Development of a high-level gene expression system for the production of bioplastics in sugarcane

Despite various approaches, the production of biodegradable plastics such as polyhydroxybutyrate (PHB) in transgenic plants has met with limited success due largely to low expression levels. Even in the few instances where high levels of protein expression have been reported, the transgenic plants have been stunted indicating PHB is phytotoxic (Poirier 2002). This PhD describes the application of a novel virus-based gene expression technology, termed InPAct („In Plant Activation.), for the production of PHB in tobacco and sugarcane. InPAct is based on the rolling circle replication mechanism by which circular ssDNA viruses replicate and provides a system for controlled, high-level gene expression. Based on these features, InPAct was thought to represent an ideal system to enable the controlled, high-level expression of the three phb genes (phbA, phbB and phbC) required for PHB production in sugarcane at a preferred stage of plant growth. A Tobacco yellow dwarf virus (TbYDV)-based InPAct-phbA vector, as well as linear vectors constitutively expressing phbB and phbC were constructed and different combinations were used to transform tobacco leaf discs. A total of four, eight, three and three phenotypically normal tobacco lines were generated from discs transformed with InPAct-phbA, InPAct-phbA + p1300-TaBV P-phbB/phbC- 35S T, p1300-35S P-phbA-NOS T + p1300-TaBV P-phbB/phbC-35S T and InPAct-GUS, respectively. To determine whether the InPAct cassette could be activated in the presence of the TbYDV Rep, leaf samples from the eight InPActphbA + p1300-TaBV P-phbB/phbC-35S T plants were agroinfiltrated with p1300- TbYDV-Rep/RepA. Three days later, successful activation was indicated by the detection of episomes using both PCR and Southern analysis. Leaf discs from the eight InPAct-phbA + p1300-TaBV P-phbB/phbC-35S T transgenic plant lines were agroinfiltrated with p1300-TbYDV-Rep/RepA and leaf tissue was collected ten days post-infiltration and examined for the presence of PHB granules. Confocal microscopy and TEM revealed the presence of typical PHB granules in five of the eight lines, thus demonstrating the functionality of InPActbased PHB production in tobacco. However, analysis of leaf extracts by HPLC failed to detect the presence of PHB suggesting only very low level expression levels. Subsequent molecular analysis of three lines revealed low levels of correctly processed mRNA from the catalase intron contained within the InPAct cassette and also the presence of cryptic splice sites within the intron. In an attempt to increase expression levels, new InPAct-phb cassettes were generated in which the castorbean catalase intron was replaced with a synthetic intron (syntron). Further, in an attempt to both increase and better control Rep/RepA-mediated activation of InPAct cassettes, Rep/RepA expression was placed under the control of a stably integrated alc switch. Leaf discs from a transgenic tobacco line (Alc ML) containing 35S P-AlcR-AlcA P-Rep/RepA were supertransformed with InPAct-phbAsyn or InPAct-GUSsyn using Agrobacterium and three plants (lines) were regenerated for each construct. Analysis of the RNA processing of the InPAct-phbAsyn cassette revealed highly efficient and correct splicing of the syntron, thus supporting its inclusion within the InPAct system. To determine the efficiency of the alc switch to activate InPAct, leaf material from the three Alc ML + InPAct-phbAsyn lines was either agroinfiltrated with 35S P-Rep/RepA or treated with ethanol. Unexpectedly, episomes were detected not only in the infiltrated and ethanol treated samples, but also in non-treated samples. Subsequent analysis of transgenic Alc ML + InPAct-GUS lines, confirmed that the alc switch was leaky in tissue culture. Although this was shown to be reversible once plants were removed from the tissue culture environment, it made the regeneration of Alc ML + InPAct-phbsyn plant lines extremely difficult, due to unintentional Rep expression and therefore high levels of phb expression and phytotoxic PHB production. Two Alc ML + InPAct-phbAsyn + p1300-TaBV P-phbB/phbC-35S T transgenic lines were able to be regenerated, and these were acclimatised, alcohol-treated and analysed. Although episome formation was detected as late as 21 days post activation, no PHB was detected in the leaves of any plants using either microscopy or HPLC, suggesting the presence of a corrupt InPAct-phbA cassette in both lines. The final component of this thesis involved the application of both the alc switch and the InPAct systems to sugarcane in an attempt to produce PHB. Initial experiments using transgenic Alc ML + InPAct-GUS lines indicated that the alc system was not functional in sugarcane under the conditions tested. The functionality of the InPAct system, independent of the alc gene switch, was subsequently examined by bombarding the 35S Rep/RepA cassette into leaf and immature leaf whorl cells derived from InPAct-GUS transgenic sugarcane plants. No GUS expression was observed in leaf tissue, whereas weak and irregular GUS expression was observed in immature leaf whorl tissue derived from two InPAct- GUS lines and two InPAct-GUS + 35S P-AlcR-AlcA P-GUS lines. The most plausible reason to explain the inconsistent and low levels of GUS expression in leaf whorls is a combination of low numbers of sugarcane cells in the DNA replication-conducive S-phase and the irregular and random nature of sugarcane cells bombarded with Rep/RepA. This study details the first report to develop a TbYDV-based InPAct system under control of the alc switch to produce PHB in tobacco and sugarcane. Despite the inability to detect quantifiable levels of PHB levels in either tobacco or sugarcane, the findings of this study should nevertheless assist in the further development of both the InPAct system and the alc system, particularly for sugarcane and ultimately lead to an ethanol-inducible InPAct gene expression system for the production of bioplastics and other proteins of commercial value in plants.

