Tissue engineering is a field devoted to the design and creation of replacement tissues with the ultimate goal of one day providing replacement organs. Traditional strategies to accomplish this through the bulk seeding of cells onto a single monolithic porous bio-scaffold are unable to realise a precise architecture, thus the inability to mimic the cells natural micro-environment found within the body. Bio-printing approaches are the current state of the art with the ability to accurately mimic the complex 3D hierarchical structure of tissue. However, a functional construct also requires high strength to provide adequate support in load bearing applications such as bone and cartilage tissue engineering, and to maintain the open geometry of a large intricate channel network, which is crucial for the transport of nutrients and wastes. Typical approaches utilise materials which have processing parameters more amendable for cell incorporation, thus they can be simultaneously deposited with scaffolding material. However, the resulting construct is typically of low strength. This thesis explores the automation of a printing and “tissue assembly” process with the ability to incorporate delicate cell aggregates or spheroids within a high strength bio-scaffold requiring harsh processing parameters, at precise locations. The 3D printed bio-scaffold has a lattice architecture which enables a frictional fit to be formed between the particle and scaffold, thus preventing egress. To achieve this the pore must be expanded before the delivery of a single 1mm particle. Novel subsystems were developed to automate this process and provide the ability to achieve scalable, flexible, complex constructs with accurate architecture. A system architecture employing the benefits of modularity was devised. The main subsystems developed were the singulation device, to ensure the separation of a single particle; the injection device, to deliver and seed particles into the scaffold, and the control system, to facilitate the operation of the devices. Three generations of singulation devices have been developed ranging from mechanical to fluid manipulation methods alone. The first prototype utilised mechanical methods, with simple control methods. However the inability to correctly position the lead particle within the singulation chamber, resulted in damage to the test alginate particles. In the second prototype a fully fluidics based device utilised two trapping sites to capture the leading particles. Singulation success rates of up to 88% was achieved. Higher rates were limited by the trapped particle’s interaction with the lagging particles during capture. In a similar concept to the second prototype, the third prototype utilised only a single trapped particle, and achieved much higher throughput, and 100% singulation accuracy. The injection device, utilised a conical expanding rod within a thin outer sheath. It was able to expand the pore, with minimal damage to the scaffold, providing an unobstructed path for the delivery of the particle into the pore. A decentralised control system was devised to integrate the process operation for the electro-mechanical devices. Separate microcontrollers were able to sense, interact and communicate with one another, and the master control PC, to execute specific tasks to automate the process. The development of systems to automate the process has addressed the ability to accurately incorporate delicate cells with a high strength bio-scaffold, and will enable the realisation and investigation of intricate complex constructs, unachievable with current manual processes. Thus features found within the body may be more closely mimicked and functionalised, which may provide the necessary signals, micro-environment and infrastructure to correctly regulate the formation of complex functional tissue, supported by the adequate mass transport of nutrients and wastes. This may one day lead to 3D printing or assembly of viable replacement tissue, accurate in vitro model systems for laboratory testing, or even whole organs.

Adiponectin, a hormone that homo-oligomerizes into trimer, hexamer, or higher molecular weight (HMW) species, is involved in maintaining insulin sensitivity in muscle and liver. Interestingly, its functions appear to be oligomer-specific. Recent data suggest that HMW levels are decreased in obesity and insulin resistance, although, the cause for this decrease is not known. Impaired assembly to the octadecamer represents one possible reason for decreased HMW adiponectin in insulin resistance and type 2 diabetes, but mechanisms by which HMW adiponectin assembles are unknown. This dissertation discusses the progress that we have made regarding formation of HMW adiponectin in vitro.I found that disulfide bonds are important in the assembly process to octadecameric adiponectin, but are not required for stability of the octadecamer itself. We showed that hydrogen peroxide accelerated oligomerization to the octadecamer through formation of disulfide bonds, while alkylation of the cysteines led to inhibition of both oligomerization and disulfide bond formation. Using comparative native/denaturing polyacrylamide gel electrophoresis (PAGE), dynamic light scattering, and tandem mass spectrometry, we demonstrated that octadecamer is stable in the absence of disulfide bonds by using multiple biochemical and biophysical assays. In addition, oxidized adiponectin oligomerizes to octadecamer far slower than reduced adiponectin. To further evaluate the role of disulfide bonds in the formation to octadecamer, we analyzed the role of reduction potential on adiponectin oligomerization. We observed that under immediate oxidizing conditions, hexamers and trimers form. Oxidized hexamer can form HMW adiponectin through disulfide bond rearrangement using beta-mercaptoethanol (βME) or increasing the total concentration of glutathione under oxidizing conditions. To further understand the role of disulfide bonds, we showed that zinc increased the oligomerization to octadecamer. This effect was associated with decreased initial disulfide bonding during the assembly to the octadecamer. In summary, these data suggest the rate of disulfide bond formation and the ability to undergo disulfide bond isomerization are important in the oligomerization process of HMW adiponectin.

