The evolution of apomixis in the Asplenium monanthes fern complex

Asexually reproducing eukaryotes provide a window into the evolution and maintenance of sexual reproduction, and are challenging our concept of a species. In plants, asexual reproduction (apomixis) is known to cause taxonomic problems and has been indicated to have a disparately high frequency in homosporous ferns. The reasons for such a high frequency of apomictic taxa are unclear, and only add to the enigmatic nature of these ferns. Contemporary studies in ferns are focussing on such questions, and are providing valuable insights into the evolutionary dynamics of apomictic ferns. In this thesis, I investigate the evolution of apomixis in the Asplenium monanthes complex. First, I perform a biosystematic study of the complex, based upon plastid and nuclear DNA sequence data, reproductive mode and polyploidy. I present evidence for reticulate evolution and multiple apomictic lineages. Second, I address the problem of species delimitation in an apomictic species complex. I performed a comparative analysis of AFLP data and sequence data using a variety of species delimitation methods. Results supported the inferences of independent lineages and reticulate evolution made in the previous chapter, but the AFLP data did not support inferences of parentage. Third, I investigated the evolution of genome size in the complex based on DNA C-value data, and tested the utilisation of spore size data to infer ploidy level based on the relationship between genome size and spore size. Genome size variation was shown not only to be due to polyploidy, but also due to expansion of the monoploid genome / chromosome size. Moreover, the evolution of spore size and genome size were not correlated, indicating that spore size is not a good indicator of ploidy level in apomictic complexes. Finally, I investigate the origins of apomixis in A.monanthes based upon AFLP data, sequence data and DNA C-values. I find evidence that the observed genetic and karyological diversity is explained by a single origin of apomixis followed by the spread of apomixis by hybridisation with closely related sexual species by the male function. There is also evidence for post genetic divergence by other mechanisms such as genetic segregation, somatic mutation and unequal meiosis. This thesis presents the first thorough investigation of this complex and has increased our understanding of the evolutionary dynamics of apomixis in ferns

Of Mice and Materials: Payoffs of UNSGC Research Infrastructure Awards

A versatile test facility has been designed and built to study space environments effects on small satellites and system components. Testing for potentially environmental-induced modifications of small satellites is critical to avoid possible deleterious or catastrophic effects over the duration of space mission. This is increasingly more important as small satellite programs have longer mission lifetimes, expand to more harsh environments (such as polar or geosynchronous orbits), make more diverse and sensitive measurements, minimize shielding to reduce mass, and utilize more compact and sensitive electronics (often including untested off-the-shelf components). The vacuum chamber described here is particularly well suited for cost-effective, long-duration tests of modifications due to exposure to simulated space environment conditions for CubeSats, system components, and small scale materials samples of \u3e10 cm X 10 cm. The facility simulates critical environmental components including the neutral gas atmosphere, the FUV/UVMS/NIR solar spectrum, electron plasma fluxes, and temperature. The solar spectrum (-120 nm to 2500 nm) is simulated using an Solar Simulator and Kr resonance lamps at up to four Suns intensity. Low and intermediate electron flood guns and a Sr90 β radiation source provide uniform, stable, electron flux (~ 20 eV to 2.5 MeV) over the CubeSat surface at \u3e5X intensities of the geosynchronous spectrum. Stable temperatures from 100 K to 450 K are possible. An automated data acquisition system periodically monitors and records the environmental conditions, sample photographs, UVMS/NIR reflectivity, IR absorptivity/emissivity, and surface voltage over the CubeSat face and in situ calibration standards during the sample exposure cycle

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source.

The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B(4)C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources

Developing a biodiversity-based indicator for large-scale environmental assessment: a case study of proposed shale gas extraction sites in Britain

1. Environmental impact assessments are important tools for predicting the consequences of development and changes in land use. These assessments generally use a small subset of total biodiversity – typically rare and threatened species and habitats – as indicators of ecological status. However, these indicators do not necessarily reflect changes in the many more widespread (but increasingly threatened) species, which are important for ecosystem functions. In addition, assessment of threatened species through field surveys is time-consuming and expensive and, therefore, only possible at small spatial scales. In contrast, planning changes in land use over large spatial scales (e.g. national infrastructure projects) require assessment and prioritization of biodiversity over large spatial extents. 2. Here, we provide a method for the assessment of biodiversity, which takes account of species diversity across larger spatial scales, based on occurrence records from 5553 species across 11 taxonomic groups. We compare the efficacy of the biodiversity-based indicator we developed against one based on threatened species only and then use it to consider spatial and temporal patterns in ecological status across Great Britain. Finally, we develop a case study to investigate biodiversity status in regions proposed for shale gas extraction in Great Britain. 3. Our results show a strong relationship between the ecological status of areas defined by all biodiversity versus only threatened species, although they also demonstrate that significant exceptions do exist where threatened species do not always accurately indicate the ecological status of wider biodiversity. 4. Spatial and temporal analyses show large variation in ecological status across Great Britain both within the area made available for shale gas licensing and within individual environmental zones. In total, however, 63% of hectads across Britain have suffered a net reduction in our biodiversity-based indicator since 1970. 5. Synthesis and applications. We provide a method and develop a biodiversity-based indicator for the assessment and prioritization of biodiversity at large spatial scales. We highlight the potential applications of this approach for the prioritization of areas that would benefit from conservation and restoration. We also emphasize the danger of insufficient consideration of more widespread species and not just rare and threatened species and habitats as indicators of ecological status when prioritizing large-scale national infrastructure projects. Our method should be a useful tool to complement existing environmental impact assessment methods