Individual user behaviour modelling for effective web recommendation

With the growth of the Web, E-commerce activities are also becoming popular. Product recommendation is an effective way of marketing a product to potential customers. Based on a user’s previous searches, most recommendation methods employ two dimensional models to find relevant items. Such items are then recommended to a user. Further too many irrelevant recommendations worsen the information overload problem for a user. This happens because such models based on vectors and matrices are unable to find the latent relationships that exist between users and searches. Identifying user behaviour is a complex process, and usually involves comparing searches made by him. In most of the cases traditional vector and matrix based methods are used to find prominent features as searched by a user. In this research we employ tensors to find relevant features as searched by users. Such relevant features are then used for making recommendations. Evaluation on real datasets show the effectiveness of such recommendations over vector and matrix based methods.

Multifractal characterisation and analysis of complex networks

Complex networks have been studied extensively due to their relevance to many real-world systems such as the world-wide web, the internet, biological and social systems. During the past two decades, studies of such networks in different fields have produced many significant results concerning their structures, topological properties, and dynamics. Three well-known properties of complex networks are scale-free degree distribution, small-world effect and self-similarity. The search for additional meaningful properties and the relationships among these properties is an active area of current research. This thesis investigates a newer aspect of complex networks, namely their multifractality, which is an extension of the concept of selfsimilarity. The first part of the thesis aims to confirm that the study of properties of complex networks can be expanded to a wider field including more complex weighted networks. Those real networks that have been shown to possess the self-similarity property in the existing literature are all unweighted networks. We use the proteinprotein interaction (PPI) networks as a key example to show that their weighted networks inherit the self-similarity from the original unweighted networks. Firstly, we confirm that the random sequential box-covering algorithm is an effective tool to compute the fractal dimension of complex networks. This is demonstrated on the Homo sapiens and E. coli PPI networks as well as their skeletons. Our results verify that the fractal dimension of the skeleton is smaller than that of the original network due to the shortest distance between nodes is larger in the skeleton, hence for a fixed box-size more boxes will be needed to cover the skeleton. Then we adopt the iterative scoring method to generate weighted PPI networks of five species, namely Homo sapiens, E. coli, yeast, C. elegans and Arabidopsis Thaliana. By using the random sequential box-covering algorithm, we calculate the fractal dimensions for both the original unweighted PPI networks and the generated weighted networks. The results show that self-similarity is still present in generated weighted PPI networks. This implication will be useful for our treatment of the networks in the third part of the thesis. The second part of the thesis aims to explore the multifractal behavior of different complex networks. Fractals such as the Cantor set, the Koch curve and the Sierspinski gasket are homogeneous since these fractals consist of a geometrical figure which repeats on an ever-reduced scale. Fractal analysis is a useful method for their study. However, real-world fractals are not homogeneous; there is rarely an identical motif repeated on all scales. Their singularity may vary on different subsets; implying that these objects are multifractal. Multifractal analysis is a useful way to systematically characterize the spatial heterogeneity of both theoretical and experimental fractal patterns. However, the tools for multifractal analysis of objects in Euclidean space are not suitable for complex networks. In this thesis, we propose a new box covering algorithm for multifractal analysis of complex networks. This algorithm is demonstrated in the computation of the generalized fractal dimensions of some theoretical networks, namely scale-free networks, small-world networks, random networks, and a kind of real networks, namely PPI networks of different species. Our main finding is the existence of multifractality in scale-free networks and PPI networks, while the multifractal behaviour is not confirmed for small-world networks and random networks. As another application, we generate gene interactions networks for patients and healthy people using the correlation coefficients between microarrays of different genes. Our results confirm the existence of multifractality in gene interactions networks. This multifractal analysis then provides a potentially useful tool for gene clustering and identification. The third part of the thesis aims to investigate the topological properties of networks constructed from time series. Characterizing complicated dynamics from time series is a fundamental problem of continuing interest in a wide variety of fields. Recent works indicate that complex network theory can be a powerful tool to analyse time series. Many existing methods for transforming time series into complex networks share a common feature: they define the connectivity of a complex network by the mutual proximity of different parts (e.g., individual states, state vectors, or cycles) of a single trajectory. In this thesis, we propose a new method to construct networks of time series: we define nodes by vectors of a certain length in the time series, and weight of edges between any two nodes by the Euclidean distance between the corresponding two vectors. We apply this method to build networks for fractional Brownian motions, whose long-range dependence is characterised by their Hurst exponent. We verify the validity of this method by showing that time series with stronger correlation, hence larger Hurst exponent, tend to have smaller fractal dimension, hence smoother sample paths. We then construct networks via the technique of horizontal visibility graph (HVG), which has been widely used recently. We confirm a known linear relationship between the Hurst exponent of fractional Brownian motion and the fractal dimension of the corresponding HVG network. In the first application, we apply our newly developed box-covering algorithm to calculate the generalized fractal dimensions of the HVG networks of fractional Brownian motions as well as those for binomial cascades and five bacterial genomes. The results confirm the monoscaling of fractional Brownian motion and the multifractality of the rest. As an additional application, we discuss the resilience of networks constructed from time series via two different approaches: visibility graph and horizontal visibility graph. Our finding is that the degree distribution of VG networks of fractional Brownian motions is scale-free (i.e., having a power law) meaning that one needs to destroy a large percentage of nodes before the network collapses into isolated parts; while for HVG networks of fractional Brownian motions, the degree distribution has exponential tails, implying that HVG networks would not survive the same kind of attack.

