Submitted in fulfilment for the requirement of a Degree of Doctor of Technology: Biotechnology, Durban University of Technology, 2010. / The aim of this study was to evaluate T. lanuginosus for the production of hemicellulases, its yield enhancement using mutagenesis and application of a selected xylanase on bagasse pupl to assess the improvement of pulp properties. The objectives were: To determine the localization of hemicellulases in T. lanuginosus strains, To develop high yielding strains of T. lanuginosus through mutagenensis, To investigate the synthesis of xylanase by T. lanuginosus MC134, To optimize the medium components and cultural conitions of T. lanuginosus MC134 strain, To study the influence of agitation and aeration on the production of xylanase by T. lanuginosus MC134 in a fermenter, To evaluate the bleach boosting abilities of T. lanuginosus xylanase on bagasse pulp, To evaluate simultaneous xylanase production and biobleaching potential of T. lanuginosus.

Dissertation (PhD)--University of Stellenbosch, 2003. / ENGLISH ABSTRACT: Cellulose and hemicellulose represents the two most abundant groups of renewable polysaccharides known to man. Apart from their presence in plant material, they also contribute to a significant portion of inexpensive readily available material, such as wastes and bypro ducts from forestry / agricultural origin. The chemical composition of plant material varies, but the biomass content consists of approximately 75% carbohydrate polymers (cellulose and hemicellulose) and 25% lignin. The enzymes required for the degradation of cellulose and hemicellulose are collectively called cellulases and hemicellulases. These enzymes have a broad spectrum of industrial applications including the production of fuel ethanol through fermentations, reducing the amount of chlorine required for bleaching in the pulp and paper industry, increasing dough volume in the baking industry, improving digestion and nutritional value of animal feed, increasing clarification and enhancing the filterability of wine, beer and fruit juice, etc. Therefore, a large potential market exists for cellulases and hemicellulases provided their production is economical and the product, authentic. Aspergilli occur in a wide variety of habitats including soil, stored food and feed products and decaying vegetation. The advantages for using A. niger as host for heterologous enzyme production include good protein secretion, industrial fermentation technology dating as far back as 1919, being a non-pathogenic fungus with GRAS status, no special substrate or cultivation requirements, FDA approval of numerous enzymes (homologous and heterologous) produced, etc. In this study an Aspergillus expression vector was constructed using the constitutive glyceraldehyde-3-phosphate dehydrogenase promoter (gpdp) of A. niger and the glucoamylase terminator (glaAT) of Aspergillus awamori. The cDNA copies of the eg! and xyn2 genes of Trichoderma reesei, cbhl-4 of Phanerochaete chrysosporium, man! of Aspergillus aculeatus and xyn3 of Aspergillus kawachii were introduced into the expression vector, respectively. All the plasmids were co-transformed with plasmid p3SR2 to A. niger and transformants selected for stable plasmid integration into the genome of the host. The recombinant enzymes EgI, Xyn2, Cbhl-4, Man! and XynC were successfully expressed and secreted at activity levels of 2300, 8000, 500, 6000 and 900 nkatlml, respectively. The enzymes were produced as functional entities and were subsequently characterized. The EgI, Xyn2 and ManI were evaluated as feed additives for the possible use in the animal feed industry. Improved biomass gain was observed with in vivo studies on poultry. With the possible mass production of heterologous enzymes in mind, a simple medium had to be devised for their inexpensive production. Molasses medium (available from the South African sugar industry) was therefore evaluated and the cultivation conditions