C2H2-zinc fingers (ZFs) are commonly found in transcription factors that code for nearly 3% of gene products in the human genome. ZF proteins are commonly involved in gene regulation during development, cell differentiation, and tumor suppression. Each "finger" is a domain composed of approximately 30 amino acids. Since the discovery of these domains over 25 years ago, several groups have contributed to the structural and biochemical knowledge to understand their DNA-binding properties. Taking advantage of the simplicity of manipulating the DNA-binding potential of a ZF, the technology has now evolved to make sequence-specific Zinc Finger Nucleases (ZFNs), Artificial Transcription Factors (ATFs), Zinc Finger Recombinases, and DNA detection tools. ZFPs have been used for various applications, ranging from regulating genes by ZF-ATFs to manipulating genomes in diverse organisms. ZFNs have remarkably revolutionized the field of genome engineering. ZFN-modified T-cells have now advanced into human clinical trials for cell-based therapies as a treatment against HIV. Despite the advances in the ZFN technology, one of the challenges in the field is obtaining effective ZFNs using publicly available tools. The traditional method of synthesizing custom ZF arrays was using modular assembly (MA). In this method, preselected ZFs from publicly available one-finger archives can be assembled modularly to make long arrays. MA of ZFNs provides a rapid method to create proteins that can recognize a broad spectrum of DNA sequences. However, three- and four-finger arrays often fail to produce active nucleases. The low success rate of MA ZF arrays was attributed to the fact that they suffer from finger-finger incompatibility referred to as context-dependent effects. However, we hypothesized that the low affinity of MA arrays was the limiting factor. The work presented in this dissertation describes our efforts at addressing these fundamental methodological challenges. We developed the Extended Modular Assembly method that overcomes the limitations of both the previous Modular Assembly. We performed a systematic investigation of number and composition of modules on ZFN activity and analyzed ZFN specificity both in vitro and in vivo. Our current experiments apply the ZFNs produced by our method to study the role of genetic variation in human disease.

Information is an important part of the manual assembly process. Information provides the user with the means to fulfil assembly tasks so that the right quality as well as high productivity are accomplished. This thesis addresses issues connected to information and information use in a modern manual assembly environment, and how these issues affect human operators, quality and productivity. The overall objectives of the research were to gain further knowledge on how attention affects the internal reject rate, to investigate these phenomena in industrial and laboratory environments and finally to propose a suitable evaluation method to be utilised at the design stage of an information system. Studies were performed with the purpose of investigating how the assembly personnel were affected by the information and how it affected quality and productivity. The studies were performed in an assembly plant and in the laboratory. Quantitative data collection included 10 days and nights of production where the information impact on quality was investigated. Connected to this study was a qualitative survey performed among 171 persons from the assembly personnel. The laboratory study took place during three days, approximately eight hours each day. It involved 30 persons, all experienced assembly workers from the reference assembly plant. The focus of this study was how information affected the personnel and thereby the productivity. The findings revealed that information affected the quality rates and productivity and that this can be linked to how the information is presented as well as when the information is presented. It was possible to link these findings to the outcome of a successful information search process, and to conclude that a use of an evaluation method or work process during the product lifecycle could have made it possible to avoid some of the problems connected to the information presentation. This is the basis for a proposed pragmatic evaluation method. The method was tested as a support system during the design of a prototype user interface to be used at the pilot plant. The major contribution of this research is the connection between attention and quality as well as the connection between attention and productivity. Knowledge regarding the importance of presenting the information at the right time must also be regarded as an important and proven contribution.