Analysis of conical-cylinder shells fundamental characteristics for structural health diagnostics

This paper describes the formulation for the free vibration of joined conical-cylindrical shells with uniform thickness using the transfer of influence coefficient for identification of structural characteristics. These characteristics are importance for structural health monitoring to develop model. This method was developed based on successive transmission of dynamic influence coefficients, which were defined as the relationships between the displacement and the force vectors at arbitrary nodal circles of the system. The two edges of the shell having arbitrary boundary conditions are supported by several elastic springs with meridional/axial, circumferential, radial and rotational stiffness, respectively. The governing equations of vibration of a conical shell, including a cylindrical shell, are written as a coupled set of first order differential equations by using the transfer matrix of the shell. Once the transfer matrix of a single component has been determined, the entire structure matrix is obtained by the product of each component matrix and the joining matrix. The natural frequencies and the modes of vibration were calculated numerically for joined conical-cylindrical shells. The validity of the present method is demonstrated through simple numerical examples, and through comparison with the results of previous researchers.

Feature-domain super-resolution framework for gabor-based face and iris recognition

The low resolution of images has been one of the major limitations in recognising humans from a distance using their biometric traits, such as face and iris. Superresolution has been employed to improve the resolution and the recognition performance simultaneously, however the majority of techniques employed operate in the pixel domain, such that the biometric feature vectors are extracted from a super-resolved input image. Feature-domain superresolution has been proposed for face and iris, and is shown to further improve recognition performance by capitalising on direct super-resolving the features which are used for recognition. However, current feature-domain superresolution approaches are limited to simple linear features such as Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA), which are not the most discriminant features for biometrics. Gabor-based features have been shown to be one of the most discriminant features for biometrics including face and iris. This paper proposes a framework to conduct super-resolution in the non-linear Gabor feature domain to further improve the recognition performance of biometric systems. Experiments have confirmed the validity of the proposed approach, demonstrating superior performance to existing linear approaches for both face and iris biometrics.

