Department of Biotechnology

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3,3' Diindolylmethane mediated signalling and its role in Brassica napus L. responses to vanadium
(University of the Western Cape, 2016) Gokul, Arun; Keyster, Marshall
Anthropogenic activities such as mineral mining, improper watering practices, and the use of heavy metal contaminated fertilizers have caused an influx of heavy metals into arable lands. These heavy metals may have a negative impact on plant growth, as they are able to increase ROS species within plants resulting in plant metabolism deterioration and tissue damage. Heavy metals also have the ability to render important enzymes non-functional or may decrease their activity resulting in poor growth. Vanadium was used as the heavy metal of choice in this study, as South Africa is one of the top producers of this metal worldwide. In an effort to improve growth of crop plants, mechanisms have to be identified to increase growth under vanadium stress. One method to increase growth is the use of exogenously applied signalling molecules. In this study, one such compound 3,3' Diindolylmethane (DIM) was investigated to identify whether it had growth promoting properties.
3,3'-diindolylmethane improves drought tolerance of Zea mays through enhancing antioxidant activity
(University of the Western Cape, 2018) Basson, Gerhard Leroy; Ludidi, Ndiko; Keyster, Marshall; Gokul, Arun
Maize is one of the most abundantly produced cereals and contributes to about 40% of the global cereal production. This figure will have to increase in order to feed the ever-growing human population. One of the major environmental constraints that impact maize production is drought. Plants use antioxidant defences to cope with drought stress. Understanding and improving these defence mechanisms will be important to improve overall drought tolerance. A previous study done by Gokul and authors in 2016 showed that 3,3’-diindolylmethane (DIM) improves both seed germination and seedling shoot growth in Brassica napus. Plants belonging to the Brassicaceae family have the metabolic machinery to synthesize glucosinolates such as DIM, which play vital roles in physiological and stress responses. These responses have not been investigated in plants such as maize, which lack the machinery to produce DIM. Therefore, this study investigated the effects of exogenously applied DIM on the physiological and biochemical responses of maize under drought stress. Physiological parameters such as relative water content, chlorophyll content and lipid peroxidation, were determined in order to understand how drought and DIM , as separate or combined treatments, affected the plants. Additionally, proline accumulation was also assessed because free proline plays a role as an osmoprotectant during stress. The accumulation of ROS, namely hydrogen peroxide, was measured using spectrophotometric assays to determine how the above treatments affect ROS accumulation in maize. As a result of changes in the ROS content in due to the treatments, it would only be natural to investigate the changes in antioxidants as well. Given that hydrogen peroxide was the ROS to be measured, we therefore investigated the antioxidant enzymatic activities responsible for hydrogen peroxide scavenging. Therefore, changes in Ascorbate peroxidase (APX) and catalase (CAT) were assessed. An improved drought response was observed in maize plants treated with DIM as these plants had better ability to maintain their water status than when no DIM was applied. This is indicated by water-deprived plants treated with DIM having a higher RWC than water-deprived plant without DIM.
A comparative ancestry analysis of Y-chromosome DNA haplogroups using high resolution melting
(University of the Western Cape, 2018) Michelle Burrows, Adria; Eugenia D'Amato, Maria
The objective of this study is to deduce paternal ancestry using ancestry informative single nucleotide polymorphisms (SNPs) by means of High Resolution Melting (HRM). This was completed by producing a multiplex system that was designed in a hierarchical manner according to the YSNP tree. This project mainly focused on African ancestry and was used to infer paternal ancestral lineages on the Johannesburg Coloured population. South Africa has a diverse population that has ancestral history from across the globe. The South African Coloured population is the most admixed population as it is derived from at least five different population groups: these being Khoisan, Bantu, Europeans, Indians and Southeast Asians. There have been studies done on the Western Cape/ Cape Town Coloured populations before but this study focused on the Johannesburg Coloured population. The first step was to design the multiplex system. This was done by using inhouse SNPs. A total of seven multiplexes were designed and optimised, each consisting of two, three or four different SNPs respectively. A total of 143 saliva and buccal samples were collected from male Johannesburg Coloureds. DNA was extracted from the saliva samples using an optimised organic method. DNA was extracted from the buccal samples using an optimised salting out method. DNA was successfully extracted from 77 of the male samples. A total of 69 samples were screened using Multiplex 1; of the 69 samples 56 samples were successfully screened to infer the paternal lineage of the samples. The results show that the most frequent haplogroup of the Johannesburg male samples was haplogroup CF (39%). The second most frequent haplogroup was haplogroup DE (38%). Under further analysis of haplogroup DE it was seen that 37% of those samples were derived for the haplogroup E1b1b.
