Browsing Faculty of Natural Sciences by Issue Date
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Baker, Gillian; Smith, J.J.; Cowan, Donald A. (Elsevier, 2003)[more][less]
Abstract: The Polymerase Chain Reaction (PCR) has facilitated the detection of unculturable microorganisms in virtually any environmental source and has thus been used extensively in the assessment of environmental microbial diversity. This technique relies on the assumption that the gene sequences present in the environment are complementary to the “universal” primers used in their amplification. The recent discovery of new taxa with 16S rDNA sequences not complementary to standard universal primers suggests that current 16S rDNA libraries are not representative of true prokaryotic biodiversity. Here we re-assess the specificity of commonly used 16S rRNA gene primers and present these data in tabular form designed as a tool to aid simple analysis, selection and implementation. In addition, we present two new primer pairs specifically designed for effective ‘universal’ Archaeal 16S rDNA sequence amplification. These primers are found to amplify sequences from Crenarchaeote and Euryarchaeote type strains and environmental DNA. URI: http://hdl.handle.net/10566/169 Files in this item: 1
BakerReviewReanalysis2003.pdf (969.0Kb) -
Adesemowo, A. Kayode; Tucker, William D. (Telkom, 2003)[more][less]
Abstract: As mobile devices and networks become more data-centric, text messaging requires an extension of co-presence capabilities for better interactive discussion between input/output handicapped handheld users and their free form desktop counterparts. Given some degree of co-presence (online presence and awareness) in text-based Instant Messaging, we hope to increase this co-presence on a handheld with fast-track feedback (FF) mechanisms. These are user-defined gestures, such as emoticons, and prioritised messages. We are building a system that facilitates gesture input within an interactive text-based chat over a wireless network running Session Initiation Protocol (SIP). The chat bridges a robust desktop environment and a small number of handhelds. This work in progress looks into the SIP Instant Messaging and Presence Leveraging Extensions as a platform to provide fast-track interactive and co-presence feedback. The aim is to rubberise a hitherto plastic and limited instant messaging conversation. We shall measure co-presence levels between FF and standard IM environments in and without desktop and handhelds by engaging two groups of users in chats session. We expect to demonstrate that there exists high co-presence notion in open (work by Sun Research Awarenex Group and AT&T Hubbubme in similar domain were in closed systems) FF text messaging open environment as we would like to show that this higher presence brings a much more enhanced interactive discourse. The envisaged results are intended to extrapolate to online aware co-presence in the up and coming smart phones on 3G packet networks. URI: http://hdl.handle.net/10566/539 Files in this item: 1
AdesemowoTuckerMobileDevices2003.pdf (180.9Kb) -
Benjamin, Anita; Tucker, William D. (Telkom, 2003)[more][less]
Abstract: We have built a hybrid voice/text web–board that utilizes floor control for handling resources such as microphone and interface events. The aim of this research is to determine the most appropriate floor control mechanism for a hybrid communication tool that allows conventional text and audio users to communicate with one another using a common interface. Research on floor control mechanisms provides many implementations for arbitration that are application-specific. Myers proposes a categorical explanation of the most widely used mechanisms for providing floor control and discusses these different dimensions with respect to a project called Pebbles. We have chosen to model our arbitration policies along these categories. The application will be implemented as a Java applet and gives users a view of both the text and audio aspects of the exchange. To facilitate the multi-modality of the system we will provide media conversion, using the Nuance system’s Java API. Our hypothesis is that well–known multi-tasking arbitration protocols such as FCFS, Round Robin, Token – based, and many more can be adapted to create a conferencing floor control policy for the interface of a hybrid communication environment so as to facilitate free–flowing multi-modal conversation. Measurements to determine which floor control implementation provides the best arbitration in terms of user interaction with the system will be calculated using RPT, ORT and usage tests based on the Kirkpatrick Model. We hope to show that users benefit more from an implicit arbitration mechanism than they do from an explicit one. URI: http://hdl.handle.net/10566/538 Files in this item: 1
BenjaminTuckerHybridVoice2003.pdf (123.3Kb) -
Lewis, John; Tucker, William D.; Blake, Edwin H. (Telkom, 2003)[more][less]
