1834 research outputs found
Sort by
South African Women in Science Awards (WISA)
No full textPresentations SA PhD Project Conference: Western Cape Province 13 September 2016
Commercialising research outputs
No full textPresentations SA PhD Project Conference: Gauteng Province 11 October 2016
Comparison of the HIV-1 VPU interaction with CD4 and CD74
No full textViral protein U (Vpu) is a versatile accessory protein of human immunodeficiency virus type 1 (HIV-1) and some simian immunodeficiency virus isolates. Amongst other functions, Vpu targets human CD4 for ubiquitination and proteasomal degradation. This process requires the presence of phospho-serine residues within the Vpu cytoplasmic domain in order to allow for the recruitment of beta-transducin repeat-containing protein (β-TrCP) and ultimately the E3 ligase complex. Similarly, it has been shown that the Vpu cytoplasmic domain also interacts with the human CD74 cytoplasmic region. CD74, the invariant chain of major histocompatibility complex class II (MHCII), is involved in the presentation of foreign antigens to CD4+ T cells. The Vpu/CD74 interaction may prevent the maturation of the MCHII complex resulting in the downmodulation of cell surface levels of MHCII. There are several structural similarities between the human CD4 and CD74 host proteins. Consequently, we hypothesised that HIV-1 Vpu targets human CD74 for proteasomal degradation through the binding of β-TrCP similar to that of Vpu-mediated CD4 proteasomal degradation. In view of this, this study aimed to delineate the binding interaction between HIV-1 Vpu and CD74 and to determine whether Vpu also targets CD74 for proteasomal degradation. An in silico homology study determined that the α-helices found within the cytoplasmic domains of CD4 and CD74 were similar with an RMSD of 1.437 Å. Recombinant Vpu::GFP fusion proteins were expressed in HEK 293T cells and purified in sufficient quantities and purity for use in subsequent in vitro assays. Using ELISAs, it was found that CD74 effectively prevented the binding of an anti-Vpu antibody, but not an anti-GFP antibody, to the Vpu::GFP fusion protein with an IC50 of 888.67 ± 130.08 nM. Further to this, using CD74 overlapping peptides of increasing lengths in combination with a Vpu overlapping peptide set, it was determined that the sequences “RIRERAEDSGNESEG” and “EDQKP” in the Vpu and CD74 cytoplasmic regions, respectively, contain the binding sites for this interaction. While the CD4 and CD74 cytoplasmic peptides yielded different responses after binding Vpu peptides, these two host proteins were shown to compete for binding to the Vpu protein. This provides evidence that steric hindrance has an effect on binding. Finally, total CD74 levels including cell membrane and intracellular fractions were significantly downregulated by Vpu at
24 and 48 hours (p = 0.0270 and 0.0062, respectively) as indicated by immunoprecipitation and flow cytometry in Vpu-transfected U937 cells. Notably, Vpu phosphorylation mutants (S52A and S52/56A) were unable to reduce CD74 levels within U937 cells, indicating that CD74 is not targeted for proteasomal degradation. In conclusion, this study has defined the specific Vpu/CD74 binding site and provides novel evidence that CD74 is downregulated in the presence of Vpu. Moreover, CD74 is not targeted for proteasomal degradation through the binding of β-TrCP and the recruitment of the E3 ligase complex. These findings have future relevance for HIV-1 treatment and management as CD74 downregulation is yet another mechanism by which HIV-1 impairs the host immune response.National Research Foundatio
DST-NRF postdoctoral forum
No full textPresentation DST-NRF Postdoctoral Forum: Cape Town 13-15 March 201
Can natural bio-stimulants improve agricultural productivity with reduced fertilizer input?
No full textGreen economy postdoctoral fellowships induction workshop 201
Advances in random forests with application to classification
No full texte, a novel random forest framework, viz. oblique random rotation
forests, is proposed. Although not entirely satisfactory, the framework
serves as an example of a heuristic approach towards novel proposals based on
bias-variance analyses, instead of an ad hoc approach, as is often found in the
literature.
The analysis of comparative studies regarding advances in random forest algo rithms is also considered. It is of interest to critically evaluate the conclusions
that can be drawn from these studies, and to infer whether novel random forest
algorithms are found to significantly outperform Forest-RI. For this purpose,
a meta-analysis is conducted in which an evaluation is given of the state of research
on random forests based on all (34) papers that could be found in which
a novel random forest algorithm was proposed and compared to already existing
random forest algorithms. Using the reported performances in each paper,
a novel two-step procedure is proposed, which allows for multiple algorithms
to be compared over multiple data sets, and across different papers. The metaanalysis
results indicate weighted voting strategies and variable weighting in
high-dimensional settings to provide significantly improved performances over
the performance of Breiman’s popular Forest-RI algorithm.National Research Foundatio
Towards standardised reef fish monitoring: an assessment of stereo-video techniques to sample shallow and deep reef fish assemblages
No full textBaited remote underwater stereo-video systems (stereo-BRUVs) were developed to
determine fish abundance and size structure in a more unbiased, and relatively non-invasive
manner across a broader range of depths and habitats than conventional sampling methods
achieve. These characteristics make stereo-BRUVs particularly useful for research inside
marine protected areas (MPAs) where researchers are required to minimize disturbance to
the protected environment.
Although stereo-BRUVs have been widely used around the world, they are novel to South
Africa and standardised protocols for their application are required. As such, this study
aimed to address i) the effect of different bait types, namely pilchard (Sardinops sagax),
squid (Loligo reynaudi) and bivalves (Crassostrea gigas and Perna perna) on the observed
reef fish assemblage structure and ii) the effect of artificial illumination (lighting) on the
observed reef fish assemblage structure sampled with stereo-BRUVs.
