A cDNA subtraction approach to isolate male-specific genes from Ceratitis capitata : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University

The Mediterranean fruit fly, Ceraritis capitata (medfly), is a significant world wide agricultural pest. Sterile Insect Technique (SIT) is a biological method that has been used to control medfly successfully in several parts of the world for around two decades. SIT involves the release of sterile insects into wild populations which, due to sterile matings, lead to a reduction in the size of the wild population. The effectiveness of this technique is significantly increased when only sterile males are released. This can be achieved by using sexing strains, but these strains are prone to breakdown as a result of recombination leading to the disassociation of the selection gene from the Y chromosome. An alternative system, that could be more robust, would involve the control of the expression of the male determining gene. The aim of this thesis was to identify the male determining gene of medfly by creating subtracted cDNA libraries enriched for male-specific transcripts. Subtracted libraries were made by subtractive suppression PCR, using the ClonTech cDNA subtraction kit. The libraries were screened by Southern hybridisation analysis using male and female total cDNA probes. Only one clone appeared to display a bias toward male-specific hybridisation, but this was found to be a result of unequal transfer of DNA. A selection of clones were individually used to probe membrane bound genomic DNA. These hybridisation analyses indicated a general lack of male-specific enrichment. In addition to this, sequence analysis of a selection of clones revealed a number of mitochondrial gene fragments, showing that there had been insufficient subtraction. As results indicated that the creation of subtracted, male-specifically enriched libraries had been unsuccessful another approach to the identification of the male determining gene was attempted. Genomic DNA was screened with an Sxl probe, under low stringency hybridisation conditions, to identify Y-linked encoding RNA binding proteins distantly related Sxl, which could represent the male determining gene. This screen showed that there were no male-specific RNA binding proteins, of the SXL family in medfly

Quantifying the structure of free association networks across the life span.

We investigate how the mental lexicon changes over the lifespan using free association data from over 8,000 individuals, ranging from 10 to 84 years of age, with more than 400 cue words per age group. Using network analysis, with words as nodes and edges defined by the strength of shared associations, we find that associative networks evolve in a nonlinear (U-shaped) fashion over the lifespan. During early life, the network converges and becomes increasingly structured, with reductions in average path length, entropy, clustering coefficient, and small world index. Into late life, the pattern reverses but shows clear differences from early life. The pattern is independent of the increasing number of word types produced per cue across the lifespan, consistent with a network encoding an increasing number of relations between words as individuals age. Lifetime variability is dominantly driven by associative change in the least well-connected words

The ethics of curriculum development:Engineers and technicians in a context of development: Engineers and technicians in a context of development

South African higher education has, for the last twenty years, attempted to confront the legacy its past, particularly the lack of access to science, technology, engineering and mathematics-based (STEM) education by the vast majority of potential students. The current policy environment is dominated by a drive towards high skills jobs and innovation that links research to new forms of production and new services. With the promulgation of a new "Higher Education Qualifications Sub-framework" (HEQSF, 2013) in South Africa there has been considerable curriculum development work across a number of fields and disciplines to enable the "high skills" agenda. Many programs that served as entry qualifications to employment as computer engineering technicians have been subject to upward re-curriculation towards engineering programs. A concern is the lack of clarity around appropriate qualifications and skills levels for a developing country and what might differentiate engineering technician programs from professional engineering programs. There are deep concerns in South Africa about the need to transform society, in particular to ensure that the legitimate aspirations of black South Africans are met and that talented young citizens are able to access higher education and obtain qualifications that enable them to enter the workplace and contribute meaningfully to development. In this paper we discuss the ethics of curriculum development, and argue for an ethical framework to assist institutions to guide curricular decision-making in engineering. A methodology for curricular comparison was developed from the work of Karl Maton on "semantic waves" that was used to construct a systematic comparison between a technician and engineering programme in the field of computer engineering. We show distinct knowledge differences between two programs, one a technician's diploma and the other an professional engineering degree program. We use the findings to illustrate wider concerns about the ethics of/in engineering curriculum development in South Africa as a developing country with a transformation agenda