Abstract: Instant Messaging is traditionally a text only a air. However, there are instances when it would be useful to bridge to other types of media, like speech. The SoftBridge is an application framework that enables this kind of communications bridging using instant messages. Its use of protocols like the Jabber Instant Messaging Protocol and the Simple Object Access Protocol makes it simple, open and extensible. It also allows bridging to non IP communications infrastructure, like the telephone network. We describe the design and architecture of the system, protocol and extensibility mechanism. Finally we describe our experimental methodology and discuss the results of our initial experiments. URI: http://hdl.handle.net/10566/537 Files in this item: 1
LewisTuckerBlakeInstantMessaging2003.pdf (202.4Kb) -
Buecher, Emmanuelle; Gibbons, Mark J. (NISC (Pty) Ltd and Taylor& Francis, 2003)[more][less]
Abstract: Diel vertical migration (DVM) of six common species of hydromedusae was investigated during two drogue studies conducted in St Helena Bay on the west coast of South Africa in February 1995. Clytia spp., Obelia spp. and Bougainvillia macloviana, were largely confined to surface waters and did not appear to display any DVM. By contrast, Leuckartiara octona and Euphysa aurata displayed clear DVM and, like Proboscidactyla menoni, were found at greater depths than the other species. The depth distribution and amplitude of migration varied between surveys for most species, so definitive interpretations of patterns could not be made. URI: http://hdl.handle.net/10566/377 Files in this item: 1
BuecherDielVerticalMigration2003.pdf (121.3Kb) -
Sparks, Conrad, A.J.; Gibbons, Mark J. (Taylor & Francis and NISC, 2003)[more][less]
Abstract: A total of 242 zooplankton samples from the upper 100 m of the water column was collected discontinuously from March 1997 to January 1999 off the Orange River mouth on the west coast of southern Africa. Six species of hydromedusae were recovered at generally low abundance, of which Euphysa aurata, Leuckartia octona and Proboscidactyla menoni were dominant. E. aurata and L. octona showed evidence of seasonality in abundance. The low diversity of the fauna was remarkable and it is hypothesized that this might be attributable in part to sedimentation from the Orange River, and in part to locally weak circulation and the wide extent of the continental shelf. URI: http://hdl.handle.net/10566/380 Files in this item: 1
SparksHydromedusaeOrangeRiver2003.pdf (57.50Kb) -
Gibbons, Mark J.; Buecher, Emmanuelle; Thibault-Botha, Delphine (NISC (Pty) Ltd and Taylor& Francis, 2003)[more][less]
Abstract: The vertical distribution, abundance and size composition of a population of Pleurobrachia pileus was studied during a six-day drogue study conducted off the west coast of South Africa in February 1995. The population was centred in deep water, possibly because of the presence of a potential predator, Beroe sp., at shallower depths. The population of P. pileus failed to display clear patterns of migration, although nocturnal recruitment from deeper water resulted in a deepening of the depth of occupation then. The population was dominated by individuals <4 mm polar diameter, and large animals were confined to the upper water layers. These results are discussed with reference to possible spawning activities. Using published equations relating size to clearance rates, it was estimated that the population could remove up to 27% of integrated mesozooplankton standing stocks, and in excess of 100% (293%) at some depths. URI: http://hdl.handle.net/10566/373 Files in this item: 1
GibbonsPleurobrachia2003.pdf (270.1Kb) -
Sjoling, Sara; Cowan, Donald A. (Springer Verlag, 2003)[more][less]
Abstract: The microbial diversity in maritime meltwater pond sediments from Bratina Island, Ross Sea, Antarctica was investigated by 16S rDNA-dependent molecular phylogeny. Investigations of the vertical distribution, phylogenetic composition, and spatial variability of Bacteria and Archaea in the sediment were carried out. Results revealed the presence of a highly diverse bacterial population and a significantly depthrelated composition. Assessment of 173 partial 16S rDNA clones analyzed by amplified rDNA restriction analysis (ARDRA) using tetrameric restriction enzymes (HinP1I 5'GVCGC3'and Msp I. 5'CVGG3', BioLabs) revealed 153 different bacterial OTUs (operational taxonomic units). However, only seven archaeal OTUs were detected, indicating low archaeal diversity. Based on ARDRA results, 30 bacterial clones were selected for sequencing and the sequenced clones fell into seven major lineages of the domain Bacteria; the a, c, and d subdivisions of Proteobacteria, the Cytophaga–Flavobacterium– Bacteroides, the Spirochaetaceae, and the Actinobacteria. All of the archaeal clones sequenced belonged to the group Crenarchaeota and phylogenetic analysis revealed close relationships with members of the deep-branching Group 1 Marine Archaea. URI: http://hdl.handle.net/10566/148 Files in this item: 1
Sjoling16SrDNA.pdf (543.4Kb) -
Tucker, William D.; Glaser, Meryl; Lewis, John (Telkom, 2003)[more][less]