Actinobacteria associated with two diverse soil environments and their multicopper oxidase diversity
(University of the Western Cape, 2024) Prins, Alaric; McCullough, Bronwyn Kirby
The Cape Floristic Region (CFR) is a biodiverse region boasting unique plant diversity with a rich concentration of endemic plants. Aspalathus linearis (Rooibos) is an indigenous plant that grows in the Clanwilliam region of the Western Cape and is cultivated for its use as an herbal tea. Emerging peatlands in the CFR have gained increasing attention over recent years through research aiming to understand the microbial diversity associated with these environments. Little is known about the actinobacterial diversity of these regions, and as such, it is necessary to investigate the diversity of the actinobacteria associated with these environments, whilst simultaneously gaining knowledge on whether the associated actinobacteria may produce enzymes of biotechnological interest. Two CFR regions (the Rooibos environment – Clanwillian, and the Springfield emerging peatland environment – Agulhas) were explored through culture-based and genomic screening. Metabarcoding analyses using actinobacterial-specific 16S rRNA gene primers showed that the major taxa contributing to the Rooibos environment were members of the families Mycobacteriaceae, Pseudonocardiaceae, Frankiaceae and Geodermatophilaceae. Members of the families Mycobacteriaceaea, Pseudonocardiaceae, Acidimicrobiaceae and Nocardioiaceae was identified as the major taxa for the Springfield environment. Through selective isolation techniques, actinobacteria from rare (underrepresented) genera were isolated, including members of the genera Dactylosporangium, Actinokineospora, Curtobacterium, Modestobacter, Leifsonia and Actinomadura. The top strains, selected based on exhibiting extracellular multicopper oxidase (MCO) activity through culture-based screening, were subjected to whole genome sequence analysis. These rare genera are also vastly underrepresented among 3 400 bacterial MCO sequences found in the Laccase and Multicopper Oxidase Engineering Database (LccED).
Actinobacterial and archaeal diversity in lake Magadi, Kenya
(University of the Western Cape, 2013) Halimat, Olubukola Ibrahim; Cowan, D. A.
Microorganisms of the class Actinobacteria and domain Archaea are interesting from a biotechnological perspective owing to their metabolic attributes as producers of secondary metabolites and resilience under harsh environmental conditions respectively. Lake Magadi is a soda lake well studied in terms of its geology and limnology. Research attention has also been drawn to the microbial populations which thrive in this unique habitat but currently there are no reports on the assessment of its microflora using molecular methods. This study aimed to assess the actinobacterial and archaeal communities within Lake Magadi, Kenya a hypersaline –highly alkaline habitat using metagenomic methods as a preliminary study to identify potential candidates for exploitative biology Samples from two sites dubbed Lake Magadi station 2 (LM2) and Lake Magadi salt pan 4 (LMS4) within the Lake Magadi were analyzed using the 16S rRNA gene as a phylogenetic marker. Cluster analysis of taxon-specific 16S rDNA PCR-DGGE profiles revealed moderately heterogeneous actinobacterial and archaeal populations across the sample sites under investigation which is probably a reflection of the differences in abiotic conditions at the study sites. This observation was also confirmed from the multi-dimensional scaling (MDS) plot. PCR-based clonal libraries of actinobacterial and archaeal communities of both study sites retrieved a total of thirty-two clones (twenty actinobacterial and twelve archaeal) were sequenced. Analysis of the sequences revealed cultured and uncultured signatures of microorganisms typical of hypersaline and or highly alkaline niches. A few (3) sequences presented novelty (<96%) in identities with any previously identified organism. It was concluded that the species dominance at site LMS4 [situated within the salt flats of Lake Magadi and site for exploration of trona and its mineralized extensions (nacholite and gayllusite)] is likely to be dictated by anthropogenic stress since most of the microbial signals associated with the study site are typical of saline and or alkaline environmental samples exposed to especially mining but also agricultural and waste management practices. Isolation studies also revealed previously identified strains peculiar to hypersaline brines and sediments. The strains retrieved were affiliated to the taxonomically diverse genus Bacillus and Halomonas sp. The true applications and potential opportunities these isolates have for biotechnology have been well documented. Observations made from the culture dependent and culture independent methods suggests strongly that study site LMS4 is subjected to environmental conditions more severe than at site LM2. This study is a guide for future studies as it provides primary information on the haloalkaliphilic representatives of the actinobacteria phylum and domain Archaea within the soda lake environment. It can serve as a pedestal for investigation into the molecular machinery that supports the haloalkaliphilic lifestyles of inhabiting microorganisms and consequently give leads as to how they can be commercially exploited.