optimized for it's possible use as cultivation substrate for A. niger. The evaluation was done on the grounds of EgI and Xyn2 activity produced which was monitored over time. This study highlighted the possible use of A. niger for the heterologous production of enzymes, the use of industrial substrate for cultivation and paved the way for the high level expression of industrially important genes at low cost and a positive environmental impact. / AFRIKAANSE OPSOMMING: Sellulose en hemisellulose verteenwoordig die twee vollopste herwinbare polisakkariede bekend. Behalwe vir hul teenwoordigheid in plantmateriaal, dra hulle ook by tot 'n beduidende fraksie van goedkoop, maklik bekombare materiaal soos afval- en byprodukte van bosbou I landbou oorsprong. Soos te verwagte, varieër die chemiese samestelling van die plantmateriaal, maar die biomassa-inhoud bestaan uit naastenby 25% lignien en 75% koolhidraatpolimere (sellulose and hemicellulose). Die ensieme benodig vir die afbraak van sellulose en hemisellulose staan gesamentlik as sellulases en hemisellulases bekend. Hierdie ensieme het 'n breë spektrum van industriële toepassings insluitende die produksie van brandstofalkohol d.m.v. fermentasies, vermindering in die hoeveelheid chloor benodig vir die bleikproses in die pulp-en-papier industrie, toename in deegvolume in die bakkersindustrie, verbetering van verteerbaarheid en verhoging van voedingswaarde van dierevoer, toename in verheldering en verbeterde filtreerbaarheid van wyn, bier en vrugtesap, ens. Dus bestaan daar 'n groot potensiële mark vir sellulases en hemisellulases, mits hul produksie ekonomies en die produk outentiek is. Aspergilli kom in 'n wye verskeidenheid van omgewings voor, insluitende grond, gestoorde voedsel- en voerprodukte asook ontbindende plante materiaal. Die voordele vir die gebruik van A. niger as gasheer vir heteroloë ensiemproduksie sluit in 'n goeie proteïen produseerder, industriële fermentasietegnologie dateer sover terug as 1919, 'n nie-patogeniese fungus met GRAS-status, benodig geen spesiale substrate of kwekingskondisies nie, FDA goedkeuring vir 'n groot aantal ensieme (homoloog sowel as heteroloog) wat reeds geproduseer word, ens. In hierdie studie is 'n Aspergillus uitdrukkingsvektor gekonstrueer deur van die konstitutiewe gliseraldehied-3-fosfaat dehidrogenase promoter (gpdp) van A. niger en die glukoamilase termineerder (glaAT) van Aspergillus awamori gebruik te maak. Die cDNA kopiee van die die eg! en xyn2 van Trichoderma reesei, cbhl-4 van Phanerochaete chrysosporium, man! van Aspergillus aculeatus en die xynC van Aspergillus kawachii was onderskeidelik na die uitdrukkingsplasmied oorgedra. Alle plasmiede is gesamentlik met die p3 SR2 plasmied na A. niger getransformeer en vir stabiele integrasie in die gasheergenoom geselekteer. Die rekombinante ensieme Egl, Xyn2, Cbhl-4, Manl en Xyn3 is suksesvol uitgedruk en teen aktiviteitsvlakke van 2300, 8000, 500, 6000 en 900 nkat/ml, onderskeidelik uitgeskei. Die ensieme is as funksionele entiteite geproduseer en vervolgens gekaraktiriseer. Die Egl, Xyn2 en Manl is as voertoevoegings vir die moontlike gebruik in die dierevoerindustrie geëvalueer. Verbeterde biomassa toename is in die in vivo studie op pluimvee waargeneem. Met die moontlikheid van grootskaalse heteroloë ensiemproduksie in gedagte, moes 'n eenvoudige substraat vir hul goedkoop produksie gevind word. Molasse medium (verkrygbaar vanaf die Suid Afrikaanse suiker industrie) was derhalwe geëvalueer en die kwekingskondisies geoptimiseer vir die moontlike gebruik as kwekingssubstraat vir A. niger. Vir die evaluasie is die Egl en Xyn2 aktiwiteite onder verskillende toestande geproduseer en oor tyd gemonitor. Hierdie studie beklemtoon die moontlike gebruik van A. niger vir heteroloë produksie van ensieme, die gebruik van industriële substrate as kwekingsmedium en baan die weg vir ekonomiese, hoëvlakuitdrukking van industrieelbelangrike ensieme met 'n positiewe implikasie op die omgewing.