Abstract: Following on several partial prototypes, we built an automated Deaf Telephony bridging application with the SoftBridge platform. The SoftBridge performs multi-modal bridging in real-time using Text-to-Speech (TTS) and Automatic Speech Recognition (ASR) utilities accessed via web services. To perform Action Research with the Deaf community in Cape Town, we invited a Deaf user (DU) to participate in a pilot study. We conducted three tests varying the input/output modalities of the hearing user (HU). The DU had a standard text in/text out Instant Messaging client. The HU client used the following specific modality combinations: Text & TTS in/Text out, TTS in/Text out and TTS in/Text & ASR out. The SoftBridge logged the conversations for subsequent analysis. The trial showed a largely successful conversation. Success factors include a) a text and computer literate DU who is familiar with research practise, b) using the system to explain the research as we conducted it and c) that the multi-modal bridging capabilities overcame the expected shortcomings of TTS and especially ASR. The lessons learned from this trial will be applied to the next trial once the necessary modifications have been implemented. URI: http://hdl.handle.net/10566/535 Files in this item: 1
TuckerDeafTelephony2003.pdf (108.8Kb) -
Ah Tow, Lemese; Cowan, Donald A. (Society for General Microbiology, 2003)[more][less]
Abstract: Our results allow us to conclude that there appears to be significant conservation between the tuf genes of Planococcus, Planomicrobium and Staphylococcus spp., and that although the primer set TstaG422/TStag765 has been shown to possess high specificity, its use for the definitive identification of Staphylococcus spp. must be treated with some caution. Description: Published as a "Microbiology Comment": this provides a platform for readers of Microbiology to communicate their personal observations and opinions in a more informal way than through the submission of papers. URI: http://hdl.handle.net/10566/143 Files in this item: 1
AhTow&Cowan2003.PDF (251.5Kb) -
Cowan, Donald A.; Ah Tow, Lemese (Annual Reviews, 2004)[more][less]
Abstract: The Antarctic continent harbors a range of specialized and sometimes highly localized microbial biotopes. These include biotopes associated with desiccated mineral soils, rich ornithogenic soils, glacial and sea ice, ice-covered lakes, translucent rocks, and geothermally heated soils. All are characterized by the imposition of one or more environmental extremes (including low temperature, wide temperature fluctuations, desiccation, hypersalinity, high periodic radiation fluxes, and low nutrient status). As our understanding of the true microbial diversity in these biotopes expands from the application of molecular phylogenetic methods, we come closer to the point where we can make an accurate assessment of the impacts of environmental change, human intervention, and other natural and unnatural impositions. At present, it is possible to make reasonable predictions about the physical effects of local climate change, but only general predictions on possible changes in microbial community structure. The consequences of some direct human impacts, such as physical disruption of microbial soil communities, are obvious if not yet quantitated. Others, such as the dissemination of nonindigenous microorganisms into indigenous microbial communities, are not yet understood. URI: http://hdl.handle.net/10566/145 Files in this item: 1
Endangered Antarctic Environments.docx (12.30Kb) -
Julius, Elroy P.; Tucker, William D. (Telkom, 2004)[more][less]
Abstract: This research aims to find an empirical solution for guaranteeing the delivery of synchronous and asynchronous messages within a semi-synchronous IP-based communication domain. The communication infrastructure that is needed between the Deaf and hearing communities forms the application domain within which the research is situated. SoftBridging is a framework for multi-modal bridging as well as multiuser, multi-modal conversation sessions. An implementation of this concept called SoftBridge, is a communication platform that allows a hearing and Deaf person to communicate inside a single uniform space. The system is based on an asynchronous transport mechanism that makes use of various web services to do the actual data conversions such as voice to text and text to voice. Publish-subscribe systems are an emerging paradigm for building a range of distributed applications. The architecture of publish-subscribe systems make use of Message Oriented Middleware (MOM) to guarantee reliable delivery of messages within a communication domain. We will choose one of these systems and incorporate it within the overall architecture of a SoftBridge system. We will modify the existing architecture of a SoftBridge system to reliably transport synchronous as well as asynchronous data over a synchronous established session. We will use the Session Initiation Protocol (SIP) to establish a synchronous session between various users and a SoftBridge system. The system will then be used as a basis for developing a Deaf telephony application that guarantees the delivery of messages no matter the synchrony. URI: http://hdl.handle.net/10566/463 Files in this item: 1