Actinobacterial diversity of the Ethiopian Rift Valley lakes
(University of the Western Cape, 2011) Du Plessis, Gerda; Cowan, D.A.; Tuffin, Marla
The class Actinobacteria consists of a heterogeneous group of filamentous, Gram-positive bacteria that colonise most terrestrial and aquatic environments. The industrial and biotechnological importance of the secondary metabolites produced by members of this class has propelled it into the forefront of metagenomics studies. The Ethiopian Rift Valley lakes are characterized by several physical extremes, making it a polyextremophilic environment and a possible untapped source of novel actinobacterial species. The aims of the current study were to identify and compare the eubacterial diversity between three geographically divided soda lakes within the ERV focusing on the actinobacterial subpopulation. This was done by means of a culture-dependent (classical culturing) and culture-independent (DGGE and ARDRA) approach. The results indicate that the eubacterial 16S rRNA gene libraries were similar in composition with a predominance of α-Proteobacteria and Firmicutes in all three lakes. Conversely, the actinobacterial 16S rRNA gene libraries were significantly different and could be used to distinguish between sites. The actinobacterial OTUs detected belonged to both the Rubrobacterales and Actinomycetales orders with members of the genus Arthrobacter being found in all three lakes. Geochemical properties were significantly different between the lakes, although more than one property attributed to the variance between community compositions. The diversity detected in the culture-based study differed significantly and all isolates belonged to the genus Streptomyces. Two novel strains were characterized by means of phylogenetic (16S rRNA gene sequence), physiological, morphological and biochemical analyses. Both novel isolates were capable of growing under "extreme" conditions- pH 12, 10% NaCl and 45°C. Partial enzyme characterization revealed that both strains produced xylanase enzymes that were active at pH 6.5 and 8.5 with an increase in activity up to 45°C. The results obtained revealed a previously undetected diversity of actinobacteria in the Ethiopian Rift Valley with a potentially novel subpopulation adapted to haloalkaline conditions. The low 16S rRNA sequence similarity of a substantial proportion of the libraries suggests that culture-based isolation may play a vital role in deciphering the community fingerprint.
An investigation of the zinc binding characteristics of the RING finger domain from the human RBBP6 protein using heteronuclear NMR spectroscopy.
(University of the Western Cape, 2007) Mulaudzi, Takalani; Pugh, David J.R.; Magister Scientiae - MSc; Faculty of Science
Retinoblastoma binding prot ein 6 (RBBP6) is a 250 kDa human splicing-associated protein that is also known to interact with tumour suppresso r proteins p53 and pRb and to mediate ubiquitination of p53 via its intera ction with Hdm2. RBBP6 is highly up regulated in oesophageal cancer, and has been shown to be a promising target for immunotherapy against the disease. RBBP6 is also known to play a role in mRNA splicing, cell cycle control and apoptosis.
Analysis of ammonia-oxidizing bacteria associated with the roots of Proteaceae plant species in soils of Fynbos ecosystem
(University of the Western Cape, 2005) Cowan, D. A.
Molecular methods were used to investigate the microbial diversity and community structure of ammonia-oxidizing bacteria (AOB) associated with the roots of the Proteaceae plant family. The identification of ammonia oxidizing bacteria in this ecosystem is of particular interest since Proteaceae are adapted to acidic, low nutrient (e.g. nitrogen) soils. The ammonia monooxygenase operon was used as a molecular marker to identify ammonia-oxidizing bacteria associated with the proteoid roots of the three Proteaceae members and compared to non-plant associated soil. PCR amplification using primer sets targeting the ammonia monooxygenase gene (amoA subunits) were used to construct a clone library. Sequence diversity was determined by RFLP analysis of amoA to identify major groups of AOB of the ~-subclass of Proteobacteria in total community DNA, and DNA sequencing and phylogenetic analysis were also applied. DGGE analysis was performed to determine the community structure and distribution of ammonia-oxidizing bacteria in plant-associated and non-plant associated soils. The AOB genotypic diversity was similar in the plant-associated samples and non-plant associated soil. All AOB phylotypes belonged to Nitrosospira species and clustered with Nitrosospira cluster 3. The abundance of the amoA was quantified to be approximately 4.2 x 107 copies/g of dry soil, using a real-time PCR assay. These data suggest that the Nitrosospira species are the dominant phylotypes in that environment. This investigation provides new insights into the relationships between plants and ammonia-oxidizing bacteria in natural Fynbos ecosystems.