Statistical modelling of wind effects on signal propagation for wireless sensor networks

A wireless sensor network system must have the ability to tolerate harsh environmental conditions and reduce communication failures. In a typical outdoor situation, the presence of wind can introduce movement in the foliage. This motion of vegetation structures causes large and rapid signal fading in the communication link and must be accounted for when deploying a wireless sensor network system in such conditions. This thesis examines the fading characteristics experienced by wireless sensor nodes due to the effect of varying wind speed in a foliage obstructed transmission path. It presents extensive measurement campaigns at two locations with the approach of a typical wireless sensor networks configuration. The significance of this research lies in the varied approaches of its different experiments, involving a variety of vegetation types, scenarios and the use of different polarisations (vertical and horizontal). Non–line of sight (NLoS) scenario conditions investigate the wind effect based on different vegetation densities including that of the Acacia tree, Dogbane tree and tall grass. Whereas the line of sight (LoS) scenario investigates the effect of wind when the grass is swaying and affecting the ground-reflected component of the signal. Vegetation type and scenarios are envisaged to simulate real life working conditions of wireless sensor network systems in outdoor foliated environments. The results from the measurements are presented in statistical models involving first and second order statistics. We found that in most of the cases, the fading amplitude could be approximated by both Lognormal and Nakagami distribution, whose m parameter was found to depend on received power fluctuations. Lognormal distribution is known as the result of slow fading characteristics due to shadowing. This study concludes that fading caused by variations in received power due to wind in wireless sensor networks systems are found to be insignificant. There is no notable difference in Nakagami m values for low, calm, and windy wind speed categories. It is also shown in the second order analysis, the duration of the deep fades are very short, 0.1 second for 10 dB attenuation below RMS level for vertical polarization and 0.01 second for 10 dB attenuation below RMS level for horizontal polarization. Another key finding is that the received signal strength for horizontal polarisation demonstrates more than 3 dB better performances than the vertical polarisation for LoS and near LoS (thin vegetation) conditions and up to 10 dB better for denser vegetation conditions.

Robotics toolbox for MATLAB, release 9 [Software]

The ninth release of the Toolbox, represents over fifteen years of development and a substantial level of maturity. This version captures a large number of changes and extensions generated over the last two years which support my new book “Robotics, Vision & Control”. The Toolbox has always provided many functions that are useful for the study and simulation of classical arm-type robotics, for example such things as kinematics, dynamics, and trajectory generation. The Toolbox is based on a very general method of representing the kinematics and dynamics of serial-link manipulators. These parameters are encapsulated in MATLAB ® objects - robot objects can be created by the user for any serial-link manipulator and a number of examples are provided for well know robots such as the Puma 560 and the Stanford arm amongst others. The Toolbox also provides functions for manipulating and converting between datatypes such as vectors, homogeneous transformations and unit-quaternions which are necessary to represent 3-dimensional position and orientation. This ninth release of the Toolbox has been significantly extended to support mobile robots. For ground robots the Toolbox includes standard path planning algorithms (bug, distance transform, D*, PRM), kinodynamic planning (RRT), localization (EKF, particle filter), map building (EKF) and simultaneous localization and mapping (EKF), and a Simulink model a of non-holonomic vehicle. The Toolbox also including a detailed Simulink model for a quadcopter flying robot.

Intensity pulsations in distributed feedback Yb:Phosphate waveguide lasers

The intensity pulsations of a cw 1030 nm Yb:Phosphate monolithic waveguide laser with distributed feedback are described. We show that the pulsations could result from the coupling of the two orthogonal polarization modes through the two photon process of cooperative luminescence. The predictions of the presented theoretical model agree well with the observed behaviour.

SeqSLAM : visual route-based navigation for sunny summer days and stormy winter nights

Learning and then recognizing a route, whether travelled during the day or at night, in clear or inclement weather, and in summer or winter is a challenging task for state of the art algorithms in computer vision and robotics. In this paper, we present a new approach to visual navigation under changing conditions dubbed SeqSLAM. Instead of calculating the single location most likely given a current image, our approach calculates the best candidate matching location within every local navigation sequence. Localization is then achieved by recognizing coherent sequences of these “local best matches”. This approach removes the need for global matching performance by the vision front-end - instead it must only pick the best match within any short sequence of images. The approach is applicable over environment changes that render traditional feature-based techniques ineffective. Using two car-mounted camera datasets we demonstrate the effectiveness of the algorithm and compare it to one of the most successful feature-based SLAM algorithms, FAB-MAP. The perceptual change in the datasets is extreme; repeated traverses through environments during the day and then in the middle of the night, at times separated by months or years and in opposite seasons, and in clear weather and extremely heavy rain. While the feature-based method fails, the sequence-based algorithm is able to match trajectory segments at 100% precision with recall rates of up to 60%.

