Poly(glutamic acid) promoted assembly of nucleosome cores on the histone gene quintet of psammechinus miliaris

Bibliography: leaves 194-217.This thesis investigates whether DNA and histones contain sufficient information to direct nucleosome cores into specific positions. The "in vitro" assembly of nucleosome cores promoted by poly(glutamic acid) has been optimized with respect to rate and yield. This was achieved by paying attention to the purity of the core constituents and in particular by the use of histones in their octameric form. The suitability of a number of octamer purification protocols, to produce pure undenatured histone octamers, has been investigated and the methodology improved. The particles assembled on random DNA have been found to be indistinguishable from native nucleosome cores by the following criteria: Their S value on sucrose gradient centrifugation, resistance to Micrococcal nuclease digestion, DNase I digestion patterns, DNase I digestion kinetics at the susceptible sites, electronmicroscopic appearance, hi stone content and electrophoretic mobility. Cores were also assembled on unique DNA, namely the intact h22 histone quintet of Psammechinus miliaris. Low resolution mapping, by indirect endlabelling of polycores assembled on the quintet, did not reveal any preferred sites of assembly. To investigate the core associated DNA at single base pair resolution, a series of fragments, excised from the H2A-Hl and the Hl-H4 spacer areas, were inserted into pGV403 plasmids. These plasmids can be strand specifically end-labelled with the Klenow fragment at the two different Tth 111 I excision sites utilised to isolate the propagated insert. On the free linearised DNA a complex digestion pattern is produced due to the sequence specificities of Micrococcal nuclease and DNase I. When cores are assembled on this DNA the digestion pattern is changed. This pattern reveals two preferential frames of assembly and indicates that in the remainder of the fragments cores are assembled, randomly, or in a number of overlapping frames. It is concluded that the DNA fragments investigated and the hi stone octamer contain enough structural information to influence the positions occupied by some nucleosome cores. The implications of these findings are discussed

Methods for multi-spectral image fusion: identifying stable and repeatable information across the visible and infrared spectra

Fusion of images captured from different viewpoints is a well-known challenge in computer vision with many established approaches and applications; however, if the observations are captured by sensors also separated by wavelength, this challenge is compounded significantly. This dissertation presents an investigation into the fusion of visible and thermal image information from two front-facing sensors mounted side-by-side. The primary focus of this work is the development of methods that enable us to map and overlay multi-spectral information; the goal is to establish a combined image in which each pixel contains both colour and thermal information. Pixel-level fusion of these distinct modalities is approached using computational stereo methods; the focus is on the viewpoint alignment and correspondence search/matching stages of processing. Frequency domain analysis is performed using a method called phase congruency. An extensive investigation of this method is carried out with two major objectives: to identify predictable relationships between the elements extracted from each modality, and to establish a stable representation of the common information captured by both sensors. Phase congruency is shown to be a stable edge detector and repeatable spatial similarity measure for multi-spectral information; this result forms the basis for the methods developed in the subsequent chapters of this work. The feasibility of automatic alignment with sparse feature-correspondence methods is investigated. It is found that conventional methods fail to match inter-spectrum correspondences, motivating the development of an edge orientation histogram (EOH) descriptor which incorporates elements of the phase congruency process. A cost function, which incorporates the outputs of the phase congruency process and the mutual information similarity measure, is developed for computational stereo correspondence matching. An evaluation of the proposed cost function shows it to be an effective similarity measure for multi-spectral information

Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA

<p>Abstract</p> <p>Background</p> <p>The interpretability of microarray data can be affected by sample quality. To systematically explore how RNA quality affects microarray assay performance, a set of rat liver RNA samples with a progressive change in RNA integrity was generated by thawing frozen tissue or by <it>ex vivo </it>incubation of fresh tissue over a time course.</p> <p>Results</p> <p>Incubation of tissue at 37°C for several hours had little effect on RNA integrity, but did induce changes in the transcript levels of stress response genes and immune cell markers. In contrast, thawing of tissue led to a rapid loss of RNA integrity. Probe sets identified as most sensitive to RNA degradation tended to be located more than 1000 nucleotides upstream of their transcription termini, similar to the positioning of control probe sets used to assess sample quality on Affymetrix GeneChip^®arrays. Samples with RNA integrity numbers less than or equal to 7 showed a significant increase in false positives relative to undegraded liver RNA and a reduction in the detection of true positives among probe sets most sensitive to sample integrity for <it>in silico </it>modeled changes of 1.5-, 2-, and 4-fold.</p> <p>Conclusion</p> <p>Although moderate levels of RNA degradation are tolerated by microarrays with 3'-biased probe selection designs, in this study we identify a threshold beyond which decreased specificity and sensitivity can be observed that closely correlates with average target length. These results highlight the value of annotating microarray data with metrics that capture important aspects of sample quality.</p