Analysis of ammonia-oxidizing bacteria associated with the roots of Proteaceae plant species in soils of Fynbos ecosystem
(University of the Western Cape, 2005) Lako, Joseph; Cowan, Don A.; Dept. of Biotechnology; Faculty of Science
The major objective of this study was to investigate soil ammonia-oxidizing bacterial diversity and composition associated with plant roots of Proteaceae plants and to compare it with non-plant associated soil.
Analysis of the early events in the interaction between Venturia inaequalis and the susceptible Golden Delicious apple (Malus x domestica Borkh.)
(University of the Western Cape, 2014) Hüsselmann, Lizex Hollenbach Hermanus; Ndimba, Bongani K.
Apple (Malus x domestica) production in the Western Cape, South Africa, is one of the major contributors to the gross domestic product (GDP) of the region. The production of apples is affected by a number of diseases. One of the economically important diseases is apple scab that is caused by the pathogenic fungus, Venturia inaequalis. Research to introduce disease resistance ranges from traditional plant breeding through to genetic manipulation. Parallel disease management regimes are also implemented to combat the disease, however, such strategies are increasingly becoming more ineffective since some fungal strains have become resistant to fungicides. The recently sequenced apple genome has opened the door to study the plant pathogen interaction at a molecular level. This study reports on proteomic and transcriptomic analyses of apple seedlings infected with Venturia inaequalis. In the proteomic analysis, two-dimensional gel electrophoresis (2-DE) in combination with mass spectrometry (MS) was used to separate, visualise and identify apple leaf proteins extracted from infected and uninfected apple seedlings. Using MelanieTM 2-DE Gel Analysis Software version 7.0 (Genebio, Geneva, Switzerland), a comparative analysis of leaf proteome expression patterns between the uninfected and infected apple leaves were conducted. The results indicated proteins with similar expression profiles as well as qualitative and quantitative differences between the two leaf proteomes. Thirty proteins from the apple leaf proteome were identified as differentially expressed. These were selected for analysis using a combination of MALDI-TOF and MALDI-TOF-TOF MS, followed by database searching. Of these spots, 28 were positively identified with known functions in photosynthesis and carbon metabolism (61%), protein destination and storage (11%), as well as those involved in redox/response to stress, followed by proteins involved in protein synthesis and disease/defence (7%), nucleotide and transport (3%). RNA-Seq was used to identify differentially expressed genes in response to the fungal infection over five time points namely Day 0, 2, 4, 8 and 12. cDNA libraries were constructed, sequenced using Illumina HiScan SQTM and MiSeqTM instruments. Nucleotide reads were analysed by aligning it to the apple genome using TopHat spliceaware aligner software, followed by analysis with limma/voom and edgeR, R statistical packages for finding differentially expressed genes. These results showed that 398 genes were differentially expressed in response to fungal infection over the five time points. These mapped to 1164 transcripts in the apple transcripts database, which were submitted to BLAST2GO. Eighty-six percent of the genes obtained a BLAST hit to which 77% of the BLAST hits were assigned GO terms. These were classed into three ontology categories i.e. biological processes, molecular function and cellular components. By focussing on the host responsive genes, modulation of genes involved in signal perception, transcription, stress/detoxification, defence related proteins, transport and secondary metabolites have been observed. A comparative analysis was performed between the Day 4 proteomic and Day 4 transcriptomic data. In the infected and uninfected apple leaf proteome of Day 4, we found 9 proteins responsive to fungal infection were up-regulated. From the transcriptome data of Day 4, 162 genes were extracted, which mapped to 395 transcripts in the apple transcripts. These were submitted to BLAST2GO for functional annotation. Proteins encoded by the up-regulated transcripts were functionally categorised. Pathways affected by the up-regulated genes are carbon metabolism, protein synthesis, defence, redox/response to stress. Up-regulated genes were involved in signal perception, transcription factors, stress/detoxification, defence related proteins, disease resistance proteins, transport and secondary metabolites. We found that the same pathways including energy, disease/defence and redox/response to stress were affected for the comparative analysis. The results of this study can be used as a starting point for targeting host responsive genes in genetic manipulation of apple cultivars.