Children and the environment

Children and the environment cover a broad, interdisciplinary field of research and practice. The social sciences often use the word “environment” to mean the social, political, or economic context of children’s lives, but this bibliography covers physical settings. It focuses on a place-based scale that children can see, hear, taste, smell, touch, and navigate: not large, abstract scales such as national identities or population dynamics, or small scales such as environmental impacts on genes or cell functions. Attention to the everyday settings of children’s lives grew in the 18th century, when Romantic literature introduced the theme of children and nature. In the 19th century, concern for children’s welfare included an interest in conditions for children in burgeoning industrial cities, and justifications for early streetcar and railroad suburbs included claims that they would save children from the dangers of cities and provide the healthful benefits of natural surroundings. In the 20th century, academic disciplines developed different lines of inquiry about the impact of the physical environment on children and how children relate to places: ethnographic studies of children in different parts of the world in the fields of anthropology and geography; sociological studies of different populations of children in different settings; educational research on the learning opportunities that different school and out-of-school settings afford; medical research to understand disease vectors and the impact of pollutants on children; and efforts in the field of environment and behavior research more broadly, to understand how built and designed environments affect children physically, cognitively, socially, and emotionally. At the beginning of the 21st century, children and the environment is an active area of inquiry seeking to understand rapidly changing conditions for children as the world urbanizes, opportunities for free play outdoors and independent mobility erode in many parts of the world, media environments consume more of children’s time, and awareness grows that children need opportunities to contribute to creating sustainable societies.

Wolbachia uses host microRNAs to manipulate host gene expression and facilitate colonization of the dengue vector Aedes aegypti

The obligate endosymbiont Wolbachia pipientis is found in a wide range of invertebrates where they are best known for manipulating host reproduction. Recent studies have shown that Wolbachia also can modulate the lifespan of host insects and interfere with the development of human pathogens in mosquito vectors. Despite considerable study, very little is known about the molecular interactions between Wolbachia and its hosts that might mediate these effects. Using microarrays, we show that the microRNA (miRNA) profile of the mosquito, Aedes aegypti, is significantly altered by the wMelPop-CLA strain of W. pipientis. We found that a host miRNA (aae-miR-2940) is induced after Wolbachia infection in both mosquitoes and cell lines. One target of aae-miR-2940 is the Ae. aegypti metalloprotease gene. Interestingly, expression of the target gene was induced after Wolbachia infection, ectopic expression of the miRNA independent of Wolbachia, or transfection of an artificial mimic of the miRNA into mosquito cells. We also confirmed the interaction of aae-miR-2940 with the target sequences using GFP as a reporter gene. Silencing of the metalloprotease gene in both Wolbachia-infected cells and adult mosquitoes led to a significant reduction in Wolbachia density, as did inhibition of the miRNA in cells. These results indicate that manipulation of the mosquito metalloprotease gene via aae-miR-2940 is crucial for efficient maintenance of the endosymbiont. This report shows how Wolbachia alters the host miRNA profile and provides insight into the mechanisms of host manipulation used by this widespread endosymbiont.

A dual-polarized microstrip antenna array with port decoupling for MIMO systems

Utilization of multiport-antennas represents an appropriate way for the mitigation of multi-path fading in wireless communication systems. However, to obtain low correlation between the signals from different antenna ports and to prevent gain reduction by cross-talk, large antenna elements spacing is expected. Polarization diversity allows signal separation even with small antenna spacing. Although it is effective, polarization diversity alone does not suffice once the number of antennas exceeds the number of orthogonal polarizations. This paper presents an approach which combines a novel array concept with the use of dual polarization. The theory is verified by a compact dual polarized patch antenna array, which consists of four elements and a decoupling network.