ITC/USA 2011 Conference Proceedings / The Forty-Seventh Annual International Telemetering Conference and Technical Exhibition / October 24-27, 2011 / Bally's Las Vegas, Las Vegas, Nevada / In geometrically complex indoor industrial environments, such as factories, health care facilities, or offices, it can be challenging to determine where each telemetry receiver needs to be located to collect data from one or more mobile transmitters. Accurately estimating the areas that each transmitter frequently travels, rarely travels, and quickly travels through, helps to simplify the telemetry system planning problem and establishes which areas may be acceptable to provide marginal coverage. This paper discusses how using A* (A-Star) for transmitter path planning can assist in the telemetry system planning problem.

published_or_final_version / Mechanical Engineering / Doctoral / Doctor of Philosophy

Submitted in fulfillment of the requirements of the degree of Master of Technology (Biotechnology), Durban University of Technology, Durban, South Africa, 2014. / Microbial enzymes are gaining worldwide attention due to their potential industrial applications. Microorganisms producing thermostable -xylanase and their associated hemicellulases have significant application in the paper and pulp, food, animal feed, and textile industries. The potential of partially purified xylanase from Thermomyces lanuginosus MC 134, Luminase PB 100, Luminase PB 200 (a commercial xylanase) and T. lanuginosus DSM 5826 (Sigma Aldrich) was evaluated in bleaching of bagasse pulp. The temperature and pH optima for all the enzymes were 60°C and pH 6, respectively. The temperature (50- 80°C) and pH (5-8) stability of the enzymes were also assessed. All the enzymes were relatively stable at 60°C and pH 6 for 180 min. T. lanuginosus MC 134 retained 80% of its activity at 60°C and pH 6 for 180 min and PB 200 retained 75% of its activity at 80°C for 180 min. T. lanuginosus MC 134 also exhibited good alkaline stability at pH 8. The commercial xylanases Luminase PB 100, Luminase PB 200, T. lanuginosus DSM 5826 (Sigma Aldrich) were purified to homogeneity using a gel filtration column packed with sephadex G-100 and characterized for Km and Vmax. However extracellular crude xylanases from T. lanuginosus MC 134 was purified to homogeneity using (N )2S04 precipitation and gel filtration column, packed with sephadex G-100. The purified xylanases exhibited a molecular mass of- 26 to 24 kDa, given range as determined by SDS page. The Km and Vmax values of Luminase PB 100, Luminase PB 200, T. lanuginosus MC 134, and T. lanuginosus DSM 5826, xylanases were determined by the Michaelis-Menten equation using birchwood xylan as the substrate. The Km value for Luminase PB 100, Luminase PB 200, T. lanuginosus DSM 5826 and T. lanuginosus MC 134 were, 8.1 mg/mL, 11.7 mg/mL and 14.3 mg/mL respectively. The Vmax for Luminase PB 100, Luminase PB 200, T lanuginosus DSM 5826 and T lanuginosus MC 134 were 232.6, 454.6 and 74.6 !Jl11ol/min/mg. Biobleaching conditions of the xylanases were also optimised and the release of reducing sugars and lignin derived compounds showed that an enzyme dosage of 50U/g of pulp was ideal for biobleaching at pH 6 and 60°C for 180 min. This brightness for T lanuginosus MC 134, Luminase PB 200, Luminase PB 100 was 45.5 ± 0.11%, 44.1 ± 0.007% and 42.7 ± 0.03% respectively at pH 6, compared to untreated samples. Reducing sugars and UV-absorbing lignin-derived compound values were considerably higher in xylanase-treated samples. All the enzymes analysed exhibited similar trends in the release of lignin derived compounds and reducing sugars which indicated their potential in the pulp and paper industry. / PDF Full-text unavailable. Please refer to hard copy for Full-text / M

Orientador: Ivan de Godoy Maia / Banca: Celso Luis Marino / Banca: Marcio José da Silva / Resumo: A identificação de promotores com expressão tecido-específica é uma alternativa viável para substituição dos promotores com expressão ubíqua geralmente utilizados em transgenia. Nesse contexto, o presente trabalho teve como objetivos caracterizar funcionalmente o promotor de um gene de eucalipto que codifica um transportador de potássio com expressão específica em raiz bem como isolar e caracterizar a região promotora de um gene de eucalipto selecionado como apresentando expressão específica em folha. Plantas transgênicas de tabaco (Nicotiana tabacum SR1) contendo um cassete de expressão composto pelo promotor de raiz fusionado ao gene repórter GUS (que codifica a β-glucoronidase) foram usadas em ensaios histoquímicos e histológicos