Guidelines for restoring Lowland Sand Fynbos ecosystems

CITATION: Holmes, P.M., et al. 2022. Guidelines for restoring Lowland Sand Fynbos ecosystems. Stellenbosch: Stellenbosch Univesity, Department of Conservation Ecology and Entomology.The original publication is available at http://biodiversityadvisor.sanbi.org/planning-and-assessment/ecological-restoration/Lowland Sand Fynbos ecosystems are among the most threatened terrestrial systems in South Africa. Of the ten Sand Fynbos veld types, seven are Critically Endangered or Endangered according to the IUCN Red List of Ecosystems. They are all either poorly protected, or not protected at all in the conservation network. Sand Fynbos ecosystems harbour unique biodiversity, but owing to their lowland locations experience extensive losses to other land uses. Some natural pockets remain scattered within agricultural or urban developments. They are, however degraded due to invasive alien plants, inappropriate fire regimes or pollution and are an urgent priority to restore. National biodiversity targets aim for a minimum proportion of an ecosystem type to be retained in a natural or near-natural state. The minimum target for Sand Fynbos ecosystems is mostly 30% of the original extent – a target no longer attainable for several of these ecosystems, such as Cape Flats Sand Fynbos. For many of these precious systems, this means a necessary focus on their restoration. The purpose of these guidelines is to assist managers and landowners of degraded Sand Fynbos vegetation to restore biodiversity and contribute to the conservation of these threatened ecosystems. The guidelines outline appropriate methods to restore degraded Sand Fynbos ecosystems, based on the latest research and field trial outcomes.Hans Hoheisen Charitable TrustBiodiversity Management Branch, City of Cape TownSANBI - South African National Biodiversity InstituteHans Hoheisen Charitable TrustPublishers versio

Use of a mixed tissue RNA design for performance assessments on multiple microarray formats

The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range assessments on multiple formats. We designed and tested a complex biological reagent for performance measurements on three commercial oligonucleotide array formats that differ in probe design and signal measurement methodology. The reagent is a set of two mixtures with different proportions of RNA for each of four rat tissues (brain, liver, kidney and testes). The design provides four known ratio measurements of >200 reference probes, which were chosen for their tissue-selectivity, dynamic range coverage and alignment to the same exemplar transcript sequence across all three platforms. The data generated from testing three biological replicates of the reagent at eight laboratories on three array formats provides a benchmark set for both laboratory and data processing performance assessments. Close agreement with target ratios adjusted for sample complexity was achieved on all platforms and low variance was observed among platforms, replicates and sites. The mixed tissue design produces a reagent with known gene expression changes within a complex sample and can serve as a paradigm for performance standards for microarrays that target other species

Die probleem van die sedelike kwaad

Verhandeling (M.A.) -- Universiteit van Stellenbosch, 1936.Full text to be digitised and attached to bibliographic record

Uncertainties in the South African wind load design formulation

CITATION: Botha, J., Retief, J. V. & Viljoen, C. 2018. Uncertainties in the South African wind load design formulation. Journal of the South African Institution of Civil Engineering, 60(3):16-29, doi:10.17159/2309-8775/2018/v60n3a2.The original publication is available at http://www.scielo.org.zaThis paper presents an investigation of the uncertainties inherent in the South African formulation of design wind loads on structures, as stipulated by SANS 10160-3:2011. The investigation follows from the identification of anomalous values in the existing South African probabilistic wind load models during a reliability assessment of SANS 10160. The primary wind load components which have the greatest effect on the total wind load uncertainty are identified as the time variant free-field wind pressure, followed by the time invariant pressure coefficients and terrain roughness factors. A rational and transparent reliability framework for the quantification of the uncertainties inherent in the formulation of these components is then presented. Probabilistic models of these components were developed following independent investigations of each component. The results from these investigations show that the existing probabilistic wind load models underestimate the uncertainty of the wind load components, particularly when considering the time invariant components.http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S1021-20192018000300002&lng=en&nrm=iso&tlng=enPublisher's versio

Variability of time independent wind load components

This paper investigates the variability of the primary time independent components of the design wind load formulation. It is shown that the variability of these components has a significant influence on the total reliability of wind loads. The use of comparative studies of international wind load standards as an indicator of the variability of the time independent wind load components is discussed. A two part comparative study is done to determine the variability. It is found that the existing representative probability model of wind load components underestimates even a lower limit estimate of the variability of these components, particularly for pressure coefficients. Furthermore, insight is gained into the effects of various structural and wind load parameters on the total variability of wind loads.Non UBCUnreviewedThis collection contains the proceedings of ICASP12, the 12th International Conference on Applications of Statistics and Probability in Civil Engineering held in Vancouver, Canada on July 12-15, 2015. Abstracts were peer-reviewed and authors of accepted abstracts were invited to submit full papers. Also full papers were peer reviewed. The editor for this collection is Professor Terje Haukaas, Department of Civil Engineering, UBC Vancouver.Facult