Analysis of the proteome of red and green leaf phenotypes of 'Bon Rouge' pear trees \trus communrls L. by 2-dimensional gel electrophoresis
(University of the Western Cape, 2007) Sehata, Majimi James; du Preez, Marlene; Ndimba, Bongani; Rees, Jasper
The 'Bon Rouge' pear is a red pear cultivar derived from a rare, spontaneous bud mutation which occurred on the green pear 'William's Bon Chretien' (Bartlett). 'Bon Rouge' pear cultivar was observed to be reverting back to its original phenotypic green colour. To study the cellular changes occurring within the cells both the mutated red phenotype and the wild type green phenotype of 'Bon Rouge' were investigated using proteomics approach. The proteins from the tissues of interest were precipitated in the presence of l0o/o TCA and solubilized in urea/thiourea lysis buffer. The proteins were separated onl2Yo SDS-PAGE and2D PAGE in order to compare their protein expression profiles. The results from SDS-PAGE and 2D PAGE profiles show an elevated level of 53 kDa protein in green pears which was either absent or less expressed in red phenotype and this protein appears to be the only differentiating factor between the red and green 'Bon Rouge' phenotypes. This protein was subsequently identified by the MALDI-TOFMS to be large subunit of RuBisCO. Expression proteomics is a preferred method due to its reproducibility and it has a potential to provide direct identification of cultivars related proteins. Additionally, proteomics approaches could help the fruit crop gtowers andbreeders, to select and determine types of different cultivars at various growth stages.
Analysis, expression profiling and characterization of hsa-miR-5698 target genes as putative dynamic network biomarkers for prostate cancer: a combined in silico and molecular approach
(University of the Western Cape, 2019) Lombe, Chipampe Patricia; Pretorius, Ashley; Meyer, Mervin
2018, the International Agency for Research on Cancer (IARC) estimated that prostate cancer (PCa) was the second leading cause of death in males worldwide. The number of deaths are expected to raise by 50 % in the next decade. This rise is attributed to the shortcomings of the current diagnostic, prognostic, and therapeutic biomarkers used in the management of the disease. Therefore, research into more sensitive, specific and effective biomarkers is a requirement. The use of biomarkers in PCa diagnosis and management takes advantage of the genetic alterations and abnormalities that characterise the disease. In this regard, a microRNA, hsa-miR-5698 was identified in a previous study as a differentiating biomarker between prostate adenocarcinoma and bone metastasis. Six putative translational targets (CDKN1A, CTNND1, FOXC1, LRP8, ELK1 and BIRC2) of this microRNA were discovered using in silico approaches. The aim of this study was to analyse via expression profiling and characterization, the target genes of hsa-miR-5698 in order to determine their ability to act as putative dynamic network biomarkers for PCa. The study was conducted using a combined in silico and molecular approach. The in silico part of the study investigated the putative transcriptional effects of hsa-miR-5698 on the promotors of its translational targets, the correlation between hsa-miR-5698 and mRNA expression profiles as well as the co-expression analysis, pathway analysis and prognostic ability of the target genes. A number of computational software were employed for these purposes, including, R Studio, Trident algorithm, STRING, KEGG, MEME Suite, SurvExpress and ProGgene. The molecular part of the study involved expression profiling of the genes in two PCa cell line LNCaP and PC3 via qPCR.
Ancient Genes in Cancer Gene Expression?