para investigar a especificidade da expressão determinada pelo promotor em estudo. Os resultados evidenciaram que o promotor investigado dirige a expressão do gene repórter em tecido vascular de folhas e raízes. A expressão em feixes vasculares de folhas e raízes foi confirmada em cortes histológicos. Visando avaliar a resposta deste promotor a baixas concentrações de potássio, duas linhagens da geração T2 foram submetidas à deficiência de potássio, e a expressão relativa do gene repórter GUS foi determinada por PCR em tempo real. Nas linhagens submetidas a estresse de potássio observou-se um aumento da expressão relativa do gene repórter GUS em função da privação do elemento. Em paralelo, um gene selecionado in silico como apresentando expressão em folha de eucalipto teve seu perfil de expressão validado por RT-PCR. A construção de um cassete de expressão contendo o referido promotor fusionado ao gene repórter GUS foi empreendida visando futuras validações funcionais / Abstract: The identification of tissue-specific promoters is of great value to substitute the ubiquitous promoters generally used in transgenic production. In this context, the present study aimed to functionally characterize the promoter of a Eucalyptus grandis gene encoding a potassium transporter showing root specific expression, and to isolate and functionally characterize the promoter region of an E. grandis gene selected as showing specific expression in leaf. Transgenic tobacco plants (Nicotiniana tabacum SR1) harboring a promoter:GUS fusion were used to investigate the expression specificity of the selected root promoter. The results showed that the investigated promoter drives a reporter gene expression in vascular tissues of leaves and roots. The expression in vascular bundles of leaves and roots was confirmed in histological crosssections. To evaluate the promoter responsiveness to low potassium concentrations, two transgenic lines (T2) were submitted to potassium starvation and the relative expression of the GUS reporter gene was determined by real time PCR. An increase in the relative expression of GUS in response to potassium starvation was observed. In parallel, the expression pattern of a gene showing leaf specific expression in Eucalyptus grandis was validated by RT-PCR. The construction of an expression cassette containing this promoter fused to the GUS reporter gene was performed aiming future functional characterization / Mestre

Chen, Yanmin. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 140-160). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Cheng, Zhenzhou. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references. / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Silicon photonics is the study and application of photonic systems, which use silicon as an optical medium. Data is transferred in the systems by optical rays. This technology is seen as the substitutions of electric computer chips in the future and the means to keep tack on the Moore’s law. Cavity optomechanics is a rising field of silicon photonics. It focuses on the interaction between light and mechanical objects. Although it is currently at its early stage of growth, this field has attracted rising attention. Here, we present highly sensitive optical detection of acceleration using an optomechanical accelerometer. The core part of this accelerometer is a slot-type photonic crystal cavity with strong optomechanical interactions. We first discuss theoretically the optomechanical coupling in the air-slot mode-gap photonic crystal cavity. The dispersive coupling gom is numerically calculated. Dynamical parametric oscillations for both cooling and amplification, in the resolved and unresolved sideband limit, are examined numerically, along with the displacement spectral density and cooling rates for the various operating parameters. Experimental results also demonstrated that the cavity has a large optomechanical coupling rate. The optically induced spring effect, damping and amplification of the mechanical modes are observed with measurements both in air and in vacuum. Then, we propose and demonstrate our optomechanical accelerometer. It can operate with a resolution of 730 ng/Hz¹/² (or equivalently 40.1 aN/Hz¹/²) and with a transduction bandwidth of ≈ 85 kHz. We also demonstrate an integrated photonics device, an on-chip spectroscopy, in the last part of this thesis. This new type of on-chip microspectrometer is based on the Vernier effect of two cascaded micro-ring cavities. It can measure optical spectrum with a bandwidth of 74nm and a resolution of 0.22 nm in a small footprint of 1.5 mm².

