Thesis (MSc (Genetics. Institute of Plant Biotechnology))--Stellenbosch University, 2008. / Sugarcane (Saccharum spp.) is an important crop which is cultivated worldwide for the high sucrose content in its stem. Conventional plant breeding has proven to be very successful over the years with regard to the enhancement of yield characteristics but due to the exhaustion of genetic potential in the commercial sugarcane germplasm recent progress has been slow. Genetic engineering seems to be a more attractive approach to enhance sucrose content and pest resistance in the stems but requires appropriate transgenes and suitable promoter. A promoter is essential to drive the transcription of a gene and is therefore critical to the success of transgenic approaches in sugarcane crop improvement. A negligible number of strong stem-specific promoters is available for use in sugarcane and this is one of the major limitations to genetic engineering. The goal of this project was to isolate a stemspecific promoter from maize and sorghum to drive stem-specific transgene expression in sugarcane. The approach used was to source promoters from non-sugarcane grass species with less complex genomes to simplify isolation and possibly counteract silencing. A cDNA sequence (SS) (EST clone, Accession number AW746904) from sugarcane was shown by Northern and Southern analysis to be stem-specific and to have an appropriately low copy number. The SS gene sequence was not expressed in the leaves of maize, sorghum or the sugarcane cultivars and prominent expression was observed only in the stems of the sugarcane hybrids N19 and 88H0019. The SS gene sequence was used to isolate its upstream regions from a Lambda genomic library of maize (Zea mays) and a sorghum (Sorghum bicolor) Bacterial Artificial Chromosome library (BAC). Of the four sorghum and six maize clones obtained in this study, a 4500 bp maize genomic DNA fragment (λ5) was sub-cloned in three fragments into separate pBluescript vectors using the ‘forced’ cloning approach for sequence and database (BLASTN) analysis. This revealed the complete SS gene sequence (975 bp), the promoter and a 300 bp intron region. A stretch of DNA sequence from nucleotides 664-3194 from the maize clone 5 sequence was designated the maize5-pro. Following sequence alignment of the maize and sugarcane promoter regions, significant sequence identity (68%) was observed between nucleotide 1675 and 3194 in maize and nucleotide 1506 and 2947 in sugarcane. The distance between the putative TATA-box and the TSS for this promoter (30 bp) was found to fall within the expected range of 32± 7 bp. The promoter region was analysed for possible cis-acting regulatory elements and revealed several promoter elements that are common in other plant promoters. The comparisons made between the putative transcription factors in maizepro-5 and the sugarcane promoter show that both promoter sequences are very similar as they share ten of the same transcription factors. However, the transcriptional factors WBOX, SRE and SP8BFIBSP8BIB are unique to the maize5-pro and the TAAG motif to the sugarcane promoter. Primers were designed with appropriate restriction sites and the promoter and intron (2850 bp) region was amplified by PCR (Polymerase chain reaction). The amplified fragment was fused inframe to the GUS reporter gene encoding β-glucuronidase to produce a transformation test vector. This will be used in future work to assess the functionality of the promoter through the production of stable transformants in which GUS activity can be measured in a range of tissues.

Rhodotorula (Rhodosporidium) toruloides is an oleaginous basidiomycete yeast with great biotechnological potential. Capable of accumulating lipid up to 76 % of its dry biomass and well suited to the metabolism of lignocellulosic hydrolysate, it is a good candidate for production of advanced biofuels as well as a host of other potential roles in industry. However, molecular genetic tools for manipulation of this yeast are lacking and its high genomic GC content can make routine cloning difficult. Agrobacterium tumefaciens-mediated transformation of R. toruloides CBS 14 was demonstrated, and plasmid vectors were developed for transformation of R. toruloides, including elements for Saccharomyces cerevisiae in-yeast assembly. In-yeast assembly is robust to the manipulation of GC-rich DNA and of large plasmids. Using these vectors and an EGFP reporter, a screen to identify inducible promoters was performed, and promoters from the genes NAR1, ICL1, CTR3, and MET16 identified. These promoters have independent induction/repression conditions and different levels and rates of induction. Minimal inducible promoters were determined, which are as small as 200 bp. As well as showing tight regulation of the EGFP marker, the NAR1 promoter was able to drive conditional rescue of a leu2 mutant strain. In parallel, as a proof of principle for production of advanced biofuels, hydrocarbon biosynthesis pathways were expressed in R. toruloides and analysed by GC-MS. After co-expression of Synechococcus elongatus fatty acyl-ACP reductase and fatty aldehyde decarbonylase, and E. coli ferredoxin and ferredoxin reductase, production of the alkane heptadecane was observed. To increase the availability of free fatty acids (FFA) for production of hydrocarbons by other pathways, Thermomyces lanuginosus lipase 2 was expressed, resulting in a 1.3-fold increase in the concentration of FFAs.