The energy use of commercial building operations is a significant contributor to the total global energy demand, and lighting is one of the largest end uses of electricity in commercial buildings. Convention Centers as commercial buildings are examples of big energy consumers, and they present a unique opportunity to showcase benefits of green building techniques due to their large size and broad range of visitors; however, the individual nature of convention centers makes it challenging to find design improvements which will be helpful in general for many convention centers. One exception to this rule of individuality is the presence of public assembly rooms, which are ubiquitous in nature and are used heavily. Traditionally, public assembly rooms are fully enclosed to allow for full control of illumination levels with artificial lighting, particularly fluorescent light. This represents a missing opportunity to utilize daylight or energy efficient artificial light to reduce energy use while enhancing human visual comfort. The objective of this research is to analyze the potential impact of the use of daylight in public assembly rooms. We present the results of a set of computer simulations performed using IES VE software. The simulations are performed as an iterative process, using as base case a north-facing public assembly room in the Tucson Convention Center, and progressively updating the lighting scheme using the software to analyze the illuminance levels for each case. The results are used to propose a lighting scheme for the north-facing public assembly room which uses 100% daylight to achieve a uniform level of illumination and meets the compliance of illumination requirements for public assembly rooms.

We report a new chameleon-like Anolis species from Hispaniola that is ecomorphologically similar to congeners found only on Cuba. Lizards from both clades possess short limbs and a short tail and utilize relatively narrow perches, leading us to recognize a novel example of ecomorphological matching among islands in the well-known Greater Antillean anole radiation. This discovery supports the hypothesis that the assembly of island faunas can be substantially deterministic and highlights the continued potential for basic discovery to reveal new insights in well-studied groups. Restricted to a threatened band of midelevation transitional forest near the border of the Dominican Republic and Haiti, this new species appears to be highly endangered.

Résumé : Les transferts d’électrons photo-induits et d’énergie jouent un rôle primordial dans un grand nombre de processus photochimiques et photobiologiques, comme la respiration ou la photosynthèse. Une très grande quantité de systèmes à liaisons covalentes ont été conçus pour copier ces processus de transferts. Cependant, les progrès sont, en grande partie, limités par les difficultés rencontrées dans la synthèse de nouveaux couples de types donneurs-accepteurs. Récemment, des espèces utilisant des liaisons non-covalentes, comme les liaisons hydrogènes, les interactions [pi]-[pi], les liaisons de coordination métal-ligands ou encore les interactions électrostatiques sont le centre d’un nouvel intérêt du fait qu’ils soient plus faciles à synthétiser et à gérer pour obtenir des comportements de transferts d’électrons ou d’énergie plus flexibles et sélectifs. C’est dans cette optique que le travail de cette thèse a été mené, i.e. de concevoir des composés auto-assemblés avec des porphyrines et un cluster de palladium pour l’étude des transferts d’électrons photo-induits et d’énergie. Cette thèse se divise en quatre parties principales. Dans la première section, le chapitre 3, deux colorants porphyriniques, soit le 5-(4-carboxylphényl)-10, 15, 20-tristolyl(porphyrinato)zinc(II) (MCP, avec Na+ comme contre-ion) et 5, 15-bis(4-carboxylphényl)-15, 20-bistolyl(porphyrinato)zinc(II) (DCP, avec Na+ comme contre-ion) ont été utilisés comme donneurs d’électrons, et le [Pd3(dppm)3(CO)]2+ ([Pd32+], dppm = (Ph2P)2CH2, PF6‾ est le contre-ion) a été choisi comme accepteur d’électrons. La structure de l’assemblage [Pd32+]•••porphyrine a été élucidée par l’optimisation des géométries à l’aide de calculs DFT. La spectroscopie d’absorption transitoire (TAS) montre la vitesse de transferts d’électrons la plus rapide (< 85 fs, temps inférieurs