Exploration and Exploitation of Victorian Science in Darwin's Reading Notebooks

Search in an environment with an uncertain distribution of resources involves a trade-off between exploitation of past discoveries and further exploration. This extends to information foraging, where a knowledge-seeker shifts between reading in depth and studying new domains. To study this decision-making process, we examine the reading choices made by one of the most celebrated scientists of the modern era: Charles Darwin. From the full-text of books listed in his chronologically-organized reading journals, we generate topic models to quantify his local (text-to-text) and global (text-to-past) reading decisions using Kullback-Liebler Divergence, a cognitively-validated, information-theoretic measure of relative surprise. Rather than a pattern of surprise-minimization, corresponding to a pure exploitation strategy, Darwin's behavior shifts from early exploitation to later exploration, seeking unusually high levels of cognitive surprise relative to previous eras. These shifts, detected by an unsupervised Bayesian model, correlate with major intellectual epochs of his career as identified both by qualitative scholarship and Darwin's own self-commentary. Our methods allow us to compare his consumption of texts with their publication order. We find Darwin's consumption more exploratory than the culture's production, suggesting that underneath gradual societal changes are the explorations of individual synthesis and discovery. Our quantitative methods advance the study of cognitive search through a framework for testing interactions between individual and collective behavior and between short- and long-term consumption choices. This novel application of topic modeling to characterize individual reading complements widespread studies of collective scientific behavior.Comment: Cognition pre-print, published February 2017; 22 pages, plus 17 pages supporting information, 7 pages reference

The same, but different: Stochasticity in binary destruction

Observations of binaries in clusters tend to be of visual binaries with separations of 10s - 100s au. Such binaries are 'intermediates' and their destruction or survival depends on the exact details of their individual dynamical history. We investigate the stochasticity of the destruction of such binaries and the differences between the initial and processed populations using N-body simulations. We concentrate on Orion Nebula Cluster-like clusters, where the observed binary separation distribution ranges from 62 - 620 au. We find that, starting from the same initial binary population in statistically identical clusters, the number of intermediate binaries that are destroyed after 1 Myr can vary by a factor of >2, and that the resulting separation distributions can be statistically completely different in initially substructured clusters. We also find that the mass ratio distributions are altered (destroying more low mass ratio systems), but not as significantly as the binary fractions or separation distributions. We conclude that finding very different intermediate (visual) binary populations in different clusters does not provide conclusive evidence that the initial populations were different.Comment: 11 pages, 7 figures, accepted for publication in MNRA

Non-contact, non-destructive mapping of thermal diffusivity and surface acoustic wave speed using transient grating spectroscopy

We present new developments of the laser-induced transient grating spectroscopy (TGS) technique that enable the measurement of large area 2D maps of thermal diffusivity and surface acoustic wave speed. Additional capabilities include targeted measurements and the ability to accommodate samples with increased surface roughness. These new capabilities are demonstrated by recording large TGS maps of deuterium implanted tungsten, linear friction welded aerospace alloys and high entropy alloys with a range of grain sizes. The results illustrate the ability to view grain microstructure in elastically anisotropic samples, and to detect anomalies in samples, for example due to irradiation and previous measurements. They also point to the possibility of using TGS to quantify grain size at the surface of polycrystalline materials.Comment: The following article has been submitted to Review of Scientific Instruments. After it is published, it will be found at https://aip.scitation.org/journal/rs

Global Sensitivity Analysis of OnGuard Models Identifies Key Hubs for Transport Interaction in Stomatal Dynamics.

