond distances. The application of infrared and Raman spectroscopy to the study of ludlamite enables the molecular structure of the pegmatite mineral ludlamite to be assessed.

The difference of thermal stability between Fe-substituted palygorskite and Al-rich palygorskite

Sedimentary palygorskite (SP) and hydrothermal palygorskite (HP) were characterized by XRF, TG/DSC, andXRD. The total iron and dissociative iron in palygorskite were detected using spectrophotometry. The results showed that about 3.57 wt% of Fe2O3 was detected in SP in contrast with 0.4 wt% in HP. SP was a Fe-substituted palygorskite, and HP was an Al-rich palygorskite. The occurrence of Fe substitution in SP resulted in two mass loss steps of coordinated water and resulted in a larger d spacing. The SP showed greater thermal stability than the HP. It was proposed the change of (200) diffraction peak and (240) diffraction peak reflect changes of tetrahedral and octahedral structures in palygorskite.