à la limite de détection) jamais enregistrée pour ce type de système (porphyrine-accepteur auto-assemblés). Généralement, ces processus sont de l’ordre de l’échelle de la ps-ns. Cette vitesse est comparable aux plus rapides transferts d’électrons rapportés dans le cas de systèmes covalents de type porphyrine-accepteur rapide (< 85 fs, temps inférieurs à la limite de détection). Ce transfert d’électrons ultra-rapide (ket > 1.2 × 1013 s-1) se produit à l’état énergétique S1 des colorants dans une structure liée directement par des interactions ioniques, ce qui indique qu’il n’est pas nécessaire d’avoir de forts liens ou une géométrie courbée entre le donneur et l’accepteur. Dans une deuxième section, au chapitre 4, nous avons étudié en profondeur l’effet de l’utilisation de porphyrines à systèmes π-étendus sur le comportement des transferts d’électrons. Le colorant 9, 18, 27, 36-tétrakis-meso-(4-carboxyphényl)tétrabenzoporphyrinatozinc(II) (TCPBP, avec Na+ comme contre-ion) a été sélectionné comme candidat, et le 5, 10, 15, 20-tétrakis-meso-(4-carboxyphényl)porphyrineatozinc(II) (TCPP, avec Na+ comme contre-ion) a aussi été utilisé à des fins de comparaisons. TCPBP et TCPP ont, tous deux, été utilisés comme donneurs d’électrons pour fabriquer des assemblages supramoléculaires avec le cluster [Pd32+] comme accepteur d’électrons. Les calculs DFT ont été réalisés pour expliquer les structures de ces assemblages. Dans les conditions expérimentales, ces assemblages sont composés principalement d’une porphyrine avec 4 équivalents de clusters. Ces systèmes ont aussi été investigués par des mesures de quenching (perte de luminescence), par électrochimie et par d’autres techniques. Les transferts d’électrons (< 85 fs; temps inférieurs à la limite de détection) étaient aussi observés, de façon similaire aux assemblages MCP•••[Pd32+] et [Pd32+]•••DCP•••[Pd32+]. Les résultats nous indiquent que la modification de la structure de la porphyrine vers la tétrabenzoporphyrine ne semble pas influencer le comportement des cinétiques de transferts d’électrons (aller ou retour). Dans la troisième section, le chapitre 5, nous avons synthétisé la porphyrine hautement [pi]-conjuguée: 9, 18, 27, 36-tétra-(4-carboxyphényléthynyl)tétrabenzoporphyrinatozinc(II) (TCPEBP, avec Na+ comme contre-ion) par des fonctionnalisations en positions meso- et β, β-, qui présente un déplacement vers le rouge de la bande de Soret et des bandes Q. TCPEBP était utilisé comme donneur d’électrons pour fabriquer des motifs supramoléculaires avec le [Pd32+] comme accepteur d’électrons. Des expériences en parallèle ont été menées en utilisant la 5, 10, 15, 20-tétra-(4-carboxyphényl)éthynylporphyrinatozinc(II) (TCPEP, avec Na+ comme contre-ion). Des calculs DFT et TDDFT ont été réalisés pour de nouveau déterminer de façon théorique les structures de ces systèmes. Les constantes d’association pour les assemblages TCPEBP•••[Pd32+]x sont les plus élevées parmi tous les assemblages entre des porphyrines et le cluster de palladium rencontrés dans la littérature. La TAS a montré, encore une fois, des processus de transferts d’électrons dans des échelles de l’ordre de 75-110 fs. Cependant, les transferts de retour d’électrons sont aussi très rapides (< 1 ps), ce qui est un obstacle potentiel pour des applications en cellules solaires à pigment photosensible (DSSCs). Dans la quatrième section, le chapitre 6, les transferts d’énergie triplets (TET) ont été étudiés pour les assemblages MCP•••[Pd32+] et [Pd32+]•••DCP•••[Pd32+]. Les analyses spectrales des états transitoires dans l’échelle de temps de la ns-[mu]s démontrent de façon évidente les TETs; ceux-ci présentent des transferts d’énergie lents et/ou des vitesses moyennes pour des transferts d’énergie T1-T1 (3dye*•••[Pd32+] → dye•••3[Pd32+]*) opérant à travers exclusivement le mécanisme de Förster avec des valeurs de kET autour de ~ 1 × 105 s-1 selon les mesures d’absorption transitoires à 298 K. Des forces motrices non-favorables rendent ces types de processus non-opérants ou très lents dans les états T1. L’état T1 de [Pd32+] (~8190 cm-1) a été qualitativement déterminé par DFT et par la mise en évidence de l’émission S0 ← Tn retardée à 680-700 nm provenant de l’annihilation T1-T1, ce qui fait que ce cluster peut potentiellement agir comme un donneur à partir de ses états Tn, et