The physical requirement for charge to balance across biological membranes means that the transmembrane transport of each ionic species is interrelated, and manipulating solute flux through any one transporter will affect other transporters at the same membrane, often with unforeseen consequences. The OnGuard systems modeling platform has helped to resolve the mechanics of stomatal movements, uncovering previously unexpected behaviors of stomata. To date, however, the manual approach to exploring model parameter space has captured little formal information about the emergent connections between parameters that define the most interesting properties of the system as a whole. Here, we introduce global sensitivity analysis to identify interacting parameters affecting a number of outputs commonly accessed in experiments in Arabidopsis (Arabidopsis thaliana). The analysis highlights synergies between transporters affecting the balance between Ca2+ sequestration and Ca2+ release pathways, notably those associated with internal Ca2+ stores and their turnover. Other, unexpected synergies appear, including with the plasma membrane anion channels and H+-ATPase and with the tonoplast TPK K+ channel. These emergent synergies, and the core hubs of interaction that they define, identify subsets of transporters associated with free cytosolic Ca2+ concentration that represent key targets to enhance plant performance in the future. They also highlight the importance of interactions between the voltage regulation of the plasma membrane and tonoplast in coordinating transport between the different cellular compartments

Do binaries in clusters form in the same way as in the field?

We examine the dynamical destruction of binary systems in star clusters of different densities. We find that at high densities (10^4 - 10^5 Msun pc^-3) almost all binaries with separations > 10^3 AU are destroyed after a few crossing times. At low densities (order(10^2) Msun pc^-3) many binaries with separations > 10^3 AU are destroyed, and no binaries with separations > 10^4 AU survive after a few crossing times. Therefore the binary separations in clusters can be used as a tracer of the dynamical age and past density of a cluster. We argue that the central region of the Orion Nebula Cluster was around 100 times denser in the past with a half-mass radius of only 0.1 - 0.2 pc as (a) it is expanding, (b) it has very few binaries with separations > 10^3 AU, and (c) it is well-mixed and therefore dynamically old. We also examine the origin of the field binary population. Binaries with separations < 10^2 AU are not significantly modified in any cluster, therefore at these separations the field reflects the sum of all star formation. Binaries with separations in the range 10^2 - 10^4 AU are progressively more and more heavily affected by dynamical disruption in increasingly dense clusters. If most star formation is clustered, these binaries must be over-produced relative to the field. Finally, no binary with a separation > 10^4 AU can survive in any cluster and so must be produced by isolated star formation, but only if all isolated star formation produces extremely wide binaries.Comment: 12 pages, 6 figures, accepted for publication in MNRA

Massive, wide binaries as tracers of massive star formation

Massive stars can be found in wide (hundreds to thousands AU) binaries with other massive stars. We use N-body simulations to show that any bound cluster should always have approximately one massive wide binary: one will probably form if none are present initially; and probably only one will survive if more than one are present initially. Therefore any region that contains many massive wide binaries must have been composed of many individual subregions. Observations of Cyg OB2 show that the massive wide binary fraction is at least a half (38/74) which suggests that Cyg OB2 had at least 30 distinct massive star formation sites. This is further evidence that Cyg OB2 has always been a large, low-density association. That Cyg OB2 has a normal high-mass IMF for its total mass suggests that however massive stars form they 'randomly sample' the IMF (as the massive stars did not 'know' about each other)

The dynamical evolution of very-low mass binaries in open clusters

Very low-mass binaries (VLMBs), with system masses <0.2 Msun appear to have very different properties to stellar binaries. This has led to the suggestion that VLMBs form a distinct and different population. As most stars are born in clusters, dynamical evolution can significantly alter any initial binary population, preferentially destroying wide binaries. In this paper we examine the dynamical evolution of initially different VLMB distributions in clusters to investigate how different the initial and final distributions can be. We find that the majority of the observed VLMB systems, which have separations <20 au, cannot be destroyed in even the densest clusters. Therefore, the distribution of VLMBs with separations <20 au now must have been the birth population (although we note that the observations of this population may be very incomplete). Most VLMBs with separations >100 au can be destroyed in high-density clusters, but are mainly unaffected in low-density clusters. Therefore, the initial VLMB population must contain many more binaries with these separations than now, or such systems must be made by capture during cluster dissolution. M-dwarf binaries are processed in the same way as VLMBs and so the difference in the current field populations either points to fundamentally different birth populations, or significant observational incompleteness in one or both samples.Comment: 11 pages, 10 figues, accepted for publication in MNRA