(University of the Western Cape, 2004) Panji, Sumir; Hide, Winston
Backsround: The Cancer/testis (CT) antigens are a division of germ cell specific genes not expressed in somatic cells, exceptions being placental cells and 20Vo - 4OVo of cancer types. The aptitude of CT antigens to elicit humoral immune responses, their restricted expression profile, absence of major histocompatability complex expression in male germline cells have contributed to the emergent attraction of CT antigens as ideal, prospective cancer vaccination candidates. Motivation: Presently there are M CT gene families containing a total of 97 gene products and isoforms. Due to the promulgation in sensitivity and specificity of rapid serological immunodetection assays e.g. serial analysis of recombinant cDNA expression libraries (SEREX), the magnitude of novel CT genes and gene families will increase. Hence, characteization of this unique subset of CT genes is fundamental to our erudition of this rapidly emerging novel subset of genes. Obiectives: The sequencing of the human genome provides a useful biological framework for the categoization and systematization of rapidly accumulating biological information. A genomic approach was used to ascertain the locations of the CT genes in the human genome and determine if the genomic locations of the CT genes is nonrandom. An in-silico expression study was conducted for the CT genes with the aim of establishing if CT gene expression is restricted to the testis. A portion of the human genome housing the largest proportion of the CT genes was selected for analysis in order to determine if the surrounding genomic architecture influences CT gene expression. A comparative genomics approach was used in determining if the CT genes are "ancient genes.
Antibacterial effects of biogenic silver nanoparticles synthesized using manihot esculenta (cassava) leaf aqueous extract
(University of the Western Cape, 2023) Oliver, Toni Charlize Alexia; Madiehe, Abram
Antimicrobial resistance (AMR) is a growing global health concern that poses a serious threat to the health of humans, animals, and plants. The major public health problem of AMR is primarily caused by the incorrect use of antibiotics, which is further compounded by the reduced novel antibiotics discovery rate. AMR bacteria cause infections that are difficult to treat, resulting in prolonged hospital stays and increased healthcare costs. Moreover, AMR is associated with a high risk of morbidity and mortality. Current therapeutic strategies for AMR infections are often inefficacious, associated with side effects, and may further exacerbate AMR. Therefore, there is an urgent need to develop alternative strategies to treat AMR bacterial infections.
The antimicrobial activity of zinc oxide nanoparticles synthesized with plant extracts against Staphylococcus aureus
(University of the Western Cape, 2019) Kriek, Gisela; Antunes, Edith
Nanoparticles using a green synthesis production method is of increasing interest for biomedical applications. Zinc oxide is currently used in medicinal and cosmetic formulations, and zinc oxide nanoparticles have potential in biomedical applications. Antibiotic-resistant bacterial infections are of growing concern globally, and novel antimicrobial agents are drastically needed. In this work, zinc oxide nanoparticles were synthesized using Calendula officinalis flowers aqueous extract and zinc nitrate hexahydrate using a single-pot green synthesis approach. The synthesized particles were calcined and characterised using UV-Vis spectrophotometry, Dynamic Light Scattering (DLS), X-Ray Diffraction (XRD), Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Thermogravimetric Analysis (TGA), Fourier-Transform Infrared Spectroscopy (FTIR) and Nuclear Magnetic Resonance Imaging (NMR). Quasi-spherical, hexagonal phase zinc oxide nanoparticles with core size <10nm according to TEM and average size of ~53nm according to XRD were successfully synthesized. The particles tended towards agglomeration. Antioxidant assays were run to determine the reducing power, antioxidant activity, and presence of polyphenols in the final products. The final product possessed antioxidant activity, polyphenols and had reducing power, confirming the constituents from Calendula officinalis playing a role in the reduction of the zinc ions and capping of the zinc oxide nanoparticles. Minimum inhibitory concentration of the samples by tube dilution was conducted to determine potential of the samples as antimicrobial agent against methicillin-resistant Staphylococcus aureus, using Clindamycin as control. Results of antimicrobial studies indicate the need for investigation of MIC using a variety of concentrations of the samples, and a variety of solvents, in order to determine exact MIC values. Further work is needed to improve the methodology to obtain particles that have a narrow size distribution, that are well dispersed, and are of higher concentration to be considered for antimicrobial use in the biomedical field.