accepteur à partir de T1 à l’intérieur de ces assemblages. Des pertes d’intensités de types statiques pour la phosphorescence dans le proche-IR sont observées à 785 nm. Ce travail démontre une efficacité modérée des colorants à base de porphyrines pour être impliquée dans des TETs avec des fragments organométalliques, et ce, même attachées grâce à des interactions ioniques. En conclusion, les assemblages ioniques à base de porphyrines et de clusters de palladium présentent des propriétés de transferts d’électrons S1 ultra-rapides, et des transferts d’énergie T1 de vitesses modérées, ce qui est utile pour de possibles applications comme outils optoélectroniques. D’autres études, plus en profondeur, sont présentement en progrès. / Abstract : Photoinduced electron and energy transfers play the pivotal role in various photochemical and photobiological redox processes including photosynthesis and respiration. Abundant covalently bonded systems have been designed to mimic the natural electron and energy transfer processes. However, the progress is often interfered by the difficulties to synthesize novel and versatile covalent donor-acceptor pairs. Recently, entities utilizing non-covalent interactions including hydrogen-bonding, [pi]-[pi] stacking, metal-ligand coordination and electrostatic interactions are becoming a hot topic since they are easy to be fabricated and tuned for selective and flexible electron and energy transfer behaviors. In this respect, the work presented in this thesis designed self-assemblies with porphyrins and a palladium cluster for photoinduced electron and energy transfers. It includes four main sections. In the first section, Chapter 3, two porphyrinic dyes, 5-(4-carboxylphenyl)-10, 15, 20-tristolyl(porphyrinato)zinc(II) (MCP, as sodium salt) and 5, 15-bis(4-carboxylphenyl)-15, 20-bistolyl(porphyrinato)zinc(II) (DCP, as sodium salt), were used as electron donors, and [Pd3(dppm)3(CO)]2+ ([Pd32+], dppm = (Ph2P)2CH2, as PF6‾ salt) cluster was adopted as the electron acceptor. The structure of [Pd32+]•••porphyrin assemblies was elucidated by geometry optimization using Density Functional Theory (DFT) calculations. Transient absorption spectroscopy (TAS) indicated a record fast electron transfer rate (< 85 fs, the time resolution limit) among the porphyrin-acceptor self-assemblies. Typically, these occur in ps-ns time scale. This rate is also comparable to the fastest electron transfer rate reported for the covalently linked porphyrin-acceptor systems (~ 50 fs, the time resolution limit). The ultrafast photo-induced electron transfers (ket > 1.2 × 1013 s-1) occurring at the S1 levels of the dyes in the structurally well-defined “straight up” ionic assemblies indicate that it is not necessary to have a strong bond and bent geometry between the donor and acceptor. In the second section, Chapter 4, we further studied the effect of using π-extended porphyrins on the electron transfer behavior of these assemblies. 9, 18, 27, 36-Tetrakis-meso-(4-carboxyphenyl)tetrabenzoporphyrinatozinc(II) (TCPBP, as a sodium salt) was selected as the candidate, and the 5, 10, 15, 20-tetrakis-meso-(4-carboxyphenyl)porphyrinatozinc(II) (TCPP, as a sodium salt) dye was also studied for comparison purposes. TCPBP and TCPP were both utilized as electron donors to fabricate supramolecular assemblies with the [Pd32+] cluster as the electron acceptor. DFT calculations were used to explain the structure of these assemblies. Under the experimental conditions used, these assemblies mainly exist in the form of one porphyrin with four equivalent clusters. These systems were also investigated by quenching measurements, electrochemistry, and other techniques. Ultrafast electron transfers (< 85 fs; time resolution limit) were also observed, which is similar as those for MCP•••[Pd32+] and [Pd32+]•••DCP•••[Pd32+] assemblies. The results indicate the structural modification from porphyrin to tetrabenzoporphyrin does not seemingly influence the kinetic behavior of the forward and back electron transfers. In the third section, Chapter 5, we synthesized a highly [pi]-conjugated porphyrin, 9, 18, 27, 36-tetra-(4-carboxyphenylethynyl)tetrabenzoporphyrinatozinc(II) (TCPEBP, as a sodium salt) by meso- and β, β-bifunctionalization, which exhibits large red shift of the Soret and Q-bands. TCPEBP was utilized