The diploma thesis in the first part deals with a theoretical description of coating technologies, textile materials used in coatings, types of coated polymers and properties of coatings - especially adhesion. The experimental part of the work is devoted to the preparation of textile coatings from polyester fabric and coating based on addition silicone. Using the developed method of sample preparation for T-peel testing of the adhesive strength, the improvement of the adhesion of the coating by chemical adhesion with the support of adhesive agents was studied. The second method studied the change in compactness and adhesion of the coating to the fabric after shaking as a function of breathability. The influence of side reactions of reagents on silicone cohesion was studied by preparing dogbones for testing tensile-deformation properties. The research also included the characterization of silicone samples using ATR-FTIR, monitoring the weight gain and thickness of the fabric after coating, the feel and color stability of the applied fabric and observing the coating under an optical microscope.

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No description available.

The specific goal of this study was to construct and test transcriptional fusions of zein promoters and a yeast reporter gene that will serve as part of a two plasmid system that will allow for the identification of maize transcriptional regulators of zein genes. Zein genes are expressed coordinately and tempO~ly during endosperm development and are controlled at the transcriptional level (Pedersen et aL, 1980; Kodryzcki et al. t 1989). The accumulation of zein proteins in the endosperm presents an ideal model system to study plant gene regulation. These proteins are synthesized only in the endosperm tissue, and their concentration in the endosperm determine the nutritional quality of the seed. Because of the coordinate and temporal regulation of zein gene transcription, there is a strong likelihood that there exists positive regulatory elements of zein gene expression during early endosperm development. We know that the control of storage protein gene expression is mediated by regulatory elements in the endosperm of maize seeds. It has been shown that the recessive mutation opaque-2 (02) specifically reduces the 22,000 zein polypeptide .. Schmidt et at (1990) and Aukennan et at (1991) show that the wild-type 02 encodes a protein containing a basic leucine zipper domain / Master of Science

Dissertation submitted in partial compliance with the requirements for a Masters Degree in Technology: Homoeopathy, Durban University of Technology, 2008. / Introduction This study investigated the effectiveness of homoeopathic dilutions of abscisic acid (ABA), molybdenum and allopurinol on inhibiting or promoting the germination of barley seeds (Hordeum vulgare cv. Stirling, ex Caledon, Western Cape, South Africa, 1998 harvest). Recent research involving ABA and seed germination has shown mixed results, with Bruni (2001), finding there to be statistically significant biological effects, but Couchman (2001) not. Objective/Aim/Purpose The purpose of this study was to evaluate the effectiveness of homoeopathic dilutions of ABA, molybdenum and allopurinol (two substances which have an effect on ABA metabolism), especially those above the 10-23 level (Avogadro’s dilution limit), on germination, in light of recent findings. Abscisic acid, a plant hormone and molybdenum, a trace element, both play an essential role in inducing dormancy of the seed. Allopurinol, a therapeutic drug, has also been shown to affect ABA metabolism and therefore seed germination. The study used all three substances individually and in combination, in homoeopathic dilutions ranging from 4CH to 200CH potency. Methodology There were 7 treatments with 5 potencies per treatment (4CH, 9CH, 15CH, 30CH and 200CH). Each potency level for each treatment had a control, which meant there were 5 controls per treatment. The seeds (distally cut) were placed in 9cm Petri dishes (20 seeds in each), with 5 repetitions, 100 seeds per dilution level with one control of 20 seeds. There were thus 600 (120 x 5) seeds per treatment and 4200 seeds in total (600 x 7 treatments). Seeds were germinated in the dark at a constant temperature. Counts were done every 24 hours for 3 days and the data recorded. The criterion for germination was radical emergence. Results The data was analysed statistically using Univariate Analysis of Variance (STATISTICA version 6). The results showed statistically significant interaction between treatments and potencies and a One-Way Anova was then used to analyse each treatment to determine the effectiveness of each potency. Statistically significant differences were noted between potencies for each treatment. From the results it was clear that the most effective treatment for stimulating germination was the treatment utilizing homoeopathic dilutions of allopurinol. The most effective treatment for inhibiting germination was the treatment utilizing ABA in homoeopathic dilutions. The 30CH (10-60) showed a statistically significant effect on the stimulation of germination across almost all treatments, whereas the 15CH (10-30) showed a statistically significant effect in inhibiting germination in most treatments. Conclusion It is evident from the results of this study that all the treatments produced distinct biological effects, whether it be stimulating germination or inhibiting germination in homoeopathic dilution.

