1834 research outputs found
Sort by
A novel approach for targeted elimination of CSPG4-positive triple negative breast cancer using a MAP-tau based fusion protein
No full textChondroitin sulfate proteoglycan 4 (CSPG4) has been identified as a highly promising target antigen for immunotherapy of triple‐negative breast cancer (TNBC). TNBC represents a highly aggressive heterogeneous group of tumors lacking expression of estrogen, progesterone and human epidermal growth factor receptor 2. TNBC is particularly prevalent among young premenopausal women. No suitable targeted therapies are currently available and therefore, novel agents for the targeted elimination of TNBC are urgently needed. Here, we present a novel cytolytic fusion protein (CFP), designated αCSPG4(scFv)‐MAP, that consists of a high affinity CSPG4‐specific single‐chain antibody fragment (scFv) genetically fused to a functionally enhanced form of the human microtubule‐associated protein (MAP) tau. Our data indicate that αCSPG4(scFv)‐MAP efficiently targets CSPG4+ TNBC‐derived cell lines MDA‐MB‐231 and Hs 578T and potently inhibits their growth with IC50 values of ∼200 nM. Treatment with αCSPG(scFv)‐MAP resulted in induction of the mitochondrial stress pathway by activation of caspase‐9 as well as endonuclease G translocation to the nucleus, while induction of the caspase‐3 apoptosis pathway was not detectable. Importantly, in vivo studies in mice bearing human breast cancer xenografts revealed efficient targeting to and accumulation of αCSPG4(scFv)‐MAP at tumor sites resulting in prominent tumor regression. Taken together, this preclinical proof of concept study confirms the potential clinical value of αCSPG4(scFv)‐MAP as a novel targeted approach for the elimination of CSPG4‐positive TNBC.National Research Foundation (South Africa
Seasonality of leaf and fig production in Ficus squamosa, a fig tree with seeds dispersed by water
No full textThe phenology of plants reflects selection generated by seasonal climatic factors and interactions with other plants and animals, within constraints imposed by their phylogenetic history. Fig trees (Ficus) need to produce figs year-round to support their short-lived fig wasp pollinators, but this requirement is partially de-coupled in dioecious species, where female trees only develop seeds, not pollinator offspring. This allows female trees to concentrate seed production at more favorable times of the year. Ficus squamosa is a riparian species whose dispersal is mainly by water, rather than animals. Seeds can float and travel in long distances. We recorded the leaf and reproductive phenology of 174 individuals for three years in Chiang Mai, Northern Thailand. New leaves were produced throughout the year. Fig production occurred year-round, but with large seasonal variations that correlated with temperature and rainfall. Female and male trees initiated maximal fig crops at different times, with production in female trees confined mainly to the rainy season and male figs concentrating fig production in the preceding months, but also often bearing figs continually. Ficus squamosa concentrates seed production by female plants at times when water levels are high, favouring dispersal by water, and asynchronous flowering within male trees allow fig wasps to cycle there, providing them with potential benefits by maintaining pollinators for times when female figs become available to pollinateNational Research Foundation (South Africa
Floral constraint resulting from intersexual mimicry in a gynodioecious fig tree
No full textFig trees (Ficus: Moraceae) are pollinated by female fig wasps (Agaonidae) whose larvae develop inside galled flowers of unusual inflorescences (figs). Most fig trees also support communities of non‐pollinating fig wasps. Figs of different species display great size variation and contain tens to tens of thousands of flowers. Around one‐half the species of fig trees have the gynodioecious breeding system, where female trees have figs that produce seeds and male trees have figs that support development of pollinators. Mutual mimicry between receptive male and female figs ensures that pollinators enter female figs, even though the insects will die without reproducing, but the need to give no sex‐specific cues to the pollinators may constrain differences in size between receptive male and female figs. We compared relationships between inflorescence size and some measures of reproductive success in male and female figs of Ficus montana grown under controlled conditions in the presence of the pollinator Kradibia tentacularis and its main parasitoid Sycoscapter sp. indesc. Female figs that contained more flowers produced more seeds, but male figs did not increase the production of female pollinator K. tentacularis fig wasps in proportion of the flower number. Although more flowers were galled by the pollinators in male figs containing more female flowers, the high larval mortality caused by parasitism and nutritional limitation prevented the increase in the production of adult female offspring. Selection may favor the increase in flower numbers within figs in female plants of F. montana, but contrarily constrain this attribute in male plants.National Research Foundation (South Africa
Starving seabirds: unprofitable foraging and its fitness consequences in Cape gannets competing with fisheries in the Benguela upwelling ecosystem