as electron donors to fabricate supramolecular motifs with [Pd32+] cluster as the electron acceptor. Parallel experiments were conducted using 5, 10, 15, 20-tetra-(4-carboxyphenyl)ethynylporphyrinatozinc(II) (TCPEP, as a sodium salt). DFT and TDDFT calculations were applied to elucidate the structure of these assemblies. Binding constants for TCPEBP•••[Pd32+]x is the largest one among all the assemblies with porphyrin and palladium cluster. TAS showed again the ultrafast electron transfer process within the 75-110 fs time frame. However, the back electron transfers are also very fast (< 1 ps), which may be a potential obstacle for future applications in dye-sensitized solar cells (DSSCs). In the fourth section, Chapter 6, triplet energy transfers (TET) of the assemblies MCP•••[Pd32+] and [Pd32+]•••DCP•••[Pd32+] were studied. The transient spectral analysis in the ns-[mu]s time scale clearly demonstrates evidence for TET, which shows a slow to medium T1-T1 energy transfer (3dye*•••[Pd32+] → dye•••3[Pd32+]*) operating through a Förster mechanism exclusively with kET values of ~ 1 × 105 s-1 based on transient absorption measurements at 298 K. Unfavourable reductive and oxidative driving forces make this type of process inoperative or very slow in the T1 states. The T1 state of [Pd32+] (~8190 cm-1) has been quantitatively determined by DFT computations and by evidence for a delayed S0 ← Tn emission at 680-700 nm arising from T1-T1 annihilation, which makes this cluster potentially acting as the energy donor from its Tn state, and T1 acceptor within the assemblies. The static quenching of their near-IR phosphorescence at 785 nm was observed. This work demonstrated a moderate efficiency of the porphyrin dye to be involved in TET with an organometallic fragment, even when attached through ionic interactions. Conclusively, ionic assemblies with porphyrins and palladium clusters exhibit ultrafast S1 electron transfer and moderate T1 energy transfer properties, which is useful for possible application as optoelectronic devices. Further research in more depth is in progress.

1-eicosanethiolate molecules form relatively weak bonds with the surface of InSb(100) limiting the order of the self-assembled monolayer despite the long length of the alkyl chain. Heating to only 225 °C in vacuum completely desorbed the eicosanethiolate layer from the surface based on x-ray photoelectron spectroscopy. Even after deposition times as long as 20 h in ethanol, the asymmetric methylene stretch was at 2925 cm-1 in the attenuated total reflection Fourier transform infrared spectrum, which is indicative of alkane chains that are incompletely ordered. Atomic force microscopy images combined with ellipsometry showed that the eicosanethiolate layer conformed to the rough InSb(100) starting surface (2.3±0.2 nm RMS). The reoxidation kinetics in air of InSb(100) and InSb(111)B covered with eicosanethiolate layers was the same despite the lower surface roughness of the latter (0.64±0.14 nm). The bond that the S head group makes with the substrate is the primary factor that determines the cohesiveness of the molecules on the surface. Although interactions between the alkane chains in the layer are sufficient to form a self-assembled layer, the fluidity of the molecules in the layer compromised the chemical passivation of the surface resulting in reoxidation in air after 20 minutes.

No description available.

The first chapter discusses the concept of macros: its definition, structure, usage, design goals, and the related prior work. This thesis principally concerns my work on OLMP (an On-Line Macro Processor for the Motorola 6800 Microprocessor), which is a macro processor which interacts with the user. It takes Motorola assembler source code and macro definitions as its input; after the appropriate editing and expansions, it outputs the expanded assembler source statements. The functional objectives, the design for implementation of OLMP, the basic macro format, and the macro definition construction are specified in Chapter Two. The software and the hardware environment of OLMP are discussed in the third chapter. The six modules of OLMP are the main spine of the fourth chapter. The comments on future improvement and how to link OLMP with the Motorola 6800 assembler are the major concern of the final chapter.