One key component of the stereo-BRUVs methodology is the application of bait to attract
fish into the field of view. Globally, pilchard is the most often used bait type for stereoBRUVs,
however, its suitability has never been tested comparatively against other bait types
for South African conditions. Significant differences in fish abundance and assemblage
structure were recorded between stereo-BRUVs deployments when applying the different
bait types. The bivalve baits, oyster and mussel, were typically poor when sampling the reef
fish assemblages of the region. Pilchard and squid were sampled in similar communities and
were able to attract the majority of the reef fish from the region, suggesting they are
suitable bait types for stereo-BRUVs in the Agulhas ecoregion. However, a power analysis
indicated that roughly twice the amount of samples are required to effectively sample the
same abundances of Chrysoblephus laticeps (roman) and Cheilodactylidae (fingerfins)
II
species when sampling with squid as opposed to pilchard. Both bait types can be locally
sourced, however, squid is considerably more expensive than pilchard. Considering the
difference in cost, together with the fact that twice as much squid bait is required, squid is
not a cost-effective option relative to pilchard. As such this study recommends that pilchard
is the most appropriate bait for the Agulhas ecoregion of South Africa.
Due to low light levels, artificial lighting is required when conducting remote video research
in the sub-photic zone. Blue light has a shorter wavelength than other colour lights and
attenuates slower through water. In addition, blue lighting has no recorded effect on fish
behaviour and has proven to be a successful light colour for underwater sampling. The use
of lighting is unavoidable for sub-photic stereo-BRUVs sampling and is recommended for all
stereo-BRUVs sampling for comparability of data from environments characterised by
different light levels. A study was conducted to test the necessity of artificial lighting when
sampling from environments characterised by ambient light levels adequate for stereoBRUVs
sampling, a comparative to measure the effect of light on the fish assemblage
structure. Of the more commonly detected fish species (those observed in >50% of the
samples), most were seen at similar abundances in samples using lighting and in those
without lighting. No significant differences were observed in fish length data between
samples collected with and samples collected without lighting. This suggests that
standardised stereo-BRUVs sampling across photic zones on the continental shelf of South
Africa can be collected without blue lighting when ambient light levels are sufficient to see
the survey area.National Research Foundatio
Swimming with the giant: coexistence patterns of a new redfin minnow Pseudobarbus skeltoni from a global biodiversity hot spot
No full textEcological niche theory predicts that coexistence is facilitated by resource partitioning
mechanisms that are influenced by abiotic and biotic interactions.
Alternative hypotheses suggest that under certain conditions, species may
become phenotypically similar and functionally equivalent, which invokes the
possibility of other mechanisms, such as habitat filtering processes. To test these
hypotheses, we examined the coexistence of the giant redfin Pseudobarbus
skeltoni, a newly described freshwater fish, together with its congener Pseudobabus
burchelli and an anabantid Sandelia capensis by assessing their scenopoetic
and bionomic patterns. We found high habitat and isotope niche overlaps
between the two redfins, rendering niche partitioning a less plausible sole mechanism
that drives their coexistence. By comparison, environment–trait relationships
revealed differences in species–environment relationships, making habitat
filtering and functional equivalence less likely alternatives. Based on P. skeltoni’s
high habitat niche overlap with other species, and its large isotope niche width,
we inferred the likelihood of differential resource utilization at trophic level as
an alternative mechanism that distinguished it from its congener. In comparison,
its congener P. burchelli appeared to have a relatively small trophic niche,
suggesting that its trophic niche was more conserved despite being the most
abundant species. By contrast, S. capensis was distinguished by occupying a
higher trophic position and by having a trophic niche that had a low probability
of overlapping onto those of redfins. Therefore, trophic niche partitioning
appeared to influence the coexistence between S. capensis and redfins. This
study suggests that coexistence of these fishes appears to be promoted by their
differences in niche adaptation mechanisms that are probably shaped by historic
evolutionary and ecological processes.Rufford Small Grants for Nature Conservation and MBZ
Emergent effects of structural complexity and temperature on predator–prey interactions
No full textEphemeral aquatic environments are important habitats for a variety of species. They are highly
variable with regards to vegetation structure and physico-chemical features that potentially mediate outcomes
of biotic interactions. Multiple environmental variables and their emergent impacts on the relationship between
prey consumption rate by a predator and prey density (functional response), however, are rarely assessed.
Here, we investigated the combined effects of temperature and habitat complexity on the functional response
of the freshwater predatory notonectid Enithares sobria on the cladoceran prey organism Daphnia longispina. A
Type II functional response was observed for E. sobria predating on D. longispina and while temperature and
habitat complexity had no effect on the response type, these environmental variables interacted with consequences
for the magnitude of the functional responses. Overall, structural complexity favored the predator
as greater consumption was observed in the most complex habitat treatment. Temperature effects were also
evident although these effects were not unidirectional with regard to treatment factor gradients as predators
were the most successful at intermediary temperatures. Furthermore, there was a complex interplay between
habitat complexity and temperature, with attack rates being greatest at low and high complexities within intermediate
temperatures, while at zero complexity attack rates were greatest at the lowest temperature. The effect
of habitat on handling times was only evident in the low temperature treatments which decreased steadily with
each increase in complexity. Through the application of functional responses the synergistic effects of multiple
environmental drivers on predator–prey interaction outcomes have been highlighted, adding insight into how
interactions among species may be affected by natural or artificially induced environmental variability