No full textFisheries are often accused of starving vulnerable seabirds, yet evidence for this claim is scarce. Foraging energetics may provide efficient, short-term indicators of the fitness status of seabirds competing with fisheries. We used this approach in Cape gannets (Morus capensis) from Malgas Island, South Africa, which feed primarily on small pelagic fish in the southern Benguela upwelling region, thereby competing with purse-seine fisheries. During their 2011–2014 breeding seasons, we determined body condition of breeding adult Cape gannets and measured their chick growth rates. In addition to these conventional fitness indices, we assessed the daily energy expenditure of breeding adults using a high-resolution time-energy budget derived from GPS-tracking and accelerometry data. For these same individuals, we also determined prey intake rates using stomach temperature recordings. We found that adult body condition and chick growth rates declined significantly during the study period. Crucially, most birds (73 %) studied with electronic recorders spent more energy than they gained through foraging, and 80–95 % of their feeding dives were unsuccessful. Our results therefore point to unprofitable foraging in Cape gannets, with a longer-term fitness cost in terms of adult body condition and reproductive performance that corresponds to a local population decline. Based on this evidence, we advocate a revision of regional fishing quotas for small pelagic fish and discuss the possibility of an experimental cessation of purse-seine fishing activities off the west coast of South Africa. These measures are needed for the ecological and socio-economical persistence of the broader southern Benguela upwelling ecosystem.National Research Foundation (South Africa
The effect of commercial forestry plantations and roads on southern afrotemperate forest arthropod diversity
No full textWith only about 12% of the Earth’s surface under some form of official protection and the
human population on the rise exponentially, production landscapes can and should contribute
significantly towards biodiversity conservation in the future. Globally, management practices
that balance production and conservation are important for creating sustainable agriculture
and timber production landscape. This study aims to determine how a heterogeneous,
unfenced national park in South Africa, containing a mosaic of commercial plantations, natural
forests and fynbos is affected by land transformation. This was achieved by focussing on
artificially created and natural edges found in this landscape, through analysing and comparing
the composition and species richness of arthropods across linear transects. Specifically I
determined if natural edges next to southern Cape Afrotemperate forests are altered by
anthropogenic influences such as forestry plantations, and their felling, as measured by
epigaeic arthropod diversity. The effects of different road types, and directions that these roads
dissect the forest, were also assessed. I found that pine plantations provide little suitable
habitat for either forest or fynbos arthropods. The natural fynbos-forest ecotone harbours a
unique composition of arthropod assemblages, with the smallest edge effect into the forest.
Once this is replaced by commercial pine plantations, an edge effect up to 30 m into the forests
from the plantation edge is detected. When plantations bordering natural forests are felled,
the edge effect increases to 50 m into natural forests. Research on edge effects created by
roads showed that both wider, arterial roads as well as secondary roads affected the diversity
of forest arthropods up to 50 m into the natural forest. These effects are therefore similar to
that observed after clear felling of plantations except that, in contrast to possible regeneration
of natural edge habitat after clear felling, these edges are now permanent fragmentary
features in the forest with little chance of recovery. Even hiking trails affected overall arthropod
assemblages in the adjacent forests up to 10 m. Although this likely does not lead to forest
fragmentation due to an in-tact forest canopy, these areas alter natural assemblages with
unknown population dynamic consequences. I also show that east-west directed roads have
Stellenbosch University https://scholar.sun.ac.za
stronger fragmentary effects as determined by arthropod diversity, along their southern edge
than north-south directed roads, with east and west facing edges. Increased sunlight
penetration, with its accompanying changes in microclimatic conditions is put forward to
explain these differences. Habitat loss due to the establishment of commercial plantation
forestry in the region not only leads to a decrease in suitable fynbos habitat, but also impacts
adjacent natural forest arthropod diversity. The remaining southern Cape Afrotemperate
forests are greatly fragmented by a network of roads. Due to the uniqueness of these forests,
special management is needed to ensure that the biodiversity in the region is optimally
conserved without adversely affecting production yields. Some possible mitigation actions are
put forward. However, these should be assessed for their effectiveness in future research studies before they are implemented.National Research Foundatio
Die identifisering, beskrywing en riglyne vir die ontwikkeling van veerkragtigheidskenmerke in gesinne waarvan ʼn ouer alkohol misbruik: ʼn gesinsperspektief
No full textAlcohol abuse is a major problem worldwide and in South Africa which not only affects
individuals, but families and communities as well. In South Africa, the Western Cape is the
province with the highest prevalence of alcohol abuse. Alcohol abuse is also the most prevalent
amongst the coloured population group and in rural areas. Despite the potentially negative
impact that parental alcohol abuse can have on families, some families are capable of coping
with and overcoming this adversity. Families who have the ability to withstand and rebound
from disruptive life challenges, such as when a parent in the family abuses alcohol, are referred
to as resilient families.