Simulation Chamber for Space Environment Survivability Testing

A vacuum chamber was designed and built that simulates the space environment making possible the testing of material modification due to exposure of solar radiation. Critical environmental components required include an ultra high vacuum (10-9 Torr), a UV/VIS/NIR solar spectrum source, an electron gun and charge plasma, temperature extremes, and long exposure duration. To simulate the solar spectrum, a solar simulator was attached to the chamber with a range of 200nm to 2000nm. The exposure time can be accelerated by scaling the solar intensity up to four suns. A Krypton lamp imitates the 120 nm ultraviolet hydrogen Lymann alpha emission not produced by the solar simulator. A temperature range from 100K to 450K is achieved using an attached cryogenic reservoir and resistance heaters. An electron flood gun (mono-energetic, 20 eV to 15keV) is calibrated to replicate solar wind at desired distances from the sun. The chamber maintains 98% uniformity of the electron and electromagnetic radiation exposure relative to the center. The chamber allows for a cost-effective investigation of multiple small-scale samples. An automated data acquisition system monitors and records the reflectivity, absorptivity, and emissivity of the samples throughout the test. An integrating sphere and an IR absorptivity/emissivity probe are used to collect this data. The system allows for measurements to be taken while the samples are still under vacuum and exposed to radiation. With these accurate simulations we can closely predict the material’s behavior in near proximity to the sun. This information is vital in determining materials for satellites, probes, and any other spacecraft

Visible Light Photo-oxidation of Model Pollutants Using CaCu3Ti4O12: An Experimental and Theoretical Study of Optical Properties, Electronic Structure, and Selectivity

[Image: see text] Charge transfer between metal ions occupying distinct crystallographic sublattices in an ordered material is a strategy to confer visible light absorption on complex oxides to generate potentially catalytically active electron and hole charge carriers. CaCu(3)Ti(4)O(12) has distinct octahedral Ti(4+) and square planar Cu(2+) sites and is thus a candidate material for this approach. The sol−gel synthesis of high surface area CaCu(3)Ti(4)O(12) and investigation of its optical absorption and photocatalytic reactivity with model pollutants are reported. Two gaps of 2.21 and 1.39 eV are observed in the visible region. These absorptions are explained by LSDA+U electronic structure calculations, including electron correlation on the Cu sites, as arising from transitions from a Cu-hybridized O 2p-derived valence band to localized empty states on Cu (attributed to the isolation of CuO(4) units within the structure of CaCu(3)Ti(4)O(12)) and to a Ti-based conduction band. The resulting charge carriers produce selective visible light photodegradation of 4-chlorophenol (monitored by mass spectrometry) by Pt-loaded CaCu(3)Ti(4)O(12) which is attributed to the chemical nature of the photogenerated charge carriers and has a quantum yield comparable with commercial visible light photocatalysts

Anaesthesia – what has the University of Cape Town contributed?

From humble beginnings, the University of Cape Town’s Department of Anaesthesia has played a major role in the development of anaesthesia as a speciality, in South Africa and internationally. We highlight these contributions in clinical service, teaching and research, with particular emphasis on the department’s leading role in the evolution of anaesthetic safety in adults and children: from the development of the treatment of malignant hyperthermia, to unique studies in mortality associated with anaesthesia, and modern contributions to improved drug safety. Innovations in anaesthetic techniques have contributed to significant surgical developments, including the first heart transplant. Furthermore, our research has contributed to major advances in obstetric and endocrine anaesthesia, and training in the department is recognised as being among the best in the world

A novel retinoblastoma therapy from genomic and epigenetic analyses.

Retinoblastoma is an aggressive childhood cancer of the developing retina that is initiated by the biallelic loss of RB1. Tumours progress very quickly following RB1 inactivation but the underlying mechanism is not known. Here we show that the retinoblastoma genome is stable, but that multiple cancer pathways can be epigenetically deregulated. To identify the mutations that cooperate with RB1 loss, we performed whole-genome sequencing of retinoblastomas. The overall mutational rate was very low; RB1 was the only known cancer gene mutated. We then evaluated the role of RB1 in genome stability and considered non-genetic mechanisms of cancer pathway deregulation. For example, the proto-oncogene SYK is upregulated in retinoblastoma and is required for tumour cell survival. Targeting SYK with a small-molecule inhibitor induced retinoblastoma tumour cell death in vitro and in vivo. Thus, retinoblastomas may develop quickly as a result of the epigenetic deregulation of key cancer pathways as a direct or indirect result of RB1 loss

DNA methylation at a nutritionally sensitive region of the PAX8 gene is associated with thyroid volume and function in Gambian children.

Funder: Wellcome TrustPAX8 is a key thyroid transcription factor implicated in thyroid gland differentiation and function, and PAX8 gene methylation is reported to be sensitive to the periconceptional environment. Using a novel recall-by-epigenotype study in Gambian children, we found that PAX8 hypomethylation at age 2 years is associated with a 21% increase in thyroid volume and an increase in free thyroxine (T4) at 5 to 8 years, the latter equivalent to 8.4% of the normal range. Free T4 was associated with a decrease in DXA-derived body fat and bone mineral density. Furthermore, offspring PAX8 methylation was associated with periconceptional maternal nutrition, and methylation variability was influenced by genotype, suggesting that sensitivity to environmental exposures may be under partial genetic control. Together, our results demonstrate a possible link between early environment, PAX8 gene methylation and thyroid gland development and function, with potential implications for early embryonic programming of thyroid-related health and disease