<p>Promoter detection, especially in prokaryotes, has always been an uphill task and may remain so, because of the many varieties of sigma factors employed by various organisms in transcription. The situation is made more complex by the fact, that any seemingly unimportant sequence segment may be turned into a promoter sequence by an activator or repressor (if the actual promoter sequence is made unavailable). Nevertheless, a computational approach to promoter detection has to be performed due to number of reasons. The obvious that comes to mind is the long and tedious process involved in elucidating promoters in the &lsquo / wet&rsquo / laboratories not to mention the financial aspect of such endeavors. Promoter detection/prediction of an organism with few characterized promoters (M.tuberculosis) as envisaged at the beginning of this work was never going to be easy. Even for the few known Mycobacterial promoters, most of the respective sigma factors associated with their transcription were not known. If the information (promoter-sigma) were available, the research would have been focused on categorizing the promoters according to sigma factors and training the methods on the respective categories. That is assuming that, there would be enough training data for the respective categories. Most promoter detection/prediction studies have been carried out on E.coli because of the availability of a number of experimentally characterized promoters (+- 310). Even then, no researcher to date has extended the research to the entire E.coli genome.</p>

The thermochemical process converts almost any kind of biomass to a desired final product, i.e. gaseous or liquid transportation fuels and chemicals. The transportation fuels obtained in this way are renewable biofuels, which are alternatives to fossil fuels. During the last few years, thermochemical plants for the production of bioethanol have been launched and another is under construction. A total of about 290 million liters of ethanol are expected to be processed per year, mostly using municipal solid waste. Considerable efforts have been made in order to find a more selective catalyst for the conversion of biomass-derived syngas to ethanol. The thesis is the summary of five publications. The first two publications (Papers I and II) review the state of the art of ethanol and higher alcohols production from biomass, as well as the current status of synthetic fuels production by other processes such as the Fischer-Tropsch synthesis. Paper III analyses the catalytic performance of a mesoporous Rh/MCM-41 (MCM-41 is a hexagonal mesoporous silica) in the synthesis of ethanol which is compared to a typical Rh/SiO2 catalyst. Exhaustive catalytic testing including the addition of water vapor and modifying the hydrogen partial pressure in the syngas feed-stream which, in addition to the catalyst characterization (XRD, BET, XPS, chemisorption, TEM and TPR) before and after the catalytic testing, have allowed concluding that some water vapor can be concentrated in the pores of the Rh/MCM-41 catalyst. The concentration of water-vapor promotes the occurrence of the water gas shift reaction, which in turn induces some secondary reactions that change the product distribution, as compared to results obtained from the typical Rh/SiO2 catalyst. These results have been verified in a wide range of syngas conversion levels (1-68 %) and for different catalyst activation procedures (catalyst reduction at 200 °C, 500 °C and no-reduction) as shown in Paper IV. Finally, similar insights about the use of mesoporous catalyst have been found over a Cu/MCM-41 catalyst, shown in Paper V. Also in Paper V, the effect of metal promoters (Fe and K) has been studied; a noticeable increase of ethanol reaction rate was found over Cu-Fe-K/MCM-41 catalyst as compared to Cu/MCM-41. / <p>QC 20161125</p>