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Tucker, William D.; Blake, Edwin H.; Marsden, Gary (Telkom, 2004)[more][less]
Abstract: We looked for and found two situations within the South African Digital Divide where constant and severe macro-scale latencies would most likely interfere with the usage of Information and Communication Technology (ICT) solutions. We describe how these systems tend to exhibit both social and technical macro-scale delays. Our experience building bridges for these communities has inspired several innovations with respect to the design, development and measurement of IP communications systems. The main contribution is the Open User Interconnect (OUI) stack, a communications system model that explicitly includes the user in relation to the underlying network. The OUI stack is orthogonal to the Open System Interconnect stack. There are two outcomes from including the user in the model. First, the OUI approach necessitates the adoption of usercentred methods such as Participatory Design and in the case of the South African Digital Divide, the adoption of Action Research principles. The second outcome is a user-centred measurement notion, called Quality of Communication (QoC), that is a macro-scale spin on Quality of Service. QoC explicitly includes the measurement of user behaviour in addition to system metrics. In conclusion, we suggest that these Digital Divide-inspired contributions may be applicable to IP communications system design, development and measurement in general. The paper concludes with a brief dissertation completion plan. URI: http://hdl.handle.net/10566/485 Files in this item: 1
TuckerDigitalDivide2004.pdf (131.4Kb) -
Chetty, Marshini; Tucker, William D.; Blake, Edwin H. (SAICSIT, in assocation with ACM, 2004)[more][less]
Abstract: The digital divide between rural and urban areas within developing countries is vast. We investigate how to address this divide by introducing Information and Communication Technologies (ICTs) into remote rural areas. Our aim is to discover how to create locally relevant software applications with appropriate content for these areas. We use a user centred design approach and a modified software development lifecycle that is participatory, iterative and cyclical. This process is based on principles from Participatory Design and Action Research. This paper presents our initial experience of developing a telemedicine application for a rural village in the Eastern Cape Province of South Africa using this process. We present an overview of the methodology, describe the software application we have developed and cite several challenges we have faced. Finally we conclude that an inter-organisational and inter-disciplinary approach is needed to develop software for remote areas. URI: http://hdl.handle.net/10566/532 Files in this item: 1
ChettyTuckerBlakeICT2004.pdf (386.9Kb) -
Cowan, Donald A. (Elsevier, 2004)[more][less]
Abstract: The newly isolated hyperthermophilic archaeal strain 121 grows slowly at 121 8C and even survives short periods at 130 8C. This is another organism that grows best at temperatures well in excess of 100 8C! We should not be astonished so much by the numerical increments but by the biochemical implications of this fact, and we should be excited by the scope provided by this and similar organisms to further our understanding of the evolution and adaptation of molecular structures and systems. And what about the upper limit of life? It appears improbable that the end-point of this search is represented by strain 121. The consensus view is that the true upper limit, where the energetic burden imposed by molecular repair and resynthesis becomes unsustainable, will probably lie in the region of 140–150 8C URI: http://hdl.handle.net/10566/147 Files in this item: 1
CowanUpperTemperature2004.pdf (331.8Kb) -
Cowan, Donald A.; Sayed, Muhammed F.; Tsekoa, Tsepo L.; Cameron, Rory A.; Sewell, B. Trevor (Academy of Science of South Africa (ASSAf), 2004)[more][less]
Abstract: Microbial nitrile hydratases are important industrial enzymes that catalyse the conversion of nitriles to the corresponding amides. Bacillus strain RAPc8 nitrile hydratase has recently been cloned and functionally expressed in E. coli. Here, the purification, crystallization and preliminary X-ray diffraction data of this nitrile hydratase are described. The heterotetrameric enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 30% PEG 400, 0.1 M MES (pH 6.5) and 0.1 M magnesium chloride were selected for X-ray diffraction studies. A data set complete to 2.5 Å was collected under cryoconditions at the in-house X-ray source at the University of the Western Cape. The space group was determined to be primitive tetragonal (P41212) with unit cell dimensions a = 106.61 Å, b = 106.61 Å, c=83.23 Å, = = =90°; with one dimer per asymmetric unit. Solution of the three-dimensional structure via molecular replacement is in progress. URI: http://hdl.handle.net/10566/167 Files in this item: 1
TsekoaPurification2004.pdf (784.0Kb) -