The extraordinary growth of parallelism in high-performance computing requires efficient data communication for scaling compute performance. High-performance computing systems have been using photonic links for communication of large bandwidth-distance product during the last decade. Photonic interconnection networks, however, should not be a wire-for-wire replacement based on conventional electrical counterparts. Features of photonics beyond high bandwidth, such as transparent bandwidth steering, can implement important functionalities needed by applications. In another aspect, application characteristics can be exploited to design better photonic interconnects. Therefore, this thesis explores codesign opportunities at the intersection between photonic interconnect architectures and high-performance computing applications. The key accomplishments of this thesis, ranging from system level to node level, are as follows. Chapter 2 presents a system-level architecture that leverages photonic switching to enable a reconfigurable interconnect. The architecture, called Flexfly, reconfigures the inter-group level of the widely-used Dragonfly topology using information about the application’s communication pattern. It can steal additional direct bandwidth for communication-intensive group pairs. Simulations with applications such as GTC, Nekbone and LULESH show up to 1.8x speedup over Dragonfly paired with UGAL routing, along with halved hop count and latency for cross-group messages. To demonstrate the effectiveness of our approach, we built a 32-node Flexfly prototype using a silicon photonic switch connecting four groups and demonstrated 820 ns interconnect reconfiguration time. This is the first demonstration of silicon photonic switching and bandwidth steering in a high-performance computing cluster. Chapter 3 extends photonic switching to the node level and presents a reconfigurable silicon photonic memory interconnect for many-core architectures. The interconnect targets at important memory access issues, such as network-on-chip hot-spots and non-uniform memory access. Integrated with the processor through 2.5D/3D stacking, a fast-tunable silicon photonic memory tunnel can transparently direct traffic from any off-chip memory to any on-chip interface – thus alleviating the hot-spot and non-uniform access effects. We demonstrated the operation of our proposed architecture using a tunable laser, a 4-port silicon photonic switch (four wavelength-routed memory channels) and a 4x4 mesh network-on-chip synthesized by FPGA. The emulated system achieves a 15-ns channel switching time. Simulations based on a 12-core 4-memory model show that for such switching speeds the interconnect system can realize a 2x speedup for the STREAM benchmark in the hot-spot scenario and a reduction of execution time for data-intensive applications such as 3D stencil and K-means clustering by 23% and 17%, respectively. Chapters 4 explores application-level characteristics that can be exploited to hide photonic path setup delays. In view of the frequent reuse of optical circuits by many applications, we proposed a circuit-cached scheme that amortizes the setup overhead by maximizing circuit reuses. In order to improve circuit “hit” rates, we developed a reuse-distance based replacement policy called “Farthest Next Use”. We further investigated the tradeoffs between the realized hit rate and energy consumption. Finally, we experimentally demonstrated the feasibility of the proposed concept using silicon photonic devices in an FPGA-controlled network testbed. Chapter 5 proceeds to develop an application-guided circuit-prefetch scheme. By learning temporal locality and communication patterns from upper-layer applications, the scheme not only caches a set of circuits for reuses, but also proactively prefetches circuits based on predictions. We applied this technique to communication patterns from a spectrum of science and engineering applications. The results show that setup delays via circuit misses are significantly reduced, showing how the proposed technique can improve circuit switching in photonic interconnects.