G-quadruplex secondary structures are four-stranded globular nucleic acid structures that form in specific DNA and RNA G-rich sequences with biological significance, such as those found in human telomeres, oncogene promoter regions, replication initiation sites, and 5’- and 3’-untranslated (UTR) regions, which have been identified as novel drug targets. The non-canonical G-quadruplex secondary structures readily form under physiologically relevant ionic conditions, and exhibit great diversity in their topologies and loop conformations depending on the DNA or RNA sequences at hand. The structural diversity of these unique secondary structures is essential to their specific recognition by different regulatory proteins or small molecule compounds. A significant amount of research has been done in this field that provides compelling evidence for the existence, biological significance, and potential druggability of G-quadruplexes. In this dissertation, I explore G-quadruplex formation in the promoters of BCL2, PDGFR-β and c-Myc oncogenes and their interactions with small molecule compounds or proteins. Firstly, I investigated a newly-identified G-quadruplex (P1G4) forming immediately upstream of the human BCL2 gene, which has been found to be overexpressed in several human tumors. In this research, I have found that P1G4 acts as a transcription repressor, and that its inhibitory effect can be enriched by the G-quadruplex-interactive compound, TMPyP4. Both P1G4 and the previously reported Pu39 G-quadruplexes form independently in adjacent regions within the BCL2 P1 promoter, but P1G4 appears to play a more dominant role in repressing transcriptional activity. NMR and CD studies have shown that the P1G4 G-quadruplex appears to comprise a novel dynamic equilibrium of two parallel structures, one regular, with two 1-nt loops and a 12-nt middle loop, and another broken-stranded, with three 1-nt loops and an 11-nt middle loop; both structures adopt a novel hairpin (stem-loop duplex) conformation in the long central loop. This dynamic equilibrium of two closely-related G-quadruplex structures with a unique hairpin loop conformation may provide a specific target for small molecules to modulate BCL2 gene transcription. I also explored the 3’ end G-quadruplex that forms within the core promoter of PDGFR-β, which has also been observed to be present at abnormal levels in a variety of clinical pathologies, including malignancies. The 3′-end G-quadruplex formed in the PDGFR-β promoter NHE appears to be selectively stabilized by an ellipticine analog, GSA1129, which can shift the dynamic equilibrium in the full-length sequence to favor the 3′-end G-quadruplex, and can repress PDGFR-β activity in cancer cell lines. NMR studies in combination with biophysical experiments have shown that in the wild-type extended 3ʼ-end NHE sequences, two novel intramolecular G-quadruplexes can be formed in a potassium solution, one with a 3’-flanking distant guanine inserted into the 3’-external tetrad (3’-insertion G-quadruplex), and another with a 5’-flanking distant guanine inserted into the 5’-external tetrad (5’-insertion G-quadruplex). Further investigation of the elongated PDGFR-β 3′-end sequence containing both the 5’- and 3’- flanking guanine sequences showed the formation of a combination of the two G-quadruplexes existing in equilibrium. Importantly, it was observed that GSA1129 can bind to and increase the stability of each of the end-insertion G-quadruplexes, raising their Tₘ by 25 degrees. This study highlights the dynamic nature of the 3′-end NHE sequence and the importance of identifying the proper sequence for the formation of biologically relevant G-quadruplex structures. Significantly, the dynamic nature of the 3′-end G-quadruplex suggests that it may be an attractive target for drug regulation. I then analyzed two proteins, Nucleolin and NM23-H2, which interact with the c-Myc G-quadruplex structure that forms in the proximal promoter region of the c-Myc gene; this is one of the most commonly deregulated genes in the human neoplasm. Nucleolin is known to be a transcriptional repressor for c-Myc, binding to and stabilizing the c-Myc G-quadruplex, whereas NM23-H2 is known to be a transcriptional activator that unwinds and destabilizes the c-Myc G-quadruplex. An investigation of the molecular mechanisms of the interaction between the c-Myc G-quadruplex and nucleolin showed that the minimal binding domains required for a tight binding of the protein to the c-Myc G-quadruplex are the four RNA binding domains (RBDs) of nucleolin, referred to as Nuc1234, and that the RGG domain is unnecessary for c-Myc G-quadruplex binding. The stable G-quadruplex formed within Pu27 using G-tract runs I, II, IV and V was determined to be the best substrate (Myc1245T) for nucleolin binding, showing the highest affinity. 3D NMR experiments performed on the free protein Nuc1234 and its complex with the Myc1245T G-quadruplex have shown that upon complex formation, only the disordered linker regions of the protein display significant chemical shift changes, whereas most other residues show chemical shift values similar to those of the free protein. The c-Myc G-quadruplex has three loops that flip outward in a solvent containing K⁺, according to its structure. The hypothesis for this association is that nucleolin wraps around the G-quadruplex and interacts specifically with the flipped-outward loop regions of the c-Myc G-quadruplex via its own inter-RBD linker regions, with little structural change in the RBDs themselves. A definitive determination of the 3D molecular structure of nucleolin and its complex with Myc1245T is currently in development. Biophysical and structural studies were then conducted to investigate the interactions of the protein NM23-H2/NDP kinase B with the c-Myc G-quadruplex. NM23-H2 binds to single-stranded guanine- and cytosine-rich sequences, but not to double-stranded DNA in the NHE III₁ region; the binding therefore appears structure-specific, rather than sequence-specific. Moreover, increasing concentrations of the strong G-quadruplex-interactive compound TMPyP4, a porphyrin-based drug, inhibits the binding of NM23-H2 to the NHE III₁ region; this suggests that the stabilization of the G-quadruplex hinders the recognition and remodeling function of the NM23-H2. By conducting Forster Resonance Energy Transfer (FRET) assays in combination with Circular Dichroism (CD) studies, I demonstrated that NM23-H2 can actively resolve the c-Myc G-quadruplex. Taken together, these results show that the use of small molecules to prevent NM23-H2 from binding to and resolving the NHE III₁ region G-quadruplex may have the potential to inhibit c-Myc transcription for cancer therapeutic purposes. This underlines the importance of understanding the mechanism of function operating between NM23-H2 and the c-Myc G-quadruplex. Understanding molecular mechanism between NM23-H2 and c-Myc is under investigation.