Antimicrobial, anticancer and catalytic activities of green synthesized Avocado seed extract-gold nanoparticles
(University of the Western Cape, 2019) Ngungeni, Yonela; Madiehe, Abram; Dube, Admire
Nature through billions of years of trial and error has produced an immeasurable amount of natural systems like plants, birds and animals. The intelligence of nature is hidden in these natural systems and researchers are turning towards “Nature’s intelligence” to find inspiration and advance novelty in the development of nanomaterials. Gold nanoparticles (AuNPs) have unique optical, electronic and physicochemical features which has gained them popularity and widespread exploitation in various applications. The conventional methods used for AuNPs synthesis employs toxic chemicals which makes these NPs unsafe for biomedical applications. Hence, there is a search for new, ‘green’ and more cost effective methods for AuNPs synthesis. Plant extracts are regarded as a highly desirable system for nanoparticle synthesis due to their tremendous capability to produce a wide range of phytochemicals that can act as reducing agents. The main goal of this study was to synthesize AuNPs in a cost effective manner without the use of toxic chemicals in the synthesis process. Avocado seeds which are an agricultural waste by-product were used for the biosynthesis of AuNPs. The study reports on the synthesis optimization, characterization and activities of the biogenic AuNPs. The avocado seed extract mediated - AuNPs (AvoSE-AuNPs) were optimized by varying reaction parameters and characterized by UV-visible, Dynamic Light Scattering (DLS) and High Resolution Transmission Electron Microscopy (HRTEM), Zetasizer and Fourier Transform Infrared Spectroscopy (FTIR). The formation of AvoSE-AuNPs had an absorption maximum at 534 nm. HRTEM and DLS confirmed that the NPs were polydispersed and present in different shapes. The presence of phytochemical constituents on the AvoSE-AuNPs were confirmed by FTIR. Their potential antibacterial activity was tested on bacterial strains known to exhibit resistance to a number of current antibiotics. The catalytic activity of AvoSE-AuNPs was also assessed as a means to contribute to the development of new methods aimed at alleviating organic pollutants such as nitrophenols in the environment. The AvoSE-AuNPs demonstrated excellent catalytic activity in the reduction of 4-NP by NaBH4 as shown by the rapid decrease in the nitrophenolate absorption band at 400 nm and the appearance of new absorption band at 298 nm, revealing the formation of the 4-aminophenol. Furthermore, the rate constants calculated demonstrated that the reaction occurs faster in the presence AvoSEAuNPs. The AvoSE-AuNPs showed low significant cytotoxicity. Cell cycle analysis was conducted to further investigate the apparent exhibited toxicity of the AvoSE-AuNPs. The results showed that in both cell lines treated with AvoSE-AuNPs and AvoSE there was a ii | P a g e disruption in the regulation of cell cycle. Cell cycle analysis helped improve understanding of the low cytotoxicity observed by the MTT assay results. The results presented in this study clearly demonstrate the feasibility of using AvoSE for the synthesis of AuNPs. This study demonstrated that AvoSE mediated AuNPs synthesis is a greener alternative as it abides by the green chemistry principles. Furthermore, the study outcomes contributed to minimizing environmental pollution by finding use for agricultural waste and thus ultimately adding value to the field.
Aptamer selection against GFRa1 for its application in the prognosis of breast cancer
(University of the Western Cape, 2019) Swartz, Lauren Taryn; Meyer, Mervin
Breast cancer is the second most common cancer amongst South African women. Despite ongoing efforts to combat breast cancer, current prognostic and/or therapeutic monitoring methods are limited since very little improvement, in the rate of long term recurrence of breast cancer, has been observed. Considering this, developing novel strategies to detect breast cancer recurrence – at an early onset – is crucial for monitoring the disease and potentially preventing disease progression. Methods currently used for the detection of BC are costly and can also be very uncomfortable for the patient. These methods are also too costly to use as a routine test, following surgery or treatment to assess disease progression. Thus, developing a cost-effective detection method appears to be an appealing alternative. Serum/blood-based biomarkers are ideal targets for the development of low cost detection assays. Two candidate biomarkers, unique ligand binding protein 2 (ULBP2) and glial cell line-derived neurotrophic factor family receptor alpha 1 (GFR1) were identified using bioinformatics and proteomics, respectively. These biomarkers have demonstrated to be useful prognostic biomarkers for breast cancer. The selection of aptamers against these biomarkers can facilitate the development of cost-effective detection methods. Aptamers are short DNA or RNA oligonucleotides that have very high affinity and specificity for its targets and can potentially replace antibodies as tools for molecular recognition in detection systems, such as the enzyme-linked immunosorbent assay (ELISA), lateral flow assays and electrochemical biosensors.
The assessment of the bactericidal effect of green synthesized silver nanoparticles against a panel of infectious microorganisms
(University of the Western Cape, 2016) Mokone, Mmola; Beukes, D. R.; Antunes, E. M.; Meyer, M.