The main objective of this investigation was to determine which family characteristics can be
associated with positive adaptation in families in which a parent abuses alcohol in a rural area
of the Western Cape among the coloured population, based on family membersʼ views. The
secondary objective of this investigation was to provide guidelines based on family membersʼ
perspectives for how these characteristics can be developed in order to help families cope with
the crisis of alcohol abuse.
Although family resilience studies regarding parental alcohol abuse were found in the
international literature, there is a lack of similar studies in South Africa. The lack of local
studies that are qualitative in nature, that focus on family resilience rather than individual
resilience and where the parent is the family member that abuses alcohol, allows for an
investigation in which the unique factors of this group of participants can be identified and
described.
Participants were 18 families of which one or both parents had been abusing alcohol for six
months or longer. In 15 cases, the mother acted as the representative of the family, and in one
case the father. In two cases both the mother and a daughter who still lives with them at home
participated on behalf of the family. Data were collected by means of semi-structured
interviews and analysed thematically.
Stellenbosch University https://scholar.sun.ac.za
vi
The results are presented in four sections, namely participants’ descriptions of how their
families are characterised, participants’ experiences of the negative effect of alcohol abuse,
participants’ descriptions of family resilience characteristics, and participants’ suggestions for
guidelines for the development of an intervention programme for families with parental alcohol
abuse. Themes that related to participants’ descriptions of how their families are characterised
were: alcohol abuse is at its worst over weekends and in the month of December; other family
members are against alcohol abuse; domestic violence; more than one family member abuses
alcohol; only the parent that abuses alcohol can help him-/herself; the parent has been abusing
alcohol his/her whole life and has had relapses; the parent does not want to admit the problem
or the severity of the problem; and stressors. Themes that related to participants’ experiences
of the negative effect of alcohol abuse were the negative effects of alcohol abuse on finances,
the community, the family, health, the marriage, children and careers.
Themes that related to participants’ descriptions of family resilience factors included family
problem-solving communication, family time and routines, religion, support from community
resources, social support, and other factors. Themes that related to participants’ suggestions for
guidelines for the development of an intervention programme were: to emphasise the
importance of the youth; to involve families with parental alcohol abuse in the community; to
link the programme to a religious component; to help people to not start drinking, drink less or
stop drinking; to make the intervention programme prolonged and continuous; as well as to
receive rehabilitation, counselling or therapy.
Based on the identified resilience characteristics and advice to other families, suggestions are
made for how these factors can be implemented in order to develop a family resilience
intervention programme for families with parental alcohol abuse.National Research Foundatio
Machine learning approach to radio frequency interference(RFI) classification in radio astronomy
No full textRadio frequency interference (RFI) presents a large problem for radio tele-
scopes. Interference prevents observations from being made, or extends the
duration required for observations. This thesis investigates di erent methods
to automatically classify RFI signals. Data from di erent sources was cap-
tured at the SKA site. Both Gaussian Mixture Model (GMM) and K-nearest
neighbors (KNN) classi ers were used to analyse the data. Both performed
adequately, with the KNN slightly outperforming the GMM. Di erent feature
extraction methods were also investigated.National Research Foundatio
Design, synthesis and evaluation of 3-hydroxypyridin-4-ones as inhibitors of catechol-O-methyltransferase
No full textParkinson’s disease is a bradykinetic disorder that is the result of the death of dopaminergic neurons in the basal ganglia of the brain. This, in turn, leads to the depletion of dopamine in the striatum, which is responsible for the characteristic motor symptoms of the disease. The most effective treatment for restoring central dopamine levels is levodopa, the metabolic precursor of dopamine. However, due to extensive peripheral enzymatic metabolism by dopa decarboxylase (DDC) and O-methylation by catechol-O-methyltransferase (COMT), less than 1% of levodopa reaches the brain unchanged. Thus, by preventing levodopa metabolism and increasing the availability of levodopa for uptake into the brain, the inhibition of COMT would be beneficial in Parkinson’s disease. COMT serves as a catalyst in the methyl transmission from S-adenosyl-L-methionine (SAMe/SAM) to a hydroxy group of a catechol substrate. Nitrocatechol COMT inhibitors, such as tolcapone and entacapone, have been used in the treatment of Parkinson’s disease. Poor bioavailability and undesirable side-effect profiles sometimes limit the clinical use of nitrocatechol COMT inhibitors. The aim of this study therefore was to discover new non-nitrocatechol COMT inhibitors for the treatment of Parkinson’s disease. In the present study, the 3-hydroxypyridin-4-one scaffold was selected for the design of non-nitrocatechol COMT inhibitors since the COMT inhibitory potential of this class has been illustrated. 3-Hydroxypyridin-4-ones are isosteric to the catechol ring, but are not O-methylated by the enzyme themselves. Further, it has been illustrated that non-nitrocatechol COMT inhibitors can be MB-COMT (membrane bound COMT) specific, which may be beneficial when considering peripheral side-effects.