Corneal changes following near work in myopic anisometropia

PURPOSE: To examine the symmetry of corneal changes following near work in the fellow eyes of non-amblyopic myopic anisometropes. METHODS: Thirty-four non-amblyopic myopic anisometropes (minimum 1 D spherical equivalent anisometropia) were recruited. Corneal topography was measured with the Medmont E300 Videokeratoscope before and after a controlled near task. Subjects were positioned to minimise head movements and read continuous text on a computer monitor for 10 minutes at an angle of 25 degrees downward gaze and an accommodation demand of 2.5 D. Measures of palpebral aperture morphology during primary and downward gaze were also obtained using digital photography and analysed with customised software. RESULTS: Significant changes in corneal topography were observed after ten minutes of reading. Localised superior regions of corneal topographical change (a hyperopic shift in corneal power) were typically exhibited in both eyes following the near task. The mean change in the corneal sphero-cylinder was +0.02/-0.11 x 113 and +0.02/-0.06 x 68 for the more and less myopic eyes respectively for a 6 mm corneal diameter. A significantly greater change in corneal astigmatism power vector J0 (a larger increase in against the rule astigmatism) was observed in the more myopic eyes (p < 0.01 for a 6 mm diameter). The more and less myopic eyes exhibited a high degree of interocular symmetry for measures of palpebral aperture morphology during both primary and downward gaze. Changes in corneal power vectors following reading were associated with eyelid position during downward gaze. CONCLUSIONS: Changes in corneal topography observed following a controlled reading task were highly symmetrical between the fellow eyes of myopic anisometropes due to the interocular symmetry of the palpebral aperture. However, the more myopic eye did exhibit a small but significantly greater magnitude of change in corneal astigmatism compared to the less myopic eye following reading. These findings may have implications for understanding the mechanism of development of non-amblyopic myopic anisometropia.

Setting up a platform for plant-based influenza virus vaccine production in South Africa

Background During a global influenza pandemic, the vaccine requirements of developing countries can surpass their supply capabilities, if these exist at all, compelling them to rely on developed countries for stocks that may not be available in time. There is thus a need for developing countries in general to produce their own pandemic and possibly seasonal influenza vaccines. Here we describe the development of a plant-based platform for producing influenza vaccines locally, in South Africa. Plant-produced influenza vaccine candidates are quicker to develop and potentially cheaper than egg-produced influenza vaccines, and their production can be rapidly upscaled. In this study, we investigated the feasibility of producing a vaccine to the highly pathogenic avian influenza A subtype H5N1 virus, the most generally virulent influenza virus identified to date. Two variants of the haemagglutinin (HA) surface glycoprotein gene were synthesised for optimum expression in plants: these were the full-length HA gene (H5) and a truncated form lacking the transmembrane domain (H5tr). The genes were cloned into a panel of Agrobacterium tumefaciens binary plant expression vectors in order to test HA accumulation in different cell compartments. The constructs were transiently expressed in tobacco by means of agroinfiltration. Stable transgenic tobacco plants were also generated to provide seed for stable storage of the material as a pre-pandemic strategy. Results For both transient and transgenic expression systems the highest accumulation of full-length H5 protein occurred in the apoplastic spaces, while the highest accumulation of H5tr was in the endoplasmic reticulum. The H5 proteins were produced at relatively high concentrations in both systems. Following partial purification, haemagglutination and haemagglutination inhibition tests indicated that the conformation of the plant-produced HA variants was correct and the proteins were functional. The immunisation of chickens and mice with the candidate vaccines elicited HA-specific antibody responses. Conclusions We managed, after synthesis of two versions of a single gene, to produce by transient and transgenic expression in plants, two variants of a highly pathogenic avian influenza virus HA protein which could have vaccine potential. This is a proof of principle of the potential of plant-produced influenza vaccines as a feasible pandemic response strategy for South Africa and other developing countries.

Diversity of dicotyledenous-infecting geminiviruses and their associated DNA molecules in Southern Africa, including the South-west Indian Ocean Islands

The family Geminiviridae comprises a group of plant-infecting circular ssDNA viruses that severely constrain agricultural production throughout the temperate regions of the world, and are a particularly serious threat to food security in sub-Saharan Africa. While geminiviruses exhibit considerable diversity in terms of their nucleotide sequences, genome structures, host ranges and insect vectors, the best characterised and economically most important of these viruses are those in the genus Begomovirus. Whereas begomoviruses are generally considered to be either monopartite (one ssDNA component) or bipartite (two circular ssDNA components called DNA-A and DNA-B), many apparently monopartite begomoviruses are associated with additional subviral ssDNA satellite components, called alpha- (DNA-αs) or betasatellites (DNA-βs). Additionally, subgenomic molecules, also known as defective interfering (DIs) DNAs that are usually derived from the parent helper virus through deletions of parts of its genome, are also associated with bipartite and monopartite begomoviruses. The past three decades have witnessed the emergence and diversification of various new begomoviral species and associated DI DNAs, in southern Africa, East Africa, and proximal Indian Ocean islands, which today threaten important vegetable and commercial crops such as, tobacco, cassava, tomato, sweet potato, and beans. This review aims to describe what is known about these viruses and their impacts on sustainable production in this sensitive region of the world. © 2012 by the authors licensee MDPI, Basel, Switzerland.