The emergence of multiple drug resistant microorganisms poses a major threat to human life. These microorganisms have made the currently used antibiotics ineffective and therefore continue to thrive. Therefore, there is a need for development of new, broad-secptrum antibiotics which is effective against almost every infectious microorganism. These antibiotics should ensure high effectiveness against the infectious pathogens while it is less detrimental to human health. Thus the search is channelled in nanoscience and nanotechnology in order to develop antibiotics that can kill infectious microorganisms effectively and hindering the development of drug resistance by these microorganisms. Nanoscience is the study of properties of a material when reduced to it smallest size (below 100 nm). It is a newly developing field of science which includes chemistry, physics and biology and has made it easy to synthesise nanomaterials for applications in many sectors of life including in medicine. The synthesis of nanoparticles can be achieved by physical and chemical methods. However, these methods are energy and capital intensive. Additionally, chemical method of synthesis uses chemicals that may be toxic which restrict the use of resultant nanoparticles in medicine. Therefore, there is a need for the use of eco-friendly methods of nanoparticle synthesis. The synthesis of silver and gold nanoparticles in this study was carried out by a green synthesis method, at room temperature, using an aqueous extract from the endemic brown alga Sargassum incisifolium. For comparison, commercially available brown algal fucoidans were also used to synthesise these nanoparticle, in addition to conventional methods of synthesis. The formation of nanoparticles was followed by the use of UV-Vis spectrophotometry. The characterization of the nanoparticles was done by TEM, XRD, DLZ and FT-IR. The rate of nanoparticle formation varied with specific reducing agent used. The faster reaction rate was recorded with S. incisifolium aqueous extracts pretreated with organic solvents while extracts obtained without this pretreatment produced slightly slower reaction rates. However, the commercially available fucoidans were less effective and required elevated temperatures for nanoparticle formation. Sodium borohydride reduction of silver nitrate was faster than the biological methods while the reduction of auric chloride by the S. incisifolium extracts and sodium citrate proceeded at similar rates. The nanoparticles synthesised with the help of the untreated aqueous extract were bigger than those synthesised from pre-treated extracts with both giving irregular shaped of nanoparticles. Also the nanoparticles formed from commercially available fucoidans were not of the same size, with bigger sizes recorded with Macrocystis fucoidan and smaller sizes with Fucus fucoidan. The shapes of nanoparticles from these fucoidans were spherical. From the conventional method, the nanoparticle sizes were smaller compared to the green synthesised nanoparticles and were predominantly spherical. The silver nanoparticles synthesised from the Sargassum aqueous extracts showed excellent antimicrobial activity against five pathogenic microorganisms including A. baumannii, K. pneumoniae, E. faecalis, S. aureus, and C. albicans. The gold nanoparticles were much less effective. To adequately assess the antimicrobial activities of the nanoparticles, it is or paramount importance to also asses their cytotoxicity activity. Three cell lines were used in this study namely, MCF-7, HT-29 and MCF-12a. The silver nanoparticles were found to be toxic to HT-29 and MCF-7 cell lines, exhibiting sligtly less toxicity against MCF-12a cells. The gold nanoparticles showed lower toxicity but a similar trend was observed.
An assessment of the dietary intake of pregnant women in the West Coast / Winelands region, Western Cape Province: relation to low birth weight
(University of the Western Cape, 2008) Jaffer, Sharmilah; Swart, E.C.; Jackso, D.; Faculty of Community and Health Sciences
This secondary analysis aimed to develop dietary scores to assess the dietary intake of pregnant women in the West Coast/ Winelands region and determine the association with LBW. Further to determine the association between the dietary scores and maternal socioeconomic and socio-demographic characteristics and maternal smoking and/or alcohol consumption during pregnancy.
Association between antioxidant activities and drought responses of two contrasting sugar beet genotypes
(University of the Western Cape, 2017) Majola, Anelisa; Ludidi, Ndiko
Sugar beet (Beta vulgaris L), which belongs to the Amaranthaceae family is a biennial crop widely used as a source of domestic sugar in the European countries, United States, China and Japan. However, in South Africa, sugar cane is the sole source of natural sugar and therefore sugar beet is a potential source of bioethanol since it would not be in direct competition with a food crop for sugar production. Thus, sugar beet can be utilized as a renewable source of energy, reducing the need and use of fossil fuels (such as petrol) that produce greenhouse gases and consequently cause global warming and climate change. Nonetheless, drought stress is one of the major factors limiting the growth of sugar beet, resulting in sugar beet yield reductions worldwide.

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