The present study thus reports the synthesis of new members of the 3-hydroxypyridin-4-one class of compounds, which may act as COMT inhibitors. Such compounds may represent useful agents for the treatment of Parkinson’s disease with improved safety profiles compared to nitrocatechol COMT inhibitors. Different structural aspects of the nitrogen substituent that were explored included simple aromatic and aliphatic substitution (JDB1, JDB10 and JDB11), chain elongation and increasing flexibility (JDB3, JDB4, JDB5 and JDB9), as well as halogen and methyl substitution of the side chain phenyl ring (JDB12, JDB13 and JDB14). Molecular modelling studies (Discovery Studio 3.1, Accelrys) were conducted in a preliminary attempt to predict the inhibition activities of the proposed 3-hydroxypyridin-4-one derivatives. All the derivatives fitted within the catechol binding site of COMT and formed productive interactions with the residues of the enzyme. Therefore the potential inhibition activities of these compounds were confirmed. The compounds were synthesised by reacting maltol with a suitable primary amine in an acidic environment, with ethanol serving as co-solvent. Nuclear magnetic resonance spectroscopy (NMR), infrared spectroscopy (IR) and mass spectrometry (MS) were used to characterise the structures. The purities of the compounds were estimated by high-performance liquid chromatography (HPLC) analysis.
COMT obtained from porcine liver was used as enzyme source to evaluate the in vitro COMT inhibitory properties of the synthesised 3-hydroxypyridin-4-ones. A HPLC method with fluorescence detection was validated and employed to measure COMT activity. The natural COMT substrate, (-)-norepinephrine (NE), was incubated with COMT in the presence of various concentrations of the test inhibitors. The formation of normetanephrine (NMN), the O-methylated product of NE metabolism, was measured by the validated HPLC system. From the inhibition data IC50 (inhibitor concentration at 50% inhibition) values for the inhibition of COMT were calculated. The synthesised 3-hydroxypyridin-4-ones were found to be inhibitors of COMT with IC50 values ranging from 4.55 to 19.79 μM. Compared to the reference COMT inhibitors, entacapone (IC50 = 0.00047 μM) and tolcapone (IC50 = 0.00675 μM), the 3-hydroxypyridin-4-ones were significantly lower potency COMT inhibitors. 1-Benzyl-3-hydroxy-2-methylpyridin-4-one (JDB3) was the most potent compound with an IC50 value of 4.55 μM. Some preliminary structure-activity relationships (SARs) were derived, for example, benzyl substitution of the 3-hydroxypyridin-4-one moiety yielded the most potent COMT inhibitors of the series. Phenylethyl, phenylpropyl and phenylbutyl substitution yielded lower potency inhibitors. This shows that chain elongation of the substituent reduces COMT inhibition potency. In conclusion, several 3-hydroxypyridin-4-one derivatives were synthesised and their COMT inhibitory activities were determined. Although these compounds are not highly potent inhibitors, they may act as leads for the development of non-nitrocatechol COMT inhibitors with possibly better safety profiles. Such compounds would be appropriate for the treatment of Parkinson’s disease.National Research Foundatio
A computational perspective of influenza a virus targets: neuraminidase and endonuclease
No full textThrough the ages the viruses have plagued mankind claiming the lives of millions, pre-dating
any advancements in the medicinal sciences. One such pathogenic virus is influenza A, which
has been implicated in the 1918-Spanish flu, the 2006-avian flu outbreak and the 2009-swine
flu pandemic. It is a highly sophisticated species, alluding efforts to thwart the spread of
disease and infection. One of the main reasons influenza has survived this long is simple
evolution. Natural mutation within the genome of virions expressed in proteins, enzymes or
molecular structure render us unable to predict or take preventative measures against possible
infection. Thus, research efforts toward the competitive inhibition of biological pathways that
lead to the spread of disease, have become attractive targets.