Vuza, Xolisa; Tucker, William D. (Telkom, 2004)[more][less]
Abstract: We intend adding video messaging and conferencing to Multimodal Telemedicine Intecommunicator (MuTI), a previous system that has already been in place in the target environment. This is to allow a semi-synchronous communication to occur over the Internet Protocol. Videoconferencing can be used to communicate synchronously and video messaging in a store and forward fashion can be used to communicate asynchronously. MuTI supports store and forward of still images, voicemail and text. The system also supports real time communication by means of audio. The aim of this research is to learn how to bridge the digital divide by building applications that are useful and relevant to the users we build for. We are developing this application together with the users of the application in an iterative fashion where we build the prototypes and show the users at each cycle. The feedback that we get from the users plays an important role in building a prototype for the next cycle. The software will be instrumented to provide statistics about the system usage. We are also going to get data from the users by using questionnaires and compare this data with the statistics about software usage to see how much the system has been used and which features in the system do the users like. We are using a rural South African context in conducting this research. We hope to bring about guidelines and recommendations on how to develop applications to bridge the digital divide in a developing world context. URI: http://hdl.handle.net/10566/435 Files in this item: 1
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Cowan, Donald A.; Arslanoglu, A.; Burton, Stephanie; Cameron, Rory A.; Baker, Gillian; Smith, Jacques J.; Meyer, Quinton (Portland Press, 2004)[more][less]
Abstract: With the rapid development of powerful protein evolution and enzyme-screening technologies, there is a growing belief that optimum conditions for biotransformation processes can be established without the constraints of the properties of the biocatalyst. These technologies can then be applied to find the ‘ideal biocatalyst’ for the process. In identifying the ideal biocatalyst, the processes of gene discovery and enzyme evolution play major roles. However, in order to expand the pool genes for in vitro evolution, new technologies, which circumvent the limitations of microbial culturability, must be applied. These technologies, which currently include metagenomic library screening, gene-specific amplification methods and even full metagenomic sequencing, provide access to a volume of ‘sequence space’ that is not addressed by traditional screening. URI: http://hdl.handle.net/10566/142 Files in this item: 1
CowanMetagenomicsGeneDiscovery2004.pdf (575.0Kb) -
Tucker, William D. (ACM, 2004)[more][less]
Abstract: Connecting people across the Digital Divide is as much a social effort as a technological one. We are developing a community-centered approach to learn how interaction techniques can compensate for poor communication across the Digital Divide. Preliminary trials have yielded interfaces that deal with poor quality by adapting Instant Messaging techniques for multiple modalities, providing improved semi-synchronous communication. Lessons learned suggest new ways to design user interfaces specifically for the developing world. URI: http://hdl.handle.net/10566/591 Files in this item: 1
Tucker-CHI2004.pdf (81.56Kb) -
Adesemowo, A. Kayode; Tucker, William D. (Telkom, 2004)[more][less]
Abstract: A text only Instant Messaging (IM) built on the IETF open standard SIP/SIMPLE has been developed in line with our proposed introduction of a user-defined text Hotkey feature. These act as an on-click Affective Gesture (AG): in similitude to Face-to-Face (F2F) expressive gesture-like abilities. Given that text communication possesses expressive discourse with some presence level, we seek to show that one-click text-gesture fast-tracking enhances text communication further. For this study, we are taking a hybrid quantitative and qualitative approach. Initial Pre-trial results have shown that an AG approach is more likely to improve IM chat spontaneity/response rate. Further experimental trials are being undertaken. Mobile devices and networks are becoming more data-centric (evident in Japanese I-mode) even as mobile network voice Average Revenue Per User (ARPU) are declining, new stream of data services are required which must take cognisance of handhelds features albeit their small screen estate and input/output limitation. Given that IM is entrenched in the social space, especially among teenagers and gaining wide adoption in the business place, we believe extensions are required for IM steep uptake in the mobile world, much as SMS has gained prominence. Enhanced input mechanisms for handheld IM system are expected to increase co-presence between handheld users and their desktop-based counterparts while in a synchronous discussion. URI: http://hdl.handle.net/10566/548 Files in this item: 1
AdesemowoTuckerInstantMessaging2004.pdf (165.2Kb)