The influenza A virus has a number of chemotherapeutic targets, such as:
1) The surface antigens, hemagglutinin and neuraminidase,
2) RNA-dependent RNA polymerase, and
3) The M2 proton channel.
Influenza RNA polymerase is composed of three large segments encoding polymerase acidic
protein (PA), polymerase basic protein 1 (PB1) and polymerase basic protein 2 (PB2). The
PA protein is an N-terminal domain subunit which contains the endonuclease activity. The
influenza virus is incapable of synthesizing a 5’-mRNA cap, so it has adapted a cap-snatching
mechanism whereby the PB2 subunit binds to the 5’-end of host mRNA, after which 10-14
nucleotides downstream the PA-subunit (aka PAN) cleaves the strand forming a primer for viral
mRNA synthesis which is catalysed by the PB1 subunit. Influenza target identification is based
primarily on evidence suggesting sequence conservation of each entity and its selective
expression in the virus and not the host.
In this thesis two enzymatic targets were investigated, the PA protein of RNA polymerase and
neuraminidase. The studies focussed on using computational tools to:
1) provide insight into the mechanism of drug-resistance,
2) describe the conformational structure of the protein in the presence of point mutations
and in complex with an inhibitor,
3) determine the essential binding pharmacophoric features to aid the design of new drug
therapies.
An array of computational techniques were employed in the studies, such as: molecular
dynamics (MD) simulation, structure-based and ligand-based in silico screening, principal
component analysis, radius of gyration analysis, binding free energy calculations and solventaccessible
surface area analysis.
The first study (Chapter 5) determined the mechanism of drug-resistance in influenza A
neuraminidase as a consequence of antigenic variations. Two distinct mutations in the enzyme
sequence that were investigated are H274Y and I222K. The active site residues of
neuraminidase are conserved among the subtypes of influenza A. However, it was discovered
that the occurrence of resistance to the drug oseltamivir, in the H1N1 species was different to
the H5N1 virus. Although both systems shared a loss in hydrophobicity of the active site, the
conformational distortion of the active site pocket distinguished the enzyme of the two viral
entities, from one another.
The discoveries made in the first study laid the foundation for the second study (Chapter 6),
which was based on the in silico design and screen of potential neuraminidase inhibitors. As
a result 10 characteristic molecular scaffolds were suggested as potential inhibitors. The
pharmacophore design was constructed with consideration to the new conformational structure
of the active site pocket.
Chapter 7 is the third study of this thesis. The active site pocket enclosing the endonuclease
activity of the PA subunit was investigated. Using molecular dynamics simulations and postdynamic
analyses, a description of the protein conformation was offered. Subsequently, a
pharmacophore was proposed as a potential scaffold to which endonuclease inhibitors may be
modelled upon. It is my belief that the impact of the results derived from the above mentioned studies would
greatly contribute to the development of new and effective anti-influenza drugs.National Research Foundatio
Politics and prosthesis: representing disability in South Africa's truth and reconciliation commission
No full textThis dissertation aims to put two seemingly stable and unchanging categories, namely the 'nation' and the 'body', into conversation with each other in order to interrogate how the disabled body, in particular, became a site for nation building in South Africa's transition from apartheid to democracy in the 1990s. More specifically, this dissertation aims to explore how, framed by the Truth and Reconciliation Commission (TRC), different bodies took on disparate meanings that both affirmed and challenged the emergence of the euphemistically termed, 'New Nation'. Relying on insights from disability studies, postcolonial scholarship and critical race and gender studies, this dissertation endeavours to interrogate how the emergent post-apartheid state relied on the collective memory and identity generated through particular ideas of violence and politics evidenced by the injured bodies on display at the TRC. Drawing on the TRC transcripts, the TRC Final Report and the Truth Commission Special Report coverage of the proceedings, this dissertation seeks to ask new questions about the shifting and uneven sites of embodied meaning-making in post-apartheid South Africa.National Research Foundatio